fastgenomicsRclient

Connect to any FASTGenomics instance and manipulate / retrieve data.

Installation

You can install the development version like this:

install.packages("devtools")
library(devtools)
install_github("FASTGenomics/r_client")

Example

You need to get a bearer token to use this api. You can get this token at: https://fastgenomics.org/ids/Account/ApiTokenLogin

WARNING: Never commit this token to a repository or share it otherwise! It can be used to impersonate you

connection <- fastgenomicsRclient::connect("https://fastgenomics.org/", "Bearer Token")
datasets <- fastgenomicsRclient::get_datasets(connection)
print(datasets@content) # all datasets available to you

Run tests

If you want the unit tests of this package, set two envrionment variables

Sys.setenv(FGBEARERTOKEN = "YOUR TOKEN")
Sys.setenv(FGBASEURL = "URL")

then run the tests through RStudio (Build -> Test Pakcage) or run devtools::test()

Troubleshooting

HTTP2 framing error

If you encounter an HTTP2 framing error try disabling HTTP2 with

library("httr")
httr::set_config(config(http_version = 0))

User permissions

If you get 403 FORBIDDEN errors when using the API, your user account has not the necessary permissions for an operation. Please contact us at feedback@fastgenomics.org to get access to such functions.

Compression of submitted data

We internally use the zip function, which by default uses a system-dependent compression program ("zip" by default). Make sure to have zip installed if you wan to submit compressed data. On Windows one solution is to get it with the Rtools package, just make sure to check the update PATH checkbox when installing it.