Open Microscopy Environment

we had an issue and would like your feedback, if possible. at this we are using the omerocli to import and attach H5 tables to these images. at some point last night we starting getting this error

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/usr/lib/python2.5/site-packages/pyslid/features.pyc in link(conn,
iid, scale, fids, features, set, field, rid, pixels, channel, zslice,
timepoint, debug)
     703             #table for cell level features (roi == regions of
interest)
     704             table = conn.getSharedResources().newTable( 1,
'iid-' + str(iid) + '_feature-' + str(set) + '_roi.h5' )
--> 705         table.initialize(columns)
     706
     707         try:
AttributeError: 'NoneType' object has no attribute 'initialize'


since i know this error occurs when the table is nonetype i tried making a dummy table and got the same result. i restarted omero and the problem remained. then i restarted the node and now it works. we figure out there might be a memory leak. do you have any recommendations on how to handle this particular issue?

I'd guess that there was an exception creating the Table. We'd have to see the Tables-0.log to see what might have happened.

how are exceptions reported in the log file? it would be easier to grep for a line. we have more than ten log files at the moment.

ERROR would be a good start, Ivan, but really just the latest log file (var/log/Tables-0.log) would probably be the most useful. ~J.

Hi,

same problem here. Working through the example code in http://trac.openmicroscopy.org.uk/ome/w ... MEROtables fails on newTable() resulting in type(table) == NoneType.

@icaoberg: Have you solved your issue?

Here is the complete Table-0.log after OMERO restart:

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2012-06-12 16:24:07,697 INFO  [                       omero.util.Server] (MainThread) Stopped
2012-06-12 16:24:07,698 INFO  [                       omero.util.Server] (MainThread) ********************************************************************************
2012-06-12 16:24:07,701 INFO  [                    omero.util.Resources] (Thread-2  ) Halted
2012-06-12 16:24:18,728 INFO  [                       omero.util.Server] (MainThread) ********************************************************************************
2012-06-12 16:24:18,728 INFO  [                       omero.util.Server] (MainThread) Starting
2012-06-12 16:24:18,728 INFO  [                       omero.util.Server] (MainThread) Loaded dependency numpy (1.4.1)
2012-06-12 16:24:18,728 INFO  [                       omero.util.Server] (MainThread) Loaded dependency tables (2.1.2, hdf=1.8.4-patch1)
2012-06-12 16:24:18,729 INFO  [                    omero.util.Resources] (Thread-2  ) Starting
2012-06-12 16:24:31,305 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 1
2012-06-12 16:24:41,483 INFO  [                       omero.util.Server] (MainThread) Entering main loop
2012-06-12 16:28:13,656 INFO  [                            omero.remote] (Dummy-3   )  Meth: TablesI.getTable
2012-06-12 16:28:13,656 INFO  [                    omero.tables.TablesI] (Dummy-3   ) getTable: 18301 {}
2012-06-12 16:28:14,536 INFO  [                       omero.util.Server] (MainThread) ********************************************************************************
2012-06-12 16:28:14,536 INFO  [                       omero.util.Server] (MainThread) Starting
2012-06-12 16:28:14,536 INFO  [                       omero.util.Server] (MainThread) Loaded dependency numpy (1.4.1)
2012-06-12 16:28:14,536 INFO  [                       omero.util.Server] (MainThread) Loaded dependency tables (2.1.2, hdf=1.8.4-patch1)
2012-06-12 16:28:14,537 INFO  [                    omero.util.Resources] (Thread-2  ) Starting
2012-06-12 16:28:14,655 INFO  [                       omero.util.Server] (MainThread) Entering main loop


\m/ Christian

If you try the following Christian can you then create a table?

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...
$ bin/omero admin ice 'server stop Tables-0'
...


What that does is just restart the OMERO.tables process.

Hi,

Thank you for your advice. But the reason for my issue was a broken PyTables setup. PyTables tried to use outdated HDF5 shared libs from a Matlab installation.

Best,

\m/ Christian