X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fbin%2FCache.java;h=a64e86994d8cfa35add4fd6eb44fb9f4d518913e;hb=3dcec29e9be7607122fb981050ff2198cef2a746;hp=fc9dddab4dd49cbaeebffb9f33dfd1738c114d53;hpb=0f72eae506d32d20f11908522330d49889818f10;p=jalview.git

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index fc9ddda..a64e869 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -43,6 +43,7 @@ import java.util.Collections;
 import java.util.Date;
 import java.util.Enumeration;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Locale;
 import java.util.Map;
 import java.util.Properties;
@@ -52,7 +53,9 @@ import java.util.TreeSet;
 import javax.swing.LookAndFeel;
 import javax.swing.UIManager;
 
-import jalview.analytics.GoogleAnalytics4;
+import jalview.analytics.Plausible;
+import jalview.bin.argparser.Arg;
+import jalview.bin.argparser.ArgParser;
 import jalview.datamodel.PDBEntry;
 import jalview.gui.Preferences;
 import jalview.gui.UserDefinedColours;
@@ -128,7 +131,7 @@ import jalview.ws.sifts.SiftsSettings;
  * service</li>
  * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
  * service</li>
- * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
+ * <li>USAGESTATS (false - user prompted) Enable analytics tracker for
  * collecting usage statistics</li>
  * <li>SHOW_OVERVIEW boolean for overview window display</li>
  * <li>ANTI_ALIAS boolean for smooth fonts</li>
@@ -140,6 +143,10 @@ import jalview.ws.sifts.SiftsSettings;
  * <li>WRAP_ALIGNMENT</li>
  * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
  * style check</li>
+ * <li>BITMAP_SCALE - scale factor for PNG export - default 0.0 - native
+ * resolution</li>
+ * <li>BITMAP_HEIGHT - height bound for PNG export or 0 for unbound</li>
+ * <li>BITMAP_WIDTH - width bound for PNG export or 0 for unbound</li>
  * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
  * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
  * $SEQUENCE_ID$</li>
@@ -406,9 +413,9 @@ public class Cache
           fis = new URL(propertiesFile).openStream();
           if (!Jalview.quiet())
           {
-            System.out.println(
+            jalview.bin.Console.outPrintln(
                     "Loading jalview properties from : " + propertiesFile);
-            System.out.println(
+            jalview.bin.Console.outPrintln(
                     "Disabling Jalview writing to user's local properties file.");
           }
           propsAreReadOnly = true;
@@ -439,7 +446,8 @@ public class Cache
       } catch (Exception ex)
       {
         if (!Jalview.quiet())
-          System.out.println("Error reading properties file: " + ex);
+          jalview.bin.Console
+                  .outPrintln("Error reading properties file: " + ex);
       }
     }
 
@@ -496,7 +504,8 @@ public class Cache
     } catch (Exception ex)
     {
       if (!Jalview.quiet())
-        System.out.println("Error reading author details: " + ex);
+        jalview.bin.Console
+                .outPrintln("Error reading author details: " + ex);
       authorDetails = null;
     }
     if (authorDetails == null)
@@ -582,10 +591,10 @@ public class Cache
             {
               if (!Jalview.quiet())
               {
-                System.out.println(
+                jalview.bin.Console.errPrintln(
                         "Non-fatal exception when checking version at "
                                 + remoteBuildPropertiesUrl + ":");
-                System.out.println(ex);
+                jalview.bin.Console.printStackTrace(ex);
               }
               remoteVersion = getProperty("VERSION");
             }
@@ -635,8 +644,8 @@ public class Cache
         url = Cache.class.getResource(resourcePath).toString();
       } catch (Exception ex)
       {
-        System.err.println("Failed to resolve resource " + resourcePath
-                + ": " + ex.getMessage());
+        jalview.bin.Console.errPrintln("Failed to resolve resource "
+                + resourcePath + ": " + ex.getMessage());
       }
     }
     else
@@ -686,7 +695,8 @@ public class Cache
     } catch (Exception ex)
     {
       if (!Jalview.quiet())
-        System.out.println("Error reading build details: " + ex);
+        jalview.bin.Console
+                .outPrintln("Error reading build details: " + ex);
       applicationProperties.remove("VERSION");
     }
     String codeVersion = getProperty("VERSION");
@@ -706,8 +716,9 @@ public class Cache
     new BuildDetails(codeVersion, null, codeInstallation);
     if (printVersion && reportVersion)
     {
-      System.out.println(ChannelProperties.getProperty("app_name")
-              + " version: " + codeVersion + codeInstallation);
+      jalview.bin.Console
+              .outPrintln(ChannelProperties.getProperty("app_name")
+                      + " version: " + codeVersion + codeInstallation);
     }
   }
 
@@ -783,8 +794,27 @@ public class Cache
       } catch (NumberFormatException e)
       {
         if (!Jalview.quiet())
-          System.out.println("Error parsing int property '" + property
-                  + "' with value '" + string + "'");
+          jalview.bin.Console.errPrintln("Error parsing int property '"
+                  + property + "' with value '" + string + "'");
+      }
+    }
+
+    return def;
+  }
+
+  public static float getDefault(String property, float def)
+  {
+    String string = getProperty(property);
+    if (string != null)
+    {
+      try
+      {
+        def = Float.parseFloat(string);
+      } catch (NumberFormatException e)
+      {
+        if (!Jalview.quiet())
+          jalview.bin.Console.errPrintln("Error parsing float property '"
+                  + property + "' with value '" + string + "'");
       }
     }
 
@@ -834,7 +864,7 @@ public class Cache
     } catch (Exception ex)
     {
       if (!Jalview.quiet())
-        System.out.println(
+        jalview.bin.Console.errPrintln(
                 "Error setting property: " + key + " " + obj + "\n" + ex);
     }
     return oldValue;
@@ -866,7 +896,7 @@ public class Cache
       } catch (Exception ex)
       {
         if (!Jalview.quiet())
-          System.out.println("Error saving properties: " + ex);
+          jalview.bin.Console.errPrintln("Error saving properties: " + ex);
       }
     }
   }
@@ -954,146 +984,41 @@ public class Cache
   }
 
   /**
-   * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
-   * enabled.
+   * Initialise the tracker if it is not done already.
    */
-  protected static Object tracker = null;
-
-  protected static Class trackerfocus = null;
-
-  protected static Class jgoogleanalyticstracker = null;
-
-  private static boolean useGA4 = true;
-
-  /**
-   * Initialise the google tracker if it is not done already.
-   */
-  public static void initGoogleTracker()
+  public static void initAnalytics()
   {
-    if (useGA4)
-    {
-      GoogleAnalytics4.setEnabled(true);
+    Plausible.setEnabled(true);
 
-      String appName = ChannelProperties.getProperty("app_name")
-              + " Desktop";
-      String version = Cache.getProperty("VERSION") + "_"
-              + Cache.getDefault("BUILD_DATE", "unknown");
-      String path;
-      /* we don't want to encode ':' as "%3A" for backward compatibility with the UA setup
-      try
-      {
-        path = "/" + String.join("/", URLEncoder.encode(appName, "UTF-8"),
-                URLEncoder.encode(version, "UTF-8"),
-                URLEncoder.encode(APPLICATION_STARTED, "UTF-8"));
-      } catch (UnsupportedEncodingException e)
-      {
-      */
-      path = ("/" + String.join("/", appName, version, APPLICATION_STARTED))
-              .replace(' ', '+');
-      /*
-      }
-      */
-      GoogleAnalytics4 ga4 = GoogleAnalytics4.getInstance();
-
-      // This will add a page_view similar to the old UA analytics.
-      // We probably want to get rid of this once the application_launch event
-      // is being processed properly.
-      ga4.sendAnalytics("page_view", "page_location", path, "page_title",
-              APPLICATION_STARTED);
-
-      // This will send a new "application_launch" event with parameters
-      // including the old-style "path", the channel name and version
-      ga4.sendAnalytics("application_launch", true, "page_location", path);
-    }
-    else
+    String appName = ChannelProperties.getProperty("app_name") + " Desktop";
+    String version = Cache.getProperty("VERSION") + "_"
+            + Cache.getDefault("BUILD_DATE", "unknown");
+    String path;
+    /* we don't want to encode ':' as "%3A" for backward compatibility with the UA setup
+    try
     {
-      if (tracker == null)
-      {
-        if (jgoogleanalyticstracker == null)
-        {
-          // try to get the tracker class
-          try
-          {
-            jgoogleanalyticstracker = Cache.class.getClassLoader()
-                    .loadClass(
-                            "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
-            trackerfocus = Cache.class.getClassLoader().loadClass(
-                    "com.boxysystems.jgoogleanalytics.FocusPoint");
-          } catch (Exception e)
-          {
-            Console.debug(
-                    "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
-            tracker = null;
-            jgoogleanalyticstracker = null;
-            trackerfocus = null;
-            return;
-          }
-        }
-        // now initialise tracker
-        Exception re = null, ex = null;
-        Error err = null;
-        String vrs = "No Version Accessible";
-        try
-        {
-          // Google analytics tracking code for Library Finder
-          tracker = jgoogleanalyticstracker
-                  .getConstructor(new Class[]
-                  { String.class, String.class, String.class })
-                  .newInstance(new Object[]
-                  { ChannelProperties.getProperty("app_name") + " Desktop",
-                      (vrs = Cache.getProperty("VERSION") + "_"
-                              + Cache.getDefault("BUILD_DATE", "unknown")),
-                      "UA-9060947-1" });
-          jgoogleanalyticstracker
-                  .getMethod("trackAsynchronously", new Class[]
-                  { trackerfocus })
-                  .invoke(tracker, new Object[]
-                  { trackerfocus
-                          .getConstructor(new Class[]
-                          { String.class })
-                          .newInstance(new Object[]
-                          { APPLICATION_STARTED }) });
-        } catch (RuntimeException e)
-        {
-          re = e;
-        } catch (Exception e)
-        {
-          ex = e;
-        } catch (Error e)
-        {
-          err = e;
-        }
-        if (re != null || ex != null || err != null)
-        {
-          if (re != null)
-          {
-            Console.debug("Caught runtime exception in googletracker init:",
-                    re);
-          }
-          if (ex != null)
-          {
-            Console.warn(
-                    "Failed to initialise GoogleTracker for Jalview Desktop with version "
-                            + vrs,
-                    ex);
-          }
-          if (err != null)
-          {
-            Console.error(
-                    "Whilst initing GoogleTracker for Jalview Desktop version "
-                            + vrs,
-                    err);
-          }
-        }
-        else
-        {
-          Console.debug("Successfully initialised tracker.");
-        }
-      }
+      path = "/" + String.join("/", URLEncoder.encode(appName, "UTF-8"),
+              URLEncoder.encode(version, "UTF-8"),
+              URLEncoder.encode(APPLICATION_STARTED, "UTF-8"));
+    } catch (UnsupportedEncodingException e)
+    {
+    */
+    List<String> pathParts = new ArrayList<>();
+    pathParts.add(appName);
+    pathParts.add(version);
+    pathParts.add(APPLICATION_STARTED);
+    path = ("/" + String.join("/", pathParts)).replace(' ', '+');
+    /*
     }
+    */
+    Plausible plausible = Plausible.getInstance();
+
+    // This will send a new "application_launch" event with parameters
+    // including the old-style "path", the channel name and version
+    plausible.sendEvent("application_launch", path, true);
   }
 
-  private static final String APPLICATION_STARTED = "Application Started.";
+  private static final String APPLICATION_STARTED = "Application Started";
 
   /**
    * get the user's default colour if available
@@ -1161,8 +1086,9 @@ public class Cache
         return date_format.parse(val);
       } catch (Exception ex)
       {
-        System.err.println("Invalid or corrupt date in property '"
-                + propertyName + "' : value was '" + val + "'");
+        jalview.bin.Console
+                .errPrintln("Invalid or corrupt date in property '"
+                        + propertyName + "' : value was '" + val + "'");
       }
     }
     return null;
@@ -1185,8 +1111,8 @@ public class Cache
         return Integer.valueOf(val);
       } catch (NumberFormatException x)
       {
-        System.err.println("Invalid integer in property '" + property
-                + "' (value was '" + val + "')");
+        jalview.bin.Console.errPrintln("Invalid integer in property '"
+                + property + "' (value was '" + val + "')");
       }
     }
     return null;
@@ -1250,7 +1176,8 @@ public class Cache
       } catch (Exception ex)
       {
         if (!Jalview.quiet())
-          System.out.println("Error loading User ColourFile\n" + ex);
+          jalview.bin.Console
+                  .outPrintln("Error loading User ColourFile\n" + ex);
       }
     }
     if (!files.equals(coloursFound.toString()))
@@ -1524,11 +1451,10 @@ public class Cache
                 if (customProxySet &&
                 // we have a username but no password for the scheme being
                 // requested
-                        (protocol.equalsIgnoreCase("http")
-                                && (httpUser != null
-                                        && httpUser.length() > 0
-                                        && (httpPassword == null
-                                                || httpPassword.length == 0)))
+                (protocol.equalsIgnoreCase("http")
+                        && (httpUser != null && httpUser.length() > 0
+                                && (httpPassword == null
+                                        || httpPassword.length == 0)))
                         || (protocol.equalsIgnoreCase("https")
                                 && (httpsUser != null
                                         && httpsUser.length() > 0
@@ -1738,26 +1664,36 @@ public class Cache
     }
     if (file == null || !file.exists())
     {
+      if (file != null)
+      {
+        jalview.bin.Console
+                .errPrintln("Could not load bootstrap preferences file '"
+                        + file.getPath() + "'");
+      }
       String channelPrefsFilename = ChannelProperties
               .getProperty("preferences.filename");
       String propertiesFilename = System.getProperty("user.home")
               + File.separatorChar + channelPrefsFilename;
+      jalview.bin.Console.errPrintln(
+              "Using default properties file '" + propertiesFilename + "'");
       file = new File(propertiesFilename);
     }
     if (file == null || !file.exists())
+
     {
       String releasePrefsFilename = fallbackPropertiesFile;
       String releasePropertiesFilename = System.getProperty("user.home")
               + File.separatorChar + releasePrefsFilename;
+      jalview.bin.Console.errPrintln("Falling back to properties file '"
+              + releasePropertiesFilename + "'");
       file = new File(releasePropertiesFilename);
     }
 
-    if (filename == null)
-      return null;
     if (!file.exists())
     {
-      System.err.println("Could not load bootstrap preferences file '"
-              + filename + "'");
+      jalview.bin.Console
+              .errPrintln("Could not load bootstrap preferences file '"
+                      + file.getPath() + "'");
       return null;
     }
 
@@ -1773,11 +1709,12 @@ public class Cache
       }
     } catch (FileNotFoundException e)
     {
-      System.err.println("Could not find bootstrap preferences file '"
-              + file.getAbsolutePath() + "'");
+      jalview.bin.Console
+              .errPrintln("Could not find bootstrap preferences file '"
+                      + file.getAbsolutePath() + "'");
     } catch (IOException e)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "IOException when loading bootstrap preferences file '"
                       + file.getAbsolutePath() + "'");
     }
@@ -1796,4 +1733,10 @@ public class Cache
   {
     return key == null ? null : sessionProperties.get(key);
   }
+
+  public static boolean getArgCacheDefault(Arg a, String pref, boolean def)
+  {
+    ArgParser ap = Jalview.getInstance().getArgParser();
+    return ap.isSet(a) ? ap.getBoolean(a) : getDefault(pref, def);
+  }
 }