X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=9e51d67b32e11de34d9dde2b3d2259e009008c4d;hb=76cfeb5e50dd69a3ba963096556f9677c9eea55a;hp=35d6aa381ff2e2e2fb783e37f77f5fb3acb60af5;hpb=510131abf452a7389d0d40afa323d0bec8bb9f0d;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 35d6aa3..9e51d67 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -20,16 +20,6 @@
  */
 package jalview.bin;
 
-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.ws.sifts.SiftsSettings;
-
 import java.awt.Color;
 import java.io.BufferedReader;
 import java.io.File;
@@ -37,6 +27,8 @@ import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.io.StringWriter;
 import java.text.DateFormat;
 import java.text.SimpleDateFormat;
 import java.util.Collections;
@@ -46,12 +38,26 @@ import java.util.Locale;
 import java.util.Properties;
 import java.util.StringTokenizer;
 import java.util.TreeSet;
+import java.util.regex.Pattern;
+
+import javax.swing.LookAndFeel;
+import javax.swing.UIManager;
 
 import org.apache.log4j.ConsoleAppender;
 import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 import org.apache.log4j.SimpleLayout;
 
+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.ws.sifts.SiftsSettings;
+
 /**
  * Stores and retrieves Jalview Application Properties Lists and fields within
  * list entries are separated by '|' symbols unless otherwise stated (|) clauses
@@ -161,6 +167,8 @@ import org.apache.log4j.SimpleLayout;
  * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
  * respond to selections made in other alignments containing the same sequences.
  * </li>
+ * <li>SHOW_JWS2_SERVICES (true) when set to false, jalview will not
+ * auto-discover JABAWS services</li>
  * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
  * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
  * warning dialog box is displayed.</li>
@@ -168,8 +176,8 @@ import org.apache.log4j.SimpleLayout;
  * when shading by annotation</li>
  * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
  * when shading by annotation</li>
- * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
- * requests to be redirected to a mirror of http://www.jalview.org</li>
+ * <li>www.jalview.org (https://www.jalview.org) a property enabling all HTTP
+ * requests to be redirected to a mirror of https://www.jalview.org</li>
  * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
  * alignment figure to accommodate even the longest sequence ID or annotation
  * label.</li>
@@ -189,6 +197,10 @@ import org.apache.log4j.SimpleLayout;
  * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
  * </li>
  * 
+ * <li>NONEWS - when set disables Jalview News from automatically appearing</li>
+ * <li>NOHTMLTEMPLATES - when set, the
+ * https://github.com/jalview/exporter-templates/tree/master/biojs repository is
+ * not downloaded automatically</li>
  * </ul>
  * Deprecated settings:
  * <ul>
@@ -309,6 +321,10 @@ public class Cache
       // 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);
@@ -422,7 +438,7 @@ public class Cache
                     DEFAULT_CACHE_THRESHOLD_IN_DAYS));
 
     IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
-            "http://www.jalview.org/services/identifiers"));
+            "https://www.jalview.org/services/identifiers"));
     IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
 
     StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
@@ -435,8 +451,8 @@ public class Cache
 
     String jnlpVersion = System.getProperty("jalview.version");
 
-    // jnlpVersion will be null if a latest version check for the channel needs to
-    // be done
+    // jnlpVersion will be null if a latest version check for the channel needs
+    // to be done
     // Dont do this check if running in headless mode
 
     if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
@@ -446,9 +462,12 @@ public class Cache
 
       class VersionChecker extends Thread
       {
+
         @Override
         public void run()
         {
+          String buildPropertiesUrl = Cache.getAppbaseBuildProperties();
+
           String orgtimeout = System
                   .getProperty("sun.net.client.defaultConnectTimeout");
           if (orgtimeout == null)
@@ -462,28 +481,19 @@ public class Cache
           {
             System.setProperty("sun.net.client.defaultConnectTimeout",
                     "5000");
-            java.net.URL url = new java.net.URL(Cache
-                    .getDefault("www.jalview.org", "http://www.jalview.org")
-                    + "/webstart/jalview.jnlp");
+            java.net.URL url = new java.net.URL(buildPropertiesUrl);
+
             BufferedReader in = new BufferedReader(
                     new InputStreamReader(url.openStream()));
-            String line = null;
-            while ((line = in.readLine()) != null)
-            {
-              if (line.indexOf("jalview.version") == -1)
-              {
-                continue;
-              }
-
-              line = line.substring(line.indexOf("value=") + 7);
-              line = line.substring(0, line.lastIndexOf("\""));
-              remoteVersion = line;
-              break;
-            }
+
+            Properties remoteBuildProperties = new Properties();
+            remoteBuildProperties.load(in);
+            remoteVersion = remoteBuildProperties.getProperty("VERSION");
           } catch (Exception ex)
           {
-            System.out.println(
-                    "Non-fatal exception when checking version at www.jalview.org :");
+            System.out
+                    .println("Non-fatal exception when checking version at "
+                            + buildPropertiesUrl + ":");
             System.out.println(ex);
             remoteVersion = getProperty("VERSION");
           }
@@ -555,8 +565,8 @@ public class Cache
     new BuildDetails(codeVersion, null, codeInstallation);
     if (printV && reportVersion)
     {
-      System.out
-            .println("Jalview Version: " + codeVersion + codeInstallation);
+      System.out.println(
+              "Jalview Version: " + codeVersion + codeInstallation);
     }
   }
 
@@ -1099,16 +1109,23 @@ public class Cache
   public static String getVersionDetailsForConsole()
   {
     StringBuilder sb = new StringBuilder();
-    sb.append("Jalview Version: " + jalview.bin.Cache.getDefault("VERSION", "TEST"));
+    sb.append("Jalview Version: ");
+    sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST"));
     sb.append("\n");
-    sb.append("Jalview Installation: "
-            + jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
+    sb.append("Jalview Installation: ");
+    sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
     sb.append("\n");
-    sb.append("Build Date: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+    sb.append("Build Date: ");
+    sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
     sb.append("\n");
-    sb.append("Java version: " + System.getProperty("java.version"));
+    sb.append("Java version: ");
+    sb.append(System.getProperty("java.version"));
     sb.append("\n");
-    sb.append(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version"));
+    sb.append(System.getProperty("os.arch"));
+    sb.append(" ");
+    sb.append(System.getProperty("os.name"));
+    sb.append(" ");
+    sb.append(System.getProperty("os.version"));
     sb.append("\n");
     appendIfNotNull(sb, "Install4j version: ",
             System.getProperty("sys.install4jVersion"), "\n", null);
@@ -1116,9 +1133,23 @@ public class Cache
             System.getProperty("installer_template_version"), "\n", null);
     appendIfNotNull(sb, "Launcher version: ",
             System.getProperty("launcher_version"), "\n", null);
-    if (jalview.bin.Cache.getDefault("VERSION", "TEST").equals("DEVELOPMENT")) {
+    LookAndFeel laf = UIManager.getLookAndFeel();
+    String lafName = laf == null ? "Not obtained" : laf.getName();
+    String lafClass = laf == null ? "unknown" : laf.getClass().getName();
+    sb.append("LookAndFeel: ");
+    sb.append(lafName);
+    sb.append(" (");
+    sb.append(lafClass);
+    sb.append(")\n");
+    // Not displayed in release version ( determined by possible version number
+    // regex 9[9.]*9[.-_a9]* )
+    if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
+            jalview.bin.Cache.getDefault("VERSION", "TEST")))
+    {
       appendIfNotNull(sb, "Getdown appdir: ",
               System.getProperty("getdownappdir"), "\n", null);
+      appendIfNotNull(sb, "Getdown appbase: ",
+              System.getProperty("getdownappbase"), "\n", null);
       appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
               "\n", "unknown");
     }
@@ -1135,4 +1166,69 @@ public class Cache
     // eg 'built from Source' or update channel
     return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
   }
+
+  public static String getStackTraceString(Throwable t)
+  {
+    StringWriter sw = new StringWriter();
+    PrintWriter pw = new PrintWriter(sw);
+    t.printStackTrace(pw);
+    return sw.toString();
+  }
+
+  /**
+   * Getdown appbase methods
+   */
+
+  private static final String releaseAppbase;
+
+  private static String getdownAppbase;
+
+  private static String getdownDistDir;
+
+  static
+  {
+    Float specversion = Float
+            .parseFloat(System.getProperty("java.specification.version"));
+    releaseAppbase = (specversion < 9)
+            ? "https://www.jalview.org/getdown/release/1.8"
+            : "https://www.jalview.org/getdown/release/11";
+  }
+
+  // look for properties (passed in by getdown) otherwise default to release
+  private static void setGetdownAppbase()
+  {
+    if (getdownAppbase != null)
+    {
+      return;
+    }
+    String appbase = System.getProperty("getdownappbase");
+    String distDir = System.getProperty("getdowndistdir");
+    if (appbase == null)
+    {
+      appbase = releaseAppbase;
+      distDir = "release";
+    }
+    if (appbase.endsWith("/"))
+    {
+      appbase = appbase.substring(0, appbase.length() - 1);
+    }
+    if (distDir == null)
+    {
+      distDir = appbase.equals(releaseAppbase) ? "release" : "alt";
+    }
+    getdownAppbase = appbase;
+    getdownDistDir = distDir;
+  }
+
+  public static String getGetdownAppbase()
+  {
+    setGetdownAppbase();
+    return getdownAppbase;
+  }
+
+  public static String getAppbaseBuildProperties()
+  {
+    String appbase = getGetdownAppbase();
+    return appbase + "/" + getdownDistDir + "/build_properties";
+  }
 }