Make a separate base class for command and conda CLI configs.

Right now, the conda CLI config only works on windows.

src/main/java/fiji/plugin/trackmate/util/cli/CLIConfigurator.java

@@ -1,6 +1,5 @@
 package fiji.plugin.trackmate.util.cli;
 
-import java.io.File;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -18,8 +17,6 @@ public abstract class CLIConfigurator
 
 	protected final List< Argument< ? > > arguments = new ArrayList<>();
 
-	protected final ExecutablePath executable = new ExecutablePath();
-
 	protected final List< SelectableArguments > selectables = new ArrayList<>();
 
 	protected final Map< Command< ? >, Function< Object, List< String > > > translators = new HashMap<>();
@@ -29,19 +26,21 @@ public abstract class CLIConfigurator
 	 */
 
 	/**
-	 * Returns the list of arguments in this CLI config. All arguments are
-	 * present, regardless of whether they are in {@link SelectableArguments}.
-	 * 
+	 * Returns the list of arguments (plus the command) in this CLI config. All
+	 * arguments are present, regardless of whether they are in
+	 * {@link SelectableArguments}, {@link Argument#visible} or not,
+	 * {@link Argument#inCLI} or not.
+	 *
 	 * @return the list of arguments.
 	 */
-	public List< Argument< ? > > getArguments()
+	public List< Command< ? > > getArguments()
 	{
 		return Collections.unmodifiableList( arguments );
 	}
 
 	/**
 	 * Returns the list of {@link SelectableArguments} in this CLI config.
-	 * 
+	 *
 	 * @return the list of {@link SelectableArguments}.
 	 */
 	public List< SelectableArguments > getSelectables()
@@ -54,7 +53,7 @@ public List< SelectableArguments > getSelectables()
 	 * only the arguments that are selected if they are in a
 	 * {@link SelectableArguments}, and those who are not in a
 	 * {@link SelectableArguments}.
-	 * 
+	 *
 	 * @return the selected arguments.
 	 */
 	public List< Argument< ? > > getSelectedArguments()
@@ -65,18 +64,6 @@ public List< SelectableArguments > getSelectables()
 		return selectedArguments;
 	}
 
-	/*
-	 * EXECUTABLE.
-	 */
-
-	/**
-	 * Exposes the executable path argument.
-	 */
-	public ExecutablePath getExecutableArg()
-	{
-		return executable;
-	}
-
 	/*
 	 * VALUE TRANSLATOR.
 	 */
@@ -518,10 +505,10 @@ protected ChoiceAdder addChoiceArgument()
 	{
 		return new ChoiceAdder();
 	}
-	
+
 	/**
 	 * Adds an extra argument, defined by other means than the adder methods.
-	 * 
+	 *
 	 * @param extraArg
 	 *            the argument to add to this CLI config.
 	 * @return the argument
@@ -978,7 +965,7 @@ public String toString()
 		/**
 		 * Sets the value of this argument via the specified object. This is
 		 * used when deserializing TrackMate settings map.
-		 * 
+		 *
 		 * @param val
 		 *            the object to set the value from
 		 * @see TrackMateSettingsBuilder
@@ -988,14 +975,14 @@ public String toString()
 		/**
 		 * Returns an object built from the value of this argument, if it has
 		 * one. This is used in TrackMate settings map serialization.
-		 * 
+		 *
 		 * @return the value object.
 		 * @see TrackMateSettingsBuilder
 		 */
 		public abstract Object getValueObject();
 	}
 
-	public static class ExecutablePath extends Command< ExecutablePath >
+	public static class ExecutablePath extends Argument< ExecutablePath >
 	{
 
 		private String value = null;
@@ -1087,12 +1074,12 @@ public String getArgument()
 		{
 			return argument;
 		}
-		
+
 		/**
 		 * If <code>false</code>, this argument won't be used in the command
 		 * line generator. This is useful to add extra parameters to the GUI
 		 * that are required by TrackMate but not by the CLI tool.
-		 * 
+		 *
 		 * @param inCLI
 		 *            whether this argument should be used when generating
 		 *            commands. By default: <code>true</code>.
@@ -1125,31 +1112,11 @@ public String toString()
 	{
 		final StringBuilder str = new StringBuilder();
 		str.append( super.toString() + "\n" );
-		str.append( executable.toString() );
 		arguments.forEach( str::append );
 		return str.toString();
-
-	}
-
-	protected String checkExecutable()
-	{
-		if ( !executable.isSet() )
-		{
-			return "Executable path is not set.\n" ;
-		}
-		else
-		{
-			final String path = executable.getValue();
-			final File file = new File(path);
-			if ( !file.exists() )
-				return "Executable path " + path + " does not exist.\n";
-			if ( !file.canExecute() )
-				return "Executable " + path + " cannot be run.\n";
-		}
-		return null;
 	}
 
-	protected String checkArguments()
+	public String check()
 	{
 		final StringBuilder str = new StringBuilder();
 		for ( final Argument< ? > arg : getSelectedArguments() )
@@ -1167,11 +1134,10 @@ protected String checkArguments()
 		return str.length() == 0 ? null : str.toString();
 	}
 
-	public String check()
-	{
-		final String out = checkExecutable();
-		if ( out != null )
-			return out;
-		return checkArguments();
-	}
+	/**
+	 * Returns the command object of this tool.
+	 *
+	 * @return the command object.
+	 */
+	public abstract Command< ? > getCommandArg();
 }

src/main/java/fiji/plugin/trackmate/util/cli/CliGuiBuilder.java

@@ -51,6 +51,7 @@
 import fiji.plugin.trackmate.util.cli.CLIConfigurator.Argument;
 import fiji.plugin.trackmate.util.cli.CLIConfigurator.ArgumentVisitor;
 import fiji.plugin.trackmate.util.cli.CLIConfigurator.ChoiceArgument;
+import fiji.plugin.trackmate.util.cli.CLIConfigurator.Command;
 import fiji.plugin.trackmate.util.cli.CLIConfigurator.DoubleArgument;
 import fiji.plugin.trackmate.util.cli.CLIConfigurator.ExecutablePath;
 import fiji.plugin.trackmate.util.cli.CLIConfigurator.Flag;
@@ -80,7 +81,7 @@ public class CliGuiBuilder implements ArgumentVisitor, StyleElementVisitor
 
 	private final List< StyleElement > elements = new ArrayList<>();
 
-	private CliGuiBuilder( final ExecutablePath executableArg )
+	private CliGuiBuilder()
 	{
 		this.panel = new CliConfigPanel();
 		final GridBagLayout layout = new GridBagLayout();
@@ -92,9 +93,6 @@ private CliGuiBuilder( final ExecutablePath executableArg )
 		c.gridwidth = 1;
 		c.gridx = 0;
 		c.gridy = 0;
-
-		if ( executableArg.isVisible() )
-			visit( executableArg );
 	}
 
 	private void setCurrentButtonGroup( final ButtonGroup buttonGroup )
@@ -521,7 +519,7 @@ private void addLastRow()
 
 	public static CliConfigPanel build( final CLIConfigurator cli )
 	{
-		final CliGuiBuilder builder = new CliGuiBuilder( cli.getExecutableArg() );
+		final CliGuiBuilder builder = new CliGuiBuilder();
 
 		/*
 		 * Iterate over CLI arguments.
@@ -531,7 +529,7 @@ public static CliConfigPanel build( final CLIConfigurator cli )
 		final Map< SelectableArguments, ButtonGroup > buttonGroups = new HashMap<>();
 
 		// Iterate over arguments, taking care of selectable group.
-		for ( final Argument< ? > arg : cli.getArguments() )
+		for ( final Command< ? > arg : cli.getArguments() )
 		{
 			if ( !arg.isVisible() )
 				continue;
@@ -583,5 +581,4 @@ public void refresh()
 			elements.forEach( e -> e.update() );
 		}
 	}
-
 }

src/main/java/fiji/plugin/trackmate/util/cli/CommandBuilder.java

@@ -27,10 +27,9 @@ public class CommandBuilder implements ArgumentVisitor
 
 	private final Map< Command< ? >, Function< Object, List< String > > > translators;
 
-	protected CommandBuilder( final ExecutablePath executableArg, final Map< Command< ? >, Function< Object, List< String > > > translators )
+	protected CommandBuilder( final Map< Command< ? >, Function< Object, List< String > > > translators )
 	{
 		this.translators = translators;
-		visit( executableArg );
 	}
 
 	@Override
@@ -177,7 +176,7 @@ public void visit( final ChoiceArgument arg )
 
 	public static List< String > build( final CLIConfigurator cli )
 	{
-		final CommandBuilder cb = new CommandBuilder( cli.getExecutableArg(), cli.translators );
+		final CommandBuilder cb = new CommandBuilder( cli.translators );
 		cli.getSelectedArguments()
 				.stream()
 				.filter( a -> a.isInCLI() )

src/main/java/fiji/plugin/trackmate/util/cli/CommandCLIConfigurator.java

@@ -0,0 +1,60 @@
+package fiji.plugin.trackmate.util.cli;
+
+import java.io.File;
+
+/**
+ * Base class for CLI config that are based on an executable, reachable by a
+ * path.
+ */
+public abstract class CommandCLIConfigurator extends CLIConfigurator
+{
+
+	protected final ExecutablePath executable;
+
+	protected CommandCLIConfigurator()
+	{
+		this.executable = new ExecutablePath();
+	}
+
+	@Override
+	public ExecutablePath getCommandArg()
+	{
+		return executable;
+	}
+
+	protected String checkExecutable()
+	{
+		if ( !executable.isSet() )
+		{
+			return "Executable path is not set.\n";
+		}
+		else
+		{
+			final String path = executable.getValue();
+			final File file = new File( path );
+			if ( !file.exists() )
+				return "Executable path " + path + " does not exist.\n";
+			if ( !file.canExecute() )
+				return "Executable " + path + " cannot be run.\n";
+		}
+		return null;
+	}
+
+	@Override
+	public String check()
+	{
+		final String out = checkExecutable();
+		if ( out != null )
+			return out;
+		return super.check();
+	}
+
+	@Override
+	public String toString()
+	{
+		final StringBuilder str = new StringBuilder();
+		str.append( executable.toString() );
+		str.append( super.toString() + "\n" );
+		return str.toString();
+	}
+}

src/main/java/fiji/plugin/trackmate/util/cli/CondaCLIConfigurator.java

@@ -4,7 +4,7 @@
 import java.util.Arrays;
 import java.util.List;
 
-public class CondaCLIConfigurator extends CLIConfigurator
+public abstract class CondaCLIConfigurator extends CLIConfigurator
 {
 
 	public static final String KEY_CONDA_ENV = "CONDA_ENV";
@@ -28,12 +28,11 @@ protected CondaCLIConfigurator()
 				.inCLI( false )
 				.get();
 
-		// Don't show the executable arg in the UI: must be set by subclass, and
-		// only conda env required configurating.
-		getExecutableArg().visible( false );
+		// Add it first to the list of arguments
+		this.arguments.add( condaEnv );
 
 		// Add the translator to make a proper cmd line calling conda first.
-		setTranslator( getExecutableArg(), s -> {
+		setTranslator( condaEnv, s -> {
 			final String executableName = ( String ) s;
 			// Split by spaces
 			final String[] split = executableName.split( " " );
@@ -46,14 +45,18 @@ protected CondaCLIConfigurator()
 		} );
 	}
 
-	public ChoiceArgument getCondaEnv()
+	@Override
+	public Command< ? > getCommandArg()
 	{
 		return condaEnv;
 	}
 
-	@Override
-	public String check()
-	{
-		return checkArguments();
-	}
+	/**
+	 * Returns the command that must be run in the configured conda environment.
+	 * In case the command is made of several tokens, they can be returned
+	 * separated by space (as in a normal command line).
+	 *
+	 * @return the command for this tool.
+	 */
+	protected abstract String getCommand();
 }

src/main/java/fiji/plugin/trackmate/util/cli/TrackMateSettingsBuilder.java

@@ -36,7 +36,7 @@ private static void fromMap( final Map< String, Object > settings, final Command
 	 */
 	public static void toTrackMateSettings( final Map< String, Object > settings, final CLIConfigurator cli )
 	{
-		toMap( cli.getExecutableArg(), settings );
+		toMap( cli.getCommandArg(), settings );
 		cli.getArguments().forEach( arg -> toMap( arg, settings ) );
 	}
 
@@ -52,7 +52,7 @@ public static void toTrackMateSettings( final Map< String, Object > settings, fi
 	 */
 	public static final void fromTrackMateSettings( final Map< String, Object > settings, final CLIConfigurator cli )
 	{
-		fromMap( settings, cli.getExecutableArg() );
+		fromMap( settings, cli.getCommandArg() );
 		cli.getArguments().forEach( arg -> fromMap( settings, arg ) );
 	}
 }