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CCPNMR  March 2010

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Subject:

Re: ECI database deposition

From:

Wayne Boucher <[log in to unmask]>

Reply-To:

CcpNmr software mailing list <[log in to unmask]>

Date:

Wed, 17 Mar 2010 11:35:26 +0000

Content-Type:

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TEXT/PLAIN (119 lines)

Ah, so that did need an update.  I updated my repository version again and 
checked the diffs and I can see that the only real change was that two 
lines moved down in the code, but an import also changed (from msd to 
pdbe) so I had to edit the 2.1.3 version rather than just upload the 
current repository version.  But hopefully it is sorted now.

(But we're likely to be doing a 2.1.4 release soon(ish) because of this 
msd --> pdbe change, and also Tim is getting through the documentation, so 
when that is done it's probably time to do a release.)

Wayne

On Wed, 17 Mar 2010, Chris Penkett wrote:

> Hi Wayne,
>
> You'll need to add ccpnmr/eci/EntryCompletionFrame.py to the update server 
> first as there was a new bug in the DB reference section.
>
> Chris
>
>
>
> On 17 Mar 2010, at 10:53, Wayne Boucher wrote:
>
>> Hello,
>> 
>> I've checked with Chris and he said those bugs were fixed and I checked the 
>> 2.1.3 release code and what is in our repository and they are the same in 
>> both cases, and I can see that the second bug is definitely fixed (the 
>> first is harder for me to determine).  And the line numbers don't match. So 
>> I think your release must not be 2.1.3 (the 2.1.2 release did have the 
>> second bug in it).  So assuming I haven't got this all wrong, I'd recommend 
>> upgrading to 2.1.3.
>> 
>> Wayne
>> 
>> On Wed, 17 Mar 2010, Phelan, Marie wrote:
>> 
>>> Hi
>>> 
>>> I have spotted a couple of bugs whilst using the ECI database deposition, 
>>> I can't seem to set a Database Name in the ECI Deposition  form under the 
>>> tab Molecules - there is a drop down menu but it doesn't seem to want to 
>>> select anything. The traceback looks like this:
>>> 
>>> Exception in Tkinter callback
>>> Traceback (most recent call last):
>>> File 
>>> "/home/mjfi9jc3/programs/ccpnmr/ccpnmr/python2.5/lib/python2.5/lib-tk/Tkinter.py", 
>>> line 1403, in __call__
>>>   return self.func(*args)
>>> File 
>>> "/home/mjfi9jc3/programs/ccpnmr/ccpnmr/ccpnmr2.1/python/memops/gui/PulldownList.py", 
>>> line 402, in <lambda>
>>>   command = lambda n=index: self.setIndex(n, True)
>>> File 
>>> "/home/mjfi9jc3/programs/ccpnmr/ccpnmr/ccpnmr2.1/python/memops/gui/PulldownList.py", 
>>> line 183, in setIndex
>>>   self.callback(obj)
>>> File "ccpnmr2.1/python/ccpnmr/eci/EntryCompletionFrame.py", line 3676, in 
>>> setMoleculeDbName
>>> AttributeError: 'NoneType' object has no attribute 'code'
>>> 
>>> Also is it possible to produce a NMRSTAR file whilst the Report is 
>>> incomplete? At the moment my report's missing constraints and structures 
>>> and clicking the 'Export as NMR-STAR 3.1' button I get the following 
>>> traceback:
>>> 
>>> Cannot CCPN map value for 
>>> contactPerson.currentPersonInGroup.group.organisation.addresses, function 
>>> <bound method Ccpn_To_NmrStar.getThirdAddressLine of 
>>> <msd.nmrStar.IO.Ccpn_To_NmrStar.Ccpn_To_NmrStar instance at 0xb24f36ec>>
>>> Exception in Tkinter callback
>>> Traceback (most recent call last):
>>> File 
>>> "/home/mjfi9jc3/programs/ccpnmr/ccpnmr/python2.5/lib/python2.5/lib-tk/Tkinter.py", 
>>> line 1403, in __call__
>>>   return self.func(*args)
>>> File "ccpnmr2.1/python/ccpnmr/eci/EntryCompletionFrame.py", line 7717, in 
>>> exportNmrStar31
>>> File "ccpnmr2.1/python/msd/nmrStar/IO/NmrStarExport.py", line 199, in 
>>> createFile
>>> File "ccpnmr2.1/python/msd/nmrStar/IO/NmrStarExport.py", line 290, in 
>>> loopSaveFrameData
>>> File "ccpnmr2.1/python/msd/nmrStar/IO/NmrStarExport.py", line 405, in 
>>> setSaveFrameData
>>> File "ccpnmr2.1/python/msd/nmrStar/IO/NmrStarExport.py", line 690, in 
>>> loopStarLevelObjects
>>> File "ccpnmr2.1/python/msd/nmrStar/IO/NmrStarExport.py", line 440, in 
>>> setTableData
>>> File "ccpnmr2.1/python/msd/nmrStar/IO/NmrStarExport.py", line 654, in 
>>> loopStarLevelObjects
>>> File "ccpnmr2.1/python/msd/nmrStar/IO/NmrStarExport.py", line 1080, in 
>>> setStarTags
>>> File "ccpnmr2.1/python/msd/nmrStar/IO/NmrStarExport.py", line 2008, in 
>>> getCcpnMapValue
>>> File "ccpnmr2.1/python/msd/nmrStar/IO/Ccpn_To_NmrStar.py", line 2884, in 
>>> getThirdAddressLine
>>> File "ccpnmr2.1/python/msd/nmrStar/IO/Ccpn_To_NmrStar.py", line 2902, in 
>>> getArrayEntryIndexToEnd
>>> NameError: global name 'string' is not defined
>>> 
>>> 
>>> 
>>> 
>>> cheers
>>> 
>>> Marie
>>> 
>>> 
>>> NMR Centre
>>> Biological Sciences
>>> University of Liverpool
>>> Crown Street
>>> Liverpool
>>> L697ZB
>>> 0151 795 4398

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