Yes, unicode creates Analysis problems. That is the acute e and the most
likely places for that are in some citation or name or organisation or
something. Given that Leeds is not in France hopefully it's pretty
obvious where the offending character might be. You should be able to
edit the relevant xml file to change it (to "e", say), but if you have any
problem finding it then let me know.
Wayne
On Tue, 20 Nov 2012, Gary Thompson wrote:
> Hi Wayne
>
> many thanks fotr the file I just created one myself and it works ! ;-) howevere all is not cured I now have a UnicodeEncodeError: 'ascii' codec can't encode character u'\xe9' in position 34: ordinal not in range(128) on save i presume somewhere i copied some unicode and it doesn't like it???
>
>
> regards
> gary
>
> ________________________________________
> From: CcpNmr software mailing list [[log in to unmask]] On Behalf Of Wayne Boucher [[log in to unmask]]
> Sent: 20 November 2012 16:33
> To: [log in to unmask]
> Subject: Re: [CCPNMR] more weirdness constraint must_point_to_valid_KeywordDefinition
>
> OK, that was the issue I just emailed you about off list (!). (So crossed
> postings.)
>
> Analysis creates ResidueValidations but it checks that the relevant
> KeywordDefinitions exist, and creates them if they do not. So somehow
> some other program (I think) created (by copying??) ResidueValidations but
> seemingly did not create (copy) the KeywordDefinitions.
>
> If you have any project with a ccp/general/KeywordDefinition/***.xml file
> then you should be able to copy that into that project and it ought to
> work.
>
> I'll email you one off list in case you cannot find one.
>
> Wayne
>
> On Tue, 20 Nov 2012, Gary Thompson wrote:
>
>> Hi
>>
>> i have just loaded a set of astructures into my data deposition project and I now get the following stack trace when i try and reload the datamodel after a save
>>
>>
>> Using CCPN version 2.0.5, NMR-STAR version 3.1.
>> Warning: No Ccpn__2_0_5__To_NmrStar__3_1__ conversion class available, using Ccpn_To_NmrStar default.
>> Warning: No Ccpn__2_0_5__To_NmrStar__3_1__ constants dictionary available, using Ccpn_To_NmrStar default.
>> Error loading file for: <ccp.molecule.Validation.ValidationStore ['RMSD_p7_meth_depo_garyt_2012-11-20-12-13-12-339_00001']>
>> Reading: <open file '/home/garyt/projects/p7/p7_backbone/p7_meth_depo_broken_revovery2/ccp/molecule/Validation/RMSD_p7_meth_depo_garyt_2012_11_20_12_13_12_339_00001+p7_meth_depo_garyt_2012-11-20-12-14-36-697_00001.xml', mode 'r' at 0x15006ed0>
>> Last xml tag read: _StorageUnit
>> Parser state was: checking validity
>> Object stack was empty
>> Error loading file for: <ccp.molecule.MolStructure.StructureEnsemble [<ccp.molecule.MolSystem.MolSystem ['MS1']>, 1]>
>> Reading: <open file '/home/garyt/projects/p7/p7_backbone/p7_meth_depo_broken_revovery2/ccp/molecule/MolStructure/_ccp_molecule_MolSystem_MolSystem___MS1___+1+p7_meth_depo_garyt_2012-11-20-12-13-12-339_00001.xml', mode 'r' at 0x15006e40>
>> Last xml tag read: COOR.Residue.residueValidations
>> Parser state was: reading
>> Current object was: <ccp.molecule.MolStructure.Residue [<ccp.molecule.MolSystem.MolSystem ['MS1']>, 1, 'A', 2]>
>> Traceback (most recent call last):
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisGui.py", line 226, in <module>
>> main(projectDir, max_size, glDirect)
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisGui.py", line 111, in main
>> top.initProject(project)
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisPopup.py", line 1622, in initProject
>> self.openActivePopups()
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisPopup.py", line 857, in openActivePopups
>> func()
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisPopup.py", line 2706, in startECI
>> popup = self.openPopup('entry_completion_interface', EntryCompletionPopup)
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisPopup.py", line 1785, in openPopup
>> transient=transient, *args, **kw)
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/eci/EntryCompletionPopup.py", line 83, in __init__
>> BasePopup.__init__(self, parent, title='Deposition Entry Completion Interface', **kw)
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/memops/editor/BasePopup.py", line 85, in __init__
>> memops.gui.BasePopup.BasePopup.__init__(self, parent, *args, **kw)
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/memops/gui/BasePopup.py", line 128, in __init__
>> self.initial_focus = self.body(frame)
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/eci/EntryCompletionPopup.py", line 93, in body
>> frame.updateAll()
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/eci/EntryCompletionFrame.py", line 2847, in updateAll
>> self.updateEntries()
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/eci/EntryCompletionFrame.py", line 2974, in updateEntries
>> self.changeEntry(entry)
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/eci/EntryCompletionFrame.py", line 2905, in changeEntry
>> self.updateAll()
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/eci/EntryCompletionFrame.py", line 2850, in updateAll
>> self.selectTab(self.tabbedFrame.selected)
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/eci/EntryCompletionFrame.py", line 2838, in selectTab
>> func()
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/eci/EntryCompletionFrame.py", line 3019, in updateMain
>> self.updateReport()
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/eci/EntryCompletionFrame.py", line 2987, in updateReport
>> results = checkNmrEntryCompleteness(self.entry, submissionType=self.submissionType)
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/eci/CompletenessCheck.py", line 861, in checkNmrEntryCompleteness
>> ccpnObjDict = checkCcpnObjects(nmrEntry, submissionType)
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccpnmr/eci/CompletenessCheck.py", line 764, in checkCcpnObjects
>> elif not structureGeneration.structureEnsemble.models:
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccp/api/molecule/MolStructure.py", line 10133, in getModels
>> self.load()
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/memops/api/Implementation.py", line 25419, in load
>> self.loadFrom(repositories[0])
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/memops/api/Implementation.py", line 25453, in loadFrom
>> XmlIO.loadTopObject(repository.url.getDataLocation(), self)
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/memops/format/xml/XmlIO.py", line 236, in loadTopObject
>> return loadFromStream(open(filePath), topObjId=topObjId, topObject=topObject)
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/memops/format/xml/XmlIO.py", line 267, in loadFromStream
>> partialLoad=partialLoad)
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/memops/xml/Implementation.py", line 5043, in loadFromStream
>> value = clazz.getByKey(oo,vv[1:-1])
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccp/api/molecule/Validation.py", line 11698, in getByKey
>> obj1.load()
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/memops/api/Implementation.py", line 25419, in load
>> self.loadFrom(repositories[0])
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/memops/api/Implementation.py", line 25453, in loadFrom
>> XmlIO.loadTopObject(repository.url.getDataLocation(), self)
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/memops/format/xml/XmlIO.py", line 236, in loadTopObject
>> return loadFromStream(open(filePath), topObjId=topObjId, topObject=topObject)
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/memops/format/xml/XmlIO.py", line 273, in loadFromStream
>> partialLoad=partialLoad)
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/memops/xml/Implementation.py", line 5125, in loadFromStream
>> obj.checkValid()
>> File "/home/garyt/programs/ccpnmr/ccpnmr2.2/python/ccp/api/molecule/Validation.py", line 11443, in checkValid
>> + ": %s" % (self,)
>> memops.general.Implementation.ApiError: ccp.molecule.Validation.ResidueValidation.checkValid:
>> constraint must_point_to_valid_KeywordDefinition violated: <ccp.molecule.Validation.ResidueValidation ['RMSD_p7_meth_depo_garyt_2012-11-20-12-13-12-339_00001', 98]>
>>
>>
>> anyone have any ideas
>>
>> from my analysis there seem to be no keywords in the keyword store and it is looking for thinsg like all and O
>>
>>
>> regards
>> gary
>
