MUSIT to Specify Migration

This repository serves as a knowledge base and workspace for migrating the Norwegian MUSIT system to Specify.

Documentation

The full documentation is available in the docs/ directory. If viewing on GitHub Pages, visit the Documentation Site.

Repository Structure

• charts/: Kubernetes Helm charts (including specify7).
• config/: Configuration files (local settings).
• docs/: Knowledge base source files (Markdown).
• scripts/: Python scripts for migration logic.
• specify7/: [Submodule] Official Specify 7 repository.

Development Setup

1. Install Requirements:

   pip install -r requirements.txt

2. Configuration:

   • Copy config/local_specify_settings.py (if missing, see the template using the bootstrap.py logic) and configure your database credentials.
   • Note: config/local_specify_settings.py is git-ignored.

3. Running Scripts: Scripts in scripts/ utilize a bootstrap.py helper to load the Specify 7 environment dynamically.

   python scripts/test_setup.py
   python scripts/test_setup.py

Dev / Migration Container

For advanced debugging, database proxying, and running migration scripts inside the cluster, see the Dev Container Guide. For the current Prefect in-cluster workflow, see the Prefect Runbook.

It supports:

• Building with Podman (x86/amd64).
• Proxying Oracle and MariaDB to your local machine.
• Running scripts with full ORM access in the cluster.

Kubernetes Deployment

A custom Helm chart is provided in charts/specify7 to deploy a staging environment.

Features:

• Official Specify 7 images (no custom builds).
• Split architecture: Backend (Gunicorn) + Static Server (Nginx).
• Shared Assets via ReadWriteMany PVC.
• Integrated MariaDB (Bitnami) for self-contained staging.

Quick Start:

helm install staging ./charts/specify7

Versioning & Release

The project uses automatic semantic versioning. See Versioning and Release Process for details on how releases are cut and how the Helm chart is updated.