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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