OMERO.DataQueryWorker

OMERO.DataQueryWorker is a private, OMERO-agnostic service for bounded SQL queries over immutable DuckDB, SQLite, and CSV files. It is designed to run as a separate container beside an authenticated application such as OMERO.Analysis. It does not connect to OMERO or authorize end users.

The worker stores source files and bounded CSV query results in its own persistent cache. Every query runs in a disposable subprocess with a timeout, row and byte limits, disabled DuckDB external access, and a restrictive SQL policy. SQLite uses the standard-library engine in immutable, query-only mode. A CSV source is imported once and exposed as the table data.

Run locally

python -m venv .venv
. .venv/bin/activate
python -m pip install -e '.[test]'export DQW_API_TOKEN='replace-with-at-least-16-characters'export DQW_CACHE_DIR="$PWD/cache"
omero-data-query-worker

OpenAPI is available at http://localhost:8080/docs. All /v1/* requests require Authorization: Bearer <DQW_API_TOKEN>. /health/live and /health/ready intentionally return only minimal status.

Source and query flow

1. Call POST /v1/sources/resolve with an opaque scope and immutable source reference.
2. On a miss, stream the file to POST /v1/sources as multipart form data.
3. Inspect GET /v1/sources/{source_id}/schema.
4. Submit one parameterized SELECT to POST /v1/sources/{source_id}/query.
5. Download the complete bounded result from GET /v1/results/{result_id}/download.

Named parameters use $name placeholders and typed values:

{
"sql": "SELECT * FROM measurements WHERE area >= $minimum",
"parameters": {
"minimum": {"type": "float", "value": 12.5}
}
}

Deterministic results are cached by source digest, normalized SQL, typed parameters, engine/policy version, and configured limits. Queries containing volatile time, random, sequence, or UUID functions bypass the result cache.

Configuration

Variable	Default
DQW_API_TOKEN	required, at least 16 characters
DQW_CACHE_DIR	/var/lib/omero-data-query-worker
TMPDIR	/var/lib/omero-data-query-worker/tmp in the container
DQW_SOURCE_CACHE_MAX_BYTES	100 GiB
DQW_RESULT_CACHE_MAX_BYTES	10 GiB
DQW_SOURCE_TTL_SECONDS	7 days
DQW_RESULT_TTL_SECONDS	24 hours
DQW_MAX_SOURCE_BYTES	20 GiB
DQW_QUERY_TIMEOUT_SECONDS	30
DQW_MAX_RESULT_ROWS	100,000
DQW_MAX_RESULT_BYTES	64 MiB
DQW_MAX_CONCURRENT_QUERIES	4
DQW_DUCKDB_MEMORY_LIMIT	1GB
DQW_DUCKDB_THREADS	2

The cache volume contains source data and query results in plaintext and must be treated as trusted server storage. Run one worker replica per cache volume. Container deployments should keep TMPDIR under that writable volume. The multipart parser spools large streamed uploads there before atomic ingestion; the separate /tmp tmpfs can therefore remain small and constrained.

Verification

pytest
ruff check .
mypy src
python scripts/smoke_container.py

The smoke test builds the container, queries fixtures for all three formats, checks result caching and unsafe-SQL rejection, restarts the service, and confirms that its cache survives.

License

Copyright NL-BioImaging contributors. Licensed under AGPL-3.0-or-later.