Revert "closes #122 - updating Apache Commons CLI usage to avoid depr…

…ecated classes"

This reverts commit 93e9f86.

src/java/boa/BoaMain.java

@@ -24,7 +24,7 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.PosixParser;
 
 /**
  * The main entry point for Boa-related tools.
@@ -46,7 +46,7 @@ public static void main(final String[] args) throws IOException {
                 printHelp(options, null);
                 return;
             } else {
-                final CommandLine cl = new DefaultParser().parse(options, new String[] { args[0] });
+                final CommandLine cl = new PosixParser().parse(options, new String[] { args[0] });
                 final String[] tempargs = new String[args.length - 1];
                 System.arraycopy(args, 1, tempargs, 0, args.length - 1);
 

src/java/boa/compiler/BoaCompiler.java

@@ -39,9 +39,9 @@
 import org.stringtemplate.v4.ST;
 
 import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
+import org.apache.commons.cli.PosixParser;
 import org.apache.log4j.Logger;
 
 import org.scannotation.ClasspathUrlFinder;
@@ -383,7 +383,7 @@ private static CommandLine processCommandLineOptions(final String[] args) {
 
 		final CommandLine cl;
 		try {
-			cl = new DefaultParser().parse(options, args);
+			cl = new PosixParser().parse(options, args);
 		} catch (final org.apache.commons.cli.ParseException e) {
 			System.err.println(e.getMessage());
 			new HelpFormatter().printHelp("Boa Compiler", options);
@@ -422,7 +422,7 @@ private static CommandLine processParseCommandLineOptions(final String[] args) {
 
 		final CommandLine cl;
 		try {
-			cl = new DefaultParser().parse(options, args);
+			cl = new PosixParser().parse(options, args);
 		} catch (final org.apache.commons.cli.ParseException e) {
             printHelp(options, e.getMessage());
 			return null;

src/java/boa/datagen/BoaGenerator.java

@@ -20,9 +20,9 @@
 import java.io.IOException;
 
 import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
+import org.apache.commons.cli.PosixParser;
 
 import boa.datagen.forges.github.GetGithubRepoByUser;
 import boa.datagen.forges.github.LocalGitSequenceGenerator;
@@ -43,7 +43,7 @@ public static void main(final String[] args) throws IOException {
 
 		final CommandLine cl;
 		try {
-			cl = new DefaultParser().parse(options, args);
+			cl = new PosixParser().parse(options, args);
 		} catch (final org.apache.commons.cli.ParseException e) {
 			System.err.println(e.getMessage());
 			new HelpFormatter().printHelp("BoaCompiler", options);

src/java/boa/evaluator/BoaEvaluator.java

@@ -25,8 +25,9 @@
 import java.util.UUID;
 
 import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
+import org.apache.commons.cli.PosixParser;
 import org.apache.commons.io.FileUtils;
 
 import boa.BoaMain;
@@ -74,7 +75,7 @@ public static void main(final String[] args) {
 				printHelp(options, null);
 				return;
 			} else {
-				final CommandLine cl = new DefaultParser().parse(options, args);
+				final CommandLine cl = new PosixParser().parse(options, args);
 
 				if (cl.hasOption('i') && cl.hasOption('d')) {
 					final BoaEvaluator evaluator;

src/java/boa/runtime/BoaRunner.java

@@ -1,7 +1,6 @@
 /*
- * Copyright 2017, Anthony Urso, Hridesh Rajan, Robert Dyer, 
- *                 Iowa State University of Science and Technology
- *                 and Bowling Green State University
+ * Copyright 2014, Anthony Urso, Hridesh Rajan, Robert Dyer, 
+ *                 and Iowa State University of Science and Technology
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -20,11 +19,11 @@
 import java.io.IOException;
 
 import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionBuilder;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
+import org.apache.commons.cli.PosixParser;
 
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.conf.Configured;
@@ -106,21 +105,21 @@ public Job job(final Path[] ins, final Path out) throws IOException {
 	static {
 		options.addOption("p", "profile", false, "if true, profiles the execution of 1 map task");
 		options.addOption("b", "block", false, "if true, wait for job to finish and show status");
-		options.addOption(Option.builder("j").longOpt("job")
-										.desc("sets the MySql ID to update with this job's status")
+		options.addOption(OptionBuilder.withLongOpt("job")
+										.withDescription("sets the MySql ID to update with this job's status")
 										.hasArg()
-										.argName("ID")
-										.build());
-		options.addOption(Option.builder("a").longOpt("ast")
-										.desc("which INPUT to use for ASTs")
+										.withArgName("ID")
+										.create("j"));
+		options.addOption(org.apache.commons.cli.OptionBuilder.withLongOpt("ast")
+										.withDescription("which INPUT to use for ASTs")
 										.hasArg()
-										.argName("INPUT")
-										.build());
-		options.addOption(Option.builder("c").longOpt("comments")
-										.desc("which INPUT to use for comments")
+										.withArgName("INPUT")
+										.create("a"));
+		options.addOption(org.apache.commons.cli.OptionBuilder.withLongOpt("comments")
+										.withDescription("which INPUT to use for comments")
 										.hasArg()
-										.argName("INPUT")
-										.build());
+										.withArgName("INPUT")
+										.create("c"));
 	}
 
 	protected static Options getOptions() { return options; }
@@ -129,7 +128,7 @@ public static CommandLine parseArgs(String[] args, String usage) {
 		CommandLine line = null;
 
 		try {
-			line = new DefaultParser().parse(options, args);
+			line = new PosixParser().parse(options, args);
 		} catch (ParseException exp) {
 			System.err.println(exp.getMessage());
 			printHelp(usage);