Note

This documentation is for OMERO 5.2. This version is now in maintenance mode and will only be updated in the event of critical bugs or security concerns. OMERO 5.3 is expected in the first quarter of 2017.

Moving objects between groups

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

$ bin/omero chgrp -h

The chgrp command will remove 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 --include and --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 a --report option. A --dry-run option can be used to report on what objects would be moved without actually moving them.

Examples

Basic move

$ bin/omero chgrp 5 OriginalFile:101
$ bin/omero chgrp Group:5 Project:51
$ bin/omero chgrp ExperimenterGroup:5 Project:51
$ bin/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.

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

Moving lower level objects

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

$ bin/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:

$ bin/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:

$ bin/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:

$ bin/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:

$ bin/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:

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

would be equivalent to making three separate calls:

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

--report

Provide a detailed report of what is moved:

$ bin/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 --report to provide a detailed confirmation of what would be moved before running the move itself.