CLI

Optimus provides a CLI for pipeline maintenance and analysis tasks. The CLI is separate from Kedro's built-in commands and focuses on catalog management, data validation, and publication figure generation.

uv run cli --help

Commands

checksum

Compute the BLAKE2b hash of a file or directory. Optionally compare against an expected value.

# Compute checksum
uv run cli checksum data/landing/bgee/expression.parquet

# Compare against expected value
uv run cli checksum data/landing/bgee/expression.parquet --expected b7a669ddabfa209e

This is the same BLAKE2b algorithm used by ChecksumHooks to validate catalog entries.

sync-catalog

The primary maintenance command. Synchronizes catalog YAML files with the actual data on disk by updating schemas and checksums.

# Sync all catalog entries
uv run cli sync-catalog

# Sync a specific dataset
uv run cli sync-catalog --dataset bronze.bgee

# Sync an entire layer
uv run cli sync-catalog --layer silver

# Validate without modifying files
uv run cli sync-catalog --validate

# Preview changes without writing
uv run cli sync-catalog --dry-run

When syncing, the CLI:

1. Reads the Parquet file on disk to extract the actual schema
2. Updates the load_args.schema in the catalog YAML to match
3. Computes the BLAKE2b checksum of the file
4. Updates the metadata.checksum field in the YAML

The YAML formatting is preserved (comments, ordering, indentation) using regex-based patching rather than full file rewriting.

metrics

Generate metrics from the gold knowledge graph. Produces summary statistics for node counts, edge counts, and graph properties.

uv run cli metrics

figure

A subcommand group for generating publication-quality figures from the knowledge graph data. Each subcommand produces a specific type of analysis visualization:

# List available figure commands
uv run cli figure --help

Available figure types: