JAL-4193 JAL-4194 sessionProperties layer in Cache, CLI arg Opts to deal with -Pkey...

diff --git a/help/help/html/features/clarguments-reference.html b/help/help/html/features/clarguments-reference.html
index fc4f0a0..0221a67 100644 (file)
--- a/help/help/html/features/clarguments-reference.html
+++ b/help/help/html/features/clarguments-reference.html
@@ -103,6 +103,11 @@
     </tr>
 
     <tr valign="top">
     </tr>
 
     <tr valign="top">

+    <td><code>&#8209;&#8209;nostartupfile</code></td>
+    <td>Don't show the default startup file.</td>
+    </tr>
+
+    <tr valign="top">

     <td><code>&#8209;&#8209;webservicediscovery / &#8209;&#8209;nowebservicediscovery</code></td>
     <td>Attempt (/ or don't attempt) to connect to JABAWS web services.</td>
     </tr>
     <td><code>&#8209;&#8209;webservicediscovery / &#8209;&#8209;nowebservicediscovery</code></td>
     <td>Attempt (/ or don't attempt) to connect to JABAWS web services.</td>
     </tr>

@@ -124,6 +129,13 @@
 
 <!--
     <tr valign="top">
 
 <!--
     <tr valign="top">

+    <td><code>&#8209;&#8209;P<em>PREFERENCE=VALUE</em></code></td>
+    <td>Set a Jalview preference for this session only.  Experimental.</td>
+    </tr>
+-->
+
+<!--
+    <tr valign="top">

     <td><code>&#8209;&#8209;initsubstitutions / &#8209;&#8209;noinitsubstitutions</code></td>
     <td>Set <code>&#8209;&#8209;substitutions</code> to be initially enabled (or initially disabled).</td>
     </tr>
     <td><code>&#8209;&#8209;initsubstitutions / &#8209;&#8209;noinitsubstitutions</code></td>
     <td>Set <code>&#8209;&#8209;substitutions</code> to be initially enabled (or initially disabled).</td>
     </tr>

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index f4c8854..b966af6 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -42,7 +42,9 @@ import java.util.Collection;
 import java.util.Collections;
 import java.util.Date;
 import java.util.Enumeration;
 import java.util.Collections;
 import java.util.Date;
 import java.util.Enumeration;

+import java.util.HashMap;

 import java.util.Locale;
 import java.util.Locale;

+import java.util.Map;

 import java.util.Properties;
 import java.util.StringTokenizer;
 import java.util.TreeSet;
 import java.util.Properties;
 import java.util.StringTokenizer;
 import java.util.TreeSet;

@@ -310,6 +312,24 @@ public class Cache
   // in-memory only storage of proxy password, safer to use char array
   public static char[] proxyAuthPassword = null;
 
   // in-memory only storage of proxy password, safer to use char array
   public static char[] proxyAuthPassword = null;
 

+  /**
+   * Session properties, set by command line, try not to affect stored
+   * properties!
+   */
+  private static Map<String, String> sessionProperties = new HashMap<>();
+
+  private static boolean bypassSessionProperties = false;
+
+  public static void enableSessionProperties()
+  {
+    bypassSessionProperties = false;
+  }
+
+  public static void disableSessionProperties()
+  {
+    bypassSessionProperties = true;
+  }
+

   /** Jalview Properties */
   public static Properties applicationProperties = new Properties()
   {
   /** Jalview Properties */
   public static Properties applicationProperties = new Properties()
   {

@@ -712,7 +732,21 @@ public class Cache
    */
   public static String getProperty(String key)
   {
    */
   public static String getProperty(String key)
   {

-    String prop = applicationProperties.getProperty(key);
+    return getProperty(key, false);
+  }
+
+  public static String getProperty(String key,
+          boolean skipSessionProperties)
+  {
+    String prop = null;
+    if (!(skipSessionProperties || bypassSessionProperties))
+    {
+      prop = getSessionProperty(key);
+    }
+    if (prop == null)
+    {
+      prop = applicationProperties.getProperty(key);
+    }

     if (prop == null && Platform.isJS())
     {
       prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
     if (prop == null && Platform.isJS())
     {
       prop = applicationProperties.getProperty(Platform.getUniqueAppletID()

@@ -782,8 +816,16 @@ public class Cache
     try
     {
       oldValue = applicationProperties.setProperty(key, obj);
     try
     {
       oldValue = applicationProperties.setProperty(key, obj);

-      if (propertiesFile != null && !propsAreReadOnly)
+      if (propertiesFile != null && !propsAreReadOnly
+      // don't rewrite if new value is same as old value
+              && !((obj == null && oldValue == null)
+                      || (obj != null && obj.equals(oldValue))))

       {
       {

+        // reset the session property too
+        if (sessionProperties.containsKey(key))
+        {
+          sessionProperties.remove(key);
+        }

         FileOutputStream out = new FileOutputStream(propertiesFile);
         applicationProperties.store(out, "---JalviewX Properties File---");
         out.close();
         FileOutputStream out = new FileOutputStream(propertiesFile);
         applicationProperties.store(out, "---JalviewX Properties File---");
         out.close();

@@ -1695,4 +1737,17 @@ public class Cache
     }
     return bootstrapProps;
   }
     }
     return bootstrapProps;
   }

+
+  public static void setSessionProperty(String key, String val)
+  {
+    if (key != null)
+    {
+      sessionProperties.put(key, val);
+    }
+  }
+
+  public static String getSessionProperty(String key)
+  {
+    return key == null ? null : sessionProperties.get(key);
+  }

 }
 }

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index dc97549..b29d9d7 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -343,6 +343,25 @@ public class Jalview
       }
     }
 
       }
     }
 

+    // set individual session preferences
+    if (bootstrapArgs.contains(Arg.P))
+    {
+      for (String kev : bootstrapArgs.getValueList(Arg.P))
+      {
+        if (kev == null)
+        {
+          continue;
+        }
+        int equalsIndex = kev.indexOf(ArgParser.EQUALS);
+        if (equalsIndex > -1)
+        {
+          String key = kev.substring(0, equalsIndex);
+          String val = kev.substring(equalsIndex + 1);
+          Cache.setSessionProperty(key, val);
+        }
+      }
+    }
+

     // Move any new getdown-launcher-new.jar into place over old
     // getdown-launcher.jar
     String appdirString = System.getProperty("getdownappdir");
     // Move any new getdown-launcher-new.jar into place over old
     // getdown-launcher.jar
     String appdirString = System.getProperty("getdownappdir");

@@ -720,18 +739,18 @@ public class Jalview
           testoutput(argparser, Arg.WEBSERVICEDISCOVERY);
         }
 
           testoutput(argparser, Arg.WEBSERVICEDISCOVERY);
         }
 

-        boolean usagestats = bootstrapArgs.getBoolean(Arg.USAGESTATS);
+        boolean usagestats = !bootstrapArgs.getBoolean(Arg.NOUSAGESTATS);

         if (aparser.contains("nousagestats"))
           usagestats = false;
         if (usagestats)
         {
           startUsageStats(desktop);
         if (aparser.contains("nousagestats"))
           usagestats = false;
         if (usagestats)
         {
           startUsageStats(desktop);

-          testoutput(argparser, Arg.USAGESTATS);
+          testoutput(argparser, Arg.NOUSAGESTATS);

         }
         else
         {
           System.out.println("CMD [-nousagestats] executed successfully!");
         }
         else
         {
           System.out.println("CMD [-nousagestats] executed successfully!");

-          testoutput(argparser, Arg.USAGESTATS);
+          testoutput(argparser, Arg.NOUSAGESTATS);

         }
 
         boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE);
         }
 
         boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE);

@@ -1114,7 +1133,8 @@ public class Jalview
 
     if (!Platform.isJS() && !headless && file == null
             && Cache.getDefault("SHOW_STARTUP_FILE", true)
 
     if (!Platform.isJS() && !headless && file == null
             && Cache.getDefault("SHOW_STARTUP_FILE", true)

-            && !cmds.commandArgsProvided())
+            && !cmds.commandArgsProvided()
+            && !bootstrapArgs.getBoolean(Arg.NOSTARTUPFILE))

     // don't open the startup file if command line args have been processed
     // (&& !Commands.commandArgsProvided())
     /**
     // don't open the startup file if command line args have been processed
     // (&& !Commands.commandArgsProvided())
     /**

@@ -1840,7 +1860,7 @@ public class Jalview
   }
 
   /*
   }
 
   /*

-   * testoutput for boolean values
+   * testoutput for boolean and unary values

    */
   protected static void testoutput(ArgParser ap, Arg a)
   {
    */
   protected static void testoutput(ArgParser ap, Arg a)
   {

@@ -1883,7 +1903,15 @@ public class Jalview
 
   private static void testoutput(boolean yes, Arg a)
   {
 
   private static void testoutput(boolean yes, Arg a)
   {

-    System.out.println("[TESTOUTPUT] arg "
-            + (yes ? a.argString() : a.negateArgString()) + " was set");
+    String message = null;
+    if (a.hasOption(Opt.BOOLEAN))
+    {
+      message = (yes ? a.argString() : a.negateArgString()) + " was set";
+    }
+    else if (a.hasOption(Opt.UNARY))
+    {
+      message = a.argString() + (yes ? " was set" : " was not set");
+    }
+    System.out.println("[TESTOUTPUT] arg " + message);

   }
 }
   }
 }

diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index 0d6e3b1..f7588cb 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -44,9 +44,10 @@ public enum Arg
   QUESTIONNAIRE(Type.CONFIG,
           "Show (or don't show) the questionnaire if one is available.",
           true, Opt.BOOLEAN, Opt.BOOTSTRAP),
   QUESTIONNAIRE(Type.CONFIG,
           "Show (or don't show) the questionnaire if one is available.",
           true, Opt.BOOLEAN, Opt.BOOTSTRAP),

-  USAGESTATS(Type.CONFIG,
-          "Send (or don't send) initial launch usage stats.", true,
-          Opt.BOOLEAN, Opt.BOOTSTRAP),
+  NOUSAGESTATS(Type.CONFIG, "Don't send initial launch usage stats.",
+          Opt.UNARY, Opt.BOOTSTRAP),
+  NOSTARTUPFILE(Type.CONFIG, "Don't show the default startup file.",
+          Opt.UNARY, Opt.BOOTSTRAP),

   WEBSERVICEDISCOVERY(Type.CONFIG,
           "Attempt (or don't attempt) to connect to JABAWS web services.",
           true, Opt.BOOLEAN, Opt.BOOTSTRAP),
   WEBSERVICEDISCOVERY(Type.CONFIG,
           "Attempt (or don't attempt) to connect to JABAWS web services.",
           true, Opt.BOOLEAN, Opt.BOOTSTRAP),

@@ -65,6 +66,9 @@ public enum Arg
   INITSUBSTITUTIONS(Type.CONFIG,
           "Set ‑‑substitutions to be initially enabled (or initially disabled).",
           true, Opt.BOOLEAN, Opt.BOOTSTRAP, Opt.NOACTION, Opt.SECRET),
   INITSUBSTITUTIONS(Type.CONFIG,
           "Set ‑‑substitutions to be initially enabled (or initially disabled).",
           true, Opt.BOOLEAN, Opt.BOOTSTRAP, Opt.NOACTION, Opt.SECRET),

+  P(Type.CONFIG, "Set a Jalview preference value for this session.",
+          Opt.PREFIXKEV, Opt.PRESERVECASE, Opt.STRING, Opt.BOOTSTRAP,
+          Opt.MULTI, Opt.NOACTION, Opt.SECRET), // keep this secret for now.

 
   // Opening an alignment
   OPEN(Type.OPENING,
 
   // Opening an alignment
   OPEN(Type.OPENING,

@@ -399,6 +403,14 @@ public enum Arg
      * A LAST arg gets moved to appear last in the usage statement (within type)
      */
     LAST(null),
      * A LAST arg gets moved to appear last in the usage statement (within type)
      */
     LAST(null),

+    /*
+     * After other args are checked, the following args can prefix a KEY=VALUE argument
+     */
+    PREFIXKEV("prefixes key=value"),
+    /*
+     * do not lowercase the name when getting the arg name or arg string
+     */
+    PRESERVECASE(null),

     //
     ;
 
     //
     ;
 

@@ -486,15 +498,15 @@ public enum Arg
   private Arg(Type type, String alternativeName, String description,
           boolean defaultBoolean, Opt... options)
   {
   private Arg(Type type, String alternativeName, String description,
           boolean defaultBoolean, Opt... options)
   {

+    this.type = type;
+    this.description = description;
+    this.defaultBoolValue = defaultBoolean;
+    this.setOptions(options);

     this.argNames = alternativeName != null
             ? new String[]
             { this.getName(), alternativeName }
             : new String[]
             { this.getName() };
     this.argNames = alternativeName != null
             ? new String[]
             { this.getName(), alternativeName }
             : new String[]
             { this.getName() };

-    this.type = type;
-    this.description = description;
-    this.defaultBoolValue = defaultBoolean;
-    this.setOptions(options);

   }
 
   public String argString()
   }
 
   public String argString()

@@ -544,7 +556,9 @@ public enum Arg
 
   public String getName()
   {
 
   public String getName()
   {

-    return this.name().toLowerCase(Locale.ROOT).replace('_', '-');
+    String name = hasOption(Opt.PRESERVECASE) ? this.name()
+            : this.name().toLowerCase(Locale.ROOT);
+    return name.replace('_', '-');

   }
 
   @Override
   }
 
   @Override

@@ -794,7 +808,16 @@ public enum Arg
     argSb.append(
             a.hasOption(Opt.BOOLEAN) ? booleanArgString(a) : a.argString());
     if (a.hasOption(Opt.STRING))
     argSb.append(
             a.hasOption(Opt.BOOLEAN) ? booleanArgString(a) : a.argString());
     if (a.hasOption(Opt.STRING))

-      argSb.append("=value");
+    {
+      if (a.hasOption(Opt.PREFIXKEV))
+      {
+        argSb.append("key=value");
+      }
+      else
+      {
+        argSb.append("=value");
+      }
+    }

     return argSb.toString();
   }
 
     return argSb.toString();
   }
 

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index f08e678..1558065 100644 (file)
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -48,7 +48,7 @@ public class ArgParser
 
   protected static final String DOUBLEDASH = "--";
 
 
   protected static final String DOUBLEDASH = "--";
 

-  protected static final char EQUALS = '=';
+  public static final char EQUALS = '=';

 
   protected static final String NEGATESTRING = "no";
 
 
   protected static final String NEGATESTRING = "no";
 

@@ -302,12 +302,34 @@ public class ArgParser
         Arg a = argMap.get(argName);
         // check for boolean prepended by "no" e.g. --nowrap
         boolean negated = false;
         Arg a = argMap.get(argName);
         // check for boolean prepended by "no" e.g. --nowrap
         boolean negated = false;

-        if (a == null && argName.startsWith(NEGATESTRING) && argMap
-                .containsKey(argName.substring(NEGATESTRING.length())))
+        if (a == null)

         {
         {

-          argName = argName.substring(NEGATESTRING.length());
-          a = argMap.get(argName);
-          negated = true;
+          if (argName.startsWith(NEGATESTRING) && argMap
+                  .containsKey(argName.substring(NEGATESTRING.length())))
+          {
+            argName = argName.substring(NEGATESTRING.length());
+            a = argMap.get(argName);
+            negated = true;
+          }
+          else
+          {
+            // after all other args, look for Opt.PREFIXKEV args if still not
+            // found
+            for (Arg potentialArg : EnumSet.allOf(Arg.class))
+            {
+              if (potentialArg.hasOption(Opt.PREFIXKEV) && argName != null
+                      && argName.startsWith(potentialArg.getName())
+                      && equalPos > -1)
+              {
+                val = argName.substring(potentialArg.getName().length())
+                        + EQUALS + val;
+                argName = argName.substring(0,
+                        potentialArg.getName().length());
+                a = potentialArg;
+                break;
+              }
+            }
+          }

         }
 
         // check for config errors
         }
 
         // check for config errors

@@ -464,7 +486,8 @@ public class ArgParser
               val = LINKEDIDDIRNAME + File.separator + LINKEDIDBASENAME
                       + val.substring(MATCHALLLINKEDIDS.length());
             }
               val = LINKEDIDDIRNAME + File.separator + LINKEDIDBASENAME
                       + val.substring(MATCHALLLINKEDIDS.length());
             }

-            else if (a.hasOption(Opt.OUTPUTFILE) && a.hasOption(Opt.ALLOWALL)
+            else if (a.hasOption(Opt.OUTPUTFILE)
+                    && a.hasOption(Opt.ALLOWALL)

                     && val.startsWith(MATCHOPENEDLINKEDIDS))
             {
               // --output=open*.ext is shorthand for --opened --output
                     && val.startsWith(MATCHOPENEDLINKEDIDS))
             {
               // --output=open*.ext is shorthand for --opened --output

diff --git a/src/jalview/bin/argparser/BootstrapArgs.java b/src/jalview/bin/argparser/BootstrapArgs.java
index e1ad1d7..4b7b180 100644 (file)
--- a/src/jalview/bin/argparser/BootstrapArgs.java
+++ b/src/jalview/bin/argparser/BootstrapArgs.java
@@ -4,6 +4,7 @@ import java.io.File;
 import java.util.AbstractMap;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.AbstractMap;
 import java.util.ArrayList;
 import java.util.Arrays;

+import java.util.EnumSet;

 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;

@@ -108,6 +109,24 @@ public class BootstrapArgs
           }
         }
 
           }
         }
 

+        // after all other args, look for Opt.PREFIX args if still not found
+        if (!ArgParser.argMap.containsKey(argName))
+        {
+          for (Arg potentialArg : EnumSet.allOf(Arg.class))
+          {
+            if (potentialArg.hasOption(Opt.PREFIXKEV) && argName != null
+                    && argName.startsWith(potentialArg.getName())
+                    && val != null)
+            {
+              val = argName.substring(potentialArg.getName().length())
+                      + ArgParser.EQUALS + val;
+              argName = argName.substring(0,
+                      potentialArg.getName().length());
+              break;
+            }
+          }
+        }
+

         if (ArgParser.argMap.containsKey(argName) && val == null)
         {
           val = "true";
         if (ArgParser.argMap.containsKey(argName) && val == null)
         {
           val = "true";

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 35fdf6a..c4f32c3 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -156,6 +156,9 @@ public class Preferences extends GPreferences
   public static List<String> groupURLLinks;
   static
   {
   public static List<String> groupURLLinks;
   static
   {

+    // don't populate with session properties
+    Cache.disableSessionProperties();
+

     // get links selected to be in the menu (SEQUENCE_LINKS)
     // and links entered by the user but not selected (STORED_LINKS)
     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
     // get links selected to be in the menu (SEQUENCE_LINKS)
     // and links entered by the user but not selected (STORED_LINKS)
     String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");

@@ -180,6 +183,9 @@ public class Preferences extends GPreferences
      */
 
     groupURLLinks = new ArrayList<>();
      */
 
     groupURLLinks = new ArrayList<>();

+
+    // reenable
+    Cache.enableSessionProperties();

   }
 
   JInternalFrame frame;
   }
 
   JInternalFrame frame;

@@ -248,6 +254,9 @@ public class Preferences extends GPreferences
   private Preferences()
   {
     super();
   private Preferences()
   {
     super();

+    // don't populate with session properties
+    Cache.disableSessionProperties();
+

     frame = new JInternalFrame();
     frame.setFrameIcon(null);
     frame.setContentPane(this);
     frame = new JInternalFrame();
     frame.setFrameIcon(null);
     frame.setContentPane(this);

@@ -689,6 +698,8 @@ public class Preferences extends GPreferences
      * Set Startup tab defaults
      */
 
      * Set Startup tab defaults
      */
 

+    // re-enable
+    Cache.enableSessionProperties();

   }
 
   /**
   }
 
   /**

@@ -701,6 +712,8 @@ public class Preferences extends GPreferences
   protected void setupOutputCombo(JComboBox<Object> comboBox,
           String propertyKey)
   {
   protected void setupOutputCombo(JComboBox<Object> comboBox,
           String propertyKey)
   {

+    Cache.disableSessionProperties();
+

     comboBox.addItem(promptEachTimeOpt);
     comboBox.addItem(lineArtOpt);
     comboBox.addItem(textOpt);
     comboBox.addItem(promptEachTimeOpt);
     comboBox.addItem(lineArtOpt);
     comboBox.addItem(textOpt);

@@ -722,6 +735,8 @@ public class Preferences extends GPreferences
     {
       comboBox.setSelectedItem(promptEachTimeOpt);
     }
     {
       comboBox.setSelectedItem(promptEachTimeOpt);
     }

+
+    Cache.enableSessionProperties();

   }
 
   /**
   }
 
   /**

@@ -733,6 +748,8 @@ public class Preferences extends GPreferences
   @Override
   public void ok_actionPerformed(ActionEvent e)
   {
   @Override
   public void ok_actionPerformed(ActionEvent e)
   {

+    Cache.disableSessionProperties();
+

     if (!validateSettings())
     {
       return;
     if (!validateSettings())
     {
       return;

@@ -746,6 +763,7 @@ public class Preferences extends GPreferences
     /*
      * Save Visual settings
      */
     /*
      * Save Visual settings
      */

+

     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
             Boolean.toString(seqLimit.isSelected()));
     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
             Boolean.toString(seqLimit.isSelected()));
     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",

@@ -1020,10 +1038,14 @@ public class Preferences extends GPreferences
     } catch (Exception ex)
     {
     }
     } catch (Exception ex)
     {
     }

+
+    Cache.enableSessionProperties();

   }
 
   public void saveProxySettings()
   {
   }
 
   public void saveProxySettings()
   {

+    Cache.disableSessionProperties();
+

     String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
             : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
                     : Cache.PROXYTYPE_SYSTEM;
     String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
             : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
                     : Cache.PROXYTYPE_SYSTEM;

@@ -1044,6 +1066,8 @@ public class Preferences extends GPreferences
       wsPrefs.update++;
     }
     previousProxyType = newProxyType;
       wsPrefs.update++;
     }
     previousProxyType = newProxyType;

+
+    Cache.enableSessionProperties();

   }
 
   /**
   }
 
   /**

@@ -1075,6 +1099,8 @@ public class Preferences extends GPreferences
   @Override
   public void startupFileTextfield_mouseClicked()
   {
   @Override
   public void startupFileTextfield_mouseClicked()
   {

+    Cache.disableSessionProperties();
+

     // TODO: JAL-3048 not needed for Jalview-JS
     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
     JalviewFileChooser chooser = JalviewFileChooser
     // TODO: JAL-3048 not needed for Jalview-JS
     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
     JalviewFileChooser chooser = JalviewFileChooser

@@ -1096,6 +1122,8 @@ public class Preferences extends GPreferences
       startupFileTextfield
               .setText(chooser.getSelectedFile().getAbsolutePath());
     }
       startupFileTextfield
               .setText(chooser.getSelectedFile().getAbsolutePath());
     }

+
+    Cache.enableSessionProperties();

   }
 
   /**
   }
 
   /**

@@ -1405,6 +1433,7 @@ public class Preferences extends GPreferences
      */
     String viewerPath = "";
     List<String> paths = null;
      */
     String viewerPath = "";
     List<String> paths = null;

+    Cache.disableSessionProperties();

     try
     {
       ViewerType viewerType = ViewerType.valueOf(selectedItem);
     try
     {
       ViewerType viewerType = ViewerType.valueOf(selectedItem);

@@ -1430,6 +1459,7 @@ public class Preferences extends GPreferences
     {
       // only valid entries should be in the drop-down
     }
     {
       // only valid entries should be in the drop-down
     }

+    Cache.enableSessionProperties();

     structureViewerPath.setText(viewerPath);
 
     paths.add(0, structureViewerPath.getText());
     structureViewerPath.setText(viewerPath);
 
     paths.add(0, structureViewerPath.getText());

diff --git a/test/jalview/bin/CommandLineOperationsNG.java b/test/jalview/bin/CommandLineOperationsNG.java
index 049e9a8..30a1b9f 100644 (file)
--- a/test/jalview/bin/CommandLineOperationsNG.java
+++ b/test/jalview/bin/CommandLineOperationsNG.java
@@ -333,9 +333,8 @@ public class CommandLineOperationsNG
   public void testAllInputOperations(String expectedString,
           String failureMsg)
   {
   public void testAllInputOperations(String expectedString,
           String failureMsg)
   {

-    if ("[TESTOUTPUT] arg --nousagestats was set".equals(expectedString))
-      Assert.assertTrue(successfulCMDs.contains(expectedString),
-              failureMsg);
+    Assert.assertTrue(successfulCMDs.contains(expectedString),
+            failureMsg + "; was expecting '" + expectedString + "'");

   }
 
   @Test(
   }
 
   @Test(

@@ -352,7 +351,8 @@ public class CommandLineOperationsNG
     file.deleteOnExit();
     Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
     assertNotNull(worker, "worker is null");
     file.deleteOnExit();
     Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
     assertNotNull(worker, "worker is null");

-    String msg = "Didn't create an output" + type + " file.[" + cmd + "]";
+    String msg = "Didn't create an output" + type + " file '" + fileName
+            + "'. [" + cmd + "]";

     assertTrue(file.exists(), msg);
     FileAssert.assertFile(file, msg);
     FileAssert.assertMinLength(file, expectedMinFileSize);
     assertTrue(file.exists(), msg);
     FileAssert.assertFile(file, msg);
     FileAssert.assertMinLength(file, expectedMinFileSize);