add -DFout option to BeastMain #894

src/beast/app/BeastMCMC.java

@@ -94,6 +94,8 @@ public void parseArgs(String[] args) throws IOException, XMLParserException, JSO
         boolean resume = false;
         boolean useStrictVersions = false;
         boolean sampleFromPrior = false;
+        boolean hasDF = false;
+        String outFile = null;
         Map<String, String> parserDefinitions = new HashMap<>();
 
         File beastFile = null;
@@ -166,6 +168,10 @@ public void parseArgs(String[] args) throws IOException, XMLParserException, JSO
                 			Log.warning("Found definition of " + key + " " + jsonDictionary.getString(key).length());
                             parserDefinitions.put(key, jsonDictionary.getString(key));
                 		}
+                		hasDF = true;
+                        i += 2;     
+                    } else if (args[i].equals("-DFout")) {
+                    	outFile = args[i + 1];                    	 
                         i += 2;                    
                     } else if (args[i].equals("-strictversions")) {
                     	useStrictVersions = true;
@@ -189,6 +195,14 @@ public void parseArgs(String[] args) throws IOException, XMLParserException, JSO
             throw new IllegalArgumentException("Error parsing command line arguments: " + Arrays.toString(args) + "\nArguments ignored\n\n" + getUsage());
         }
 
+        if (hasDF && outFile == null && beastFile != null) {
+        	outFile = beastFile.getAbsolutePath();
+        	if (outFile.toLowerCase().endsWith(".xml")) {
+        		outFile = outFile.substring(0, outFile.length() - 4);
+        	}
+    		outFile = outFile + ".out.xml";
+        }        	
+
         if (beastFile == null) {
             // Not resuming so get starting options...
 
@@ -308,7 +322,7 @@ public void parseArgs(String[] args) throws IOException, XMLParserException, JSO
             m_runnable = new JSONParser(parserDefinitions).parseFile(beastFile, sampleFromPrior);
         } else {        	
         	try {
-				m_runnable = new XMLParser(parserDefinitions).parseFile(beastFile, sampleFromPrior);
+				m_runnable = new XMLParser(parserDefinitions, outFile).parseFile(beastFile, sampleFromPrior);
 			} catch (SAXException | ParserConfigurationException e) {
 				throw new IllegalArgumentException(e);
 			}

src/beast/app/beastapp/BeastMain.java

@@ -284,7 +284,8 @@ public static void main(final String[] args) throws java.io.IOException {
                         new Arguments.Option("version", "Print version and stop"),
                         new Arguments.Option("strictversions", "Use only package versions as specified in the 'required' attribute"),
                         new Arguments.StringOption("D", "DEFINITIONS", "attribute-value pairs to be replaced in the XML, e.g., -D \"arg1=10,arg2=20\"").allowMultipleUse(),
-                        new Arguments.StringOption("DF", "DEFINITIONFILE", "as -D, but attribute-value pairs defined in file in a JSON file").allowMultipleUse(),
+                        new Arguments.StringOption("DF", "DEFINITIONFILE", "as -D, but attribute-value pairs defined in file in JSON format").allowMultipleUse(),
+                        new Arguments.StringOption("DFout", "DEFINITIONRESULTFILE", "BEAST XML file written when -DF option is used"),
                         new Arguments.Option("sampleFromPrior", "samples from prior for MCMC analysis (by adding sampleFromPrior=\"true\" in the first run element)"),
                 });
 
@@ -547,6 +548,10 @@ public void write(int b) {
                 MCMCargs.add(optionVal);
             }
         }
+        if (arguments.hasOption("DFout")) {
+            MCMCargs.add("-DFout");
+            MCMCargs.add(arguments.getStringOption("DFout"));
+        }
 
         if (beagleShowInfo) {
             Log.info.println("\n--- BEAGLE RESOURCES ---\n");

src/beast/util/XMLParser.java

@@ -264,6 +264,13 @@ public HashMap<String, String> getElement2ClassMap() {
      */
     RequiredInputProvider requiredInputProvider = null;
     PartitionContext partitionContext = null;
+
+    /**
+     * if outFile is not null, an XML file merged with parser definitions processed 
+     * will be saved here
+     */
+    String outFile;
+
 
     public XMLParser() {
         this.parserDefinitions = new HashMap<>();
@@ -273,6 +280,10 @@ public XMLParser(java.util.Map<String,String> parserDefinitions) {
 		this.parserDefinitions = parserDefinitions;
 	}
 
+	public XMLParser(java.util.Map<String,String> parserDefinitions, String outFile) {
+		this.parserDefinitions = parserDefinitions;
+		this.outFile = outFile;
+	}
 
 
     public Runnable parseFile(final File file) throws SAXException, IOException, ParserConfigurationException, XMLParserException {
@@ -288,14 +299,17 @@ public Runnable parseFile(final File file, boolean sampleFromPrior) throws SAXEx
         	xml = xml.replaceAll("\\$\\(" + key + "\\)", parserDefinitions.get(key));
         }
 
-//        try {
-//	        FileWriter outfile = new FileWriter("/tmp/beast.xml");
-//	        outfile.write(xml);
-//	        outfile.close();
-//	        System.exit(0);
-//        } catch (IOException e) {
-//        	// ignore
-//        }
+        try {
+        	if (parserDefinitions != null && parserDefinitions.size() > 1) {
+	    		Log.warning("Outputting merged file to " + outFile);
+		        FileWriter outfile = new FileWriter(outFile);
+		        outfile.write(xml);
+		        outfile.close();
+        	}
+        } catch (IOException e) {
+        	// ignore
+    		Log.warning("Something went wroting outputting merged file: " + e.getMessage());
+        }
 
 
         doc = factory.newDocumentBuilder().parse(new ByteArrayInputStream(xml.getBytes()));

src/test/beast/integration/ExampleXmlParsingTest.java

@@ -172,17 +172,23 @@ public void checkExit(int status)
         try {
         BeastMain.main(new String[]{
         		"-D", "chainLength=1000",
-        		"-DF", dir + "/RSV2.json", 
+        		"-DF", dir + "/RSV2.json",
+        		"-DFout", "/tmp/RSV2.out.xml",
         		dir + "/RSV2.xml"});
         } catch (ExitException e) {
         	if (e.status != 0) {
         		e.printStackTrace();
         		throw new RuntimeException("Exitted with status = " + e.status);
         	}
         }
-                
+
         // reinstate System.exit() behaviour
         System.setSecurityManager(sm) ;
+
+        if (!new File("/tmp/RSV2.out.xml").exists()) {
+    		throw new RuntimeException("Could not find file /tmp/RSV2.out.xml");
+        }
+
     } // test_ThatParameterisedXmlExamplesRuns