added groovy argument for launching a groovy script from the command line

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index bfd6d70..5d0b9d6 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -18,7 +18,9 @@
  */
 package jalview.bin;
 
+import java.io.File;
 import java.io.IOException;
+import java.lang.reflect.Constructor;
 import java.util.*;
 
 import javax.swing.*;
@@ -78,6 +80,7 @@ public class Jalview
                       + "-noquestionnaire\tTurn off questionnaire check."
                       + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments."
                       + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them."
+                      + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed."
                       + "\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
       System.exit(0);
     }
@@ -160,6 +163,9 @@ public class Jalview
     jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
     Vector getFeatures = null; // vector of das source nicknames to fetch features from
     // loading is done.
+    String groovyscript = null; // script to execute after all loading is completed one way or another
+    // extract groovy argument and execute if necessary
+    groovyscript = aparser.getValue("groovy");
     file = aparser.getValue("open");
 
     if (file == null && desktop == null)
@@ -272,6 +278,19 @@ public class Jalview
           }
         }
       }
+      if (groovyscript!=null)
+      {
+        // Execute the groovy script after we've  done all the rendering stuff
+        // and before any images or figures are generated.
+        if (jalview.bin.Cache.groovyJarsPresent())
+        {
+          System.out.println("Executing script "+groovyscript);
+          executeGroovyScript(groovyscript, desktop);
+        } else {
+          System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript);
+        }
+        groovyscript = null;
+      }
       String imageName = "unnamed.png";
       while (aparser.getSize() > 1)
       {
@@ -345,6 +364,7 @@ public class Jalview
       startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
               format);
       getFeatures = checkDasArguments(aparser);
+      // extract groovy arguments before anything else.
     }
     // Once all loading is done. Retrieve features.
     if (getFeatures!=null)
@@ -354,6 +374,77 @@ public class Jalview
         startFeatureFetching(getFeatures);
       }
     }
+    if (groovyscript!=null)
+    {
+      if (jalview.bin.Cache.groovyJarsPresent())
+      {
+        System.out.println("Executing script "+groovyscript);
+        executeGroovyScript(groovyscript, desktop);
+      } else {
+        System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript);
+      }
+    }
+
+    // Once all other stuff is done, execute any groovy scripts (in order)
+  }
+  /**
+   * Locate the given string as a file and pass it to the groovy interpreter.
+   * @param groovyscript the script to execute
+   * @param jalviewContext the Jalview Desktop object passed in to the groovy binding as the 'Jalview' object.
+   */
+  private static void executeGroovyScript(String groovyscript, Object jalviewContext)
+  {
+    if (jalviewContext==null)
+    {
+      System.err.println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
+    }
+    File sfile = new File(groovyscript);
+    if (!sfile.exists())
+    {
+      System.err.println("File '"+groovyscript+"' does not exist.");
+      return;
+    }
+    if (!sfile.canRead())
+    {
+      System.err.println("File '"+groovyscript+"' cannot be read.");
+      return;
+    }
+    if (sfile.length()<1)
+    {
+      System.err.println("File '"+groovyscript+"' is empty.");
+      return;
+    }
+    try {
+      /* The following code performs the GroovyScriptEngine invocation using reflection,
+       * and is equivalent to this fragment from the embedding groovy documentation on 
+       * the groovy site:
+       * <code>
+         import groovy.lang.Binding;
+         import groovy.util.GroovyScriptEngine;
+        
+         String[] roots = new String[] { "/my/groovy/script/path" };
+         GroovyScriptEngine gse = new GroovyScriptEngine(roots);
+         Binding binding = new Binding();
+         binding.setVariable("input", "world");
+         gse.run("hello.groovy", binding);
+         * </code>
+         */
+        ClassLoader cl = jalviewContext.getClass().getClassLoader();
+        Class   gbindingc = cl.loadClass("groovy.lang.Binding");
+        Constructor gbcons = gbindingc.getConstructor(null);
+        Object gbinding = gbcons.newInstance(null);
+        java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable", new Class[] { String.class, Object.class} );
+        setvar.invoke(gbinding, new Object[] { "Jalview", jalviewContext});
+        Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
+        Constructor gseccons = gsec.getConstructor(new Class[] { String[].class });
+        Object gse = gseccons.newInstance(new Object[] { new String[] { groovyscript } });
+        java.lang.reflect.Method run = gsec.getMethod("run", new Class[]{ String.class, gbindingc });
+        run.invoke(gse, new Object[] { sfile.getName(), gbinding });
+    } catch (Exception e)
+    {
+      System.err.println("Exception Whilst trying to execute file "+sfile+" as a groovy script.");
+      e.printStackTrace(System.err);
+    }
   }
   /**
    * Check commandline for any das server definitions or any fetchfrom switches