iSkyLIMS 3.1.1

What's Changed

iSkyLIMS 3.1.1 improves API security, adds bulk sample queries and adopts the BU-ISCIII deployment standard for Docker and Podman.

Security

• Removed request-controlled eval() calls from the sample-information API. Requested fields are validated through Django's model metadata API and accessed safely.
• Updated Django, cryptography and Paramiko dependencies.

Application

• Added the sample-project-values-bulk API endpoint to retrieve selected project values for multiple RELECOV samples. #401
• Fixed SampleSheet username resolution for dash-delimited identifiers and database usernames containing dots. #396

Deployment and installation

• Adopted the BU-ISCIII deployment standard, with separate image staging and runtime bootstrap, configuration validation, readiness checks and smoke tests.
• Added protected per-service settings, generated Compose environments and externally mounted Django settings.
• Added persistent volumes for documents and static files, with rootless Podman ownership and permission repair.
• Standardized standalone service names and scoped Apache, database and configuration resources to the deployment.
• Added ordered Apache configuration generated from protected settings and configurable /server-status, restricted to localhost by default.
• Improved container healthchecks, database bootstrap, fixture loading, timezone support and host-database access.
• Fixed production file downloads through the shared documents volume.
• Improved supercronic job generation and cron status checks, including fallback when system crontab is unavailable.

Upgrading

This release changes the deployment layout and replaces legacy container and Apache configuration paths. Review the deployment runbook and installation settings before upgrading.

• Upgrades validate committed migrations before applying database migrations.
• The existing Django signing key is preserved from protected settings.
• Persistent services and application data are retained during application container rebuilds.
• Upgrades avoid implicit fixture and demo-data loads.
• Updated documentation covers backup, restore, rollback, migration verification and permission repair.

Dependencies

Package	Previous	New
biopython	1.84	1.87
cryptography	44.0.3	48.0.1
Django	4.2.28	4.2.30
paramiko	3.4.1	5.0.0

Contributors

Thanks to @saramonzon, @ESapenaVentura and @svarona.

Release PR: #412

Full Changelog: 3.1.0...3.1.1