OMERO 5.1.0 introduced a new implementation of ObjectGraphs
offered through the API via :slicedoc_blitz:Chgrp2 <omero/cmd/Chgrp2.html>, :slicedoc_blitz:Chown2 <omero/cmd/Chown2.html>, :slicedoc_blitz:Delete2 <omero/cmd/Delete2.html>, and their superclass :slicedoc_blitz:GraphModify2 <omero/cmd/GraphModify2.html>. OMERO 5.1.2 added :slicedoc_blitz:Chmod2 <omero/cmd/Chmod2.html>. The corresponding deprecated legacy request operations are removed in OMERO 5.3. Client code must be adjusted accordingly.
For specifying which model objects to operate on, instead of using one request for each object, use :slicedoc_blitz:GraphModify2 <omero/cmd/GraphModify2.html>'s targetObjects
which allows specification of multiple model object classes, each with an unordered list of IDs, all in a single request. To specify a type, no longer use /
-delimited paths, but instead just the class name, e.g. Image
instead of /Image
. To achieve a root-anchored subgraph operation use :slicedoc_blitz:SkipHead <omero/cmd/SkipHead.html> to wrap your request: for instance, for /Image/Pixels/RenderingDef
, set the SkipHead
request's targetObjects
to the image(s), and set startFrom
to RenderingDef
.
:slicedoc_blitz:GraphModify2 <omero/cmd/GraphModify2.html> offers childOptions
, an ordered list of :slicedoc_blitz:ChildOption <omero/cmd/graphs/ChildOption.html> instances, each of which allows its applicability to annotations to be limited by namespace. Some examples:
- To move a dataset with all its images, removing those images from other datasets where necessary, use
Chgrp2
with aChildOption
'sincludeType
set toImage
. - To delete a dataset without deleting any images at all from it, use
Delete2
with aChildOption
'sexcludeType
set toImage
. - To delete annotations except for the tags that are in a specific namespace, use
Delete2
with aChildOption
'sexcludeType
set toTagAnnotation
andincludeNs
set to that namespace.
chgrps = DoAll()
chgrps.requests = [Chgrp(type="/Image", id=n, grp=5) for n in [1,2,3]]
sf.submit(chgrps)
used in OMERO 5.0 should now be written as,
chgrp = Chgrp2(targetObjects={'Image': [1,2,3]}, groupId=5)
sf.submit(chgrp)
keepAnn = {"/Annotation": "KEEP"}
delete = Delete(type="/Plate", id=8, options=keepAnn)
sf.submit(delete)
used in OMERO 5.0 should now be written as,
keepAnn = [ChildOption(excludeType=['Annotation'])]
delete = Delete2(targetObjects={'Plate': [8]}, childOptions=keepAnn)
sf.submit(delete)
delete = Delete(type="/Image/Pixels/RenderingDef", id=6)
sf.submit(delete)
used in OMERO 5.0 should now be written as,
anchor = {'Image': [6]}
targets = ['RenderingDef']
delete = SkipHead(targetObjects=anchor, startFrom=targets,
request=Delete2())
sf.submit(delete)
A utility class :java_gateway_source:Requests.java <src/main/java/omero/gateway/util/Requests.java> provides convenient instantiation of graph requests. This class allows the requests from the above Python examples to be created by,
// move images
Chgrp2 example1 = Requests.chgrp().target("Image").id(1L,2L,3L)
.toGroup(5L).build();
// delete plate, but not annotations
ChildOption childOption = Requests.option()
.excludeType("Annotation").build();
Delete2 example2 = Requests.delete().target("Plate").id(8L)
.option(childOption).build();
// delete an image's rendering settings
SkipHead example3 = Requests.skipHead().target("Image").id(6L)
.startFrom("RenderingDef").request(Delete2.class).build();