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Changelog

Source: NEWS.md

sevenbridges 1.19.3

Bug Fixes

  • Fixed issue of stoping when fetching project with tags

sevenbridges 1.19.2

Improvements

  • Transfer package maintainership.

sevenbridges 1.19.1

Bug Fixes

  • Fixed an API issue on invalid JSON when running tasks.
  • Fixed a subtle column class mismatch issue when binding data frames since R 4.0.0.

Improvements

sevenbridges 1.17.1

Bug Fixes

  • Fix build issues in R 4.0.0, in which the the default value for stringsAsFactors is changed to FALSE. Updated the affected data.frame() calls which rely on the default automatic vector expansion behavior with explicit stringsAsFactors = TRUE.

sevenbridges 1.15.2

Improvements

  • Added a new argument authorization in Auth and api() to allow specifying the token as the access token from Seven Bridges single sign-on (SSO).

sevenbridges 1.15.1

Improvements

  • Added new fields created_by, created_on, and modified_on to the Project class following the recent API improvements. This enables better project filtering when querying projects. See the vignette for details.

sevenbridges 1.13.5

Improvements

  • Added new platform options for the recently introduced environments. Now we can choose from "aws-us", "aws-eu", "ali-cn", "cgc", "cavatica", and "f4c" in Auth() calls.

sevenbridges 1.13.4

New Features

Improvements

  • Added a new field description to the Files class following the recent API improvements.
  • Updated the API vignette to reflect the platform default setting update for spot instances (spot is now enabled by default).

sevenbridges 1.13.3

New Features

Improvements

  • Removed unnecessary package dependencies to optimize the time needed for package installation and loading.
  • New look for the documentation website with improved text readability.

sevenbridges 1.13.2

New Features

Improvements

  • Added floating TOC and changed the vignette theme for the HTML vignettes available on Bioconductor, to improve the browsing experience for long vignettes.

Bug Fixes

  • Fixed Docker image build issue and updated Bunny version.

sevenbridges 1.13.1

New Features

sevenbridges 1.11.5

Bug Fixes

  • Fixed issues related to hints when creating CWL tools (#65) in R 3.5.x.

sevenbridges 1.11.4

Bug Fixes

  • Fixed several compatibility issues for CWL app conversion caused by newly introduced fields.

sevenbridges 1.11.3

Improvements

  • Added better support for the spot instance feature, by introducing the new argument use_interruptible for project_new() and use_interruptible_instances for task_add(). This will allow users to enable/disable the spot instance feature on both the project level and individual task level. See the new section “Run tasks using spot instances” in the API vignette for details.

sevenbridges 1.11.2

Improvements

  • Further remove all words related to the previous installation method per Bioconductor’s request.

sevenbridges 1.11.1

Improvements

  • Use the new Bioconductor package manager BiocManager for installation instructions.

sevenbridges 1.9.1

Bug Fixes

  • Removed functions that prevents Shiny apps to load when the package is loaded (#63).

sevenbridges 1.7.5

Improvements

  • Update rabix-cli (Bunny) to 1.0.2 for the Docker container.

sevenbridges 1.7.4

Bug Fixes

  • Fixed the baseCommand conversion issue (#59).

sevenbridges 1.7.3

Improvements

  • Use system font stack instead of Google Fonts in vignettes to avoid pandoc SSL issue.

sevenbridges 1.7.2

Bug Fixes

  • Fixed task creation issues by introducting the new field use_interruptible_instances which supports the latest spot instance feature (ea14d5c).

sevenbridges 1.7.1

New Features

  • Added a new argument (global option) advance_access for enabling the access to Advance Access features.

sevenbridges 1.5.9

New Features

Seven Bridges Command Line Uploader Interface

With this update, users are able to download the Seven Bridges command line uploader (Java-based) for the corresponding platform, and control the command line uploader within R directly. This offers another option for uploading (large) files in addition to API file uploading. Related changes are:

For detailed usage of these functions, please check this section in the vignette.

Bug Fixes

  • Fixed task output files download issue (#52).
  • Fixed IDE Docker image build issues; removed the libssl-dev dependency; updated Dockerfile (#50).

Improvements

  • New function get_token() for getting the authentication token for different Seven Bridges platforms. The old function misc_get_token() is deprecated.
  • misc_make_metadata() is deprecated, use Metadata() for metadata constructor instead.
  • API status code has been updated to the latest version.
  • Added docker pull stats badge (#49).

sevenbridges 1.5.8

Bug Fixes

  • Fixed task creation issues introduced by the recently added field created_time in the API (#51).

  • Fixed the user configuration file path (from ~/.sevenbridges/credential to ~/.sevenbridges/credentials), following the authentication specification. Thanks: Fabian Zimmer

sevenbridges 1.5.6

Improvements

API Client

  • Added fields as query default in API calls, the same with limit, offset; now requests on file details will use fields = "_all" directly so that only one request is issued. The same applies to updating a upload logic for folder/multiple files (54488bc). Thanks: Raunaq Malhotra.

  • Added functions input_matrix() and output_matrix() (2ec7c84) to extract input/output matrix from CWL JSON files directly, without converting CWL JSON to Tool or Flow objects. This is a faster implementation compared to the old method, and more stable to custom fields.

CWL

  • Added more default SBG fields to fix conversion errors; support array type enum (79274b8, 8ff4c68).

Bug Fixes

CWL

  • Fixed filename and fileContent conversion to Expression (4c0a686).

sevenbridges 1.5.5

Improvements

API Client (Authentication)

  • Support three authentication methods: direct authentication, via environment variables, or via user configuration file. Compliant with the new API client authentication specification. Please check the latest vignette vignette("api", package = "sevenbridges") for the current authentication methods.
  • Updated platform types: now users can choose from "cgc", "aws-us", "aws-eu", "gcp", and "cavatica" in Auth() to avoid using API base URLs explicitly.
  • Removed credential information parsing when package is loaded.

API Client (Task and Upload)

  • File ID support on task input (directly) (#27)
  • New argument keep_test for task_add() added: when users push a Tool object with no sbg:job information, can still use keep_test = TRUE to keep previous test information. (#31)
  • Support manifest file upload with fitler and subsetting for uploader (#46)

Docker Image

  • Migrated Docker images to Seven Bridges Docker Hub account (#43), now users could use docker pull sevenbridges/sevenbridges-r

CWL Support

  • Improved robustness of convert_app() when a CWL JSON has more fields than defined (#44)

Miscellaneous

  • New vignette style (#38)

sevenbridges 1.5.4

Bug Fixes

  • Big fix for batch mode: (b6a91f2)
  • Bug fix in IDE Dockerfile (838856b)

Improvements

  • Decoupled Files class and (CWL) File class; updated Files class to support the latest API
  • Updated error status code to the latest version

sevenbridges 1.5.3

Bug Fixes

  • Fixed build error under Windows caused by unexpected UTF-8 characters (b03ed45)
  • Removed BiocStyle to avoid naming scheme conflicts
  • Added essential dependencies, such as miniUI, shiny, and rstudioapi to be ready for RStudio addins
  • Fixed batch mode input checking. Thanks: Fabian Zimmer

Improvements

  • New website for function references and vignettes: https://sbg.github.io/sevenbridges-r/
  • Added continuous integration (with new badge) for Windows
  • Structural and style improvements for README.md
  • General R code style improvements

sevenbridges 1.1.16

New Features

  • Full support for API V2, user-friendly call from R
  • CWL Draft 2+ generator in R, create JSON/YAML tool directly
  • 5 Vignettes added for comprehensive tutorials and reference
  • Three examples inlcuded under inst/docker for CWL app examples
  • Auth configuration file to maintain multiple platforms and user account
  • Works for multiple Seven Bridges supported platforms
  • More features like task hook function to ease the automation

sevenbridges 1.0.0

New Features

  • Initial version
  • All the APIs of the SBG platform are supported
  • First vignette added