magmaRset {magmaR}

Set up your magma environment and authentication

Description

Set up your magma environment and authentication

Usage

magmaRset(
  token = NULL,
  url = "https://magma.ucsf.edu",
  opts = list(followlocation = FALSE)
)

Arguments

token

Single string. Your personal token from https://janus.ucsf.edu.

When not explicitly given, you will be prompted to input it via the console.

url

Single string. The url of the production, staging, or development version of magma that you you would like to target. See authentication-and-environments for more information.

opts

A named list of curl options and the values to give them (ex: list(followlocation = FALSE, othersetting = 42)). Generally, most users can ignore this input, but it can be useful for adjusting proxy settings for particular development environment setup.

Details

This function compiles a list, from the given inputs, of the information needed by other magmaR functions to properly route and authenticate a call to magma.

Value

A list with three components: token, url, and opts.

Examples

if (interactive()) {
    
    # THE DEFAULT:
    # When run in this way, it will ask you to give your token.
    # And the resulting $url will be the standard, production, magma url.
    prod <- magmaRset()
    print(prod)
         
    # TARGET = staging:
    # Give the proper url.
    # Again, because we are not providing our token to the call, it will ask.
    stage <- magmaRset(url = "https://magma-stage.ucsf.edu")
    print(stage)
    
    # We can also give additional curl options to the 'opts' input:
    prod_opts <- magmaRset(token = prod$token,
        opts = list(proxyport = 1234))
    print(prod_opts)
    
    # Now we can retrieve data with...
    retrieve(
        target = prod,
        projectName = "example",
        modelName = "rna_seq",
        recordNames = "all",
        attributeNames = "all",
        filter = "")
}