Hi,
After upgrading a v1 project to v2 using the online upgrade script,
analysis 2.1 and 2.1.1 fail to open the project with the following error
popup:
Cannot add child - key already in use:
ccp.molecule.ChemComp.StdChemComp:<memops.Implementation.MemopsRootid:109832656>:('protein':'Xxx')
It also produces the following traceback:
Error loading file for: <ccp.molecule.ChemComp.StdChemComp ['protein',
'Xxx']>
Reading: <open file
'/usr/local64/ccpnmr2.1.1/ccpnmr2.1/data/ccp/molecule/ChemComp/protein
+Xxx+pdbe_ccpnRef_2009-07-30-11-31-14-656_00001.xml', mode 'r' at
0x58dfbe8>
Last xml tag read: CHEM.ChemComp.chemAtomSets
Parser state was: handling version compatibility
Object stack was empty
Error during Exo link dereferencing. Object was:
<ccp.molecule.Molecule.MolResidue ['FH19-20', 129]>
values were: ['msd_ccpnRef_2007-12-11-10-20-10_00007']
tag name was: chemComp
Error loading file for: <ccp.molecule.Molecule.Molecule ['FH19-20']>
Reading: <open file
'/media/KINGSTON/FH1920_MUTS/HUS_MUTS/FH19_20/ccp/molecule/Molecule/FH19_20+FH19_20_user_2009-10-29-16-07-33_00023.xml', mode 'r' at 0x58dfcd8>
Last xml tag read: _StorageUnit
Parser state was: postprocessing data
Object stack was empty
Error loading file for: <ccp.molecule.MolSystem.MolSystem ['FH19-20']>
Reading: <open file
'/media/KINGSTON/FH1920_MUTS/HUS_MUTS/FH19_20/ccp/molecule/MolSystem/FH19_20+FH19_20_user_2009-10-29-16-07-33_00124.xml', mode 'r' at 0x58dfc60>
Last xml tag read: _StorageUnit
Parser state was: checking validity
Object stack was empty
Error loading file for: <ccp.nmr.Nmr.NmrProject ['FH19-20']>
Reading: <open file
'/media/KINGSTON/FH1920_MUTS/HUS_MUTS/FH19_20/ccp/nmr/Nmr/FH19_20
+FH19_20_user_2009-10-29-16-07-33_00125.xml', mode 'r' at 0x5c166c0>
Last xml tag read: NMR.AtomSet.atoms
Parser state was: reading
Current object was: <ccp.nmr.Nmr.AtomSet ['FH19-20', 1]>
Traceback (most recent call last):
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/ccpnmr/analysis/AnalysisGui.py", line 231, in <module>
main(projectDir, max_size, glDirect)
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/ccpnmr/analysis/AnalysisGui.py", line 109, in main
project = loadProject(top, path=projectDir)
File "/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/ccp/gui/Io.py", line
92, in loadProject
if isinstance(dataStore, NumericMatrix) and not
dataStore.nmrDataSources:
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/ccp/api/general/DataLocation.py", line 6147, in getNmrDataSources
tobj.load()
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/api/Implementation.py", line 5066, in load
self.loadFrom(repositories[0])
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/api/Implementation.py", line 5100, in loadFrom
XmlIO.loadTopObject(repository.url.getDataLocation(), self)
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/format/xml/XmlIO.py",
line 236, in loadTopObject
return loadFromStream(open(filePath), topObjId=topObjId,
topObject=topObject)
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/format/xml/XmlIO.py",
line 267, in loadFromStream
partialLoad=partialLoad)
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/xml/Implementation.py", line 4805, in loadFromStream
val[ii] = clazz.getByKey(oo,vv[1:-1])
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/ccp/api/molecule/MolSystem.py", line 1583, in getByKey
obj1.load()
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/api/Implementation.py", line 5066, in load
self.loadFrom(repositories[0])
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/api/Implementation.py", line 5100, in loadFrom
XmlIO.loadTopObject(repository.url.getDataLocation(), self)
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/format/xml/XmlIO.py",
line 236, in loadTopObject
return loadFromStream(open(filePath), topObjId=topObjId,
topObject=topObject)
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/format/xml/XmlIO.py",
line 273, in loadFromStream
partialLoad=partialLoad)
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/xml/Implementation.py", line 4881, in loadFromStream
obj.checkValid()
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/ccp/api/molecule/MolSystem.py", line 20389, in checkValid
('molResidues', self.seqId),
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/api/Implementation.py", line 4013, in getByNavigation
result.load()
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/api/Implementation.py", line 5066, in load
self.loadFrom(repositories[0])
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/api/Implementation.py", line 5100, in loadFrom
XmlIO.loadTopObject(repository.url.getDataLocation(), self)
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/format/xml/XmlIO.py",
line 236, in loadTopObject
return loadFromStream(open(filePath), topObjId=topObjId,
topObject=topObject)
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/format/xml/XmlIO.py",
line 273, in loadFromStream
partialLoad=partialLoad)
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/xml/Implementation.py", line 4853, in loadFromStream
delayedLoadLinksExo(topObjByGuid, exoTopLinkData)
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/xml/Implementation.py", line 5165, in delayedLoadLinksExo
root.refreshTopObjects(packageName)
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/api/Implementation.py", line 16542, in refreshTopObjects
topObject = XmlIO.loadFromFile(self, filePath, partialLoad=True)
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/format/xml/XmlIO.py",
line 251, in loadFromFile
partialLoad=partialLoad)
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/format/xml/XmlIO.py",
line 273, in loadFromStream
partialLoad=partialLoad)
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/xml/Implementation.py", line 4862, in loadFromStream
linkChildData(delayDataDict, result, mapping, linkTopToParent,
doOutOfPackage)
File
"/usr/local64/ccpnmr2.1.1/ccpnmr2.1/python/memops/xml/Implementation.py", line 5069, in linkChildData
+ ": %s:%s:%s" % (obj.getQualifiedName(), obj.getParent(), key)
memops.general.Implementation.ApiError: Cannot add child - key already
in use:
ccp.molecule.ChemComp.StdChemComp:<memops.Implementation.MemopsRoot
id:109832656>:('protein', 'Xxx')
>>>
The project works fine in analysis 2.0.
Cheers
Andy
--
Dr Andy Herbert
Department of Chemistry
University of Edinburgh
West Mains Road
Edinburgh
UK
EH9 3JJ
Tel: +44 (0)131 651 3042 or 650 4792
Email: [log in to unmask]
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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