[ome-users] Couple of admin questions

[Josh Moore]

On Oct 17, 2011, at 2:57 AM, Leon Kolchinsky wrote:

> Hello Josh,

Hi Leon,

> Here is the output from 2 Omero servers -
> 
> Server1:
> [omero at vera143 pil]$ make
> python t1.py
>  Found PIL.Image: <module 'PIL.Image' from
> '/usr/lib64/python2.6/site-packages/PIL/Image.pyc'>
> python t2.py
>  Found Image:<module 'Image' from
> '/usr/lib64/python2.6/site-packages/PIL/Image.pyc'>
> python t3.py
>  Found PIL.Image: <module 'PIL.Image' from
> '/usr/lib64/python2.6/site-packages/PIL/Image.pyc'>
>  Reimported Image: <module 'Image' from
> '/usr/lib64/python2.6/site-packages/PIL/Image.pyc'>
> 
> Server2:
> [omero at vera145 pil]$ make
> python t1.py
>  Found PIL.Image: <module 'PIL.Image' from
> '/usr/lib64/python2.6/site-packages/PIL/Image.pyc'>
> python t2.py
>  Found Image:<module 'Image' from
> '/usr/lib64/python2.6/site-packages/PIL/Image.pyc'>
> python t3.py
>  Found PIL.Image: <module 'PIL.Image' from
> '/usr/lib64/python2.6/site-packages/PIL/Image.pyc'>
>  Reimported Image: <module 'Image' from
> '/usr/lib64/python2.6/site-packages/PIL/Image.pyc'>
> 
> Seems OK, right?
> I guess I'll check it again with the new version of Omero (when it's
> released).

It does look correct, i.e. no other mismatched libraries, etc. Let us know how the web client functions without the patch.

Cheers,
~Josh.


> Thanks,
> Leon Kolchinsky
> 
> 
> 
> On Wed, Oct 12, 2011 at 20:04, Josh Moore <josh at glencoesoftware.com> wrote:
> 
>> 
>> On Oct 12, 2011, at 1:50 AM, Leon Kolchinsky wrote:
>> 
>>> Hi,
>>> 
>>> 
>>> On Tue, Oct 11, 2011 at 20:00, Josh Moore <josh at glencoesoftware.com>
>> wrote:
>>> 
>>>> 
>>>> On Oct 11, 2011, at 6:43 AM, Leon Kolchinsky wrote:
>>>> 
>>>>> Hello,
>>>>> 
>>>>> 1. How do I run auto "cleanse" job via cron (so it won't ask me for
>>>> username
>>>>> and password)?
>>>>> 
>>>>> "$ /srv/omeroserver/bin/omero -s localhost admin cleanse
>> /srv/omerodata"
>>>> -
>>>>> asks for username/pass
>>>>> "$ /srv/omeroserver/bin/omero -s root at localhost admin cleanse
>>>>> /srv/omerodata" - asks for pass
>>>> 
>>>> There's currently no way to login passwordlessly, but I've added
>>>> https://trac.openmicroscopy.org.uk/ome/ticket/6957 in order to examine
>>>> adding support for that. Until then, you'll need to follow the recipes
>> on
>>>> the backup-and-restore page:
>>>> 
>>>> 
>>>> 
>> https://www.openmicroscopy.org/site/support/omero4/server/backup-and-restore
>>> 
>>> 
>>> Thanks, I'll try that.
>>> 
>>>> 
>>>> 
>>>>> 2. Is it possible to include this patch into Omero releases (from Chris
>>>>> Allan):
>>>>> 
>>>> 
>> http://users.openmicroscopy.org.uk/~cxallan/pil_image_import_inline.patch
>>>>> 
>>>>> It solves some client issues for us (python 2.6).
>>>>> 
>>>>> This is how I patch OMERO web client:
>>>>> [root at vera144 log]# cd /srv/OMERO.server-Beta-4.3.2/lib/python/
>>>>> [root at vera144 python]# wget
>>>>> 
>>>> 
>> http://users.openmicroscopy.org.uk/~cxallan/pil_image_import_inline.patch
>>>>> [root at vera144 python]# cp omeroweb/webclient/webclient_gateway.py
>>>>> omeroweb/webclient/webclient_gateway.py.orig
>>>>> [root at vera144 python]# patch -p0 < pil_image_import_inline.patch
>>>>> patching file omeroweb/webclient/webclient_gateway.py
>>>>> [root at vera144 python]# chown omero.omero
>>>>> omeroweb/webclient/webclient_gateway.pyl
>>>> 
>>>> Unfortunately, it's still unclear why this patch is only necessary for
>> your
>>>> installation, and therefore, it's likely that adding this would break
>> other
>>>> installations. The import block at the top of that file:
>>>> 
>>>> try:
>>>>  from PIL import Image, ImageDraw # see ticket:2597
>>>> except ImportError:
>>>>  try:
>>>>      import Image, ImageDraw # see ticket:2597
>>>>  except:
>>>>      logger.error("You need to install the Python Imaging Library. Get
>> it
>>>> at http://www.pythonware.com/products/pil/")
>>>>      logger.error(traceback.format_exc())
>>>> 
>>>> should definitely have already imported "Image". If there are any
>> generic
>>>> fixes you can make to that block so that your installation works without
>>>> Chris' patch, that would be something we could add to the main codebase.
>>>> 
>>> Hmm, I'm not a python user myself so it's kinda Chinese for me.
>>> Sorry, I don't have any python skills (except of installing one and it's
>>> modules.....)
>>> Anyway AFAIK, additional "Import" shouldn't break anything in theory.
>> 
>> The issue with the import is that without the try/except block on any
>> system that requires the "PIL" prefix, it will fail. I'm attaching a zip
>> with a make file, could you unpack it and run it on your system:
>> 
>> /tmp $ unzip pil.zip
>> Archive:  pil.zip
>>  creating: pil/
>> inflating: pil/Makefile
>> inflating: pil/t1.py
>> inflating: pil/t2.py
>> inflating: pil/t3.py
>> /tmp $ cd pil
>> /tmp/pil $ make
>> python t1.py
>> Found PIL.Image: <module 'PIL.Image' from
>> '/usr/local/lib/python2.6/site-packages/PIL/Image.pyc'>
>> python t2.py
>> Found Image:<module 'Image' from
>> '/usr/local/lib/python2.6/site-packages/PIL/Image.pyc'>
>> python t3.py
>> Found PIL.Image: <module 'PIL.Image' from
>> '/usr/local/lib/python2.6/site-packages/PIL/Image.pyc'>
>> Reimported Image: <module 'Image' from
>> '/usr/local/lib/python2.6/site-packages/PIL/Image.pyc'>
>> 
>> 
>> Cheers,
>> ~Josh.
>> 
>>>> Cheers,
>>>> ~Josh.
>>>> 
>>>> 
>>>>> Thank you,
>>>>> Leon Kolchinsky
>>>> 
>>> 
>>> Thanks,
>>> Leon
>> 
>> 

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