Releases: sbg/sevenbridges-r
Releases · sbg/sevenbridges-r
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 functionmisc_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 functionmisc_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 functionmisc_get_token()
is deprecated. misc_make_metadata()
is deprecated, useMetadata()
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 withlimit
,offset
; now requests on file details will usefields = "_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()
andoutput_matrix()
(2ec7c84) to extract input/output matrix from CWL JSON files directly, without converting CWL JSON toTool
orFlow
objects. This is a faster implementation compared to the old method, and more stable to custom fields.
CWL
Bug Fixes
CWL
- Fixed
filename
andfileContent
conversion toExpression
(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"
inAuth()
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
fortask_add()
added: when users push a Tool object with nosbg:job
information, can still usekeep_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
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
, andrstudioapi
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