mixs-source

This repo contains the draft MIxS schema for environmental packages and checklists.

Pages generated by this code will be served via https://github.com/GenomicsStandardsConsortium/gensc.github.io.

This repo may be merged with https://github.com/GenomicsStandardsConsortium/mixs

The source files are here:

• model/
  • schema/ -- schema files
    • mixs.yaml - container module
    • terms.yaml - all terms (fields/slots)
    • checklists.yaml - checklists, e.g. MIMAG
    • soil.yaml - soil package
    • ...OTHER PACKAGES HERE

These are the files that should be edited

Workflow for adding new CHECKLISTS

Edit checklists.yaml

The easiest thing to do is to copy and paste an existing checklist, modifying the values

You will need to specify both slots and slot_usage

Workflow for adding new TERMS

Edit terms.yaml

The easiest thing to do is to copy and paste an existing term, e.g.

  barometric_press:
    is_a: environment field
    aliases:
    - barometric pressure
    description: Force per unit area exerted against a surface by the weight of air
      above that surface
    range: quantity value
    examples:
    - value: 5 millibar
    comments:
    - 'Preferred unit: millibar'
    slot_uri: MIXS:0000096

The range field will be one of:

• string
• integer
• float
• quantity value
• an enum

Workflow for creating a new ENUM

TODO

Workflow for adding new ENVIRONMENTAL PACKAGES

Create a NEW file in model/schema

The easiest thing to do is to copy a

Deploying Documentation

This is currently in a different repo

There is a demo of a fork of the github pages repo with markdown generated in this repo copied over:

https://cmungall.github.io/gensc.github.io/mixs6/

We can consider merging repos, but for now these are distinct, and docs are copied from one to another like this:

make gen-docs
cp docs/*.md ../gensc.github.io/mixs6/

Seeding the schema from google sheets

An early version of terms.yaml was by converting the legacy spreadhseet for MIxS6 using mixs_converter.py. After the release of MIxS6, the yaml will switch to being Source of Truth, and there will be no need to generate from sheets.

In the interim phase, see the Makefile for details on regenerating the yaml from google sheets/excel.