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Throw CommandLineParserInternalException for immutable collections #102

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Throw CommandLineParserInternalException for immutable collections #102

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f42fa6f
Throw CommandLineParserInternalException for immutable collections
magicDGS Oct 11, 2017
d0a4dcf
Address comments
magicDGS Oct 30, 2017
4f2e0c7
Fix build by suppressing warnings
magicDGS Oct 31, 2017
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48 changes: 32 additions & 16 deletions src/main/java/org/broadinstitute/barclay/argparser/CommandLineArgumentParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
import java.lang.reflect.Field;
import java.lang.reflect.InvocationTargetException;
import java.util.*;
import java.util.function.Consumer;
import java.util.stream.Collectors;
import java.util.stream.Stream;

Expand Down Expand Up @@ -599,7 +600,7 @@ private void setPositionalArgument(final String stringValue) {
c.add(value);
}

@SuppressWarnings("unchecked")
@SuppressWarnings({"unchecked", "rawtypes"})
private void setArgument(ArgumentDefinition argumentDefinition, List<String> values) {
//special treatment for flags
if (argumentDefinition.isFlag() && values.isEmpty()){
Expand All @@ -616,9 +617,8 @@ private void setArgument(ArgumentDefinition argumentDefinition, List<String> val
// if this is a collection then we only want to clear it once at the beginning, before we process
// any of the values, unless we're in APPEND_TO_COLLECTIONS mode, in which case we leave the initial
// and append to it
@SuppressWarnings("rawtypes")
final Collection c = (Collection) argumentDefinition.getFieldValue();
c.clear();
System.err.println("Clear collection");
applyToCollection(argumentDefinition, Collection::clear);
}
values = expandListFile(values);
}
Expand Down Expand Up @@ -680,21 +680,37 @@ private void setArgument(ArgumentDefinition argumentDefinition, List<String> val

// check the argument range
checkArgumentRange(argumentDefinition, value);
// set the already parsed argument
setParsedArgumentValue(argumentDefinition, value);
}
}

if (argumentDefinition.isCollection) {
@SuppressWarnings("rawtypes")
final Collection c = (Collection) argumentDefinition.getFieldValue();
if (value == null) {
//user specified this arg=null which is interpreted as empty list
c.clear();
} else {
c.add(value);
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@cmnbroad cmnbroad Oct 27, 2017 •
edited
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There is at least one other place in this method that calls clear on a collection (line 627). We should scan the code for any places that need to be changed.

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Done. I added a method to catch the exception while applying a consumer (either clear/add, but in the future may be others).

}
argumentDefinition.hasBeenSet = true;
@SuppressWarnings({"unchecked", "rawtypes"})
private void setParsedArgumentValue(final ArgumentDefinition argumentDefinition, final Object value) {
if (argumentDefinition.isCollection) {
if (value == null) {
applyToCollection(argumentDefinition, Collection::clear);
} else {
argumentDefinition.setFieldValue(value);
argumentDefinition.hasBeenSet = true;
applyToCollection(argumentDefinition, c -> c.add(value));
}
argumentDefinition.hasBeenSet = true;
} else {
argumentDefinition.setFieldValue(value);
argumentDefinition.hasBeenSet = true;
}
}

// apply a function to a collection, catching UnsuportedOperationException into a more informative
@SuppressWarnings("rawtypes")
private void applyToCollection(final ArgumentDefinition argumentDefinitionCollection, final Consumer<Collection> function) {

final Collection c = (Collection) argumentDefinitionCollection.getFieldValue();
try {
function.accept(c);
} catch (UnsupportedOperationException e) {
throw new CommandLineException.CommandLineParserInternalException(String.format("Collection arguments seems immutable: \"%s\". Initialized collection should support the clear and add methods, but %s does not.",
argumentDefinitionCollection.getLongName(),
c.getClass().getName()));
}
}

Expand Down
30 changes: 30 additions & 0 deletions src/test/java/org/broadinstitute/barclay/argparser/CollectionArgumentUnitTests.java
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Original file line number Diff line number Diff line change
Expand Up @@ -277,6 +277,36 @@ public void testCollectionThatCannotBeAutoInitialized() {
new CommandLineArgumentParser(o);
}

class ImmutableCollectionArguments {
@Argument(optional = true)
public List<String> LIST = Arrays.asList("T");
}

@DataProvider
public Object[][] argsForImmmutableCollectionTest() {
return new Object[][] {
// replace mode
{Collections.EMPTY_SET, // parser options
new String[]{"--LIST", "A"}}, // arguments (real)
// replace mode
{Collections.EMPTY_SET, // parser options
new String[]{"--LIST", "null"}}, // arguments (null)

// append mode
{Collections.singleton(CommandLineParserOptions.APPEND_TO_COLLECTIONS), // parser options
new String[]{"--LIST", "A"}}, // arguments (real)
// append mode
{Collections.singleton(CommandLineParserOptions.APPEND_TO_COLLECTIONS), // parser options
new String[]{"--LIST", "null"}}, // arguments (null)
};
}

@Test(dataProvider = "argsForImmmutableCollectionTest", expectedExceptions = CommandLineException.CommandLineParserInternalException.class)
public void testCollectionThatIsImmmutable(final Set<CommandLineParserOptions> opts, final String[] args) {
final ImmutableCollectionArguments o = new ImmutableCollectionArguments();
new CommandLineArgumentParser(o, Collections.emptyList(), opts).parseArguments(System.err, args);
}

//////////////////////////////////////////////////////////////////
// Helper methods

Expand Down