import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
+import java.io.FileNotFoundException;
import java.io.FileOutputStream;
+import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.net.URL;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
+import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collection;
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;
import java.util.StringTokenizer;
import java.util.TreeSet;
import javax.swing.LookAndFeel;
import javax.swing.UIManager;
+import jalview.analytics.Plausible;
import jalview.datamodel.PDBEntry;
import jalview.gui.Preferences;
import jalview.gui.UserDefinedColours;
* 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>
* <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>
*/
public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
+ // for tests
+ public static final String BOOTSTRAP_TEST = "BOOTSTRAP_TEST";
+
/**
* Sifts settings
*/
// 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()
{
/** Default file is ~/.jalview_properties */
static String propertiesFile;
+ private static final String fallbackPropertiesFile = ".jalview_properties";
+
private static boolean propsAreReadOnly = Platform.isJS();
public static boolean isPropsAreReadOnly()
{
String channelPrefsFilename = ChannelProperties
.getProperty("preferences.filename");
- String releasePrefsFilename = ".jalview_properties";
+ String releasePrefsFilename = fallbackPropertiesFile;
propertiesFile = System.getProperty("user.home") + File.separatorChar
+ channelPrefsFilename;
releasePropertiesFile = System.getProperty("user.home")
{
// props file provided as URL
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.");
+ if (!Jalview.quiet())
+ {
+ jalview.bin.Console.outPrintln(
+ "Loading jalview properties from : " + propertiesFile);
+ jalview.bin.Console.outPrintln(
+ "Disabling Jalview writing to user's local properties file.");
+ }
propsAreReadOnly = true;
} catch (Exception ex)
{
fis.close();
} catch (Exception ex)
{
- System.out.println("Error reading properties file: " + ex);
+ if (!Jalview.quiet())
+ jalview.bin.Console
+ .outPrintln("Error reading properties file: " + ex);
}
}
}
} catch (Exception ex)
{
- System.out.println("Error reading author details: " + ex);
+ if (!Jalview.quiet())
+ jalview.bin.Console
+ .outPrintln("Error reading author details: " + ex);
authorDetails = null;
}
if (authorDetails == null)
if (orgtimeout == null)
{
orgtimeout = "30";
- System.out.println("# INFO: Setting default net timeout to "
- + orgtimeout + " seconds.");
+ Console.debug("Setting default net timeout to " + orgtimeout
+ + " seconds.");
}
String remoteVersion = null;
if (remoteBuildPropertiesUrl.startsWith("http"))
remoteVersion = remoteBuildProperties.getProperty("VERSION");
} catch (Exception ex)
{
- System.out.println(
- "Non-fatal exception when checking version at "
- + remoteBuildPropertiesUrl + ":");
- System.out.println(ex);
+ if (!Jalview.quiet())
+ {
+ jalview.bin.Console.errPrintln(
+ "Non-fatal exception when checking version at "
+ + remoteBuildPropertiesUrl + ":");
+ jalview.bin.Console.printStackTrace(ex);
+ }
remoteVersion = getProperty("VERSION");
}
}
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
}
} catch (Exception ex)
{
- System.out.println("Error reading build details: " + ex);
+ if (!Jalview.quiet())
+ jalview.bin.Console
+ .outPrintln("Error reading build details: " + ex);
applicationProperties.remove("VERSION");
}
String codeVersion = getProperty("VERSION");
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);
}
}
*/
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()
def = Integer.parseInt(string);
} catch (NumberFormatException e)
{
- System.out.println("Error parsing int property '" + property
- + "' with value '" + string + "'");
+ if (!Jalview.quiet())
+ 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 + "'");
}
}
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();
}
} catch (Exception ex)
{
- System.out.println(
- "Error setting property: " + key + " " + obj + "\n" + ex);
+ if (!Jalview.quiet())
+ jalview.bin.Console.errPrintln(
+ "Error setting property: " + key + " " + obj + "\n" + ex);
}
return oldValue;
}
out.close();
} catch (Exception ex)
{
- System.out.println("Error saving properties: " + ex);
+ if (!Jalview.quiet())
+ jalview.bin.Console.errPrintln("Error saving properties: " + ex);
}
}
}
}
/**
- * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
- * enabled.
- */
- protected static Object tracker = null;
-
- protected static Class trackerfocus = null;
-
- protected static Class jgoogleanalyticstracker = null;
-
- /**
- * Initialise the google tracker if it is not done already.
+ * Initialise the tracker if it is not done already.
*/
- public static void initGoogleTracker()
+ public static void initAnalytics()
{
- if (tracker == null)
+ 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
{
- 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";
+
/**
* get the user's default colour if available
*
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;
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;
}
} catch (Exception ex)
{
- System.out.println("Error loading User ColourFile\n" + ex);
+ if (!Jalview.quiet())
+ jalview.bin.Console
+ .outPrintln("Error loading User ColourFile\n" + ex);
}
}
if (!files.equals(coloursFound.toString()))
String appbase = getGetdownAppbase();
return appbase + "/" + getdownDistDir + "/build_properties";
}
+
+ private static final Collection<String> bootstrapProperties = new ArrayList<>(
+ Arrays.asList(JALVIEWLOGLEVEL, BOOTSTRAP_TEST));
+
+ public static Properties bootstrapProperties(String filename)
+ {
+ Properties bootstrapProps = new Properties();
+ File file = null;
+ if (filename != null)
+ {
+ file = new File(filename);
+ }
+ 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 (!file.exists())
+ {
+ jalview.bin.Console
+ .errPrintln("Could not load bootstrap preferences file '"
+ + file.getPath() + "'");
+ return null;
+ }
+
+ try
+ {
+ FileInputStream in = new FileInputStream(file.getAbsoluteFile());
+ Properties props = new Properties();
+ props.load(in);
+ for (String prop : bootstrapProperties)
+ {
+ if (props.containsKey(prop))
+ bootstrapProps.put(prop, props.getProperty(prop));
+ }
+ } catch (FileNotFoundException e)
+ {
+ jalview.bin.Console
+ .errPrintln("Could not find bootstrap preferences file '"
+ + file.getAbsolutePath() + "'");
+ } catch (IOException e)
+ {
+ jalview.bin.Console.errPrintln(
+ "IOException when loading bootstrap preferences file '"
+ + file.getAbsolutePath() + "'");
+ }
+ 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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff