Hmmm, I just looked at the Aria code and it seems there are quite a few 
Unix system commands being run, e.g. "csh", "cp", "rm" and "gzip". (There 
are pure Pythonic ways of doing cp, rm and gzip, so those should not be in 
there, and even the csh I'm not sure is needed.)

Has anyone ever gotten Aria 2.* to work on Windows???

Evidently one of the "cp" commands is being triggered when you click on 
that Analysis button (which calls the Aria setup function). I'm not an 
Aria expert so I'm not sure which of the occurrences of this is the likely 
culprit, but I suspect even if that one is fixed there would need to be 
some more serious surgery required.

Wayne

On Fri, 11 Jan 2013, McElroy, Craig wrote:

> Wayne,
>
> Thanks again for your response.
>
> Firstoff, just to be clear, I am not running Analysis through Cygwin... I am simply double clicking on the Analysis.exe icon. If I try and run it through Cygwin I get:
>
> 	Fatal Python error: PyEval_RestoreThread: NULL tstate
>
> 	This application has requested the Runtime to terminate it in an unusual way.
> 	Please contact the application's support team for more information.
>
> Rather, I have the ARIA and CNS environment variables set in Windows so that they get passed as system variables to the python shell that gets called when I double click on the Analysis.exe.
>
> I'm not sure what was causing the problems that I asked about before, but I was encountering other strange issues (like trying to import structures and getting a message that said something like "atoms will not be created if MatrixData exists"), so I reinstalled Analysis and now I don't get the previous error messages anymore.
>
> Now if I click on "Setup Project" in the CCPN-ARIA module it will copy the directory structure and toppar files etc to the proper location but then doesn't write the ARIA XML project file and says:
>
> 	'cp' is not recognized as an internal or external command, operable program or batch file.
> 	MESSAGE [Project]: Directory tree created.
> 	MESSAGE [Project]: Copying data files into local data-directory...
>
> 	Done.
>
> 	For running ARIA: aria2 None
>
> The message about 'cp' is the same message you get if you type 'cp' in a MS-DOS command shell, so I assume it's because I'm not running through a shell. Any idea on how I can get it to create the XML file.
>
> I would just set up the CCPN project and then run the ARIA gui from the Cygwin shell, but if I set up the project in CCPN and then start the gui from a command line I can import a CCPN project and the molecule etc  from the project, but for some reason when I try and import peak lists/spectra it tells me that there is no peak list or spectrum associated with the molecule, so I was hoping I could set up the aria project in CCPN, but that doesn't work either.
>
> Thanks again for all of your help... I appreciate it very much.
>
> Thanks
> Craig
>
> -----Original Message-----
> From: CcpNmr software mailing list [mailto:[log in to unmask]] On Behalf Of Wayne Boucher
> Sent: Thursday, January 10, 2013 10:46 AM
> To: [log in to unmask]
> Subject: Re: CCPN and ARIA on windows
>
> Hello,
>
> I'm glad the / \ issue is resolved.
>
> On the compatibility front, you should get the updates (Project --> Updates).  (In Windows you have to run the program as administrator but I don't know what cygwin would do for that.)  That should let you load new data.  (I assume you have some data created with SpecView or ChemBuild, otherwise I'm puzzled how this message was even triggered.)
>
> For the other issues, I can't see any sensible way they could be being triggered, which makes me wonder if running it through cygwin is causing the problem.  One way to diagnose the "not a modeled attribute" error a bit more is to go into the CCPN\ccpn\python\ccp\api\nmr\NmrCalc.py file and where it is complaining, at line 6652, you should see code like:
>
>         for key, value in attrlinks.iteritems():
>           try:
>             func = getattr(self.__class__, key).fset
>           except:
>             raise ApiError("%s: error setting %s - not a modeled attribute"
>                            % (self, key))
>
> You could change that to just:
>
>         for key, value in attrlinks.iteritems():
>           func = getattr(self.__class__, key).fset
>
> (the "f" in "func" should line up under the "r" in "for") and see what the error message is according to Python (rather than as CCPN is massaging it).  When key is "groupId" it is triggering the exception but it shouldn't be since "groupId" is an attribute.
>
> I couldn't trigger this exception on my Windows version, so it created a RunParameter with groupId as an attribute ok.
>
> Wayne
>
> On Wed, 9 Jan 2013, McElroy, Craig wrote:
>
>> Wayne,
>>
>> Thank you so much for the prompt reply. I know I'm probably crazy for trying this on a windows machine, but I don't have a linux box anymore, so windows 7 is my only option at the moment.
>>
>> So the problem from the aria side was an issue with the back slashes. On the command line for Cygwin it needs the \ before a space or other special character like a ( so I included them in the environment variable. However, it seems when that gets passed to python it gets misinterpreted. Once I fixed that to: setenv PYTHONPATH '/cygdrive/c/Program Files (x86)/CCPN/ccpn/python' it is being recognized and I can import the ccpnmr module. However, if I try and load a ccpn project in the aria gui I get an error:
>>
>> Could not import
>> Memops.format.compatability.downgrad.v_2_1_1
>> Forwards compatibility from 2.1.1 to 2.0.5 missing Trying to load
>> new-version data with old-version code?
>>
>> On the other side: The CCPN Data Model is version 2.0.5 and the _fieldNames does include 'groupId'.
>> I have the CNS environment variables defined in windows and there are no odd characters. I also discovered that even just moving the mouse over the region where you define the path for the CNS executable and aria calculations I get the error.
>>
>> Thanks for all your help in trying to trouble shoot this.
>>
>> Thanks
>> Craig
>>
>>
>> -----Original Message-----
>> From: CcpNmr software mailing list [mailto:[log in to unmask]] On
>> Behalf Of Wayne Boucher
>> Sent: Wednesday, January 09, 2013 1:25 PM
>> To: [log in to unmask]
>> Subject: Re: CCPN and ARIA on windows
>>
>> Hello,
>>
>> Windows, we love it.
>>
>> Both your variants of setting the PYTHONPATH look ok to me, although I don't know about / vs \ for paths in cygwin, nor how it copes with spaces in path names.  If you are able to run a python (I have a feeling we don't distribute that as is in Windows) command in some shell, after setting the PYTHONPATH, then can you try, at the Python prompt:
>>
>>>>> import ccpnmr
>>
>> That is what Aria tries to do in check.py.  Well, it does a bit more but that is the first thing it tries.  If that doesn't work then it is worth also doing:
>>
>>>>> import sys
>>>>> print sys.path
>>
>> And see if the correct CCPN python directory is indeed listed.
>>
>> That first error in the other direction, about groupId, is a puzzle.  So that is a modeled attribute in all the versions I've managed to check.  As it happens, it's about to be eliminated as an attribute but in theory nobody in the outside world should have seen that yet, which is worrying (!).  If you look at the top of:
>>
>> C:\Program Files (x86)\CCPN\ccpn\python\ccp\api\nmr\NmrCalc.py
>>
>> can you tell me what the CCPN Data Model version is?  It ought to be 2.0.5 if this is Analysis 2.2.2.  In any case, you should also check the class RunParameter in that file (search for "class RunParameter" starting at the first column).  Just below that there is a list of _fieldNames in alphabetic order, and that ought to include 'groupId'.
>>
>> That Unicode error is happening (I think) when it is trying to check if the CNS executable path exists.  Is there some odd character in that path??
>>
>> Wayne
>>
>> On Wed, 9 Jan 2013, Craig McElroy wrote:
>>
>>> Hi all,
>>> Sorry for the long e-mail... I have a number of issues because I'm trying to get CCPN 2.2.2 and ARIA 2.3 working together on a windows machine. I have CNS 1.21 and ARIA 2.3 compiled and functioning in cygwin. I haven't been able to successfully compile CCPN 2.2.2 in cygwin so I have been using the precompiled windows version. However, the directory structure of the precompiled windows version seems to be different than the linux version such that I'm not sure how to set the environment variables in my cshrc file for cygwin. I currently have them set to:
>>> setenv CCPNMR_TOP_DIR '/cygdrive/c/Program\ Files\ \(x86\)/CCPN/ccpn'
>>> setenv PYTHONPATH '$CCPNMR_TOP_DIR/python:$PYTHONPATH'
>>>
>>> but have also tried
>>> setenv CCPNMR_TOP_DIR '/cygdrive/c/Program\ Files\ \(x86\)/CCPN/'
>>> setenv PYTHONPATH '$CCPNMR_TOP_DIR/ccpn/python:$PYTHONPATH'
>>>
>>> in either case ARIA 2.3 can't find ccpn when I run the check.py script.
>>>
>>> On the other side I have set the environment variable for ARIA2 in windows and CCPN recognizes it (at least it doesn't give the no local aria error) but I get a number of errors when trying to use the ARIA module. In the window when I click on the Run Settings tab I get:
>>>
>>>>>> ERROR in ccp.nmr.NmrCalc.RunParameter.__init__
>>> WARNING Error in clean-up of incorrectly created object.
>>>        Data may be left in an illegal state Exception in Tkinter
>>> callback Traceback (most recent call last):
>>>  File "Tkinter.pyo", line 1410, in __call__  File "C:\Program Files
>>> (x86)\CCPN\ccpn\python\paris\aria\AriaRunFrame.py", line 152, in
>>> updateEntryParams  File "C:\Program Files
>>> (x86)\CCPN\ccpn\python\ccp\util\NmrCalc.py", line 81, in
>>> setRunParameter  File "C:\Program Files
>>> (x86)\CCPN\ccpn\python\ccp\api\nmr\NmrCalc.py", line 5499, in
>>> newRunParameter  File "C:\Program Files
>>> (x86)\CCPN\ccpn\python\ccp\api\nmr\NmrCalc.py", line 6652, in
>>> __init__
>>> ApiError: <ccp.nmr.NmrCalc.RunParameter ['AT3', 'ARIA', 1, None]>:
>>> error setting groupId - not a modeled attribute
>>>
>>> when I press the Launch ARIA GUI button I get:
>>>>>> Exception in Tkinter callback
>>> Traceback (most recent call last):
>>>  File "Tkinter.pyo", line 1410, in __call__  File "C:\Program Files
>>> (x86)\CCPN\ccpn\python\paris\aria\AriaExtendNmrFrame.py", line 244,
>>> in runAriaGui  File "C:\Program Files
>>> (x86)\CCPN\ccpn\python\paris\aria\AriaExtendNmrFrame.py", line 221,
>>> in checkProjectPath  File "genericpath.pyo", line 18, in exists
>>> TypeError: coercing to Unicode: need string or buffer, NoneType found
>>>
>>> and when I press the Setup Project button I get:
>>>>>> Exception in Tkinter callback
>>> Traceback (most recent call last):
>>>  File "Tkinter.pyo", line 1410, in __call__  File "C:\Program Files
>>> (x86)\CCPN\ccpn\python\paris\aria\AriaExtendNmrFrame.py", line 250,
>>> in setupAriaProject  File "C:\Program Files
>>> (x86)\CCPN\ccpn\python\paris\aria\AriaExtendNmrFrame.py", line 221,
>>> in checkProjectPath  File "genericpath.pyo", line 18, in exists
>>> TypeError: coercing to Unicode: need string or buffer, NoneType found
>>>
>>> Any help/suggestions/comments would be welcome.
>>> Thanks
>>> Craig
>>>
>>
>