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 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 (c6c4245)
• Added essential dependencies, such as miniUI, shiny, and rstudioapi to be ready for RStudio addins
• Removed BiocStyle to avoid naming scheme conflicts
• 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 1.3.8

v1.3.8

version bump

sevenbridges 1.3.7

v1.3.7

bump versino, also udpate bioc