submission-schema

The home of the NMDC submission schema. Not the home of sheets_and_friends. In development: GH pages hosted NMDC DataHarmonizer interface.

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

Here's how you can update the submission schema to use a new version of nmdc-schema:

1. Update the one occurrence of the nmdc-schema version number in project.Makefile:

   local/nmdc.yaml:
   -        wget -O $@ https://raw.githubusercontent.com/microbiomedata/nmdc-schema/v11.0.1/nmdc_schema/nmdc_materialized_patterns.yaml
   +        wget -O $@ https://raw.githubusercontent.com/microbiomedata/nmdc-schema/v11.1.0/nmdc_schema/nmdc_materialized_patterns.yaml

2. Update all the nmdc-schema version numbers in sheets_and_friends/tsv_in/import_slots_regardless.tsv

   - Biosample	https://raw.githubusercontent.com/microbiomedata/nmdc-schema/v11.0.1/nmdc_schema/nmdc_materialized_patterns.yaml	abs_air_humidity ...
   + Biosample	https://raw.githubusercontent.com/microbiomedata/nmdc-schema/v11.1.0/nmdc_schema/nmdc_materialized_patterns.yaml	abs_air_humidity ...

   That is one of the many occurrences in that file.

   Note: The above search-and-replacement (of all occurrences in that file) can be done inside Vim via:

   :%s/nmdc-schema\/v11.0.1/nmdc-schema\/v11.1.0/g

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. (Optional) Delete the container image:

   docker image rm submission-schema-builder

Direct process

Prerequisites

• yq is installed on your computer, such that the following command shows a version number instead of an error message.

  bash -c 'yq --version'

  If yq is not installed, you can install it by running this, assuming you're using macOS:

  brew install yq

• wget is installed on your computer, such that the following command shows a version number instead of an error message.

  bash -c 'wget --version'

  If wget is not installed, you can install it by running this, assuming you're using macOS:

  brew install wget

Procedure

1. Install Python dependencies:

   poetry shell
   poetry install

2. Generate the release artefacts:

   make all

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

   git add .
   git commit -m "11.1.0"

Credits

this project was made with linkml-project-cookiecutter