Dear Brian,
The error message says that there are two ExpPrototypes with serial 253
found in the project. 2.2.2 has an ExpPrototype with that serial, and
2.1.5 does not, so that part makes sense. The likely reason is that you
have added an ExpPrototype of your own, with the serial 253, and that it
lives in the project itself (ccp/nmr/NmrExpPrototype). If you delete that
one you should be OK. Of course if it is in use that wil break some
things, so you may have to unset the ExpPrototype for experiments hta
use it, upgrade, and then remake your new ExpPrototype so it gets a new
serial (or you could change the serial by hand).
We do not really have a good solution to this problem at the moment. When
more ExpPrototypes are added to the refrence data, it uses up serials that
may be taken in individual projects. We would likely have to give each
ExpProtype a unique name as a key. It will certainly not be for the next
six months, though.
Yours,
Rasmus
---------------------------------------------------------------------------
Dr. Rasmus H. Fogh Email: [log in to unmask]
Dept. of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002
On Mon, 30 Apr 2012, Brian Smith wrote:
> I'm having trouble reading a project that loads without fuss in 2.1.5. My
> guess is that there's some incompatible ExpType in the project:
>
> Error loading file for: <ccp.nmr.NmrExpPrototype.NmrExpPrototype [253]>
> Reading: <open file
> '/usr/local/ccpnmr/ccpnmr2.2/data/ccp/nmr/NmrExpPrototype/253+Expts_vicky_2010-12-14-13-22-07-063_00001.xml',
> mode 'r' at 0x125d9c00>
> Last xml tag read: NMRX.NmrExpPrototype.atomSites
> Parser state was: postprocessing data
> Object stack was empty
> Error loading file for: <ccp.nmr.Nmr.NmrProject ['proteinX']>
> Reading: <open file
> '/home/gillian/analysis/ATG8B/ATG8Bg/ccp/nmr/Nmr/proteinX+proteinX_kirstyh_2009-12-01-11-46-02-205_00002.xml',
> mode 'r' at 0x871a660>
> Last xml tag read: _StorageUnit
> Parser state was: handling version compatibility
> Object stack was empty
> Traceback (most recent call last):
> File "/usr/local/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisGui.py",
> line 226, in <module>
> main(projectDir, max_size, glDirect)
> File "/usr/local/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisGui.py",
> line 102, in main
> project = loadProject(top, path=projectDir)
> File "/usr/local/ccpnmr/ccpnmr2.2/python/ccp/gui/Io.py", line 92, in
> loadProject
> if isinstance(dataStore, NumericMatrix) and not dataStore.nmrDataSources:
> File "/usr/local/ccpnmr/ccpnmr2.2/python/ccp/api/general/DataLocation.py",
> line 5628, in getNmrDataSources
> tobj.load()
> File "/usr/local/ccpnmr/ccpnmr2.2/python/memops/api/Implementation.py",
> line 25419, in load
> self.loadFrom(repositories[0])
> File "/usr/local/ccpnmr/ccpnmr2.2/python/memops/api/Implementation.py",
> line 25453, in loadFrom
> XmlIO.loadTopObject(repository.url.getDataLocation(), self)
> File "/usr/local/ccpnmr/ccpnmr2.2/python/memops/format/xml/XmlIO.py", line
> 236, in loadTopObject
> return loadFromStream(open(filePath), topObjId=topObjId,
> topObject=topObject)
> File "/usr/local/ccpnmr/ccpnmr2.2/python/memops/format/xml/XmlIO.py", line
> 267, in loadFromStream
> partialLoad=partialLoad)
> File "/usr/local/ccpnmr/ccpnmr2.2/python/memops/xml/Implementation.py",
> line 5103, in loadFromStream
> Converters1.minorPostProcess(fileVersion, result, delayDataDict,
> objectDict, mapping, topObjElem)
> File
> "/usr/local/ccpnmr/ccpnmr2.2/python/memops/format/compatibility/part1/Converters1.py",
> line 924, in minorPostProcess
> mod.Minor.correctData(topObj, delayDataDict, toNewObjDict, mapping)
> File
> "/usr/local/ccpnmr/ccpnmr2.2/python/memops/format/compatibility/upgrade/v_2_0_b3/Minor.py",
> line 72, in correctData
> Minor204.correctData(topObj, delayDataDict, toNewObjDict, mapping)
> File
> "/usr/local/ccpnmr/ccpnmr2.2/python/memops/format/compatibility/upgrade/v_2_0_4/Minor.py",
> line 84, in correctData
> fixNmr(topObj, delayDataDict)
> File
> "/usr/local/ccpnmr/ccpnmr2.2/python/memops/format/compatibility/upgrade/v_2_0_4/Minor.py",
> line 121, in fixNmr
> remapPrototypeLink)
> File
> "/usr/local/ccpnmr/ccpnmr2.2/python/memops/format/compatibility/upgrade/v_2_0_a1/Minor.py",
> line 203, in setNmrExpPrototypeLink
> obj.root.refreshTopObjects(clazz._packageName)
> File "/usr/local/ccpnmr/ccpnmr2.2/python/memops/api/Implementation.py",
> line 17701, in refreshTopObjects
> topObject = XmlIO.loadFromFile(self, filePath, partialLoad=True)
> File "/usr/local/ccpnmr/ccpnmr2.2/python/memops/format/xml/XmlIO.py", line
> 251, in loadFromFile
> partialLoad=partialLoad)
> File "/usr/local/ccpnmr/ccpnmr2.2/python/memops/format/xml/XmlIO.py", line
> 273, in loadFromStream
> partialLoad=partialLoad)
> File "/usr/local/ccpnmr/ccpnmr2.2/python/memops/xml/Implementation.py",
> line 5106, in loadFromStream
> linkChildData(delayDataDict, result, mapping, linkTopToParent,
> doOutOfPackage)
> File "/usr/local/ccpnmr/ccpnmr2.2/python/memops/xml/Implementation.py",
> line 5313, in linkChildData
> + ": %s:%s:%s" % (obj.getQualifiedName(), obj.getParent(), key)
> memops.general.Implementation.ApiError: Cannot add child - key already in
> use:
> ccp.nmr.NmrExpPrototype.NmrExpPrototype:<memops.Implementation.MemopsRoot
> id:198842384>:253
>
>
>
> Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
> Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
> College of Medical, Veterinary & Life Sciences,
> Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
> Tel: 0141 330 5167/6459/3089 Fax: 0141 330 4600
> ----------------------------------------------------------------------
> The University of Glasgow, charity number SC004401
>
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