NEWS
BaseSpaceR 1.13.1
BUG FIXES
Changed Access token and projects ID used in the vignette to reflect changes in
the permission enforcements performed by BaseSpace
BaseSpaceR 1.7
NEW FEATURES
- Improved API design and a cleaner representation of the BaseSpace Data Model.
- New countRESOURCE methods. These methods should be used to get the number of
instances of a particular resource which are visible under the current scope.
For example, the total number of Samples within a Project. Or the total number
of Files for a given AppResults.
- Improved authentication process. One can now seamlessly used the R SDK from with
Native Apps or Web Apps. New 'AppSessionAuth' class to handle the authentication
in this cases. It extends the 'AppAuth' class, by keeping track of the AppSession Id.
User-level constructors:
'authWebClient()' and
'authNativeClient()'
generator .AppSessionAuth().
- New mechanism for handling the BaseSpace server responses. 'ResponseStatus' class
is now used for tracking the HTTP/server response status and integrated in the
'AppAuth' interface. 'x$showResponse()' can now be used to print the (JSON) body
of the last response from the server.
- Integration with some Bioconductor data structures. BAM data from BaseSpace can now
be easily map to 'BamFile' objects.
SIGNIFICANT USER-VISIBLE CHANGES
- 'authenticateClient()' function remove and replaced by 'authWebClient()' and
'authNativeClient()'. 'AppAuth' instances are used for desktop Apps only.
BUG FIXES
- Minor bug fixes with the authentication process.
- Method dispatchment now works as intended for 'listFiles' and 'Files'.
BaseSpaceR 1.1
NEW FEATURES
- New high level function performOAuth() makes the App authentication easier.
- initializeAuth() now fires up a browser window and starts the OAuth v2 process.
Users can use 'useBrowser' parameter to control this behaviour.
SIGNIFICANT USER-VISIBLE CHANGES
- requestAccessToken() now returns an integer giving the status of request:
* 1 if the request was succesful and an access_token was received
* -1 if the AppAuth handle already contains a feasible access token
* An integer larger than one if the request fails.
There is also a new 'verbose' parameter controling the messages shown to
the user. By default 'verbose = TRUE'
BUG FIXES
- Added end of line character to some messages.
- fileItem$Size is now stored as a numeric, thus allowing for file larger than 2GB.
BaseSpaceR 1.0.0
PACKAGE FEATURES
- BaseSpaceR is a R SDK for Illumina's BaseSpace cloud computing environment,
enabling the rapid prototyping and development of production ready application
for next-gen sequencing data.
- It provides a set of S4 classes and methods to interface with BaseSpace data model.
- It allows for persistent connections with BaseSpace REST server and offers
support for the REST API query parameters.
- It allows for queries across multiple Projects, Samples, Files, AppResults, etc.,
using vectorized operations in line with the R semantic.