Omero-gallery: lock-up issue and different viewer option

Hi OME team,

For our public-access OMERO instance on AWS (https://omero.lincsclarion.org/webclient/userdata/?experimenter=52) I’m trying to set up omero-gallery with the new IDR front-end as a shiny example. At this time I’m still on OMERO 5.5.1 so I’m limited to gallery 3.1.1 (is that correct?) so for now I can only get the Default UI (which is fine until I upgrade to 5.6, when I plan to use the Categories UI).

However, when initiating gallery for a user with access to the Public group (which has > 500k images over many plates and screens and some individual images in Projects/Datasets) the Blitz processes peg up to 100% and the server becomes unresponsive for a while until it auto-recovers 10-15 minutes later. I don’t see much happening in the Blitz log. When I do the same for user that is not part of the Public group i.e. a group that has only a small number of images in it, gallery works fine. Is there anything I can do to make this work for now with 5.5.1 and gallery 3.1.1 for the Public group?

Question 2: the default viewer in gallery is the regular viewer. Is there a way to configure gallery to use iviewer? Or is that governed by the “system-wide” default viewer (set with omero.web.viewer.view)?

Thanks,
Damir

Hi Damir,

The default UI won’t be any use to you since it never supported Screens/Plates (only Projects).
You should be fine to use omero-gallery 3.2.0a8. https://github.com/ome/omero-gallery/releases/tag/v3.2.0a8
This is what’s currently running on IDR (OMERO 5.5.1).
See: https://github.com/IDR/deployment/blob/90c1d6a4ba15076373636c07946dbe9f2bbbc57f/ansible/group_vars/omero-hosts.yml#L182

This was the last tag/release before we made the Python 3/Django 1.11 updates for gallery 3.3.0. It may even be possible to run gallery 3.3.0 on 5.5.1 but I haven’t tried.

With the Categories UI in gallery, images will be opened in the default webclient viewer (omero.web.viewer.view), so if you’ve configured iviewer to be your default viewer then you should be fine.

Cheers,

Will.

Hi Will,

Thanks!! 3.2.0a8 indeed gets me a lot further while still on OMERO 5.5.1. I am trying a few things using the Categories UI and that brought up a few more questions:

  1. this one may be a bug: when I start gallery while logged in as a user that has no access to any Screens in any groups they have access to, the initial gallery screen shows: “Loading Studies…” and nothing else. If, however, I add a dummy empty Screen, then gallery shows the expected display. When it hangs on “Loading Studies” the OMEROweb.log and Blitz.log show errors such as:
  File "/home/omero/OMERO.server/lib/python/omero/gateway/__init__.py", line 4700, in __call__
    return self.f(*args, **kwargs)
  File "/home/omero/OMERO.server/lib/python/omero_api_IQuery_ice.py", line 857, in projection
    return _M_omero.api.IQuery._op_projection.invoke(self, ((query, params), _ctx))
ApiUsageException: exception ::omero::ApiUsageException
{
    serverStackTrace = ome.conditions.ApiUsageException: unexpected end of subtree [select chl.parent.id, count(chl.id) from ome.model.screen.ScreenPlateLink chl where chl.parent.id in () group by chl.parent.id]; nested exception is org.hibernate.hql.ast.QuerySyntaxException: unexpected end of subtree [select chl.parent.id, count(chl.id) from ome.model.screen.ScreenPlateLink chl where chl.parent.id in () group by chl.parent.id]
        at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:672)
        at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:416)
        at org.springframework.orm.hibernate3.HibernateTemplate.doExecute(HibernateTemplate.java:416)
...etc...
  1. In the Categories UI, there is no logout “button” as there is in the Default UI. Would be nice to have that for non-public logged-in users.

  2. The Categories UI gives a huge number of great features but there’s one in the Default UI that I was hoping I could get back for very rudimentary access: simply clicking down into a Study and seeing the images without getting exposed to the more complex OMERO webclient view. Any way to still get that?

  3. Are advanced config settings such as super_categories safe to use? Especially that functionality would be very useful for what I’m trying to do, namely give individual research projects their own “area” on the same public server.

  4. I have one glitch with the “simplest case” Categories UI config when connecting as the public user (https://omero.lincsclarion.org/gallery/): the thumbnails for the Studies are not showing up (see below). This only happens for the public user. All is fine for a logged-in user with access to the same data. Any suggestions where I need to look?

The examples from IDR are very useful to figure out what’s all possible. Thanks for referring me to that.

Thanks,
Damir

On question 5, it probably has something to do with my omero.web.public.url_filter. I currently have:

omero.web.public.url_filter=^/(iviewer|api|figure(?!/new)|webadmin/myphoto/|webclient/(?!(script_ui|ome_tiff|figure_script|download_|ome_tiff_script|archived_files/download|download_orig_metadata))|webgateway/(?!(archived_files|download_as)))

I’m guessing I have to add something “gallery”-related in there somewhere, right?

Thanks,
Damir

Hi Damir,

Yes, for 5. you need to allow https://omero.lincsclarion.org/gallery/gallery-api/thumbnails/?project=152 in your public.url_filter.

  1. That is a bug - There’s an assumption you have at least 1 Screen. Actually, that’s a bug in the main omero-web JSON api, since /api/v0/m/screens/?childCount=true fails if you have no Screens. Issue created at https://github.com/ome/omero-web/issues/146

  2. Logout button issue created at https://github.com/ome/omero-gallery/issues/58 (I assume this should behave the same as in the webclient?)

  3. No way see Images within a Study yet. Really this means covering all of Project > Dataset > Image and Screen > Plate > Wells which is a fair bit of work, but it is something we’ve planned to do at some point for Gallery. I created https://github.com/ome/omero-gallery/issues/59

  4. Super_categories are OK but I’ve only tested using 2 of them. Since the IDR only needed 2, I haven’t tried to optimise the UI layout with other numbers, but certainly give it a try.

  5. See above.

Thanks for the feedback and for being the guinea pig for the Gallery (outside of IDR).

Hope that helps,

Will

Hi Will,

Thanks for all the answers.

  1. Yes, with the public.url_filter fixed, the thumbs show up and things work.
  2. The dummy Screen is a good-enough work-around.
  3. Yes, logout button/menu item with same behavior as in webclient would be useful to have.
  4. Understood and going through the regular webclient is fine for now.
  5. It works with more but the layout is kinda messy so for now best to stick with 2 super-categories. Would be nice to have it handle multi super-categories in the future.

Thanks a bunch,
Damir

Hi Damir,

I created an issue for multiple super-categories.

Regards,
Will.