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25.8.0 (LabID-PROV Workflow Run Support & UI Enhancements)

This release introduces advanced workflow management with comprehensive Workflow Run support and improved integration with WorkflowHub. Numerous user interface enhancements have been made, including online visualization for supported dataset file types.

Workflow Run Management

  • Workflow runs (WFRuns) are now fully supported for creation, viewing, and management within the UI.
  • Datasets can be linked or unlinked to WorkflowRuns as inputs, outputs, reports, configurations, or logs.
  • Workflow run metadata can be imported from Galaxy, with LabID maintaining references to the original Galaxy history and workflow invocation rather than copying datasets.
  • Workflow runs can be registered via the labid register CLI tool, simplifying imports from workflow management systems like snakemake and nextflow.
    • A generic WF run sniffer is available for pattern-based imports
    • Custom "WF run sniffers" can be plugged in to customize your needs
  • WF runs imported as RO-Crate objects have extra management safeguards to maintain RO-Crate validity over time. Connected datasets cannot be unlinked from the WF runs or deleted individually.
  • Versioned workflows can now be imported and exported with the WorkflowHub repository, and WF runs can be exported as RO-Crate objects.

Viewing Datasets online

  • The "View File" button in datafile copy detail pages and table views enables instant visualization of files with supported mime types, without requiring download.
  • Files not compatible with online viewing can be downloaded instead.

Data Management & Storage

  • S3 storage now displays HTTP URLs and allows searching by these URLs for easier data access and sharing.
  • Assay pages now offer data archiving, enabling streamlined transfer of all assay datasets to cold storage.
  • Improved handling of longer names for attachments, datafile copies, and data session directories.
  • Content types and mimetypes for datafile copies are now correctly set to ensure proper handling and visualization.
  • Fixed the ability to restore datasets and archives from detail pages.
  • Managers and data managers can register data for other users in their group using the labid register CLI tool. Registered items (datasets, assays, WF Runs, samples) are owned by the specified user, while the registering manager retains creator status and full permissions. This feature also supports automated data registration.

User Interface Improvements & Fixes

  • Menus now auto-close on mobile devices and display legacy items properly.
  • Better visual cues throughout the interface to identify deleted objects. Protocol lists now show clear indicators for deleted protocols and improved filtering options.
  • Larger text in breadcrumbs and better handling of long item names that might overflow.
  • Improved pagination controls and styling for better experience when browsing large item collections.
  • Fixed styling issues with dropdown menus and resolved associated display problems.
  • Fixed z-index issues where buttons would appear over text editor toolbars.
  • Improved error handling and redirect behavior when login errors occur.
  • Better error handling when network connection is lost, with automatic redirection to appropriate pages.
  • The system now automatically tracks when items are modified and by whom.
  • Fixed WorkflowHub URLs to properly resolve to version-specific formats.
  • Updated default email addresses to use example.com instead of embl.de for better privacy.
  • New installations now use freetsa.org as the default timestamping service.
  • Fixed site-wide search toggle and redirect behavior.
  • Resolved console errors that occurred when logging out from pages with attachments.
  • Fixed API configuration issues that affected file download functionality.

Development Experience

  • Developers now see helpful welcome messages in the browser console.