Merge branch 'scripts'

This topic branch brings fixes required by the script editor (so that
errors are shown in the script editor, not in the console that might
be hidden from the user by the operating system).

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>

Author: dscho

src/main/java/org/scijava/script/ScriptModule.java

@@ -32,6 +32,8 @@
 package org.scijava.script;
 
 import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintWriter;
 import java.io.Reader;
 import java.io.Writer;
 
@@ -146,7 +148,13 @@ public void run() {
 		engine.put(ScriptEngine.FILENAME, path);
 		final ScriptContext scriptContext = engine.getContext();
 		if (output != null) scriptContext.setWriter(output);
-		if (error != null) scriptContext.setErrorWriter(error);
+		final PrintWriter errorPrinter;
+		if (error != null) {
+			scriptContext.setErrorWriter(error);
+			errorPrinter = new PrintWriter(error);
+		} else {
+			errorPrinter = null;
+		}
 
 		// populate bindings with the input values
 		for (final ModuleItem<?> item : getInfo().inputs()) {
@@ -164,11 +172,15 @@ public void run() {
 			setOutput(RETURN_VALUE, language.decode(returnValue));
 			setResolved(RETURN_VALUE, true);
 		}
-		catch (final ScriptException e) {
-			log.error(e.getCause());
-		}
-		catch (final Throwable e) {
-			log.error(e);
+		catch (Throwable e) {
+			while (e instanceof ScriptException && e.getCause() != null) {
+				e = e.getCause();
+			}
+			if (error == null) {
+				log.error(e);
+			} else {
+				e.printStackTrace(errorPrinter);
+			}
 		}
 
 		// populate output values
@@ -180,6 +192,20 @@ public void run() {
 			final Object typed = ConversionUtils.convert(decoded, item.getType());
 			setOutput(name, typed);
 		}
+
+		if (output != null) try {
+			output.flush();
+		} catch (IOException e) {
+			if (error == null) {
+				log.error(e);
+			} else {
+				e.printStackTrace(errorPrinter);
+			}
+		}
+
+		if (errorPrinter != null) {
+			errorPrinter.flush();
+		}
 	}
 
 	// -- Contextual methods --