/* * Copyright (c) 2010 The Broad Institute * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation * files (the "Software"), to deal in the Software without * restriction, including without limitation the rights to use, * copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the * Software is furnished to do so, subject to the following * conditions: * * The above copyright notice and this permission notice shall be * included in all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ package org.broadinstitute.sting.commandline; import org.broadinstitute.sting.utils.Utils; import java.util.regex.Matcher; import java.util.regex.Pattern; /** * Holds a pattern, along with how to get to the argument definitions that could match that pattern. */ public abstract class ParsingMethod { private final Pattern pattern; private final DefinitionMatcher definitionMatcher; /** * Create a new parsing method with the given identifying / validating pattern and definition matcher. * @param pattern The pattern * @param definitionMatcher The definition matcher. */ private ParsingMethod( Pattern pattern, DefinitionMatcher definitionMatcher ) { this.pattern = pattern; this.definitionMatcher = definitionMatcher; } /** * Can the given token be parsed by this parsing method? * @param token Token to validate. * @return True if the given token matches. */ public boolean matches( String token ) { Matcher matcher = pattern.matcher(token); return matcher.matches(); } /** * Find the best match for a given token at a given position from among the provided * argument definitions. * @param definitions List of argument definitions. * @param token The token from the command line to match. Should be validated using * ParsingMethod's matches() tester. * @param position Position at which this command-line argument occurs. Will be used * for validation later. * @return An argument match. Definition field will be populated if a match was found or * empty if no appropriate definition could be found. */ public ArgumentMatch match( ArgumentDefinitions definitions, String token, int position ) { // If the argument is valid, parse out the argument. Matcher matcher = pattern.matcher(token); // Didn't match? Must be bad input. if( !matcher.matches() ) throw new IllegalArgumentException( String.format("Unable to parse token %s with pattern %s", token, pattern.pattern()) ); String argument = matcher.group(1).trim(); Tags tags = new Tags(); if(matcher.group(2) != null) { for(String tag: Utils.split(matcher.group(2),",")) { // Check for presence of an '=' sign, indicating a key-value pair in the tag line. int equalDelimiterPos = tag.indexOf('='); if(equalDelimiterPos >= 0) { // Sanity check; ensure that there aren't multiple '=' in this key-value pair. if(tag.indexOf('=',equalDelimiterPos+1) >= 0) throw new ArgumentException(String.format("Tag %s passed to argument %s is malformed. Please ensure that " + "key-value tags are of the form =, and neither key " + "nor value contain the '=' character", tag, argument)); tags.addKeyValueTag(tag.substring(0,equalDelimiterPos),tag.substring(equalDelimiterPos+1)); } else tags.addPositionalTag(tag); } } // Find the most appropriate argument definition for the given argument. ArgumentDefinition argumentDefinition = definitions.findArgumentDefinition( argument, definitionMatcher ); // Try to find a matching argument. If found, label that as the match. If not found, add the argument // with a null definition. ArgumentMatch argumentMatch = new ArgumentMatch(argument,argumentDefinition,position,tags); return argumentMatch; } /** * A command-line argument always starts with an alphabetical character or underscore followed by any word character. */ private static final String ARGUMENT_TEXT = "[A-Za-z_][\\w\\-\\.]*"; /** * Tags, on the other hand, can start with any word character. */ private static final String TAG_TEXT = "[\\w\\-\\.\\=]*"; public static ParsingMethod FullNameParsingMethod = new ParsingMethod(Pattern.compile(String.format("\\s*--(%1$s)(?:\\:(%2$s(?:,%2$s)*))?\\s*",ARGUMENT_TEXT,TAG_TEXT)), ArgumentDefinitions.FullNameDefinitionMatcher) {}; public static ParsingMethod ShortNameParsingMethod = new ParsingMethod(Pattern.compile(String.format("\\s*-(%1$s)(?:\\:(%2$s(?:,%2$s)*))?\\s*",ARGUMENT_TEXT,TAG_TEXT)), ArgumentDefinitions.ShortNameDefinitionMatcher) {}; }