Open Microscopy Environment

Hi Everybody,

Recently I tried to add OMERO.figure to the fully working OMERO . During installation something went wrong and OMERO.insight stopped working. So the question is which files are overwritten when command "bin/omero config append omero.web.apps '"figure"' " executes and how to revert changes or uninstall OMERO.figure ??

Regards slozosnitram

Here is the screenshot of whats going on. What do I need to modify to fix this ?

Hi Martins,

Can we please see the output of

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[user@servername ~]$ OMERO-CURRENT/bin/omero config get --hide-password | grep omero.web

All the best,

Kenny

Hi Martins,

So it looks like the "config append" step has happened twice.

You can set the `omero.web.apps` config to just "figure", removing the duplicate, with the following:

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bin/omero config set omero.web.apps '["figure"]'


Best,

Kenny

OK I executed the command reloaded OMERO and everything works. Thank you very much !!

slozosnitram wrote:OK I executed the command reloaded OMERO and everything works. Thank you very much !!

We're very glad to hear it, and you're most welcome.

For completeness, to answer your initial question, the figure install updates the OMERO configuration via `bin/omero config update` CLI commands.

Specifically, the `omero.web.apps` and `omero.web.ui.top_links` configuration properties, which are a list of the names of "apps" which can be written and installed to extend the functionality of OMERO.web [1] and a list of hyperlinks which appear in the OMERO.web UI at the top of the page [2].

[1] https://www.openmicroscopy.org/site/sup ... -omero-web

[2] https://www.openmicroscopy.org/site/sup ... .top_links

Sorry guys one more question,

I have unexpected difficulties with "Upload figure export script (need to be Admin)"
Instructions says to do this: path/to/bin/omero script upload omero/figure_scripts/Figure_To_Pdf.py --official
so when I'm doing it I'm getting following password problem

What I'm doing wrong ??

slozosnitram wrote:Sorry guys one more question,

Absolutely no worries.

slozosnitram wrote:I'm getting following password problem
What I'm doing wrong ??

So there are two distinct issues going on here. Let's deal with the first one, the password problem.

You appear to be trying to log into OMERO as 'omero-system-user', and it's failing.

The user you're trying to log in with, 'omero-system-user' has a name which implies 'operating system user' - and you can see, in this case, your shell tells you that you are logged into this linux server as 'omero-system-user'. This will most likely be the operating system user that OMERO is running as. i.e. a linux user.

OMERO has it's own concept of users/groups, known as 'OMERO users', distinct from the users the operating system knows about [1]. So an OMERO instance will start off it's life with a single Administrative OMERO user (i.e. not a linux or operating system user), called 'root'. It is with the 'root' OMERO user account one would log in to OMERO to set up the rest of the system for the users of OMERO.

So you likely need to log into OMERO with an _OMERO_ administrative account, not an operating system account. Find out what admin account you normally use to manage the server, and try a CLI log-in, and let us know if you are still having problems there.

i.e.

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bin/omero login

[1] https://www.openmicroscopy.org/site/sup ... g-password

The second issue is one of paths:

slozosnitram wrote:Instructions says to do this: path/to/bin/omero script upload omero/figure_scripts/Figure_To_Pdf.py --official

There is another instruction, just before `path/to/bin/omero script upload`: as follows:

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$ cd figure/scripts       # NB: important to be in this directory

before running

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$ path/to/bin/omero script upload omero/figure_scripts/Figure_To_Pdf.py --official

From your screenshot, you are in the operating system user's homedir. You'll need to change directory to the `figure/scripts` folder first. i.e.

So using the example from the OMERO.figure docs, i.e. `lib/python/omeroweb` [1]

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cd ~/OMERO.server/lib/python/omeroweb/figure/scripts
~/OMERO.server/bin/omero script upload omero/figure_scripts/Figure_To_Pdf.py --official


[1] http://figure.openmicroscopy.org/