# 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 - Use `data.table::rbindlist()` when possible to increase the data frame binding performance. # 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](https://sbg.github.io/sevenbridges-r/articles/api.html#filter-by-project-creation-date-modification-date-and-creator) 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 - Added support for Markers API (Advance Access feature). See the [Markers API section in the vignette](https://sbg.github.io/sevenbridges-r/articles/api.html#markers) for details. - Added support for Actions API. See the [Actions API section in the vignette](https://sbg.github.io/sevenbridges-r/articles/api.html#actions) for details. ## Improvements - Added a new field `description` to the `Files` class following the recent API improvements. - Updated the API [vignette](https://sbg.github.io/sevenbridges-r/articles/api.html#run-tasks-using-spot-instances) to reflect the platform default setting update for spot instances (spot is now enabled by default). # sevenbridges 1.13.3 ## New Features - Added support for Enterprise API. See the [Enterprise API section in the vignette](https://sbg.github.io/sevenbridges-r/articles/api.html#enterprise) for details. ## Improvements - Removed unnecessary package dependencies to optimize the time needed for package installation and loading. - New look for the [documentation website](https://sbg.github.io/sevenbridges-r/) with improved text readability. # sevenbridges 1.13.2 ## New Features - Added support for Folder API. See the [Folders API section in the vignette](https://sbg.github.io/sevenbridges-r/articles/api.html#folders) for details. ## 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 - Added support for setting [execution hints per task run](https://sbg.github.io/sevenbridges-r/articles/api.html#execution-hints-per-task-run) when drafting new tasks. # sevenbridges 1.11.5 ## Bug Fixes - Fixed issues related to hints when creating CWL tools ([#65](https://github.com/sbg/sevenbridges-r/issues/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"](https://sbg.github.io/sevenbridges-r/articles/api.html#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](https://github.com/sbg/sevenbridges-r/issues/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](https://github.com/sbg/sevenbridges-r/issues/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](https://www.sevenbridges.com/spot-instances-cost-reduction/) ([ea14d5c](https://github.com/sbg/sevenbridges-r/commit/ea14d5c6333b999e754ebb760fc93f89ecdf6019)). # 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: - New function `get_uploader()` for downloading Seven Bridges command line uploader for specific platforms. The old function `misc_get_uploader()` is deprecated. - New functions `cli_upload()`, `cli_list_projects()`, `cli_list_tags()` as the R interface for Seven Bridges command line uploader. The old function `misc_upload_cli()` is deprecated. For detailed usage of these functions, please check [this section](https://sbg.github.io/sevenbridges-r/articles/api.html#upload-files-via-command-line-uploader) in the vignette. ## Bug Fixes - Fixed task output files download issue ([#52](https://github.com/sbg/sevenbridges-r/issues/52)). - Fixed IDE Docker image build issues; removed the libssl-dev dependency; updated Dockerfile ([#50](https://github.com/sbg/sevenbridges-r/issues/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](https://github.com/sbg/sevenbridges-r/issues/49)). # sevenbridges 1.5.8 ## Bug Fixes - Fixed task creation issues introduced by the recently added field `created_time` in the API ([#51](https://github.com/sbg/sevenbridges-r/issues/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](https://github.com/sbg/sevenbridges-r/commit/54488bcaa77e999b198999e81af8c6c471908d9f)). Thanks: Raunaq Malhotra. - Added functions `input_matrix()` and `output_matrix()` ([2ec7c84](https://github.com/sbg/sevenbridges-r/commit/2ec7c84ede491e50639502ca0d34bae04c5cde8f)) 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](https://github.com/sbg/sevenbridges-r/commit/79274b8d75f838934d736c30f11da417416030c5), [8ff4c68](https://github.com/sbg/sevenbridges-r/commit/8ff4c6832e7aff63fbdeb0904d0d7f937334eb0c)). ## Bug Fixes ### CWL - Fixed `filename` and `fileContent` conversion to `Expression` ([4c0a686](https://github.com/sbg/sevenbridges-r/commit/4c0a6867b597d0c6e882ed63216c7c3882257404)). # 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](https://github.com/sbg/sevenbridges-r/issues/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](https://github.com/sbg/sevenbridges-r/issues/31)) - Support manifest file upload with fitler and subsetting for uploader ([#46](https://github.com/sbg/sevenbridges-r/issues/46)) ### Docker Image - Migrated Docker images to Seven Bridges Docker Hub account ([#43](https://github.com/sbg/sevenbridges-r/issues/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](https://github.com/sbg/sevenbridges-r/issues/44)) ### Miscellaneous - New vignette style ([#38](https://github.com/sbg/sevenbridges-r/issues/38)) # sevenbridges 1.5.4 ## Bug Fixes - Big fix for batch mode: ([b6a91f2](https://github.com/sbg/sevenbridges-r/commit/b6a91f2fbbb59cbe6dc40b63f6b7057064e25c19)) - Bug fix in IDE Dockerfile ([838856b](https://github.com/sbg/sevenbridges-r/commit/838856bd1dfb4ea8bc143f246a152deda3c76d92)) ## 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](https://github.com/sbg/sevenbridges-r/commit/b03ed45d5c9495196df311b58a2e275b3f2ea44a)) - 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