nmdc-submission-schema 11.17.0

The NMDC submission schema

submission-schema

The NMDC submission schema.

Note that the while this repo is named submission-schema, the generated artifacts are named nmdc_submission_schema for disambiguation purposes when publishing to PyPI.

Website

• https://microbiomedata.github.io/submission-schema

Repository Structure

• examples/ - example data
• project/ - project files (do not edit these)
• src/ - source files (edit these)
  • nmdc_submission_schema
    • schema -- LinkML schema (edit this)
• datamodel -- Generated python datamodel
• tests - python tests

Developer Documentation

Updating the submission schema

The version of nmdc-schema used as a basis when building the submission schema is controlled by a dependency in the dev group, specified in pyproject.toml. You can update the version used by running:

poetry add nmdc-schema==X.Y.Z --group dev  # replace X.Y.Z with the desired version

[!NOTE]
It is important to use the == version constraint to ensure the exact version is installed.

Building the submission schema

Here's how you can generate the submission schema release artifacts:

Container-based process

Prerequisites

• Docker is installed on your computer
• You are in the root directory of the repository

Procedure

1. Build the container image you will later use to build the submission schema:

   docker build -t submission-schema-builder -f builder.Dockerfile .
   

2. Use that container image to build the submission schema:

   docker run --rm -it -v ${PWD}:/submission-schema submission-schema-builder
   

3. Commit the changes, using the new nmdc-schema version number as the commit message; like this:

   git add .
   git commit -m "X.Y.Z"  # replace X.Y.Z with the nmdc-schema version
   

4. (Optional) Delete the container image:

   docker image rm submission-schema-builder
   

Direct process

Procedure

1. Install Python dependencies:

   poetry install
   

2. Generate the release artefacts:

   make clean all
   

3. Commit the changes, using the new nmdc-schema version number as the commit message; like this:

   git add .
   git commit -m "X.Y.Z"  # replace X.Y.Z with the nmdc-schema version
   

Credits

this project was made with linkml-project-cookiecutter