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Execute Robot Commands

robot.Rd

Light wrapper for OBO Foundry ROBOT program (OBO Foundry). See ROBOT documentation for information about subcommands and arguments.

Usage

robot(..., .robot_path = NULL)

Arguments

...

Command(s) passed on to ROBOT, including subcommand(s), either as a single string or named strings, where the name corresponds to the long or short form of the option and the value being the option value. Where options do not use a value, use "". Subcommands should be unnamed.

Examples:

  • Subcommands: "query", "export"

  • Common options:

    • "--input doid.owl" or input = "doid.owl" (named argument).

    • "-o result.owl" (i.e. --output) or o = "result.owl" (named argument).

    • "--remove-annotations" (option of annotate) or "remove-annotations" = "" (named argument form).

.robot_path

The path to a ROBOT executable or .jar file, as a string. When NULL (default), if a system ROBOT executable is available it will be used, otherwise an error will be signaled.

NOTE: DO.utils caches the last ROBOT used for future use.

ROBOT Setup

  • Requires installation of Java (supported versions are listed under the "Getting Started" section at http://robot.obolibrary.org/).

  • Can use OBO Foundry ROBOT tool installed on the system path. This may be achieved with install_robot() or as described at http://robot.obolibrary.org/.

  • Can also use a standalone robot.jar file (.robot_path must be specified) in which case it is executed with java -Xmx10G -jar (10 GB memory).

  • On the first use of each R session, the ROBOT executable/.jar specified will be tested. It must succeed prior to any command execution. On success, robot() will announce the version & path being used. If at any time a new .robot_path is specified, this previous version will be replaced with a new announcement.

Citation

R.C. Jackson, J.P. Balhoff, E. Douglass, N.L. Harris, C.J. Mungall, and J.A. Overton. ROBOT: A tool for automating ontology workflows. BMC Bioinformatics, vol. 20, July 2019.