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CCPNMR  May 2012

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Subject:

Re: Trouble reading 2.1.5 project with 2.2.2: experiment prototypes?

From:

Rasmus Fogh <[log in to unmask]>

Reply-To:

CcpNmr software mailing list <[log in to unmask]>

Date:

Tue, 1 May 2012 10:02:46 +0100

Content-Type:

TEXT/PLAIN

Parts/Attachments:

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TEXT/PLAIN (127 lines)

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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