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Remove old Apache CLI-based arg system. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@604 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-05-06 18:37:51 +00:00
parent 521aa40baa
commit ef211f96b1
6 changed files with 13 additions and 840 deletions
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1
ivy.xml
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@ -7,7 +7,6 @@
<dependency org="junit" name="junit" rev="4.4" />
<dependency org="log4j" name="log4j" rev="1.2.15" />
<dependency org="colt" name="colt" rev="1.2.0" />
<dependency org="commons-cli" name="commons-cli" rev="1.2" />
<dependency org="bcel" name="bcel" rev="5.1" />
<!-- The following are all castor dependencies. Remove when transitive dependencies are working -->

2
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -4,8 +4,6 @@ import edu.mit.broad.picard.reference.ReferenceSequenceFile;
import edu.mit.broad.picard.reference.ReferenceSequenceFileFactory;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMFileReader.ValidationStringency;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionBuilder;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.executive.MicroScheduler;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;

617
java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
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@ -1,617 +0,0 @@
package org.broadinstitute.sting.utils.cmdLine;
import org.apache.commons.cli.*;
import org.apache.log4j.Logger;
import java.lang.reflect.Array;
import java.lang.reflect.Constructor;
import java.lang.reflect.Field;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Modifier;
import java.lang.reflect.ParameterizedType;
import java.util.Arrays;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.HashSet;
import java.util.Set;
import org.broadinstitute.sting.utils.Pair;
/**
* User: aaron
* Date: Mar 19, 2009
* Time: 6:54:15 PM
* <p/>
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
* This software and its documentation are copyright 2009 by the
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
* <p/>
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
*/
public class ArgumentParser {
// what program are we parsing for
private String programName;
// the command-line options received.
private CommandLine cmd;
// where we eventually want the values to land
private HashMap<String,Field> m_storageLocations = new HashMap<String,Field>();
// create Options object
protected Options m_options = new Options();
/**
* our log, which we want to capture anything from org.broadinstitute.sting
*/
protected static Logger logger = Logger.getLogger(ArgumentParser.class);
// the reference to the command line program to fill in
Object prog;
public ArgumentParser(String programName, Object prog) {
this.programName = programName;
this.prog = prog;
}
/**
* print out the help information
*/
public void printHelp() {
// automatically generate the help statement
org.apache.commons.cli.HelpFormatter formatter = new org.apache.commons.cli.HelpFormatter();
formatter.printHelp(100,
"java -Xmx4096m -jar dist/GenomeAnalysisTK.jar",
"",
m_options,
"",
true);
}
/**
* addOptionalArg
* <p/>
* Adds an optional argument to check on the command line
*
* @param name the name of the argument, the long name
* @param letterform the short form
* @param description the description of the argument
* @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()
.withDescription(description)
.create(letterform);
// add it to the option
AddToOptionStorage(opt, fieldname);
}
public void addOptionalArg(Option opt, String fieldname) {
// add it to the option
AddToOptionStorage(opt, fieldname);
}
/**
* Used locally to add to the options storage we have, for latter processing
*
* @param opt the option
* @param fieldname what field it should be stuck into on the calling class
*/
private void AddToOptionStorage(Option opt, String fieldname) {
AddToOptionStorage( opt, getField(prog, fieldname) );
}
/**
* Used locally to add to the options storage we have, for latter processing
*
* @param opt the option
* @param field what field it should be stuck into on the calling class
*/
private void AddToOptionStorage(Option opt, Field field ) {
// first check to see if we've already added an option with the same name
if (m_options.hasOption( opt.getOpt() ))
throw new IllegalArgumentException(opt.getOpt() + " was already added as an option");
// Doesn't make much sense to have a single (ungrouped) required option. Force to unrequired.
if( !opt.hasArg() && opt.isRequired() )
opt.setRequired(false);
// add to the option list
m_options.addOption(opt);
// add the object with it's name to the storage location
m_storageLocations.put( opt.getLongOpt(), field );
}
/**
* Used locally to add a group of mutually exclusive options to options storage.
* @param options A list of pairs of param, field to add.
*/
private void AddToOptionStorage( List<Pair<Option,Field>> options ) {
// Create an option group and mark it 'required'. If any of its constituent parameters
// are NOT required, they'll unset the required bit for the whole group.
OptionGroup optionGroup = new OptionGroup();
optionGroup.setRequired(true);
for( Pair<Option,Field> option: options ) {
if (m_options.hasOption(option.first.getOpt()) )
throw new IllegalArgumentException(option.first.getOpt() + " was already added as an option");
optionGroup.addOption(option.first);
m_storageLocations.put( option.first.getLongOpt(), option.second );
optionGroup.setRequired( optionGroup.isRequired() & option.first.isRequired() );
}
m_options.addOptionGroup(optionGroup);
}
private Field getField( Object obj, String fieldName ) {
try {
return obj.getClass().getField(fieldName);
} catch (NoSuchFieldException e) {
logger.fatal("Failed to find the field specified by the fieldname parameter.");
throw new RuntimeException(e.getMessage());
}
}
/**
* addRequiredArg
* <p/>
* Adds a required argument to check on the command line
*
* @param name the name of the argument, the long name
* @param letterform the short form
* @param description the description of the argument
* @param fieldname what field it should be stuck into on the calling class
*/
public void addRequiredArg(String name, String letterform, String description, String fieldname) {
// we always want the help option to be available
Option opt = OptionBuilder.isRequired()
.withLongOpt(name)
.withArgName(name)
.hasArg()
.withDescription("(Required Option) " + description)
.create(letterform);
// add it to the option
AddToOptionStorage( opt, fieldname );
}
/**
* addOptionalArg
* <p/>
* Adds an optional argument to check on the command line
*
* @param name the name of the argument, the long name
* @param letterform the short form
* @param description the description of the argument
* @param fieldname what field it should be stuck into on the calling class
*/
public void addOptionalArgList(String name, String letterform, String description, String fieldname) {
// we always want the help option to be available
Option opt = OptionBuilder.withLongOpt(name).withArgName(name)
.hasArgs()
.withDescription(description)
.create(letterform);
// add it to the option
AddToOptionStorage( opt, fieldname );
}
/**
* addRequiredArg
* <p/>
* Adds a required argument to check on the command line
*
* @param name the name of the argument, the long name
* @param letterform the short form
* @param description the description of the argument
* @param fieldname what field it should be stuck into on the calling class
*/
public void addRequiredArgList(String name, String letterform, String description, String fieldname) {
// we always want the help option to be available
Option opt = OptionBuilder.isRequired()
.withLongOpt(name)
.withArgName(name)
.hasArgs()
.withDescription("(Required Option) " + description)
.create(letterform);
// add it to the option
AddToOptionStorage(opt, fieldname);
}
/**
* addOptionalFlag
* <p/>
* Adds an optional argument to check on the command line
*
* @param name the name of the argument, the long name
* @param letterform the short form
* @param description the description of the argument
* @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( opt, fieldname );
}
/**
* This function is called to validate all the arguments to the program.
* If a required Arg isn't found, we generate the help message, and
* exit the program
*
* @param args the command line arguments we recieved
* @param allowIncomplete whether to allow incomplete command-line arguments
*/
public void processArgs(String[] args, boolean allowIncomplete) throws ParseException {
OurPosixParser parser = new OurPosixParser();
try {
parser.parse(m_options, args, false);
}
catch( ParseException e ) {
boolean isIncomplete = e instanceof org.apache.commons.cli.MissingArgumentException ||
e instanceof MissingOptionException ||
e instanceof UnrecognizedOptionException;
if( !(allowIncomplete && isIncomplete) ) {
logger.warn(e.getMessage());
throw e;
}
}
// Apache CLI can ignore unrecognized arguments with a boolean flag, but
// you can't get to the unparsed args. Override PosixParser with a class
// that can reach in and extract the protected command line.
this.cmd = parser.getCmd();
}
public void loadArgumentsIntoObject( Object obj ) {
Collection<Option> opts = m_options.getOptions();
// logger.info("We have " + opts.size() + " options");
for (Option opt : opts) {
//logger.info("looking at " + m_storageLocations.get(opt.getLongOpt()));
Field field = m_storageLocations.get(opt.getLongOpt());
// Check to see if the object contains the specified field. Iterate through
// the array rather than doing a name lookup in case field names overlap between
// multiple classes in the application.
List<Field> fieldsInObj = Arrays.asList(obj.getClass().getFields());
if( !fieldsInObj.contains(field) )
continue;
if (cmd.hasOption(opt.getOpt())) {
try {
if (opt.hasArg())
field.set(obj, constructFromString(field, cmd.getOptionValues(opt.getOpt())));
else
field.set(obj, new Boolean(true));
} catch (IllegalAccessException e) {
logger.fatal("processArgs: cannot convert field " + field.toString());
throw new RuntimeException("processArgs: Failed conversion " + e.getMessage());
}
}
else {
if( hasDefaultValue( field ) ) {
try {
field.set(obj, constructFromString(field, new String[] { getDefaultValue(field) }) );
}
catch (IllegalAccessException e) {
logger.fatal("processArgs: cannot convert field " + field.toString());
throw new RuntimeException("processArgs: Failed conversion " + e.getMessage());
}
}
}
}
}
/**
* Returns whether this field is annotated with a default value.
* @param f the field to check for a default.
* @return whether a default value exists.
*/
private boolean hasDefaultValue( Field f ) {
return getDefaultValue( f ) != null;
}
/**
* Gets the String representation for the default value of a given argument.
* @return The string of a default value, or null if no default exists.
*/
private String getDefaultValue( Field f ) {
Argument arg = f.getAnnotation( Argument.class );
if( arg == null )
return null;
String defaultValue = arg.defaultValue().trim();
if( defaultValue.length() == 0 )
return null;
return defaultValue;
}
/**
* Simple class to wrap the posix parser and get access to the parsed cmd object.
*/
private class OurPosixParser extends PosixParser {
public CommandLine getCmd() { return cmd; }
}
/**
* Extract arguments stored in annotations from fields of a given class.
* @param source Source of arguments, probably provided through Argument annotation.
*/
public void addArgumentSource( CommandLineProgram clp, Class source ) {
Field[] fields = source.getFields();
for( Set<Field> optionGroup: groupExclusiveOptions(fields) ) {
List<Pair<Option,Field>> options = new ArrayList<Pair<Option,Field>>();
for( Field field: optionGroup ) {
Argument argument = field.getAnnotation(Argument.class);
Option option = createOptionFromField( clp.getArgumentSourceName( source ), field, argument );
options.add( new Pair<Option,Field>( option, field ) );
}
if( options.size() == 1 )
AddToOptionStorage( options.get(0).first, options.get(0).second );
else {
AddToOptionStorage( options );
}
}
}
/**
* Group mutually exclusive options together into sets. Non-exclusive options
* will be alone a set. Every option should appear in exactly one set.
* WARNING: Has no concept of nested dependencies.
* @param fields list of fields for which to check options.
* @return groupings of mutually exclusive options.
*/
private List<Set<Field>> groupExclusiveOptions( Field[] fields ) {
List<Set<Field>> optionGroups = new ArrayList<Set<Field>>();
for(Field field: fields) {
Argument argument = field.getAnnotation(Argument.class);
if(argument == null)
continue;
String[] exclusives = argument.exclusive().split(",");
if( exclusives.length != 0 ) {
HashSet<Field> matchingFields = new HashSet<Field>();
// Find the set of all options exclusive to this one.
matchingFields.add( field );
for( Field candidate: fields ) {
for( String exclusive: exclusives ) {
if( candidate.getName().equals( exclusive.trim() ) )
matchingFields.add( candidate );
}
}
// Perform a set intersection to see whether this set of fields intersects
// with any existing set.
//
// If so, add any additional elements to the list.
boolean setExists = false;
for( Set<Field> optionGroup: optionGroups ) {
Set<Field> working = new HashSet<Field>(optionGroup);
working.retainAll( matchingFields );
if( working.size() > 0 ) {
optionGroup.addAll( matchingFields );
setExists = true;
}
}
// Otherwise, add a new option group.
if( !setExists )
optionGroups.add( matchingFields );
}
}
return optionGroups;
}
/**
* Given a field with some annotations, create a command-line option. If not enough data is
* available to create a command-line option, return null.
* @param sourceName Source class containing the field.
* @param field Field
* @return Option representing the field options.
*/
private Option createOptionFromField( String sourceName, Field field, Argument argument ) {
String fullName = (argument.fullName().length() != 0) ? argument.fullName() : field.getName().trim().toLowerCase();
String shortName = (argument.shortName().length() != 0) ? argument.shortName() : fullName.substring(0,1);
String description = argument.doc();
boolean isRequired = argument.required();
boolean isFlag = (field.getType() == Boolean.class) || (field.getType() == Boolean.TYPE);
boolean isCollection = field.getType().isArray() || Collection.class.isAssignableFrom(field.getType());
if( isFlag && isCollection )
throw new IllegalArgumentException("Can't have an array of flags.");
OptionBuilder.withLongOpt(fullName);
if( !isFlag ) {
OptionBuilder.withArgName(fullName);
if( isCollection )
OptionBuilder.hasArgs();
else
OptionBuilder.hasArg();
}
if( isRequired ) {
OptionBuilder.isRequired();
description = String.format("(Required Option) %s", description);
}
sourceName = sourceName.trim();
if( sourceName.length() > 0 )
description = String.format("[%s] %s", sourceName, description );
if( description.length() != 0 ) OptionBuilder.withDescription( description );
return OptionBuilder.create( shortName );
}
/**
* Constructs a command-line argument given a string and field.
* @param f Field type from which to infer the type.
* @param strs Collection of parameter strings to parse.
* @return Parsed object of the inferred type.
*/
private Object constructFromString(Field f, String[] strs) {
Class type = f.getType();
if( Collection.class.isAssignableFrom(type) ) {
Collection collection = null;
Class containedType = null;
// If this is a parameterized collection, find the contained type. If blow up if only one type exists.
if( f.getGenericType() instanceof ParameterizedType ) {
ParameterizedType parameterizedType = (ParameterizedType)f.getGenericType();
if( parameterizedType.getActualTypeArguments().length > 1 )
throw new IllegalArgumentException("Unable to determine collection type of field: " + f.toString());
containedType = (Class)parameterizedType.getActualTypeArguments()[0];
}
else
containedType = String.class;
// If this is a generic interface, pick a concrete implementation to create and pass back.
// Because of type erasure, don't worry about creating one of exactly the correct type.
if( Modifier.isInterface(type.getModifiers()) || Modifier.isAbstract(type.getModifiers()) )
{
if( java.util.List.class.isAssignableFrom(type) ) type = ArrayList.class;
else if( java.util.Queue.class.isAssignableFrom(type) ) type = java.util.ArrayDeque.class;
else if( java.util.Set.class.isAssignableFrom(type) ) type = java.util.TreeSet.class;
}
try
{
collection = (Collection)type.newInstance();
}
catch( Exception ex ) {
// Runtime exceptions are definitely unexpected parsing simple collection classes.
throw new IllegalArgumentException(ex);
}
for( String str: strs )
collection.add( constructSingleElement(f,containedType,str) );
return collection;
}
else if( type.isArray() ) {
Class containedType = type.getComponentType();
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);
}
}
}
}
*/

6
java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
View File

@ -204,7 +204,7 @@ public abstract class CommandLineProgram {
// return the result
System.exit(result);
}
catch (org.apache.commons.cli.ParseException e) {
catch (ParseException e) {
logger.fatal("Unable to pass command line arguments: " + e.getMessage() );
clp.parser.printHelp();
}
@ -257,7 +257,7 @@ public abstract class CommandLineProgram {
* this function checks the logger level passed in on the command line, taking the lowest
* level that was provided.
*/
private void setupLoggerLevel() throws org.apache.commons.cli.ParseException {
private void setupLoggerLevel() throws ParseException {
Level par = Level.ERROR;
if (logging_level.equals("DEBUG")) {
@ -280,7 +280,7 @@ public abstract class CommandLineProgram {
}
else {
// we don't understand the logging level, let's get out of here
throw new org.apache.commons.cli.ParseException("Unable to match: " + logging_level + " to a logging level, make sure it's a valid level (INFO, DEBUG, ERROR, FATAL, OFF)");
throw new ParseException("Unable to match: " + logging_level + " to a logging level, make sure it's a valid level (INFO, DEBUG, ERROR, FATAL, OFF)");
}
logger.setLevel(par);

14
java/src/org/broadinstitute/sting/utils/cmdLine/ParsingEngine.java
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@ -49,7 +49,7 @@ public class ParsingEngine {
/**
* our log, which we want to capture anything from org.broadinstitute.sting
*/
protected static Logger logger = Logger.getLogger(ArgumentParser.class);
protected static Logger logger = Logger.getLogger(ParsingEngine.class);
public ParsingEngine() {
parsingMethods.add( new ParsingMethod(Pattern.compile("\\s*--([\\w\\.]+)\\s*"), ArgumentDefinitions.FullNameDefinitionMatcher) );
@ -467,10 +467,16 @@ class MissingArgumentException extends StingException {
}
}
class ParseException extends StingException {
public ParseException( String message ) {
super( message );
}
}
/**
* An exception for undefined arguments.
*/
class InvalidArgumentException extends StingException {
class InvalidArgumentException extends ParseException {
public InvalidArgumentException( Collection<ArgumentMatch> invalidArguments ) {
super( formatArguments(invalidArguments) );
}
@ -486,7 +492,7 @@ class InvalidArgumentException extends StingException {
/**
* An exception for values that can't be mated with any argument.
*/
class InvalidArgumentValueException extends StingException {
class InvalidArgumentValueException extends ParseException {
public InvalidArgumentValueException( ArgumentMatch invalidValues ) {
super( formatArguments(invalidValues) );
}
@ -503,7 +509,7 @@ class InvalidArgumentValueException extends StingException {
/**
* An exception indicating that too many values have been provided for the given argument.
*/
class TooManyValuesForArgumentException extends StingException {
class TooManyValuesForArgumentException extends ParseException {
public TooManyValuesForArgumentException( Collection<ArgumentMatch> arguments ) {
super( formatArguments(arguments) );
}

213
java/test/org/broadinstitute/sting/utils/cmdLine/ArgumentParserTest.java
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@ -1,213 +0,0 @@
// our package
package org.broadinstitute.sting.utils.cmdLine;
// the imports for unit testing.
import org.junit.*;
import static org.junit.Assert.*;
import org.apache.commons.cli.ParseException;
import org.broadinstitute.sting.BaseTest;
/**
* The ArgumentParserTest test class. In JUnit 4, you don't have to extent the
* TestCase class, instead we use annotations (@Test, @Before, @After)
* to indicate the test pattern.
* <p/>
* The basic idea of a test workflow in Junit 4 is:
* <p/>
* 1) run the method tagged @BeforeClass
* 2) for each method tagged with @Test {
* run all methods tagged with @Before
* run the @Test tagged method
* run all methods tagged with @After
* 3) run the method tagged with @AfterClass
* <p/>
* You should use the methods like
*/
public class ArgumentParserTest extends BaseTest {
// our argument parser
private ArgumentParser m_parser = null;
public Boolean testBool = false;
public String testString = "";
public Integer testInt = 0;
public Float testFloat = 0.0f;
/**
* This function (because of the @BeforeClass tag) gets called only once ever,
* before any tests are run
*/
@BeforeClass
public static void doBeforeAnyTests() {
}
/**
* Tears down the test fixture after each call.
* <p/>
* Called after every test case method.
*/
@AfterClass
public static void doAfterAllTests() {
}
/**
* This function does the setup of our parser, before each method call.
* <p/>
* Called before every test case method.
*/
@Before
public void doForEachTest() {
// we don't need something done to setup each test
// setup the parser
m_parser = new ArgumentParser("Test Program", this);
m_parser.addOptionalFlag("testBool", "B", "our test bool", "testBool");
m_parser.addRequiredArg("testString", "S", "our test string", "testString");
m_parser.addRequiredArg("testInt", "I", "our test int", "testInt");
m_parser.addRequiredArg("testFloat", "F", "our test float", "testFloat");
}
/**
* Tears down the test fixture after each call.
* <p/>
* Called after every test case method.
*/
@After
public void undoForEachTest() {
// release objects under test here, if necessary
m_parser = null;
}
/**
* Tests that we got a string parameter in correctly
*/
@Test
public void testStringParameter() {
logger.warn("Executing testStringParameter");
// setup the parameter list
String[] params = {"-B", "-S", "String", "-I", "100", "-F", "100.0"};
try {
// process the arguments
m_parser.processArgs(params,false);
m_parser.loadArgumentsIntoObject(this);
} catch (ParseException e) {
fail("We received an unexpected parsing exception");
}
// assert that none of the parameters are still null
org.junit.Assert.assertNotNull(testString);
assertEquals(testString.equals("String"), true);
}
/**
* Tests that we got a Boolean parameter in correctly
*/
@Test
public void testBooleanParameter() {
logger.warn("Executing testBooleanParameter");
// setup the parameter list
String[] params = {"-B", "-S", "String", "-I", "100", "-F", "100.0"};
try {
// process the arguments
m_parser.processArgs(params,false);
m_parser.loadArgumentsIntoObject(this);
} catch (ParseException e) {
fail("We received an unexpected parsing exception");
}
assertEquals((boolean) testBool, true);
}
/**
* Tests that we got a Boolean parameter in correctly
*/
@Test
public void testFloatParameter() {
logger.warn("Executing testFloatParameter");
// setup the parameter list
String[] params = {"-B", "-S", "String", "-I", "100", "-F", "100.0"};
try {
// process the arguments
m_parser.processArgs(params,false);
m_parser.loadArgumentsIntoObject(this);
} catch (ParseException e) {
fail("We received an unexpected parsing exception");
}
assertEquals((testFloat.compareTo(100.0f)), 0);
}
/**
* Tests that we got a Integer parameter in correctly
*/
@Test
public void testIntegerParameter() {
logger.warn("Executing testIntegerParameter");
// setup the parameter list
String[] params = {"-B", "-S", "String", "-I", "100", "-F", "100.0"};
try {
// process the arguments
m_parser.processArgs(params,false);
m_parser.loadArgumentsIntoObject(this);
} catch (ParseException e) {
fail("We received an unexpected parsing exception");
}
assertEquals(testInt.compareTo(100), 0);
}
/**
* Tests that if we dont pass a required parameter we get an exception
*/
@Test
public void testForUnpassedParameter() {
logger.warn("Executing testForUnpassedParameter");
// add a new required flag we won't send it
m_parser.addRequiredArg("testNotTHere", "N", "our should be provided test", "testFloat");
// setup the parameter list
String[] params = {"-B", "-S", "String", "-I", "100", "-F", "100.0"};
try {
// process the arguments
m_parser.processArgs(params,false);
fail("We should have received a missing argument exception");
} catch (ParseException e) {
// do nothing but consume the exception
}
}
/**
* test to see if we pass a bad field name we get an runtime exception
*/
@Test
public void testForBadArgFieldName() {
logger.warn("Executing testForBadArgFieldName");
try {
// add a new required flag we won't send it
m_parser.addRequiredArg("testNotTHere", "N", "our should be provided test", "testDoesNotExist");
fail("We should of recieved a runtime exception, add unavailable fields is Baaad");
} catch (RuntimeException e) {
// do nothing but consume the exception
}
}
}