added some cleanup of code, and new junit targets to the build file

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@177 348d0f76-0448-11de-a6fe-93d51630548a

build.xml

@@ -48,6 +48,53 @@
         <ivy:retrieve/>
     </target>
 
+
+    <!-- where to put reports and tests-->
+    <property name="report" value="build/report"/>
+    <property name="test.classes" value="build/testclasses"/>
+    <property name="test.output" value="dist/test"/>
+    <property name="test.sources" value="java/test"/>
+    <property name="classes" value="classes"/>
+
+
+    <target name="test.compile" depends="compile" description="Compile test cases">
+        <echo message="Sting: Compiling test cases!"/>
+        <mkdir dir="${test.classes}"/>
+        <javac destdir="${test.classes}" debug="on" optimize="on">
+            <src path="${test.sources}"/>
+            <classpath>
+                <path refid="thirdparty.dependencies"/>
+                <pathelement location="build"/>
+                <pathelement location="lib/junit-4.4.jar"/>
+            </classpath>
+        </javac>
+    </target>
+
+
+    <!-- TEST -->
+    <target name="test" depends="test.compile">
+        <mkdir dir="${report}"/>
+        <echo message="Sting: Running test cases!"/>
+        <junit printsummary="yes" clonevm="yes" haltonfailure="yes">
+            <formatter type="plain"/>
+            
+            <classpath>
+                <path refid="thirdparty.dependencies"/>
+                <pathelement location="build"/>
+                <pathelement location="${test.classes}"/>
+                <pathelement location="lib/junit-4.4.jar"/>
+            </classpath>
+
+            <batchtest fork="yes" todir="${report}">
+                <fileset dir="${test.classes}">
+                    <include name="**/*.class"/>
+                </fileset>
+            </batchtest>
+        </junit>
+
+    </target>
+
+
     <target name="init">
         <!-- Create the time stamp -->
         <tstamp/>

java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java

@@ -66,6 +66,7 @@ public class ArgumentParser {
                 true);
     }
 
+
     /**
      * addOptionalArg
      * <p/>
@@ -77,6 +78,7 @@ public class ArgumentParser {
      * @param fieldname   the field to set when we've parsed this option
      */
     public void addOptionalArg(String name, String letterform, String description, String fieldname) {
+
         // we always want the help option to be available
         Option opt = OptionBuilder.withLongOpt(name).withArgName(name)
                 .hasArg()
@@ -98,9 +100,15 @@ public class ArgumentParser {
      * @param opt        the option
      */
     private void AddToOptionStorage(String name, String letterform, String fieldname, Option opt) {
+
         // add to the option list
         m_options.addOption(opt);
 
+        // first check to see if we've already added an option with the same name
+        if (m_option_names.contains(letterform)) {
+            throw new IllegalArgumentException(letterform + " was already added as an option");
+        }
+
         // add the object with it's name to the storage location
         try {
             m_storageLocations.put(name, prog.getClass().getField(fieldname));
@@ -159,6 +167,7 @@ public class ArgumentParser {
     }
 
 
+
     /**
      * addRequiredlArg
      * <p/>
@@ -170,6 +179,7 @@ public class ArgumentParser {
      * @param fieldname   what field it should be stuck into on the calling class
      */
     public void addRequiredlArgList(String name, String letterform, String description, String fieldname) {
+
         // we always want the help option to be available
         Option opt = OptionBuilder.isRequired()
                 .withLongOpt(name)
@@ -193,11 +203,22 @@ public class ArgumentParser {
      * @param fieldname   what field it should be stuck into on the calling class
      */
     public void addOptionalFlag(String name, String letterform, String description, String fieldname) {
+
+        // if they've passed a non-Boolean as a object, beat them
+        try {
+            if (!(prog.getClass().getField(fieldname).getType() == Boolean.class)) {
+                throw new IllegalArgumentException("Fields to addOptionalFlag must be of type Boolean");
+            }
+        } catch (NoSuchFieldException e) {
+            throw new IllegalArgumentException("Fields to addOptionalFlag must exist!");
+        }
+        
         // we always want the help option to be available
         Option opt = OptionBuilder.withLongOpt(name)
                 .withDescription(description)
                 .create(letterform);
 
+
         // add it to the option
         AddToOptionStorage(name, letterform, fieldname, opt);
 
@@ -215,6 +236,16 @@ public class ArgumentParser {
      * @param fieldname   what field it should be stuck into on the calling class
      */
     public void addRequiredlFlag(String name, String letterform, String description, String fieldname) {
+
+        // if they've passed a non-Boolean as a object, beat them
+        try {
+            if (!(prog.getClass().getField(fieldname).getType() == Boolean.class)) {
+                throw new IllegalArgumentException("Fields to addRequiredlFlag must be of type Boolean");
+            }
+        } catch (NoSuchFieldException e) {
+            throw new IllegalArgumentException("Fields to addRequiredlFlag must exist!");
+        }
+
         // we always want the help option to be available
         Option opt = OptionBuilder.isRequired()
                 .withLongOpt(name)
@@ -234,7 +265,7 @@ public class ArgumentParser {
      *
      * @param args the command line arguments we recieved
      */
-    public void processArgs(String[] args) {
+    public void processArgs(String[] args) throws ParseException {
         CommandLineParser parser = new PosixParser();
 
         try {
@@ -254,8 +285,7 @@ public class ArgumentParser {
                             logger.fatal("processArgs: cannot convert field " + f.toString());
                             throw new RuntimeException("processArgs: Failed conversion " + e.getMessage());
                         }
-                    }
+                    } else {
-                    else {
 
                         Field f = m_storageLocations.get(opt.getLongOpt());
                         try {
@@ -271,12 +301,6 @@ public class ArgumentParser {
         } catch (UnrecognizedOptionException e) {
             // we don't care about unknown exceptions right now
             logger.warn(e.getMessage());
-        } catch (ParseException e) {
-            // we didn't get all the required arguments,
-            // print out the help
-            e.printStackTrace();
-            this.printHelp();
-            System.exit(1);
         }
     }