Open Microscopy Environment

Hi all,

Trying to use the tagging feature to improve our workflow and help users find stuff and I'm bumping into a number of issues (on OMERO 5.1.2):

1) Took me a while to figure out how to delete tags using CLI. Good to update the documentation on: http://www.openmicroscopy.org/site/supp ... i/tag.html saying to use: "omero delete TagAnnotation:xxxx"
2) Have not been able to figure out how to delete a TagSet with CLI.
3) One can create tagsets in CLI and Insight but not in Web? And in Insight, one can create a tagset but there is no way to move tags into an existing tagset? And in Web, same problem with moving tags into tagsets.
4) In CLI empty tagsets do not show up at all with "omero tag listsets". And in Web, tagsets cannot be deleted at all.
5) I'd like to use Tag Search from Douglas's great WebTagging (1.2.0) package but it only supports tags associated with projects, datasets, and images and not tags associated with screens and plates. Feature request?

Hope this helps squashing some bugs in future releases.
Thanks,
- Damir

Hi Damir,

I'm not going to respond to the CLI questions since someone else will handle those...

Tagsets is unfortunately just one of those features where the web client has not caught up with Insight. But this is certainly something that will be addressed at some point.

In Insight, you should be able to "copy" and "paste" tags into Tag Sets (using right-click menu or toolbar buttons) or use drag-n-drop to move them. Also, if you select a Tag Set and create a new Tag, it should be placed in the Tag set.

For webtagging, it would be best if you could create a new Issue on the repo at https://github.com/MicronOxford/webtagging/issues since this app is supported by Oxford.

Many thanks for your feedback,

Will.

Hi Damir,

First of all, thanks for the feedback. I'll address the CLI issues and let Will get back to you on the web and Insight issues.

dsudar wrote:1) Took me a while to figure out how to delete tags using CLI. Good to update the documentation on: http://www.openmicroscopy.org/site/supp ... i/tag.html saying to use: "omero delete TagAnnotation:xxxx"

Deletion is documented at http://www.openmicroscopy.org/site/supp ... elete.html though deleting a TagAnnotation does not have a direct example. But yes the documentation could definitely be improved, I'll look at improving that with an example and a crosslink.

dsudar wrote:2) Have not been able to figure out how to delete a TagSet with CLI.

A TagSet is itself a TagAnnotation so your delete command above should do the job. By default any Tags in the TagSet will not be deleted:

Code: Select all

$ omero tag list
+- 8:'Set2'
|\
| +- 6:'Tag6'
| +- 5:'Tag5'
| +- 4:'Tag4'

+- 7:'Set2'
|\
| +- 5:'Tag5'
| +- 4:'Tag4'
| +- 3:'Tag3'

$ omero delete TagAnnotation:8
omero.cmd.Delete2 TagAnnotation 8... ok

$ omero tag list
+- 7:'Set2'
|\
| +- 5:'Tag5'
| +- 4:'Tag4'
| +- 3:'Tag3'

Orphaned tags:
> 6:'Tag6'


but you can force the Tags in the TagSet to be deleted (depending on permissions and ownership):

Code: Select all

$ omero delete TagAnnotation:7 --include TagAnnotation
omero.cmd.Delete2 TagAnnotation 7... ok
$ omero tag list
Orphaned tags:
> 6:'Tag6'


dsudar wrote:4) In CLI empty tagsets do not show up at all with "omero tag listsets".

Thanks, I've added a card https://trello.com/c/ZV7AexGM/44-cli-list-empty-tagsets to deal with this in some ongoing CLI work.

Cheers,

Colin

Thanks Will and Colin. Very helpful responses
Damir

Colin provides fine examples but unfortunately "--include" is rarely used and turns out to be overzealous: "--include TagAnnotation" could even delete other tag sets! I think that https://github.com/mtbc/openmicroscopy/commit/bebb09d3 fixes this and, once properly checked, that or some other fix should make it into OMERO 5.1.4. My apologies for not noticing this problem much sooner.

Cheers,

Mark