From: Ben Soares <b.soares@dundee.ac.uk>
Date: Thu, 18 May 2023 16:16:42 +0000 (+0100)
Subject: JAL-629 fixes to typed args
X-Git-Tag: Release_2_11_4_0~316
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=45502494dee1b9f2d7a5a1d62dc00ed24acfc6f4;p=jalview.git

JAL-629 fixes to typed args
---

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 8bc3e1b..3d20d3c 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -494,9 +494,8 @@ public class Jalview
     {
       if (bootstrapArgs.containsType(Type.HELP))
       {
-        System.out.println("##### HERE");
-        System.out
-                .println(Arg.usage(bootstrapArgs.getArgsOfType(Type.HELP)));
+        List<Arg> helpArgs = bootstrapArgs.getArgsOfType(Type.HELP);
+        System.out.println(Arg.usage(helpArgs));
         Jalview.exit(null, 0);
       }
       if (aparser.contains("help") || aparser.contains("h"))
diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index a7fc0f7..a9cacbd 100644
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -18,7 +18,7 @@ public enum Arg
 
   // Initialising arguments (BOOTSTRAP)
   HELP(Type.HELP, "h", "Display this help statement", Opt.UNARY,
-          Opt.BOOTSTRAP, Opt.HASTYPE),
+          Opt.BOOTSTRAP, Opt.HASTYPE, Opt.MULTI),
   /*
    * Other --help-type Args will be added by the static block.
    */
@@ -319,8 +319,10 @@ public enum Arg
     OUTPUT("Arguments used to save data from a processed alignment"),
     IMAGE("Arguments used to export an image of an alignment"),
     FLOW("Arguments that control processing of the other arguments"),
+    HELP("Arguments to provide help text"), // --help
     ALL("All arguments"), // mostly just a place-holder for --help-all
-    HELP("Arguments to provide help text");
+    NONE("No specific arguments"), // mostly a place-holder for --help
+    INVALID("This type of argument doesn't exist");
 
     private String description;
 
diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 4e1793d..6d1251c 100644
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -283,9 +283,15 @@ public class ArgParser
           Arg potentialArg = argMap.get(potentialArgName);
           if (potentialArg != null && potentialArg.hasOption(Opt.HASTYPE))
           {
-            argName = argName.substring(0, dashPos);
             String typeName = argName.substring(dashPos + 1);
-            type = Type.valueOf(typeName);
+            try
+            {
+              type = Type.valueOf(typeName);
+            } catch (IllegalArgumentException e)
+            {
+              type = Type.INVALID;
+            }
+            argName = argName.substring(0, dashPos);
           }
         }
 
diff --git a/src/jalview/bin/argparser/BootstrapArgs.java b/src/jalview/bin/argparser/BootstrapArgs.java
index 1c54355..faa4a43 100644
--- a/src/jalview/bin/argparser/BootstrapArgs.java
+++ b/src/jalview/bin/argparser/BootstrapArgs.java
@@ -7,6 +7,7 @@ import java.util.Arrays;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Set;
 import java.util.stream.Collectors;
@@ -64,46 +65,50 @@ public class BootstrapArgs
         String val = null;
         Type type = null;
         // remove "--"
-        arg = arg.substring(ArgParser.DOUBLEDASH.length());
+        argName = arg.substring(ArgParser.DOUBLEDASH.length());
 
         // look for equals e.g. --arg=value
-        int equalPos = arg.indexOf(ArgParser.EQUALS);
-        if (equalPos > -1
-                && ArgParser.argMap.containsKey(arg.substring(0, equalPos)))
+        int equalPos = argName.indexOf(ArgParser.EQUALS);
+        if (equalPos > -1)
         {
-          argName = arg.substring(0, equalPos);
-          val = arg.substring(equalPos + 1);
+          val = argName.substring(equalPos + 1);
+          argName = argName.substring(0, equalPos);
         }
+
         // check for boolean prepended by "no"
-        else if (arg.startsWith(ArgParser.NEGATESTRING)
+        if (argName.startsWith(ArgParser.NEGATESTRING)
                 && ArgParser.argMap.containsKey(
-                        arg.substring(ArgParser.NEGATESTRING.length())))
+                        argName.substring(ArgParser.NEGATESTRING.length())))
         {
-          argName = arg.substring(ArgParser.NEGATESTRING.length());
           val = "false";
+          argName = argName.substring(ArgParser.NEGATESTRING.length());
         }
-        else if (ArgParser.argMap.containsKey(arg))
-        {
-          argName = arg;
-          val = "true";
-        }
-        else
+
+        // look for type modification e.g. --help-opening
+        int dashPos = argName.indexOf(ArgParser.SINGLEDASH);
+        if (dashPos > -1)
         {
-          // look for type modification e.g. --help-opening
-          int dashPos = arg.indexOf(ArgParser.SINGLEDASH);
-          if (dashPos > -1)
+          String potentialArgName = argName.substring(0, dashPos);
+          Arg potentialArg = ArgParser.argMap.get(potentialArgName);
+          if (potentialArg != null && potentialArg.hasOption(Opt.HASTYPE))
           {
-            String potentialArgName = arg.substring(0, dashPos);
-            Arg potentialArg = ArgParser.argMap.get(potentialArgName);
-            if (potentialArg != null && potentialArg.hasOption(Opt.HASTYPE))
+            String typeName = argName.substring(dashPos + 1);
+            try
             {
-              argName = arg.substring(0, dashPos);
-              String typeName = arg.substring(dashPos + 1);
-              type = Type.valueOf(typeName);
+              type = Type.valueOf(typeName.toUpperCase(Locale.ROOT));
+            } catch (IllegalArgumentException e)
+            {
+              type = Type.INVALID;
             }
+            argName = argName.substring(0, dashPos);
           }
         }
 
+        if (ArgParser.argMap.containsKey(argName) && val == null)
+        {
+          val = "true";
+        }
+
         Arg a = ArgParser.argMap.get(argName);
 
         if (a == null || !a.hasOption(Opt.BOOTSTRAP))