Telemetry package for R

A package for crafting API requests to the telemetry database API.

Package Design and Philosophy

The telemetry package is a utility for crafting valid API requests for the telemetry database from R. It handles:

login and session management
creating POST requests to the API
converting input data from R into JSON data payloads,
marshalling JSON responses from the API into R data structures.

Importantly, the telemetry package is designed to be flexible while also providing moderate user convienence.

Login and Session Management

A session for the API is started via the start_session() function,

my_session = start_session(uname = "My Name",
                           pwd = "my_password",
                           api_baseurl = "some_url")

The returned object (my_session in this case) is an R list with identifying information about the newly created session, including base URL and the unique token assigned for this login. This unique token is required for every subsequent interaction with the API.

Multiple sessions can be started simultaneously for the same user, as can multiple simultaneous sessions for different users. Each unique session is identified by the unique token for that session.

A note on the api_baseurl parameter: To be flexible, this can be any valid URL, include one local to the user's machine (e.g. localhost:). The functions in the telemetry package will extract the URL from the session object to automatically submit requests to the URL for that session. This is useful in cases where e.g. you might want to test two sessions simultaenously, one for a locally running database API and another for a web-hosted API.

By default, a single session's unique token will be valid for 30 min. Each interaction with the API will refresh a token for another 30 min. A session can be ended manually via the end_session() function.

Downloading Data

Existing data in the database is downloaded via the download_data() function. This function takes two optional arguments, region and speciesID. If omitted, all data the user has access to will be downloaded, including registrations for tagID's not in the database. When region is specified, only detections for antennas in the specified region are returned. When speciesID is provided, only tags of that species are returned. Important - tagIDs not in the database will have an unknown species, hence are not returned when speciesID is provided.

The downloaded data takes the form of a complete SQLite database, subset according to the above. If the db_file() is not provided, this is saved to a tempfile(). The file path to the saved database is returned.

For convenience, all tables from this SQLite database can be extracted into R data.frames with extract_data() - by default these tables are extracted into a separate environment that is returned by the function

fish_db = download_data(my_session, ...)

fish_data = extract_data(fish_db)

In this example, fish_data is an environment and the tables within can be accessed via the $ operator.

fish_data$Tags

Documentation on the database can be found here.

Sending API Requests

All API requests are submitted via the send_api_request() function. This function takes a session object and then a set of key = value pairs. These key = value pairs are marshalled to JSON in the format expected by the API. By design, the telemetry package mirrors the API itself. The keys must match the expected values for each API endpoint - any extra keys are ignored. The values must also match the expected data type for the API end point specified. In cases where the value is a complex data structure (e.g. a data.frame or array), it will be marshalled to JSON prior to submission.

Bug Reports