JAL-3671 hardwire log4j.root logger to INFO to supress jetty and httpclient log output

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

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index bb26c13..3208a36 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -20,21 +20,8 @@
  */
 package jalview.bin;
 
-import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
-import jalview.datamodel.PDBEntry;
-import jalview.gui.UserDefinedColours;
-import jalview.schemes.ColourSchemeLoader;
-import jalview.schemes.ColourSchemes;
-import jalview.schemes.UserColourScheme;
-import jalview.structure.StructureImportSettings;
-import jalview.urls.IdOrgSettings;
-import jalview.util.ColorUtils;
-import jalview.util.Platform;
-import jalview.ws.sifts.SiftsSettings;
-
 import java.awt.Color;
 import java.io.BufferedReader;
-import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.InputStream;
@@ -55,6 +42,18 @@ import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 import org.apache.log4j.SimpleLayout;
 
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.datamodel.PDBEntry;
+import jalview.gui.UserDefinedColours;
+import jalview.schemes.ColourSchemeLoader;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.StructureImportSettings;
+import jalview.urls.IdOrgSettings;
+import jalview.util.ColorUtils;
+import jalview.util.Platform;
+import jalview.ws.sifts.SiftsSettings;
+
 /**
  * Stores and retrieves Jalview Application Properties Lists and fields within
  * list entries are separated by '|' symbols unless otherwise stated (|) clauses
@@ -247,10 +246,8 @@ public class Cache implements ApplicationSingletonI
   /**
    * Sifts settings
    */
-  public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
-          .getProperty("user.home") + File.separatorChar
-          + ".sifts_downloads" + File.separatorChar;
-
+  public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = Platform.getUserPath(".sifts_downloads/");
+  
   private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
 
   private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
@@ -258,8 +255,7 @@ public class Cache implements ApplicationSingletonI
   /**
    * Identifiers.org download settings
    */
-  private static final String ID_ORG_FILE = System.getProperty("user.home")
-          + File.separatorChar + ".identifiers.org.ids.json";
+  private static final String ID_ORG_FILE = Platform.getUserPath(".identifiers.org.ids.json");
 
   /**
    * Allowed values are PDB or mmCIF
@@ -332,6 +328,9 @@ public class Cache implements ApplicationSingletonI
       // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
       // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
       // Level.INFO.toString())));
+      // we shouldn't need to do this
+      org.apache.log4j.Logger.getRootLogger().setLevel(org.apache.log4j.Level.INFO); 
+
       jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
               .getDefault("logs.Jalview.level", Level.INFO.toString())));
       // laxis.addAppender(ap);
@@ -363,8 +362,7 @@ public class Cache implements ApplicationSingletonI
     propertiesFile = propsFile;
     if (propsFile == null && !propsAreReadOnly)
     {
-      propertiesFile = System.getProperty("user.home") + File.separatorChar
-              + ".jalview_properties";
+      propertiesFile = Platform.getUserPath(".jalview_properties");
     }
     else
     {
@@ -1052,11 +1050,16 @@ public class Cache implements ApplicationSingletonI
   public static Date getDateProperty(String propertyName)
   {
     String val = getProperty(propertyName);
+    
     if (val != null)
     {
       try
       {
-        return date_format.parse(val);
+        if ((val = val.trim()).indexOf(",") < 0 && val.indexOf("-") >= 0 && val.indexOf(" ") == val.lastIndexOf(" ")) {
+          val = val.replace(" ",", ").replace('-',' ');
+        }
+        Date date =  date_format.parse(val);
+        return date;
       } catch (Exception ex)
       {
         System.err.println("Invalid or corrupt date in property '"