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.

Using the new 5.1 graph requests

Migration is required

OMERO 5.1.0 introduced a new implementation of Model graph operations offered through the API via Chgrp2, Chown2, Delete2, and their superclass GraphModify2. OMERO 5.1.2 added Chmod2. The legacy request operations Chgrp, Chmod, Chown, Delete, and their superclass GraphModify, are now deprecated and will be removed in OMERO 5.3. Now is the time to adjust client code accordingly so that the OME team can fix any regressions before the release of OMERO 5.3.

Target objects

For specifying which model objects to operate on, instead of using one request for each object through GraphModify‘s type and id data members, use GraphModify2‘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 SkipHead 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.

Translating options

GraphModify‘s options data member has its related analog in GraphModify2‘s childOptions, an ordered list of ChildOption 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 a ChildOption‘s includeType set to Image.
• To delete a dataset without deleting any images at all from it, use Delete2 with a ChildOption‘s excludeType set to Image.
• To delete annotations except for the tags that are in a specific namespace, use Delete2 with a ChildOption‘s excludeType set to TagAnnotation and includeNs set to that namespace.

GraphUtil.java includes the translateOptions method that may give additional insight on how to translate the previous style of option. This method too will be removed in OMERO 5.3.

Examples in Python

Move images

chgrps = DoAll()
chgrps.requests = [Chgrp(type="/Image", id=n, grp=5) for n in [1,2,3]]
sf.submit(chgrps)

becomes,

chgrp = Chgrp2(targetObjects={'Image': [1,2,3]}, groupId=5)
sf.submit(chgrp)

Delete plate, but not annotations

keepAnn = {"/Annotation": "KEEP"}
delete = Delete(type="/Plate", id=8, options=keepAnn)
sf.submit(delete)

becomes,

keepAnn = [ChildOption(excludeType=['Annotation'])]
delete = Delete2(targetObjects={'Plate': [8]}, childOptions=keepAnn)
sf.submit(delete)

Delete an image’s rendering settings

delete = Delete(type="/Image/Pixels/RenderingDef", id=6)
sf.submit(delete)

becomes,

anchor = {'Image': [6]}
targets = ['RenderingDef']
delete = SkipHead(targetObjects=anchor, startFrom=targets,
                  request=Delete2())
sf.submit(delete)

Java request factory

A utility class 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("Image", Arrays.asList(1L,2L,3L), 5L);

// delete plate, but not annotations
ChildOption childOption = Requests.option(null, "Annotation");
Delete2 example2 = Requests.delete("Plate", 8L, childOption);

// delete an image's rendering settings
SkipHead example3 =
    Requests.skipHead("Image", 6L, "RenderingDef", new Delete2());