Direct authentication

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 were explicitly specified.

Note: platform and url should not be specified at the same time.

Authentication via system environment variables

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>"
)

See if 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"
)

Authentication via user configuration file

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_user

Please 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.

Advance Access Features

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] FALSE

For 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] TRUE

Send 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()

Query Parameter fields

All 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:

1. No fields parameter specified: returns all fields for each resource returned (TBD for Apps).

2. 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")).

3. 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.

4. 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.

5. Negations and nesting can be combined freely, so, for example, you can issue p$list_files(fields = c("id", "name", "size", "!metadata.library", "!origin")).

Rate Limits

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: 25

General API error handlers

We should also mention that there are 3 types of general API errors that are handled by the client sevenbridges2 package:

• Rate limit sleeper which pauses the execution of any API call if rate limit is breached. The execution will automatically continue when the required break time expires,
• Maintenance sleeper which pauses the execution if Seven Bridges API is under maintenance and
• General error sleeper which pauses the execution if response status code is equal or larger than 500 (if some server error occurred).

Billing groups

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:

• analysis breakdown
• storage breakdown
• egress breakdown.

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 objcet
my_billing_group$reload()

Invoices

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_bg

Keep 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: 357.88

If something changes, you can always refresh your local Invoice object by reloading it with:

# Reload Invoice object
invoice$reload()