Add custom Map/Dictionary argument handlers

src/main/java/imsam/DynamicBinaryWeightedSSA.java

@@ -15,29 +15,25 @@
 
 package imsam;
 
-import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileNotFoundException;
-import java.io.FileReader;
 import java.io.IOException;
-import java.util.*;//ArrayList;
-//import java.util.List;
-//import java.util.Dictionary;
-//import java.util.NoSuchElementException;
-import java.lang.Math;
+//ArrayList;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
 
 import org.apache.logging.log4j.Logger;
 import org.kohsuke.args4j.Option;
 
-import parser.ast.ModulesFile;
+import imsam.args4j.MapDoubleOptionHandler;
 import parser.Values;
-
+import parser.ast.ModulesFile;
+import prism.ModelGenerator;
 import prism.Prism;
 import prism.PrismDevNullLog;
 import prism.PrismException;
 import prism.PrismLog;
-import prism.ModelGenerator;
-
 import simulator.RandomNumberGenerator;
 import simulator.SimulatorEngine;
 
@@ -74,8 +70,11 @@ public class DynamicBinaryWeightedSSA extends Command {
 	@Option(name="--const",usage="Model constant name=value")
 	public String modelConstant = "";
 
+	@Option(name="--weight",usage="TODO: needs description",handler=MapDoubleOptionHandler.class)
+	public Map<String,Double> predilections = Map.of("[r3]", 1e20);
+
 	public String argsToString() {
-		return String.format("TMAX=%f Nruns=%d modelFile=%s ", TMAX, Nruns, modelFileName);
+		return String.format("TMAX=%f Nruns=%d modelFile=%s weights=%s", TMAX, Nruns, modelFileName, predilections);
 	}
 	public String argsRawToString() {
 		return String.format("%f\t%d", TMAX, Nruns);
@@ -90,19 +89,16 @@ public String argsRawToString() {
     public SimulatorEngine    sim;
     public ModelGenerator     info;
 
-    private int               constraintIndex;
-    private int               objectiveIndex;
+    //private int               constraintIndex;
+    //private int               objectiveIndex;
     private RandomNumberGenerator rng = new RandomNumberGenerator();
-    private Dictionary        predilections = new Hashtable();
 
 	@Override
 	public int exec() throws IOException, PrismException {
 
 		logger.debug("Running Dynamic Binary Weighted SSA");
 
 		loadModel();
-		Double d=1e20;
-		predilections.put("[r3]",d);
 
 		double sum       = 0.0;
 		long   binarySum = 0;

src/main/java/imsam/Main.java

@@ -1,5 +1,7 @@
 package imsam;
 
+import java.util.stream.Stream;
+
 import org.apache.logging.log4j.Level;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -11,7 +13,6 @@
 import org.kohsuke.args4j.Argument;
 import org.kohsuke.args4j.CmdLineException;
 import org.kohsuke.args4j.CmdLineParser;
-import org.kohsuke.args4j.spi.OptionHandler;
 import org.kohsuke.args4j.spi.SubCommand;
 import org.kohsuke.args4j.spi.SubCommandHandler;
 import org.kohsuke.args4j.spi.SubCommands;
@@ -95,14 +96,10 @@ public static void printUsage(CmdLineException ex) {
     private static void _printUsage(CmdLineParser parser, boolean includeSubcommand) {
         System.err.println("Usage:");
         System.err.print(" ./bin/run.sh");
-        for (OptionHandler arg : Main.parser.getArguments()) {
-            System.err.print(" " + arg.getDefaultMetaVariable());
-        }
-        if (includeSubcommand) {
-            for (OptionHandler arg : parser.getArguments()) {
-                System.err.print(" " + arg.getDefaultMetaVariable());
-            }
-        }
+        Stream.concat(
+            Main.parser.getArguments().stream(),
+            parser.getArguments().stream()
+        ).forEachOrdered(opt -> System.err.print(" "+opt.getDefaultMetaVariable()));
         System.err.println(" [OPTIONS]...\n");
         parser.printUsage(System.err);
     }

src/main/java/imsam/args4j/MapDoubleOptionHandler.java

@@ -0,0 +1,21 @@
+package imsam.args4j;
+
+import java.util.Map;
+
+import org.kohsuke.args4j.CmdLineParser;
+import org.kohsuke.args4j.OptionDef;
+import org.kohsuke.args4j.spi.Setter;
+
+public class MapDoubleOptionHandler extends MultiMapOptionHandler {
+
+    public MapDoubleOptionHandler(CmdLineParser parser, OptionDef option, Setter<? super Map<?, ?>> setter) {
+        super(parser, option, setter);
+    }
+
+    @Override
+    @SuppressWarnings({"rawtypes", "unchecked"})
+    protected void addToMap(Map m, String key, String value) {
+        m.put(key, Double.parseDouble(value));
+    }
+
+}

src/main/java/imsam/args4j/MapIntOptionHandler.java

@@ -0,0 +1,21 @@
+package imsam.args4j;
+
+import java.util.Map;
+
+import org.kohsuke.args4j.CmdLineParser;
+import org.kohsuke.args4j.OptionDef;
+import org.kohsuke.args4j.spi.Setter;
+
+public class MapIntOptionHandler extends MultiMapOptionHandler {
+
+    public MapIntOptionHandler(CmdLineParser parser, OptionDef option, Setter<? super Map<?, ?>> setter) {
+        super(parser, option, setter);
+    }
+
+    @Override
+    @SuppressWarnings({"rawtypes", "unchecked"})
+    protected void addToMap(Map m, String key, String value) {
+        m.put(key, Integer.parseInt(value));
+    }
+
+}

src/main/java/imsam/args4j/MultiMapOptionHandler.java

@@ -0,0 +1,34 @@
+package imsam.args4j;
+
+import java.util.Map;
+
+import org.kohsuke.args4j.CmdLineException;
+import org.kohsuke.args4j.CmdLineParser;
+import org.kohsuke.args4j.OptionDef;
+import org.kohsuke.args4j.spi.MapOptionHandler;
+import org.kohsuke.args4j.spi.Parameters;
+import org.kohsuke.args4j.spi.Setter;
+
+public class MultiMapOptionHandler extends MapOptionHandler  {
+
+    protected static final String delimiterRegex = ",";
+
+    protected final CmdLineParser parser;
+    protected final OptionDef option;
+
+    public MultiMapOptionHandler(CmdLineParser parser, OptionDef option, Setter<? super Map<?,?>> setter) {
+        super(parser, option, setter);
+        this.parser = parser;
+        this.option = option;
+    }
+
+    @Override
+    public int parseArguments(Parameters params) throws CmdLineException {
+        for (String arg : params.getParameter(0).split(delimiterRegex)) {
+            Parameters splitParam = new ParametersImpl(new String[]{arg}, parser, option);
+            super.parseArguments(splitParam);
+        }
+        return 1;
+    }
+
+}

src/main/java/imsam/args4j/ParametersImpl.java

@@ -0,0 +1,50 @@
+package imsam.args4j;
+
+import org.kohsuke.args4j.CmdLineException;
+import org.kohsuke.args4j.CmdLineParser;
+import org.kohsuke.args4j.OptionDef;
+import org.kohsuke.args4j.spi.Parameters;
+
+public class ParametersImpl implements Parameters {
+
+    private final CmdLineParser parser;
+    private final OptionDef option;
+
+    private final String[] args;
+    private int pos;
+
+    ParametersImpl(String[] args, CmdLineParser parser, OptionDef option) {
+        this.parser = parser;
+        this.option = option;
+        this.args = args;
+        pos = 0;
+    }
+
+    @Override
+    @SuppressWarnings("deprecation")    // Use CmdLineException without localization
+    public String getParameter(int idx) throws CmdLineException {
+        if (pos+idx >= args.length || pos+idx < 0) {
+            String msg = String.format("Option \"{0}\" takes an operand", option.toString());
+            throw new CmdLineException(parser, msg);
+        }
+        return args[pos+idx];
+    }
+
+    @Override
+    public int size() {
+        return args.length - pos;
+    }
+
+    public boolean hasMore() {
+        return pos < args.length;
+    }
+
+    public String getCurrentToken() {
+        return args[pos];
+    }
+
+    public void proceed(int n) {
+        pos += n;
+    }
+
+}

src/test/java/imsam/args4j/Test_MapDoubleOptionHandler.java

@@ -0,0 +1,45 @@
+package imsam.args4j;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import org.junit.jupiter.api.Test;
+import org.kohsuke.args4j.CmdLineException;
+import org.kohsuke.args4j.CmdLineParser;
+import org.kohsuke.args4j.Option;
+import org.opentest4j.AssertionFailedError;
+
+public class Test_MapDoubleOptionHandler {
+
+    protected class TestClass {
+        @Option(name="--dict", metaVar="dict", handler=MapDoubleOptionHandler.class)
+        public Map<String,Double> dictionary = new HashMap<>();
+    }
+
+    protected Map<String,Double> parse(String[] args) throws CmdLineException {
+        TestClass testClass = new TestClass();
+        CmdLineParser parser = new CmdLineParser(testClass);
+        parser.parseArgument(args);
+        return testClass.dictionary;
+    }
+
+    @Test
+    public void test_MapStringDouble() throws CmdLineException {
+        String[] args = "--dict foo=1.11 --dict bar=2.22 --dict baz=3.33".split("\\s+");
+        Map<String,Double> map = parse(args);
+        try {
+            assertTrue(map.size() == 3);
+            assertEquals(1.11, map.get("foo"));
+            assertEquals(2.22, map.get("bar"));
+            assertEquals(3.33, map.get("baz"));
+        }
+        catch (AssertionFailedError ex) {
+            System.err.println(map);
+            throw ex;
+        }
+    }
+
+}

src/test/java/imsam/args4j/Test_MapIntOptionHandler.java

@@ -0,0 +1,45 @@
+package imsam.args4j;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import org.junit.jupiter.api.Test;
+import org.kohsuke.args4j.CmdLineException;
+import org.kohsuke.args4j.CmdLineParser;
+import org.kohsuke.args4j.Option;
+import org.opentest4j.AssertionFailedError;
+
+public class Test_MapIntOptionHandler {
+
+    protected class TestClass {
+        @Option(name="--dict", metaVar="dict", handler=MapIntOptionHandler.class)
+        public Map<String,Integer> dictionary = new HashMap<>();
+    }
+
+    protected Map<String,Integer> parse(String[] args) throws CmdLineException {
+        TestClass testClass = new TestClass();
+        CmdLineParser parser = new CmdLineParser(testClass);
+        parser.parseArgument(args);
+        return testClass.dictionary;
+    }
+
+    @Test
+    public void test_MapStringInt() throws CmdLineException {
+        String[] args = "--dict foo=1 --dict bar=2 --dict baz=3".split("\\s+");
+        Map<String,Integer> map = parse(args);
+        try {
+            assertTrue(map.size() == 3);
+            assertEquals(1, map.get("foo"));
+            assertEquals(2, map.get("bar"));
+            assertEquals(3, map.get("baz"));
+        }
+        catch (AssertionFailedError ex) {
+            System.err.println(map);
+            throw ex;
+        }
+    }
+
+}

src/test/java/imsam/args4j/Test_MultiMapOptionHandler.java

@@ -0,0 +1,70 @@
+package imsam.args4j;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import org.junit.jupiter.api.Test;
+import org.kohsuke.args4j.CmdLineException;
+import org.kohsuke.args4j.CmdLineParser;
+import org.kohsuke.args4j.Option;
+import org.opentest4j.AssertionFailedError;
+
+public class Test_MultiMapOptionHandler {
+
+    protected class TestClass {
+        @Option(name="--dict", metaVar="dict", handler=MultiMapOptionHandler.class)
+        public Map<String,String> dictionary = new HashMap<>();
+    }
+
+    protected Map<String,String> parse(String[] args) throws CmdLineException {
+        TestClass testClass = new TestClass();
+        CmdLineParser parser = new CmdLineParser(testClass);
+        parser.parseArgument(args);
+        return testClass.dictionary;
+    }
+
+    @Test
+    public void test_Empty() throws CmdLineException {
+        String[] args = {};
+        Map<String,String> map = parse(args);
+        assertTrue(map.isEmpty());
+    }
+
+    @Test
+    public void test_MapStringString() throws CmdLineException {
+        String[] args = "--dict foo=Hello --dict bar=World".split("\\s+");
+        Map<String,String> map = parse(args);
+        try {
+            assertEquals(2, map.size());
+            assertEquals("Hello", map.get("foo"));
+            assertEquals("World", map.get("bar"));
+        }
+        catch (AssertionFailedError ex) {
+            System.err.println(map);
+            throw ex;
+        }
+    }
+
+    @Test
+    public void test_MultiMap() throws CmdLineException {
+        String[] args = "--dict foo=99,bar=88,baz=77".split("\\s+");
+        Map<String,String> map = parse(args);
+        try {
+            assertEquals(3, map.size());
+            assertEquals("99", map.get("foo"));
+            assertEquals("88", map.get("bar"));
+            assertEquals("77", map.get("baz"));
+        }
+        catch (AssertionFailedError ex) {
+            System.err.println("size="+map.size());
+            map.forEach((key, value) -> {
+                System.err.println("'"+key+"' : '"+value+"'");
+            });
+            throw ex;
+        }
+    }
+
+}