We're Hiring!

OMERO Figure - XML not well-formed

Having a problem deploying OMERO? Please ask new questions at https://forum.image.sc/tags/omero
Please note:
Historical discussions about OMERO. Please look for and ask new questions at https://forum.image.sc/tags/omero

The OMERO.server installation documentation begins here and you can find OMERO.web deployment documentation here.

OMERO Figure - XML not well-formed

Postby mattc » Mon Jul 30, 2018 2:26 pm

Hi,

i've added the Figure plugin but when I try and open an image with it I get a "XML Parsing Error: not well-formed" message. When I visit the URL the data seems to be there but its JSON rather than XML. Is there a config option that could fix this?

Thanks,

Matt.
mattc
 
Posts: 41
Joined: Thu Jun 05, 2014 2:03 pm

Re: OMERO Figure - XML not well-formed

Postby kennethgillen » Tue Jul 31, 2018 4:33 pm

Hi mattc,

Could you please paste the omero config for your OMERO.web client deployment?

That'll let us see if the plugin is properly installed. (also - did you restart OMERO.web after installing the plugin?)

In the corresponding folder of your OMERO.web deployment:
Code: Select all
bin/omero config get


Best,

Kenny
kennethgillen
 
Posts: 254
Joined: Mon Nov 05, 2012 3:39 pm

Re: OMERO Figure - XML not well-formed

Postby mattc » Wed Aug 01, 2018 3:58 pm

Thanks for getting back to me Kenny. My config looks like this:

Code: Select all
omero.db.name=image_db
omero.db.pass=********
omero.db.user=omero_user
*** ldap stuff ***
omero.web.application_server=wsgi-tcp
omero.web.apps=["omero_iviewer", "omero_figure"]
omero.web.open_with=[["Image viewer", "webgateway", {"supported_objects": ["image"], "script_url": "webclient/javascript/ome.openwith_viewer.js"}], ["omero_iviewer", "omero_iviewer_index", {"supported_objects": ["images", "dataset", "well"], "script_url": "omero_iviewer/openwith.js", "label": "OMERO.iviewer"}], ["omero_figure", "new_figure", {"supported_objects": ["images"], "target": "_blank", "label": "OMERO.figure"}]]
omero.web.ui.top_links=[["Data", "webindex", {"title": "Browse Data via Projects, Tags etc"}], ["History", "history", {"title": "History"}], ["Help", "https://help.openmicroscopy.org/", {"target": "new", "title": "Open OMERO user guide in a new tab"}], ["Figure", "figure_index", {"target": "_blank", "title": "Open Figure in new tab"}]]
omero.web.viewer.view=omero_iviewer.views.index


I realised after I posted that Figure is working well for some images on our DB but with others we get the spinning progress icon but nothing loads. I did try restarting OMERO.web without success i'm afraid.
mattc
 
Posts: 41
Joined: Thu Jun 05, 2014 2:03 pm

Re: OMERO Figure - XML not well-formed

Postby kennethgillen » Fri Aug 03, 2018 4:43 pm

Hi Matt,

The plugin configuration looks good to me.

The only other two times we've come across that particular error message it's been issues like an upgrade of the plugin with browsers or Django caching parts of the the old version.

See the two threads at

http://lists.openmicroscopy.org.uk/pipe ... 06607.html
and
viewtopic.php?f=4&t=8318

Did you replace an older or different version of the plugin with a new one?

Or if this is a fresh install, perhaps it's worth checking the versions of the prerequisites.

Is python-reportlab successfully installed in the same e.g. virtualenv which OMERO.web is using?

Best,

Kenny
kennethgillen
 
Posts: 254
Joined: Mon Nov 05, 2012 3:39 pm


Return to Installation and Deployment

Who is online

Users browsing this forum: No registered users and 0 guests