From b1bab6945931fb2798ef5d5dd9797cabf4a83326 Mon Sep 17 00:00:00 2001
From: Jan Eglinger <jan.eglinger@fmi.ch>
Date: Sun, 25 Oct 2020 21:33:55 +0100
Subject: [PATCH] Always ignore commented script parameters

Before this commit, commented-out new-style (#@) script parameters were ignored when in the script body, but parsed when in the script header, because they matched the pattern for old-style parameter syntax.
We now explicitly omit lines with new-style syntax preceded by non-word characters from being matched, so the behavior is consistent independent of the position of the parameter in the script.

Without this change in ParameterScriptProcessor, the test added in this commit would fail with:

[ERROR]   ParameterScriptProcessorTest.testScriptParameterParsing:49 expected null, but was:<commentedHeaderParameter: required=true, persisted=true>
---
 .../process/ParameterScriptProcessor.java     |  6 ++-
 .../process/ParameterScriptProcessorTest.java | 54 +++++++++++++++++++
 2 files changed, 58 insertions(+), 2 deletions(-)
 create mode 100644 src/test/java/org/scijava/script/process/ParameterScriptProcessorTest.java

diff --git a/src/main/java/org/scijava/script/process/ParameterScriptProcessor.java b/src/main/java/org/scijava/script/process/ParameterScriptProcessor.java
index fb73cdc16..0ed4d7212 100644
--- a/src/main/java/org/scijava/script/process/ParameterScriptProcessor.java
+++ b/src/main/java/org/scijava/script/process/ParameterScriptProcessor.java
@@ -129,7 +129,7 @@ public void begin(final ScriptInfo scriptInfo) {
 
 	@Override
 	public String process(final String line) {
-		// parse new-style parameters starting with @# anywhere in the script.
+		// parse new-style parameters starting with #@ anywhere in the script.
 		if (line.matches("^#@.*")) {
 			final int at = line.indexOf('@');
 			return process(line, line.substring(at + 1));
@@ -140,7 +140,9 @@ public String process(final String line) {
 			// NB: Check if line contains an '@' with no prior alphameric
 			// characters. This assumes that only non-alphanumeric characters can
 			// be used as comment line markers.
-			if (line.matches("^[^\\w]*@.*")) {
+			// NB: In addition, to allow for commented-out new-style parameters, we exclude
+			// lines that have the new-style #@ preceded by non-alphanumeric characters.
+			if (line.matches("^[^\\w]*[^\\w#]@.*")) {
 				final int at = line.indexOf('@');
 				return process(line, line.substring(at + 1));
 			}
diff --git a/src/test/java/org/scijava/script/process/ParameterScriptProcessorTest.java b/src/test/java/org/scijava/script/process/ParameterScriptProcessorTest.java
new file mode 100644
index 000000000..3e29007bb
--- /dev/null
+++ b/src/test/java/org/scijava/script/process/ParameterScriptProcessorTest.java
@@ -0,0 +1,54 @@
+package org.scijava.script.process;
+
+import static org.junit.Assert.*;
+
+import java.io.StringReader;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.scijava.Context;
+import org.scijava.script.ScriptInfo;
+
+public class ParameterScriptProcessorTest {
+
+	private Context context;
+
+	@Before
+	public void setUp() {
+		context = new Context();
+	}
+
+	@After
+	public void tearDown() {
+		context.dispose();
+	}
+
+	@Test
+	public void testScriptParameterParsing() {
+		String script = "" + //
+				"% @String legacyStyleParameter\n" +
+				"% #@ String commentedHeaderParameter\n" +
+				"% ############## Some Comment ###########\n" +
+				"#@ String implicitInputParameter\n" +
+				"#@input String explicitInputParameter\n" +
+				"\n" +
+				"% @String legacyStyleBodyParameter\n" +
+				"% #@ String commentedBodyParameter\n" +
+				"\n" +
+				"#@output implicitlyTypedOutputParameter\n" +
+				"#@output String explicitlyTypedOutputParameter\n";
+		final ScriptInfo info = new ScriptInfo(context, ".bsizes", new StringReader(script));
+		assertEquals("legacyStyleParameter", info.getInput("legacyStyleParameter").getName());
+		assertEquals("implicitInputParameter", info.getInput("implicitInputParameter").getName());
+		assertEquals("explicitInputParameter", info.getInput("explicitInputParameter").getName());
+
+		assertEquals("implicitlyTypedOutputParameter", info.getOutput("implicitlyTypedOutputParameter").getName());
+		assertEquals("explicitlyTypedOutputParameter", info.getOutput("explicitlyTypedOutputParameter").getName());
+
+		assertNull(info.getInput("commentedHeaderParameter"));
+		assertNull(info.getInput("legacyStyleBodyParameter"));
+		assertNull(info.getInput("commentedBodyParameter"));
+	}
+
+}