Package org.obolibrary.robot

Class CommandLineHelper

java.lang.Object

org.obolibrary.robot.CommandLineHelper

public class CommandLineHelper
extends Object

Convenience methods for working with command line options.

Constructor Summary

Constructors

Constructor	Description
CommandLineHelper()

Method Summary

Modifier and Type	Method	Description
static List<String>	cleanAxiomStrings(org.apache.commons.cli.CommandLine line)	Given a command line, get the 'axioms' option(s) and make sure all are properly split and return one axiom selector per list entry.
static Map<String,String>	getAddPrefixes(org.apache.commons.cli.CommandLine line)	Given a command line, get a map of all prefixes to use and add to the output.
static Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>>	getAxiomValues(org.apache.commons.cli.CommandLine line)	Deprecated. split into methods cleanAxiomStrings(CommandLine) and others in RelatedObjectsHelper
static List<String>	getBaseNamespaces(org.apache.commons.cli.CommandLine line, IOHelper ioHelper)	Given a command line and an IOHelper, return a list of base namespaces from the '--base-iri' option.
static boolean	getBooleanValue(org.apache.commons.cli.CommandLine line, String name, boolean defaultValue)	Get the boolean value of a command-line option with the given name.
static boolean	getBooleanValue(org.apache.commons.cli.CommandLine line, String name, boolean defaultValue, boolean optionalArg)	Given a command line, an argument name, the boolean default value, and boolean if the arg is optional, return the value of the command-line option 'name'.
static String	getCommand(org.apache.commons.cli.CommandLine line)	Given a command line, return its first argument, which should be the name of the command to execute.
static org.apache.commons.cli.CommandLine	getCommandLine(String usage, org.apache.commons.cli.Options options, String[] args)	Parse the command line, handle help and other common options, (May exit!) and return a CommandLine.
static org.apache.commons.cli.Options	getCommonOptions()	Create a new Options object with shared options for 'help' and 'version'.
static String	getDefaultValue(org.apache.commons.cli.CommandLine line, String name, String defaultValue)	Get the value of the command-line option with the given name, or return a default value if the option is not found.
static String	getIndexValue(org.apache.commons.cli.CommandLine line, int index)	Given a command line and an index, return the argument at that index.
static List<org.semanticweb.owlapi.model.OWLOntology>	getInputOntologies(IOHelper ioHelper, org.apache.commons.cli.CommandLine line)	Given an IOHelper and a command line, check input options and return a list of loaded input ontologies.
static List<org.semanticweb.owlapi.model.OWLOntology>	getInputOntologies(IOHelper ioHelper, org.apache.commons.cli.CommandLine line, boolean allowEmpty)	Given an IOHelper and a command line, check for required options and return a list of loaded input ontologies.
static List<org.semanticweb.owlapi.model.OWLOntology>	getInputOntologies(IOHelper ioHelper, org.apache.commons.cli.CommandLine line, String catalogPath)	Given an IOHelper, a command line, and the path to a catalog file, check input options and return a list of loaded input ontologies with the catalog file.
static org.semanticweb.owlapi.model.OWLOntology	getInputOntology(IOHelper ioHelper, org.apache.commons.cli.CommandLine line)	Given an IOHelper and a command line, check for required options and return a loaded input ontology.
static org.semanticweb.owlapi.model.OWLOntology	getInputOntology(IOHelper ioHelper, org.apache.commons.cli.CommandLine line, String catalogPath)	Given an IOHelper, a command line, and a path to a catalog, return an OWLOntology loaded from input or input-iri using the specified catalog (or null).
static IOHelper	getIOHelper(org.apache.commons.cli.CommandLine line)	Given a command line, return an initialized IOHelper.
static String	getOptionalValue(org.apache.commons.cli.CommandLine line, String name)	Get the value of the command-line option with the given name.
static List<String>	getOptionalValues(org.apache.commons.cli.CommandLine line, String name)	Get the value of the command-line options with the given name.
static List<String>	getOptionValues(org.apache.commons.cli.CommandLine line, String name)	Given a command line, return the values for an option as a list.
static File	getOutputFile(org.apache.commons.cli.CommandLine line)	Given a command line, check for the required options and return a File for saving data.
static org.semanticweb.owlapi.model.IRI	getOutputIRI(org.apache.commons.cli.CommandLine line)	Given a command line, check for the required options and return an IRI to be used as the OntologyIRI for the output ontology.
static org.semanticweb.owlapi.reasoner.OWLReasonerFactory	getReasonerFactory(org.apache.commons.cli.CommandLine line)	Given a string of a reasoner name from user input, return the reasoner factory.
static org.semanticweb.owlapi.reasoner.OWLReasonerFactory	getReasonerFactory(org.apache.commons.cli.CommandLine line, boolean allowEMR)	Given a string of a reasoner name from user input, return the reasoner factory.
static String	getRequiredValue(org.apache.commons.cli.CommandLine line, String name, String message)	Get the value of the command-line option with the given name, or throw an IllegalArgumentException with a given message if the option is not found.
static Set<org.semanticweb.owlapi.model.IRI>	getTerms(IOHelper ioHelper, org.apache.commons.cli.CommandLine line)	Given an IOHelper and a command line, check for the required options and return a set of IRIs for terms.
static Set<org.semanticweb.owlapi.model.IRI>	getTerms(IOHelper ioHelper, org.apache.commons.cli.CommandLine line, boolean allowEmpty)	As getTerms, but allow the list to be empty.
static Set<org.semanticweb.owlapi.model.IRI>	getTerms(IOHelper ioHelper, org.apache.commons.cli.CommandLine line, String singles, String paths)	Given an IOHelper and a command line, and the names of two options, check for the required options and return a set of IRIs for terms.
static void	handleException(Exception exception)	Shared method for dealing with exceptions, printing help, and exiting.
static void	handleException(String usage, org.apache.commons.cli.Options options, Exception exception)	Shared method for dealing with exceptions, printing help, and exiting.
static boolean	hasFlagOrCommand(org.apache.commons.cli.CommandLine line, String name)	Return true if a command line include the option with the given name, or the command with the given name.
static org.semanticweb.owlapi.model.IRI	maybeCreateIRI(IOHelper ioHelper, String term, String field)	Try to create an IRI from a string input.
static org.apache.commons.cli.CommandLine	maybeGetCommandLine(String usage, org.apache.commons.cli.Options options, String[] args, boolean stopAtNonOption)	Parse the command line, handle help and other common options, and return null or a CommandLine.
static void	maybeSaveOutput(org.apache.commons.cli.CommandLine line, org.semanticweb.owlapi.model.OWLOntology ontology)	Given a command line and an ontology, for each `--output` option (if any), save a copy of the ontology to the specified path.
static List<String>	parseArgList(String toProcess)	Given a single string, return a list of strings split at whitespace but allowing for quoted values, as a command-line parser does.
static String[]	parseArgs(String toProcess)	Given a single string, return an array of strings split at whitespace but allowing for quoted values, as a command-line parser does.
static void	printHelp(String usage, org.apache.commons.cli.Options options)	Print a help message for a command.
static void	printVersion()	Print the ROBOT version
protected static List<String>	splitSelects(String selects)	Given an input string, return a list of the string split on whitespace, while ignoring any whitespace in single string quotes.
static CommandState	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	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 inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CommandLineHelper

public CommandLineHelper()

Method Detail

parseArgList

public static List<String> parseArgList(String toProcess)
                                 throws Exception

Given a single string, return a list of strings split at whitespace but allowing for quoted values, as a command-line parser does.

Parameters:

toProcess - the string to parse

Returns:

a string list, split at whitespace, with quotation marks removed

Throws:

Exception - on parsing problems

parseArgs

public static String[] parseArgs(String toProcess)
                          throws Exception

Given a single string, return an array of strings split at whitespace but allowing for quoted values, as a command-line parser does. Adapted from org.apache.tools.ant.types.Commandline

Parameters:

toProcess - the string to parse

Returns:

a string array, split at whitespace, with quotation marks removed

Throws:

Exception - on parsing problems

getOptionValues

public static List<String> getOptionValues(org.apache.commons.cli.CommandLine line,
                                           String name)

Given a command line, return the values for an option as a list. This is just a convenience function for turning an array into a list.

Parameters:

line - the command line to use

name - the name of the option to find

Returns:

the option values as a list of strings, maybe empty

getIndexValue

public static String getIndexValue(org.apache.commons.cli.CommandLine line,
                                   int index)

Given a command line and an index, return the argument at that index.

Parameters:

line - the command line to use

index - the index of the argument

Returns:

the argument at the given index

getCommand

public static String getCommand(org.apache.commons.cli.CommandLine line)

Given a command line, return its first argument, which should be the name of the command to execute.

Parameters:

line - the command line to use

Returns:

the name of the command to execute

hasFlagOrCommand

public static boolean hasFlagOrCommand(org.apache.commons.cli.CommandLine line,
                                       String name)

Return true if a command line include the option with the given name, or the command with the given name.

Parameters:

line - the command line to use

name - the name of the flag or argument to check for

Returns:

true if a flag or first argument match the given name, false otherwise

cleanAxiomStrings

public static List<String> cleanAxiomStrings(org.apache.commons.cli.CommandLine line)

Given a command line, get the 'axioms' option(s) and make sure all are properly split and return one axiom selector per list entry.

Parameters:

line - the command line to use

Returns:

cleaned list of input axiom type strings

getBaseNamespaces

public static List<String> getBaseNamespaces(org.apache.commons.cli.CommandLine line,
                                             IOHelper ioHelper)

Given a command line and an IOHelper, return a list of base namespaces from the '--base-iri' option.

Parameters:

line - the command line to use

ioHelper - the IOHelper to resolve prefixes

Returns:

list of full base namespaces

getBooleanValue

public static boolean getBooleanValue(org.apache.commons.cli.CommandLine line,
                                      String name,
                                      boolean defaultValue,
                                      boolean optionalArg)

Given a command line, an argument name, the boolean default value, and boolean if the arg is optional, return the value of the command-line option 'name'.

Parameters:

line - the command line to use

name - the name of the option to find

defaultValue - the default value to use if the option is not provided

optionalArg - if true, the option without an arg will return true

Returns:

the option value as boolean, or the default if not found

getAxiomValues

@Deprecated
public static Set<Class<? extends org.semanticweb.owlapi.model.OWLAxiom>> getAxiomValues(org.apache.commons.cli.CommandLine line)

Deprecated.

split into methods cleanAxiomStrings(CommandLine) and others in RelatedObjectsHelper

Given a command line, return the value of --axioms as a set of classes that extend OWLAxiom.

Parameters:

line - the command line to use

Returns:

set of OWLAxiom types

getBooleanValue

public static boolean getBooleanValue(org.apache.commons.cli.CommandLine line,
                                      String name,
                                      boolean defaultValue)

Get the boolean value of a command-line option with the given name.

Parameters:

line - the command line to use

name - the name of the option to find

defaultValue - the default value to use

Returns:

the option value as boolean, or the default if not found

getOptionalValue

public static String getOptionalValue(org.apache.commons.cli.CommandLine line,
                                      String name)

Get the value of the command-line option with the given name.

Parameters:

line - the command line to use

name - the name of the option to find

Returns:

the option value as a string, or null if not found

getOptionalValues

public static List<String> getOptionalValues(org.apache.commons.cli.CommandLine line,
                                             String name)

Get the value of the command-line options with the given name.

Parameters:

line - the command line to use

name - the name of the option to find

Returns:

the option value as a list of strings, maybe empty

getDefaultValue

public static String getDefaultValue(org.apache.commons.cli.CommandLine line,
                                     String name,
                                     String defaultValue)

Get the value of the command-line option with the given name, or return a default value if the option is not found.

Parameters:

line - the command line to use

name - the name of the option to find

defaultValue - the default value to use

Returns:

the option value as a string, or the default if the option not found

getRequiredValue

public static String getRequiredValue(org.apache.commons.cli.CommandLine line,
                                      String name,
                                      String message)
                               throws IllegalArgumentException

Get the value of the command-line option with the given name, or throw an IllegalArgumentException with a given message if the option is not found.

Parameters:

line - the command line to use

name - the name of the option to find

message - the message for the exception

Returns:

the option value as a string

Throws:

IllegalArgumentException - if the option is not found

getIOHelper

public static IOHelper getIOHelper(org.apache.commons.cli.CommandLine line)
                            throws IOException

Given a command line, return an initialized IOHelper. The --prefix, --add-prefix, --prefixes, --add-prefixes, --noprefixes, --xml-entities, and --base options are handled.

Parameters:

line - the command line to use

Returns:

an initialized IOHelper

Throws:

IOException - on issue creating IOHelper with given context

getInputOntology

public static org.semanticweb.owlapi.model.OWLOntology getInputOntology(IOHelper ioHelper,
                                                                        org.apache.commons.cli.CommandLine line)
                                                                 throws IllegalArgumentException,
                                                                        IOException

Given an IOHelper and a command line, check for required options and return a loaded input ontology. Currently handles --input and --input-iri options.

Parameters:

ioHelper - the IOHelper to load the ontology with

line - the command line to use

Returns:

the input ontology

Throws:

IllegalArgumentException - if requires options are missing

IOException - if the ontology cannot be loaded

getInputOntology

public static org.semanticweb.owlapi.model.OWLOntology getInputOntology(IOHelper ioHelper,
                                                                        org.apache.commons.cli.CommandLine line,
                                                                        String catalogPath)
                                                                 throws IllegalArgumentException,
                                                                        IOException

Given an IOHelper, a command line, and a path to a catalog, return an OWLOntology loaded from input or input-iri using the specified catalog (or null).

Parameters:

ioHelper - the IOHelper to load the ontology with

line - the command line to use

catalogPath - the catalog to use to load imports

Returns:

the input ontology

Throws:

IllegalArgumentException - if requires options are missing

IOException - if the ontology cannot be loaded

getInputOntologies

public static List<org.semanticweb.owlapi.model.OWLOntology> getInputOntologies(IOHelper ioHelper,
                                                                                org.apache.commons.cli.CommandLine line,
                                                                                boolean allowEmpty)
                                                                         throws IllegalArgumentException,
                                                                                IOException

Given an IOHelper and a command line, check for required options and return a list of loaded input ontologies. Currently handles --input, --input-iri, and --inputs options.

Parameters:

ioHelper - the IOHelper to load the ontology with

line - the command line to use

allowEmpty - if an empty list may be returned (when chaining commands, an input was already provided)

Returns:

the list of input ontologies

Throws:

IllegalArgumentException - if requires options are missing

IOException - if the ontology cannot be loaded

updateInputOntology

public static CommandState updateInputOntology(IOHelper ioHelper,
                                               CommandState state,
                                               org.apache.commons.cli.CommandLine line)
                                        throws IllegalArgumentException

Given an IOHelper, a state object, and a command line, update the state with the ontology.

Parameters:

ioHelper - the IOHelper to load the ontology with

state - the input state, maybe null

line - the command line to use

Returns:

the updated state

Throws:

IllegalArgumentException - if requires options are missing

updateInputOntology

public static CommandState updateInputOntology(IOHelper ioHelper,
                                               CommandState state,
                                               org.apache.commons.cli.CommandLine line,
                                               boolean required)
                                        throws IllegalArgumentException

Given an IOHelper, a state object, a command line, and a "required" flag, update the state with the ontology. If the state contains an ontology, use it. If the state is null or does not contain an ontology, use the `--input` option. If the state has an ontology and there's an `--input` throw an exception warning the use to use two commands instead of a chain of commands.

Parameters:

ioHelper - the IOHelper to load the ontology with

state - the input state, maybe null

line - the command line to use

required - when true, throw an exception if ontology is not found

Returns:

the updated state

Throws:

IllegalArgumentException - if requires options are missing

getOutputFile

public static File getOutputFile(org.apache.commons.cli.CommandLine line)
                          throws IllegalArgumentException

Given a command line, check for the required options and return a File for saving data.

Parameters:

line - the command line to use

Returns:

the File for output; may be null; may not exist!

Throws:

IllegalArgumentException - if required options are not found

getOutputIRI

public static org.semanticweb.owlapi.model.IRI getOutputIRI(org.apache.commons.cli.CommandLine line)

Given a command line, check for the required options and return an IRI to be used as the OntologyIRI for the output ontology.

Parameters:

line - the command line to use

Returns:

the IRI for the output ontology, or null

maybeSaveOutput

public static void maybeSaveOutput(org.apache.commons.cli.CommandLine line,
                                   org.semanticweb.owlapi.model.OWLOntology ontology)
                            throws IOException

Given a command line and an ontology, for each `--output` option (if any), save a copy of the ontology to the specified path.

Parameters:

line - the command lien to use

ontology - the ontology to save

Throws:

IOException - on any problem

maybeCreateIRI

public static org.semanticweb.owlapi.model.IRI maybeCreateIRI(IOHelper ioHelper,
                                                              String term,
                                                              String field)

Try to create an IRI from a string input. If the term is not in a valid format (null), an IllegalArgumentException is thrown to prevent null from being passed into other methods.

Parameters:

ioHelper - IOHelper to use

term - the term to convert to an IRI

field - the field in which the term was entered, for reporting

Returns:

the new IRI if successful

getAddPrefixes

public static Map<String,String> getAddPrefixes(org.apache.commons.cli.CommandLine line)
                                               throws IOException

Given a command line, get a map of all prefixes to use and add to the output.

Parameters:

line - the command line to use

Returns:

a map of prefixes to add to output

Throws:

IOException - if the prefixes are not formatted correctly or a JSON file cannot be read

getTerms

public static Set<org.semanticweb.owlapi.model.IRI> getTerms(IOHelper ioHelper,
                                                             org.apache.commons.cli.CommandLine line)
                                                      throws IllegalArgumentException,
                                                             IOException

Given an IOHelper and a command line, check for the required options and return a set of IRIs for terms. Handles --terms and --term-file options.

Parameters:

ioHelper - the IOHelper to use for loading the terms

line - the command line to use

Returns:

a set of term IRIs

Throws:

IllegalArgumentException - if the required options are not found

IOException - if the term file cannot be loaded

getTerms

public static Set<org.semanticweb.owlapi.model.IRI> getTerms(IOHelper ioHelper,
                                                             org.apache.commons.cli.CommandLine line,
                                                             boolean allowEmpty)
                                                      throws IllegalArgumentException,
                                                             IOException

As getTerms, but allow the list to be empty.

Parameters:

ioHelper - the IOHelper to use for loading the terms

line - the command line to use

allowEmpty - true if empty lists of properties are allowed

Returns:

a set of term IRIs

Throws:

IllegalArgumentException - if the required options are not found

IOException - if the term file cannot be loaded

getTerms

public static Set<org.semanticweb.owlapi.model.IRI> getTerms(IOHelper ioHelper,
                                                             org.apache.commons.cli.CommandLine line,
                                                             String singles,
                                                             String paths)
                                                      throws IllegalArgumentException,
                                                             IOException

Given an IOHelper and a command line, and the names of two options, check for the required options and return a set of IRIs for terms. Handles single term options and term-file options. Allows empty returns.

Parameters:

ioHelper - the IOHelper to use for loading the terms

line - the command line to use

singles - the option name for single terms, or null

paths - the option name for term file paths, or null

Returns:

a set of term IRIs

Throws:

IllegalArgumentException - if the required options are not found

IOException - if the term file cannot be loaded

getReasonerFactory

public static org.semanticweb.owlapi.reasoner.OWLReasonerFactory getReasonerFactory(org.apache.commons.cli.CommandLine line)

Given a string of a reasoner name from user input, return the reasoner factory. If the user input is not valid, throw IllegalArgumentExcepiton. By default, EMR is not allowed.

Parameters:

line - the command line to use

Returns:

OWLReasonerFactory if successful

getReasonerFactory

public static org.semanticweb.owlapi.reasoner.OWLReasonerFactory getReasonerFactory(org.apache.commons.cli.CommandLine line,
                                                                                    boolean allowEMR)

Given a string of a reasoner name from user input, return the reasoner factory. If the user input is not valid, throw IllegalArgumentExcepiton.

Parameters:

line - the command line to use

allowEMR - boolean specifying if EMR can be returned

Returns:

OWLReasonerFactory if successful

printHelp

public static void printHelp(String usage,
                             org.apache.commons.cli.Options options)

Print a help message for a command.

Parameters:

usage - the usage information for the command

options - the command line options for the command

printVersion

public static void printVersion()
                         throws IOException

Print the ROBOT version

Throws:

IOException - on issue getting info from JAR

getCommonOptions

public static org.apache.commons.cli.Options getCommonOptions()

Create a new Options object with shared options for 'help' and 'version'.

Returns:

a new Options object with some options added

maybeGetCommandLine

public static org.apache.commons.cli.CommandLine maybeGetCommandLine(String usage,
                                                                     org.apache.commons.cli.Options options,
                                                                     String[] args,
                                                                     boolean stopAtNonOption)
                                                              throws org.apache.commons.cli.ParseException,
                                                                     IOException

Parse the command line, handle help and other common options, and return null or a CommandLine.

Parameters:

usage - the usage string for this command

options - the command-line options for this command

args - the command-line arguments provided

stopAtNonOption - same as CommandLineParser

Returns:

a new CommandLine object or null

Throws:

org.apache.commons.cli.ParseException - if the arguments cannot be parsed

IOException - on issue printing version

getCommandLine

public static org.apache.commons.cli.CommandLine getCommandLine(String usage,
                                                                org.apache.commons.cli.Options options,
                                                                String[] args)
                                                         throws org.apache.commons.cli.ParseException,
                                                                IOException

Parse the command line, handle help and other common options, (May exit!) and return a CommandLine.

Parameters:

usage - the usage string for this command

options - the command-line options for this command

args - the command-line arguments provided

Returns:

a new CommandLine object or exit(0)

Throws:

org.apache.commons.cli.ParseException - if the arguments cannot be parsed

IOException - on issue printing version

handleException

public static void handleException(Exception exception)

Shared method for dealing with exceptions, printing help, and exiting. Currently prints the error message, stack trace (DEBUG), usage, and then exits.

Parameters:

exception - the exception to handle

handleException

public static void handleException(String usage,
                                   org.apache.commons.cli.Options options,
                                   Exception exception)

Shared method for dealing with exceptions, printing help, and exiting. Currently prints the error message, stack trace (DEBUG), usage, and then exits.

Parameters:

usage - the usage string for this command; WARN: not used

options - the command-line options for this command; WARN: not used

exception - the exception to handle

splitSelects

protected static List<String> splitSelects(String selects)

Given an input string, return a list of the string split on whitespace, while ignoring any whitespace in single string quotes.

Parameters:

selects - String of select options to split

Returns:

List of split strings

getInputOntologies

public static List<org.semanticweb.owlapi.model.OWLOntology> getInputOntologies(IOHelper ioHelper,
                                                                                org.apache.commons.cli.CommandLine line)
                                                                         throws IllegalArgumentException,
                                                                                IOException

Given an IOHelper and a command line, check input options and return a list of loaded input ontologies.

Parameters:

ioHelper - the IOHelper to load the ontology with

line - the command line to use

Returns:

the list of input ontologies

Throws:

IllegalArgumentException - on bad pattern

IOException - if the ontology cannot be loaded

getInputOntologies

public static List<org.semanticweb.owlapi.model.OWLOntology> getInputOntologies(IOHelper ioHelper,
                                                                                org.apache.commons.cli.CommandLine line,
                                                                                String catalogPath)
                                                                         throws IOException

Given an IOHelper, a command line, and the path to a catalog file, check input options and return a list of loaded input ontologies with the catalog file.

Parameters:

ioHelper - the IOHelper to load the ontology with

line - the command line to use

catalogPath - the catalog file to use

Returns:

the list of input ontologies

Throws:

IOException - if the ontology cannot be loaded