In the Molecule directory:
Molecule_1+AGR2_pryank_2009-03-26-10-44-01-852_00001.xml
Molecule_1+AGR2_pryank_2009-03-26-10-44-01-852_00001.xml.bak
Pryank
Wayne Boucher wrote:
> So in the original project directory what files are in the Molecule
> directory?
>
> Wayne
>
> On Fri, 17 Apr 2009, Dr. Pryank Patel wrote:
>
>
>> Hi Wayne,
>> In the [backup]/ccp/molecule, there is no Molecule directory, only the
>> MolSystem directory. I had hoped that by copying over the Molecule directory
>> from the original project directory that it would solve the issue, but the
>> same error messages still appear.
>>
>> I don't know if this is of any use, but I have attached the output of a "diff
>> -r [project] [project_backup]".
>>
>> Best wishes,
>> Pryank
>>
>>
>> Wayne Boucher wrote:
>>
>>> Hello,
>>>
>>> I've had a quick chat with Rasmus and we don't know what has gone wrong. So
>>> it is loading a chain in a MolSystem (specifically chain A of molSystem
>>> MS1) and each such chain points to a molecule. Now the molecule it is
>>> looking for has the (arcane) key AGR2_pryank_2009_03_26-10-44-01-852_00001
>>> (unfortunately the error message does not give the name of the molecule but
>>> presumably you know what chain A's molecule ought to be).
>>>
>>> What files do you see in the directory ccp/molecule/Molecule? There is
>>> supposed to be one ending with that horrid key above (+ (.xml"). The file
>>> is actually prefixed with the molecule name (with underscores replacing
>>> spaces). Look in both the backup directory and the original project
>>> directory because I guess it's possible that the molecule file (for some
>>> reason) is only in the original directory. (Which would tend to indicate
>>> that the backup failed in its job.)
>>>
>>> Wayne
>>>
>>> On Fri, 17 Apr 2009, Dr. Pryank Patel wrote:
>>>
>>>
>>>
>>>> Hi Wayne,
>>>> Thanks for the information. I have tried to open a backup project before
>>>> but failed, which is why I asked, to see where I went wrong. I tried to
>>>> open the backup project from the Open Project dialog, and received a
>>>> "Project invalid" box error message, saying "Project invalid, please quit,
>>>> fix and restart: Linked-to object with ID not found:
>>>> <ccp.molecule.MolSystem.Chain['MS1',
>>>> 'A']>:molecule:AGR2_pryank_2009_03_26-10-44-01-852_00001". The error
>>>> message in the console is as follows:
>>>>
>>>>
>>>>
>>>>>>> Error during Exo link dereferencing. Object was:
>>>>>>>
>>>> <ccp.molecule.MolSystem.Chain ['MS1', 'A']>
>>>> values were: ['AGR2_pryank_2009-03-26-10-44-01-852_00001']
>>>> tag name was: molecule
>>>> Error loading file for: <ccp.molecule.MolSystem.MolSystem ['MS1']>
>>>> Reading: <open file
>>>> '/home/pryank/nmr-projects/AGR2-P40/AGR2_backup/ccp/molecule/MolSystem/MS1+AGR2_pryank_2009-03-26-10-44-03-588_00001.xml',
>>>> mode 'r' at 0x59f2580>
>>>> Last xml tag read: _StorageUnit
>>>> Parser state was: postprocessing data
>>>> Object stack was empty
>>>> Error loading file for: <ccp.nmr.Nmr.NmrProject ['AGR2']>
>>>> Reading: <open file
>>>> '/home/pryank/nmr-projects/AGR2-P40/AGR2_backup/ccp/nmr/Nmr/AGR2+AGR2_pryank_2009-03-25-13-41-03-886_00002.xml',
>>>> mode 'r' at 0x59f24f8>
>>>> Last xml tag read: NMR.AtomSet.atoms
>>>> Parser state was: reading
>>>> Current object was: <ccp.nmr.Nmr.AtomSet ['AGR2', 1]>
>>>> Error loading file for: <ccpnmr.Analysis.AnalysisProject ['AGR2']>
>>>> Reading: <open file
>>>> '/home/pryank/nmr-projects/AGR2-P40/AGR2_backup/ccpnmr/Analysis/AGR2+AGR2_pryank_2009-03-25-13-41-03-887_00001.xml',
>>>> mode 'r' at 0x59f23e8>
>>>> Last xml tag read: ANAL.AnalysisSpectrum.dataSource
>>>> Parser state was: reading
>>>> Current object was: <ccpnmr.Analysis.AnalysisSpectrum ['AGR2', None]>
>>>>
>>>>
>>>> If I try and open the backup project in your recommended way, renaming
>>>> xyz_backup to xyz, the same set of messages appear as above, but with an
>>>> added traceback message at the end
>>>>
>>>> Error during Exo link dereferencing. Object was:
>>>> <ccp.molecule.MolSystem.Chain ['MS1', 'A']>
>>>> values were: ['AGR2_pryank_2009-03-26-10-44-01-852_00001'] tag name was:
>>>> molecule Error loading file for: <ccp.molecule.MolSystem.MolSystem
>>>> ['MS1']> Reading: <open file
>>>> '/home/pryank/nmr-projects/AGR2-P40/AGR2/ccp/molecule/MolSystem/MS1+AGR2_pryank_2009-03-26-10-44-03-588_00001.xml',
>>>> mode 'r' at 0x58cbcf0> Last
>>>> xml tag read: _StorageUnit Parser state was: postprocessing data Object
>>>> stack was empty Error loading file for: <ccp.nmr.Nmr.NmrProject ['AGR2']>
>>>> Reading: <open file
>>>> '/home/pryank/nmr-projects/AGR2-P40/AGR2/ccp/nmr/Nmr/AGR2+AGR2_pryank_2009-03-25-13-41-03-886_00002.xml',
>>>> mode 'r' at 0x58c1f10> Last xml tag read: NMR.AtomSet.atoms Parser state
>>>> was: reading Current object was: <ccp.nmr.Nmr.AtomSet ['AGR2', 1]> Error
>>>> loading file for: <ccpnmr.Analysis.AnalysisProject ['AGR2']> Reading:
>>>> <open file
>>>> '/home/pryank/nmr-projects/AGR2-P40/AGR2/ccpnmr/Analysis/AGR2+AGR2_pryank_2009-03-25-13-41-03-887_00001.xml',
>>>> mode 'r' at 0x4b4e828> Last xml tag read:
>>>> ANAL.AnalysisSpectrum.dataSource Parser state was: reading Current object
>>>> was: <ccpnmr.Analysis.AnalysisSpectrum ['AGR2', None]> Traceback (most
>>>> recent call last): File
>>>> "/home/pryank/programs/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/AnalysisGui.py",
>>>> line 224, in <module>
>>>> main(projectDir, max_size, glDirect) File
>>>> "/home/pryank/programs/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/AnalysisGui.py",
>>>> line 111, in main
>>>> top.initProject(project) File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/AnalysisPopup.py",
>>>> line 1004, in initProject
>>>> Analysis.initProject(self, project) File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/Analysis.py",
>>>> line 257, in initProject
>>>> self.initTopObjects(project) File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/Analysis.py",
>>>> line 228, in initTopObjects
>>>> self.analysisProject.isThreadingAllowed = False File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/ccpnmr/api/Analysis.py",
>>>> line 10239, in setIsThreadingAllowed
>>>>
>>>> File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/api/Implementation.py",
>>>> line 5036, in load File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/api/Implementation.py",
>>>> line 5070, in loadFrom File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/format/xml/XmlIO.py",
>>>> line 236, in loadTopObject File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/format/xml/XmlIO.py",
>>>> line 267, in loadFromStream File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/xml/Implementation.py",
>>>> line 4724, in loadFromStream File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/ccp/api/nmr/Nmr.py",
>>>> line 16393, in getByKey File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/api/Implementation.py",
>>>> line 5036, in load
>>>> File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/api/Implementation.py",
>>>> line 5070, in loadFrom
>>>> File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/format/xml/XmlIO.py",
>>>> line 236, in loadTopObject
>>>> File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/format/xml/XmlIO.py",
>>>> line 273, in loadFromStream
>>>> File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/xml/Implementation.py",
>>>> line 4724, in loadFromStream
>>>> File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/ccp/api/molecule/MolSystem.py",
>>>> line 1278, in getByKey
>>>> File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/api/Implementation.py",
>>>> line 5036, in load
>>>> File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/api/Implementation.py",
>>>> line 5070, in loadFrom
>>>> File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/format/xml/XmlIO.py",
>>>> line 236, in loadTopObject
>>>> File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/format/xml/XmlIO.py",
>>>> line 273, in loadFromStream
>>>> File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/xml/Implementation.py",
>>>> line 4772, in loadFromStream
>>>> File
>>>> "/home/pryank/programs/ccpnmr/temporaryReleaseDir/ccpnmr/ccpnmr2.0/python/memops/xml/Implementation.py",
>>>> line 5089, in delayedLoadLinksExo
>>>> memops.general.Implementation.ApiError: Linked-to object with ID not
>>>> found: <ccp.molecule.MolSystem.Chain ['MS1',
>>>> 'A']>:molecule:AGR2_pryank_2009-03-26-10-44-01-852_00001
>>>> Best wishes,
>>>> Pryank
>>>>
>>>>
>>>> Wayne Boucher wrote:
>>>>
>>>>
>>>>> Hello,
>>>>>
>>>>> I forgot to answer the question about the automated backup. Here is a
>>>>> general blurb about backups.
>>>>>
>>>>> There are two types of backup. One backup happens when you do a save, so
>>>>> it copies an existing *.xml file to *.xml.bak. To use those you just
>>>>> have to rename the *.xml.bak as *.xml. Right now I'm not sure if all the
>>>>> *.xml.bak taken together are guaranteed to be in a consistent state (i.e.
>>>>> if you copy them all over then it will work). The main point of these
>>>>> *.bak files is in case your disk is nearly full and writing out a new
>>>>> *.xml file is not completed. So generally you probably wouldn't use
>>>>> these backups.
>>>>>
>>>>> The other backup (and I think the one the question was about) is one you
>>>>> can generate automatically (or on demand) via the Project --> Backup
>>>>> dialog. The default here is that if your project is called Xyz then the
>>>>> backup directory is Xyz_backup. When you open up a project you can just
>>>>> use that directory rather than Xyz, i.e. instead of
>>>>>
>>>>> analysis Xyz
>>>>>
>>>>> you could do:
>>>>>
>>>>> analysis Xyz_backup
>>>>>
>>>>> This will warn you that some paths have changed. Instead of doing it
>>>>> this way I'd generally recommend that instead you rename Xyz_backup to
>>>>> Xyz (after backing up Xyz by hand just in case!).
>>>>>
>>>>> (You can also open up the backup via the Open Project dialog. You would
>>>>> see the backup project row in the dialog coloured yellow instead of
>>>>> green, but only because the project file is called Xyz.xml instead of
>>>>> Xyz_backup.xml, which analysis can cope with perfectly well, but it's
>>>>> warning you that this is not a standard naming.)
>>>>>
>>>>> Wayne
>>>>>
>>>>> On Wed, 15 Apr 2009, Dr. Pryank Patel wrote:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>> ...
>>>>>
>>>>>
>>>>>
>>>>>> PS: is there any documentation on using the Backup system in Analysis?
>>>>>> ie: how to load up a project from automated backup.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
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