fairscape-conversion

Turns metadata you already have (a datasheet, a data package, a workflow engine’s run output) into a FAIRSCAPE RO-Crate, so you don’t have to type it in again. It can also export a crate to other formats.

It is the create step of FAIRSCAPE, next to fairscape_models.

Install

pip install fairscape-conversion

Example

mkdir my-crate
python -m fairscape_conversion.core.cli convert d4d import datasheet.yaml my-crate/ro-crate-metadata.json

From Python:

import yaml
from fairscape_conversion.plugins import d4d

crate = d4d.convert("import", yaml.safe_load(open("datasheet.yaml")))

Every format works the same way: convert <format> <import|export> INPUT [OUTPUT].

Formats

Import from	Input
`d4d`	Datasheet for Datasets (YAML or JSON)
`snakemake`	records JSON from `snakemake --reporter fairscape`
`cromwell`	`metadata.json` from `cromwell run -m`
`galaxy`	an invocation export (`.tar.gz`, `.zip`, folder) or a `.ga` file
`mlflow`	an `mlruns` dir or tracking URI, with `--experiment NAME` (needs `pip install mlflow`)
`wrroc`	a Workflow Run RO-Crate `ro-crate-metadata.json` (CWL, Galaxy, …)
`redcap`	the data dictionary CSV, plus `--records DATA.csv` if you want the records too
`frictionless`	a `datapackage.json` or its folder
`c2m2`	a CFDE C2M2 datapackage folder
`cpm`	a CPM RO-Crate folder with its PROV bundle files

Export to
`croissant`	MLCommons Croissant
`d4d`	Datasheet for Datasets
`wrroc`	Workflow Run RO-Crate
`frictionless`	Frictionless `datapackage.json`
`cpm`	PROV-JSON (or PROV-N with `--provn`)

Details

Try every converter with no data of your own. python examples/run_all.py runs each one on the sample input that ships in plugins/<format>/ and checks the result against a reviewed golden file. examples/mlflow/mlflow_to_rocrate.ipynb is a full walk-through.
Linking crates. If this run’s inputs were another run’s outputs, pass --link-crate /path/to/upstream-crate. The new crate reuses the upstream identifiers, so the evidence graph can follow one crate into the other. See examples/linked-crates/.
Adding a format. A converter is a folder with two CSV mapping files and a small plugin class. See docs/NEW-PLUGIN.md, docs/INTERNALS.md and MAPPING-SCHEMA.md.

Source: github.com/fairscape/fairscape_conversion