Obtain a SIRIUS job configuration — getSIRIUSConfig • patRoon

This function obtains a JobSubmission configuration object for use with generateFormulasSIRIUS and generateCompoundsSIRIUS.

Usage

getSIRIUSConfig(
  config = NULL,
  import = NULL,
  login = "check",
  alwaysLogin = FALSE,
  SIRIUSAPI = NULL
)

Arguments

config

A configuration specification. Use NULL to obtain the server default, a character string to fetch a named configuration, NA to list available configuration names, or a list / RSirius::JobSubmission object to use directly.

import

Path to a JSON file to import the configuration from, e.g. exported from the SIRIUS GUI. Cannot be used together with config.

login, alwaysLogin

Specifies if and how account logging of SIRIUS should be handled:

login=FALSE: no automatic login is performed and the active login status is not checked.

login="check": aborts if no active login is present.

login="interactive": interactively ask for login (using getPass).

login=c(username="...", password="..."): perform the login with the given details. For security reasons, please do not enter the details directly, but use e.g. environment variables or store/retrieve them with the keyring package.

if alwaysLogin=TRUE then a login is always performed, otherwise only if SIRIUS reports no active login.

See the SIRIUS website and patRoon handbook for more information.

NOTE: By loggin in you will accept the terms of the Service and Privacy Policy of the SIRIUS Webservice.

SIRIUSAPI

An rsirius_api object for connecting to the SIRIUS API. If NULL, a new connection will be started automatically.

Value

A RSirius::JobSubmission object with the job configuration, or a character vector of configuration names when config = NA.

Details

The function can return the server default configuration, fetch a named configuration, import a configuration from a JSON file, or use a provided configuration object/list. If needed, the SIRIUS API is started automatically and a login can be performed. There are many configuration options available in SIRIUS. It is probably easiest to explore and configure them through the SIRIUS GUI, save or export the configuration profile and then load it via the config or import arguments.