Well that did the trick, but where did the Xxx come from in the first
place? I can't find any reference to it in the old project.
cheers
Andy
On Thu, 2009-10-29 at 16:29 +0000, Wayne Boucher wrote:
> Xxx, is that a real amino acid???
>
> Anyway, I think that in v2.0, Xxx was not included in the release, but it
> seems to be in v2.1 for whatever reason. So my guess is that you have a
> version of Xxx in your project directory and there is another one in the
> reference data directory (so that file it mentions in the error message).
> The simplest solution will be to delete the version in your project
> directory (so look for a file name that contains "Xxx" and ends in ".xml"
> and lives in a directory called ccp/molecule/ChemComp). (Well, you might
> want to move that file rather than delete it.)
>
> Wayne
>
> On Thu, 29 Oct 2009, Dr Andy Herbert wrote:
>
> > 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.
> >
>
--
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.
