MOUSE OpenBIS Uploader

A small CLI tool to upload MOUSE SAXS measurement batches to OpenBIS based on a YMD day code (e.g. 20251220). It reads the measurement metadata from the Excel logbook and uploads/updates OpenBIS objects and datasets (RAW and PROCESSED).

The general structure is as follows:

Install (editable)

python -m venv .venv
source .venv/bin/activate
pip install -U pip
pip install -e .

Token-based authentication

The CLI uses a token stored in a file (default: ~/.datastore_token).

• Make sure the token file exists and contains a non-empty token string.
• Override the path via --datastore-token-path.

Usage

Minimal (only required argument is the YMD code):

openbis-mouse-uploader 20251220

More verbose logging:

openbis-mouse-uploader 20251220 --log-level DEBUG

Continue from a later row in the logbook:

openbis-mouse-uploader 20251220 --start-row 50

Dry-run (no writes; logs intended actions):

openbis-mouse-uploader 20251220 --dry-run

Notes on behavior

• People collections are grouped by proposal year: PEOPLE_<proposal-year>.
• Duplicate objects should not exist. If they do, the uploader logs a warning and deletes duplicates permanently until a single object remains.
• If the project-leader BAM record is not found, the project_leader_bam property is omitted.

Development

• Formatting/linting: ruff
• Typing: mypy (configured to ignore missing third-party stubs)
• Pre-commit: pre-commit

Setup:

pip install -e ".[dev]"
pre-commit install

Example:

ruff format .
ruff check .
mypy src
pytest