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)

v0.17.0

Added

• Adding incremental retry backoffs to FireCloud & GCS API errors (5 times, adds 15 sec. per retry) (#189)
  • Also includes blacklist of methods/URLs to not increment backoff in cases of UI blocking (#189)

Changed

• Refactoring UploadCleanupJob to retry pushing files to FireCloud on failure (up to 3 times over 10 minutes) (#189)
• Study.storage_sanity_check will now also push missing files using UploadCleanupJob (#189)
• Updated rack to 2.0.6 re: CVE-2018-16470/1 (#189)
• Updated Docker base image version to 1.6 (#189)
• Updated yarn to 1.12.3 (#189)

Fixed

• Fixing bug with StudyFileBundles not cleaning up after themselves on deletion of parent file (either during or after upload has completed) (#189)

v0.16.1

Fixed

• Correctly unsetting default cluster & annotation when deleting metadata or cluster files (#187)
• Fixed issue with caches not correctly clearing when changing cluster point size, border, or alpha settings (#187)

v0.16.0

Added

• Bundled files (e.g. 10X Genes/Barcodes, BAM Indexes) can now be uploaded asynchronously once parent file has begun the upload process (#184)
• Accession field for GenomeAssembly model (#186)
• Python data pipeline to process genome reference data (#183)

Changed

• Updated 'selenium-webdriver' to 3.14.1 (#184)

Fixed

• Resolved 'closed stream' issue on file localization for parsing due to GCS returning closed file handle (#184)
• Fixed range request issue on chunked downloads of files with gzip Content-Encoding from GCS (#184)

v0.15.2

Changed

• Orphaned delayed_jobs now automatically restart on daemon restart (#182)

Fixed

• Chunked downloads for parse localization no longer fail after completion with sporadic 'closed stream' error (#182)
• Re-parsing gene-barcode matrices from sync page no longer fails with erroneous 'repeated cells' validation (#182)

v0.15.1

Fixed

• Adding support for gene-barcode matrices without gene IDs in the genes file to prevent parsing failures (#180)

v0.15.0

Added

• Terms of Service (specific to Broad Institute) (#177)
• New integration tests for study administrative actions and species ingest (#176)
• Added genome annotation attributes to admin species ingest from file (#178)

Changed

• Updated Docker image to latest version of Phusion/Passenger (#176)
• Updated Ruby version to 2.5.1, including minor gem updates (#175)
• UI Regression suite can now run headlessly (#176)

Fixed

• Fix legend overlapping scatter plot (#174)

v0.14.0

Added

• Taxon, GenomeAssembly, and GenomeAnnotation models for collecting and assigning species-relating information about Study and StudyFile objects (#169)
  • Includes validations and form updates
  • Also includes administrative interface for registering approved species information
  • Migration to auto-populate default species & assemblies from a list of common research targets (#171)
• StudyFileBundle model for more robust management of files that are 'bundled' together, such as 10X gene-barcode matrix file triplets, and BAMs with index files. (#172)
• REST API (#172)
  • Rails-style resources for Study, StudyFile, StudyShare, StudyFileBundle, and DirectoryListing models
  • Swagger documentation available at https://portals.broadinstitute.org/single_cell/api

Changed

• Display "Genome" tab whenever a BAM is available (#173)
• Remove hard-coded species data in genome visualizations (#168)
• Updating google-cloud-storage gem and dependencies (now v1.14.2) (#171)

Fixed

• Renaming folders in GCP buckets no longer causes 'Sync Workspace' feature to error out (#167)

v0.13.1

Fixed

• Users not registered for FireCloud no longer experience errors when trying to add new Studies

v0.13.0

Changed

• Migrate from Sprockets to Webpack where feasible, yielding faster page loads (#164)

Fixed

• Corrected file write mode when localizing large files for parsing (#165)