Changes in version 1.19.3
Bug Fixes
- Fixed issue of stoping when fetching project with tags
Changes in version 1.19.2
Improvements
- Transfer package maintainership.
Changes in version 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.
Changes in version 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.
Changes in version 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).
Changes in version 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.
Changes in version 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.
Changes in version 1.13.4
New Features
- Added support for Markers API (Advance Access feature). See the
Markers API section in the vignette for details.
- Added support for Actions API. See the Actions API section in the
vignette for details.
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).
Changes in version 1.13.3
New Features
- Added support for Enterprise API. See the Enterprise API section in
the vignette for details.
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.
Changes in version 1.13.2
New Features
- Added support for Folder API. See the Folders API section in the
vignette 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.
Changes in version 1.13.1
New Features
- Added support for setting execution hints per task run when drafting
new tasks.
Changes in version 1.11.5
Bug Fixes
- Fixed issues related to hints when creating CWL tools (#65) in
R 3.5.x.
Changes in version 1.11.4
Bug Fixes
- Fixed several compatibility issues for CWL app conversion caused by
newly introduced fields.
Changes in version 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.
Changes in version 1.11.2
Improvements
- Further remove all words related to the previous installation method
per Bioconductor's request.
Changes in version 1.11.1
Improvements
- Use the new Bioconductor package manager BiocManager for
installation instructions.
Changes in version 1.9.1
Bug Fixes
- Removed functions that prevents Shiny apps to load when the package
is loaded (#63).
Changes in version 1.7.5
Improvements
- Update rabix-cli (Bunny) to 1.0.2 for the Docker container.
Changes in version 1.7.4
Bug Fixes
- Fixed the baseCommand conversion issue (#59).
Changes in version 1.7.3
Improvements
- Use system font stack instead of Google Fonts in vignettes to avoid
pandoc SSL issue.
Changes in version 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).
Changes in version 1.7.1
New Features
- Added a new argument (global option) advance_access for enabling the
access to Advance Access features.
Changes in version 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).
Changes in version 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
Changes in version 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).
Changes in version 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)
Changes in version 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
Changes in version 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
Changes in version 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
Changes in version 1.0.0
New Features
- Initial version
- All the APIs of the SBG platform are supported
- First vignette added