Error creating table on local server installation


I’m having trouble running a script to create an OMERO table on a local virtual OMERO server.
When I run the script on the demo omero server, things go smoothly. I can reproduce the error with this example script

#!/usr/bin/env python
# -*- coding: utf-8 -*-
import omero
from credentials import HOST, USER, PASSWORD

c = omero.client(HOST)
s = c.createSession(USER, PASSWORD)
r = s.sharedResources()
m = r.repositories()
i = m.descriptions[0].id.val
t = r.newTable(i, "/example.h5")
lc = omero.grid.LongColumn('name', 'desc', None)
lc.values = [1, 2, 3, 4]
ids = t.getWhereList('(name==1)', {}, 0, 0, 0)
data = t.readCoordinates(ids)
data = t.slice([0], [0])

On the demo server the output is, as expected


but on my instance I get the following error.

Traceback (most recent call last):
  File "<input>", line 1, in <module>
  File "/home/julio/.local/share/JetBrains/Toolbox/apps/PyCharm-P/ch-0/193.6494.30/plugins/python/helpers/pydev/_pydev_bundle/", line 197, in runfile
    pydev_imports.execfile(filename, global_vars, local_vars)  # execute the script
  File "/home/julio/.local/share/JetBrains/Toolbox/apps/PyCharm-P/ch-0/193.6494.30/plugins/python/helpers/pydev/_pydev_imps/", line 18, in execfile
    exec(compile(contents+"\n", file, 'exec'), glob, loc)
  File "/home/julio/PycharmProjects/OMERO.metrics/", line 11, in <module>
    t = r.newTable(i, "/example.h5")
  File "/home/julio/PycharmProjects/OMERO.metrics/venv/lib64/python3.7/site-packages/", line 393, in newTable
    return _M_omero.grid.SharedResources._op_newTable.invoke(self, ((repoId, path), _ctx))
omero.InternalException: exception ::omero::InternalException
    serverStackTrace = 
    serverExceptionClass = 
    message = null table as argument

Only changes are, I believe, the credentials. There must be something wrong in my OMERO installation. Do yo have an idea of what it could be?

Cheers, Julio

Hi Julio
Could you check your OMERO.server/var/log/Tables-0.log file for messages matching the time you ran the script?

Hmmm. That log fine isn’t there. I have Blitz-0.log Indexer-0.log master.err master.out PixelData-0 and Processor-0.log

Sounds like your Tables service isn’t running. Do you have PyTables installed in the OMERO.server virtualenv?

Yes! That’s it. I must have missed that line in the server installation docs. I’m sorry.


I’ve added an issue regarding the error message: