Allow script processors to modify the script

In particular, we want the #@ processing directives to disappear from
the executed version of the script, since they are invalid syntax for
many of the script languages.

This change gives ScriptProcessor plugins the flexibility to modify each
line of the script however they choose, although our initial use case
here will simply blank out lines which have been handled.

What processors should not do is change the number of lines; we want the
line numbers in error messages to match those of the original script.

Author: ctrueden

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

@@ -84,6 +84,9 @@ public class ScriptInfo extends AbstractModuleInfo implements Contextual {
 	@Parameter
 	private ScriptProcessorService scriptProcessorService;
 
+	/** Final version of the script, after script processing. */
+	private String processedScript;
+
 	/** True iff the return value should be appended as an output. */
 	private boolean appendReturnValue;
 
@@ -216,6 +219,16 @@ public BufferedReader getReader() {
 		return new BufferedReader(new StringReader(script), PARAM_CHAR_MAX);
 	}
 
+	/**
+	 * Gets the script contents <em>after</em> script processing.
+	 * 
+	 * @return The processed script.
+	 * @see ScriptProcessorService#process
+	 */
+	public String getProcessedScript() {
+		return processedScript;
+	}
+
 	/** Gets the scripting language of the script. */
 	public ScriptLanguage getLanguage() {
 		if (scriptLanguage == null) {
@@ -275,7 +288,7 @@ public List<ScriptCallback> callbacks() {
 	public void parseParameters() {
 		clearParameters();
 		try {
-			scriptProcessorService.process(this);
+			processedScript = scriptProcessorService.process(this);
 		}
 		catch (final IOException exc) {
 			// TODO: Consider a better error handling approach.

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

@@ -31,10 +31,8 @@
 
 package org.scijava.script;
 
-import java.io.FileReader;
 import java.io.IOException;
 import java.io.PrintWriter;
-import java.io.Reader;
 import java.io.Writer;
 
 import javax.script.ScriptContext;
@@ -158,9 +156,7 @@ public void run() {
 			}
 
 			// execute script!
-			final Reader reader = getInfo().getReader();
-			if (reader == null) returnValue = engine.eval(new FileReader(path));
-			else returnValue = engine.eval(reader);
+			returnValue = engine.eval(getInfo().getProcessedScript());
 		}
 		catch (Throwable e) {
 			while (e instanceof ScriptException && e.getCause() != null) {

src/main/java/org/scijava/script/process/ParameterScriptProcessor.java

@@ -127,12 +127,11 @@ public void begin(final ScriptInfo scriptInfo) {
 	}
 
 	@Override
-	public void process(final String line) {
+	public String process(final String line) {
 		// parse new-style parameters starting with @# anywhere in the script.
 		if (line.matches("^#@.*")) {
 			final int at = line.indexOf('@');
-			parseParam(line.substring(at + 1));
-			return;
+			return process(line, line.substring(at + 1));
 		}
 
 		// parse old-style parameters in the initial script header
@@ -142,10 +141,12 @@ public void process(final String line) {
 			// be used as comment line markers.
 			if (line.matches("^[^\\w]*@.*")) {
 				final int at = line.indexOf('@');
-				parseParam(line.substring(at + 1));
+				return process(line, line.substring(at + 1));
 			}
 			else if (line.matches(".*\\w.*")) header = false;
 		}
+
+		return line;
 	}
 
 	@Override
@@ -160,34 +161,40 @@ public void end() {
 
 	// -- Helper methods --
 
-	private void parseParam(final String param) {
+	private String process(final String line, final String param) {
+		if (parseParam(param)) return "";
+		log.warn("Ignoring invalid parameter: " + param);
+		return line;
+	}
+
+	private boolean parseParam(final String param) {
 		final int lParen = param.indexOf("(");
 		final int rParen = param.lastIndexOf(")");
-		if (rParen < lParen) { warnInvalid(param); return; }
-		if (lParen < 0) parseParam(param, parseAttrs("()"));
-		else {
-			final String cutParam =
-				param.substring(0, lParen) + param.substring(rParen + 1);
-			final String attrs = param.substring(lParen + 1, rParen);
-			parseParam(cutParam, parseAttrs(attrs));
-		}
+		if (rParen < lParen) return false;
+		if (lParen < 0) return parseParam(param, parseAttrs("()"));
+		final String cutParam =
+			param.substring(0, lParen) + param.substring(rParen + 1);
+		final String attrs = param.substring(lParen + 1, rParen);
+		return parseParam(cutParam, parseAttrs(attrs));
 	}
 
-	private void parseParam(final String param, final Map<String, Object> attrs) {
+	private boolean parseParam(final String param,
+		final Map<String, Object> attrs)
+	{
 		final String[] tokens = param.trim().split("[ \t\n]+");
-		if (tokens.length < 1) { warnInvalid(param); return; }
+		if (tokens.length < 1) return false;
 		final String typeName, varName;
 		final String maybeIOType = tokens[0].toUpperCase();
 		if (isIOType(maybeIOType)) {
 			// assume syntax: <IOType> <type> <varName>
-			if (tokens.length < 3) { warnInvalid(param); return; }
+			if (tokens.length < 3) return false;
 			attrs.put("type", maybeIOType);
 			typeName = tokens[1];
 			varName = tokens[2];
 		}
 		else {
 			// assume syntax: <type> <varName>
-			if (tokens.length < 2) { warnInvalid(param); return; }
+			if (tokens.length < 2) return false;
 			typeName = tokens[0];
 			varName = tokens[1];
 		}
@@ -197,14 +204,16 @@ private void parseParam(final String param, final Map<String, Object> attrs) {
 		}
 		catch (final ScriptException exc) {
 			log.warn("Invalid class: " + typeName, exc);
-			return;
+			return false;
 		}
 
 		if (ScriptModule.RETURN_VALUE.equals(varName)) {
 			// NB: The return value variable is declared as an explicit parameter.
 			// So we should not append the return value as an extra output.
 			info.setReturnValueAppended(false);
 		}
+
+		return true;
 	}
 
 	/** Parses a comma-delimited list of {@code key=value} pairs into a map. */
@@ -216,10 +225,6 @@ private boolean isIOType(final String token) {
 		return convertService.convert(token.toUpperCase(), ItemIO.class) != null;
 	}
 
-	private void warnInvalid(final String param) {
-		log.warn("Ignoring invalid parameter: " + param);
-	}
-
 	private <T> void addItem(final String name, final Class<T> type,
 		final Map<String, Object> attrs, final boolean explicit)
 	{

src/main/java/org/scijava/script/process/ScriptProcessor.java

@@ -48,7 +48,7 @@
 public interface ScriptProcessor extends SingletonPlugin {
 
 	void begin(ScriptInfo info);
-	void process(String line);
+	String process(String line);
 	default void end() {}
 
 }

src/main/java/org/scijava/script/process/ScriptProcessorService.java

@@ -56,7 +56,7 @@ public interface ScriptProcessorService extends
 	 * Invokes all {@link ScriptProcessor} plugins on the given script, line by
 	 * line in sequence.
 	 */
-	default void process(final ScriptInfo info) throws IOException {
+	default String process(final ScriptInfo info) throws IOException {
 		final List<ScriptProcessor> processors = getPlugins().stream().map(
 			p -> pluginService().createInstance(p)).collect(Collectors.toList());
 
@@ -69,19 +69,25 @@ default void process(final ScriptInfo info) throws IOException {
 			p.begin(info);
 		}
 
+		final StringBuilder sb = new StringBuilder();
+
 		try (final BufferedReader in = reader) {
 			while (true) {
-				final String line = in.readLine();
+				String line = in.readLine();
 				if (line == null) break;
 				for (final ScriptProcessor p : processors) {
-					p.process(line);
+					line = p.process(line);
 				}
+				sb.append(line);
+				sb.append("\n");
 			}
 		}
 
 		for (final ScriptProcessor p : processors) {
 			p.end();
 		}
+
+		return sb.toString();
 	}
 
 	// -- PTService methods --

src/main/java/org/scijava/script/process/ShebangScriptProcessor.java

@@ -64,15 +64,17 @@ public void begin(final ScriptInfo scriptInfo) {
 	}
 
 	@Override
-	public void process(final String line) {
-		if (!first) return;
+	public String process(final String line) {
+		if (!first) return line;
+		first = false;
 		if (line.startsWith("#!")) {
 			// shebang!
 			final String langName = line.substring(2);
 			final ScriptLanguage lang = scriptService.getLanguageByName(langName);
 			if (lang != null) info.setLanguage(lang);
 			else log.warn("Unknown script language: " + langName);
+			return "";
 		}
-		first = false;
+		return line;
 	}
 }