OpenCloning_LinkML

A LinkML data model for OpenCloning, a standardized schema for describing molecular cloning strategies and DNA assembly protocols.

Website

You can access the model documentation at https://opencloning.github.io/OpenCloning_LinkML

Migration from previous versions of the schema

If you have json files in older formats, you can migrate them to the latest version using the migrate command:

python -m opencloning_linkml.migrations.migrate file.json

This will create a new file with the same name but with the suffix _backup.json with the original data, and overwrite the original file with the migrated data.

You can also specify a target version to migrate to:

python -m opencloning_linkml.migrations.migrate file.json --target-version 0.2.9

And you can skip the backup (simply edit in place):

python -m opencloning_linkml.migrations.migrate file.json --no-backup

Developer Documentation

The python package can be installed from PyPI:

pip install opencloning-linkml

Use the `make` command to generate project artefacts:

• make all: make everything
• make deploy: deploys site

Creating a migration

To add a migration from version X.Y.Z to a new version A.B.C, follow these steps:

1. Archive the current model: Save a copy of the current Pydantic model to src/opencloning_linkml/migrations/model_archive/vA_B_C.py. This file should contain the complete model classes for version A.B.C (typically copied from src/opencloning_linkml/datamodel/_models.py after generating the new version).

2. Create the transformation file: Create a new file src/opencloning_linkml/migrations/transformations/vX_Y_Z_to_vA_B_C.py with a migration function

3. Register the migration: Add the migration to src/opencloning_linkml/migrations/__init__.py:

   • Import the migration function: from .transformations.vX_Y_Z_to_vA_B_C import migrate_X_Y_Z_to_A_B_C
   • Add it to the load_migrations() return dictionary: ("X.Y.Z", "A.B.C"): migrate_X_Y_Z_to_A_B_C

4. Add a test: Add a test to tests/test_migration.py to ensure the migration works as expected.

Example: See v0_2_8_to_v0_2_9.py for a simple transformation example, or v0_2_9_to_v_0_4_0.py for a more complex migration with ID remapping and structural changes.

Credits

This project was made with linkml-project-cookiecutter.