Dataset Citation Metadata

This repo holds the schema and associated scripts used by the Dataset Citation Metadata project.

The Dataset Citation Metadata is a project aimed at ensuring that appropriate citation information exists for data entering and/or produced by biological and environmental research platforms to allow credit to be attributed to those who produced the data.

• Dataset Citation Metadata
  • Metadata Schema
    • Schema Diagram
  • Software Installation
    • Useful commands
      • JSON Schema data validation
  • Developers
    • Add pygraphviz locally with uv add

Metadata Schema

The Dataset Citation Metadata schema is maintained in LinkML format; other formats (including the python class) can be generated from the LinkML schema file.

See the LinkML documentation for full details on using the LinkML format and the related tools.

Full schema documentation can be found at https://kbase.github.io/credit_engine/.

See also some additional information on the schema design.

Schema Diagram

Generated from the Pydantic version of the Dataset Credit Metadata Schema using erdantic.

See below for how to regenerate the ER diagram after making changes to the schema.

Software Installation

This repo uses uv to manage the python environment and dependencies.

See the uv docs for uv installation instructions.

Install the project dependencies and create a virtual environment:

uv sync

Run tests or other scripts:

uv run <command>
uv run pytest tests/

Useful commands

These assume that you have already run uv sync to install the credit engine virtual environment and dependencies.

generate derived files in all formats and save them to the project directory:

uv run gen-project -d project/ schema/dcm/linkml/credit_metadata.yaml

lint the LinkML schema file:

uv run linkml-lint -f terminal schema/dcm/linkml/credit_metadata.yaml

validate data (in file data.yaml) against the schema:

uv run linkml-validate -s schema/dcm/linkml/credit_metadata.yaml data.yaml

generate JSON Schema version:

uv run gen-json-schema schema/dcm/linkml/credit_metadata.yaml > schema/dcm/jsonschema/credit_metadata.schema.json

generate Python classes:

uv run gen-python schema/dcm/linkml/credit_metadata.yaml > schema/dcm/python/credit_metadata.py

generate Pydantic classes:

uv run gen-pydantic schema/dcm/linkml/credit_metadata.yaml > schema/dcm/python/credit_metadata_pydantic.py

generate an ER diagram from the Pydantic classes using erdantic (assumes that erdantic has been installed already):

uv run erdantic schema.dcm.python.credit_metadata_pydantic.CreditMetadata -o schema/dcm/dcm-schema.png

JSON Schema data validation

install the JSONschema check script:

# install with Homebrew
brew install check-jsonschema

or

# install with pip
pip install check-jsonschema

To test a file or files against the schema, use the command:

check-jsonschema --schemafile schema/dcm/jsonschema/credit_metadata.schema.json data_file_1.json data_file_2.json

or

check-jsonschema --schemafile schema/dcm/jsonschema/credit_metadata.schema.json sample_data/**/*_dcm.json

Developers

Add pygraphviz locally with uv add

Assumes that Graphviz has been installed using Homebrew.

uv add --config-settings="--global-option=build_ext" --config-settings="--global-option=-I$(brew --prefix graphviz)/include/"  --config-settings="--global-option=-L$(brew --prefix graphviz)/lib/" pygraphviz --dev

See pygraphviz installation instructions for more information.