Uses of Class
org.obolibrary.robot.CommandState

Uses of CommandState in org.obolibrary.robot

Methods in org.obolibrary.robot that return CommandState

Modifier and Type	Method	Description
CommandState	AnnotateCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, add or remove ontology annotations and return the modified state.
CommandState	CollapseCommand.execute(CommandState state, String[] args)
CommandState	Command.execute(CommandState inputState, String[] args)	All commands offer an execute method that can be chained from previous commands.
CommandState	CommandManager.execute(CommandState state, String[] args)	Given an input state and command-line arguments, execute one or more commands.
CommandState	ConvertCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, save the ontology to a new format and return the state unchanged.
CommandState	DiffCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, report on the differences between ontologies, if any, and return the state unchanged.
CommandState	ExpandCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, expand macro relations, and add axioms to the input ontology, returning a state with the updated ontology.
CommandState	ExplainCommand.execute(CommandState state, String[] args)
CommandState	ExportCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, build a new ontology from the given template, and return a state with the new ontology.
CommandState	ExportPrefixesCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, export the current prefixes and return the state unchanged.
CommandState	ExtractCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, extract a new ontology and return an new state.
CommandState	FilterCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, filter axioms from its ontology, modifying it, and return a state with the modified ontology.
CommandState	MaterializeCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, run a reasoner, and add axioms to the input ontology, returning a state with the updated ontology.
CommandState	MeasureCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, compute metrics in ontology.
CommandState	MergeCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, merge all ontology axioms into the first ontology and return a state with the merged ontology.
CommandState	MirrorCommand.execute(CommandState state, String[] args)	Mirrors the input ontologgy and its imports closure.
CommandState	PythonCommand.execute(CommandState state, String[] args)	Runs ROBOT accessible via Python.
CommandState	QueryCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, query the ontolgy.
CommandState	ReasonCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, run a reasoner, and add axioms to the input ontology, returning a state with the updated ontology.
CommandState	ReduceCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, run a reasoner, and add axioms to the input ontology, returning a state with the updated ontology.
CommandState	RelaxCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, run a reasoner, and add axioms to the input ontology, returning a state with the updated ontology.
CommandState	RemoveCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, create a new ontology with removed axioms and return a new state.
CommandState	RenameCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, rename the entity IRIs in the ontology.
CommandState	RepairCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, repair a new ontology and return an new state.
CommandState	ReportCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, report a new ontology and return an new state.
CommandState	TemplateCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, build a new ontology from the given template, and return a state with the new ontology.
CommandState	UnmergeCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, unmerge all ontology axioms into the first ontology and return a state with the unmerged ontology.
CommandState	ValidateProfileCommand.execute(CommandState state, String[] args)
CommandState	VerifyCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, verify that the SPARQL queries return no results.
CommandState	CommandManager.executeCommand(CommandState state, List<String> globalOptionArgs, List<String> arguments)	Given an input state, global option strings, and remaining command-line argument strings, use as many arguments as needed to execute a single command.
static CommandState	CommandLineHelper.updateInputOntology(IOHelper ioHelper, CommandState state, org.apache.commons.cli.CommandLine line)	Given an IOHelper, a state object, and a command line, update the state with the ontology.
static CommandState	CommandLineHelper.updateInputOntology(IOHelper ioHelper, CommandState state, org.apache.commons.cli.CommandLine line, boolean required)	Given an IOHelper, a state object, a command line, and a "required" flag, update the state with the ontology.

Methods in org.obolibrary.robot with parameters of type CommandState

Modifier and Type	Method	Description
CommandState	AnnotateCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, add or remove ontology annotations and return the modified state.
CommandState	CollapseCommand.execute(CommandState state, String[] args)
CommandState	Command.execute(CommandState inputState, String[] args)	All commands offer an execute method that can be chained from previous commands.
CommandState	CommandManager.execute(CommandState state, String[] args)	Given an input state and command-line arguments, execute one or more commands.
CommandState	ConvertCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, save the ontology to a new format and return the state unchanged.
CommandState	DiffCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, report on the differences between ontologies, if any, and return the state unchanged.
CommandState	ExpandCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, expand macro relations, and add axioms to the input ontology, returning a state with the updated ontology.
CommandState	ExplainCommand.execute(CommandState state, String[] args)
CommandState	ExportCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, build a new ontology from the given template, and return a state with the new ontology.
CommandState	ExportPrefixesCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, export the current prefixes and return the state unchanged.
CommandState	ExtractCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, extract a new ontology and return an new state.
CommandState	FilterCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, filter axioms from its ontology, modifying it, and return a state with the modified ontology.
CommandState	MaterializeCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, run a reasoner, and add axioms to the input ontology, returning a state with the updated ontology.
CommandState	MeasureCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, compute metrics in ontology.
CommandState	MergeCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, merge all ontology axioms into the first ontology and return a state with the merged ontology.
CommandState	MirrorCommand.execute(CommandState state, String[] args)	Mirrors the input ontologgy and its imports closure.
CommandState	PythonCommand.execute(CommandState state, String[] args)	Runs ROBOT accessible via Python.
CommandState	QueryCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, query the ontolgy.
CommandState	ReasonCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, run a reasoner, and add axioms to the input ontology, returning a state with the updated ontology.
CommandState	ReduceCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, run a reasoner, and add axioms to the input ontology, returning a state with the updated ontology.
CommandState	RelaxCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, run a reasoner, and add axioms to the input ontology, returning a state with the updated ontology.
CommandState	RemoveCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, create a new ontology with removed axioms and return a new state.
CommandState	RenameCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, rename the entity IRIs in the ontology.
CommandState	RepairCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, repair a new ontology and return an new state.
CommandState	ReportCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, report a new ontology and return an new state.
CommandState	TemplateCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, build a new ontology from the given template, and return a state with the new ontology.
CommandState	UnmergeCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, unmerge all ontology axioms into the first ontology and return a state with the unmerged ontology.
CommandState	ValidateProfileCommand.execute(CommandState state, String[] args)
CommandState	VerifyCommand.execute(CommandState state, String[] args)	Given an input state and command line arguments, verify that the SPARQL queries return no results.
CommandState	CommandManager.executeCommand(CommandState state, List<String> globalOptionArgs, List<String> arguments)	Given an input state, global option strings, and remaining command-line argument strings, use as many arguments as needed to execute a single command.
static CommandState	CommandLineHelper.updateInputOntology(IOHelper ioHelper, CommandState state, org.apache.commons.cli.CommandLine line)	Given an IOHelper, a state object, and a command line, update the state with the ontology.
static CommandState	CommandLineHelper.updateInputOntology(IOHelper ioHelper, CommandState state, org.apache.commons.cli.CommandLine line, boolean required)	Given an IOHelper, a state object, a command line, and a "required" flag, update the state with the ontology.