Open Microscopy Environment

Hi,

I'm following the instructions here : https://www.openmicroscopy.org/site/sup ... ebrew.html and I end up with OMERO 4.4.9 instead of OMERO as advertised.

Is it possible you forgot to update the formula?

Thanks!

Hi,

sorry for the confusion. Indeed the default OMERO formula is still OMERO 4.4.10. To install OMERO 5.0.0-rc1 via Homebrew, you can currently use the --devel option, i.e.

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brew install omero --devel


Note that once OMERO 5.0.0 is released (in the upcoming next weeks obviously), we will archive the OMERO 4.4.x formulas and the default installation will be OMERO 5 (see https://trac.openmicroscopy.org.uk/ome/ticket/11891)

Best regards,
Sebastien

Thanks Sebastien! That did it. The installation completed with no errors and this message:

For non-homebrew Python, you need to set your PYTHONPATH:
export PYTHONPATH=/usr/local/Cellar/omero/5.0.0-rc1/lib/python:$PYTHONPATH

To finish the installation, execute omero_python_deps in your
shell:
./usr/local/Cellar/omero/5.0.0-rc1/bin/omero_python_deps

Running omero_python_deps also didn't throw any errors.

I homebrewed Python so I understand I wouldn't need to set pythonpath. I tried both setting it and not but I still get the same error when I try to run omero :

Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6

I was trying to run in the terminal some of your code to see where it breaks and it's something in the init script, I suppose, as it fails at :

>>> from omero.util import get_user
Fatal Python error: Interpreter not initialized (version mismatch?)
Abort trap: 6

FYI I'm running this on Mountain Lion with

python --version
Python 2.7.6
$ which python
/usr/local/bin/python

Do you have any ideas how I could fix this?

Hi again,

Unluckily, you seem to have installed OMERO while some breaking changes had been committed in the upstream Homebrew repository upsetting all formulas with Python bindings (see https://github.com/Homebrew/homebrew/issues/26218, https://github.com/Homebrew/homebrew/issues/26197 or https://github.com/Homebrew/homebrew/issues/26228). Minimally, any formula with Python binding seemed to end up getting compiled against the system Python even if Homebrew Python was installed.

The following error message suggests you are in this exact situation:

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Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6

The issue we are talking about seems to have been solved upstream as of today (see https://github.com/Homebrew/homebrew/pull/26229). We reactivated our testing job for Homebrew installation this afternoon which uses Homebrew Python. The last run has been successful, see http://ci.openmicroscopy.org/job/OME-5. ... ebrew/343/.

So at the moment, your formulas have certainly been compiled against the wrong Python, you should be able to safely reinstall Ice and OMERO. Assuming you used the default formula (i.e. with Ice 3.5), could you try reinstalling and testing Ice first:

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brew reinstall ice
python -c "import Ice"


If you have Homebrew Python, the last command should not throw any fatal error. Then, try to reinstall OMERO

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brew reinstall omero --devel


Let me know if anything does not work,
Sebastien

Hi Sebastien,

Thanks for all the help. I was able to install it now but with the system python, not the homebrew one. I uninstalled all pythons , removed links and installed one again via mac ports.

I hope the dependencies and database setup will go smooth.

Thanks,
ilinca

Hi,

In principle I have everything installed now. After I start the web server I follow the link in the terminal and try to login with the credentials on the documentation page I get this error : "Error: Client version does not match server, please contact administrator.". Can someone explain what this means?

Thanks,
ilinca

Hi ilinca,

glad to know you've been able to get that far.
And thanks for reporting your bug which is an issue on our side since to the version number is not set in the case of the OMERO 5 formula. I just opened a Pull Request to fix this bug. Hopefully this will be tested and included in the tap in the upcoming days. With it, I would expect the client/server communication to be restored.

I will keep you posted. Best,
Sebastien

Hi Ilinca,

the bug fix I mentioned yesterday just got merged in our Homebrew tap. Could you try reinstalling OMERO via

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brew update
brew reinstall omero --devel


and start the server/web client again? This should fix the error you reported.

Best,
Sebastien

Hi Sebastien,

yes, this fixed it. Thanks, I now have both the server and client working.

Thanks,
ilinca