Administrators with restricted privileges

Summary

OMERO allows you to create administrators with a subset of the full administrator privileges. This is a way to cater for the need for more powerful users acting on behalf of all other OMERO users, with no group membership but with access to all groups and data of all users in OMERO. This should be achieved without creating new full administrators in OMERO. In the real world, these administrators with restricted privileges (restricted admins) will typically be imaging facility managers, image analysts, or anybody who needs to organize users and data of others in OMERO.

Full administrators in OMERO can create new administrators with restricted privileges using the OMERO.web interface, see the facility managers guide in our Help documentation. OMERO.cli does not yet support easy management of restrictions nor does it offer the helpful permissions mapping but advanced users may use OMERO.cli to adjust the restrictions on an administrator.

We suggest here four setups that should cover the four mainstream workflows. Nevertheless, you can combine the privileges (check the checkboxes in the OMERO.web interface) in any way you see fit. The privileges were designed in such a way that they still bear useful functionality even when used in isolation. For example, checking the Chown checkbox will give the new administrator with restricted privileges the power to transfer ownership of other users’ data. For exact server-side definitions of the privileges displayed in OMERO.web interface see Administrator restrictions: relating OMERO.webadmin to OMERO.server.

Four suggested workflows

Required Privileges Data viewer Importer Analyst Group and Data Organizer
Sudo N Y N N
Write Data N N Y Y
Delete Data N N N Y
Chgrp N N N Y
Chown N N Y (O) Y
Create and Edit Groups N N N Y
Create and Edit Users N N N Y
Add Users to Groups N N N Y
Upload Scripts N N Y N
Y
privilege required, checkbox in OMERO.web interface is checked
N
privilege not required, checkbox is not checked
O
privilege optional for the workflow

Note

Restricted admins workflows in OMERO.clients

Please do not expect for any workflows mentioned here that all OMERO.clients OMERO.web, OMERO.insight, command line interface (CLI) are fully equipped to execute them (see details below). New features will be added in OMERO.clients in the 5.4.x series of OMERO releases.

Note

Group membership

All the workflows here assume that the administrator with restricted privileges is not a member of any group except the System group. This does not preclude such administrator from being a member of any number of groups. Inside the groups the restricted admin is a member of, they have the same privileges as other group members of that group additionally to their administrative privileges.

Note

Deleting privileges

Sudo privilege includes ability to delete the data of the user whom the administrator is working on behalf of. If you want to prevent the restricted admin from deleting others’ data entirely, do not give Delete Data and do not give Sudo privileges.

Note

Privilege escalation

The administrators with restricted privileges (restricted admins) are prevented from escalation of their privileges. Creation of a restricted admin with higher privileges than the creator, and creation of a full administrator, are prevented. Furthermore, although a restricted admin can Sudo on behalf of a full administrator, their privileges will not expand to the full administrator privilege set by this action. See also Sudo.

Workflow 1: Data viewer

If you do not give any explicit privileges to the administrator with restricted privileges, this administrator still has some useful privileges. These include browsing and viewing all the data of all users in all groups (including the groups where they are not members). The administrator with restricted privileges is also able to download all the data in all types of groups. Furthermore, they can view user and group information, such as usernames, e-mail addresses, group permission levels and lists of all users and groups. They are not able to annotate, edit or delete any of the data or change any user or group information though. Note that any administrator with restricted privileges described below or otherwise created combining the privileges at will would be able to perform the Data viewer workflow as well.

Client Details:

  • OMERO.insight: is not designed to show any groups, or data belonging to any groups, you are not a member of. The Data Viewer workflow is preferably executed using OMERO.web or CLI.

  • OMERO.web: allows viewing and downloading the data, see Viewing Data.

  • CLI: allows listing all images, groups and users and downloading the data:

    # List all users on server
$ bin/omero user list
# List all groups on server
$ bin/omero group list
# List all images on server
$ bin/omero fs images

Workflow 2: Importer

The Importer role is to import images into OMERO for other users, i.e. in such a manner that the imported images are owned by the users in OMERO, not by the user in the role of the Importer. The Importer role is typically used by an imaging facility manager who is importing data acquired by users on microscopes into OMERO.

The importer workflow can be achieved with only the Sudo privilege (first line in the above table). This privilege allows them to “become” the user they are importing the data for. The Importer role may need to reorganize the imported data. For example, they made a mistake, Sudoed as a wrong user in a wrong group and need to rectify the mistake using the command line interface (CLI) client. Whilst being sudoed, the Importer role can Delete the wrongly imported data (even without Delete privilege given, see the Note above), logout, login and Sudo as the correct user and repeat the import process. In short, whilst Sudoed, Importer role can do any action which the user they are becoming is allowed to do. In case any more post-import cleaning and data organizing is necessary for Importer, this might be enabled by giving them also privilege necessary for the Data organizers (see Workflow 4: Group and Data Organizer below).

If you have any doubts about giving the administrators with restricted privilege the Sudo privilege (which implicitly gives the ability to delete other users’ data), there are two workarounds which enable import for others without Sudo.

The first, simpler, workaround involves importing the data as Importer into the group of the future data owner and then transferring the ownership of the data (see details in Workflow 3: Analyst). The second workaround involves importing into the group of the Importer as the importer, then moving the data into the group of the prospective data owner and then changing the ownership of the data to the owner (necessary tools are described in Workflow 3: Analyst).

Client details:

  • OMERO.importer or OMERO.insight: you have to be a member of the group you want to import to in OMERO.importer or OMERO.insight. Login as the administrator with restricted privileges and perform the import for others as described in the chapter of the Help documentation import for others.

  • CLI: documentation is available covering Import images and Using import targets (see also the videos on import on the OME YouTube channel):

    # Login as the Importer and sudo as the user you want to import for
$ bin/omero --sudo Importer -u user login
# Create new containers belonging to the user
$ bin/omero obj new Dataset name=Dataset-of-user
$ bin/omero obj new Project name=Project-of-user
# Link the containers
$ bin/omero obj new ProjectDatasetLink parent=Project:17 child=Dataset:13
# Import into created Dataset
$ bin/omero import ~/Desktop/CMPO1.png -T Dataset:name:Dataset-of-user

Workflow 3: Analyst

Typically, the Analyst role in OMERO is to

  • read the data (always possible, see Workflow 1: Data viewer: Data viewer)
  • change and save the rendering settings of the images (enabled by Write Data privilege, exception is Private groups, where they cannot save rendering settings)
  • annotate the data (enabled by Write Data privilege, but not possible in Private groups)
  • draw and save ROIs on other users’ images (enabled by Write Data privilege, but no saving in Private groups possible)
  • upload and attach result files to the analyzed images (enabled by Write Data privilege, except Private groups, where attaching is not possible)
  • create Projects and Datasets for newly imported images in groups they are not a member of (enabled by Write Data privilege)
  • import new images resulting from image analysis into these Projects and Datasets
  • link new images resulting from image analysis to existing Projects and Datasets of the original data owner (enabled by Write Data privilege)
  • (possibly) changing the ownership of the newly created conainers and contained result images to the users (enabled by Chown privilege)
  • upload, edit and delete official scripts usable by all OMERO users (enabled by Upload Scripts privilege)

Client details:

  • OMERO.insight or Insight-ImageJ plugin: Analyst has to be a member of the group where the data is located. They can draw ROIs and extract analysis results from the ROIs and data in any type of group. They can save ROIs except in Private groups. They can upload official scripts in OMERO.insight (any group type, Analyst does not have to be a member of any particular group for script upload in OMERO.insight).

  • OMERO.web, OMERO.insight, Insight-ImageJ plugin: Analyst can adjust rendering settings and save them, upload attachments with results and annotate (for example tag, key-value pairs, rating, commenting). These actions are not permitted in Private groups with images belonging to others. See Help guides for rendering, annotating, attaching files, attaching data.

  • CLI: Upload of official scripts is allowed (in any group type, see OMERO.scripts user guide and below). Upload of attachments with results, annotating (not in private group), creating containers, import of resulting images into groups you are not a member of (in private groups these are invisible for the owner of the original data, unless you transfer their ownership), transferring ownership of these containers (any group type), transferring ownership of objects (images, annotations, ROIs, uploaded attachments with results) is possible too (see Command Line Interface as an OMERO client):

    # Upload an official script
$ bin/omero script upload --official /PATH/TO/YOUR_SCRIPT
# Login to the group the original data are in
$ bin/omero -g testgroup login
# Create new Dataset
$ bin/omero obj new Dataset name=new-dataset
# Import result images into the Dataset
$ bin/omero import -T Dataset:name:new-dataset /PATH/TO/RESULT/IMAGES
# Transfer the ownership of the Dataset and
# of the contained images to the user with ID:55
$ bin/omero chown 55 Dataset:112

Workflow 4: Group and Data Organizer

Group and Data Organizer role is for creation of new users and groups in OMERO and allocating the users to appropriate groups. It is also possible to change the users’ information such as e-mail and to change group permissions level. These tasks are facilitated by the privileges Create and Edit Groups, Create and Edit Users and Add Users to Groups.

The Group and Data Organizer might also be tasked with dealing with data owned by OMERO users who have left the institution. The Organizer can transfer ownership of the data owned by the leaving person (facilitated by the Chown privilege) to another user. In cases where the new owner of the data may not be a member of the data group, the Organizer first moves the data between groups (facilitated by the Chgrp privilege), and then transfers the ownership of the data. Always try to avoid the situation where owner of the data is not in data group.

For moving data between groups, usage of OMERO.web is highly recommended. The Organizer can create new containers (Projects, Datasets) on behalf of data owner in OMERO.web conveniently as part of the Move to Group command in OMERO.web (Move to Group). The containers and links of data to containers will belong to data owner. For new container creation and linking, the Write Data privilege is necessary. CLI can be used for the move action as well, see Moving objects between groups.

In case of data owner not being in the group where the data is, the Organizer can also add the data owner to the data group (facilitated by the Add Users to Groups privilege), instead of moving the data. The Organizer will transfer the ownership of the data to the new owner only after they have added the new data owner to the data group.

During all data manipulation steps, the Organizer needs the Write Data privilege to create new Projects, Datasets or Screens for the new owners of the data and to link the data to those containers or to already existing containers owned by the new owner. Since OMERO 5.4.0, OMERO.web enables Organizers with Write Data privilege to create new containers belonging to other users, see the OMERO.web in Data structure section of our Help documentation. Except the links created during creation of new Datasets inside others’ Projects in OMERO.web, any links created by the Organizer will belong to the Organizer, not the owner of the data. This will be addressed in OMERO.web in the 5.4.x series. The ownership transfer of the containers and links can be done later on the CLI. Linking of others’ data is never possible in Private groups.

After the Organizer has dealt with the data, they can remove the leaving person from any group (included in the Add Users to Groups privilege) and make the user inactive (facilitated by the Create and Edit Users privilege).

Note that the ownership of data of a user can be transferred either piecemeal, i.e. specifying each Project or Dataset to transfer (using omero chown command of CLI), or all of the data of the user can be transferred in one step. The transfer of all the data of the user in one step has to be considered an advanced feature; it may be slow and demanding of CPU resources in cases of complex data.

Quite naturally the Group and Data Organizer can be easily split into two separate roles, with the Group Organiser role having Create and Edit Groups, Create and Edit Users, Add Users to Groups privileges, and the Data Organiser role having Write Data, Delete Data, Chgrp, Chown privileges. It is of course possible to use any combination of these privileges as you see fit. It is recommended to always grant Create and Edit Users with Add Users to Groups so that the new restricted administrator is able to deactivate users.

Client Details:

  • OMERO.web: all the Data Organizing actions are possible, except transfer of ownership (possible only in CLI, will be addressed in the 5.4.x series). Creation of Projects, Datasets or Screens for other users in OMERO.web is possible since OMERO 5.4.0, see Data structure (OMERO.web). All the Group and User Organizing actions are possible if all Create and Edit Groups, Create and Edit Users and Add Users to Groups privileges are given. It is also reasonable to give Create and Edit Users and Add Users to Groups or Create and Edit Groups and Add Users to Groups. These combinations give the restricted adiminstrator good user interface experience in OMERO.web.

  • CLI: see User/group management, Moving objects between groups, Changing ownership of objects and examples below for CLI features useful for Group and Data Organizing:

    # Create new user and put them into 2 groups
$ bin/omero user add username firstname lastname group1 group2
# Edit login name of a user with ID:55
$ bin/omero obj update Experimenter:55 omeName=new-login-name
# Add a user to a group named "testgroup"
$ bin/omero group adduser --name testgroup --user-name newbieingroup
$ bin/omero group removeuser --name testgroup --user-name thegoner
# Make a user a group owner. Works also when the owner-to-be
# is already a member of the group
$ bin/omero group adduser --name group --user-name ownertobe --as-owner
# Remove a group owner from ownership of the group. Does not remove
# the formerowner from group, just unsets the ownership.
$ bin/omero user leavegroup testgroup --name formerowner  --as-owner
# Move a Dataset hierarchy to group 5 and include all annotations
# on the Dataset and objects linked to the Dataset
$ bin/omero chgrp 5 Dataset:51 --include Annotation
# Transfer ownership to user 55 of the Project 112
$ bin/omero chown 55 Project:112
# Transfer the ownership of a Project-Dataset link. Useful in case the
# link was created by the Organizer and links objects of others
$ bin/omero chown 55 ProjectDatasetLink:123
# Transfer the ownership of Dataset-Image link
$ bin/omero chown 55 DatasetImageLink:154
# Transfer all data of user 5 to user 11 (advanced, might be slow)
$ bin/omero chown 11 Experimenter:5

Key

Add Users to Groups
Administrator can add or remove users to groups. See Workflow 4: Group and Data Organizer for more details.
Analyst
Administrator who performs image analysis on others’ images in OMERO. See more details in Workflow 3: Analyst.
Chgrp
Administrator can move others’ data to a different Group. See Workflow 4: Group and Data Organizer for more details.
Chown
Administrator can transfer others’ data to a different Owner. See Workflow 4: Group and Data Organizer for more details.
Create and Edit Groups
Administrator can create and edit groups (but not add or remove users). See Workflow 4: Group and Data Organizer for more details.
Create and Edit Users
Administrator can create and edit other users (but not add them to groups). See Workflow 4: Group and Data Organizer for more details.
Data Viewer
Administrator who views and downloads data of others. See more details in Workflow 1: Data viewer.
Delete Data
Administrator can delete other users’ data. See Note on Delete for more details. Integral part of Workflow 4: Group and Data Organizer.
Group and Data Organizer
Administrator who creates new users and groups in OMERO and allocates or removes the users to or from appropriate groups. This administrator also deals with data left after OMERO users which left the institution, or otherwise is tasked with reorganizing of others’ data. See more details in Workflow 4: Group and Data Organizer.
Importer
Administrator who imports images into OMERO for other users. The imported images are owned by the users in OMERO, not by the Importer. This is typically an imaging facility manager who is importing data acquired by users on microscopes into OMERO. See more details in Workflow 2: Importer.
Sudo
Administrator can log in as another user, with all the permissions of that user. When the restricted admin is working on behalf of a user and using Sudo, their privileges are a common least denominator of the privileges of the user and of the restricted admin (i.e. if a restricted administrator is using Sudo on behalf of a full administrator, they do not have full admin rights to perform actions not covered by their own privileges). See also Note on privilege escalation, Note on Delete and Workflow 2: Importer for more details.
Upload Scripts
Administrator can upload “official” OMERO.scripts to the server. See Workflow 3: Analyst for more details.
Write Data
Administrator can create data in groups of which he/she is not a member. Also allows annotating, adding attachments to and editing and linking of other users’ data. See Workflow 3: Analyst for more details.