From e400c2aa8fe74794d496b72689ec73fd337edfa8 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Fri, 5 May 2023 10:42:55 +0100
Subject: [PATCH] JAL-629 test fixes

---
 src/jalview/gui/Desktop.java                  |    6 ++-
 test/jalview/bin/CommandLineOperationsNG.java |   62 +++++++++++++------------
 2 files changed, 38 insertions(+), 30 deletions(-)

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index cd62c9f..fb3bbc0 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -435,7 +435,11 @@ public class Desktop extends jalview.jbgui.GDesktop
     {
       if (LaunchUtils.getJavaVersion() >= 11)
       {
-        jalview.bin.Console.info(
+        /*
+         * Send this message to stderr as the warning that follows (due to
+         * reflection) also goes to stderr.
+         */
+        System.err.println(
                 "Linux platform only! You may have the following warning next: \"WARNING: An illegal reflective access operation has occurred\"\nThis is expected and cannot be avoided, sorry about that.");
       }
       try
diff --git a/test/jalview/bin/CommandLineOperationsNG.java b/test/jalview/bin/CommandLineOperationsNG.java
index 12072f7..049e9a8 100644
--- a/test/jalview/bin/CommandLineOperationsNG.java
+++ b/test/jalview/bin/CommandLineOperationsNG.java
@@ -39,6 +39,8 @@ import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import io.github.classgraph.ClassGraph;
+import io.github.classgraph.ModuleRef;
+import io.github.classgraph.ScanResult;
 import jalview.gui.JvOptionPane;
 
 public class CommandLineOperationsNG
@@ -128,41 +130,38 @@ public class CommandLineOperationsNG
 
   public synchronized static String getClassPath()
   {
-    // if (scanner == null)
-    // {
-    // scanner = new ClassGraph();
-    // ScanResult scan = scanner.scan();
-    // classpath = scan.getClasspath();
-    modules = "";
-    // for (ModuleRef mr : scan.getModules())
-    // {
-    // modules.concat(mr.getName());
-    // }
-    java_exe = System.getProperty("java.home") + File.separator + "bin"
-            + File.separator + "java";
-
-    // }
-
-    // while (classpath == null)
-    // {
-    // try
-    // {
-    // Thread.sleep(10);
-    // } catch (InterruptedException x)
-    // {
-    //
-    // }
-    // }
+    if (scanner == null)
+    {
+      scanner = new ClassGraph();
+      ScanResult scan = scanner.scan();
+      classpath = scan.getClasspath();
+      modules = "";
+      for (ModuleRef mr : scan.getModules())
+      {
+        modules.concat(mr.getName());
+      }
+      java_exe = System.getProperty("java.home") + File.separator + "bin"
+              + File.separator + "java";
+
+    }
+
+    while (classpath == null)
+    {
+      try
+      {
+        Thread.sleep(10);
+      } catch (InterruptedException x)
+      {
+
+      }
+    }
     return classpath;
   }
 
   private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
           int timeout)
   {
-    // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
-    // not expanded by the shell
-    // String classpath = getClassPath();
-    getClassPath();
+    /*
     boolean win = System.getProperty("os.name").indexOf("Win") >= 0;
     String pwd = "";
     try
@@ -178,6 +177,11 @@ public class CommandLineOperationsNG
     String[] classpaths = new String[] { pwd + "/bin/main",
         pwd + "/j11lib/*", pwd + "/resources", pwd + "/help" };
     String classpath = String.join(win ? ";" : ":", classpaths);
+    getClassPath();
+    */
+    // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
+    // not expanded by the shell
+    String classpath = getClassPath();
     String _cmd = java_exe + " "
             + (withAwt ? "-Djava.awt.headless=true" : "") + " -classpath "
             + classpath
-- 
1.7.10.2