--- title: "Authentication and Billing reference guide for Seven Bridges API R Client" date: "`r Sys.Date()`" output: rmarkdown::html_document: toc: true toc_float: true toc_depth: 4 number_sections: false theme: "flatly" highlight: "textmate" css: "sevenbridges.css" vignette: > %\VignetteEngine{knitr::rmarkdown} %\VignetteIndexEntry{Authentication and Billing reference guide for Seven Bridges API R Client} %\VignetteEncoding{UTF-8} --- ```{r, include = FALSE} knitr::opts_chunk$set( collapse = TRUE, comment = "#>", eval = FALSE ) ``` # Authentication Before you can interact with the API, you need to construct an `Auth` object which stores the following information: - Your authentication token. This is used to authenticate your credentials with the API. Learn more about obtaining your authentication token on the [Seven Bridges Platform](https://docs.sevenbridges.com/v1.0/docs/get-your-authentication-token), [Cancer Genomics Cloud (CGC)](https://docs.cancergenomicscloud.org/v1.0/docs/get-your-authentication-token), [BioData Catalyst (BDC)](https://sb-biodatacatalyst.readme.io/docs/get-your-authentication-token#find-your-authentication-token), and [CAVATICA](https://docs.cavatica.org/docs/get-your-authentication-token#your-authentication-token). The approach for obtaining the authentication token also applies to the other Seven Bridges platforms. - The path for the API (base URL). - The name of the platform you are using. This is an optional field, as the base URL of the API ultimately decides where the API calls will be sent to. This field will only be blank when the URL was directly provided, and the platform name could not be inferred from that URL. The general authentication logic for `Auth$new()` is as follows: 1. The package will use the direct authentication method if the `from` parameter is not specified explicitly or is specified as `from = "direct`. 2. The package will load the authentication information from environment variables when `from = "env"`, or user configuration file when `from = "file"`. ## Direct authentication To use direct authentication, users need to specify one of `platform` or `url`, with the corresponding `token`. Examples of direct authentication: ```{r} # Direct authentication with setting platform parameter a <- Auth$new( token = "", platform = "aws-us" ) ``` The above will use the Seven Bridges Platform on AWS (US). ```{r} # Direct authentication with setting url parameter a <- Auth$new( 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. ```{r} # Direct authentication on default aws-us platform a <- Auth$new(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: ```{r} # Set environment variables sevenbridges2:::sbg_set_env( url = "https://cgc-api.sbgenomics.com/v2", token = "" ) ``` See if the environment variables are correctly set: ```{r} # Check environment variables sevenbridges2:::sbg_get_env("SB_API_ENDPOINT") ## "https://cgc-api.sbgenomics.com/v2" sevenbridges2:::sbg_get_env("SB_AUTH_TOKEN") ## "" ``` Now you can create the `Auth` object: ```{r} # Authenticate using environment variables a <- Auth$new(from = "env") ``` To unset the two environment variables: ```{r} # Unset environment variables Sys.unsetenv("SB_API_ENDPOINT") Sys.unsetenv("SB_AUTH_TOKEN") ``` If you need to be logged into multiple accounts at the same time it is essential that you provide environment variables for each of the accounts. Of course, these variables must have different names. If you do not have pre-set environment variables, you can create them in the following way: ```{r} # Set environment variables for the first account sevenbridges2:::sbg_set_env( url = "https://api.sbgenomics.com/v2", token = "", sysenv_url_name = "account_1_url", sysenv_token_name = "account_1_token" ) # Set environment variables for the second account sevenbridges2:::sbg_set_env( url = "https://api.sb.biodatacatalyst.nhlbi.nih.gov/v2/", token = "", sysenv_url_name = "account_2_url", sysenv_token_name = "account_2_token" ) ``` Now you are ready to create an authentication object for these two accounts: ```{r} # Authenticate using the first account a <- sevenbridges2::Auth$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: ```{r} # Authenticate using file configuration a <- Auth$new(from = "file") ``` To load the user profile `aws-us-` from this configuration file, change the `profile_name`: ```{r} # Authenticate using file configuration and specific profile a <- Auth$new(from = "file", profile_name = "aws-us-") ``` To use a user configuration file from other locations (not recommended), please specify the file path using the argument `config_file`. For example: ```{r} # Authenticate using specific file configuration on custom path a <- Auth$new( from = "file", config_file = "~/sevenbridges.cfg", profile_name = "aws-us-" ) ``` ***Note:*** If you edited the `credentials` file, please use `Auth$new()` to re-authenticate.

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# API general information ## 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: ```{r} # Load package and check advance access option library("sevenbridges2") getOption("sevenbridges2")$advance_access ``` ``` ## [1] FALSE ``` For example, if we try to use the Markers API to list markers available on a BAM file with the `advance_access` option disabled, it will return an error message: ```{r} # Authenticate first a <- Auth$new(token = "", platform = "aws-us") # Try to send request to list markers req <- a$api( path = "genome/markers?file={bam_file_id}", method = "GET" ) ``` ``` ## !HTTP Status 400: Advance access feature needs X-SBG-Advance-Access: advance header. ``` To enable the Advance Access features, one can use ```{r} # Enable advance access option opt <- getOption("sevenbridges2") opt$advance_access <- TRUE options(sevenbridges2 = opt) ``` at the beginning of their scripts. Let's check if the option has been enabled: ```{r} # Check advance_access option again getOption("sevenbridges2")$advance_access ``` ``` ## [1] TRUE ``` Send the API call again: ```{r} # Send request again to list markers req <- a$api( path = "genome/markers?file={bam_file_id}", method = "GET" ) ``` The information on the markers available on that BAM file will be returned: ```{r} # 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() ```

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## 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"))`.

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## Rate Limits This call returns information about your current rate limit. This is the number of API calls you can make in one hour. ```{r} # 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 ```

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## 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). # List All API Calls 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. ```{r} # List all API paths a$api() ```

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# Users 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. ```{r} # Return your information a$user() # Return user RFranklin's information a$user(username = "RFranklin") ```

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# Billing Groups and Invoices ## 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. ```{r} # Get specific billing group my_billing_group <- a$billing_groups$get(id = "") # You can still print the billing group info by calling the print method my_billing_group$print() ``` You can also get detailed information for a specific billing group. The following options are available to you: - analysis breakdown - storage breakdown - egress breakdown. To get an analysis breakdown for a billing group which contains information on both the tasks and Data Studio analyses, call: ```{r} # Get analysis breakdown my_billing_group$analysis_breakdown() ``` To get storage breakdown for a billing group, call: ```{r} # Get storage breakdown my_billing_group$storage_breakdown() ``` Finally, you may want to get egress breakdown for a billing group: ```{r} # Get egress breakdown my_billing_group$egress_breakdown() ``` If something changes in the billing group, you can refresh your `Billing` object by reloading it with: ```{r} # Reload Billing objcet my_billing_group$reload() ```

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## 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. ```{r} # List invoices of specific billing group invoices_bg <- a$invoices$query(billing_group = "") # 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. ```{r} # Get specific invoice by ID invoice <- a$invoices$get(id = "") # Print invoice ``` ``` ── Invoice info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── • approval_date: 2022-02-01T00:00:00Z • pending: FALSE • invoice_id: • href: https://api.sbgenomics.com/v2/billing/invoices/ • 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: ```{r} # Reload Invoice object invoice$reload() ```

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# Send a feedback item 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. ```{r} # Send feedback a$send_feedback( "This is a test for sending feedback via API. Please ignore this message.", type = "thought" ) ```

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