JAL-629 Add --nowebdiscovery. Distinguish arg=="open" as old style. Increase timeout...

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 5f1f228..e384a0b 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -39,7 +39,9 @@ import java.security.CodeSource;
 import java.security.PermissionCollection;
 import java.security.Permissions;
 import java.security.Policy;
+import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Locale;
 import java.util.Map;
 import java.util.Properties;
@@ -64,8 +66,9 @@ import com.threerings.getdown.util.LaunchUtil;
 //import edu.stanford.ejalbert.launching.IBrowserLaunching;
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
-import jalview.bin.ArgParser.Arg;
-import jalview.bin.ArgParser.BootstrapArgs;
+import jalview.bin.argparser.Arg;
+import jalview.bin.argparser.ArgParser;
+import jalview.bin.argparser.BootstrapArgs;
 import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
@@ -280,12 +283,14 @@ public class Jalview
    */
   void doMain(String[] args)
   {
-
     if (!Platform.isJS())
     {
       System.setSecurityManager(null);
     }
 
+    if (args == null)
+      args = new String[] {};
+
     // Move any new getdown-launcher-new.jar into place over old
     // getdown-launcher.jar
     String appdirString = System.getProperty("getdownappdir");
@@ -415,6 +420,8 @@ public class Jalview
     String usrPropsFile = bootstrapArgs.contains(Arg.PROPS)
             ? bootstrapArgs.get(Arg.PROPS)
             : aparser.getValue("props");
+    // if usrPropsFile == null, loadProperties will use the Channel
+    // preferences.file
     Cache.loadProperties(usrPropsFile);
     if (usrPropsFile != null)
     {
@@ -427,12 +434,14 @@ public class Jalview
     // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
     if (bootstrapArgs.contains(Arg.ARGFILE))
     {
-      argparser = ArgParser
-              .parseArgFiles(bootstrapArgs.getList(Arg.ARGFILE));
+      argparser = ArgParser.parseArgFiles(
+              bootstrapArgs.getList(Arg.ARGFILE),
+              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
     }
     else
     {
-      argparser = new ArgParser(args);
+      argparser = new ArgParser(args,
+              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
     }
 
     if (!Platform.isJS())
@@ -442,8 +451,12 @@ public class Jalview
      * @j2sIgnore
      */
     {
-      if (aparser.contains("help") || aparser.contains("h")
-              || argparser.getBool(Arg.HELP))
+      if (bootstrapArgs.contains(Arg.HELP))
+      {
+        System.out.println(Arg.usage());
+        Jalview.exit(null, 0);
+      }
+      if (aparser.contains("help") || aparser.contains("h"))
       {
         showUsage();
         Jalview.exit(null, 0);
@@ -483,26 +496,40 @@ public class Jalview
       }
     }
 
-    String defs = aparser.getValue("setprop");
-    while (defs != null)
+    List<String> setprops = new ArrayList<>();
+    if (bootstrapArgs.contains(Arg.SETPROP))
+    {
+      setprops = bootstrapArgs.getList(Arg.SETPROP);
+    }
+    else
+    {
+      String sp = aparser.getValue("setprop");
+      while (sp != null)
+      {
+        setprops.add(sp);
+        sp = aparser.getValue("setprop");
+      }
+    }
+    for (String setprop : setprops)
     {
-      int p = defs.indexOf('=');
+      int p = setprop.indexOf('=');
       if (p == -1)
       {
-        System.err.println("Ignoring invalid setprop argument : " + defs);
+        System.err
+                .println("Ignoring invalid setprop argument : " + setprop);
       }
       else
       {
-        System.out.println("Executing setprop argument: " + defs);
+        System.out.println("Executing setprop argument: " + setprop);
         if (Platform.isJS())
         {
-          Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
+          Cache.setProperty(setprop.substring(0, p),
+                  setprop.substring(p + 1));
         }
         // DISABLED FOR SECURITY REASONS
         // TODO: add a property to allow properties to be overriden by cli args
-        // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
+        // Cache.setProperty(setprop.substring(0,p), setprop.substring(p+1));
       }
-      defs = aparser.getValue("setprop");
     }
     if (System.getProperty("java.awt.headless") != null
             && System.getProperty("java.awt.headless").equals("true"))
@@ -541,7 +568,9 @@ public class Jalview
 
     if (!(headless || headlessArg))
     {
-      Desktop.nosplash = aparser.contains("nosplash");
+      Desktop.nosplash = "false".equals(bootstrapArgs.get(Arg.SPLASH))
+              || aparser.contains("nosplash")
+              || Cache.getDefault("SPLASH", "true").equals("false");
       desktop = new Desktop();
       desktop.setInBatchMode(true); // indicate we are starting up
 
@@ -601,7 +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();
         }
@@ -648,14 +682,16 @@ public class Jalview
                   .println("CMD [-noquestionnaire] executed successfully!");
         }
 
-        if (!aparser.contains("nonews")
-                || Cache.getProperty("NONEWS") == null)
+        if ((!aparser.contains("nonews")
+                && Cache.getProperty("NONEWS") == null
+                && !"false".equals(bootstrapArgs.get(Arg.NEWS)))
+                || "true".equals(bootstrapArgs.get(Arg.NEWS)))
         {
           desktop.checkForNews();
         }
 
         if (!aparser.contains("nohtmltemplates")
-                || Cache.getProperty("NOHTMLTEMPLATES") == null)
+                && Cache.getProperty("NOHTMLTEMPLATES") == null)
         {
           BioJsHTMLOutput.updateBioJS();
         }
@@ -705,7 +741,7 @@ public class Jalview
     groovyscript = aparser.getValue("groovy", true);
     file = aparser.getValue("open", true);
 
-    if (file == null && desktop == null)
+    if (file == null && desktop == null && !commandsSuccess)
     {
       Jalview.exit("No files to open!", 1);
     }
@@ -1599,7 +1635,6 @@ public class Jalview
 
   public static void exit(String message, int exitcode)
   {
-    System.err.println("####### EXITING HERE!");
     Console.debug("Using Jalview.exit");
     if (message != null)
       if (exitcode == 0)