Open Microscopy Environment

Hi OME team (pre-emptive thanks to Will for offering help via twitter),

BACKGROUND: we're playing with Open Science Notebooks here: [https://raphazlabcommons.wordpress.com/] and want to get the raw data (already in OMERO) out to the public.

Having finally managed to get ports open to the outside world, I'm realising that making available public data is not quite as easy as I had at first thought.

Good news is that I have the public user set up such that I can share single images using:
http://myserver.com/webgateway/img_detail/123456/

That's great, but I wanted to make a dataset available and can't figure out an easy way to do that without linking to 20 or so separate images.

Looking over the documentation, it's not clear to me whether webgateway is set up to serve Datasets/Projects. All I'm looking to do is have people able to view and optionally download the data via the Public user account.

Thanks in anticipation,

Dave Mason

Hi Dave,

could you possibly send us your current web configuration (bin/omero config get | grep web) as well as which version you are using?

Happy Friday,
~Josh.

Hi Josh,

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$ omero config get|grep web

omero.web.apps=["figure", "autotag", "tagsearch"]
omero.web.public.enabled=True
omero.web.public.password=[###removed###]
omero.web.public.server_id=1
omero.web.public.url_filter=/webgateway
omero.web.public.user=public
omero.web.ui.center_plugins=[["Auto Tag", "autotag/auto_tag_init.js.html", "auto_tag_panel"]]
omero.web.ui.top_links=[["Figure", "figure_index"], ["Tag Search", "tagsearch"]]


And...

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$ omero admin diagnostics
================================================================================
OMERO Diagnostics 5.0.8-ice34-b60
================================================================================

Commands:   java -version                  1.6.0     (/usr/bin/java)
Commands:   python -V                      2.7.3     (/usr/bin/python)
Commands:   icegridnode --version          3.4.2     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.4.2     (/usr/bin/icegridadmin)
Commands:   psql --version                 9.1.15    (/usr/bin/psql)


Although I'm about to bump to Ubuntu 14.04 LTS so a bunch of those packages will be updated (including ICE 3.5).

Sorry for the complication. Should have sorted this out before posting. Just bumped Ubuntu versions, so now I'm running 5.0.8 ICE35:

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$ omero admin diagnostics
================================================================================
OMERO Diagnostics 5.0.8-ice35-b60
================================================================================
Commands:   java -version                  1.7.0     (/usr/bin/java)
Commands:   python -V                      2.7.6     (/usr/bin/python)
Commands:   icegridnode --version          3.5.1     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.5.1     (/usr/bin/icegridadmin)
Commands:   psql --version                 9.3.6     (/usr/bin/psql)


Hi Dave,

Apologies - there isn't an 'out-of-the-box' public gallery in webgateway.
I think you have 2 main options:

- You can make the main webclient UI publicly available, as has been done by http://ssbd.qbic.riken.jp/ See: http://ssbd.qbic.riken.jp/omero/webclie ... =dataset-1
If you are happy for users to use this UI, then you just need to disable various features that shouldn't be publicly available - E.g. Creating data, running scripts, etc. since this UI wasn't originally designed for 'public' use.

- You can add a public 'gallery' via an additional web app, although this will involve a bit more work. One prototype example is https://github.com/will-moore/gallery. I need to update the install docs there but it's essentially the same as https://github.com/will-moore/webmobile.

For smaller numbers of images you could always manually construct static pages to show thumbnails and links to image viewers - but this is obviously very limited.

I'll update the docs for webgallery and test it with latest OMERO, so it's ready to try out.

Hope we can find a suitable solution for you.

Regards,

Will.

Hi Will,

Thanks for the reply (especially on the weekend!). That's just what I needed to get started. I'll definitely look into the gallery app, but I think providing access to the UI is likely what I need.

I'll have a play next week, see how far I can get and report back with any questions,

Best,

Dave

Hi Dave,

I added install instructions and some screenshots to the OMERO.gallery docs at https://github.com/will-moore/gallery.

Seems to be working fine with the latest OMERO (5.1 and 5.0).

There are a few obvious little things to fix (E.g. footer) but I think it's generally looking pretty good.

Let us know if you need any help etc.

Cheers,

Will.

Hi Will,

I shouldn't be surprised, but gallery is lovely. I think it would be a real benefit for others like me who just want a quick and easy public gallery if this were to become "built-in". I don't know if you're taking feature suggestions, but it would be great to have a "download original" link at the project/dataset/image level.

Anyway, the one niggle that I have about the public user is that when I navigate to my server, it automatically logs me in as Public user, and I have to go to http://your_host/webclient/login/ to get to the login page.

Is there some way to reverse this behaviour so that "your_host" directs to the login page and "yourhost/public" directs me to gallery? I've been playing with the nginx configuration file and I can't seem to get it to work.

Thanks,

Dave

Hi Dave,

You need to change your url filter to

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bin/omero config set omero.web.public.url_filter '/(webgateway|gallery|webclient/render_thumbnail/\w+)'

That should help and public data will be available http://YOUR_HOST/gallery. If you go to http://YOUR_HOST/ you get login page

Will is going to clean up links after that you won't need third filter.
Ola

Hi Dave,

I just fixed the gallery app to only use thumbnails from webgateway https://github.com/will-moore/gallery/c ... d15b2e7936
so you shouldn't need to include the webclient/render_thumbnail/\w+ in your url filter for public users.

Cheers,

Will.