C2M2 → FAIRSCAPE RO-Crate converter

C2M2 datapackage to FAIRSCAPE RO-Crate.

Install

Python 3.10+ is required. Install the dependencies:

python3 -m venv .venv && source .venv/bin/activate
pip install -r requirements.txt

Usage

Run from the src/ directory:

cd src
python3 convert.py <datapackage-dir> [--output-path DIR]

How it maps

A C2M2 datapackage has three kinds of tables, each becoming a different part of the @graph:

C2M2 table kind	Becomes	Example
Entity	a typed FAIRSCAPE node	subject→Patient, biosample/collection→Sample, file→Dataset
CV (controlled vocabulary)	a schema.org DefinedTerm (@id = resolved ontology IRI)	disease, anatomy, assay_type, … (14 tables)
Association	an edge between the above (no node of its own)	subject_disease → Patient.diagnosis → disease DefinedTerm

So a patient with a diagnosis is a Patient node whose diagnosis (from subject_disease) points at a disease DefinedTerm (from the disease CV table). See MAPPING-SCHEMA.md for the full mapping reference.

Module map

File	Role
convert.py	Main entry point. The mapping-driven engine (MappingC2M2Converter): loads the mappings, explodes rows into typed nodes, builds the root + provenance, writes the crate.
base.py	Base mapper (C2M2ToROCrateMapper) that convert.py subclasses: datapackage plumbing, generic per-table Dataset/evi:Schema reflection, the preservation layer (datapackage.json + sqlite), and the Computation/Software pair.
ontology.py	Pure CV-value → ontology IRI resolution (resolve_term) + the schema.org PropertyValue/IdentifierValue helpers. No converter or model imports.
parsers.py	The fixed parser registry the JSON mappings refer to by name (imports from base + ontology).
mappings/	The declarative heart — manifest.json (load order), root.json, the entity mappings (file/subject/biosample/collection), and cv/ (the 14 controlled-vocabulary tables → DefinedTerm).
MAPPING-SCHEMA.md	Full reference for the mapping JSON format.
test_convert.py	End-to-end test suite for convert.py.
test_base.py	Base-layer tests guarding base.py (the class convert.py subclasses).
examples/, test-data/	Datapackage fixtures and reference crates used by the tests.

Import graph: convert.py → base.py, parsers.py; parsers.py → base.py, ontology.py. ontology.py and base.py have no sibling dependencies.

Tests

python3 -m pytest -q        # runs test_convert.py + test_base.py