X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=1021a697f5152bdd5cd78cfe529e46a2f5e9513a;hb=79456f40b33e73e2fb5420a3287ae80854281ef6;hp=e384a0bc50be0480a2bb96146032c5f64c00a189;hpb=13cb17a0bdff818a32d253e2199105d9def58796;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index e384a0b..1021a69 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -67,6 +67,7 @@ import com.threerings.getdown.util.LaunchUtil;
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
 import jalview.bin.argparser.Arg;
+import jalview.bin.argparser.Arg.Opt;
 import jalview.bin.argparser.ArgParser;
 import jalview.bin.argparser.BootstrapArgs;
 import jalview.ext.so.SequenceOntology;
@@ -133,6 +134,17 @@ public class Jalview
 
   public static AlignFrame currentAlignFrame;
 
+  public ArgParser argparser = null;
+
+  public BootstrapArgs bootstrapArgs = null;
+
+  private boolean QUIET = false;
+
+  public static boolean quiet()
+  {
+    return Jalview.getInstance() != null && Jalview.getInstance().QUIET;
+  }
+
   static
   {
     if (!Platform.isJS())
@@ -291,35 +303,18 @@ public class Jalview
     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");
-    if (appdirString != null && appdirString.length() > 0)
-    {
-      final File appdir = new File(appdirString);
-      new Thread()
-      {
-        @Override
-        public void run()
-        {
-          LaunchUtil.upgradeGetdown(
-                  new File(appdir, "getdown-launcher-old.jar"),
-                  new File(appdir, "getdown-launcher.jar"),
-                  new File(appdir, "getdown-launcher-new.jar"));
-        }
-      }.start();
-    }
-
     // get args needed before proper ArgParser
-    BootstrapArgs bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
+    bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
 
     if (!Platform.isJS())
     {
       // are we being --quiet ?
       if (bootstrapArgs.contains(Arg.QUIET))
       {
+        QUIET = true;
         OutputStream devNull = new OutputStream()
         {
+
           @Override
           public void write(int b)
           {
@@ -333,29 +328,56 @@ public class Jalview
           System.setErr(new PrintStream(devNull));
         }
       }
-    }
 
-    System.out
-            .println("Java version: " + System.getProperty("java.version"));
-    System.out.println("Java Home: " + System.getProperty("java.home"));
-    System.out.println(System.getProperty("os.arch") + " "
-            + System.getProperty("os.name") + " "
-            + System.getProperty("os.version"));
-
-    String val = System.getProperty("sys.install4jVersion");
-    if (val != null)
-    {
-      System.out.println("Install4j version: " + val);
+      if (bootstrapArgs.contains(Arg.HELP))
+      {
+        QUIET = true;
+      }
     }
-    val = System.getProperty("installer_template_version");
-    if (val != null)
+
+    // Move any new getdown-launcher-new.jar into place over old
+    // getdown-launcher.jar
+    String appdirString = System.getProperty("getdownappdir");
+    if (appdirString != null && appdirString.length() > 0)
     {
-      System.out.println("Install4j template version: " + val);
+      final File appdir = new File(appdirString);
+      new Thread()
+      {
+        @Override
+        public void run()
+        {
+          LaunchUtil.upgradeGetdown(
+                  new File(appdir, "getdown-launcher-old.jar"),
+                  new File(appdir, "getdown-launcher.jar"),
+                  new File(appdir, "getdown-launcher-new.jar"));
+        }
+      }.start();
     }
-    val = System.getProperty("launcher_version");
-    if (val != null)
+
+    if (!quiet())
     {
-      System.out.println("Launcher version: " + val);
+      System.out.println(
+              "Java version: " + System.getProperty("java.version"));
+      System.out.println("Java Home: " + System.getProperty("java.home"));
+      System.out.println(System.getProperty("os.arch") + " "
+              + System.getProperty("os.name") + " "
+              + System.getProperty("os.version"));
+
+      String val = System.getProperty("sys.install4jVersion");
+      if (val != null)
+      {
+        System.out.println("Install4j version: " + val);
+      }
+      val = System.getProperty("installer_template_version");
+      if (val != null)
+      {
+        System.out.println("Install4j template version: " + val);
+      }
+      val = System.getProperty("launcher_version");
+      if (val != null)
+      {
+        System.out.println("Launcher version: " + val);
+      }
     }
 
     if (Platform.isLinux() && LaunchUtils.getJavaVersion() < 11)
@@ -380,7 +402,15 @@ public class Jalview
 
     try
     {
-      String logLevel = bootstrapArgs.contains(Arg.DEBUG) ? "DEBUG" : null;
+      String logLevel = null;
+      if (bootstrapArgs.contains(Arg.TRACE))
+      {
+        logLevel = "TRACE";
+      }
+      else if (bootstrapArgs.contains(Arg.DEBUG))
+      {
+        logLevel = "DEBUG";
+      }
       if (logLevel == null && !(bootstrapProperties == null))
       {
         logLevel = bootstrapProperties.getProperty(Cache.JALVIEWLOGLEVEL);
@@ -427,21 +457,23 @@ public class Jalview
     {
       System.out.println(
               "CMD [-props " + usrPropsFile + "] executed successfully!");
+      testoutput(bootstrapArgs, Arg.PROPS,
+              "test/jalview/bin/testProps.jvprops", usrPropsFile);
     }
 
-    // new ArgParser
-    ArgParser argparser;
     // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
     if (bootstrapArgs.contains(Arg.ARGFILE))
     {
       argparser = ArgParser.parseArgFiles(
               bootstrapArgs.getList(Arg.ARGFILE),
-              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
+              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
+              bootstrapArgs);
     }
     else
     {
       argparser = new ArgParser(args,
-              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
+              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
+              bootstrapArgs);
     }
 
     if (!Platform.isJS())
@@ -458,7 +490,11 @@ public class Jalview
       }
       if (aparser.contains("help") || aparser.contains("h"))
       {
+        /*
+         * Now using new usage statement.
         showUsage();
+        */
+        System.out.println(Arg.usage());
         Jalview.exit(null, 0);
       }
 
@@ -466,7 +502,7 @@ public class Jalview
       {
         System.setProperty("java.awt.headless", "true");
         // new
-        headlessArg = argparser.getBool(Arg.HEADLESS);
+        headlessArg = bootstrapArgs.getBoolean(Arg.HEADLESS);
       }
       if (aparser.contains("nodisplay") || aparser.contains("nogui")
               || aparser.contains("headless"))
@@ -480,7 +516,9 @@ public class Jalview
       // allow https handshakes to download intermediate certs if necessary
       System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
 
-      final String jabawsUrl = aparser.getValue("jabaws");
+      String jabawsUrl = bootstrapArgs.get(Arg.JABAWS);
+      if (jabawsUrl == null)
+        jabawsUrl = aparser.getValue("jabaws");
       if (jabawsUrl != null)
       {
         try
@@ -488,6 +526,8 @@ public class Jalview
           Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
           System.out.println(
                   "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
+          testoutput(bootstrapArgs, Arg.JABAWS,
+                  "http://www.compbio.dundee.ac.uk/jabaws", jabawsUrl);
         } catch (MalformedURLException e)
         {
           System.err.println(
@@ -630,25 +670,37 @@ public class Jalview
           }
         }
 
-        boolean doWebServiceDiscovery = !aparser
-                .contains("nowebservicediscovery");
-        if (bootstrapArgs.contains(Arg.WEBSERVICEDISCOVERY))
-          doWebServiceDiscovery = bootstrapArgs
-                  .getBoolean(Arg.WEBSERVICEDISCOVERY);
-        if (doWebServiceDiscovery)
+        boolean webservicediscovery = bootstrapArgs
+                .getBoolean(Arg.WEBSERVICEDISCOVERY);
+        if (aparser.contains("nowebservicediscovery"))
+          webservicediscovery = false;
+        if (webservicediscovery)
         {
           desktop.startServiceDiscovery();
         }
-        if (!aparser.contains("nousagestats"))
+        else
+        {
+          testoutput(argparser, Arg.WEBSERVICEDISCOVERY);
+        }
+
+        boolean usagestats = bootstrapArgs.getBoolean(Arg.USAGESTATS);
+        if (aparser.contains("nousagestats"))
+          usagestats = false;
+        if (usagestats)
         {
           startUsageStats(desktop);
+          testoutput(argparser, Arg.USAGESTATS);
         }
         else
         {
-          System.err.println("CMD [-nousagestats] executed successfully!");
+          System.out.println("CMD [-nousagestats] executed successfully!");
+          testoutput(argparser, Arg.USAGESTATS);
         }
 
-        if (!aparser.contains("noquestionnaire"))
+        boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE);
+        if (aparser.contains("noquestionnaire"))
+          questionnaire = false;
+        if (questionnaire)
         {
           String url = aparser.getValue("questionnaire");
           if (url != null)
@@ -678,8 +730,9 @@ public class Jalview
         }
         else
         {
-          System.err
+          System.out
                   .println("CMD [-noquestionnaire] executed successfully!");
+          testoutput(argparser, Arg.QUESTIONNAIRE);
         }
 
         if ((!aparser.contains("nonews")
@@ -1483,7 +1536,7 @@ public class Jalview
    *          the Jalview Desktop object passed in to the groovy binding as the
    *          'Jalview' object.
    */
-  private void executeGroovyScript(String groovyscript, AlignFrame af)
+  protected void executeGroovyScript(String groovyscript, AlignFrame af)
   {
     /**
      * for scripts contained in files
@@ -1644,4 +1697,111 @@ public class Jalview
     if (exitcode > -1)
       System.exit(exitcode);
   }
+
+  /*
+   * testoutput for string values
+   */
+  protected static void testoutput(ArgParser ap, Arg a, String s1,
+          String s2)
+  {
+    BootstrapArgs bsa = ap.getBootstrapArgs();
+    if (!bsa.getBoolean(Arg.TESTOUTPUT))
+      return;
+    if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
+    {
+      Console.debug("testoutput with unmatching values '" + s1 + "' and '"
+              + s2 + "' for arg " + a.argString());
+      return;
+    }
+    boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
+            : ap.isSet(a);
+    if (!isset)
+    {
+      Console.warn("Arg '" + a.getName() + "' not set at all");
+      return;
+    }
+    testoutput(true, a, s1, s2);
+  }
+
+  protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
+          String s2)
+  {
+    if (!bsa.getBoolean(Arg.TESTOUTPUT))
+      return;
+    if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
+    {
+      Console.debug("testoutput with unmatching values '" + s1 + "' and '"
+              + s2 + "' for arg " + a.argString());
+      return;
+    }
+    if (!a.hasOption(Opt.BOOTSTRAP))
+    {
+      Console.error("Non-bootstrap Arg '" + a.getName()
+              + "' given to testoutput(BootstrapArgs bsa, Arg a, String s1, String s2) with only BootstrapArgs");
+    }
+    if (!bsa.contains(a))
+    {
+      Console.warn("Arg '" + a.getName() + "' not set at all");
+      return;
+    }
+    testoutput(true, a, s1, s2);
+  }
+
+  private static void testoutput(boolean yes, Arg a, String s1, String s2)
+  {
+    if (yes && ((s1 == null && s2 == null)
+            || (s1 != null && s1.equals(s2))))
+    {
+      System.out.println("[TESTOUTPUT] arg " + a.argString() + "='" + s1
+              + "' was set");
+    }
+  }
+
+  /*
+   * testoutput for boolean values
+   */
+  protected static void testoutput(ArgParser ap, Arg a)
+  {
+    if (ap == null)
+      return;
+    BootstrapArgs bsa = ap.getBootstrapArgs();
+    if (bsa == null)
+      return;
+    if (!bsa.getBoolean(Arg.TESTOUTPUT))
+      return;
+    boolean val = a.hasOption(Opt.BOOTSTRAP) ? bsa.getBoolean(a)
+            : ap.getBoolean(a);
+    boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
+            : ap.isSet(a);
+    if (!isset)
+    {
+      Console.warn("Arg '" + a.getName() + "' not set at all");
+      return;
+    }
+    testoutput(val, a);
+  }
+
+  protected static void testoutput(BootstrapArgs bsa, Arg a)
+  {
+    if (!bsa.getBoolean(Arg.TESTOUTPUT))
+      return;
+    if (!a.hasOption(Opt.BOOTSTRAP))
+    {
+      Console.warn("Non-bootstrap Arg '" + a.getName()
+              + "' given to testoutput(BootstrapArgs bsa, Arg a) with only BootstrapArgs");
+
+    }
+    if (!bsa.contains(a))
+    {
+      Console.warn("Arg '" + a.getName() + "' not set at all");
+      return;
+    }
+    testoutput(bsa.getBoolean(a), a);
+  }
+
+  private static void testoutput(boolean yes, Arg a)
+  {
+    System.out.println("[TESTOUTPUT] arg "
+            + (yes ? a.argString() : a.negateArgString()) + " was set");
+  }
 }