From: Ben Soares <b.soares@dundee.ac.uk>
Date: Mon, 24 Apr 2023 15:52:13 +0000 (+0100)
Subject: JAL-629 Add --nowebdiscovery. Distinguish arg=="open" as old style. Increase timeout... 
X-Git-Tag: Release_2_11_4_0~376
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=13cb17a0bdff818a32d253e2199105d9def58796;p=jalview.git

JAL-629 Add --nowebdiscovery. Distinguish arg=="open" as old style. Increase timeout for commandlineoptions tests (for failing web services?).
---

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index d70326e..e384a0b 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -630,7 +630,12 @@ public class Jalview
           }
         }
 
-        if (!aparser.contains("nowebservicediscovery"))
+        boolean doWebServiceDiscovery = !aparser
+                .contains("nowebservicediscovery");
+        if (bootstrapArgs.contains(Arg.WEBSERVICEDISCOVERY))
+          doWebServiceDiscovery = bootstrapArgs
+                  .getBoolean(Arg.WEBSERVICEDISCOVERY);
+        if (doWebServiceDiscovery)
         {
           desktop.startServiceDiscovery();
         }
diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index 07d8c28..ab3cca7 100644
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -11,11 +11,12 @@ public enum Arg
 {
   HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, ANNOTATIONS,
   COLOUR, FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, DISPLAY, GUI, NEWS,
-  SORTBYTREE, USAGESTATS, APPEND, OPEN, PROPS, QUESTIONNAIRE, SETPROP,
-  TREE, VDOC, VSESS, OUTPUT, OUTPUTTYPE, SSANNOTATIONS, NOTEMPFAC, TEMPFAC,
-  TITLE, PAEMATRIX, WRAP, NOSTRUCTURE, STRUCTURE, STRUCTUREVIEWER, IMAGE,
-  QUIT, CLOSE, DEBUG("d"), QUIET("q"), ARGFILE, INCREMENT, NPP("n++"),
-  SUBSTITUTIONS, INITSUBSTITUTIONS, NIL, SPLASH, SETARGFILE, UNSETARGFILE;
+  SORTBYTREE, USAGESTATS, APPEND, OPEN, PROPS, QUESTIONNAIRE, SETPROP, TREE,
+  VDOC, VSESS, OUTPUT, OUTPUTTYPE, SSANNOTATIONS, NOTEMPFAC, TEMPFAC, TITLE,
+  PAEMATRIX, WRAP, NOSTRUCTURE, STRUCTURE, STRUCTUREVIEWER, IMAGE, QUIT,
+  CLOSE, DEBUG("d"), QUIET("q"), ARGFILE, INCREMENT, NPP("n++"),
+  SUBSTITUTIONS, INITSUBSTITUTIONS, NIL, SPLASH, SETARGFILE, UNSETARGFILE,
+  WEBSERVICEDISCOVERY;
 
   protected static enum Opt
   {
@@ -87,6 +88,7 @@ public enum Arg
     NIL.setOptions(Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.NOACTION);
     SETARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
     UNSETARGFILE.setOptions(Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
+    WEBSERVICEDISCOVERY.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
     // Opt.BOOTSTRAP args are parsed (not linked with no SubVals so using a
     // simplified parser, see jalview.bin.argparser.BootstrapArgs)
     // before a full parse of arguments and so can be accessible at an earlier
diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index b31beab..0ab5987 100644
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -156,7 +156,8 @@ public class ArgParser
   public ArgParser(List<String> args, boolean initsubstitutions,
           boolean allowPrivate)
   {
-    // do nothing if there are no "--" args and some "-" args
+    // do nothing if there are no "--" args and (some "-" args || >0 arg is
+    // "open")
     boolean d = false;
     boolean dd = false;
     for (String arg : args)
@@ -166,7 +167,7 @@ public class ArgParser
         dd = true;
         break;
       }
-      else if (arg.startsWith("-"))
+      else if (arg.startsWith("-") || arg.equals("open"))
       {
         d = true;
       }
diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index c6d3332..9b9adf8 100644
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -54,7 +54,7 @@ public class CommandLineOperations
   }
 
   // Note longer timeout needed on full test run than on individual tests
-  private static final int TEST_TIMEOUT = 13000;
+  private static final int TEST_TIMEOUT = 23000;
 
   private static final int SETUP_TIMEOUT = 9500;
 
@@ -373,9 +373,11 @@ public class CommandLineOperations
     // since it works.
     // https://issues.jalview.org/browse/JAL-1889?focusedCommentId=21609&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-21609
     String workingDir = "test/jalview/bin/";
-    return new Object[][] { { "nodisplay -open examples/uniref50.fa",
-        " -eps", workingDir + "test_uniref50_out.eps", true,
-        MINFILESIZE_BIG, TEST_TIMEOUT },
+    return new Object[][] {
+        //
+        { "nodisplay -open examples/uniref50.fa", " -eps",
+            workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
         { "nodisplay -open examples/uniref50.fa", " -eps",
             workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
             TEST_TIMEOUT },
@@ -420,6 +422,8 @@ public class CommandLineOperations
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -jalview",
             workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
-            TEST_TIMEOUT }, };
+            TEST_TIMEOUT },
+        //
+    };
   }
 }