SLPhy can take macro now #420

examples/macro/MacroLanguage.lphy

@@ -1,3 +1,5 @@
+// It only shows the default when using studio,
+// but macro value can be replaced by SLPhy (command line application).
 data {
   L = {{L = 100}};
   taxa = taxa(names=1:{{n = 10}});

lphy-base/src/test/java/lphy/base/LPhyExamplesTest.java

@@ -56,7 +56,7 @@ public void testLPhyExamplesInDir(File exampleDir) {
             try {
                 FileReader lphyFile = new FileReader(exampleDir.getAbsoluteFile() + File.separator + fileName);
                 BufferedReader fin = new BufferedReader(lphyFile);
-                lPhyMetaParser.source(fin);
+                lPhyMetaParser.source(fin, null);
             } catch (Exception e) {
 //                    failedFiles.add(fileName);
                 System.err.println("Example " + fileName + " failed\n");

lphy-studio/src/main/java/lphystudio/app/graphicalmodelpanel/GraphicalModelPanel.java

@@ -4,7 +4,6 @@
 import lphy.core.logger.LoggerUtils;
 import lphy.core.model.*;
 import lphy.core.parser.LPhyParserDictionary;
-import lphy.core.parser.REPL;
 import lphy.core.parser.graphicalmodel.GraphicalModel;
 import lphy.core.parser.graphicalmodel.GraphicalModelListener;
 import lphy.core.simulator.Sampler;
@@ -230,7 +229,7 @@ public void layout() {
 //    }
 
     /**
-     * This is duplicated to {@link REPL#source(BufferedReader)},
+     * This is duplicated to {@link LPhyParserDictionary#source(BufferedReader, String[])},
      * but has extra code using {@link LineCodeColorizer}
      * and panel function.
      *
@@ -240,7 +239,7 @@ public void layout() {
     public void source(BufferedReader reader) throws IOException {
 
         LPhyParserDictionary metaData = component.getParserDictionary();
-        metaData.source(reader);
+        metaData.source(reader, null);
 
         repaint();
     }

lphy/src/main/java/lphy/core/io/FileConfig.java

@@ -111,9 +111,11 @@ public static class Utils {
 
         public static FileConfig createSimulationFileConfig(File lphyFile, File outDir, int numReplicates,
                                                              Long seed ) throws IOException {
+
+            String currentDir = lphyFile.getAbsoluteFile().getParent();
             // if user.dir is not the parent folder of lphyFile, then set to it
-            if (! UserDir.getUserDir().toAbsolutePath().equals(lphyFile.getParentFile())) {
-                UserDir.setUserDir(lphyFile.getParentFile().getAbsolutePath());
+            if (! UserDir.getUserDir().toAbsolutePath().equals(currentDir)) {
+                UserDir.setUserDir(currentDir);
             }
 
             if (seed != null)

lphy/src/main/java/lphy/core/io/MacroProcessor.java

@@ -1,5 +1,7 @@
 package lphy.core.io;
 
+import lphy.core.logger.LoggerUtils;
+
 import java.util.HashMap;
 import java.util.Map;
 import java.util.regex.Matcher;
@@ -15,44 +17,77 @@ public class MacroProcessor {
     public static final String CONST_MACRO = "\\{\\{\\s*(\\w+)\\s*=\\s*(.*?)\\s*\\}\\}";
     private final Pattern pattern;
 
-    public MacroProcessor(String regex) {
+    // init by user input (e.g. cmd args), if map key does not have the var name when per-processing script,
+    // then use the default from macro.
+    Map<String, String> macroMap;
+
+    public MacroProcessor(String regex, String[] constants) {
         this.pattern = Pattern.compile(regex);
+        macroMap = new HashMap<>();
+        if (constants != null)
+            // init macroMap based on user input
+            parseConstants(constants);
     }
 
-    public MacroProcessor() {
-        this(CONST_MACRO);
+    /**
+     * Process the marco in a lphy script, such as {{n = 10}}.
+     * @param constants   constants inputted by user (e.g. command line arguments),
+     *                    where each string element looks like n=10.
+     *                    Null, if no user input.
+     */
+    public MacroProcessor(String[] constants) {
+        this(CONST_MACRO, constants);
     }
 
-    // Singleton
-    private static MacroProcessor INSTANCE;
-    public static MacroProcessor getInstance() {
-        if(INSTANCE == null) {
-            INSTANCE = new MacroProcessor();
-        }
-        return INSTANCE;
-    }
 
-    public static String process(String input) {
-        Map<String, String> macroMap = getInstance().getMacroMap(input);
-        // TODO modify the macroMap based on user input?
-        return getInstance().getResult(input, macroMap);
+    /**
+     * @param input lphy string before preprocessing macros.
+     * @return a lphy string after replacing all macro into actual values.
+     */
+    public String process(String input) {
+        assignDefaultValues(input);
+        return getResult(input);
     }
 
-    public Map<String, String> getMacroMap(String input) {
-        Map<String, String> macroMap = new HashMap<>();
 
+    /**
+     * Parse command line argument into {@link #macroMap}.
+     * E.g. -D n=12;L=100 or -D n=20"
+     *
+     * @param constants
+     */
+    private void parseConstants(String[] constants) {
+        for (String arg : constants) {
+            // n = 12
+            if (arg.contains("=")) {
+                // the pattern will be applied at most limit - 1 times,
+                // the array's length will be no greater than limit,
+                // and the array's last entry will contain all input beyond the last matched delimiter.
+                String[] varVal = arg.split("=", 2);
+                if (varVal.length == 2) {
+                    // trim spaces
+                    macroMap.put(varVal[0].trim(), varVal[1].trim());
+                }
+            }
+        }
+    }
+
+    private void assignDefaultValues(String input) {
         // Populate the macroMap based on the initial matches
         Matcher matcher = pattern.matcher(input);
 
         while (matcher.find()) {
             String identifier = matcher.group(1);
             String literal = matcher.group(2);
-            macroMap.put(identifier, literal);
+            // use the default from macro, only when the var name not exist
+            if (!macroMap.containsKey(identifier))
+                macroMap.put(identifier, literal);
         }
-        return macroMap;
     }
 
-    public String getResult(String input, Map<String, String> macroMap) {
+    private String getResult(String input) {
+        if (macroMap.isEmpty()) return input;
+
         Matcher replaceMatcher = pattern.matcher(input);
         StringBuilder stringBuffer = new StringBuilder();
 
@@ -63,6 +98,9 @@ public String getResult(String input, Map<String, String> macroMap) {
                 // Slashes ('\') and dollar signs ('$') will be given no special meaning.
                 replacement = Matcher.quoteReplacement(replacement);
                 replaceMatcher.appendReplacement(stringBuffer, replacement);
+
+                LoggerUtils.log.info("Macro replaces the value of constant var : " + replaceMatcher.group(1) +
+                        " = " + replacement);
             }
         }
         replaceMatcher.appendTail(stringBuffer);
@@ -73,7 +111,8 @@ public String getResult(String input, Map<String, String> macroMap) {
     public static void main(String[] args) {
         String input = "{{identifier1 = value1}} some text {{identifier2 = value2}}";
 
-        String result = MacroProcessor.process(input);
+        MacroProcessor macroProcessor = new MacroProcessor(null);
+        String result = macroProcessor.process(input);
 
         System.out.println(result);
     }

lphy/src/main/java/lphy/core/parser/LPhyParserDictionary.java

@@ -79,11 +79,12 @@ default List<String> getKeywords() {
 
     /**
      * @param sourceFile the lphy source file
+     * @param constants      constants inputted by user using macro
      */
-    default void source(File sourceFile) throws IOException {
+    default void source(File sourceFile, String[] constants) throws IOException {
         FileReader reader = new FileReader(sourceFile);
         BufferedReader bufferedReader = new BufferedReader(reader);
-        source(bufferedReader);
+        source(bufferedReader, constants);
         reader.close();
     }
 
@@ -92,16 +93,23 @@ default void source(File sourceFile) throws IOException {
      * Before {@link #parse(String)}, the line will be preprocessed by
      * {@link MacroProcessor}, so that the marco templating language
      * will be replaced by the actual values.
+     *
      * @param bufferedReader the lphy source
+     * @param constants      constants inputted by user (e.g. command line arguments),
+     *                       where each string element looks like n=10.
+     *                       Null, if no user input.
      */
-    default void source(BufferedReader bufferedReader) throws IOException {
+    default void source(BufferedReader bufferedReader, String[] constants) throws IOException {
+        // init processor by use input if there is any
+        MacroProcessor macroProcessor = new MacroProcessor(constants);
+
         StringBuilder builder = new StringBuilder();
 
         String lineProcessed;
         String line = bufferedReader.readLine();
         while (line != null) {
             // process macro here
-            lineProcessed = MacroProcessor.process(line);
+            lineProcessed = macroProcessor.process(line);
             builder.append(lineProcessed);
             builder.append("\n");
 

lphy/src/main/java/lphy/core/simulator/NamedRandomValueSimulator.java

@@ -24,27 +24,19 @@ public NamedRandomValueSimulator() {
         simulatorListener = new ValueFileLoggerListener();
     }
 
-    public Map<Integer, List<Value>> simulateAndSaveResults(File lphyFile, int numReplicates, Long seed) throws IOException {
-        simulatorListener.start(numReplicates, lphyFile);
-        return simulate(lphyFile, numReplicates, seed);
-    }
-
-    public Map<Integer, List<Value>> simulateAndSaveResults(FileConfig fileConfig) throws IOException {
+    // must have File lphyFile, int numReplicates, Long seed
+    public Map<Integer, List<Value>> simulate(FileConfig fileConfig, String[] constants) throws IOException {
         simulatorListener.start(fileConfig);
 
         File lphyFile = fileConfig.lphyInputFile;
         int numReplicates = fileConfig.numReplicates;
         Long seed = fileConfig.seed;
 
-        return simulate(lphyFile, numReplicates, seed);
-    }
-
-    private Map<Integer, List<Value>> simulate(File lphyFile, int numReplicates, Long seed) throws IOException {
         // TODO duplicate to maps in ValueFileLoggerListener
         Map<Integer, List<Value>> simResMap = new HashMap<>();
 
         // create Sampler given a lphy script file
-        sampler = Sampler.createSampler(lphyFile);
+        sampler = Sampler.createSampler(lphyFile, constants);
 
         long start = System.currentTimeMillis();
 

lphy/src/main/java/lphy/core/simulator/SLPhy.java

@@ -41,6 +41,11 @@ public class SLPhy implements Callable<Integer> {
             "usually to create data for well-calibrated study.") int numReps = 1;
     @CommandLine.Option(names = {"-seed", "--seed"}, description = "the seed.") Long seed;
 
+    @CommandLine.Option(names = {"-D", "--data"}, split = ";",
+            description = "Replace the constant value in the lphy script, multiple constants can be split by ';', " +
+                    "but no ';' at the last: e.g. -D \"n=12;L=100\" or -D n=20")
+    String[] lphyConst = null;
+
 //    enum SPI { loggers } //TODO  functions, gendists
 //    // arity = "0" not working
 //    @CommandLine.Option(names = {"-ls", "--list"},
@@ -62,8 +67,9 @@ public Integer call() throws PicocliException {
                     .createSimulationFileConfig(infile.toFile(), outDir, numReps, seed);
 
             simulator = new NamedRandomValueSimulator();
-            simulator.simulateAndSaveResults(fileConfig);
-
+            // must provide File lphyFile, int numReplicates, Long seed
+            simulator.simulate(fileConfig, lphyConst);
+            // TODO save Map<Integer, List<Value>> simResMap ?
         } catch (IOException e) {
             throw new PicocliException(e.getMessage(), e);
         }

lphy/src/main/java/lphy/core/simulator/Sampler.java

@@ -30,13 +30,14 @@ public Sampler(LPhyParserDictionary parser) {
 
     /**
      * @param lphyFile  a File containing LPhy script.
+     * @param constants      constants inputted by user using macro
      * @return          a Sampler created by the given LPhy script.
      * @throws IOException
      */
-    public static Sampler createSampler(File lphyFile) throws IOException {
+    public static Sampler createSampler(File lphyFile, String[] constants) throws IOException {
         //*** Parse LPhy file ***//
         LPhyParserDictionary parser = new REPL();
-        parser.source(lphyFile);
+        parser.source(lphyFile, constants);
 
         // Sampler requires GraphicalLPhyParser
         Sampler sampler = new Sampler(parser);

lphy/src/main/java/lphy/core/simulator/Simulate.java

@@ -78,8 +78,9 @@ public Value<Map<String, Object>> apply() {
             FileConfig fileConfig = FileConfig.Utils
                     .createSimulationFileConfig(infile, outDir, SimulatorListener.REPLICATES_START_INDEX, seed);
 
-            values = simulator.simulateAndSaveResults(fileConfig)
-                    .get(SimulatorListener.REPLICATES_START_INDEX);
+            Map<Integer, List<Value>> allReps = simulator.simulate(fileConfig, null);
+            // only take the last replicate
+            values = allReps.get(SimulatorListener.REPLICATES_START_INDEX);
 
         } catch (IOException e) {
             LoggerUtils.log.severe("Cannot parse LPhy script file ! " + infile.getAbsolutePath());