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Add CommandLineParserConfig #126

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Add CommandLineParserConfig #126

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19 changes: 9 additions & 10 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 @@ -57,9 +57,6 @@ public final class CommandLineArgumentParser implements CommandLineParser {
public static final String COMMENT = "#";
public static final String POSITIONAL_ARGUMENTS_NAME = "Positional Argument";

// Extension for collection argument list files
static final String COLLECTION_LIST_FILE_EXTENSION = ".args";

private static final Logger logger = LogManager.getLogger();

// Map from (full class) name of each CommandLinePluginDescriptor requested and
Expand Down Expand Up @@ -113,7 +110,7 @@ private boolean inArgumentMap(ArgumentDefinition arg){
// and into which the values will be assigned.
private final Object callerArguments;

private final Set<CommandLineParserOptions> parserOptions;
private final CommandLineParserConfig config;

// null if no @PositionalArguments annotation
private Field positionalArguments;
Expand Down Expand Up @@ -151,7 +148,7 @@ public CommandLineArgumentParser(final Object callerArguments) {
this(
callerArguments,
Collections.emptyList(),
Collections.emptySet()
new CommandLineParserConfig() {}
);
}

Expand All @@ -162,17 +159,18 @@ public CommandLineArgumentParser(final Object callerArguments) {
* should be used by this command line parser to extend the list of
* command line arguments with dynamically discovered plugins. If
* null, no descriptors are loaded.
* @param parserConfig configuration for the behaviour of the parser.
*/
public CommandLineArgumentParser(
final Object callerArguments,
final List<? extends CommandLinePluginDescriptor<?>> pluginDescriptors,
final Set<CommandLineParserOptions> parserOptions) {
final CommandLineParserConfig parserConfig) {
Utils.nonNull(callerArguments, "The object with command line arguments cannot be null");
Utils.nonNull(pluginDescriptors, "The list of pluginDescriptors cannot be null");
Utils.nonNull(parserOptions, "The set of parser options cannot be null");
Utils.nonNull(parserConfig, "The parser configuration cannot be null");

this.callerArguments = callerArguments;
this.parserOptions = parserOptions;
this.config = parserConfig;

createArgumentDefinitions(callerArguments, null);
createCommandLinePluginArgumentDefinitions(pluginDescriptors);
Expand Down Expand Up @@ -622,7 +620,7 @@ private void setArgument(ArgumentDefinition argumentDefinition, List<String> val
throw new CommandLineException("Argument '" + argumentDefinition.getNames() + "' cannot be specified more than once.");
}
if (argumentDefinition.isCollection) {
if (!parserOptions.contains(CommandLineParserOptions.APPEND_TO_COLLECTIONS)) {
if (!config.getAppendToCollections()) {
// 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
Expand Down Expand Up @@ -718,8 +716,9 @@ private void setArgument(ArgumentDefinition argumentDefinition, List<String> val
*/
private List<String> expandListFile(final List<String> originalValues) {
List<String> expandedValues = new ArrayList<>(originalValues.size());

for (String stringValue: originalValues) {
if (stringValue.endsWith(COLLECTION_LIST_FILE_EXTENSION)) {
if (config.getExpansionFileExtensions().stream().anyMatch(stringValue::endsWith)) {
expandedValues.addAll(loadCollectionListFile(stringValue));
}
else {
Expand Down
51 changes: 51 additions & 0 deletions src/main/java/org/broadinstitute/barclay/argparser/CommandLineParserConfig.java
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@@ -0,0 +1,51 @@
package org.broadinstitute.barclay.argparser;

import java.util.Collection;
import java.util.Collections;

/**
* Interface for the command line parser configuration.
*
* @author Daniel Gomez-Sanchez (magicDGS)
*/
public interface CommandLineParserConfig {

/**
* Default extension for collection argument list files.
*/
public static final String DEFAULT_COLLECTION_LIST_FILE_EXTENSION = ".args";

/**
* Configuration for append/replace values in a Collection argument.
*
* <p>The default behavior is returning {@code false}, which:
*
* <p><ul>
* <li>Replace the contents of a collection argument with any values from the command line.</li>
* <li>Optionally allow the special singleton value of "null" to clear the contents of the collection.</li>
* </ul></p>
*
* <p>Returning {@code true} changes the behavior so that any collection arguments are ADDED to the
* initial values of the collection, and allows the special value "null" to be used first to clear the initial
* values.
*
* @return {@code true} if the result should be append to the initial values of the collection;
* {@code false} if they should be substituted.
*/
default public boolean getAppendToCollections() {
return false;
}

/**
* Configuration for loading Collection arguments from files ending with concrete extensions.
*
* <p>Default behaviour returns {@link #DEFAULT_COLLECTION_LIST_FILE_EXTENSION} as the file
* extension to expand.
*
* @return extension(s) for detect an argument as a file for loading a Collection argument.
*/
default Collection<String> getExpansionFileExtensions() {
return Collections.singleton(DEFAULT_COLLECTION_LIST_FILE_EXTENSION);
}

}
21 changes: 0 additions & 21 deletions src/main/java/org/broadinstitute/barclay/argparser/CommandLineParserOptions.java
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2 changes: 1 addition & 1 deletion src/main/java/org/broadinstitute/barclay/help/DefaultDocWorkUnitHandler.java
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Original file line number Diff line number Diff line change
Expand Up @@ -196,7 +196,7 @@ public void processWorkUnit(
if (argumentContainer instanceof CommandLinePluginProvider) {
pluginDescriptors = ((CommandLinePluginProvider) argumentContainer).getPluginDescriptors();
clp = new CommandLineArgumentParser(
argumentContainer, pluginDescriptors, Collections.emptySet()
argumentContainer, pluginDescriptors, new CommandLineParserConfig() {}
);
} else {
clp = new CommandLineArgumentParser(argumentContainer);
Expand Down
99 changes: 73 additions & 26 deletions src/test/java/org/broadinstitute/barclay/argparser/CollectionArgumentUnitTests.java
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Expand Up @@ -38,15 +38,21 @@ public Object[][] uninitializedCollections() {
// the same behavior on collections with no initial values
{
inputArgs,
Collections.EMPTY_SET, // replace mode
new CommandLineParserConfig() {}, // replace mode
makeList("L1", "L2"),
makeList("S1"),
makeList("HS1"),
expectedFileList
},
{
inputArgs,
Collections.singleton(CommandLineParserOptions.APPEND_TO_COLLECTIONS), // append mode
// append mode
new CommandLineParserConfig() {
@Override
public boolean getAppendToCollections() {
return true;
}
},
makeList("L1", "L2"),
makeList("S1"),
makeList("HS1"),
Expand All @@ -58,14 +64,14 @@ public Object[][] uninitializedCollections() {
@Test(dataProvider="uninitializedCollections")
public void testUninitializedCollections(
final String[] args,
final Set<CommandLineParserOptions> parserOptions,
final CommandLineParserConfig parserConfig,
final List<String> expectedList,
final List<String> expectedArrayList,
final List<String> expectedHashSet,
final List<File> expectedCollection)
{
final UninitializedCollections o = new UninitializedCollections();
final CommandLineArgumentParser clp = new CommandLineArgumentParser(o, Collections.emptyList(), parserOptions);
final CommandLineArgumentParser clp = new CommandLineArgumentParser(o, Collections.emptyList(), parserConfig);
Assert.assertTrue(clp.parseArguments(System.err, args));
Assert.assertEquals(o.LIST, expectedList);
Assert.assertEquals(o.ARRAY_LIST, expectedArrayList);
Expand All @@ -84,45 +90,52 @@ public Object[][] initializedCollections() {
final String[] inputArgsWithNullAtStart = new String[] {"--LIST", "null", "--LIST", "baz", "--LIST", "frob"};
final String[] inputArgsWithNullMidStream = new String[] {"--LIST", "baz", "--LIST", "null", "--LIST", "frob"};

final CommandLineParserConfig appendConfig = new CommandLineParserConfig() {
@Override
public boolean getAppendToCollections() {
return true;
}
};

return new Object[][]{
{
inputArgs,
Collections.singleton(CommandLineParserOptions.APPEND_TO_COLLECTIONS),
appendConfig,
makeList("foo", "bar", "baz", "frob") // original values retained
},
{
inputArgs,
Collections.emptySet(),
new CommandLineParserConfig() {},
makeList("baz", "frob") // original values replaced
},
{
inputArgsWithNullAtStart,
Collections.singleton(CommandLineParserOptions.APPEND_TO_COLLECTIONS),
appendConfig,
makeList("baz", "frob") // original values replaced
},
{
inputArgsWithNullAtStart,
Collections.emptySet(),
new CommandLineParserConfig() {},
makeList("baz", "frob") // original values replaced
},
{
inputArgsWithNullMidStream,
Collections.singleton(CommandLineParserOptions.APPEND_TO_COLLECTIONS),
appendConfig,
makeList("frob") // reset mid-stream via midstream null
},
{
inputArgsWithNullMidStream,
Collections.emptySet(),
new CommandLineParserConfig() {},
makeList("frob") // reset mid-stream via midstream null
},
{
new String[]{},
Collections.singleton(CommandLineParserOptions.APPEND_TO_COLLECTIONS),
appendConfig,
makeList("foo", "bar")
},
{
new String[]{},
Collections.singleton(Collections.emptySet()),
new CommandLineParserConfig() {},
makeList("foo", "bar")
}
};
Expand All @@ -131,13 +144,13 @@ public Object[][] initializedCollections() {
@Test(dataProvider="initializedCollections")
public void testInitializedCollections(
final String[] args,
final Set<CommandLineParserOptions> parserOptions,
final CommandLineParserConfig parserConfig,
final List<String> expectedResult) {
final InitializedCollections o = new InitializedCollections();
final CommandLineParser clp = new CommandLineArgumentParser(
o,
Collections.emptyList(),
parserOptions
parserConfig
);
Assert.assertTrue(clp.parseArguments(System.err, args));
Assert.assertEquals(o.LIST, expectedResult);
Expand All @@ -157,16 +170,22 @@ class CollectionForListFileArguments {
@DataProvider(name="listFileArguments")
public Object[][] listFileArguments() {
final String[] inputArgs = new String[] { "shmiggle0", "shmiggle1", "shmiggle2" };

return new Object[][] {
{
// replace mode
Collections.EMPTY_SET, // parser options
inputArgs, // args
new String[] {"shmiggle0", "shmiggle1", "shmiggle2"}, // expected result
// replace mode (default configuration)
new CommandLineParserConfig() {}, // parser config
inputArgs, // args
new String[] {"shmiggle0", "shmiggle1", "shmiggle2"}, // expected result
},
{
// append mode
Collections.singleton(CommandLineParserOptions.APPEND_TO_COLLECTIONS), // parser options
new CommandLineParserConfig() {
@Override
public boolean getAppendToCollections() {
return true;
}
}, // parser config
inputArgs, // args
new String[] {"foo", "bar", "shmiggle0", "shmiggle1", "shmiggle2"}, // expected result
},
Expand All @@ -176,7 +195,7 @@ public Object[][] listFileArguments() {
// Test that .list files populate collections with file contents, both mpdes
@Test(dataProvider="listFileArguments")
public void testCollectionFromListFile(
final Set<CommandLineParserOptions> parserOptions,
final CommandLineParserConfig parserConfig,
final String [] argList,
final String[] expectedList) throws IOException
{
Expand All @@ -187,7 +206,7 @@ public void testCollectionFromListFile(
final CommandLineParser clp = new CommandLineArgumentParser(
o,
Collections.emptyList(),
parserOptions
parserConfig
);

final String[] args = {"--LIST", argListFile.getAbsolutePath()};
Expand All @@ -196,14 +215,37 @@ public void testCollectionFromListFile(
Assert.assertEquals(o.LIST, makeList(expectedList));
}

@Test
public void testDoNotExpandCollectionListFile() {
final CollectionForListFileArguments o = new CollectionForListFileArguments();
final CommandLineParser clp = new CommandLineArgumentParser(
o,
Collections.emptyList(),
new CommandLineParserConfig() {
@Override
public Collection<String> getExpansionFileExtensions() {
return Collections.emptySet();
}
}
);

final String noListFile = "no_arg_list_file" + CommandLineParserConfig.DEFAULT_COLLECTION_LIST_FILE_EXTENSION;

final String[] args = {"--LIST", noListFile};
Assert.assertTrue(clp.parseArguments(System.err, args));

Assert.assertEquals(o.LIST, makeList(noListFile));
}

@DataProvider(name="mixedListFileArguments")
public Object[][] mixedListFileArguments() {
final String[] inputArgList1 = { "shmiggle0", "shmiggle1", "shmiggle2" };
final String[] inputArgList2 = { "test2_shmiggle0", "test2_shmiggle1", "test2_shmiggle2" };

return new Object[][] {
{
// replace mode
Collections.EMPTY_SET, // parser options
new CommandLineParserConfig() {}, // parser config
inputArgList1, // args list 1
inputArgList2, // args list 2
new String[] {"shmiggle0", "shmiggle1", "shmiggle2"}, // expected result list 1
Expand All @@ -217,7 +259,12 @@ public Object[][] mixedListFileArguments() {
},
{
// append mode
Collections.singleton(CommandLineParserOptions.APPEND_TO_COLLECTIONS), // parser options
new CommandLineParserConfig() {
@Override
public boolean getAppendToCollections() {
return true;
}
}, // parser config
inputArgList1, // args list 1
inputArgList2, // args list 2
new String[] {"foo", "bar", "shmiggle0", "shmiggle1", "shmiggle2"}, // expected result list 1
Expand All @@ -236,7 +283,7 @@ public Object[][] mixedListFileArguments() {
// Test that .list files intermixed with explicit command line values populate collections correctly, both mpdes
@Test(dataProvider="mixedListFileArguments")
public void testCollectionFromListFileMixed(
final Set<CommandLineParserOptions> parserOptions,
final CommandLineParserConfig parserConfig,
final String [] argList1,
final String [] argList2,
final String[] expectedList1,
Expand All @@ -250,7 +297,7 @@ public void testCollectionFromListFileMixed(
final CommandLineParser clp = new CommandLineArgumentParser(
o,
Collections.emptyList(),
parserOptions
parserConfig
);

// mix command line values and file values
Expand Down Expand Up @@ -281,7 +328,7 @@ public void testCollectionThatCannotBeAutoInitialized() {
// Helper methods

private File createListArgumentFile(final String fileName, final String[] argList) throws IOException {
final File listFile = File.createTempFile(fileName, CommandLineArgumentParser.COLLECTION_LIST_FILE_EXTENSION);
final File listFile = File.createTempFile(fileName, CommandLineParserConfig.DEFAULT_COLLECTION_LIST_FILE_EXTENSION);
listFile.deleteOnExit();
try (final PrintWriter writer = new PrintWriter(listFile)) {
Arrays.stream(argList).forEach(arg -> writer.println(arg));
Expand Down
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