v0.6.0

Added

• WorkflowConfiguration support for Smart-seq2 WDL pipeline (#102)

Changed

• Automatically adding project owner permissions for portal service account on FireCloud projects created outside of the portal when creating studies (#102)
• Docker image now supports version numbers, will default to 'latest' (#102)

Fixed

• Preventing users from changing FireCloud project references to existing studies (#102)

v0.5.0

Added

• Configurable branding groups to apply a custom look & feel to groups of studies, including scoping search and discovery (#99, #100)

Changed

• Clicking 'Sign In' now initiates authentication handshake immediately rather than requiring the user to click the 'Sign in with Google' button (#99)

v0.4.0

Added

• New files types to support 10X Genomics analyses (Matrix Market Coordinate formatted expression matrices, plus gene and barcode list files) (#97)
• Specialized 'sync' functionality for analysis workflow outputs (#97)

Changed

• Consolidating JS functions for study file sync forms into shared template (#97)
• Updating WorkflowConfiguration class to support most recent CellRanger WDL (single-cell-portal/cell-ranger-2-0-2 v3) (#97)

Fixed

• Corrected bug with deleting workspace submissions failing due to deserialization error of 'Google::Cloud::Storage::File::List' objects, job now runs in foreground instead. (#97)

v0.3.3

Changed

• Updating WorkflowConfiguration for release of CellRanger WDL pipeline (#93)

Fixed

• Fixed erroneous associations when parsing metadata files > 100K cells (#94)

v0.3.2

Added

• Migration to generate cell name lists for all previously parsed expression matrices (used for validation purposes) (#92)

Changed

• Model association queries now lazy-load where applicable (#92)
• Updated paperclip gem to 5.2.1 re: vulnerability report (#92), see thoughtbot/paperclip#2530

Fixed

• Corrected reference error when generating subsampled data_arrays for cluster_groups (had used old study_metadata collection, now correctly uses cell_metadata collection) (#92)

v0.3.1

Fixed

• Refining query in ClusterGroup#concatenate_data_arrays to prevent overplotting of points (#90)

v0.3.0

Added

• New data models (Gene, CellMetadatum) that leverage DataArrays for storage of gene expression and cell annotations, respectively. Improves data scaling where study cell counts > 100K cells. (#84)

Changed

• DataArray is now a polymorphic association for Studies, ClusterGroups, Genes, and CellMetadata (#84)
• Preserve panel toggle state for Search Options and View Options between searches (#83)
• Enable gene search by Enter key (#85)
• Responsive layout for View Options panel (#86)

Fixed

• Scatter/Distribution plot legends no longer cover plot area at smaller viewport sizes (#82)

v0.2.0

Added

• 'Reviewer' share permission for studies (user can view a private study in the portal, but cannot edit or download data either in portal or FireCloud/Google bucket)

Changed

• 'Search Genes' interface now collapses by default
• AdminConfiguration.check_api_health will now automatically recover after an API outage occurs
• Plotly.js version incrementing to 1.33.1
• StudyFiles can no longer be deleted while in the middle of parsing
• StudyFiles upload into unique subdirectories inside their parent study's data directory while parsing

Fixed

• Wizard uploader now correctly detects duplicate files before uploading

v0.1.1

Changed

• StudyMetadatum::MAX_ENTRIES increasing to 10M to address bug with studies that have > 100K cells

v0.1.0

This is the beginning of implementing release tags for Single Cell Portal releases.

Added

• New workflow analysis metadata objects in HCA analysis.json format. Currently being used in the portal as a machine-readable workflow log.

Changed

• Global gem version updates
• Backdating plotly.js version to 1.31 due to rendering bugs with 1.33 release
• Improving default drag mode to "lasso" in Create Annotations

Fixed

• Fixing delete button and small layout issue in Create Annotations