Execute Robot Commands
robot.Rd
Light wrapper for OBO Foundry ROBOT program (OBO Foundry). See ROBOT documentation for information about subcommands and arguments.
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"
orinput = "doid.owl"
(named argument)."-o result.owl"
(i.e.--output
) oro = "result.owl"
(named argument)."--remove-annotations"
(option ofannotate
) 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 withjava -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.