Bug: export/download don't search all groups

[jamoore]

See: ​https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7479

Like bin/omero hql (without the --admin option), only the current group is checked for files to download. This could be widened to search all groups.

$ bin/omero login root@localhost
Previous session expired for root on localhost:4064
Password:
Password check failed for 'root': [id=0]
Password:
Created session 437da64b-ea57-488f-a820-8be0b06ae276 (root@localhost:4064). Idle timeout: 10.0 min. Current group: system
$ bin/omero group add ExportA
Using session 437da64b-ea57-488f-a820-8be0b06ae276 (root@localhost:4064). Idle timeout: 10.0 min. Current group: system
Added group ExportA (id=853) with permissions rw----
$ bin/omero group add ExportB
Using session 437da64b-ea57-488f-a820-8be0b06ae276 (root@localhost:4064). Idle timeout: 10.0 min. Current group: system
Added group ExportB (id=854) with permissions rw----
$ bin/omero user add export_tester Export Tester ExportA ExportB
Using session 437da64b-ea57-488f-a820-8be0b06ae276 (root@localhost:4064). Idle timeout: 10.0 min. Current group: system
Please enter password for your new user (export_tester): 
Please re-enter password for your new user (export_tester): 
Added user export_tester (id=852) with password
$ bin/omero login export_tester@localhost
Password:
Created session e0d41413-59bc-4d82-89ad-52480295e41a (export_tester@localhost:4064). Idle timeout: 10.0 min. Current group: ExportA
$ echo "test" >> test.txt
$ bin/omero upload test.txt
Using session e0d41413-59bc-4d82-89ad-52480295e41a (export_tester@localhost:4064). Idle timeout: 10.0 min. Current group: ExportA
Uploaded test.txt as 26751
$ bin/omero download 26751 -
Using session e0d41413-59bc-4d82-89ad-52480295e41a (export_tester@localhost:4064). Idle timeout: 10.0 min. Current group: ExportA
test
$ bin/omero sessions group ExportB
Using session e0d41413-59bc-4d82-89ad-52480295e41a (export_tester@localhost:4064). Idle timeout: 10.0 min. Current group: ExportA
Group 'ExportA' (id=853) switched to 'ExportB' (id=854)
$ bin/omero download 26751 -
Using session e0d41413-59bc-4d82-89ad-52480295e41a (export_tester@localhost:4064). Idle timeout: 10.0 min. Current group: ExportB
Traceback (most recent call last):
  File "bin/omero", line 125, in <module>
    rv = omero.cli.argv()
  File "/opt/ome3/dist/lib/python/omero/cli.py", line 1197, in argv
    cli.invoke(args[1:])
  File "/opt/ome3/dist/lib/python/omero/cli.py", line 745, in invoke
    stop = self.onecmd(line, previous_args)
  File "/opt/ome3/dist/lib/python/omero/cli.py", line 814, in onecmd
    self.execute(line, previous_args)
  File "/opt/ome3/dist/lib/python/omero/cli.py", line 894, in execute
    args.func(args)
  File "/opt/ome3/dist/lib/python/omero/plugins/download.py", line 36, in __call__
    client.download(orig_file, filehandle=sys.stdout)
  File "/opt/ome3/dist/lib/python/omero/clients.py", line 756, in download
    ofile = self.__sf.getQueryService().get("OriginalFile", ofile.id.val)
  File "/opt/ome3/dist/lib/python/omero_api_IQuery_ice.py", line 117, in get
    return _M_omero.api.IQuery._op_get.invoke(self, ((klass, id), _ctx))
omero.SecurityViolation: exception ::omero::SecurityViolation
{
    serverStackTrace = ome.conditions.SecurityViolation: Cannot read ome.model.core.OriginalFile:Id_26751
        at ome.security.basic.BasicACLVoter.throwLoadViolation(BasicACLVoter.java:163)
        at ome.security.CompositeACLVoter.throwLoadViolation(CompositeACLVoter.java:92)
...

[jamoore]

Also fix the exception when the original file ID doesn't exist at all (which is the actual problem that the user on the forum was seeing). Thanks, Colin.

[bpindelski]

An initial attempt at fixing the issue is at ​https://github.com/bpindelski/openmicroscopy/commits/12146_all_groups. Josh (and Colin, Sebastien): if the code looks sane and the test is in the correct class, I can move forward and fix the exception handling and open a PR. Thanks for having a look.

[jamoore]

Perhaps assign to yourself if you're going to dig much deeper so no one else gives it a whirl?

[bpindelski]

Research shows that setting omero.group to -1 in ​https://github.com/openmicroscopy/openmicroscopy/blob/dev_5_0/components/tools/OmeroPy/src/omero/clients.py#L761 has a nasty side-effect of setting omero.client.uuid to an empty string. To solve the general issue this has to be fixed, as with an empty omero.client.uuid the server can't find the servant for the RawFileStore? service.

[bpindelski]

Closing. ​PR 2383 merged.

[Josh Moore <josh@…>]

(In [f1efece98d914f56022aee0e7258a09f5929425e/ome.git] on branch develop) Merge pull request #2398 from bpindelski/rebased/develop/12146_all_groups

CLI download looks for resources in all user groups (fix #12146). (rebased onto develop)

[Josh Moore <josh@…>]

(In [e9e432eca0f62dfca994745c36d568d547a4e957/ome.git] on branch develop) Merge pull request #2451 from bpindelski/rebased/develop/12146-exception

Update help and handle missing resources in download.py (see #12146). (rebased onto develop)