v0.12.1

Changed

• Upping Delayed::Worker.max_run_time to 12 hours

Fixed

• Resolving issue with chunked downloads not opening tempfiles in correct mode of 'wb'

v0.12.0

Added

• FireCloud API status checks now gracefully degrade portal functionality based on affected systems, rather than disabling all study administrative functionality & downloads (#156)
• Gene ID attribute (gene_id) to Gene model (#160)
  • Searching for genes now works with either names/symbols or gene IDs

Changed

• Improved performance on MM Coordinate Matrix parsing (#158)
  • Requires matrices to be sorted by gene indices, see here for more information
  • Syncing submission outputs from Cell Ranger WDL submissions now defaults to sorted matrices (#159)
• FireCloudClient#download_workspace_file will now perform chunked downloads on any file > 100MB when localizing to the portal for parsing (#154)
  • Uses range requests and appends output buffer to local file
  • Files under 100MB download normally as single chunk
• Global gene search results are now paginated to improve browser performance (#161)
• Updating to Plotly 1.39.3 (#156)
• Changing cluster point defaults to 3px, no borders

Fixed

• sync buttons not disabling when selecting bundled file types on study sync page(will re-enable when a bundle target is selected) (#154)
• DelayedJob deserialization error when unlocking locked jobs (#154)
• secret_key_base missing from cron environment files (#154)
• non-delivery of delayed_job_email when processes die and restart (#154)
• IGV.js error with connect-src CSP header (#154)
• Error when merging optional workflow submission parameters from study Analysis tab (#157)
• Error in DeleteQueueJob trying to call set_readonly_access on studies queued for deletion (#158)

v0.11.0

Added

• Improved igv.js integration:
  • Add genome browser to single- and multi-gene views (#140)
  • Show introns and untranslated regions (UTRs) in each gene model (#146)
  • Visually hint at the existence of more transcript models when available (#146)
  • Prevent adding duplicate BAM tracks (#146)
  • Remove default genes track, which is redundant with ours (#146)
• Global gene search to home page (#145, #148)
  • Returns violin plots for all viewable studies that contain the gene(s) queried for
• Additional content format validators, including FireCloudProfile ActiveModel (#139)
• Updated Content Security Policy header to include nonce-based JS (#143)

Changed

• Updated to Rails 5.2.0, Plotly 1.39.2, and CKEditor 5 (#141)
  • Includes global gem updates to support Rails version increase
  • Temporarily removing image upload capability in CKEditor instances
• Remove nmatrix gem, now parsing MM coordinate matrices natively as regular text files (#142)
• Decreased size of gene list in ParseUtilsTest from 33K to 100 to reduce runtime of unit tests (#141)

Fixed

• Updated associations in db/seeds.rb to conform to Rails 5.2 standards (belongs_to relationships can no longer be blank) (#141)

v0.10.2

Fixed

• Corrected typo in FireCloudClient#get_user_groups

v0.10.1

Changed

• Using absolute file path to service account credentials in FireCloudClient.initialize

Fixed

• Corrected issue with FireCloudClient not being able to access service account credentials JSON files from cron or delayed_job environments.

v0.10.0

Added

• New StudyFile types: BAM, BAM Index (#136)
• IGV.js for browsing BAM files (#136)
• Read-only service account access to public studies for rendering GCS objects client-side (#136)
  • Requires creation of a GCP service account with 'Storage Object Viewer' role
  • READ_ONLY_SERVICE_ACCOUNT_KEY environment variable for storing read-only service account credentials
  • Accessible from Study.read_only_client class instance variable
  • Makes client-side rendering for Ideogram.js & IGV.js more performant and scalable
• AdminConfiguration functionality for setting read-only access on public studies (#136)
• Support for uploading 10X Gene-barcode matrices through upload wizard (will automatically associate genes & barcodes files with MM coordinate matrix) (#136)

Changed

• FireCloudClient class now accepts service account credentials filepath as part of constructor (required for READ_ONLY_SERVICE_ACCOUNT_KEY support) (#136)
• Added devstorage.read_only scope to OAuth2 to permit reading of cloud storage assets (may require re-verification of OAuth2 client, see https://support.google.com/code/contact/oauth_app_verification for more information) (#136)

v0.9.2

Fixed

• Fixed bug with users who were not registered for FireCloud being unable to log in (broadinstitute/single_cell_portal#22)

v0.9.1

Fixed

• Updated content validators for study files to be slightly more permissive for names/labels

v0.9.0

Added

• Studies can now be shared with FireCloud user groups. Users in the specified groups will be able to view portal studies, their associated FireCloud workspaces, and GCS buckets. (#125)
• Condensed bundle of Morpheus.js dependencies (morpheus-external-r.js) (#125)
• Content format validators for all string-based model attributes that are set via forms, as well as study & gene search forms (#125)

Changed

• Updated to jquery 3.3.1, latest version of Morpheus.js
  • Removed individual Morpheus.js external dependencies (#125)
• Setting cluster point size per trace via the marker.size attribute, rather than marker_size array to more faithfully honor point size on 3d clusters (#125)
  • Also fixes issue with OSX High Sierra not properly rendering multi-trace Plotly scatter plots
• Violin plots now use native Plotly 'violin' chart type (#125)
• Main study scatter plots now auto-size to available window viewport (#125)
• User annotation creation leaves 2d scatter plots in 'scattergl' mode rather than replotting in non-gl mode
• Updated gem sprockets re: CVE-2018-3760 (#127)

Fixed

• Prevent users from changing FireCloud attributes (project & workspace) for existing studies (#125)
• Fixed issue with data points dropdown selector for box plots from not rendering/working (#125)
• User annotation form delete button now removes correct label (#125)
• Updating user annotations no longer causes source annotation to lose associations with any subsamples (if points > 1000) (#125)

v0.8.1

Fixed

• Corrected branding group query parameter name when paginating studies on home page (#118)