Open Microscopy Environment

I have installed OMERO.figure 1.2.0 into OMERO 5.2.0 and everything looks to be working correctly except the image export. I believe I have followed all the instructions on the install page.

When I try to export an image, the UI message in the green export button is "Exporting Figure.." but this never ends.

I would appreciate any advice on now to debug this problem.

Rob

Hi Rob,

Can you check whether running scripts in the main webclient is working OK?
E.g. pick an image and run script such as "Batch_Image_Export". Does the activities list show that it completed OK (can download zip etc)?

If you have just tried exporting from OMERO.figure then you will also see that activity in the same activities pane, and there may be an info or error available?

If scripts are not working, then you may also find that other actions are failing to show up in the activities panel, such as Delete and moving data to other groups?

On friday we had these exact issues when upgrading to OMERO 5.2.0 on our production server that uses Apache. I will let others give you more details if needed, but we are still trying to work out exactly what the issue is here.
We have worked around it on our production system by switching to nginx.

Regards,
Will.

Hi, did you deploy OMERO.web on Apache using mod_wsgi? If so you need to add

Code: Select all

WSGIApplicationGroup %{GLOBAL}

to your Apache config like https://github.com/openmicroscopy/openm ... che24.conf

Please let us know more about your deployment, OS, etc.

Ola

Will,

The mail webclient cannot run scripts. I tried a Batch_Image_Export and it never terminated. I had to restart OMERO.web and the server to get sane performance back again.

Deleting an image in OMERO.web also appears to cause problems with the app. Once a file has been deleted, the web app fails to respond to other actions.

There are no errors in var/log/OMEROweb.log

We are using Apache to front OMERO.web using the wsgi approach described in your docs. I don't think we have the option to move to nginx.

Rob

Rob, we realized that problem with Apache recently, adding WSGIApplicationGroup %{GLOBAL} should solve it.

Ola

Ola,

Perfect. My Apache config file was missing the entry:

WSGIApplicationGroup %{GLOBAL}

Once added, the app looks to be behaving properly.

Thanks for your suggestions.

Rob

Great, I am glad it's working for you. If you spot any more issues, please let us know imminently.

Ola