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Added an argument mode manager for group arguments and a demonstratio…
…n of how it might be used in HaplotypeCaller --dragen-mode (#7745)
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src/main/java/org/broadinstitute/hellbender/cmdline/ModeArgumentUtils.java
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| package org.broadinstitute.hellbender.cmdline; | ||
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| import org.apache.commons.lang3.StringUtils; | ||
| import org.apache.logging.log4j.LogManager; | ||
| import org.apache.logging.log4j.Logger; | ||
| import org.broadinstitute.barclay.argparser.CommandLineArgumentParser; | ||
| import org.broadinstitute.barclay.argparser.CommandLineParser; | ||
| import org.broadinstitute.barclay.argparser.NamedArgumentDefinition; | ||
| import org.broadinstitute.hellbender.exceptions.GATKException; | ||
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| import java.io.ByteArrayOutputStream; | ||
| import java.io.PrintStream; | ||
| import java.util.*; | ||
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| /** | ||
| * This class is a static helper for implementing 'mode arguments' by tools. A mode argument is defined as | ||
| * an argument which controls the setting of multiple (other) arguments to preset values, thereby resulting | ||
| * in the tool being used in a specific 'mode'. In this sense, a mode is simply a macro of sorts. A mode | ||
| * argument might be binary (in which case the associated argument and their values will be set when it is true) | ||
| * or be an enum (in which case a different set of arguments and value be set according to the selected value). | ||
| * | ||
| * The detection of the mode (i.e. the implementation of the mode argument) is the tool's responsibility. Following | ||
| * that, a public method of this class, setArgValues, can be used to install the associated argument values | ||
| * in the command parser, which will propagate them into the associate tools instance fields. | ||
| * | ||
| * The setting of the arguments is done such that argument already specified on the command line are not | ||
| * overwritten. This allows for mode refinement - i.e. the setting of the mode while turing some of its arguments | ||
| * to specific values. | ||
| * | ||
| * NOTE: This utility relies on the argument engine having already been executed. Consequently, the best place in the | ||
| * standard GATKTool would be in the #customCommandLineArgumentValidation() or at a similar stage since that gets | ||
| * executed after Barclay parsing is complete but before the tool has done anything with the filled arguments. | ||
| */ | ||
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| public final class ModeArgumentUtils { | ||
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| protected static final Logger logger = LogManager.getLogger(ModeArgumentUtils.class); | ||
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| /** | ||
| * Set a group of arguments (and associated fields) to the specified values - thereby implementing a mode | ||
| * | ||
| * The method does not overwrite arguments already set on the command line (as indicated by the parser) | ||
| * Additionally, the method emits a warning message indicating which argument were set by the mode and | ||
| * to which values. | ||
| * | ||
| * NOTE: This does not validate that the specified mode was actually set, that responsibility is left to tool authors. | ||
| * | ||
| * @param parser - commandline parser associated with the tool. This should be an instance of CommandLineArgumentParser | ||
| * @param argValues - an array of arguments and values to potentially set. The order of elements in the array | ||
| * is arg0,value0,arg1,value1 ... | ||
| * @param modeName - the name of the mode being set. This is used in textual message, such as the warning | ||
| * issued to notify the user of the changed argument and not for validation that the argument was set. | ||
| */ | ||
| public static void setArgValues(final CommandLineParser parser, final String[] argValues, final String modeName) { | ||
| final Map<String, String> modifiedArgs = new LinkedHashMap<>(); | ||
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| for ( int i = 0 ; i < argValues.length ; i += 2 ) { | ||
| if ( !hasBeenSet(parser, argValues[i]) ) { | ||
| String parserMessage = setValue(parser, argValues[i], argValues[i+1]); | ||
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| if ( StringUtils.isEmpty(parserMessage) ) { | ||
| modifiedArgs.put(argValues[i], argValues[i + 1]); | ||
| } else { | ||
| modifiedArgs.put(argValues[i], argValues[i + 1] + " (" + parserMessage + ")"); | ||
| } | ||
| } else { | ||
| logger.info("parameter not set by the '" + modeName + "' argument mode, as it was already set on the command line: " + argValues[i]); | ||
| } | ||
| } | ||
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| logModeNotice(modifiedArgs, modeName); | ||
| } | ||
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| private static boolean hasBeenSet(final CommandLineParser parser, final String alias) { | ||
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| if ( parser instanceof CommandLineArgumentParser ) { | ||
| NamedArgumentDefinition namedArg = ((CommandLineArgumentParser)parser).getNamedArgumentDefinitionByAlias(alias); | ||
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| return (namedArg != null) ? namedArg.getHasBeenSet() : false; | ||
| } else { | ||
| throw new IllegalArgumentException("command line parser is not CommandLineArgumentParser"); | ||
| } | ||
| } | ||
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| private static String setValue(final CommandLineParser parser, final String alias, final String value) { | ||
| if ( parser instanceof CommandLineArgumentParser ) { | ||
| NamedArgumentDefinition namedArg = ((CommandLineArgumentParser)parser).getNamedArgumentDefinitionByAlias(alias); | ||
| if ( namedArg == null ) { | ||
| throw new IllegalArgumentException("alias not found: " + alias); | ||
| } | ||
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| PrintStream ps = new PrintStream(new ByteArrayOutputStream()); | ||
| List<String> values = Arrays.asList(value); | ||
| namedArg.setArgumentValues((CommandLineArgumentParser)parser, ps, values); | ||
| return ps.toString(); | ||
| } else { | ||
| throw new IllegalArgumentException("command line parser is not CommandLineArgumentParser"); | ||
| } | ||
| } | ||
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| private static void logModeNotice(final Map<String, String> modifiedArgs, final String modeName) { | ||
| logger.warn("*************************************************************************"); | ||
| logger.warn(String.format("* %-69s *", "--" + modeName + " was enabled")); | ||
| logger.warn("* The following arguments have had their inputs overwritten: *"); | ||
| modifiedArgs.forEach((name, value) -> { | ||
| logger.warn(String.format("* %-69s *", "--" + name + " " + value)); | ||
| }); | ||
| logger.warn("* *"); | ||
| logger.warn("* If you would like to run this mode with different inputs for any *"); | ||
| logger.warn("* of the above arguments please manually construct the command or *"); | ||
| logger.warn("* add your specific inputs after the mode argument. This mode *"); | ||
| logger.warn("* will not override inputs explicitly provided. *"); | ||
| logger.warn("*************************************************************************"); | ||
| } | ||
| } |
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