Deleting objects

The omero delete command deletes objects. Further help is available using the -h option:

$ bin/omero delete -h

The delete command will remove entire graphs of objects based on the IDs of the topmost objects. The command can be modified to include the deletion of objects that would, by default, be excluded or exclude objects that would, by default, be included using the delete --include and delete --exclude options.

Additionally, objects of the three annotation types, FileAnnotation, TagAnnotation and TermAnnotation are not deleted by default when the objects to which they are linked are deleted.

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

By default the command confirms the deletion of the target objects but it can also provide a detailed report of all the deleted objects via a delete --report option. A delete --dry-run option can be used to report on what objects would be deleted without actually deleting them.

Examples

Basic delete

$ bin/omero delete OriginalFile:101
$ bin/omero delete Project:51

In the first line, the original file with ID 101 will be deleted. In the second, the project with ID 51 will be deleted including any datasets inside only that project and any images that are contained within deleted datasets only. Note that any linked file, tag or term annotations will not be deleted.

Deleting 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 deleting project 51 and datasets 53 and 54.

$ bin/omero delete Project:51 Dataset:53,54
$ bin/omero delete Dataset:54,53 Project:51
$ bin/omero delete Dataset:53 Project:51 Dataset:54

To delete 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.

$ bin/omero delete Project:51 Dataset:53-56 --force
$ bin/omero delete Dataset:53-56,65,101-105,201,202 --force

Note

When deleting multiple objects in a single command, if one object cannot be deleted then the whole command will fail and none of the specified objects will be deleted. The delete --dry-run option can be useful as a check before trying to delete large numbers of objects. If specifying objects with a range, it is best to pass either --dry-run or --force. Earlier versions defaulted to --dry-run if no flag was passed, but this behavior is deprecated. Future versions will default to --force.

Deleting lower level objects

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

$ bin/omero delete Project/Dataset/Image:51

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

$ bin/omero delete Project/Image:51

would have the same effect as the call above. Links can also be deleted and so:

$ bin/omero delete Project/DatasetImageLink:51 Dataset/DatasetImageLink:53

would effectively orphan all images under project 51 and dataset 53 that are not also under other datasets.

Including and excluding objects

--include

Linked objects that would not ordinarily be deleted can be included in the delete using the –include option:

$ bin/omero delete Image:51 --include FileAnnotation,TagAnnotation,TermAnnotation

As mentioned above these three annotation types are not deleted by default and so this call overrides that default by including any of the three annotation types in the delete:

$ bin/omero delete Image:51 --include Annotation

This call would also delete any annotation objects linked to the image.

--exclude

Linked objects that would ordinarily be deleted can be excluded from the delete using the –exclude option:

$ bin/omero delete Project:51 --exclude Dataset

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

The two options can be used together:

$ bin/omero delete Project/Dataset:53 --exclude Image --include FileAnnotation

This will delete 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 deleted datasets. In this case the images that are not otherwise contained in datasets will be orphaned.

For an example on deleting tags directly see Delete tags.

Further options

--ordered

Delete the objects in the order specified.

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

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

would be equivalent to making three separate calls:

$ bin/omero delete Dataset:53
$ bin/omero delete Project:51
$ bin/omero delete Dataset:54

--report

Provide a detailed report of what is deleted:

$ bin/omero delete Project:502 --report
...
omero.cmd.Delete2 Project 502... ok
Steps: 3
Elapsed time: 0.597 secs.
Flags: []
Deleted objects
Dataset:603
DatasetImageLink:303
Project:503
ProjectDatasetLink:353
Channel:203
Image:503
LogicalChannel:203
OriginalFile:460,459
Pixels:253
Fileset:203
FilesetEntry:253
FilesetJobLink:264,265,262,263,261
IndexingJob:315
JobOriginalFileLink:303
MetadataImportJob:312
PixelDataJob:313
ThumbnailGenerationJob:314
UploadJob:311
StatsInfo:72

--dry-run

Run the command and report success or failure but do not delete the objects. This can be combined with the --report to provide a detailed confirmation of what would be deleted before running the delete itself.