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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