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Fix improper detection of command-line arguments with missing values.

This commit is contained in:
Matt Hanna 2011-07-25 13:20:00 -04:00
parent 7054c5342f
commit 2ac490dbdf
3 changed files with 34 additions and 10 deletions
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3
public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
View File

@ -174,7 +174,8 @@ public class ArgumentDefinitions implements Iterable<ArgumentDefinition> {
static DefinitionMatcher VerifiableDefinitionMatcher = new DefinitionMatcher() {
public boolean matches( ArgumentDefinition definition, Object key ) {
return definition.validation != null;
// We can perform some sort of validation for anything that isn't a flag.
return !definition.isFlag;
}
};
}

2
public/java/src/org/broadinstitute/sting/commandline/ArgumentMatch.java
View File

@ -44,7 +44,7 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
public final String label;
/**
* Maps indicies of command line arguments to values paired with that argument.
* Maps indices of command line arguments to values paired with that argument.
*/
public final SortedMap<Integer,List<String>> indices = new TreeMap<Integer,List<String>>();

39
public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
View File

@ -41,6 +41,11 @@ import java.util.*;
* A parser for Sting command-line arguments.
*/
public class ParsingEngine {
/**
* The loaded argument sources along with their back definitions.
*/
private Map<ArgumentDefinition,ArgumentSource> argumentSourcesByDefinition = new HashMap<ArgumentDefinition,ArgumentSource>();
/**
* A list of defined arguments against which command lines are matched.
* Package protected for testing access.
@ -107,8 +112,13 @@ public class ParsingEngine {
*/
public void addArgumentSource( String sourceName, Class sourceClass ) {
List<ArgumentDefinition> argumentsFromSource = new ArrayList<ArgumentDefinition>();
for( ArgumentSource argumentSource: extractArgumentSources(sourceClass) )
argumentsFromSource.addAll( argumentSource.createArgumentDefinitions() );
for( ArgumentSource argumentSource: extractArgumentSources(sourceClass) ) {
List<ArgumentDefinition> argumentDefinitions = argumentSource.createArgumentDefinitions();
for(ArgumentDefinition argumentDefinition: argumentDefinitions) {
argumentSourcesByDefinition.put(argumentDefinition,argumentSource);
argumentsFromSource.add( argumentDefinition );
}
}
argumentDefinitions.add( new ArgumentDefinitionGroup(sourceName, argumentsFromSource) );
}
@ -199,16 +209,25 @@ public class ParsingEngine {
throw new InvalidArgumentException( invalidArguments );
}
// Find invalid argument values (arguments that fail the regexp test.
// Find invalid argument values -- invalid arguments are either completely missing or fail the specified 'validation' regular expression.
if( !skipValidationOf.contains(ValidationType.InvalidArgumentValue) ) {
Collection<ArgumentDefinition> verifiableArguments =
argumentDefinitions.findArgumentDefinitions( null, ArgumentDefinitions.VerifiableDefinitionMatcher );
Collection<Pair<ArgumentDefinition,String>> invalidValues = new ArrayList<Pair<ArgumentDefinition,String>>();
for( ArgumentDefinition verifiableArgument: verifiableArguments ) {
ArgumentMatches verifiableMatches = argumentMatches.findMatches( verifiableArgument );
// Check to see whether an argument value was specified. Argument values must be provided
// when the argument name is specified and the argument is not a flag type.
for(ArgumentMatch verifiableMatch: verifiableMatches) {
ArgumentSource argumentSource = argumentSourcesByDefinition.get(verifiableArgument);
if(verifiableMatch.values().size() == 0 && !verifiableArgument.isFlag && argumentSource.createsTypeDefault())
invalidValues.add(new Pair<ArgumentDefinition,String>(verifiableArgument,null));
}
// Ensure that the field contents meet the validation criteria specified by the regular expression.
for( ArgumentMatch verifiableMatch: verifiableMatches ) {
for( String value: verifiableMatch.values() ) {
if( !value.matches(verifiableArgument.validation) )
if( verifiableArgument.validation != null && !value.matches(verifiableArgument.validation) )
invalidValues.add( new Pair<ArgumentDefinition,String>(verifiableArgument, value) );
}
}
@ -515,10 +534,14 @@ class InvalidArgumentValueException extends ArgumentException {
private static String formatArguments( Collection<Pair<ArgumentDefinition,String>> invalidArgumentValues ) {
StringBuilder sb = new StringBuilder();
for( Pair<ArgumentDefinition,String> invalidValue: invalidArgumentValues ) {
sb.append( String.format("%nArgument '--%s' has value of incorrect format: %s (should match %s)",
invalidValue.first.fullName,
invalidValue.second,
invalidValue.first.validation) );
if(invalidValue.getSecond() == null)
sb.append( String.format("%nArgument '--%s' requires a value but none was provided",
invalidValue.first.fullName) );
else
sb.append( String.format("%nArgument '--%s' has value of incorrect format: %s (should match %s)",
invalidValue.first.fullName,
invalidValue.second,
invalidValue.first.validation) );
}
return sb.toString();
}