Before you can interact with the API, you need to construct an
Auth object which stores the following information:
The approach for obtaining the authentication token also applies to the other Seven Bridges platforms.
The general authentication logic for Auth$new() is as
follows:
from parameter is not specified explicitly or is specified
as from = "direct.from = "env", or user
configuration file when from = "file".To use direct authentication, users need to specify one of
platform or url, with the corresponding
token. Examples of direct authentication:
# Direct authentication with setting platform parameter
a <- Auth$new(
token = "<your_token>",
platform = "aws-us"
)The above will use the Seven Bridges Platform on AWS (US).
# Direct authentication with setting url parameter
a <- Auth$new(
token = "<your_token>",
url = "https://api.sb.biodatacatalyst.nhlbi.nih.gov/v2/"
)The above will use the specified url as the base URL for
the API calls. In this example, the url points to BioData
Catalyst powered by Seven Bridges.
# Direct authentication on default aws-us platform
a <- Auth$new(token = "<your_token>")The above will use the Seven Bridges Platform on AWS since neither
platform nor url was explicitly specified.
Note: platform and
url should not be specified at the same time.
The R API client supports reading authentication information stored in system environment variables.
To set the two environment variables in your system, use the function
sbg_set_env(). For example:
# Set environment variables
sevenbridges2:::sbg_set_env(
url = "https://cgc-api.sbgenomics.com/v2",
token = "<your_token>"
)You can check whether the environment variables are correctly set:
# Check environment variables
sevenbridges2:::sbg_get_env("SB_API_ENDPOINT")
## "https://cgc-api.sbgenomics.com/v2"
sevenbridges2:::sbg_get_env("SB_AUTH_TOKEN")
## "<your_token>"Now you can create the Auth object:
# Authenticate using environment variables
a <- Auth$new(from = "env")To unset the two environment variables:
# Unset environment variables
Sys.unsetenv("SB_API_ENDPOINT")
Sys.unsetenv("SB_AUTH_TOKEN")If you need to be logged into multiple accounts at the same time it is essential that you provide environment variables for each of the accounts. Of course, these variables must have different names.
If you do not have pre-set environment variables, you can create them in the following way:
# Set environment variables for the first account
sevenbridges2:::sbg_set_env(
url = "https://api.sbgenomics.com/v2",
token = "<your_token>",
sysenv_url_name = "account_1_url",
sysenv_token_name = "account_1_token"
)
# Set environment variables for the second account
sevenbridges2:::sbg_set_env(
url = "https://api.sb.biodatacatalyst.nhlbi.nih.gov/v2/",
token = "<your_token>",
sysenv_url_name = "account_2_url",
sysenv_token_name = "account_2_token"
)Now you are ready to create an authentication object for these two accounts:
# Authenticate using the first account
a <- sevenbridges2::Auth$new(
from = "env",
sysenv_url = "account_1_url",
sysenv_token = "account_1_token"
)
# Authenticate using the second account
b <- sevenbridges2::Auth$new(
from = "env",
sysenv_url = "account_2_url",
sysenv_token = "account_2_token"
)You can create an ini-like file named credentials under
the folder $HOME/.sevenbridges/ and maintain your
credentials for multiple accounts across various Seven Bridges
environments. An example:
[aws-us-rfranklin]
api_endpoint = https://api.sbgenomics.com/v2
auth_token = token_for_this_user
# This is a comment:
# another user on the same platform
[aws-us-rosalind-franklin]
api_endpoint = https://api.sbgenomics.com/v2
auth_token = token_for_this_user
[default]
api_endpoint = https://cgc-api.sbgenomics.com/v2
auth_token = token_for_this_user
[bdc]
api_endpoint = https://api.sb.biodatacatalyst.nhlbi.nih.gov/v2/
auth_token = token_for_this_userPlease make sure to have two fields named exactly as
api_endpoint and auth_token under each
profile.
To load the default profile (named [default]) from the
default user configuration file
($HOME/.sevenbridges/credentials), please use:
# Authenticate using file configuration
a <- Auth$new(from = "file")To load the user profile aws-us-<username> from
this configuration file, change the profile_name:
# Authenticate using file configuration and specific profile
a <- Auth$new(from = "file", profile_name = "aws-us-<username>")To use a user configuration file from other locations (not
recommended), please specify the file path using the argument
config_file. For example:
# Authenticate using specific file configuration on custom path
a <- Auth$new(
from = "file", config_file = "~/sevenbridges.cfg",
profile_name = "aws-us-<username>"
)Note: If you edited the
credentials file, please use Auth$new() to
re-authenticate.
Similar to offset and limit, every API call
accepts an argument named advance_access. This argument was
first introduced in August 2017 and controls if a special field in the
HTTP request header will be sent, which can enable access to the
“Advance Access” features in the Seven Bridges API.
In addition to modifying each API call that uses Advance Access features, the option can also be set globally at the beginning of your API script. This offers a one-button switch for users who want to experiment with Advance Access features. The option is disabled by default:
# Load package and check advance access option
library("sevenbridges2")
getOption("sevenbridges2")$advance_access## [1] FALSEFor example, if we try to use the Markers API to list markers
available on a BAM file with the advance_access option
disabled, it will return an error message:
# Authenticate first
a <- Auth$new(token = "<your_token>", platform = "aws-us")
# Try to send request to list markers
req <- a$api(
path = "genome/markers?file={bam_file_id}",
method = "GET"
)## !HTTP Status 400: Advance access feature needs X-SBG-Advance-Access: advance header.To enable the Advance Access features, one can use
# Enable advance access option
opt <- getOption("sevenbridges2")
opt$advance_access <- TRUE
options(sevenbridges2 = opt)at the beginning of their scripts. Let’s check if the option has been enabled:
# Check advance_access option again
getOption("sevenbridges2")$advance_access## [1] TRUESend the API call again:
# Send request again to list markers
req <- a$api(
path = "genome/markers?file={bam_file_id}",
method = "GET"
)The information on the markers available on that BAM file will be returned:
# Read content
httr::content(req)$href
[1] "https://api.sbgenomics.com/v2/genome/markers?file={bam_file_id}&offset=0&limit=50"
$items
$items[[1]]
$items[[1]]$href
[1] "https://api.sbgenomics.com/v2/genome/markers/{bam_file_id}"
$items[[1]]$id
[1] "{bam_file_id}"
$items[[1]]$name
[1] "Marker Title"
$items[[2]]
$items[[2]]$href
[1] "https://api.sbgenomics.com/v2/genome/markers/{bam_file_id}"
$items[[2]]$id
[1] "{bam_file_id}"
$items[[2]]$name
[1] "Marker Title"
$links
list()fieldsAll API calls take the optional query parameter fields.
This parameter enables you to specify the fields you want to be returned
when listing resources (e.g., all your projects) or getting details of a
specific resource (e.g., a given project).
The fields parameter can be used in the following
ways:
No fields parameter specified: returns all
fields for each resource returned (TBD for Apps).
The fields parameter can be set to a list of fields.
For example, to return a field’s id, name and size for files in a
project, you may issue the call
p$list_files(fields = c("id" ,"name", "size")).
The fields parameter can be used to exclude a
specific file: if you wish to omit a certain field from the response, do
so using the fields parameter with the prefix
!. For example, to get the details of a file without
listing its metadata, issue a call
p$list_files(fields = "!metadata") or to exclude multiple
fields p$list_files(fields = c("!metadata", "!tags")). The
entire metadata and tags fields will be removed from the
response.
The fields parameter can be used to include or omit
certain nested fields, in the same way as listed in 2 and 3 above: for
example, you can use metadata.sample_id or
origin.task for files.
Negations and nesting can be combined freely, so, for example,
you can issue
p$list_files(fields = c("id", "name", "size", "!metadata.library", "!origin")).
This call returns information about your current rate limit. This is the number of API calls you can make in one hour.
# Get rate limit info
a$rate_limit()It shows information about the remaining number of API calls to make in one hour, along with time when the rate limit resets, and the total and remaining number of instances available to the user.
── Rate limit ──────────────────────────────────────────────────────────────
• rate
• limit: 1000
• remaining: 998
• reset: 2023-11-27 14:24:38 CET
• instance
• limit: 25
• remaining: 25We should also mention that there are 3 types of general API errors
that are handled by the client sevenbridges2 package:
Users are able to preview all main resource paths that exist on the
public Seven Bridges API. If you do not pass any parameters to
api() from the Auth object, it will list all
API calls. Any parameters you provide will be passed to the
api() function, but you do not have to pass your input
token and path once more since the Auth object already
handles this information. The following call from the Auth
object will check the response as well.
# List all API paths
a$api()This call will return a successful response of the currently authenticated user, while if you have some advanced privileges as an Enterprise user, you can fetch information about other users when specifying their usernames.
If you did not provide a username, it will show your user information.
# Return your information
a$user()
# Return user RFranklin's information
a$user(username = "RFranklin")Billing operations are grouped under the Billing_groups
R6 Resource class and from here you can query all billing groups or
fetch a single one by its id.
When you fetch a single billing group it will be an object of the
Billing class.
# Get specific billing group
my_billing_group <- a$billing_groups$get(id = "<billing_group_id>")
# You can still print the billing group info by calling the print method
my_billing_group$print()You can also get detailed information for a specific billing group. The following options are available to you:
To get an analysis breakdown for a billing group which contains information on both the tasks and Data Studio analyses, call:
# Get analysis breakdown
my_billing_group$analysis_breakdown()To get storage breakdown for a billing group, call:
# Get storage breakdown
my_billing_group$storage_breakdown()Finally, you may want to get egress breakdown for a billing group:
# Get egress breakdown
my_billing_group$egress_breakdown()If something changes in the billing group, you can refresh your
Billing object by reloading it with:
# Reload Billing object
my_billing_group$reload()The same logic applies for the invoices - the operations available
for invoices are grouped under the Invoices class and from
here you can query or fetch a single invoice with resource operations
query() and get().
Listing all invoices doesn’t require any arguments to set, while if
you would like to list invoices of specific billing group, set the
billing_group parameter to the desired value.
# List invoices of specific billing group
invoices_bg <- a$invoices$query(billing_group = "<billing_group_id>")
# Print invoices
invoices_bgKeep in mind that the result is Collection object which
stores the returned items in the items field.
To retrieve information about a single invoice, including the costs
for analysis and storage, and the invoice period, you can use the
get() method with the id parameter set to the ID of the
invoice you are querying.
# Get specific invoice by ID
invoice <- a$invoices$get(id = "<invoice_id>")
# Print
invoice── Invoice info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
• approval_date: 2022-02-01T00:00:00Z
• pending: FALSE
• invoice_id: <your_invoice_id>
• href: https://api.sbgenomics.com/v2/billing/invoices/<your_invoice_id>
• invoice_period
• from: 2022-01-01T00:00:00Z
• to: 2022-01-31T23:59:59Z
• analysis_costs
• currency: USD
• amount: 101.77
• storage_costs
• currency: USD
• amount: 256.11
• total
• currency: USD
• amount: 357.88If something changes, you can always refresh your local
Invoice object by reloading it with:
# Reload Invoice object
invoice$reload()Lastly, to send feedback to Velsera via the API, you can use the
Auth class method send_feedback(). There are
three feedback types available: "idea",
"thought", or "problem". You can send one
feedback item per minute.
# Send feedback
a$send_feedback(
"This is a test for sending feedback via API. Please ignore this message.",
type = "thought"
)