X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=621b74b4499f573da8779e2b035b26b1879cdfd1;hb=a934d28336923f2966aeac29f7d1a877e5db1cec;hp=dcd6546ad8bd27f2210c9261761a56f33cbb46f3;hpb=4bb7ef2feb729af8a320e9c090e39aee12028375;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index dcd6546..621b74b 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -20,18 +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.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
-import jalview.ws.sifts.SiftsSettings;
-
 import java.awt.Color;
 import java.io.BufferedReader;
 import java.io.File;
@@ -39,6 +27,9 @@ 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.net.URL;
 import java.text.DateFormat;
 import java.text.SimpleDateFormat;
 import java.util.Collections;
@@ -48,12 +39,27 @@ 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.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
@@ -116,7 +122,6 @@ import org.apache.log4j.SimpleLayout;
  * service</li>
  * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
  * collecting usage statistics</li>
- * <li>DAS_LOCAL_SOURCE list of local das sources</li>
  * <li>SHOW_OVERVIEW boolean for overview window display</li>
  * <li>ANTI_ALIAS boolean for smooth fonts</li>
  * <li>RIGHT_ALIGN_IDS boolean</li>
@@ -136,9 +141,7 @@ import org.apache.log4j.SimpleLayout;
  * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
  * <li>GROUP_LINKS list of name|URL[|&lt;separator&gt;] tuples - see
  * jalview.utils.GroupURLLink for more info</li>
- * <li>DAS_REGISTRY_URL the registry to query</li>
  * <li>DEFAULT_BROWSER for unix</li>
- * <li>DAS_ACTIVE_SOURCE list of active sources</li>
  * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
  * (false)</li>
  * <li>VERSION_CHECK (true) check for the latest release version from
@@ -228,12 +231,6 @@ public class Cache
    */
   public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
 
-  public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
-
-  public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
-
-  public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
-
   /**
    * Sifts settings
    */
@@ -274,6 +271,13 @@ public class Cache
    */
   public static Logger log;
 
+  // save the proxy properties set at startup
+  public final static String[] startupProxyProperties = {
+      System.getProperty("http.proxyHost"),
+      System.getProperty("http.proxyPort"),
+      System.getProperty("https.proxyHost"),
+      System.getProperty("https.proxyPort") };
+
   /** Jalview Properties */
   public static Properties applicationProperties = new Properties()
   {
@@ -288,7 +292,9 @@ public class Cache
   /** Default file is ~/.jalview_properties */
   static String propertiesFile;
 
-  private static boolean propsAreReadOnly = false;
+  private static boolean propsAreReadOnly = Platform.isJS();
+
+  private final static String JS_PROPERTY_PREFIX = "jalview_";
 
   public static void initLogger()
   {
@@ -320,6 +326,10 @@ 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);
@@ -341,7 +351,7 @@ public class Cache
   public static void loadProperties(String propsFile)
   {
     propertiesFile = propsFile;
-    if (propsFile == null)
+    if (propsFile == null && !propsAreReadOnly)
     {
       propertiesFile = System.getProperty("user.home") + File.separatorChar
               + ".jalview_properties";
@@ -352,105 +362,111 @@ public class Cache
       propsAreReadOnly = true;
     }
 
-    try
+    if (propertiesFile == null)
+    { // BH 2019
+      Platform.readInfoProperties(JS_PROPERTY_PREFIX,
+              applicationProperties);
+    }
+    else
     {
-      InputStream fis;
       try
       {
-        fis = new java.net.URL(propertiesFile).openStream();
-        System.out.println(
-                "Loading jalview properties from : " + propertiesFile);
-        System.out.println(
-                "Disabling Jalview writing to user's local properties file.");
-        propsAreReadOnly = true;
+        InputStream fis;
+        try
+        {
+          fis = new URL(propertiesFile).openStream();
+          System.out.println(
+                  "Loading jalview properties from : " + propertiesFile);
+          System.out.println(
+                  "Disabling Jalview writing to user's local properties file.");
+          propsAreReadOnly = true;
+
+        } catch (Exception ex)
+        {
+          fis = null;
+        }
+        if (fis == null)
+        {
+          fis = new FileInputStream(propertiesFile);
+        }
+        applicationProperties.clear();
+        applicationProperties.load(fis);
 
+        // remove any old build properties
+
+        deleteBuildProperties();
+        fis.close();
       } catch (Exception ex)
       {
-        fis = null;
+        System.out.println("Error reading properties file: " + ex);
       }
-      if (fis == null)
-      {
-        fis = new FileInputStream(propertiesFile);
-      }
-      applicationProperties.clear();
-      applicationProperties.load(fis);
-
-      // remove any old build properties
-
-      deleteBuildProperties();
-      fis.close();
-    } catch (Exception ex)
-    {
-      System.out.println("Error reading properties file: " + ex);
     }
 
+    /* TO BE REPLACED WITH PROXY_TYPE SETTINGS 
     if (getDefault("USE_PROXY", false))
     {
       String proxyServer = getDefault("PROXY_SERVER", ""),
               proxyPort = getDefault("PROXY_PORT", "8080");
+    }
+    */
 
-      System.out.println("Using proxyServer: " + proxyServer
-              + " proxyPort: " + proxyPort);
-
-      System.setProperty("http.proxyHost", proxyServer);
-      System.setProperty("http.proxyPort", proxyPort);
+    // PROXY TYPE settings (now three options "none", "false", "true", but using
+    // backward compatible strings)
+    String proxyType = getDefault("USE_PROXY", "false");
+    // default to upgrading old settings
+    switch (proxyType)
+    {
+    case "none":
+      setProxyProperties(null, null, null, null);
+      break;
+    case "false": // use system settings
+      resetProxyProperties();
+      break;
+    case "true": // use specified proxy settings
+      String httpHost = getDefault("PROXY_SERVER", "");
+      String httpPort = getDefault("PROXY_PORT", "8080");
+      String httpsHost = getDefault("PROXY_SERVER_HTTPS", httpHost);
+      String httpsPort = getDefault("PROXY_PORT_HTTPS", httpPort);
+      setProxyProperties(httpHost, httpPort, httpsHost, httpsPort);
+      break;
+    default:
+      String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
+              + proxyType;
+      if (Cache.log == null)
+      {
+        System.out.println(message);
+      }
+      else
+      {
+        Cache.log.warn(message);
+      }
     }
 
     // LOAD THE AUTHORS FROM THE authors.props file
+    String authorDetails = resolveResourceURLFor("/authors.props");
+
     try
     {
-      String authorDetails = "jar:"
-              .concat(Cache.class.getProtectionDomain().getCodeSource()
-                      .getLocation().toString().concat("!/authors.props"));
-
-      java.net.URL localJarFileURL = new java.net.URL(authorDetails);
-
-      InputStream in = localJarFileURL.openStream();
-      applicationProperties.load(in);
-      in.close();
+      if (authorDetails != null)
+      {
+        URL localJarFileURL = new URL(authorDetails);
+        InputStream in = localJarFileURL.openStream();
+        applicationProperties.load(in);
+        in.close();
+      }
     } catch (Exception ex)
     {
       System.out.println("Error reading author details: " + ex);
+      authorDetails = null;
+    }
+    if (authorDetails == null)
+    {
       applicationProperties.remove("AUTHORS");
       applicationProperties.remove("AUTHORFNAMES");
       applicationProperties.remove("YEAR");
     }
 
-    // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
-    // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
-    // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
-    try
-    {
-      String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
-              .getCodeSource().getLocation().toString()
-              .concat("!/.build_properties"));
-
-      java.net.URL localJarFileURL = new java.net.URL(buildDetails);
-
-      InputStream in = localJarFileURL.openStream();
-      applicationProperties.load(in);
-      in.close();
-    } catch (Exception ex)
-    {
-      System.out.println("Error reading build details: " + ex);
-      applicationProperties.remove("VERSION");
-    }
-
-    String jnlpVersion = System.getProperty("jalview.version");
-    String codeVersion = getProperty("VERSION");
-    String codeInstallation = getProperty("INSTALLATION");
-    if (codeVersion == null)
-    {
-      // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
-      codeVersion = "Test";
-      jnlpVersion = "Test";
-      codeInstallation = "";
-    }
-    else
-    {
-      codeInstallation = " (" + codeInstallation + ")";
-    }
-    new BuildDetails(codeVersion, null, codeInstallation);
+    loadBuildProperties(false);
 
     SiftsSettings
             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
@@ -470,9 +486,6 @@ public class Cache
             "http://www.jalview.org/services/identifiers"));
     IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
 
-    System.out
-            .println("Jalview Version: " + codeVersion + codeInstallation);
-
     StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
             .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
     StructureImportSettings
@@ -480,8 +493,13 @@ public class Cache
     // StructureImportSettings
     // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
     // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
-    // jnlpVersion will be null if we're using InstallAnywhere
+
+    String jnlpVersion = System.getProperty("jalview.version");
+
+    // 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)
             && (System.getProperty("java.awt.headless") == null || System
                     .getProperty("java.awt.headless").equals("false")))
@@ -552,15 +570,84 @@ public class Cache
       }
     }
 
-    setProperty("VERSION", codeVersion);
-
     // LOAD USERDEFINED COLOURS
-    jalview.bin.Cache
-            .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
+    Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
     jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
             false);
   }
 
+  /**
+   * construct a resource URL for the given absolute resource pathname
+   * 
+   * @param resourcePath
+   * @return
+   */
+  private static String resolveResourceURLFor(String resourcePath)
+  {
+    String url = null;
+    if (Platform.isJS() || !Cache.class.getProtectionDomain()
+            .getCodeSource().getLocation().toString().endsWith(".jar"))
+    {
+      try
+      {
+        url = Cache.class.getResource(resourcePath).toString();
+      } catch (Exception ex)
+      {
+        System.err.println("Failed to resolve resource " + resourcePath
+                + ": " + ex.getMessage());
+      }
+    }
+    else
+    {
+      url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource()
+              .getLocation().toString().concat("!" + resourcePath));
+    }
+    return url;
+  }
+
+  public static void loadBuildProperties(boolean reportVersion)
+  {
+    String codeInstallation = getProperty("INSTALLATION");
+    boolean printVersion = codeInstallation == null;
+
+    /*
+     * read build properties - from the Jalview jar for a Java distribution,
+     * or from codebase file in test or JalviewJS context
+     */
+    try
+    {
+      String buildDetails = resolveResourceURLFor("/.build_properties");
+      URL localJarFileURL = new URL(buildDetails);
+      InputStream in = localJarFileURL.openStream();
+      applicationProperties.load(in);
+      in.close();
+    } catch (Exception ex)
+    {
+      System.out.println("Error reading build details: " + ex);
+      applicationProperties.remove("VERSION");
+    }
+    String codeVersion = getProperty("VERSION");
+    codeInstallation = getProperty("INSTALLATION");
+
+    if (codeVersion == null)
+    {
+      // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
+      codeVersion = "Test";
+      codeInstallation = "";
+    }
+    else
+    {
+      codeInstallation = " (" + codeInstallation + ")";
+    }
+    setProperty("VERSION", codeVersion);
+    new BuildDetails(codeVersion, null, codeInstallation);
+    if (printVersion && reportVersion)
+    {
+      System.out.println(
+              "Jalview Version: " + codeVersion + codeInstallation);
+    }
+  }
+
   private static void deleteBuildProperties()
   {
     applicationProperties.remove("LATEST_VERSION");
@@ -583,7 +670,13 @@ public class Cache
    */
   public static String getProperty(String key)
   {
-    return applicationProperties.getProperty(key);
+    String prop = applicationProperties.getProperty(key);
+    if (prop == null && Platform.isJS())
+    {
+      prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
+              + "_" + JS_PROPERTY_PREFIX + key);
+    }
+    return prop;
   }
 
   /**
@@ -602,22 +695,35 @@ public class Cache
     return def;
   }
 
-  /**
-   * These methods are used when checking if the saved preference is different
-   * to the default setting
-   */
-  public static String getDefault(String property, String def)
+  public static int getDefault(String property, int def)
   {
     String string = getProperty(property);
     if (string != null)
     {
-      return string;
+      try
+      {
+        def = Integer.parseInt(string);
+      } catch (NumberFormatException e)
+      {
+        System.out.println("Error parsing int property '" + property
+                + "' with value '" + string + "'");
+      }
     }
 
     return def;
   }
 
   /**
+   * Answers the value of the given property, or the supplied default value if
+   * the property is not set
+   */
+  public static String getDefault(String property, String def)
+  {
+    String value = getProperty(property);
+    return value == null ? def : value;
+  }
+
+  /**
    * Stores property in the file "HOME_DIR/.jalview_properties"
    * 
    * @param key
@@ -633,7 +739,7 @@ public class Cache
     try
     {
       oldValue = applicationProperties.setProperty(key, obj);
-      if (!propsAreReadOnly)
+      if (propertiesFile != null && !propsAreReadOnly)
       {
         FileOutputStream out = new FileOutputStream(propertiesFile);
         applicationProperties.store(out, "---JalviewX Properties File---");
@@ -982,22 +1088,6 @@ public class Cache
     return null;
   }
 
-  private static DasSourceRegistryI sourceRegistry = null;
-
-  /**
-   * initialise and ..
-   * 
-   * @return instance of the das source registry
-   */
-  public static DasSourceRegistryI getDasSourceRegistry()
-  {
-    if (sourceRegistry == null)
-    {
-      sourceRegistry = new DasSourceRegistry();
-    }
-    return sourceRegistry;
-  }
-
   /**
    * Set the specified value, or remove it if null or empty. Does not save the
    * properties file.
@@ -1072,4 +1162,166 @@ public class Cache
       }
     }
   }
+
+  /**
+   * Initial logging information helper for various versions output
+   * 
+   * @param prefix
+   * @param value
+   * @param defaultValue
+   */
+  private static void appendIfNotNull(StringBuilder sb, String prefix,
+          String value, String suffix, String defaultValue)
+  {
+    if (value == null && defaultValue == null)
+    {
+      return;
+    }
+    String line = prefix + (value != null ? value : defaultValue) + suffix;
+    sb.append(line);
+  }
+
+  /**
+   * 
+   * @return Jalview version, build details and JVM platform version for console
+   */
+  public static String getVersionDetailsForConsole()
+  {
+    StringBuilder sb = new StringBuilder();
+    sb.append("Jalview Version: ");
+    sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST"));
+    sb.append("\n");
+    sb.append("Jalview Installation: ");
+    sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
+    sb.append("\n");
+    sb.append("Build Date: ");
+    sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+    sb.append("\n");
+    sb.append("Java version: ");
+    sb.append(System.getProperty("java.version"));
+    sb.append("\n");
+    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);
+    appendIfNotNull(sb, "Install4j template version: ",
+            System.getProperty("installer_template_version"), "\n", null);
+    appendIfNotNull(sb, "Launcher version: ",
+            System.getProperty("launcher_version"), "\n", null);
+    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, "Java home: ", System.getProperty("java.home"),
+              "\n", "unknown");
+    }
+    return sb.toString();
+  }
+
+  /**
+   * 
+   * @return build details as reported in splashscreen
+   */
+  public static String getBuildDetailsForSplash()
+  {
+    // consider returning more human friendly info
+    // 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();
+  }
+
+  // proxy properties methods
+  public static void resetProxyProperties()
+  {
+    setProxyProperties(startupProxyProperties[0], startupProxyProperties[1],
+            startupProxyProperties[2], startupProxyProperties[3]);
+    StringBuilder sb = new StringBuilder();
+    sb.append("Setting proxy properties to: http.proxyHost=")
+            .append(startupProxyProperties[0]).append(", http.proxyPort=")
+            .append(startupProxyProperties[1]).append(", https.proxyHost=")
+            .append(startupProxyProperties[2]).append(", https.proxyPort=")
+            .append(startupProxyProperties[3]);
+    if (Cache.log == null)
+    {
+      System.err.println(sb.toString());
+    }
+    else
+    {
+      Cache.log.debug(sb.toString());
+    }
+  }
+
+  public static void setProxyProperties(String host, String port)
+  {
+    setProxyProperties(host, port, host, port);
+  }
+
+  public static void setProxyProperties(String httpHost, String httpPort,
+          String httpsHost, String httpsPort)
+  {
+    // cannot set property to null -- use clearProperty instead
+
+    // http.proxyHost
+    if (httpHost == null)
+    {
+      System.clearProperty("http.proxyHost");
+    }
+    else
+    {
+      System.setProperty("http.proxyHost", httpHost);
+    }
+
+    // http.proxyPort
+    if (httpPort == null)
+    {
+      System.clearProperty("http.proxyPort");
+    }
+    else
+    {
+      System.setProperty("http.proxyPort", httpPort);
+    }
+
+    // https.proxyHost
+    if (httpsHost == null)
+    {
+      System.clearProperty("https.proxyHost");
+    }
+    else
+    {
+      System.setProperty("https.proxyHost", httpsHost);
+    }
+
+    // https.proxyPort
+    if (httpsPort == null)
+    {
+      System.clearProperty("https.proxyPort");
+    }
+    else
+    {
+      System.setProperty("https.proxyPort", httpsPort);
+    }
+
+  }
 }