OMERO permissions querying, usage and history

Working with the OMERO 5.5.0-rc2 permissions system

Example environment

• OMERO 5.5.0-rc2 server
• IPython shell initiated by running omero shell --login

Group membership

User	private-1	read-only-1	read-write-1	read-annotate-1
user-2	Yes	Yes	No	No
user-3	No	Yes	No	Yes

Simple inserts and queries

While the ‘Default Group’ is essentially a deprecated concept, a user must be logged into one to provide a default context. It is still possible to change this default group but it is no longer required to make queries in other permissions contexts.

All remote calls to an OMERO server, since well before version 4.1.x, have the option of taking an Ice context object. Through this object, and manipulations thereof, we can affect our query context. What follows is a series of examples exploring inserts and queries using contexts that span a single group at a time.

Retrieving a user’s event context and group membership

#!python
# Session that has already been created for user-2
session = client.getSession()

# Retrieve the services we are going to use
admin_service = session.getAdminService()

ec = admin_service.getEventContext()
print ec
groups = [admin_service.getGroup(v) for v in ec.memberOfGroups]
for group in groups:
    print 'Group name: %s' % group.name.val

Example output:

object #0 (::omero::sys::EventContext)
{
    shareId = -1
    sessionId = 1783
    sessionUuid = 213adc46-2c5f-449b-81fc-fe24dec38b58
    userId = 10
    userName = user-2
    groupId = 9
    groupName = private-1
    isAdmin = False
    eventId = -1
    eventType = User
    memberOfGroups =
    {
        [0] = 9
        [1] = 8
        [2] = 1
    }
    leaderOfGroups =
    {
    }
    groupPermissions = object #1 (::omero::model::Permissions)
    {
        _restrictions =
        {
        }
        _perm1 = -120
    }
}

Group name: private-1
Group name: read-only-1
Group name: user

Here you can see and validate that, when logged in as user-2, we are a member of both the private-1 and read-only-1 groups. Membership of the user group is required in order to login. This group essentially acts as a role, letting the OMERO security system know whether or not the user is active.

Inserting and querying data from specific groups

For the purposes of this example, we will prepare a single Project in both the private-1 and read-only-1 groups and then perform various queries on those Projects.

#!python
from omero.model import *
from omero.rtypes import *
from omero.sys import ParametersI
from omero.cmd import Delete
from omero.callbacks import CmdCallbackI

# Session that has already been created for user-2
session = client.getSession()

# Project object instantiation
private_project = ProjectI()
private_project.name = rstring('private-1 project')
read_only_project = ProjectI()
read_only_project.name = rstring('read-only-1 project')

# Retrieve the services we are going to use
update_service = session.getUpdateService()
admin_service = session.getAdminService()
query_service = session.getQueryService()

# Groups we are going to write data into
private_group = admin_service.lookupGroup('private-1')
read_only_group = admin_service.lookupGroup('read-only-1')

# Save and return our two projects, setting the context correctly for each
ctx = {'omero.group': str(private_group.id.val)}
private_project = update_service.saveAndReturnObject(private_project, ctx)
ctx = {'omero.group': str(read_only_group.id.val)}
read_only_project = update_service.saveAndReturnObject(read_only_project, ctx)

private_project_id = private_project.id.val
read_only_project_id = read_only_project.id.val
print 'Created Project:%d in group private-1' % (private_project_id)
print 'Created Project:%d in group read-only-1' % (read_only_project_id)

# Query for the private project we created using private-1
#
# You will notice that this returns the Project as we have specified
# the group that the Project is in within the context passed to the
# query service.
ctx = {'omero.group': str(private_group.id.val)}
params = ParametersI()
params.addId(private_project_id)
projects = query_service.findAllByQuery(
        'select p from Project as p ' \
        'where p.id = :id', params, ctx)

print 'Found %d Project(s) with ID %d in group private-1' % \
        (len(projects), private_project_id)

# Query for the private project we created using read-only-1
#
# You will notice that this does not return the Project as we have **NOT**
# specified the group that the Project is in within the context
# passed to the query service.
ctx = {'omero.group': str(read_only_group.id.val)}
params = ParametersI()
params.addId(private_project_id)
projects = query_service.findAllByQuery(
        'select p from Project as p ' \
        'where p.id = :id', params, ctx)

print 'Found %d Project(s) with ID %d in group read-only-1' % \
        (len(projects), private_project_id)

# Use the OMERO 4.3.x introduced delete service to clean up the Projects
# we have just created.
handle = session.submit(Delete('/Project', private_project_id, None))
try:
    callback = CmdCallbackI(client, handle)
    callback.loop(10, 1000)  # Loop a maximum of ten times each 1000ms
finally:
     # Safely ensure that the Handle to the delete request is cleaned up,
     # otherwise there is the possibility of resource leaks server side that
     # will only be cleaned up periodically.
     handle.close()
handle = session.submit(Delete('/Project', read_only_project_id, None))
try:
    callback = CmdCallbackI(client, handle)
    callback.loop(10, 1000)  # Loop a maximum of ten times each 1000ms
finally:
    handle.close()

Example output:

Created Project:113 in group private-1
Created Project:114 in group read-only-1
Found 1 Project(s) with ID 113 in group private-1
Found 0 Project(s) with ID 113 in group read-only-1

Advanced queries

In OMERO 4.4.0, cross group querying was reintroduced. Again, we make use of the Ice context object. Through this object, and manipulations thereof, we can expand our query context to span all groups via the use of -1. What follows is a series of example queries using contexts that span all groups.

Querying data across groups

#!python
from omero.model import *
from omero.rtypes import *
from omero.sys import ParametersI
from omero.cmd import Delete, DoAll
from omero.callbacks import CmdCallbackI

# Session that has already been created for user-2
session = client.getSession()

# Project object instantiation
private_project = ProjectI()
private_project.name = rstring('private-1 project')
read_only_project = ProjectI()
read_only_project.name = rstring('read-only-1 project')

# Retrieve the services we are going to use
update_service = session.getUpdateService()
admin_service = session.getAdminService()
query_service = session.getQueryService()

# Groups we are going to write data into
private_group = admin_service.lookupGroup('private-1')
read_only_group = admin_service.lookupGroup('read-only-1')

# Save and return our two projects, setting the context correctly for each.
# ALL interactions with the update service where NEW objects are concerned
# must be passed an explicit context and NOT '-1'.  Otherwise the server
# has no idea which set of owners to assign to the object when persisted.
ctx = {'omero.group': str(private_group.id.val)}
private_project = update_service.saveAndReturnObject(private_project, ctx)
ctx = {'omero.group': str(read_only_group.id.val)}
read_only_project = update_service.saveAndReturnObject(read_only_project, ctx)

private_project_id = private_project.id.val
read_only_project_id = read_only_project.id.val
print 'Created Project:%d in group private-1' % (private_project_id)
print 'Created Project:%d in group read-only-1' % (read_only_project_id)

# Query for the private project we created using private-1
#
# You will notice that this returns both Projects as we have specified
# '-1' in the context passed to the query service.
ctx = {'omero.group': '-1'}
params = ParametersI()
params.addIds([private_project_id, read_only_project_id])
projects = query_service.findAllByQuery(
        'select p from Project as p ' \
        'where p.id in (:ids)', params, ctx)

print 'Found %d Project(s)' % (len(projects))

# Use the OMERO 4.3.x introduced delete service to clean up the Projects
# we have just created. The delete service uses '-1' by default for all its
# internal queries.  We are also introducing the 'DoAll' command, which
# allows for the aggregation of 'Delete' commands.
delete_requests = [
    Delete('/Project', private_project_id, None),
    Delete('/Project', read_only_project_id, None)
]
handle = session.submit(DoAll(delete_requests))
try:
    callback = CmdCallbackI(client, handle)
    callback.loop(10, 1000)  # Loop a maximum of ten times each 1000ms
finally:
    # Safely ensure that the Handle to the delete request is cleaned up,
    # otherwise there is the possibility of resource leaks server side that
    # will only be cleaned up periodically.
    handle.close()

Example output:

Created Project:117 in group private-1
Created Project:118 in group read-only-1
Found 2 Project(s)

Querying data across users in the same group

Through the use of an omero.sys.ParametersI filter, restricting a query to a given user is possible. For the purposes of these examples, we will assume that both user-2 and user-3 have a single project each in the read-only-1 group.

#!python
from omero.model import *
from omero.rtypes import *
from omero.sys import ParametersI

# Session that has already been created for user-2
session = client.getSession()

# Retrieve the services we are going to use
admin_service = session.getAdminService()
query_service = session.getQueryService()

# Groups we are going to query
read_only_group = admin_service.lookupGroup('read-only-1')

# Users we are going to query
user_2 = admin_service.lookupExperimenter('user-2')
user_3 = admin_service.lookupExperimenter('user-3')

# Print the members of 'read-only-1'
print 'Members of "read-only-1" (experimenter_id, username): %r' % \
    [(v.id.val, v.omeName.val) for v in read_only_group.linkedExperimenterList()]

# Query for all projects
ctx = {'omero.group': str(read_only_group.id.val)}
projects = query_service.findAllByQuery(
        'select p from Project as p', None, ctx)
print 'All projects in "read-only-1" (project_id, owner_id): %r' % \
    [(v.id.val, v.details.owner.id.val) for v in projects]

# Query for projects owned by 'user-2'
ctx = {'omero.group': str(read_only_group.id.val)}
params = ParametersI()
params.addId(user_2.id.val)
projects = query_service.findAllByQuery(
        'select p from Project as p ' \
        'where p.details.owner.id = :id', params, ctx)
print 'Projects owned by "user-2" in "read-only-1" (project_id, owner_id): %r' % \
    [(v.id.val, v.details.owner.id.val) for v in projects]

# Query for projects owned by 'user-3'
ctx = {'omero.group': str(read_only_group.id.val)}
params = ParametersI()
params.addId(user_3.id.val)
projects = query_service.findAllByQuery(
        'select p from Project as p ' \
        'where p.details.owner.id = :id', params, ctx)
print 'Projects owned by "user-3" in "read-only-1" (project_id, owner_id): %r' % \
    [(v.id.val, v.details.owner.id.val) for v in projects]

Example output:

Members of "read-only-1" (experimenter_id, username): [(10L, 'user-2'), (9L, 'user-3')]
All projects in "read-only-1" (project_id, owner_id): [(4L, 10L), (7L, 9L)]
Projects owned by "user-2" in "read-only-1" (project_id, owner_id): [(4L, 10L)]
Projects owned by "user-3" in "read-only-1" (project_id, owner_id): [(7L, 9L)]

Utilizing the Permissions object

Every object that is retrieved from the server via the query service, regardless of the context used, has a fully functional omero.model.PermissionsI object. This object contains various methods to allow the caller to interrogate the operations that are possible by the current user on the object:

• canAnnotate()
• canChgrp()
• canChown()
• canDelete()
• canEdit()
• canLink()

Troubleshooting permissions issues

Data disappears after a change of the primary group of a user

As outlined above, changes were made so that by default queries do not span multiple groups and the ‘Primary or Default Group’ is essentially a deprecated concept. If you have multiple groups and you are attempting to make queries by switching the ‘Active Group’ via the setSecurityContext() method of an active session (omero.cmd.SessionPrx), those queries will be scoped only to that group. If you want your queries to act more like they did in 4.1.x, setting omero.group=-1 will achieve that.

However, the reasons we made these changes have more to them than just API usage and the OMERO client history of only showing the data from one group at a time. Changing the ‘Active Group’ is both expensive because of the atomicity requirements the server enforces and can create dangerous concurrency situations. This is further complicated by the addition of the change group and delete background processes since 4.1.x. Manipulating a session’s ‘Primary or Default Group’ during these tasks can have drastic effects. Changing the ‘Active Group’ is forbidden if there are any stateful services (omero.api.RenderingPrx for example) currently open.

In short, in OMERO 5.5.0-rc2 you absolutely should not be switching the ‘Primary or Default Group’ of the user, or the ‘Active Group’ of a session, as a means to achieve cross group querying.

Listing other users’ data in read-only groups

In order to list other users’ data associated with read-only groups of which you are a member, you can also use the context object and set the omero.group to -1. In addition, you can add a filter to the query to only select the other users’ data. You can do this either by using the omero.sys.ParametersI object’s exp() method when using the IContainer service, or by an explicit query when using IQuery service.

Is the default group the primary group when not specifying the context?

The value of the groupId property of the omero.sys.EventContext is the “Active Group” for the created session. It can be modified as described above with the restrictions outlined. Unless the session has been created by means other than createSession() on an omero.client object, this will be the user’s “Primary or Default Group.” A user’s ‘Primary or Default Group’ is the first group in the collection that describes the relation Experimenter <--> ExperimenterGroup. It can be set by the setDefaultGroup() method on the IAdmin service.

What about when importing data without specifying the context object?

Exactly as outlined above. Import does nothing different or special. If you want the operating context of an import to be different from the default you must specify it as such.

Specifying the group context as -1 when deleting data

There is no need to do this. Complete graphs cannot span multiple groups and queries are only (unless otherwise filtered) restricted at the group level and not at the level of the user. Furthermore, the delete service always internally performs all its queries in the omero.group=-1 context unless another more explicit one is specified.

History

The OMERO permissions model has had a significant overhaul from version 4.1.x to 4.4.x. Users and groups have existed in OMERO since well before the initial 4.1.x releases and numerous permissions levels were possible in the 4.1.x series but it was largely assumed that an Experimenter belonged to a single Group and that the permissions of that Group were private.

The OMERO permissions system received its first significant update in 4.2.0 with the introduction of multiple group support throughout the platform and group permissions levels.

In a 4.1.x object graph Group containment was not enforced i.e. two linked objects (such as a Project and Dataset) could in theory be members of two distinct Groups. All objects continued to carry their permissions and those permissions were persisted in the database.

Things to note about 4.2.x permissions

• Objects could not be moved between groups easily.
• It was not possible to reduce the permissions level of a group.
• The delete service (introduced in OMERO 4.2.1) was made aware of the permissions system.
• ‘Default Group’ switching was required to make queries in different permissions contexts.

Note

Queries span only one group at a time. Inserts and updates as other users must be done by creating a session as that user.

Changes for OMERO 4.4.x

The second major OMERO permissions system innovations were performed in 4.4.0:

• Cross group querying was reintroduced.

• Change group was enabled, allowing the movement of graphs of objects between groups.

• Permissions level reduction was made possible for read-annotate to read-only transitions.

• A thorough user interface review resulted in the following features being made available in the UI:

  • single group browsing and user-switching (available since 4.4.0)
  • browsing data across multiple groups (available since 4.4.6 and refined in 4.4.7)

• The concept of a ‘Default or Primary Group’ was deprecated.

Note

Queries, inserts and updates span any or all groups and any user via options flags.

Changes for OMERO 5.4.x

OMERO 5.4.0 included Restricted Administrators as a new user role. See Administrators with restricted privileges and The server’s view of administrator restrictions for more information.