[ome-users] global name 'Image' is not defined?
Leon Kolchinsky
lkolchin at gmail.com
Mon Aug 15 13:51:55 BST 2011
Sure,
This is RHEL5.7 and it has python2.4.3 as a default, but I've installed
separate python instance 2.6
Here is how I've installed python:
NEW Python2.6 and modules installation:
---------------------------------------
1. Add EPEL repository to the system.
# python -V
# wget
http://download.fedora.redhat.com/pub/epel/5/x86_64/epel-release-5-4.noarch.rpm
# rpm -ivh epel-release-5-4.noarch.rpm
2. Disable this repository (no joke), otherwise it tries always to update
stuff and will break other python packages!
Edit the file /etc/yum.repos.d/epel.repo and set everywhere “enabled=0
# yum install gcc httpd-devel rpm-build atlas-devel blas-devel gcc-gfortran
gcc-c++ httpd
# yum install hdf5 hdf5-devel lzo bzip2 lzo-devel bzip2-libs bzip2-devel
# yum install python26-setuptools python26 python26-devel
python26-distribute python26-libs python26-simplejson mod_python26
--enablerepo=epel
# easy_install-2.6 pip
# pip-2.6 install virtualenv
2.1. Omero python scripts using "#!/usr/bin/env python" to find python
executable.
So to work around this issue and point Omero to python2.6 we'll do:
[root at vera144 srv]# ln -s /usr/bin/python2.6 /usr/local/bin/python
[root at vera144 srv]# export PATH=/usr/local/bin:$PATH
4. Install python modules via pip:
[root at vera144 srv]# export PATH=/usr/local/bin:$PATH
no need to install this one - (# yum install freetype freetype-devel libpng
libpng-devel libjpeg libjpeg-devel jpeg jpeg-devel)
# yum install libjpeg-devel zlib-devel freetype-devel libpng libpng-devel
[root at vera144 srv]# pip install Distutils2
[root at vera144 srv]# pip install PIL
[root at vera144 srv]# pip install numpy
[root at vera144 srv]# pip install Cython
[root at vera144 srv]# pip search numexpr
[root at vera144 srv]# pip install -U
http://www.pytables.org/svn/pytables/trunk
# pip install matplotlib
[root at vera144 srv]# pip install django
That's it.
I've even tried to reinstall PIL from source:
[root at vera144 Imaging-1.1.7]# wget
http://effbot.org/downloads/Imaging-1.1.7.tar.gz
[root at vera144 Imaging-1.1.7]# tar -xvzf Imaging-1.1.7.tar.gz
[root at vera144 Imaging-1.1.7]# cd Imaging-1.1.7
[root at vera144 Imaging-1.1.7]# python setup.py install
But I'm still getting this error:
Mon, 15 Aug 2011 13:37:29 webclient_gateway ERROR Traceback (most recent
call last):
File
"/srv/OMERO.server-Beta-4.3.1/lib/python/omeroweb/webclient/webclient_gateway.py",
line 687, in getExperimenterPhoto
photo = self.getExperimenterDefaultPhoto()
File
"/srv/OMERO.server-Beta-4.3.1/lib/python/omeroweb/webclient/webclient_gateway.py",
line 778, in getExperimenterDefaultPhoto
img = Image.open(settings.DEFAULT_USER)
NameError: global name 'Image' is not defined
Mon, 15 Aug 2011 13:37:30 views-feedback ERROR handler500: Server error
Mon, 15 Aug 2011 13:37:30 views-feedback ERROR Traceback (most recent
call last):
File "/srv/omeroserver/lib/python/django/core/handlers/base.py", line 92,
in get_response
response = callback(request, *callback_args, **callback_kwargs)
File "/srv/omeroserver/lib/python/omeroweb/webclient/views.py", line 165,
in wrapped
return f(request, *args, **kwargs)
File "/srv/omeroserver/lib/python/omeroweb/webclient/views.py", line 2366,
in myphoto
photo = conn.getExperimenterPhoto()
File
"/srv/OMERO.server-Beta-4.3.1/lib/python/omeroweb/webclient/webclient_gateway.py",
line 690, in getExperimenterPhoto
photo = self.getExperimenterDefaultPhoto()
File
"/srv/OMERO.server-Beta-4.3.1/lib/python/omeroweb/webclient/webclient_gateway.py",
line 778, in getExperimenterDefaultPhoto
img = Image.open(settings.DEFAULT_USER)
NameError: global name 'Image' is not defined
But I can import Image from command line:
[omero at vera144 ~]$ python
Python 2.6.5 (r265:79063, Feb 28 2011, 21:55:45)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-50)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Image
>>>
Here are my diagnostic messages:
[omero at vera144 ~]$ /srv/omeroserver/bin/omero admin diagnostics
================================================================================
OMERO Diagnostics 4.3.1-6d4b8c61-b2602
================================================================================
Commands: java -version 1.6.0 (/usr/bin/java)
Commands: python -V 2.6.5 (/usr/local/bin/python
-- 2 others)
Commands: icegridnode --version 3.3.1
(/opt/Ice-3.3.1/bin/icegridnode)
Commands: icegridadmin --version 3.3.1
(/opt/Ice-3.3.1/bin/icegridadmin)
Commands: psql --version 9.0.3
(/srv/PostgresPlus/9.0SS/bin/psql)
Server: icegridnode running
Server: Blitz-0 active (pid = 30320, enabled)
Server: DropBox active (pid = 30618, enabled)
Server: FileServer active (pid = 30331, enabled)
Server: Indexer-0 active (pid = 30336, enabled)
Server: MonitorServer active (pid = 30351, enabled)
Server: OMERO.Glacier2 active (pid = 30343, enabled)
Server: OMERO.IceStorm active (pid = 30350, enabled)
Server: PixelData-0 active (pid = 30338, enabled)
Server: Processor-0 active (pid = 30339, enabled)
Server: Tables-0 active (pid = 30340, enabled)
Server: TestDropBox inactive (enabled)
Log dir: /srv/omeroserver/var/log exists
Log files: Blitz-0.log 10.0 MB errors=3
warnings=249
Log files: DropBox.log 25.0 KB errors=14
warnings=12
Log files: FileServer.log 2.0 KB
Log files: Indexer-0.log 75.0 KB errors=7
warnings=12
Log files: MonitorServer.log 9.0 KB errors=0
warnings=5
Log files: OMEROweb.log 206.0 KB errors=190
warnings=146
Log files: PixelData-0.log 16.0 KB errors=7
warnings=3
Log files: Processor-0.log 15.0 KB errors=1
warnings=13
Log files: Tables-0.log 1.0 KB
Log files: TestDropBox.log n/a
Log files: master.err 4.0 KB
Log files: master.out 0.0 KB
Log files: Total size 11.19 MB
Parsing Blitz-0.log:[line:98] => Server restarted <=
Parsing Blitz-0.log:[line:10390] => Server restarted <=
Parsing Blitz-0.log:[line:18613] => Server restarted <=
Parsing Blitz-0.log:[line:53397] => Server restarted <=
Parsing Blitz-0.log:[line:55026] => Server restarted <=
Parsing Blitz-0.log:[line:61481] => Server restarted <=
Parsing Blitz-0.log:[line:65245] => Server restarted <=
Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:PATH=/usr/local/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/opt/Ice-3.3.1:/opt/Ice-3.3.1/bin:/srv/PostgresPlus/9.0SS/bin:/srv/PostgresPlus/9.0SS/pgbouncer/bin:/srv/PostgresPlus/9.0SS/pgAdmin3/bin:/srv/omeroserver/bin
Environment:ICE_HOME=/opt/Ice-3.3.1
Environment:LD_LIBRARY_PATH=/opt/Ice-3.3.1/lib64:/usr/lib64:/srv/PostgresPlus/9.0SS/pgAdmin3/lib:/srv/PostgresPlus/9.0SS/pgAgent/lib:/srv/PostgresPlus/9.0SS/lib:
Environment:DYLD_LIBRARY_PATH=/opt/Ice-3.3.1/lib64:/usr/lib64:
OMERO data dir: '/srv/omerodata/omero.144' Exists? True Is writable?
True
OMERO.web status... [RUNNING] (PID 3637)
What seems to be the problem?
Leon Kolchinsky
On Mon, Aug 15, 2011 at 22:32, Chris Allan <callan at lifesci.dundee.ac.uk>wrote:
> Couple things:
>
> "You need to install the Python Imaging Library. Get it at
> http://www.pythonware.com/products/pil/"
>
> Have you got that anywhere in your OMEROweb.log?
>
> Could you give us some idea about your deployment platform? Is this RHEL6?
> Have you compiled your own Python? Could you give us the output of
> "bin/omero admin diagnostics"?
>
> -Chris
>
> On 15 Aug 2011, at 13:12, Leon Kolchinsky wrote:
>
> > Hello Wiil,
> >
> > I've reinstalled PIL using pip:
> >
> > # pip install -U PIL
> > PIL 1.1.7 SETUP SUMMARY
> > --------------------------------------------------------------------
> > version 1.1.7
> > platform linux2 2.6.5 (r265:79063, Feb 28 2011, 21:55:45)
> > [GCC 4.1.2 20080704 (Red Hat 4.1.2-50)]
> > --------------------------------------------------------------------
> > *** TKINTER support not available
> > --- JPEG support available
> > --- ZLIB (PNG/ZIP) support available
> > --- FREETYPE2 support available
> > *** LITTLECMS support not available
> > --------------------------------------------------------------------
> > To add a missing option, make sure you have the required
> > library, and set the corresponding ROOT variable in the
> > setup.py script.
> >
> > To check the build, run the selftest.py script.
> > changing mode of build/scripts-2.6/pilprint.py from 644 to 755
> > changing mode of build/scripts-2.6/pilfont.py from 644 to 755
> > changing mode of build/scripts-2.6/pilconvert.py from 644 to 755
> > changing mode of build/scripts-2.6/pilfile.py from 644 to 755
> > changing mode of build/scripts-2.6/pildriver.py from 644 to 755
> > changing mode of /usr/bin/pilprint.py to 755
> > changing mode of /usr/bin/pilfont.py to 755
> > changing mode of /usr/bin/pilconvert.py to 755
> > changing mode of /usr/bin/pilfile.py to 755
> > changing mode of /usr/bin/pildriver.py to 755
> > Successfully installed PIL
> > Cleaning up...
> >
> >
> > The problem still persists ;(
> > When I login to webclient I'm getting this in the OMEROweb.log while
> clicking on "My account" link:
> >
> > Mon, 15 Aug 2011 13:09:36 blitz_gateway INFO created connection
> (uuid=d6f0a2b2-c22c-4969-9849-2435fa7dcecb)
> > Mon, 15 Aug 2011 13:09:36 views-admin INFO Have connection as Guest
> > Mon, 15 Aug 2011 13:09:36 views-admin INFO Client version:
> '4.3.1-6d4b8c61-b2602'; Server version: '4.3.1-6d4b8c61-b2602'
> > Mon, 15 Aug 2011 13:09:36 webgateway INFO getBlitzConnection(host=
> vera144.its.mydomain.edu.au, port=4064, ssl=False, username=myuser)
> > Mon, 15 Aug 2011 13:09:36 blitz_gateway INFO created connection
> (uuid=5bcc0d30-76d1-48bb-8bdb-f8df778497da)
> > Mon, 15 Aug 2011 13:09:41 omero.util.UpgradeCheck INFO no update
> needed
> > Mon, 15 Aug 2011 13:09:41 utils ERROR Up to date.
> >
> > Mon, 15 Aug 2011 13:09:42 blitz_gateway INFO created connection
> (uuid=5bcc0d30-76d1-48bb-8bdb-f8df778497da)
> > Mon, 15 Aug 2011 13:09:42 blitz_gateway INFO created connection
> (uuid=5bcc0d30-76d1-48bb-8bdb-f8df778497da)
> > Mon, 15 Aug 2011 13:09:59 webclient_gateway ERROR Traceback (most
> recent call last):
> > File
> "/srv/OMERO.server-Beta-4.3.1/lib/python/omeroweb/webclient/webclient_gateway.py",
> line 687, in getExperimenterPhoto
> > photo = self.getExperimenterDefaultPhoto()
> > File
> "/srv/OMERO.server-Beta-4.3.1/lib/python/omeroweb/webclient/webclient_gateway.py",
> line 778, in getExperimenterDefaultPhoto
> > img = Image.open(settings.DEFAULT_USER)
> > NameError: global name 'Image' is not defined
> >
> > Mon, 15 Aug 2011 13:10:00 views-feedback ERROR handler500: Server
> error
> > Mon, 15 Aug 2011 13:10:00 views-feedback ERROR Traceback (most recent
> call last):
> >
> > File "/srv/omeroserver/lib/python/django/core/handlers/base.py", line
> 92, in get_response
> > response = callback(request, *callback_args, **callback_kwargs)
> >
> > File "/srv/omeroserver/lib/python/omeroweb/webclient/views.py", line
> 165, in wrapped
> > return f(request, *args, **kwargs)
> >
> > File "/srv/omeroserver/lib/python/omeroweb/webclient/views.py", line
> 2366, in myphoto
> > photo = conn.getExperimenterPhoto()
> >
> > File
> "/srv/OMERO.server-Beta-4.3.1/lib/python/omeroweb/webclient/webclient_gateway.py",
> line 690, in getExperimenterPhoto
> > photo = self.getExperimenterDefaultPhoto()
> >
> > File
> "/srv/OMERO.server-Beta-4.3.1/lib/python/omeroweb/webclient/webclient_gateway.py",
> line 778, in getExperimenterDefaultPhoto
> > img = Image.open(settings.DEFAULT_USER)
> >
> > NameError: global name 'Image' is not defined
> >
> > Any idea how to fix it?
> >
> > Cheers,
> > Leon Kolchinsky
> >
> >
> >
> > On Mon, Aug 15, 2011 at 15:09, Will Moore <will at lifesci.dundee.ac.uk>
> wrote:
> > Hi,
> >
> > This looks like a failure to import PIL (python imaging library).
> >
> > You should be seeing in your log (var/lob/OMERO-web.log) something like
> this:
> > "You need to install the Python Imaging Library. Get it at
> http://www.pythonware.com/products/pil/"
> >
> > There are also some mentions on our install pages of how to install PIL.
> > Although it's not really needed in this case (default user photo is not
> critical) you will find that various other features of the webclient are
> also dependent on PIL.
> >
> > Will.
> >
> >
> > On 15 Aug 2011, at 02:11, Leon Kolchinsky wrote:
> >
> >> Hello,
> >>
> >> I'm getting those messages from the system while new users log into
> Omero web client.
> >> Any tips on how to fix it or if it's OK, how to stop those messages?
> >>
> >> Traceback (most recent call last):
> >>
> >> File "/srv/omeroserver/lib/python/django/core/handlers/base.py", line
> 92, in get_response
> >> response = callback(request, *callback_args, **callback_kwargs)
> >>
> >> File "/srv/omeroserver/lib/python/omeroweb/webclient/views.py", line
> 165, in wrapped
> >> return f(request, *args, **kwargs)
> >>
> >> File "/srv/omeroserver/lib/python/omeroweb/webclient/views.py", line
> 2366, in myphoto
> >> photo = conn.getExperimenterPhoto()
> >>
> >> File
> "/srv/OMERO.server-Beta-4.3.1/lib/python/omeroweb/webclient/webclient_gateway.py",
> line 690, in getExperimenterPhoto
> >> photo = self.getExperimenterDefaultPhoto()
> >>
> >> File
> "/srv/OMERO.server-Beta-4.3.1/lib/python/omeroweb/webclient/webclient_gateway.py",
> line 778, in getExperimenterDefaultPhoto
> >> img = Image.open(settings.DEFAULT_USER)
> >>
> >> NameError: global name 'Image' is not defined
> >>
> >>
> >> <WSGIRequest
> >> GET:<QueryDict: {}>,
> >> POST:<QueryDict: {}>,
> >> COOKIES:{'__utma':
> '192312886.1704004095.1303085135.1312265964.1313025486.33',
> >> '__utmz':
> '192312886.1312265964.32.21.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=mydomain%20eResearch',
> >> 'sessionid': '9ce727d572e0871b3d042549a2a582f7'},
> >> META:{'DOCUMENT_ROOT': '/var/www/html',
> >> 'GATEWAY_INTERFACE': 'CGI/1.1',
> >> 'HTTP_ACCEPT': '*/*',
> >> 'HTTP_ACCEPT_ENCODING': 'gzip, deflate',
> >> 'HTTP_ACCEPT_LANGUAGE': 'en-us',
> >> 'HTTP_CONNECTION': 'keep-alive',
> >> 'HTTP_COOKIE': 'sessionid=9ce727d572e0871b3d042549a2a582f7;
> __utma=175132154.1224947860.1303083934.1309411927.1313033085.5;
> __utmz=175132154.1306203174.3.2.utmccn=(organic)|utmcsr=google|utmctr=it+service+desk+mydomain|utmcmd=organic;
> __utmz=192312886.1312265964.32.21.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=mydomain%20eResearch;
> __utma=192312886.1704004095.1303085135.1312265964.1313025486.33',
> >> 'HTTP_HOST': 'vera144.its.mydomain.edu.au',
> >> 'HTTP_REFERER': '
> http://vera144.its.mydomain.edu.au/webclient/upload_myphoto/',
> >> 'HTTP_USER_AGENT': 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8)
> AppleWebKit/534.50 (KHTML, like Gecko) Version/5.1 Safari/534.50',
> >> 'PATH': '/sbin:/usr/sbin:/bin:/usr/bin',
> >> 'PATH_INFO': u'/webclient/myphoto/',
> >> 'PATH_TRANSLATED':
> '/srv/omeroserver/var/omero.fcgi/webclient/myphoto/',
> >> 'QUERY_STRING': '',
> >> 'REMOTE_ADDR': '130.194.148.244',
> >> 'REMOTE_PORT': '49846',
> >> 'REQUEST_METHOD': 'GET',
> >> 'REQUEST_URI': '/webclient/myphoto/',
> >> 'SCRIPT_FILENAME': '/srv/omeroserver/var/omero.fcgi',
> >> 'SCRIPT_NAME': u'',
> >> 'SERVER_ADDR': '130.194.245.189',
> >> 'SERVER_ADMIN': 'root at localhost',
> >> 'SERVER_NAME': 'vera144.its.mydomain.edu.au',
> >> 'SERVER_PORT': '80',
> >> 'SERVER_PROTOCOL': 'HTTP/1.1',
> >> 'SERVER_SIGNATURE': '<address>Apache/2.2.3 (Red Hat) Server at
> vera144.its.mydomain.edu.au Port 80</address>\n',
> >> 'SERVER_SOFTWARE': 'Apache/2.2.3 (Red Hat)',
> >> 'wsgi.errors': <flup.server.fcgi_base.TeeOutputStream object at
> 0x1d1cc890>,
> >> 'wsgi.input': <flup.server.fcgi_base.InputStream object at 0x1d1cc410>,
> >> 'wsgi.multiprocess': True,
> >> 'wsgi.multithread': False,
> >> 'wsgi.run_once': False,
> >> 'wsgi.url_scheme': 'http',
> >> 'wsgi.version': (1, 0)}>
> >>
> >>
> >> Cheers,
> >> Leon Kolchinsky
> >>
> >> _______________________________________________
> >> ome-users mailing list
> >> ome-users at lists.openmicroscopy.org.uk
> >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> > William Moore
> > Wellcome Trust Centre for Gene Regulation & Expression
> > College of Life Sciences
> > MSI/WTB/JBC Complex
> > University of Dundee
> > Dow Street
> > Dundee DD1 5EH
> > United Kingdom
> >
> > Phone 01382 386364
> > http://openmicroscopy.org
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
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