From 6efe596e467f27f5d689f3b766b5202b78af2c41 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 12 Apr 2023 11:19:37 +0100
Subject: [PATCH] JAL-629 allow argfiles in argfiles, but avoid looping
 argfiles

---
 src/jalview/bin/argparser/BootstrapArgs.java |   40 ++++++++++++++++++++++----
 1 file changed, 34 insertions(+), 6 deletions(-)

diff --git a/src/jalview/bin/argparser/BootstrapArgs.java b/src/jalview/bin/argparser/BootstrapArgs.java
index 90204df..408d85d 100644
--- a/src/jalview/bin/argparser/BootstrapArgs.java
+++ b/src/jalview/bin/argparser/BootstrapArgs.java
@@ -1,10 +1,13 @@
 package jalview.bin.argparser;
 
+import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import jalview.bin.argparser.Arg.Opt;
 import jalview.util.FileUtils;
@@ -14,6 +17,8 @@ public class BootstrapArgs
   // only need one
   private Map<Arg, List<String>> bootstrapArgMap = new HashMap<>();
 
+  private Set<File> argFiles = new HashSet<>();
+
   public static BootstrapArgs getBootstrapArgs(String[] args)
   {
     List<String> argList = new ArrayList<>(Arrays.asList(args));
@@ -22,13 +27,25 @@ public class BootstrapArgs
 
   private BootstrapArgs(List<String> args)
   {
-    parse(args);
+    parse(args, null);
   }
 
-  private void parse(List<String> args)
+  private void parse(List<String> args, File inArgFile)
   {
     if (args == null)
       return;
+    // avoid looping argFiles
+    if (inArgFile != null)
+    {
+      if (argFiles.contains(inArgFile))
+      {
+        System.err.println(
+                "Looped argfiles detected: '" + inArgFile.getPath() + "'");
+        return;
+      }
+      argFiles.add(inArgFile);
+    }
+
     for (int i = 0; i < args.size(); i++)
     {
       String arg = args.get(i);
@@ -69,20 +86,31 @@ public class BootstrapArgs
 
         if (a.hasOption(Opt.STRING))
         {
+          List<String> vals = null;
           if (equalPos == -1)
           {
-            addAll(a, ArgParser.getShellGlobbedFilenameValues(a, args,
-                    i + 1));
+            vals = ArgParser.getShellGlobbedFilenameValues(a, args, i + 1);
           }
           else
           {
             if (a.hasOption(Opt.GLOB))
             {
-              addAll(a, FileUtils.getFilenamesFromGlob(val));
+              vals = FileUtils.getFilenamesFromGlob(val);
             }
             else
             {
-              add(a, val);
+              vals = new ArrayList<>();
+              vals.add(val);
+            }
+          }
+          addAll(a, vals);
+
+          if (a == Arg.ARGFILE)
+          {
+            for (String filename : vals)
+            {
+              File argFile = new File(filename);
+              parse(ArgParser.readArgFile(argFile), argFile);
             }
           }
         }
-- 
1.7.10.2