Integrate the iRODS file source to support a new remote repository connection

[fairytalesbykcc]

Summary

This PR introduces iRODS as a remote repository backend for Galaxy, supporting template-driven onboarding and data lifecycle workflows.

Key Results

• Integrated iRODS Support: Implemented a new Remote File Source plugin allowing iRODS collections to be mounted as browsable repositories.
• Flexible Configuration: Supports connection via default YAML configuration or project-specific paths.
• User-Level Provisioning: Users can now create and manage their own iRODS-backed access paths via the "Manage Repositories" interface.
• Verified Data Paths: Confirmed successful Read/Write operations.
• Workflow Compatibility: Enabled Galaxy History Import/Export directly through iRODS file source paths.

Technical Implementation

Backend Logic irods.py

• Defined the iRODS file source data structures for consistent metadata handling.
• Implemented _open_fs to manage the connection lifecycle, including session construction and timeout handling.
• Overrode the _list function to correctly resolve and parse absolute logical paths from the iRODS filesystem (supporting both recursive and non-recursive traversal).

Data Models model.py

• Extended template models to include iRODS as a file source type.
• Added iRODS configuration schemas to the type-discriminated union for system-wide recognition.

Configuration & Templates irods.yml

• Created a YAML template defining the required fields for session creation.

Testing Suite test_irods.py

• Unit Tests: Used "fake" sessions and filesystem objects to verify plugin registration and configuration logic.
• Integration Tests: Performed live connectivity smoke tests, path listing validation, and read/write verification.
• Test Ergonomics: Added environment-driven settings and automated cleanup to ensure tests are reproducible and non-destructive.

Galaxy Interface

How to test the changes?

• I've included appropriate automated tests.

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.