From: Ben Soares <b.soares@dundee.ac.uk>
Date: Fri, 1 Nov 2024 17:37:54 +0000 (+0000)
Subject: JAL-4485 Extra debugging for Chimera/X and PyMol launches
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=df635455b3ff798e54f8a4c927a14e1e0e2d8260;p=jalview.git

JAL-4485 Extra debugging for Chimera/X and PyMol launches
---

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
index 668039b..ad248b2 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
@@ -55,6 +55,7 @@ import org.slf4j.LoggerFactory;
 
 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
 import ext.edu.ucsf.rbvi.strucviz2.port.ListenerThreads;
+import jalview.bin.Console;
 import jalview.ws.HttpClientUtils;
 
 /**
@@ -566,6 +567,7 @@ public class ChimeraManager
     // Do nothing if Chimera is already launched
     if (isChimeraLaunched())
     {
+      Console.debug("Chimera is already launched");
       return true;
     }
 
@@ -575,6 +577,7 @@ public class ChimeraManager
     // iterate over possible paths for starting Chimera
     for (String chimeraPath : chimeraPaths)
     {
+      Console.debug("Using '" + chimeraPath + "' to look for Chimera");
       try
       {
         // ensure symbolic links are resolved
@@ -593,6 +596,8 @@ public class ChimeraManager
         // args.add("--debug");
         addLaunchArguments(args);
         ProcessBuilder pb = new ProcessBuilder(args);
+        Console.debug("Running Chimera with '"
+                + String.join(" ", pb.command()) + "'");
         chimera = pb.start();
         error = "";
         workingPath = chimeraPath;
diff --git a/src/jalview/ext/pymol/PymolManager.java b/src/jalview/ext/pymol/PymolManager.java
index 80327b8..e09e01e 100644
--- a/src/jalview/ext/pymol/PymolManager.java
+++ b/src/jalview/ext/pymol/PymolManager.java
@@ -260,6 +260,7 @@ public class PymolManager
     String error = "Error message: ";
     for (String pymolPath : getPymolPaths())
     {
+      Console.debug("Using '" + pymolPath + "' to look for Pymol");
       try
       {
         // ensure symbolic links are resolved
@@ -269,6 +270,7 @@ public class PymolManager
         // path = new File(pymolPath + "x");
         if (!path.canExecute())
         {
+          Console.debug("Cannot execute " + path.toString());
           error += "File '" + path + "' does not exist.\n";
           continue;
         }
@@ -283,7 +285,8 @@ public class PymolManager
         }
         args.add("-R"); // https://pymolwiki.org/index.php/RPC
         ProcessBuilder pb = new ProcessBuilder(args);
-        Console.debug("Running PyMOL as " + String.join(" ", pb.command()));
+        Console.debug("Running PyMOL with '"
+                + String.join(" ", pb.command()) + "'");
         pymolProcess = pb.start();
         error = "";
         break;