extension-ancient

A MIxS extension proposal for 'radiocarbon dating' information.

Repository Structure

The repo is laid out as follows:

• feedback/
  • <date>-<eventid>: contains collated tables from community feedback sessions
• proposals/
  • <upcoming version>: contains consensus term update proposals for inclusion in the next version of the standard
• project/:
  • class-model-tsvs/: contains MIxS <= v5 style TSVs for the extension for more-human readable inspection
• scripts/: contains various helper scripts for processing JSON, YAML, and feedback data where necessary
• src/
  • mixs/: contains the structured YAML and JSON files of the latest release of the extension
• template/: contains a basic template for any YAML extension within MInAS

Technical notes

Use the YAML (in as far as possible similar format as MIxS LinkML structure) as the source of truth.

JSON Conversion

To generate the JSON version, install LinkML

pip install linkml

And run the following command, assuming root of repo:

gen-json-schema src/mixs/schema/radiocarbon-dating.yml > src/mixs/schema/radiocarbon-dating.json

MIxS TSV Style Conversion

To convert to the original MIxS TSV style, we can use a script developed by @TurboMam.

This script has been copied and modified very slightly to include the python3 shebang, and is placed under scripts until properly packaged for the MIxS project.

To use this script, you only need python3 and no other dependencies (it seems).

In the root of this directory run:

./scripts/linkml2class_tsvs.py --schema-file src/mixs/schema/radiocarbon-dating.yml --output-dir project/class-model-tsvs/