Admins can't create datasets & Undefined Dropbox behavior

[Sethur]

Hi,

we recently tried to copy some images imported by Dropbox (and thus residing in "Orphaned Images") from one user (A, an administrator) to another new user (B). While doing so we encountered a range of problems:

1) Apparently, there is no defined default or primary group in OMERO any more, so Dropbox imported the images of user A to some random group (probably the last active one), which took some time to figure out and is not documented at all (neither is the fact that the images are normally delivered to the "Orphaned Images" section).

2) We soon found out that images can only be copied inside the same group so we first moved the images to the target group which both users A and B are members of. Using OMERO.insight, it was then impossible to copy images in the "Orphaned Images" folder without CUT/PASTING (this worked) them to a dataset of user A first.

3) We then tried to copy or move this images to user B, but since this was a new user, he had no target projects or datasets yet and apparently, a copy or move operation between users is only allowed into datasets or projects (at least it did only work that way when using OMERO.insight, when trying to move directly into "Orphaned Images", the PASTE option is greyed out).

4) We then tried (since user A is an admin) to create a project or dataset for user B, but this is apparently not possible at all, even for administrators.

==> We are stuck now with the images residing in some project of user A and the only way to get them to user B would be to create a group specifically for this purpose (holding both users).

So to summarize:

1) The Dropbox import behavior should be properly documented and made more controllable. The word "group" does not even appear on http://www.openmicroscopy.org/site/support/omero5/sysadmins/dropbox.html

2) The specifics of how data can be copied and moved between groups and datasets should be documented in more detail. It should be possible to copy images between groups. It should be perfectly clear when images are physically copied or just linked.

3) The "Orphaned Images" folder should not have any special treatment when it comes to copying and moving. It should definitely be possible to move or copy data directly to another "Orphaned Images" folder.

4) There should be a way for administrators to create projects/datasets for other users, preferably directly in OMERO.web and OMERO.insight. A CLI option should also be available for this task.

Cheers,

Tristan

[cblackburn]

Hi Tristan,

Thank you for your post, you raise some interesting issues both with DropBox and our permissions system.

You are right, the DropBox documentation does not make it clear that the images will be orphaned and that as no group can be selected the last used group will be the target. I will amend the documentation to make this clear. We are also looking to enhance and improve the functionality of DropBox by allowing the file path, defined by some template, to specify the group, project and dataset. See: http://trac.openmicroscopy.org/ome/ticket/4032

Note that an image imported by user A belongs to user A. It can't be copied to user B in the sense of it then belonging to user B though it can, depending on the group permissions, be linked to a dataset belonging to user B. You can use groups to allow collaborations between users, such as annotating images, but not to transfer ownership of the data. At present it isn't possible for one user to create a project or dataset on behalf of another user other than in a very limited case, see below. Documentation aimed at system administrators explaining the permissions system can be found at: http://www.openmicroscopy.org/site/support/omero5/sysadmins/server-permissions.html while more user-focused documentation on collaborating and sharing can be found at: http://help.openmicroscopy.org/collaboration.html (this second document is likely to be updated in the near future on the release of 5.0.1).

We are always looking to improve the quality of our documentation so if you do have any specific suggestions then please do let us know.

There are a couple of ways that you can import data on another user's behalf. As an OMERO administrator you can use the "Import As" feature of Insight. This allows you to import data for another user and in the process of that import create a new project and dataset if necessary. A second way would be to use DropBox, though this would involve the person doing the import to have write access to another user's DropBox folder and so only for a very controlled environment.

"Orphaned images" is special because it contains those images that are not linked to any dataset. This can happen on import, DropBox or the CLI import, but it can also happen as a result of some move group options. It's not really a container that we have envisaged people using in an active way, more somewhere to find images that have otherwise become detached.

We will certainly look at whether administrator powers should be extended to allow them to create containers for other users.

Cheers,

Colin

[Sethur]

Hi Colin,

thanks for your reply. I already used the Dropbox-Method to get data into another user's OMERO account, but using this or the "Import As..." method of Insight is very clumsy when the data is already in the OMERO database.

Is there an implementation specific reason that disallows copying data from one user to another or at least changing the ownership of data? From a sysadmin's point of view, this would really be an important thing to be able to do.

Also, the fact that you can use Insight to move stuff out of the orphaned images folder of another user (as a sysadmin), but the same thing won't work with OMERO.web is not consistent and should be fixed (as is the fact that one cannot batch export the original image format with OMERO.web), is there a ticket for that, yet?

I saw that there is a version 5.0.1, maybe some of those issues have already been addressed there.

Cheers,

Tristan

[cblackburn]

Hi Tristan,

Thanks for the reply, you raise some pertinent points. We have a couple of key people on leave today but we'll discuss the issues you raise on Monday morning and get back to you once we know the status of any tickets.

Cheers,

Colin

[jburel]

Dear Tristan

The "Import As" feature will only work for newly imported data.
Changing ownership is currently supported by the server but has not yet been implemented in the clients.
So the feature will not be in the 5.0.1 version

The issue you raised about moving data in web will not be in 5.0.1, I will create a ticket so we can address the issue asap.
Do you want to be CC'd?

Regards
Jmarie

[Sethur]

Dear Jean-Marie, good to hear that taking ownership is already in the server code. Please put me on CC regarding the OMERO.web ticket.

Regards,

Tristan

[wmoore]

Hi Tristan,

There is a PR for web to batch download the original image files. So this should be in the next release (5.0.2). See https://github.com/openmicroscopy/openm ... /pull/2220