Omero Integration

Permissions, Filesets, Web APIs, and High-Risk Operations

This reference covers features that can broaden scope, expose original data, or mutate server state. Apply the operating contract in SKILL.md first.

Group Permissions

OMERO group permissions are commonly represented as:

• private: rw----

• read-only: rwr---

• read-annotate: rwra--

• read-write: rwrw--

The string describes group policy, not a guarantee that a specific operation is allowed. Ownership, administrator privileges, object state, and link rules also matter.

Inspect, do not infer:

image = conn.getObject("Image", image_id)
if image is None:
    raise LookupError("Image unavailable")

details = image.getDetails()
permissions = details.getPermissions()
print(
    {
        "group_id": details.getGroup().getId(),
        "owner_id": details.getOwner().getId(),
        "can_edit": permissions.canEdit(),
        "can_annotate": permissions.canAnnotate(),
        "can_link": permissions.canLink(),
        "can_delete": permissions.canDelete(),
    }
)

Do not print owner/group names or email addresses unless needed.

Cross-Group and Substitute-User Operations

conn.SERVICE_OPTS.setOmeroGroup("-1") requests all accessible groups. It can multiply query scope and expose data from collaborations not intended for the current task. Require explicit cross-group approval, a total cap, and group IDs in output.

suConn() and CLI --sudo are privileged impersonation mechanisms. Use only for an administrator-approved task with:

• initiating administrator identity;

• target user;

• target group;

• exact operation and IDs;

• audit/logging expectations;

• immediate closure of the substitute connection.

Never create a substitute connection merely to work around a permission error.

Filesets and Original Data

Filesets represent original imported file collections. One fileset may back multiple images and include nested paths:

fileset = image.getFileset()
if fileset is not None:
    print(fileset.getId())

Original-file paths and names can expose acquisition layout or identifiers. Do not enumerate them in a general inventory.

The current CLI can download one explicit object:

omero download OriginalFile:123 ./reviewed-file
omero download FileAnnotation:456 ./reviewed-file
omero download Image:789 ./reviewed-empty-directory
omero download Fileset:321 ./reviewed-empty-directory

Image and Fileset may expand to multiple files. The current download CLI looks these up with cross-group context; verify the object’s actual group first instead of relying on the session group. First inspect count/size, then use a dedicated destination with collision/symlink checks. Authenticate through a prompted stored session; do not add password or key flags.

Direct RawFileStore usage must be bounded and closed:

max_bytes = 50 * 1024 * 1024
store = conn.createRawFileStore()
try:
    store.setFileId(original_file_id, conn.SERVICE_OPTS)
    size = store.size(conn.SERVICE_OPTS)
    if size > max_bytes:
        raise ValueError("OriginalFile exceeds approved byte limit")
    chunk = store.read(0, min(size, 1024 * 1024), conn.SERVICE_OPTS)
finally:
    store.close()

This sample intentionally reads at most one chunk. A full download needs a loop with cumulative byte checks and a caller-selected safe path.

Destructive Commands

conn.deleteObjects(type, ids, wait=True) submits an OMERO command. The exact impact depends on object type, links, ownership, and server graph rules. Do not promise a cascade/orphan result from intuition.

Required delete workflow:

1. Resolve explicit object type and IDs in one group.

2. Read current object/link summaries and permissions.

3. Show counts and likely related objects from documented queries.

4. Obtain explicit approval for those exact IDs.

5. Submit with wait=True or monitor the returned command callback.

6. Inspect command response for errors.

7. Record success/failure per ID.

8. Close callbacks/handles and the gateway.

Never select delete targets by a broad name/namespace query without an ID review. Never add delete mode to inventory/export scripts.

Unlinking an annotation, table, image, or dataset is a different graph change from deleting the child. State which one is intended.

Ownership and Group Changes

Changing ownership or moving data between groups can alter access for many linked objects. Current CLI documentation says ownership changes require full admin, an appropriately privileged restricted admin, or group owner.

Before:

• enumerate exact root objects and affected links;

• confirm source and destination groups;

• confirm target owner membership;

• check whether filesets/annotations/tables move with the object graph;

• obtain administrator approval;

• use current documented CLI/API methods, not direct _obj.details.owner manipulation copied from old examples.

Do not write private model fields to bypass service-level policy.

HQL and Query Service

Use fixed HQL and typed parameters:

import omero.sys

parameters = omero.sys.ParametersI()
parameters.addLong("image_id", image_id)

query = "select i from Image i where i.id = :image_id"
model_image = conn.getQueryService().findByQuery(query, parameters, conn.SERVICE_OPTS)

Never interpolate names, namespaces, IDs, ordering, or arbitrary user text into HQL. Map user choices to allowlisted fixed query templates. Apply a server-side result limit to list queries.

Deprecated Service Surface

The current generated API marks at least these interfaces deprecated:

• IRoi

• IShare

IRoi.findByImage remains in current official Python examples, but should be isolated and version-checked. Do not build new sharing workflows on IShare; use current administrator-supported OMERO.web/public-data features instead.

Deprecation does not mean immediate removal. It means callers must not claim long-term stability or invent a replacement.

OMERO.web: What Is Publicly Supported

Official OMERO.web developer documentation says only these included apps are stable public APIs:

• api

• webgateway

Other apps, including webclient, expose internal URLs and methods that may change in minor releases. A URL currently used by the UI is not automatically a supported integration endpoint.

JSON API

The documented OMERO JSON API:

• is implemented by the api Django app;

• advertises supported major versions at GET /api/;

• advertises starting URLs at GET /api/v0/;

• reports the full API version in X-OMERO-ApiVersion;

• uses limit and offset pagination;

• reports totalCount, limit, offset, and server maxLimit;

• requires a CSRF token for POST/PUT/DELETE;

• documents login at /api/v0/login/;

• supports read endpoints for documented model types, including ROI listing;

• currently limits object creation/update to Projects, Datasets, and Screens.

Official docs describe create/read/update/delete access but also explicitly limit type coverage. Do not call it a complete generic REST interface, assume OAuth, assume token authentication, or infer endpoints not listed by the server's discovery response.

The JSON API defaults list queries to all accessible groups, unlike a typical BlitzGateway session query. Include an explicit group=<id> filter for group-scoped lists. Follow discovery URLs (including any deployment prefix), and use data for results and meta for pagination.

Authentication uses session cookies: discover url:servers and select its server ID; GET url:token for the CSRF value; POST form-encoded server, username, and password to url:login, with X-CSRFToken (or csrfmiddlewaretoken) and an HTTPS same-origin Referer. Retain cookies in the same client session and refresh the CSRF token after login before further mutations. The token endpoint is /api/v0/token/, not a bearer-token issuer; /api/v0/servers/ returns server IDs in data. Do not log login responses, which include session identifiers.

Use HTTPS. A JSON API password is sent in the documented login POST and must never be logged. Honor the returned maxLimit; apply a smaller client cap.

WebGateway

webgateway provides documented rendered images and JSON data. Confirm the current endpoint page before implementing, cap image size/quality, and use HTTPS. Do not substitute a webclient AJAX route.

Public Data and Links

Publishing is an administrator configuration, not a client-side “make public” API call. Current official guidance:

• create a dedicated read-only group;

• create/add a public user with only intended data access;

• omero.web.public.enabled defaults to false;

• public users default to GET-only;

• omero.web.public.url_filter must explicitly allow routes and otherwise matches nothing;

• download/export routes can be excluded;

• a dedicated public OMERO.web deployment may be appropriate.

OME shows examples such as webclient/?show=project-... for publication navigation, but the webclient itself is explicitly not a stable public API. Do not promise that such links are permanent integration contracts. For durable publication URLs, use administrator-owned redirects/DOIs and test them after upgrades.

Never generate a public link merely because an object is readable to the current authenticated user. Confirm:

• the public user is enabled;

• its group membership permits the object;

• GET-only remains enabled;

• URL filter permits only intended routes;

• download/export routes are intentionally allowed or blocked;

• the institution approves public release.

OMERO CLI Import/Admin Boundary

Installing omero-py provides the CLI framework, but import/admin commands also depend on a compatible extracted OMERO.server tree through OMERODIR. Do not point OMERODIR at an arbitrary or mismatched server distribution.

Remote client commands and local server administration have different risk. Before any admin command, confirm it is being run on the intended host with the intended server installation/configuration.

Advanced Operation Checklist

• Current server/client/API docs verified

• Exact user, group, object type, and IDs

• Cross-group/impersonation separately authorized

• Permission checks do not replace authorization

• Original-file count/bytes and destination reviewed

• Fixed queries with typed parameters

• Deprecated services isolated and documented

• Only api/webgateway treated as stable OMERO.web APIs

• Public access configured by administrators, not inferred

• Destructive commands previewed, confirmed, monitored, and recorded

• Every stateful service/callback/connection closed