Hello,
When you mean the backup project I assume you mean in the
PROJECTDIR_backup directory (so as created by the Auto backup procedure).
There is a slight but in how the code deals with that in that it saves
stuff to that directory but it never deletes stuff, and it's possible that
indeed it ends up not being a totally consistent project.
What I would do first (but it might not work) is to backup your existing
project directory and then, if you know which XML files, are no good in
that directory, copy just those corresponding files over from the backup
project directory. Quite likely it is just the ccp/nmr/Nmr/***.xml file
that is the problem but it might be something else, dependent on exactly
what went wrong.
If you want me to take a look then gzip up both the project directory and
the backup directory and send it to me (off list).
Wayne
On Fri, 29 Mar 2013, Patel, Pryank wrote:
>
> Hi all,
> Apologies if this has been reported before, but I cannot find anything about it. The CCPN
> Analysis project I was working on crashed suddenly, and as I had not saved it for a couple
> of hours I opened the backup project which autosaves more regularly. However, it did not
> seem to open all the windows that were open previously and, more worryingly, in the main
> CCPN Analysis toolbar, a lot of the features and options were greyed out and not clickable
> (eg: Molecule:Atom Browser, etc), and windows such as the Peak:Peak Lists window, when it
> was open before and full, were now empty. I also noticed the following error in the
> console:
>
> Error loading file for: <ccp.molecule.MolStructure.StructureEnsemble
> [<ccp.molecule.MolSystem.MolSystem ['MS1']>, 1]>
> Reading: <open file'/home/pryank/nmr-projects/CSP/1_100_backup/ccp/molecule/MolStructure/_ccp_molecule_MolSy
> stem_MolSystem___MS1___+1+1_100_pryank_2013-03-17-23-33-51-183_00001.xml', mode 'r' at
> 0xf24b8a0>
> Last xml tag read: COOR.StructureEnsemble.coordChains
> Parser state was: postprocessing data
> Object stack was empty
> Traceback (most recent call last):
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisGui.py",
> line 226, in <module>
> main(projectDir, max_size, glDirect)
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisGui.py",
> line 111, in main
> top.initProject(project)
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisPopup.py",
> line 1622, in initProject
> self.openActivePopups()
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisPopup.py",
> line 857, in openActivePopups
> func()
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisPopup.py",
> line 1923, in editPeakLists
> popup = self.openPopup('edit_peak_lists', EditPeakListsPopup)
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisPopup.py",
> line 1785, in openPopup
> transient=transient, *args, **kw)
> File
> "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/EditPeakLists.py",
> line 300, in __init__
> BasePopup.__init__(self, parent=parent, title="Peak : Peak Lists", **kw)
> File
> "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/BasePopup.py", line
> 89, in __init__
> memops.editor.BasePopup.BasePopup.__init__(self, parent, *args, **kw)
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/memops/editor/BasePopup.py", line
> 85, in __init__
> memops.gui.BasePopup.BasePopup.__init__(self, parent, *args, **kw)
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/memops/gui/BasePopup.py", line 128,
> in __init__
> self.initial_focus = self.body(frame)
> File
> "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/EditPeakLists.py",
> line 406, in body
> grid=(0,0))
> File"/home/pryank/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/frames/PeakTableFrame.py",
> line 280, in __init__
> self.updateStructures()
> File"/home/pryank/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/frames/PeakTableFrame.py",
> line 446, in updateStructures
> structures = self.getStructures()
> File"/home/pryank/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/frames/PeakTableFrame.py",
> line 481, in getStructures
> for structure in molSystem.structureEnsembles:
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/ccp/api/molecule/MolSystem.py", line
> 13530, in getStructureEnsembles
> root.refreshTopObjects('ccp.molecule.MolStructure')
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/memops/api/Implementation.py", line
> 17701, in refreshTopObjects
> topObject = XmlIO.loadFromFile(self, filePath, partialLoad=True)
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/memops/format/xml/XmlIO.py", line
> 251, in loadFromFile
> partialLoad=partialLoad)
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/memops/format/xml/XmlIO.py", line
> 267, in loadFromStream
> partialLoad=partialLoad)
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/memops/xml/Implementation.py", line
> 5106, in loadFromStream
> linkChildData(delayDataDict, result, mapping, linkTopToParent, doOutOfPackage)
> File "/home/pryank/programs/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.molecule.MolStructure.StructureEnsemble:<memops.Implementation.MemopsRoot
> id:109306704>:(<ccp.molecule.MolSystem.MolSystem ['MS1']>, 1)
>
>
> I am unable to save the backup project under another name (Project:Save and Project:Save
> As are greyed out) and, if I try and quit analysis (without saving when asked) another
> error message appears in the console:
>
> >>> Exception in Tkinter callback
> Traceback (most recent call last):
> File "/home/pryank/programs/ccpnmr/python2.6/lib/python2.6/lib-tk/Tkinter.py", line
> 1410, in __call__
> return self.func(*args)
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisPopup.py",
> line 2799, in quit
> self.destroy()
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisPopup.py",
> line 2786, in destroy
> BasePopup.destroy(self)
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/memops/editor/BasePopup.py", line
> 234, in destroy
> memops.gui.BasePopup.BasePopup.destroy(self)
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/memops/gui/BasePopup.py", line 424,
> in destroy
> Tkinter.Toplevel.destroy(self)
> File "/home/pryank/programs/ccpnmr/python2.6/lib/python2.6/lib-tk/Tkinter.py", line
> 1937, in destroy
> for c in self.children.values(): c.destroy()
> File
> "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/EditPeakLists.py",
> line 1164, in destroy
> self.administerNotifiers(self.unregisterNotify)
> File
> "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/EditPeakLists.py",
> line 648, in administerNotifiers
> notifyFunc(self.peakTableFrame.contribUpdateAfter, clazz, func)
> File "/home/pryank/programs/ccpnmr/ccpnmr2.2/python/memops/gui/BasePopup.py", line 442,
> in __getattr__
> raise AttributeError, "%s instance has no attribute '%s'" % (self.__class__.__name__,
> name)
> AttributeError: EditPeakListsPopup instance has no attribute 'peakTableFrame'
>
> "Always send" option
>
>
> Not only that, but Analysis is hanging during the exit procedure. The only way I can find
> to exit from Analysis is to manually close the console window from which Analysis is
> launched.
>
> I hasten to add that there does not seem to be a problem with the non-backup CCPN project
> directory, apart from the fact that it is now a couple of hours behind where I left it.
>
> I am using version 2.2.2.
>
> Best wishes,
> Pryank
>
>
>
>
>
>
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