Python gateway & webclient delete improvements

[ximenesuk]

This PR addresses the various items in https://trello.com/c/WMnOBpC6/31-improve-deleteobjects-deprecate-deleteobjectdirect-inpython-gateway both RFEs and deprecation of deleteObjectDirect.

Tests, both OmeroPy and OmeroWeb should pass.

Web functionality to be tested is that which deletes and unlinks P/D/I, S/P and Annotations. I.e quite wide-ranging, but concentrating on unlinking and deleting all types of annotations would be useful.

[ximenesuk]

I can't see any direct use of this method, copyImageToDataset(). Should it be removed?

[ximenesuk]

Closing temporarily

[ximenesuk]

DeleteObjects() doesn't take full advantage of the newer functionalities in Delete2 such as deleting different objects in one command. At some point a useful change might be to add something like a DeleteMultipleObjects() which takes a map of object types and ids.

[will-moore]

Code changes seem to make sense on overview. Haven't tested functionality yet.

[ximenesuk]

@sbesson the one thing I haven't done is mark deleteObjectsDirect() as deprecated. I was trying to recall if you had any luck with this or whether just adding a comment would have the same effect.

[joshmoore]

A vote for DeprecationWarning:

$ git grep -l Deprec | grep Warning
# joshuas-mbp:ome0 jamoore$ git grep -n Deprec | grep Warning
components/tools/OmeroPy/src/omero/__init__.py:129:        category=DeprecationWarning)
components/tools/OmeroPy/src/omero/gateway/__init__.py:2767:            DeprecationWarning)
components/tools/OmeroPy/src/omero/gateway/__init__.py:8873:            "Deprecated. Use getImportedImageFiles()", DeprecationWarning)
components/tools/OmeroPy/src/omero/plugins/sessions.py:169:                    " instead.", DeprecationWarning)
components/tools/OmeroPy/src/omero/plugins/sessions.py:176:                    " instead.", DeprecationWarning)
components/tools/OmeroPy/src/omero/util/script_utils.py:1225:            "future versions of OMERO", DeprecationWarning)
components/tools/OmeroPy/src/omero/util/temp_files.py:140:                DeprecationWarning)

[ximenesuk]

@joshmoore thanks. Clearly my git greping isn't up to scratch! I'll formally deprecate the method. (Especially as there is usage in the very same file!!)

[ximenesuk]

In looking through the gateway I noticed that:
https://github.com/ximenesuk/openmicroscopy/blob/python-delete-improvements/components/tools/OmeroPy/src/omero/gateway/__init__.py#L7129
has been deprecated since 4.3.2, this would probably be a good time to remove this method.

[will-moore]

Functionality of removing annotations in webclient works fine.
container.py certainly has some code that's not used now since the jsTree work, including move(), removemany() and copyImageToDataset() This will be removed as part of a full clean-up of this for 5.2.1.
Good to merge.

[joshmoore]

If they will be removed soon, deprecating sooner would be appropriate.

[will-moore]

@joshmoore I don't think that anything in the webclient can be considered an API (not like webgateway) - We don't deprecate or document changes to methods in webclient, we just go ahead and edit.

[joshmoore]

Longer-term we should really re-evaluate that since it increases the burden on consumers. Or at least it needs to be made completely obvious, e.g. s/webclient/private/

[sbesson]

The omeroweb.webclient module has certainly been exposed in the public Python API for every single release as well. I would vote for dropping the ambiguity as soon as possible.

[sbesson]

See failure in https://ci.openmicroscopy.org/job/OMERO-DEV-merge-integration-python/lastCompletedBuild/testReport/OmeroPy.test.integration.gatewaytest.test_get_objects/TestGetObject/testTraversal/

[will-moore]

@joshmoore @sbesson I would like to move all the "api" urls and view methods that power the jsTree etc into a new /url/ app, and add similar methods for other parts of the app as we go. Then mark everything remaining in webclient as non-public.

[ximenesuk]

I hadn't realised that the getDataset was still being tested despite being deprecated since 4.3.2. Its use in the test has been removed in this final commit.

[ximenesuk]

See https://ci.openmicroscopy.org/view/Failing/job/OMERO-DEV-merge-integration-python/110/

[sbesson]

Given the state of https://ci.openmicroscopy.org/view/DEV/job/OMERO-DEV-merge-integration-python/ and https://ci.openmicroscopy.org/view/DEV/job/OMERO-DEV-merge-integration-Python27/, merging this. Let's have the webclient discussion separately. @will-moore: can you provide a listing of what is meant to be public and private within webclient?

[will-moore]

Currently @dpwrussell added a number of 'api' urls, that map to corresponding functions in views.py and tree.py that load the data via projection queries and marshal it to json:

api/groups/
api/experimenters/
api/experimenters/
api/containers/
api/datasets/
api/images/
api/share_images/
api/plates/
api/plate_acquisitions/
api/links/
api/paths_to_object/
api/tags/
api/shares/

These make a good starting point for public methods in webclient. More of what the webclient needs should be moved to this architecture and made public, probably in a new 'api' Django app.