618 lines
24 KiB
Java
618 lines
24 KiB
Java
package org.broadinstitute.sting.utils.cmdLine;
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import org.apache.commons.cli.*;
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import org.apache.log4j.Logger;
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import java.lang.reflect.Array;
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import java.lang.reflect.Constructor;
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import java.lang.reflect.Field;
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import java.lang.reflect.InvocationTargetException;
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import java.lang.reflect.Modifier;
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import java.lang.reflect.ParameterizedType;
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import java.util.Arrays;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.HashMap;
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import java.util.List;
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import java.util.HashSet;
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import java.util.Set;
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import org.broadinstitute.sting.utils.Pair;
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/**
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* User: aaron
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* Date: Mar 19, 2009
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* Time: 6:54:15 PM
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* <p/>
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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* <p/>
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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public class ArgumentParser {
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// what program are we parsing for
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private String programName;
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// the command-line options received.
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private CommandLine cmd;
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// where we eventually want the values to land
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private HashMap<String,Field> m_storageLocations = new HashMap<String,Field>();
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// create Options object
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protected Options m_options = new Options();
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/**
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* our log, which we want to capture anything from org.broadinstitute.sting
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*/
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protected static Logger logger = Logger.getLogger(ArgumentParser.class);
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// the reference to the command line program to fill in
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Object prog;
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public ArgumentParser(String programName, Object prog) {
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this.programName = programName;
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this.prog = prog;
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}
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/**
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* print out the help information
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*/
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public void printHelp() {
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// automatically generate the help statement
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HelpFormatter formatter = new HelpFormatter();
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formatter.printHelp(100,
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"java -Xmx4096m -jar dist/GenomeAnalysisTK.jar",
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"",
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m_options,
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"",
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true);
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}
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/**
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* addOptionalArg
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* <p/>
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* Adds an optional argument to check on the command line
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*
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* @param name the name of the argument, the long name
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* @param letterform the short form
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* @param description the description of the argument
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* @param fieldname the field to set when we've parsed this option
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*/
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public void addOptionalArg(String name, String letterform, String description, String fieldname) {
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// we always want the help option to be available
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Option opt = OptionBuilder.withLongOpt(name).withArgName(name)
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.hasArg()
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.withDescription(description)
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.create(letterform);
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// add it to the option
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AddToOptionStorage(opt, fieldname);
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}
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public void addOptionalArg(Option opt, String fieldname) {
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// add it to the option
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AddToOptionStorage(opt, fieldname);
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}
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/**
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* Used locally to add to the options storage we have, for latter processing
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*
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* @param opt the option
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* @param fieldname what field it should be stuck into on the calling class
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*/
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private void AddToOptionStorage(Option opt, String fieldname) {
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AddToOptionStorage( opt, getField(prog, fieldname) );
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}
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/**
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* Used locally to add to the options storage we have, for latter processing
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*
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* @param opt the option
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* @param field what field it should be stuck into on the calling class
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*/
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private void AddToOptionStorage(Option opt, Field field ) {
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// first check to see if we've already added an option with the same name
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if (m_options.hasOption( opt.getOpt() ))
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throw new IllegalArgumentException(opt.getOpt() + " was already added as an option");
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// Doesn't make much sense to have a single (ungrouped) required option. Force to unrequired.
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if( !opt.hasArg() && opt.isRequired() )
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opt.setRequired(false);
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// add to the option list
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m_options.addOption(opt);
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// add the object with it's name to the storage location
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m_storageLocations.put( opt.getLongOpt(), field );
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}
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/**
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* Used locally to add a group of mutually exclusive options to options storage.
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* @param options A list of pairs of param, field to add.
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*/
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private void AddToOptionStorage( List<Pair<Option,Field>> options ) {
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// Create an option group and mark it 'required'. If any of its constituent parameters
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// are NOT required, they'll unset the required bit for the whole group.
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OptionGroup optionGroup = new OptionGroup();
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optionGroup.setRequired(true);
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for( Pair<Option,Field> option: options ) {
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if (m_options.hasOption(option.first.getOpt()) )
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throw new IllegalArgumentException(option.first.getOpt() + " was already added as an option");
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optionGroup.addOption(option.first);
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m_storageLocations.put( option.first.getLongOpt(), option.second );
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optionGroup.setRequired( optionGroup.isRequired() & option.first.isRequired() );
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}
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m_options.addOptionGroup(optionGroup);
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}
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private Field getField( Object obj, String fieldName ) {
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try {
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return obj.getClass().getField(fieldName);
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} catch (NoSuchFieldException e) {
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logger.fatal("Failed to find the field specified by the fieldname parameter.");
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throw new RuntimeException(e.getMessage());
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}
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}
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/**
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* addRequiredArg
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* <p/>
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* Adds a required argument to check on the command line
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*
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* @param name the name of the argument, the long name
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* @param letterform the short form
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* @param description the description of the argument
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* @param fieldname what field it should be stuck into on the calling class
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*/
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public void addRequiredArg(String name, String letterform, String description, String fieldname) {
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// we always want the help option to be available
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Option opt = OptionBuilder.isRequired()
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.withLongOpt(name)
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.withArgName(name)
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.hasArg()
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.withDescription("(Required Option) " + description)
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.create(letterform);
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// add it to the option
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AddToOptionStorage( opt, fieldname );
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}
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/**
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* addOptionalArg
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* <p/>
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* Adds an optional argument to check on the command line
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*
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* @param name the name of the argument, the long name
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* @param letterform the short form
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* @param description the description of the argument
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* @param fieldname what field it should be stuck into on the calling class
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*/
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public void addOptionalArgList(String name, String letterform, String description, String fieldname) {
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// we always want the help option to be available
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Option opt = OptionBuilder.withLongOpt(name).withArgName(name)
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.hasArgs()
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.withDescription(description)
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.create(letterform);
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// add it to the option
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AddToOptionStorage( opt, fieldname );
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}
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/**
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* addRequiredArg
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* <p/>
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* Adds a required argument to check on the command line
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*
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* @param name the name of the argument, the long name
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* @param letterform the short form
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* @param description the description of the argument
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* @param fieldname what field it should be stuck into on the calling class
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*/
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public void addRequiredArgList(String name, String letterform, String description, String fieldname) {
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// we always want the help option to be available
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Option opt = OptionBuilder.isRequired()
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.withLongOpt(name)
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.withArgName(name)
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.hasArgs()
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.withDescription("(Required Option) " + description)
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.create(letterform);
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// add it to the option
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AddToOptionStorage(opt, fieldname);
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}
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/**
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* addOptionalFlag
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* <p/>
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* Adds an optional argument to check on the command line
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*
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* @param name the name of the argument, the long name
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* @param letterform the short form
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* @param description the description of the argument
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* @param fieldname what field it should be stuck into on the calling class
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*/
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public void addOptionalFlag(String name, String letterform, String description, String fieldname) {
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// if they've passed a non-Boolean as a object, beat them
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try {
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if (!(prog.getClass().getField(fieldname).getType() == Boolean.class)) {
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throw new IllegalArgumentException("Fields to addOptionalFlag must be of type Boolean");
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}
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} catch (NoSuchFieldException e) {
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throw new IllegalArgumentException("Fields to addOptionalFlag must exist!");
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}
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// we always want the help option to be available
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Option opt = OptionBuilder.withLongOpt(name)
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.withDescription(description)
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.create(letterform);
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// add it to the option
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AddToOptionStorage( opt, fieldname );
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}
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/**
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* This function is called to validate all the arguments to the program.
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* If a required Arg isn't found, we generate the help message, and
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* exit the program
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*
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* @param args the command line arguments we recieved
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* @param allowIncomplete whether to allow incomplete command-line arguments
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*/
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public void processArgs(String[] args, boolean allowIncomplete) throws ParseException {
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OurPosixParser parser = new OurPosixParser();
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try {
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parser.parse(m_options, args, false);
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}
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catch( ParseException e ) {
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boolean isIncomplete = e instanceof org.apache.commons.cli.MissingArgumentException ||
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e instanceof MissingOptionException ||
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e instanceof UnrecognizedOptionException;
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if( !(allowIncomplete && isIncomplete) ) {
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logger.warn(e.getMessage());
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throw e;
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}
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}
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// Apache CLI can ignore unrecognized arguments with a boolean flag, but
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// you can't get to the unparsed args. Override PosixParser with a class
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// that can reach in and extract the protected command line.
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this.cmd = parser.getCmd();
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}
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public void loadArgumentsIntoObject( Object obj ) {
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Collection<Option> opts = m_options.getOptions();
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// logger.info("We have " + opts.size() + " options");
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for (Option opt : opts) {
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//logger.info("looking at " + m_storageLocations.get(opt.getLongOpt()));
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Field field = m_storageLocations.get(opt.getLongOpt());
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// Check to see if the object contains the specified field. Iterate through
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// the array rather than doing a name lookup in case field names overlap between
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// multiple classes in the application.
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List<Field> fieldsInObj = Arrays.asList(obj.getClass().getFields());
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if( !fieldsInObj.contains(field) )
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continue;
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if (cmd.hasOption(opt.getOpt())) {
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try {
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if (opt.hasArg())
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field.set(obj, constructFromString(field, cmd.getOptionValues(opt.getOpt())));
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else
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field.set(obj, new Boolean(true));
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} catch (IllegalAccessException e) {
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logger.fatal("processArgs: cannot convert field " + field.toString());
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throw new RuntimeException("processArgs: Failed conversion " + e.getMessage());
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}
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}
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else {
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if( hasDefaultValue( field ) ) {
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try {
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field.set(obj, constructFromString(field, new String[] { getDefaultValue(field) }) );
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}
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catch (IllegalAccessException e) {
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logger.fatal("processArgs: cannot convert field " + field.toString());
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throw new RuntimeException("processArgs: Failed conversion " + e.getMessage());
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}
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}
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}
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}
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}
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/**
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* Returns whether this field is annotated with a default value.
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* @param f the field to check for a default.
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* @return whether a default value exists.
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*/
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private boolean hasDefaultValue( Field f ) {
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return getDefaultValue( f ) != null;
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}
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/**
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* Gets the String representation for the default value of a given argument.
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* @return The string of a default value, or null if no default exists.
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*/
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private String getDefaultValue( Field f ) {
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Argument arg = f.getAnnotation( Argument.class );
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if( arg == null )
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return null;
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String defaultValue = arg.defaultValue().trim();
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if( defaultValue.length() == 0 )
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return null;
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return defaultValue;
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}
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/**
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* Simple class to wrap the posix parser and get access to the parsed cmd object.
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*/
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private class OurPosixParser extends PosixParser {
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public CommandLine getCmd() { return cmd; }
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}
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/**
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* Extract arguments stored in annotations from fields of a given class.
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* @param source Source of arguments, probably provided through Argument annotation.
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*/
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public void addArgumentSource( CommandLineProgram clp, Class source ) {
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Field[] fields = source.getFields();
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for( Set<Field> optionGroup: groupExclusiveOptions(fields) ) {
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List<Pair<Option,Field>> options = new ArrayList<Pair<Option,Field>>();
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for( Field field: optionGroup ) {
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Argument argument = field.getAnnotation(Argument.class);
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Option option = createOptionFromField( clp.getArgumentSourceName( source ), field, argument );
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options.add( new Pair<Option,Field>( option, field ) );
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}
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if( options.size() == 1 )
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AddToOptionStorage( options.get(0).first, options.get(0).second );
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else {
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AddToOptionStorage( options );
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}
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}
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}
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/**
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* Group mutually exclusive options together into sets. Non-exclusive options
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* will be alone a set. Every option should appear in exactly one set.
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* WARNING: Has no concept of nested dependencies.
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* @param fields list of fields for which to check options.
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* @return groupings of mutually exclusive options.
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*/
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private List<Set<Field>> groupExclusiveOptions( Field[] fields ) {
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List<Set<Field>> optionGroups = new ArrayList<Set<Field>>();
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for(Field field: fields) {
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Argument argument = field.getAnnotation(Argument.class);
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if(argument == null)
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continue;
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String[] exclusives = argument.exclusive().split(",");
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if( exclusives.length != 0 ) {
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HashSet<Field> matchingFields = new HashSet<Field>();
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// Find the set of all options exclusive to this one.
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matchingFields.add( field );
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for( Field candidate: fields ) {
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for( String exclusive: exclusives ) {
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if( candidate.getName().equals( exclusive.trim() ) )
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matchingFields.add( candidate );
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}
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}
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// Perform a set intersection to see whether this set of fields intersects
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// with any existing set.
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//
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// If so, add any additional elements to the list.
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boolean setExists = false;
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for( Set<Field> optionGroup: optionGroups ) {
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Set<Field> working = new HashSet<Field>(optionGroup);
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working.retainAll( matchingFields );
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if( working.size() > 0 ) {
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optionGroup.addAll( matchingFields );
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setExists = true;
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}
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}
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// Otherwise, add a new option group.
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if( !setExists )
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optionGroups.add( matchingFields );
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}
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}
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return optionGroups;
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}
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/**
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* Given a field with some annotations, create a command-line option. If not enough data is
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* available to create a command-line option, return null.
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* @param sourceName Source class containing the field.
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* @param field Field
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* @return Option representing the field options.
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*/
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private Option createOptionFromField( String sourceName, Field field, Argument argument ) {
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String fullName = (argument.fullName().length() != 0) ? argument.fullName() : field.getName().trim().toLowerCase();
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String shortName = (argument.shortName().length() != 0) ? argument.shortName() : fullName.substring(0,1);
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String description = argument.doc();
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boolean isRequired = argument.required();
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boolean isFlag = (field.getType() == Boolean.class) || (field.getType() == Boolean.TYPE);
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boolean isCollection = field.getType().isArray() || Collection.class.isAssignableFrom(field.getType());
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if( isFlag && isCollection )
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throw new IllegalArgumentException("Can't have an array of flags.");
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OptionBuilder.withLongOpt(fullName);
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if( !isFlag ) {
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OptionBuilder.withArgName(fullName);
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if( isCollection )
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OptionBuilder.hasArgs();
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else
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OptionBuilder.hasArg();
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}
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if( isRequired ) {
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OptionBuilder.isRequired();
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description = String.format("(Required Option) %s", description);
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}
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sourceName = sourceName.trim();
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if( sourceName.length() > 0 )
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description = String.format("[%s] %s", sourceName, description );
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if( description.length() != 0 ) OptionBuilder.withDescription( description );
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return OptionBuilder.create( shortName );
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}
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/**
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* Constructs a command-line argument given a string and field.
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* @param f Field type from which to infer the type.
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* @param strs Collection of parameter strings to parse.
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* @return Parsed object of the inferred type.
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*/
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private Object constructFromString(Field f, String[] strs) {
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Class type = f.getType();
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if( Collection.class.isAssignableFrom(type) ) {
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Collection collection = null;
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Class containedType = null;
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// If this is a parameterized collection, find the contained type. If blow up if only one type exists.
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if( f.getGenericType() instanceof ParameterizedType ) {
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ParameterizedType parameterizedType = (ParameterizedType)f.getGenericType();
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if( parameterizedType.getActualTypeArguments().length > 1 )
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throw new IllegalArgumentException("Unable to determine collection type of field: " + f.toString());
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containedType = (Class)parameterizedType.getActualTypeArguments()[0];
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}
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else
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containedType = String.class;
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// If this is a generic interface, pick a concrete implementation to create and pass back.
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// Because of type erasure, don't worry about creating one of exactly the correct type.
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if( Modifier.isInterface(type.getModifiers()) || Modifier.isAbstract(type.getModifiers()) )
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{
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if( java.util.List.class.isAssignableFrom(type) ) type = ArrayList.class;
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else if( java.util.Queue.class.isAssignableFrom(type) ) type = java.util.ArrayDeque.class;
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else if( java.util.Set.class.isAssignableFrom(type) ) type = java.util.TreeSet.class;
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}
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try
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{
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collection = (Collection)type.newInstance();
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}
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catch( Exception ex ) {
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// Runtime exceptions are definitely unexpected parsing simple collection classes.
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throw new IllegalArgumentException(ex);
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}
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for( String str: strs )
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collection.add( constructSingleElement(f,containedType,str) );
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return collection;
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}
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else if( type.isArray() ) {
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Class containedType = type.getComponentType();
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|
|
Object arr = Array.newInstance(containedType,strs.length);
|
|
for( int i = 0; i < strs.length; i++ )
|
|
Array.set( arr,i,constructSingleElement(f,containedType,strs[i]) );
|
|
return arr;
|
|
}
|
|
else {
|
|
if( strs.length != 1 )
|
|
throw new IllegalArgumentException("Passed multiple arguments to an object expecting a single value.");
|
|
return constructSingleElement(f,type,strs[0]);
|
|
}
|
|
}
|
|
|
|
/**
|
|
* Builds a single element of the given type.
|
|
* @param f Implies type of data to construct.
|
|
* @param str String representation of data.
|
|
* @return parsed form of String.
|
|
*/
|
|
private Object constructSingleElement(Field f, Class type, String str) {
|
|
// lets go through the types we support
|
|
if (type == Boolean.TYPE) {
|
|
boolean b = false;
|
|
if (str.toLowerCase().equals("true")) {
|
|
b = true;
|
|
}
|
|
Boolean bool = new Boolean(b);
|
|
return bool;
|
|
} else if (type == Integer.TYPE) {
|
|
Integer in = Integer.valueOf(str);
|
|
return in;
|
|
} else if (type == Float.TYPE) {
|
|
Float fl = Float.valueOf(str);
|
|
return fl;
|
|
}
|
|
else {
|
|
Constructor ctor = null;
|
|
try {
|
|
ctor = type.getConstructor(String.class);
|
|
return ctor.newInstance(str);
|
|
} catch (NoSuchMethodException e) {
|
|
logger.fatal("constructFromString:NoSuchMethodException: cannot convert field " + f.toString());
|
|
throw new RuntimeException("constructFromString:NoSuchMethodException: Failed conversion " + e.getMessage());
|
|
} catch (IllegalAccessException e) {
|
|
logger.fatal("constructFromString:IllegalAccessException: cannot convert field " + f.toString());
|
|
throw new RuntimeException("constructFromString:IllegalAccessException: Failed conversion " + e.getMessage());
|
|
} catch (InvocationTargetException e) {
|
|
logger.fatal("constructFromString:InvocationTargetException: cannot convert field " + f.toString());
|
|
throw new RuntimeException("constructFromString:InvocationTargetException: Failed conversion " + e.getMessage());
|
|
} catch (InstantiationException e) {
|
|
logger.fatal("constructFromString:InstantiationException: cannot convert field " + f.toString());
|
|
throw new RuntimeException("constructFromString:InstantiationException: Failed conversion " + e.getMessage());
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
}
|
|
|
|
|
|
/**
|
|
|
|
public static void main(String[] args) {
|
|
ArgumentParser p = new ArgumentParser("CrapApp");
|
|
p.setupDefaultArgs();
|
|
p.addRequiredArg("Flag","F","a required arg");
|
|
p.addRequiredFlag("Sub","S","a required flag");
|
|
p.addOptionalArg("Boat","T","Maybe you want a boat?");
|
|
String[] str = {"--Flag","rrr","-T","ppp", "--Flag","ttt"};
|
|
p.processArgs(str);
|
|
Iterator<String> r = map.keySet().iterator();
|
|
while (r.hasNext()) {
|
|
String key = r.next();
|
|
String[] q = map.get(key);
|
|
if (q != null) {
|
|
for (String mystr : q) {
|
|
System.err.println("key: " + key + " val: " + mystr);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
*/
|