[ome-devel] omero 4.2: OmeroPy problem

Tue Jun 22 16:33:21 BST 2010

Forwarding to list. Great to hear, Bram.

Cheers,
~Josh

On 6/22/10 4:33 PM, b.gerritsen at nki.nl wrote:
> Thanks for the help Josh!
>
> Your advice worked! I decided to migrate to ubuntu 10.4 and was able to install ALL prerequisites using the package manager alone. So I rebuilt omero 4.2 using ice 3.3. Now I have a functioning omero 4.2 and can create a connection to the server from python.
>
> Thanks again!
> Bram
> ________________________________________
> From: Josh Moore [josh.moore at gmx.de]
> Sent: Tuesday, June 22, 2010 11:38 AM
> To: Bram Gerritsen
> Cc: OME developers
> Subject: Re: [ome-devel] omero 4.2: OmeroPy problem
>
> Understood. Please do let us know when you can test with 3.3.x. We're
> planning on adding a Ice version-detector to the release, since we've
> had this problem several times[*]
>
> Cheers and thanks for helping us track this down,
> ~Josh
>
> [*]https://trac.openmicroscopy.org.uk/omero/ticket/2514
>
> On 6/22/10 11:04 AM, b.gerritsen at nki.nl wrote:
>
>> Hi Josh,
>>
>> This is the output I get from python:
>>
>>
>>
>>>>> import Ice
>>>>> import A
>>>>> A.EventContext()
>>>>>
>>>>>
>> object #0 (::Ice::Object)
>> {
>> }
>>
>>
>>>>>
>> The contents of A.ice:
>> module A {
>>        class EventContext {
>>                string text;
>>        };
>> };
>>
>> Using your other suggestion might be the solution! However, I couldn't test it yet because the older ice version was from an ubuntu package and compiled against python 2.5.2.
>>
>> Here is the output:
>>
>> PYTHONPATH=.:/var/lib/python-support/python2.5/ python
>> Python 2.6.5 (r265:79063, Jun 21 2010, 14:09:15)
>> [GCC 4.3.2] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>>
>>
>>>>> import omero
>>>>> c = omero.client()
>>>>>
>>>>>
>> Traceback (most recent call last):
>>     File "<stdin>", line 1, in<module>
>>     File "omero/__init__.py", line 22, in client
>>       import omero.clients
>>     File "omero/clients.py", line 13, in<module>
>>       model = __import__('omero.model')
>>     File "omero/model/__init__.py", line 1, in<module>
>>       from  omero.util.FactoryMap import map
>>     File "omero/util/__init__.py", line 11, in<module>
>>       import Ice
>>     File "/var/lib/python-support/python2.5/Ice.py", line 33, in<module>
>>       import IcePy
>> ImportError: /var/lib/python-support/python2.5/IcePy.so: undefined symbol: PyUnicodeUCS4_AsUTF8String
>>
>>
>>>>>
>> Cheers,
>> Bram
>> ________________________________________
>> From: Josh Moore [josh.moore at gmx.de]
>> Sent: Tuesday, June 22, 2010 10:37 AM
>> To: Bram Gerritsen
>> Cc: OME developers
>> Subject: Re: [ome-devel] omero 4.2: OmeroPy problem
>>
>> Hmm,.... if the python side hasn't worked for you, I'd say we should
>> start simpler. Can you see if you can get a very simple example running?
>>
>> $ mkdir /tmp/ice_test
>> $ cd /tmp/ice_test
>> $ cat>   A.ice<<   EOF
>>    >   module A {
>>    >     class EventContext {
>>    >       string text;
>>    >     };
>>    >   };
>>    >   EOF
>> $ slice2py A.ice
>> $ python
>> Python 2.6.5 (r265:79063, Jun 21 2010, 12:27:46)
>> [GCC 4.2.1 (Apple Inc. build 5659)] on darwin
>> Type "help", "copyright", "credits" or "license" for more information.
>>    >>>   import Ice
>>    >>>   import A
>>    >>>   A.EventConttext()
>> object #0 (::A::EventConttext)
>> {
>>        text =
>> }
>>    >>>
>>
>> This might be an issue with a mix of 32 and 64 bit python/ice versions.
>> You compiled your own Ice.... ah, I think I got it. The top of your
>> diagnostics says that you're building with version 3.3.0, but your
>> LD_LIBRARY_PATH is set to /opt/Ice-3.4.1/lib64. Could you try again with
>> everything pointing to the 3.3.0 (or a 3.3.1) install?
>>
>> *crosses fingers*
>> ~Josh.
>>
>> On 6/22/10 10:00 AM, b.gerritsen at nki.nl wrote:
>>
>>
>>> Hi Josh,
>>>
>>> The python side of the trunk build hasn't worked for me yet. At least omero.web did not start. For the older omero 4.0.3 I had a working django and was also able to connect using python. However, I did update python and ice recently.
>>>
>>> As requested I rebuilt omero. See attachment for the "build.log". The same error as shown in previous e-mail remains.
>>>
>>> Cheers,
>>> Bram
>>>
>>> ________________________________________
>>> From: ome-devel-bounces at lists.openmicroscopy.org.uk [ome-devel-bounces at lists.openmicroscopy.org.uk] On Behalf Of Josh Moore [josh.moore at gmx.de]
>>> Sent: Tuesday, June 22, 2010 8:43 AM
>>> To: ome-devel at lists.openmicroscopy.org.uk
>>> Subject: Re: [ome-devel] omero 4.2: OmeroPy problem
>>>
>>> Hi Bram,
>>>
>>> that's pretty surprising. Before you did the clean build, a trunk build
>>> worked as expected? And nothing else changed (a new Python version, a
>>> new Ice version, etc.) between the last working build and the current
>>> failing one?
>>>
>>> If so, could you possibly send us the output of the clean build:
>>>
>>>       (./build.py clean; ./build.py) 2>&1 | tee build.log
>>>
>>> As a comparison, for revision 7294 (last night around 8), I get the
>>> following:
>>>
>>> jmoore at necromancer ~/git $ PYTHONPATH=dist/lib/python:$PYTHONPATH python
>>> Python 2.6.2 (r262:71600, Sep 13 2009, 13:33:13)
>>> [GCC 4.1.2 (Gentoo 4.1.2 p1.0.2)] on linux2
>>> Type "help", "copyright", "credits" or "license" for more information.
>>>     >>>    import omero
>>>     >>>    c = omero.client(["--omero.host=foo"])
>>>     >>>
>>>
>>> Cheers,
>>> ~Josh
>>>
>>> On 6/21/10 6:06 PM, b.gerritsen at nki.nl wrote:
>>>
>>>
>>>
>>>> Dear all,
>>>>
>>>> After building a clean omero trunk (revision 7292) I was unable to use python 2.6.5 to connect to an omero server instance. See attachment for details. Could someone tell me how to solve this problem?
>>>>
>>>> Kind Regards,
>>>> Bram Gerritsen
>>>>
>>>>
>>>>