Moving objects between groups

Warning

Data does not need to be assigned to a group where the data owner is a member, and administrators may wish to change the ownership of data or move it between groups in several steps of a larger workflow. However, it is generally expected that data should end up in a group where the data owner is a member, so that they can view their data in the OMERO clients.

Who may move data

• a full administrator

• a restricted administrator with Chgrp privilege

• the owner of the data if they are a member of the target group

How to move data

• Using CLI: See below

• Using OMERO.web: See User guides

The omero chgrp command moves objects between groups. Further help is available using the -h option:

$ omero chgrp -h

This command will move entire graphs of objects based on the IDs of the topmost objects. The command can be modified to include the movement of objects that would, by default, be excluded or exclude objects that would, by default, be included using the omero chgrp --include and omero chgrp --exclude options.

It is also possible to move objects lower in the hierarchy by specifying the type and ID of a topmost object and the type of the lower object. For instance, moving all of the images under a given project.

By default the command confirms the movement of the target objects but it can also provide a detailed report of all the moved objects via an omero chgrp --report option. An omero chgrp --dry-run option can be used to report on what objects would be moved without actually moving them.

Examples

Basic move

$ omero chgrp 5 OriginalFile:101
$ omero chgrp Group:5 Project:51
$ omero chgrp ExperimenterGroup:5 Project:51
$ omero chgrp lab_group Project:51

In the first line, the original file with ID 101 will be moved to the group with ID 5. In the second and third, project 51 will be moved to group 5 including any datasets inside only that project and any images that are contained within moved datasets only. If group 5 is named ‘lab_group’ then the last line will have the same effect as the previous two. Note that any linked annotations will also be moved.

Moving multiple objects

Multiple objects can be specified with each type being followed by an ID or a comma-separated list of IDs. The order of objects or IDs is not significant, thus all three calls below are identical in moving project 51 and datasets 53 and 54 to group 5.

$ omero chgrp 5 Project:51 Dataset:53,54
$ omero chgrp 5 Dataset:54,53 Project:51
$ omero chgrp 5 Dataset:53 Project:51 Dataset:54

To move a number of objects with sequentially numbered IDs a hyphen can be used to specify an ID range. This form can also be mixed with comma-separated IDs.

$ omero chgrp 5 Project:51 Dataset:53-56
$ omero chgrp 5 Dataset:53-56,65,101-105,201,202

Note

When moving multiple objects in a single command, if one object cannot be moved then the whole command will fail and none of the specified objects will be moved. The omero chgrp --dry-run option can be useful as a check before trying to move large numbers of objects.

Moving lower level objects

To move objects below a specified top-level object the following form of the object specifier is used.

$ omero chgrp 5 Project/Dataset/Image:51

Here the all of images under the project 51 would be moved. It is not necessary to specify intermediate objects in the hierarchy and so:

$ omero chgrp 5 Project/Image:51

would have the same effect as the call above.

Including and excluding objects

--include

Linked objects that would not ordinarily be moved can be included in the move using the --include option:

$ omero chgrp 5 Image:51 --include Annotation

This call would move any annotation objects linked to the image.

--exclude

Linked objects that would ordinarily be moved can be excluded from the move using the --exclude option:

$ omero chgrp 5 Project:51 --exclude Dataset

This will move project 51 but not any datasets contained in that project.

The two options can be used together:

$ omero chgrp 5 Project/Dataset:53 --exclude Image --include FileAnnotation

This will move any datasets under project 53, that are not otherwise contained elsewhere, excluding any images in those datasets but including any file annotations linked to the moved datasets. In this case the images that are not otherwise contained in datasets will be orphaned.

Further options

--ordered

Move the objects in the order specified.

Normally all of the specified objects are grouped into a single move command. However, each object can be moved separately and in the order given. Thus:

$ omero chgrp 5 Dataset:53 Project:51 Dataset:54 --ordered

would be equivalent to making three separate calls:

$ omero chgrp 5 Dataset:53
$ omero chgrp 5 Project:51
$ omero chgrp 5 Dataset:54

--report

Provide a detailed report of what is moved:

$ omero chgrp 5 Project:502 --report

--dry-run

Run the command and report success or failure but does not move the objects. This can be combined with the omero chgrp --report to provide a detailed confirmation of what would be moved before running the move itself.