v0.23.1

Fixed

• Ideogram Annotations can now be associated with Genome Assemblies (#215)
• Corrected issue with GCS api_urls for files in subfolders (#215)
• Updating/Syncing study files will now invalidate associated caches by default (#216)
• AnalysisParameters now support optional WDL parameters (#218)

v0.23.0

Added

• StudyAccessions - permanent accessions used to generate stable, shareable links to studies that are not editable or reusable (#212)
• Study object is now a data source for AnalysisParameters (#213)
• Promoted Ideogram Annotations to first-class study file type (#213)

Changed

• Study URLs now include accession & url_safe_name (#212)

Fixed

v0.22.0

Added

• AnalysisConfigurations (#209, #203)
  • New class used to store input/output parameter definitions for WDL workflows in the FireCloud methods repository
  • Allows portal administrators to dynamically enable new analyses in the portal without writing and deploying new code
  • Can be used to dynamically generate user interfaces for both submitting analyses and synchronizing successful submissions, including setting StudyFile attributes and associations.
  • Leverages child models AnalysisParameter, AnalysisParameterFilter, and AnalysisOutputAssociation

Changed

• Updated lodash re: CVE-2018-16487 (#209)
• Removed deprecated WorfklowConfiguration class (#209)

Fixed

• Cluster subsampling selection persists when changing clusters (#208)

v0.21.1

Fixed

• Correctly rendering default images for branding groups that have not added banner/footer images

v0.21.0

Added

• Banner & footer images to Branding Groups for enhanced homepage customization (#205)

Changed

• Gem updates:
  • omniauth-google-oauth2 (0.6.0) re: Google+ API shutddown
• StudyShare validations now abort and return immediately if email format is invalid (#204)

Fixed

• Branding Group is now persisted when clicking study links from search results (#205)

v0.20.0

Added

Changed

• Refactored FireCloudClient retry logic & response/error handling (#201)
  • Only retry certain errors based on HTTP status code
  • Refined response handling & parsing
  • Only report errors externally on final error instance (5th retry)

Fixed

• Fixed bug with FireCloud user group shares not being checked when trying to bulk download study data (#201)

v0.19.0

Added

• Sentry integration for external error reporting (#199)
  • ErrorTracker module for formatting error context and reporting via Raven
• Tcell Web Application Firewall integration (#199)
• x-app-id and x-domain-id headers to all API calls to FireCloud (#199)
• Environment variables to bin/boot_docker support Sentry & Tcell integrations (#199)
  • Integration is not required for functionality, will silently deactivate if not provided
• Enable viewing all ideogram tracks at once (#198)

Changed

• Updated rails & dependencies to 5.2.2 due to CVE-2018-16477 and CVE-2018-16476 (#199)
• Updated webpack-dev-server to 3.1.11 due to CVE-2018-14732 (#199)
• bin/run_unit_tests now returns correct exit codes on failure states (#199)
• Added PORTAL_NAMESPACE environment variable to govern default FireCloud billing project (needs to be set at boot time) (#199)

Fixed

• Fixed spurious errors from test/integration/fire_cloud_client_test.rb#test_manage_workspace_configurations when configurations are unavailable (#199)

v0.18.2

Patch layout bug in viewports less than 1200 px (#197)

v0.18.1

Fixed

• Removing unused parameter in WorkflowConfiguration.get_additional_parameters (#196)

v0.18.0

Added

• New base branding styles, including new logo (#191)
• Integration for inferCNV alpha analysis (#193)
  • Extractor mechanism for .zip & .tar.gz archives
  • Cluster- & annotation-specific loading of Ideogram heatmaps
• inferCNV alpha workflow (#193)
  • Show inferCNV results for all applicable clusters and cell annotations
  • Align colors for gain and loss with those used by inferCNV
  • Refine Ideogram heatmap thresholds to better align with inferCNV
  • Pull in refined algorithm to summarize gene expression
  • Pull in upstream Ideogram.js improvements: annotation legends, heatmap track filtering, scrollable layout
• Continuous integration via Travis (#194)
• API Status endpoint (#194)