groovy scripts can be read from stdin

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 5d0b9d6..faf98db 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -18,8 +18,12 @@
  */
 package jalview.bin;
 
+import java.io.BufferedReader;
 import java.io.File;
+import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
 import java.lang.reflect.Constructor;
 import java.util.*;
 
@@ -80,7 +84,7 @@ 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."
+                      + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)"
                       + "\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
       System.exit(0);
     }
@@ -398,7 +402,32 @@ public class Jalview
     {
       System.err.println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
     }
-    File sfile = new File(groovyscript);
+    File sfile = null;
+    if (groovyscript.trim().equals("STDIN"))
+    {
+      // read from stdin into a tempfile and execute it
+      try {
+        sfile = File.createTempFile("jalview", "groovy");
+        PrintWriter outfile = new PrintWriter(new OutputStreamWriter(new FileOutputStream(sfile)));
+        BufferedReader br = new BufferedReader(new java.io.InputStreamReader(System.in));
+        String line=null;
+        while ((line=br.readLine())!=null)
+        {
+          outfile.write(line+"\n");
+        }
+        br.close();
+        outfile.flush();
+        outfile.close();
+        
+      } catch (Exception ex)
+      {
+        System.err.println("Failed to read from STDIN into tempfile "+((sfile==null) ? "(tempfile wasn't created)" : sfile.toString()));
+        ex.printStackTrace();
+        return;
+      }
+    } else {
+      sfile = new File(groovyscript);
+    }
     if (!sfile.exists())
     {
       System.err.println("File '"+groovyscript+"' does not exist.");
@@ -414,6 +443,7 @@ public class Jalview
       System.err.println("File '"+groovyscript+"' is empty.");
       return;
     }
+    boolean success = false;
     try {
       /* The following code performs the GroovyScriptEngine invocation using reflection,
        * and is equivalent to this fragment from the embedding groovy documentation on 
@@ -437,13 +467,20 @@ public class Jalview
         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 } });
+        Object gse = gseccons.newInstance(new Object[] { new String[] { sfile.toURL().toString() } });
         java.lang.reflect.Method run = gsec.getMethod("run", new Class[]{ String.class, gbindingc });
-        run.invoke(gse, new Object[] { sfile.getName(), gbinding });
+        run.invoke(gse, new Object[] { sfile.toURL().toString(), gbinding });
+        success = true;
     } catch (Exception e)
     {
       System.err.println("Exception Whilst trying to execute file "+sfile+" as a groovy script.");
       e.printStackTrace(System.err);
+      
+    }
+    if (success && groovyscript.equals("STDIN"))
+    {
+      // delete temp file that we made - but only if it was successfully executed
+      sfile.delete();
     }
   }
   /**