Biospex

Overview

Biospex is a Laravel-based web application for managing biodiversity specimen data and citizen science projects. The platform integrates with Zooniverse for crowdsourced transcription, supports automated OCR processing, and provides comprehensive data export capabilities.

Features

• Citizen Science Integration: Seamlessly connects with Zooniverse platform for specimen transcription
• Automated OCR Processing: AWS Lambda-based OCR for specimen label extraction
• Data Management: Import, export, and reconciliation of biodiversity specimen data
• Queue Processing: Background job processing for large-scale operations
• Multi-Environment Support: Separate development and production configurations

Deployment

This project deploys with GitHub Actions and Deployer 8.

Quick Deployment Commands

Production deploys automatically when main changes (normally by merging a development → main PR). The workflow calculates the next version, deploys, and creates a GitHub release:

git push origin main

Development does not deploy on push. Run the workflow manually on the development branch, either from the Actions tab (Build and Deploy → Run workflow → development) or with the GitHub CLI:

gh workflow run "Build and Deploy" --ref development

Skip deployment for a push to main by adding [skip deploy] or [no deploy] to the commit message:

git commit -m "Update documentation [skip deploy]"

From your machine (needs the deploy key), deploy either environment directly:

dep deploy production
dep deploy development

For the full deployment process, environment configuration (.env comes from AWS SSM through the shared deployer-recipes env:ssm task), and operations, see docs/operations.md and the rest of docs/.

Key Features

• ✅ CI/CD Artifacts: Assets built in GitHub Actions, no server-side building
• ✅ Queue Safety: Automatic job checking prevents interruption of active tasks
• ✅ Environment Isolation: Separate queue names for development vs production
• ✅ Skip Deployment: Use [skip deploy] in commit messages to push without deploying

Detailed Setup & Configuration

For complete deployment setup, troubleshooting, and advanced configuration:
👉 See DEPLOYMENT_SETUP.md

The detailed guide covers:

• GitHub token configuration
• CI/CD workflow explanation
• Queue configuration and environment variables
• Troubleshooting common deployment issues
• Testing procedures and best practices

License

Biospex is open-sourced software licensed under GNU General Public License v3.0.

Translation

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