I just upgraded my 4.4.10 installation to version 5.0.0 and most of it went just fine. In Insight everything appears to work perfectly (still more testing to be done) but in OMERO.Web I have the problem that in the Full Viewer" no images appear at all. The thumbnails are all fine and in the Preview tab the image appears fine but in the Full Viewer I get a grey empty image after a brief "Loading ..." message.
My diagnostics says:
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OMERO Diagnostics 5.0.0-ice34-b19
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Commands: java -version 1.7.0 (/usr/bin/java)
Commands: python -V 2.7.3 (/usr/bin/python)
Commands: icegridnode --version 3.4.2 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.4.2 (/usr/bin/icegridadmin)
Commands: psql --version 9.1.12 (/usr/bin/psql -- 2 others)
Server: icegridnode running
Server: Blitz-0 active (pid = 26589, enabled)
Server: DropBox active (pid = 26614, enabled)
Server: FileServer active (pid = 26613, enabled)
Server: Indexer-0 active (pid = 26621, enabled)
Server: MonitorServer active (pid = 26643, enabled)
Server: OMERO.Glacier2 active (pid = 26622, enabled)
Server: OMERO.IceStorm active (pid = 26625, enabled)
Server: PixelData-0 active (pid = 26623, enabled)
Server: Processor-0 active (pid = 26641, enabled)
Server: Tables-0 active (pid = 26627, enabled)
Server: TestDropBox inactive (enabled)
OMERO: SSL port 4064
OMERO: TCP port 4063
Log dir: /home/omero/OMERO.server/var/log exists
Log files: Blitz-0.log 9.0 MB errors=0 warnings=453
Log files: DropBox.log 1.0 KB
Log files: FileServer.log 0.0 KB
Log files: Indexer-0.log 87.0 KB errors=0 warnings=2
Log files: MonitorServer.log 1.0 KB
Log files: OMEROweb.log 221.0 KB errors=6 warnings=22
Log files: OMEROweb_request.log 0.0 KB errors=0 warnings=1
Log files: PixelData-0.log 4.0 KB
Log files: Processor-0.log 0.0 KB
Log files: Tables-0.log 0.0 KB
Log files: TestDropBox.log n/a
Log files: master.err 0.0 KB
Log files: master.out 0.0 KB
Log files: Total size 10.00 MB
Environment:OMERO_HOME=/home/omero/OMERO.server
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_TEMPDIR=(unset)
Environment:PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/lib/jvm/jdk1.7.0_11/bin:/usr/share/Ice-3.4.2:/usr/lib/postgresql/9.1/bin:/home/omero/OMERO.server/bin
Environment:ICE_HOME=/usr/share/Ice-3.4.2
Environment:LD_LIBRARY_PATH=/usr/share/java:/usr/lib:
Environment:DYLD_LIBRARY_PATH=(unset)
OMERO data dir: '/data/OMERO' Exists? True Is writable? True
OMERO temp dir: '/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
OMERO.web status... [RUNNING] (PID 2489)
and the errors in OMEROWeb.log include stuff such as:
2014-03-22 00:21:09,702 ERROR [ omero.gateway] (proc.27052) getThumbnail:6414 Traceback (most recent call last):
File "/home/omero/OMERO.server/lib/python/omero/gateway/__init__.py", line 6409, in getThumbnail
rv = thumb(*args)
File "/home/omero/OMERO.server/lib/python/omero/gateway/__init__.py", line 3541, in __call__
return self.handle_exception(e, *args, **kwargs)
File "/home/omero/OMERO.server/lib/python/omeroweb/webclient/webclient_gateway.py", line 1894, in handle_exception
e, *args, **kwargs)
File "/home/omero/OMERO.server/lib/python/omero/gateway/__init__.py", line 3538, in __call__
return self.f(*args, **kwargs)
File "/home/omero/OMERO.server/lib/python/omero_api_ThumbnailStore_ice.py", line 215, in getThumbnailByLongestSide
return _M_omero.api.ThumbnailStore._op_getThumbnailByLongestSide.invoke(self, ((size, ), _ctx))
InternalException: exception ::omero::InternalException
{
serverStackTrace = ome.conditions.InternalException: Wrapped Exception: (java.lang.RuntimeException):
ome.io.nio.DimensionsOutOfBoundsException: T '13' greater than sizeT '3'.
at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:248)
I'm suspecting something related to PIL and Pillow since I wasn't all the clear how to upgrade that.
Any suggestions I can try?
Thanks,
- Damir