R6 Class Representing Authentication Object

Authentication object with methods to access API endpoints. Every object could be requested from this Auth object and any action could start from this object using cascading style. Please check vignette("Authentication_and_Billing", package = "sevenbridges2") for more information.

Details

This is the main object for authentication to platforms powered by Seven Bridges.

Public fields

from: Authentication method.
platform: The platform to use.
url: Base URL for API.
sysenv_url: Name of the system environment variable storing the API base URL.
sysenv_token: Name of the system environment variable storing the auth token.
config_file: Location of the user configuration file.
profile_name: Profile name in the user configuration file.
fs: FS (FileSystem) object, for mount and unmount file system.
authorization: Is the token an API authentication token (FALSE) or an access token from the Seven Bridges single sign-on (TRUE)?
projects: Projects object, for accessing projects resources on the platform.
files: Files object, for accessing files resources on the platform.
apps: Apps object, for accessing apps resources on the platform.
volumes: Volumes object, for accessing volumes resources on the platform.
tasks: Tasks object, for accessing volumes resources on the platform.
imports: Storage imports object, for accessing volume imports resources on the platform.
exports: Storage exports object, for accessing volume exports resources on the platform.
invoices: Invoices object, for accessing invoice resources on the platform.
billing_groups: Billing_groups object, for accessing billing groups resources on the platform.

Methods

Method `new()`

Create a new Seven Bridges API Authentication object. All methods can be accessed through this object.

Usage

Auth$new(
  from = c("direct", "env", "file"),
  platform = NA,
  url = NA,
  token = NA,
  sysenv_url = NA,
  sysenv_token = NA,
  config_file = NA,
  profile_name = NA,
  fs = NA,
  authorization = FALSE
)

Arguments

from

Authentication method. Could be:

"direct" - pass the credential information to the arguments directly,
"env" - read from pre-set system environment variables, or
"file" - read configurations from a credentials file.

Default is "direct".

platform

The platform to use. If platform and url are both not specified, the default is "aws-us" (Seven Bridges Platform - US). Other possible values include:

"aws-eu" - Seven Bridges Platform - EU,
"cgc" - Cancer Genomics Cloud,
"ali-cn" - Seven Bridges Platform - China,
"cavatica" - Cavatica, and
"f4c" - BioData Catalyst Powered by Seven Bridges.

url

Base URL for API. Please only use this when you want to specify a platform that is not in the platform list above, and also leaving platform unspecified.

token

API authentication token or access_token for Seven Bridges single sign-on. Authentication token uniquely identifies you on the Seven Bridges Platform and has all your data access, app management and task execution permissions. Read more about its usage here.

sysenv_url

Name of the system environment variable storing the API base URL. By default: "SB_API_ENDPOINT".

sysenv_token

Name of the system environment variable storing the auth token. By default: "SB_AUTH_TOKEN".

config_file

Location of the user configuration file.
By default: "~/.sevenbridges/credentials".

profile_name

Profile name in the user configuration file. The default value is "default".

fs

FS (FileSystem) object, for mount and unmount file system.

authorization

Is the token an API authentication token (FALSE) or an access token from the Seven Bridges single sign-on (TRUE)?

Returns

Auth class object.

Examples

\dontrun{
 # Multiple ways to create Auth object

 # Using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # Authenticate using environment variables
 a <- Auth$new(from = "env")

 # Authenticate using file configuration
 a <- Auth$new(from = "file")

}

Method `get_token()`

Returns the authentication token read from system environment variable.

Usage

Auth$get_token()

Returns

An API authentication token in form of a string.

Examples

\dontrun{
 # Authenticate using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # Get that same token
 a$get_token()
}

Method `api()`

This method returns all API paths and pass arguments to core api() function.

Usage

Auth$api(
  ...,
  limit = getOption("sevenbridges2")$limit,
  offset = getOption("sevenbridges2")$offset,
  fields = "_all"
)

Arguments

...: Other arguments passed to core api() function, like path, query parameters or full url to some resource.
limit: The maximum number of collection items to return for a single request. Minimum value is 1. The maximum value is 100 and the default value is 50. This is a pagination-specific attribute.
offset: The zero-based starting index in the entire collection of the first item to return. The default value is 0. This is a pagination-specific attribute.
fields: Selector specifying a subset of fields to include in the response. This parameter enables you to specify the fields you want to be returned when listing resources (e.g. all your projects) or getting details of a specific resource (e.g. a given project).

For example, fields="id,name,size" to return the fields id, name and size for files. Default value is set to _all, so all fields are always returned for each resource. More details please check general API documentation.

Examples

\dontrun{
 # Authenticate using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # Create API request using request parameters directly
 a$api(params)
}

Method `user()`

Get details about the authenticated user.

Usage

Auth$user(username = NULL)

Arguments

username: The username of a user for whom you want to get basic account information. If not provided, information about the currently authenticated user will be returned.

Returns

User class object.

Examples

\dontrun{
 # Authenticate using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # Get information about the currently authenticated user
 a$user()
}

Method `rate_limit()`

Get information about current rate limit.

This call returns information about your current rate limit. This is the number of API calls you can make in one hour. This call also returns information about your current instance limit.

Usage

Auth$rate_limit()

Examples

\dontrun{
 # Authenticate using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # Get current rate limit
 a$rate_limit()
}

Method `upload()`

This method allows you to upload a single file from your local computer to the Platform.

Usage

Auth$upload(
  path,
  project = NULL,
  parent = NULL,
  filename = NULL,
  overwrite = FALSE,
  part_size = getOption("sevenbridges2")$RECOMMENDED_PART_SIZE,
  init = FALSE
)

Arguments

path: File path on local disk.
project: Project object or its ID. Project should not be used together with parent. If parent is used, the call will upload the file to the specified Platform folder, within the project to which the folder belongs. If project is used, the call will upload the file to the root of the project's files.
parent: Parent folder object (of File class) or its ID. Should not be used together with project. If parent is used, the call will upload the file to the specified Platform folder, within the project to which the folder belongs. If project is used, the call will upload the file to the root of the project's files.
filename: Optional new file name. By default the uploaded file will have the same name as the original file provided with the path parameter. If its name will not change, omit this key.
overwrite: In case there is already a file with the same name in the selected platform project or folder, this option allows you to control whether that file will be overwritten or not. If overwrite is set to TRUE and a file already exists under the name specified in the request, the existing file will be deleted and a new one created in its place.
part_size: The preferred size for upload parts in bytes. If omitted or set to a value that is incompatible with the cloud storage provider, a default value will be used.
init: If TRUE, the method will initialize and return the Upload object and stop. If FALSE, the method will return the Upload object and start the upload process immediately.

Examples

\dontrun{
 # Authenticate using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # Create upload job and set destination project
 upload_job <- a$upload(
   path = "/path/to/your/file.txt",
   project = destination_project,
   overwrite = TRUE,
   init = TRUE
 )
}

Method `list_ongoing_uploads()`

This method returns the list of all ongoing uploads.

Usage

Auth$list_ongoing_uploads()

Examples

\dontrun{
 # Authenticate using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # List ongoing uploads
 a$list_ongoing_uploads()
}

Method `upload_abort()`

This call aborts an ongoing multipart upload.

Usage

Auth$upload_abort(upload_id)

Arguments

upload_id: Upload object or ID of the upload process that you want to abort.

Examples

\dontrun{
 # Authenticate using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # Abort upload
 a$abort_upload(upload_id = "<id_of_the_upload_process>")
}

Method `send_feedback()`

Send feedback to Seven Bridges.

Send feedback on ideas, thoughts, and problems via the sevenbridges2 API package with three available types: idea, thought, and problem. You can send one feedback item per minute.

Usage

Auth$send_feedback(
  text,
  type = c("idea", "thought", "problem"),
  referrer = NULL
)

Arguments

text: Specifies the content for the feedback i.e. feedback text.
type: Specifies the type of feedback. The following are available: idea, thought and problem.
referrer: The name of the person submitting the feedback.

Examples

\dontrun{
 # Authenticate using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # Send feedback
 a$send_feedback(
  "This is a test for sending feedback via API.",
  type = "thought"
 )
}

Method `clone()`

The objects of this class are cloneable with this method.

Usage

Auth$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Examples


## ------------------------------------------------
## Method `Auth$new`
## ------------------------------------------------

if (FALSE) {
 # Multiple ways to create Auth object

 # Using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # Authenticate using environment variables
 a <- Auth$new(from = "env")

 # Authenticate using file configuration
 a <- Auth$new(from = "file")

}

## ------------------------------------------------
## Method `Auth$get_token`
## ------------------------------------------------

if (FALSE) {
 # Authenticate using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # Get that same token
 a$get_token()
}


## ------------------------------------------------
## Method `Auth$api`
## ------------------------------------------------

if (FALSE) {
 # Authenticate using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # Create API request using request parameters directly
 a$api(params)
}


## ------------------------------------------------
## Method `Auth$user`
## ------------------------------------------------

if (FALSE) {
 # Authenticate using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # Get information about the currently authenticated user
 a$user()
}

## ------------------------------------------------
## Method `Auth$rate_limit`
## ------------------------------------------------

if (FALSE) {
 # Authenticate using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # Get current rate limit
 a$rate_limit()
}


## ------------------------------------------------
## Method `Auth$upload`
## ------------------------------------------------

if (FALSE) {
 # Authenticate using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # Create upload job and set destination project
 upload_job <- a$upload(
   path = "/path/to/your/file.txt",
   project = destination_project,
   overwrite = TRUE,
   init = TRUE
 )
}

## ------------------------------------------------
## Method `Auth$list_ongoing_uploads`
## ------------------------------------------------

if (FALSE) {
 # Authenticate using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # List ongoing uploads
 a$list_ongoing_uploads()
}

## ------------------------------------------------
## Method `Auth$upload_abort`
## ------------------------------------------------

if (FALSE) {
 # Authenticate using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # Abort upload
 a$abort_upload(upload_id = "<id_of_the_upload_process>")
}

## ------------------------------------------------
## Method `Auth$send_feedback`
## ------------------------------------------------

if (FALSE) {
 # Authenticate using authentication token
 a <- Auth$new(
  token = "<your_token>",
  platform = "aws-us"
 )

 # Send feedback
 a$send_feedback(
  "This is a test for sending feedback via API.",
  type = "thought"
 )
}

R6 Class Representing Authentication Object

Details

Public fields

Methods

Public methods

Method new()

Usage

Arguments

Returns

Examples

Method get_token()

Usage

Returns

Examples

Method api()

Usage

Arguments

Examples

Method user()

Usage

Arguments

Returns

Examples

Method rate_limit()

Usage

Examples

Method upload()

Usage

Arguments

Examples

Method list_ongoing_uploads()

Usage

Examples

Method upload_abort()

Usage

Arguments

Examples

Method send_feedback()

Usage

Arguments

Examples

Method clone()

Usage

Arguments

Examples

Method `new()`

Method `get_token()`

Method `api()`

Method `user()`

Method `rate_limit()`

Method `upload()`

Method `list_ongoing_uploads()`

Method `upload_abort()`

Method `send_feedback()`

Method `clone()`