moving data between groups

[LeroyAlex]

Hi,


I have anotther question regarding the last upgrade of Omero.
In 5.0.5, when you move images between groups, even if those groups are both read-annotate, you loose all your tags/attachments, is this fixed in 5.0.8 or the 5.1.0 version to come?
If not, it'd be nice to create ticket about cause it's quite trouble to remake all the tags.

Best,

Alex.

[mtbc]

Alex,

From OMERO 5.0.5 I would not expect that upgrading to any later 5.0 version would change the behavior of move operations. Behavior is slightly adjusted in the coming 5.1.0 (developer preview m4 is soon to be released), but that work was more about improving performance and fixing some bugs. Approaching from the horizon is a more thought-through review of how move operations should be working, and associated adjustments are thus likely in rather later versions of OMERO, but those are some way off yet.

As background: every image and every annotation -- tags, attachments, comments, ratings, etc. -- is each in exactly one group. An annotation may be linked to an image only if both are in the same group. In the case of annotations like tags, where the same one may annotate multiple images, if you moved some of the images and the tag went with them, then the tag would have to move group too, and would have to be unlinked from the images that were being left behind in its previous group. So, in those cases we leave the tag behind where it was: what you are probably seeing is moved images losing annotations if the annotation was also on another image that is being left behind.

One might say that, with things like tags or ratings, perhaps it would be nice if the annotation could be copied, with a new copy of it linked to the image in the new group. There are certainly some technical issues with that, but it is conceivable that a future version of OMERO will indeed improve the situation.

Alternatively, perhaps the issue is that the annotations are not owned by the user doing the move. In the OMERO 5.1.0-m4 developer preview release, your own annotations on your own images should always move with the image when you move the image so long as those annotations are not also on images being left behind. Regardless of what else they annotate, others' file, tag, or term annotations are never moved with one's image; also, others' annotations of any kind are never moved into private groups. (There may be odd exceptions to this if it is an administrative user, a member of the system group, doing the move.) As for other cases, there are issues at the moment -- for instance, that unfortunately even other users' comments do not move with an image among read-annotate-groups -- that is part of what motivates the coming review of all this, but making the fixes is a fair bit of work. (We are very careful about making changes in this part of the code.) In the meantime, 5.1.0 should still preserve others' comments and suchlike among read-write groups, if that workaround is of any use to you.

In short: yes, you're right, and unfortunately won't be fixed in the short term, but is certainly on our radar. It's not ideal, and we have been working steadily on improving the move behavior, but there is a way yet for us to go on this because many of the edge cases are difficult and complex. Sorry about that.

Cheers,
Mark

[pwalczysko]

Hi Alex,
additionally to the overview given to you by Mark, I have tried to fathom your exact setup and expectations.
I guessed that you are putting tags which belong to you on images/datasets/projects which also belong to you and moving those images/dataset/projects between two Read-Annotate groups.
In that case, you will have only 2 options:
- either your tags are used solely on the images/datasets/projects which you are moving or
- your tags are used also on other images/datasets/projects which you are leaving behind in the "old" group

In the former case, the tags will move with your images/datasets/projects in 5.0.8 AND in 5.1.0
In the latter case, the tags will not move with your images/datasetss/projects NEITHER in 5.0.8 NOR 5.1.0

Please would you confirm that your setup is one of the two cases (which one ?) and also what would be your preferred behaviour in such case (e.g. "I want the tags duplicated so that I can use them in both groups, the original one and the target one." or "I want the tags to be used accross-groups." or similar).
As Mark suggested, the problematic is quite difficult to tackle, but any user feedback would be helpful.

Thank you
All the best
Petr
OME-Team

[LeroyAlex]

Dear Mark,

Thank you for you answer.
I appreciated it cause i got an insight of developpers thoughts.
I'd also like to apologize cause after reading my post i thought "gosh, i m whinning a lot".
Anyway, i ll try to be more constructive from now on.

Dear Peter,

To quote you:

2 options:
- either your tags are used solely on the images/datasets/projects which you are moving or
- your tags are used also on other images/datasets/projects which you are leaving behind in the "old" group

In the former case, the tags will move with your images/datasets/projects in 5.0.8 AND in 5.1.0
In the latter case, the tags will not move with your images/datasetss/projects NEITHER in 5.0.8 NOR 5.1.0

Except the fact that i'm working under omero 5.0.5, it's exactly as you said: i loose the tags when they're used on other project etc. and they are moved when only used by the moved project.

So to answer to your question:

I'd prefer to have tags across groups because other than moving your data between groups, it would be simply nice to only have to create new tags once in a group and be able to use them in every group.
For example, as a biologist i use pretty much the same set of fluorophore (hence tags for my fluorophores) in every group.

But if it' s easier to duplicate the tags, why not.

Ok the following paragraph might be completely wrong but i was just trying to figure things out:

So i don"t know how works the rights on tags but i'm gonna assume that in the current system the tags are linked to a group and not the user, it would explain why you dont have access to your tags in every group.
Regarding the tags i don't own but i used in a group read-annotate, i was wondering if it was also due to the fact that tags are linked to a group and not user, that we can do it. Now if the tags are linked to the user in order to get access to it in any group, what would happen to the tags used but not owned?
Once again this question only makes sense if it actually works like this XD.

Best,

Alex.

[mtbc]

Dear Alex,

Don't worry about sounding like you are complaining, it is important for us to know what works for our users and what doesn't. I am glad Petr is reading too because he is on the team that works on figuring out how we could improve the OMERO user experience.

Every annotation, from tags to comments, is actually both owned by a user and in a group. In groups other than private groups, users who are a member of a group can see the objects (such as tags) of their fellow group members.

I suppose that the range of use cases is challenging: You would like to use the same tags across several groups whereas, for instance, in a large department with many very separate groups under different leaders, users may not want their list of available tags cluttered by the separate work of those groups.

It may be that it is possible to move a tag into the "user" group thus making it visible to every group (perhaps with a script using the OMERO API directly, rather than from one of the standard graphical clients), and then to tag images with it that are in a normal group. There is a fair chance that it would work. If that would be a great help to you, but if you can't figure out how, we could investigate that route further, make sure it works, and consult with Petr and others on how best to make that easy for users.

Cheers,
Mark

[LeroyAlex]

Hi Mark,

n a large department with many very separate groups under different leaders, users may not want their list of available tags cluttered by the separate work of those groups.

Fair enough!
That would not be a problem in our institute though, as only a few people are in several groups and when it's the case, it's usually for collaboration so they would just use omero to show the data they own hence use the same tags to describe these data.
As the scenario is pretty rare, it might not be worth to spend time programming a python script.

Best,

Alex.