Well that is interesting. Were there any funny amino acids in the v1
project? Maybe the upgrade script did a (bad) substitution. (Or maybe it
chucks in an Xxx for fun now and again.) In the v2 project can you see
Xxx in any of the molecular sequences? And if so what was in the
equivalent spot in the v1 project?
Wayne
On Thu, 29 Oct 2009, Dr Andy Herbert wrote:
> 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.
>
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