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Bundled Helpers and OMERO.server Scripts

The local files in this skill's scripts/ directory are client-side safety helpers. They are not OMERO.server scripts and are never uploaded automatically.

Shared Safety Model

Every bundled executable:

  • uses argparse;
  • supports --help without OMERO installed;
  • imports omero only after argument parsing and only for --execute;
  • reads only named OMERO_* variables;
  • never loads .env;
  • never accepts or prints a password/session key;
  • defaults to local validation or dry-run output;
  • applies hard limits;
  • refuses unsafe output collisions/symlinks;
  • closes remote connections in finally.

Remote helpers require --execute. That flag authorizes a read-only connection, not broader scope or mutation.

Local Endpoint Validation

python -B scripts/validate_config.py
python -B scripts/validate_config.py --require-auth --json

By default it performs only local syntax checks. --resolve-host performs DNS resolution but does not connect to an OMERO port.

Output reports which named variables are present and the authentication mode. It never displays credential values.

Examples of failures:

  • host contains http://, a path, whitespace, or shell syntax;
  • port is not in 1..65535;
  • OMERO_SECURE is not a recognized boolean;
  • only one of OMERO_USER/OMERO_PASSWORD is present;
  • --require-auth is used without either a session key or complete password authentication.

Read-Only Inventory

Dry run:

python -B scripts/inventory.py \
  --object-type Image \
  --limit 50 \
  --page-size 25

Execute after reviewing endpoint/group/scope:

python -B scripts/inventory.py \
  --object-type Image \
  --limit 50 \
  --page-size 25 \
  --group-id 42 \
  --execute \
  --output ./image-inventory.json

Properties:

  • allowlisted object types only;
  • overall cap at 1000 and page cap at 200;
  • stable obj.id ordering request;
  • one optional explicit group, never cross-group -1;
  • object names redacted unless --include-names;
  • JSON output written atomically with owner-only permissions;
  • existing output refused unless --overwrite.

limit_reached means the requested cap was filled; it does not assert that more server rows exist.

Annotation and ROI Export

Dry run:

python -B scripts/export_image_metadata.py \
  --image-id 101 \
  --image-id 102 \
  --max-annotations-per-image 100 \
  --max-rois-per-image 100 \
  --max-shapes-per-roi 500 \
  --output ./selected-image-metadata.json

Execute:

python -B scripts/export_image_metadata.py \
  --image-id 101 \
  --image-id 102 \
  --group-id 42 \
  --execute \
  --output ./selected-image-metadata.json

Default redactions:

  • annotation values
  • owner names
  • FileAnnotation filenames
  • ROI/shape labels
  • mask bytes

Optional inclusion flags are independent. The helper never retrieves pixels or FileAnnotation bytes. It uses the currently documented IRoi.findByImage pattern and records that IRoi is deprecated.

Because findByImage has no page argument, the ROI caps bound serialization but may not bound server-side assembly. Do not run it on a known extreme image without reviewing the ROI count or using a site-approved paginated API.

Import/Export Planner

The planner is always local and has no --execute.

Import scan plan:

python -B scripts/plan_transfer.py import \
  --target Dataset:id:42 \
  --max-files 100 \
  --scan-depth 4 \
  ./explicit-input

It walks only explicit paths, does not follow directory symlinks, caps depth and file count, and proposes omero import -f plus a future scoped import command. It does not invoke either.

Per-image export plan:

python -B scripts/plan_transfer.py export \
  --format ome-tiff \
  --output-dir ./reviewed-existing-directory \
  Image:101 Image:102

It accepts explicit Image:<id> selectors only, proposes one output per image, and reports collisions. Dataset iteration is intentionally excluded because the official export mode is experimental and too easy to broaden.

Global --output and --overwrite arguments must precede the subcommand:

python -B scripts/plan_transfer.py \
  --output ./transfer-plan.json \
  import ./explicit-input

No proposed command includes -w, --password, -k, or a session value.

Running Local Tests

No real OMERO server is needed:

PYTHONDONTWRITEBYTECODE=1 \
  python -B -m unittest discover \
  -s tests/omero-integration \
  -p "test_*.py"

The tests use temporary directories and fake gateway objects.

OMERO.server Script Model

OMERO.server scripts are Python plugins registered with the Script Service. Clients can launch them and receive typed outputs. Inputs often include an explicit data type, object IDs, thresholds, or options.

A minimal structure:

import omero
import omero.scripts as scripts
from omero.gateway import BlitzGateway
from omero.rtypes import rlong, rstring


def main():
    client = scripts.client(
        "Bounded_Image_Summary.py",
        "Returns IDs for an explicit bounded image list.",
        scripts.List(
            "Image_IDs",
            optional=False,
            description="Explicit image IDs (maximum enforced by script)",
        ).ofType(rlong(0)),
        namespaces=[omero.constants.namespaces.NSDYNAMIC],
        version="1.0",
    )

    try:
        inputs = client.getInputs(unwrap=True)
        image_ids = list(inputs["Image_IDs"])
        if not 1 <= len(image_ids) <= 25:
            raise ValueError("Image_IDs must contain 1..25 IDs")

        conn = BlitzGateway(client_obj=client)
        found = []
        for image_id in image_ids:
            image = conn.getObject("Image", image_id)
            if image is not None:
                found.append(image.getId())

        client.setOutput("Message", rstring(f"Found {len(found)} images"))
    finally:
        client.closeSession()


if __name__ == "__main__":
    main()

The script session is supplied by OMERO. Do not read a password or create a second login inside a server script.

Server-Script Safety

Even a server script that only reads can be expensive. It must enforce:

  • maximum ID count;
  • per-container child cap;
  • plane/tile/byte limits;
  • fixed group context;
  • no cross-group fallback;
  • no user-controlled HQL/code strings;
  • bounded output size;
  • client.closeSession() in finally.

For writes, additionally require an explicit “save” input or other reviewed gate and document every created/linked object. A client-side confirmation is not enough if the server script itself accepts unbounded inputs.

Do not use Python eval() or exec() for parameters. Do not interpolate parameter text into HQL, filesystem paths, commands, or table conditions.

Upload and Launch

Uploading registers executable code and is a mutation:

omero script upload ./Bounded_Image_Summary.py
omero script list

Before upload:

  1. review source and dependencies;
  2. validate against the target OMERO.py/server pairing;
  3. confirm destination script path/category;
  4. confirm administrator authorization;
  5. record returned script ID/version.

Launching is also a remote operation:

omero script launch <SCRIPT_ID> Image_IDs=101,102

Use an already prompted session. Confirm the exact script ID, version, group, input IDs, expected writes, and resource limits. Never launch based only on a script display name.

Outputs and Temporary Files

Server scripts may return strings, objects, images, or FileAnnotations. For a file output:

  • use a server-side temporary directory designed for scripts;
  • generate a safe filename independent of user text;
  • cap bytes;
  • classify content before attaching;
  • remove local temporary files in finally;
  • close any table or raw store before closing the script session.

Do not place server paths, credentials, session IDs, or stack traces in client outputs.

Script Review Checklist

  • Client helper or server plugin clearly identified
  • Dry run and execution separated
  • Credentials absent from arguments/output
  • Object/group/file scope explicit
  • Hard bounds at every expansion
  • Output path safe and collision-aware
  • Lazy optional imports for local helpers
  • Stateful resources closed
  • IRoi/other deprecated service dependencies documented
  • No real-server test performed without explicit authorization