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.
>>>>
>>>>
>>>>
>>>>
Only in AGR2/ccp/general: DataLocation
Only in AGR2/ccp/general: Instrument
diff -r AGR2/ccp/general/Method/AGR2+AGR2_pryank_2009-03-25-13-41-04-841_00001.xml AGR2_backup//ccp/general/Method/AGR2+AGR2_pryank_2009-03-25-13-41-04-841_00001.xml
2c2
< <_StorageUnit release="2.0.b2" originator="CCPN Python XmlIO" packageGuid="www.ccpn.ac.uk_Fogh_2006-08-16-14:25:09_00027" time="Fri Apr 17 15:06:49 2009">
---
> <_StorageUnit release="2.0.b2" originator="CCPN Python XmlIO" packageGuid="www.ccpn.ac.uk_Fogh_2006-08-16-14:25:09_00027" time="Fri Apr 17 15:01:41 2009">
Only in AGR2/ccp/general/Method: AGR2+AGR2_pryank_2009-03-25-13-41-04-841_00001.xml.bak
Only in AGR2/ccp/molecule: Molecule
diff -r AGR2/ccp/molecule/MolSystem/MS1+AGR2_pryank_2009-03-26-10-44-03-588_00001.xml AGR2_backup//ccp/molecule/MolSystem/MS1+AGR2_pryank_2009-03-26-10-44-03-588_00001.xml
2c2
< <_StorageUnit release="2.0.b2" originator="CCPN Python XmlIO" packageGuid="www.ccpn.ac.uk_Fogh_2006-08-16-14:22:54_00022" time="Thu Apr 16 16:47:08 2009">
---
> <_StorageUnit release="2.0.b2" originator="CCPN Python XmlIO" packageGuid="www.ccpn.ac.uk_Fogh_2006-08-16-14:22:54_00022" time="Thu Apr 16 16:43:05 2009">
9c9
< <IMPL.AppDataInt value="1239896827">
---
> <IMPL.AppDataInt value="1239891624">
Only in AGR2/ccp/molecule/MolSystem: MS1+AGR2_pryank_2009-03-26-10-44-03-588_00001.xml.bak
diff -r AGR2/ccp/nmr/Nmr/AGR2+AGR2_pryank_2009-03-25-13-41-03-886_00002.xml AGR2_backup//ccp/nmr/Nmr/AGR2+AGR2_pryank_2009-03-25-13-41-03-886_00002.xml
2c2
< <_StorageUnit release="2.0.b2" originator="CCPN Python XmlIO" packageGuid="www.ccpn.ac.uk_Fogh_2006-08-16-14:22:46_00006" time="Fri Apr 17 15:06:49 2009">
---
> <_StorageUnit release="2.0.b2" originator="CCPN Python XmlIO" packageGuid="www.ccpn.ac.uk_Fogh_2006-08-16-14:22:46_00006" time="Fri Apr 17 15:01:41 2009">
9c9
< <IMPL.AppDataInt value="1239977209">
---
> <IMPL.AppDataInt value="1239897948">
Only in AGR2/ccp/nmr/Nmr: AGR2+AGR2_pryank_2009-03-25-13-41-03-886_00002.xml.bak
diff -r AGR2/ccpnmr/Analysis/AGR2+AGR2_pryank_2009-03-25-13-41-03-887_00001.xml AGR2_backup//ccpnmr/Analysis/AGR2+AGR2_pryank_2009-03-25-13-41-03-887_00001.xml
2c2
< <_StorageUnit release="2.0.b2" originator="CCPN Python XmlIO" packageGuid="www.ccpn.ac.uk_Fogh_2006-08-17-14:16:20_00002" time="Fri Apr 17 15:06:49 2009">
---
> <_StorageUnit release="2.0.b2" originator="CCPN Python XmlIO" packageGuid="www.ccpn.ac.uk_Fogh_2006-08-17-14:16:20_00002" time="Fri Apr 17 15:01:41 2009">
143c143
< <IMPL.AppDataInt value="1239977209">
---
> <IMPL.AppDataInt value="1239970938">
Only in AGR2/ccpnmr/Analysis: AGR2+AGR2_pryank_2009-03-25-13-41-03-887_00001.xml.bak
Only in AGR2_backup/: generalData
diff -r AGR2/memops/Implementation/AGR2.xml AGR2_backup//memops/Implementation/AGR2.xml
2c2
< <_StorageUnit release="2.0.b2" originator="CCPN Python XmlIO" packageGuid="www.ccpn.ac.uk_Fogh_2006-08-16-14:22:53_00025" time="Thu Apr 16 16:47:09 2009">
---
> <_StorageUnit release="2.0.b2" originator="CCPN Python XmlIO" packageGuid="www.ccpn.ac.uk_Fogh_2006-08-16-14:22:53_00025" time="Thu Apr 16 16:43:06 2009">
301c301
< <IMPL.AppDataInt value="1239896827">
---
> <IMPL.AppDataInt value="1239894701">
3899c3899
< <IMPL.AppDataInt value="1239896827">
---
> <IMPL.AppDataInt value="1239891624">
5146c5146
< <IMPL.AppDataInt value="1239896827">
---
> <IMPL.AppDataInt value="1239891624">
Only in AGR2/memops/Implementation: AGR2.xml.bak
Only in AGR2_backup/: userData
|
