*/
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.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.FileNotFoundException;
import java.io.FileOutputStream;
+import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.net.Authenticator;
+import java.net.PasswordAuthentication;
+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 org.apache.log4j.ConsoleAppender;
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
-import org.apache.log4j.SimpleLayout;
+import javax.swing.LookAndFeel;
+import javax.swing.UIManager;
+
+import jalview.analytics.Plausible;
+import jalview.datamodel.PDBEntry;
+import jalview.gui.Preferences;
+import jalview.gui.UserDefinedColours;
+import jalview.log.JLoggerLog4j;
+import jalview.schemes.ColourSchemeLoader;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.StructureImportSettings;
+import jalview.urls.IdOrgSettings;
+import jalview.util.ChannelProperties;
+import jalview.util.ColorUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.sifts.SiftsSettings;
/**
* Stores and retrieves Jalview Application Properties Lists and fields within
* 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>
* <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>
* 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>
* <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
* <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>
+ * <li>NOIDENTIFIERSSERVICE - when set, jalview won't automatically download
+ * available URL linkouts via www.jalview.org/services/identifiers</li>
+ * <li>
* </ul>
* Deprecated settings:
* <ul>
*/
public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
+ // for tests
+ public static final String BOOTSTRAP_TEST = "BOOTSTRAP_TEST";
+
/**
* Sifts settings
*/
/**
* Initialises the Jalview Application Log
*/
- public static Logger log;
+
+ public final static String JALVIEW_LOGGER_NAME = "JalviewLogger";
+
+ // 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"),
+ System.getProperty("http.proxyUser"),
+ System.getProperty("http.proxyPassword"),
+ System.getProperty("https.proxyUser"),
+ System.getProperty("https.proxyPassword"),
+ System.getProperty("http.nonProxyHosts") };
+
+ public final static String PROXYTYPE_NONE = "none";
+
+ // "false" and "true" for backward compatibility
+ public final static String PROXYTYPE_SYSTEM = "false";
+
+ public final static String PROXYTYPE_CUSTOM = "true";
+
+ // 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()
}
};
+ /* build Properties (not all saved to .jalview_properties) */
+ public static Properties buildProperties = new Properties();
+
/** Default file is ~/.jalview_properties */
static String propertiesFile;
+ private static final String fallbackPropertiesFile = ".jalview_properties";
+
private static boolean propsAreReadOnly = Platform.isJS();
- private final static String JS_PROPERTY_PREFIX = "jalview_";
+ public static boolean isPropsAreReadOnly()
+ {
+ return propsAreReadOnly;
+ }
- public static void initLogger()
+ public static void setPropsAreReadOnly(boolean propsAreReadOnly)
{
- if (log != null)
- {
- return;
- }
- try
- {
- // TODO: redirect stdout and stderr here in order to grab the output of
- // the log
-
- ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
- "System.err");
- ap.setName("JalviewLogger");
- org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
- // log output
- Logger laxis = Logger.getLogger("org.apache.axis");
- Logger lcastor = Logger.getLogger("org.exolab.castor");
- jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
-
- laxis.setLevel(Level.toLevel(
- Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
- lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
- Level.INFO.toString())));
- lcastor = Logger.getLogger("org.exolab.castor.xml");
- lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
- Level.INFO.toString())));
- // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
- // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
- // Level.INFO.toString())));
- jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
- .getDefault("logs.Jalview.level", Level.INFO.toString())));
- // laxis.addAppender(ap);
- // lcastor.addAppender(ap);
- // jalview.bin.Cache.log.addAppender(ap);
- // Tell the user that debug is enabled
- jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
- } catch (Exception ex)
- {
- System.err.println("Problems initializing the log4j system\n");
- ex.printStackTrace(System.err);
- }
+ Cache.propsAreReadOnly = propsAreReadOnly;
}
+ private final static String JS_PROPERTY_PREFIX = "jalview_";
+
/**
* Loads properties from the given properties file. Any existing properties
* are first cleared.
public static void loadProperties(String propsFile)
{
propertiesFile = propsFile;
+ String releasePropertiesFile = null;
+ boolean defaultProperties = false;
if (propsFile == null && !propsAreReadOnly)
{
+ String channelPrefsFilename = ChannelProperties
+ .getProperty("preferences.filename");
+ String releasePrefsFilename = fallbackPropertiesFile;
propertiesFile = System.getProperty("user.home") + File.separatorChar
- + ".jalview_properties";
+ + channelPrefsFilename;
+ releasePropertiesFile = System.getProperty("user.home")
+ + File.separatorChar + releasePrefsFilename;
+ defaultProperties = true;
}
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.");
+ // props file provided as URL
+ fis = new URL(propertiesFile).openStream();
+ 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 = null;
}
if (fis == null)
{
- fis = new FileInputStream(propertiesFile);
+ String readPropertiesFile = propertiesFile;
+ // if we're using the usual properties file and the channel properties
+ // file doesn't exist, read .jalview_properties
+ // (but we'll still save to the channel properties file).
+ if (defaultProperties && (!new File(propertiesFile).exists())
+ && (new File(releasePropertiesFile).exists()))
+ {
+ readPropertiesFile = releasePropertiesFile;
+ }
+ fis = new FileInputStream(readPropertiesFile);
}
applicationProperties.clear();
applicationProperties.load(fis);
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);
}
}
+
+ /* 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", PROXYTYPE_SYSTEM);
+ // default to upgrading old settings
+ switch (proxyType)
+ {
+ case PROXYTYPE_NONE:
+ clearProxyProperties();
+ break;
+ case PROXYTYPE_SYSTEM: // use system settings
+ resetProxyProperties();
+ break;
+ case PROXYTYPE_CUSTOM: // 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);
+ String httpUser = getDefault("PROXY_AUTH_USER", null);
+ // https.proxyUser and https.proxyPassword are not able to be
+ // independently set in Preferences yet (or http.nonProxyHosts)
+ String httpsUser = getDefault("PROXY_AUTH_USER_HTTPS", httpUser);
+ setProxyProperties(httpHost, httpPort, httpsHost, httpsPort, httpUser,
+ proxyAuthPassword, httpsUser, proxyAuthPassword, "localhost");
+ break;
+ default:
+ String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
+ + proxyType;
+ Console.warn(message);
}
// LOAD THE AUTHORS FROM THE authors.props file
- String authorDetails = resolveResourceURLFor("authors.props");
+ String authorDetails = resolveResourceURLFor("/authors.props");
try
{
if (authorDetails != null)
{
- java.net.URL localJarFileURL = new java.net.URL(authorDetails);
+ 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);
+ if (!Jalview.quiet())
+ jalview.bin.Console
+ .outPrintln("Error reading author details: " + ex);
authorDetails = null;
}
if (authorDetails == null)
{
- applicationProperties.remove("AUTHORS");
- applicationProperties.remove("AUTHORFNAMES");
- applicationProperties.remove("YEAR");
+ applicationProperties.remove("AUTHORS");
+ applicationProperties.remove("AUTHORFNAMES");
+ applicationProperties.remove("YEAR");
}
loadBuildProperties(false);
SiftsSettings
.setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
- SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
+ SiftsSettings.setSiftDownloadDirectory(Cache
.getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
SiftsSettings.setFailSafePIDThreshold(
- jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
+ Cache.getDefault("sifts_fail_safe_pid_threshold",
DEFAULT_FAIL_SAFE_PID_THRESHOLD));
SiftsSettings.setCacheThresholdInDays(
- jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
+ Cache.getDefault("sifts_cache_threshold_in_days",
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
- .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
+ StructureImportSettings.setDefaultStructureFileFormat(
+ Cache.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
StructureImportSettings
.setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
// StructureImportSettings
- // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+ // .setDefaultPDBFileParser(Cache.getDefault(
// "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
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)
&& (System.getProperty("java.awt.headless") == null || System
.getProperty("java.awt.headless").equals("false")))
{
- new Thread()
+
+ class VersionChecker extends Thread
{
+
@Override
public void run()
{
+ String remoteBuildPropertiesUrl = Cache
+ .getAppbaseBuildProperties();
+
String orgtimeout = System
.getProperty("sun.net.client.defaultConnectTimeout");
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;
- try
+ if (remoteBuildPropertiesUrl.startsWith("http"))
{
- 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");
- BufferedReader in = new BufferedReader(
- new InputStreamReader(url.openStream()));
- String line = null;
- while ((line = in.readLine()) != null)
+ try
+ {
+ System.setProperty("sun.net.client.defaultConnectTimeout",
+ "5000");
+
+ URL url = new URL(remoteBuildPropertiesUrl);
+
+ BufferedReader in = new BufferedReader(
+ new InputStreamReader(url.openStream()));
+
+ Properties remoteBuildProperties = new Properties();
+ remoteBuildProperties.load(in);
+ remoteVersion = remoteBuildProperties.getProperty("VERSION");
+ } catch (Exception ex)
{
- if (line.indexOf("jalview.version") == -1)
+ if (!Jalview.quiet())
{
- continue;
+ jalview.bin.Console.errPrintln(
+ "Non-fatal exception when checking version at "
+ + remoteBuildPropertiesUrl + ":");
+ jalview.bin.Console.printStackTrace(ex);
}
-
- line = line.substring(line.indexOf("value=") + 7);
- line = line.substring(0, line.lastIndexOf("\""));
- remoteVersion = line;
- break;
+ remoteVersion = getProperty("VERSION");
}
- } catch (Exception ex)
- {
- System.out.println(
- "Non-fatal exception when checking version at www.jalview.org :");
- System.out.println(ex);
- remoteVersion = getProperty("VERSION");
}
System.setProperty("sun.net.client.defaultConnectTimeout",
orgtimeout);
setProperty("LATEST_VERSION", remoteVersion);
}
- }.start();
+ }
+
+ VersionChecker vc = new VersionChecker();
+ vc.start();
}
else
{
url = Cache.class.getResource(resourcePath).toString();
} catch (Exception ex)
{
-
+ jalview.bin.Console.errPrintln("Failed to resolve resource "
+ + resourcePath + ": " + ex.getMessage());
}
}
else
public static void loadBuildProperties(boolean reportVersion)
{
String codeInstallation = getProperty("INSTALLATION");
- boolean printV = codeInstallation == null;
+ boolean printVersion = codeInstallation == null;
- // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
+ /*
+ * read build properties - from the Jalview jar for a Java distribution,
+ * or from codebase file in test or JalviewJS context
+ */
try
{
- String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
- .getCodeSource().getLocation().toString()
- .concat("!/.build_properties"));
-
- java.net.URL localJarFileURL = new java.net.URL(buildDetails);
-
+ String buildDetails = resolveResourceURLFor("/.build_properties");
+ URL localJarFileURL = new URL(buildDetails);
InputStream in = localJarFileURL.openStream();
- applicationProperties.load(in);
+ buildProperties.load(in);
in.close();
+ if (buildProperties.getProperty("BUILD_DATE", null) != null)
+ {
+ applicationProperties.put("BUILD_DATE",
+ buildProperties.getProperty("BUILD_DATE"));
+ }
+ if (buildProperties.getProperty("INSTALLATION", null) != null)
+ {
+ applicationProperties.put("INSTALLATION",
+ buildProperties.getProperty("INSTALLATION"));
+ }
+ if (buildProperties.getProperty("VERSION", null) != null)
+ {
+ applicationProperties.put("VERSION",
+ buildProperties.getProperty("VERSION"));
+ }
+ if (buildProperties.getProperty("JAVA_COMPILE_VERSION", null) != null)
+ {
+ applicationProperties.put("JAVA_COMPILE_VERSION",
+ buildProperties.getProperty("JAVA_COMPILE_VERSION"));
+ }
} 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");
}
setProperty("VERSION", codeVersion);
new BuildDetails(codeVersion, null, codeInstallation);
- if (printV && reportVersion)
+ if (printVersion && reportVersion)
{
- System.out
- .println("Jalview 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);
}
}
}
if (jalview.jbgui.GDesktop.class.getClassLoader()
.loadClass("uk.ac.vamsas.client.VorbaId") != null)
{
- jalview.bin.Cache.log.debug(
+ Console.debug(
"Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
vamsasJarsArePresent = 1;
- Logger lvclient = Logger.getLogger("uk.ac.vamsas");
- lvclient.setLevel(Level.toLevel(Cache
- .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
-
- lvclient.addAppender(log.getAppender("JalviewLogger"));
+ JLoggerLog4j lvclient = JLoggerLog4j.getLogger("uk.ac.vamsas",
+ Console.getCachedLogLevel("logs.Vamsas.Level"));
+ JLoggerLog4j.addAppender(lvclient, Console.log,
+ JALVIEW_LOGGER_NAME);
// Tell the user that debug is enabled
- lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
+ lvclient.debug(ChannelProperties.getProperty("app_name")
+ + " Vamsas Client Debugging Output Follows.");
}
} catch (Exception e)
{
vamsasJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Vamsas Classes are not present");
+ Console.debug("Vamsas Classes are not present");
}
}
return (vamsasJarsArePresent > 0);
if (Cache.class.getClassLoader()
.loadClass("groovy.lang.GroovyObject") != null)
{
- jalview.bin.Cache.log.debug(
+ Console.debug(
"Found Groovy (groovy.lang.GroovyObject can be loaded)");
groovyJarsArePresent = 1;
- Logger lgclient = Logger.getLogger("groovy");
- lgclient.setLevel(Level.toLevel(Cache
- .getDefault("logs.Groovy.Level", Level.INFO.toString())));
-
- lgclient.addAppender(log.getAppender("JalviewLogger"));
+ JLoggerLog4j lgclient = JLoggerLog4j.getLogger("groovy",
+ Console.getCachedLogLevel("logs.Groovy.Level"));
+ JLoggerLog4j.addAppender(lgclient, Console.log,
+ JALVIEW_LOGGER_NAME);
// Tell the user that debug is enabled
- lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
+ lgclient.debug(ChannelProperties.getProperty("app_name")
+ + " Groovy Client Debugging Output Follows.");
}
} catch (Error e)
{
groovyJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
+ Console.debug("Groovy Classes are not present", e);
} catch (Exception e)
{
groovyJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Groovy Classes are not present");
+ Console.debug("Groovy Classes are not present");
}
}
return (groovyJarsArePresent > 0);
}
/**
- * 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)
- {
- 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)
- {
- log.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[]
- { "Jalview Desktop",
- (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
- + jalview.bin.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 (log != null)
- {
- if (re != null)
- {
- log.debug("Caught runtime exception in googletracker init:",
- re);
- }
- if (ex != null)
- {
- log.warn(
- "Failed to initialise GoogleTracker for Jalview Desktop with version "
- + vrs,
- ex);
- }
- if (err != null)
- {
- log.error(
- "Whilst initing GoogleTracker for Jalview Desktop version "
- + vrs,
- err);
- }
- }
- else
- {
- if (re != null)
- {
- System.err.println(
- "Debug: Caught runtime exception in googletracker init:"
- + vrs);
- re.printStackTrace();
- }
- if (ex != null)
- {
- System.err.println(
- "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
- + vrs);
- ex.printStackTrace();
- }
+ Plausible.setEnabled(true);
- if (err != null)
- {
- System.err.println(
- "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
- + vrs);
- err.printStackTrace();
- }
- }
- }
- else
- {
- log.debug("Successfully initialised tracker.");
- }
+ 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)
+ {
+ */
+ 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
*
Color col = ColorUtils.parseColourString(colprop);
if (col == null)
{
- log.warn("Couldn't parse '" + colprop + "' as a colour for "
+ Console.warn("Couldn't parse '" + colprop + "' as a colour for "
+ property);
}
return (col == null) ? defcolour : col;
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()))
}
/**
+ * 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;
+ }
+ if (prefix != null)
+ sb.append(prefix);
+ sb.append(value == null ? defaultValue : value);
+ if (suffix != null)
+ sb.append(suffix);
+ }
+
+ /**
*
* @return Jalview version, build details and JVM platform version for console
*/
public static String getVersionDetailsForConsole()
{
- return "Jalview Version: "
- + jalview.bin.Cache.getDefault("VERSION", "TEST")
- + "\n" + "Jalview Installation: "
- + jalview.bin.Cache.getDefault("INSTALLATION",
- "unknown")
- + "\n" + "Build Date: "
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
- + "\n" + "Java version: "
- + System.getProperty("java.version") + "\n"
- + System.getProperty("os.arch") + " "
- + System.getProperty("os.name") + " "
- + System.getProperty("os.version")
- + (jalview.bin.Cache.getDefault("VERSION", "TEST")
- .equals("DEVELOPMENT")
- ? "\nGetdown appdir: " + System.getProperty("getdownappdir") + "\nJava path: "
- + System.getProperty(
- "java.home")
- + File.separator + "bin"
- + File.separator + "java"
- : "");
+ StringBuilder sb = new StringBuilder();
+ sb.append(ChannelProperties.getProperty("app_name"))
+ .append(" Version: ");
+ sb.append(Cache.getDefault("VERSION", "TEST"));
+ sb.append("\n");
+ sb.append(ChannelProperties.getProperty("app_name"))
+ .append(" Installation: ");
+ sb.append(Cache.getDefault("INSTALLATION", "unknown"));
+ sb.append("\n");
+ sb.append("Build Date: ");
+ sb.append(Cache.getDefault("BUILD_DATE", "unknown"));
+ sb.append("\n");
+ sb.append("Java version: ");
+ sb.append(System.getProperty("java.version"));
+ sb.append("\n");
+ sb.append("Java platform: ");
+ 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");
+ appendIfNotNull(sb, "Channel: ",
+ ChannelProperties.getProperty("channel"), "\n", null);
+ if (Console.isDebugEnabled()
+ || !"release".equals(ChannelProperties.getProperty("channel")))
+ {
+ appendIfNotNull(sb, "Getdown appdir: ",
+ System.getProperty("getdowninstanceappdir"), "\n", null);
+ appendIfNotNull(sb, "Getdown appbase: ",
+ System.getProperty("getdowninstanceappbase"), "\n", null);
+ appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
+ "\n", "unknown");
+ appendIfNotNull(sb, "Preferences file: ", propertiesFile, "\n",
+ "unknown");
+ }
+ return sb.toString();
}
/**
{
// consider returning more human friendly info
// eg 'built from Source' or update channel
- return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
+ return 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 clearProxyProperties()
+ {
+ setProxyProperties(null, null, null, null, null, null, null, null,
+ null);
+ }
+
+ public static void resetProxyProperties()
+ {
+ setProxyProperties(startupProxyProperties[0], startupProxyProperties[1],
+ startupProxyProperties[2], startupProxyProperties[3],
+ startupProxyProperties[4],
+ startupProxyProperties[5] == null ? null
+ : startupProxyProperties[5].toCharArray(),
+ startupProxyProperties[6],
+ startupProxyProperties[7] == null ? null
+ : startupProxyProperties[7].toCharArray(),
+ startupProxyProperties[8]);
+ StringBuilder sb = new StringBuilder();
+ sb.append("Setting proxy properties to: http.proxyHost=")
+ .append(startupProxyProperties[0]).append(", http.proxyPort=")
+ .append(startupProxyProperties[1])
+ .append(startupProxyProperties[4] != null
+ && !startupProxyProperties[4].isEmpty()
+ ? " [" + startupProxyProperties[4] + "]"
+ : "")
+ .append(", https.proxyHost=").append(startupProxyProperties[2])
+ .append(", https.proxyPort=").append(startupProxyProperties[3])
+ .append(startupProxyProperties[6] != null
+ && !startupProxyProperties[6].isEmpty()
+ ? " [" + startupProxyProperties[6] + "]"
+ : "");
+
+ Console.debug(sb.toString());
+ }
+
+ public static void setProxyPropertiesFromPreferences()
+ {
+ setProxyPropertiesFromPreferences(Cache.PROXYTYPE_SYSTEM);
+ }
+
+ public static void setProxyPropertiesFromPreferences(
+ String previousProxyType)
+ {
+ String proxyType = Cache.getDefault("USE_PROXY",
+ Cache.PROXYTYPE_SYSTEM);
+ if (previousProxyType != null
+ && !proxyType.equals(Cache.PROXYTYPE_CUSTOM) // always apply
+ // customProxy
+ && proxyType.equals(previousProxyType))
+ {
+ // no change
+ return;
+ }
+ switch (proxyType)
+ {
+ case Cache.PROXYTYPE_NONE:
+ if (!previousProxyType.equals(proxyType))
+ {
+ Console.info("Setting no proxy settings");
+ Cache.setProxyProperties(null, null, null, null, null, null, null,
+ null, null);
+ }
+ break;
+ case Cache.PROXYTYPE_CUSTOM:
+ // always re-set a custom proxy -- it might have changed, particularly
+ // password
+ Console.info("Setting custom proxy settings");
+ boolean proxyAuthSet = Cache.getDefault("PROXY_AUTH", false);
+ Cache.setProxyProperties(Cache.getDefault("PROXY_SERVER", null),
+ Cache.getDefault("PROXY_PORT", null),
+ Cache.getDefault("PROXY_SERVER_HTTPS", null),
+ Cache.getDefault("PROXY_PORT_HTTPS", null),
+ proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
+ : null,
+ proxyAuthSet ? Cache.proxyAuthPassword : null,
+ proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
+ : null,
+ proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost");
+ break;
+ default: // system proxy settings by default
+ Console.info("Setting system proxy settings");
+ Cache.resetProxyProperties();
+ }
+ }
+
+ public static void setProxyProperties(String httpHost, String httpPort,
+ String httpsHost, String httpsPort, String httpUser,
+ char[] httpPassword, String httpsUser, char[] httpsPassword,
+ String nonProxyHosts)
+ {
+ setOrClearSystemProperty("http.proxyHost", httpHost);
+ setOrClearSystemProperty("http.proxyPort", httpPort);
+ setOrClearSystemProperty("https.proxyHost", httpsHost);
+ setOrClearSystemProperty("https.proxyPort", httpsPort);
+ setOrClearSystemProperty("http.proxyUser", httpUser);
+ setOrClearSystemProperty("https.proxyUser", httpsUser);
+ // note: passwords for http.proxyPassword and https.proxyPassword are sent
+ // via the Authenticator, properties do not need to be set
+
+ // are we using a custom proxy (password prompt might be required)?
+ boolean customProxySet = getDefault("USE_PROXY", PROXYTYPE_SYSTEM)
+ .equals(PROXYTYPE_CUSTOM);
+
+ /*
+ * A bug in Java means the AuthCache does not get reset, so once it has working credentials,
+ * it never asks for more, so changing the Authenticator has no effect (as getPasswordAuthentication()
+ * is not re-called).
+ * This could lead to password leak to a hostile proxy server, so I'm putting in a hack to clear
+ * the AuthCache.
+ * see https://www.generacodice.com/en/articolo/154918/Reset-the-Authenticator-credentials
+ * ...
+ * Turns out this is only accessible in Java 8, and not in Java 9 onwards, so commenting out
+ */
+ /*
+ try
+ {
+ sun.net.www.protocol.http.AuthCacheValue
+ .setAuthCache(new sun.net.www.protocol.http.AuthCacheImpl());
+ } catch (Throwable t)
+ {
+ Cache.error(t.getMessage());
+ Cache.debug(getStackTraceString(t));
+ }
+ */
+
+ if (httpUser != null || httpsUser != null)
+ {
+ try
+ {
+ char[] displayHttpPw = new char[httpPassword == null ? 0
+ : httpPassword.length];
+ Arrays.fill(displayHttpPw, '*');
+ Console.debug(
+ "CACHE Proxy: setting new Authenticator with httpUser='"
+ + httpUser + "' httpPassword='" + displayHttpPw
+ + "'");
+ if (!Platform.isJS())
+ /* *
+ * java.net.Authenticator not implemented in SwingJS yet
+ *
+ * @j2sIgnore
+ *
+ */
+ {
+ Authenticator.setDefault(new Authenticator()
+ {
+ @Override
+ protected PasswordAuthentication getPasswordAuthentication()
+ {
+ if (getRequestorType() == RequestorType.PROXY)
+ {
+ String protocol = getRequestingProtocol();
+ boolean needProxyPasswordSet = false;
+ 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("https")
+ && (httpsUser != null
+ && httpsUser.length() > 0
+ && (httpsPassword == null
+ || httpsPassword.length == 0))))
+ {
+ // open Preferences -> Connections
+ String message = MessageManager
+ .getString("label.proxy_password_required");
+ Preferences.openPreferences(
+ Preferences.TabRef.CONNECTIONS_TAB, message);
+ Preferences.getInstance()
+ .proxyAuthPasswordCheckHighlight(true, true);
+ }
+ else
+ {
+ try
+ {
+ if (protocol.equalsIgnoreCase("http")
+ && getRequestingHost()
+ .equalsIgnoreCase(httpHost)
+ && getRequestingPort() == Integer
+ .valueOf(httpPort))
+ {
+ Console.debug(
+ "AUTHENTICATOR returning PasswordAuthentication(\""
+ + httpUser + "\", '"
+ + new String(displayHttpPw) + "')");
+ return new PasswordAuthentication(httpUser,
+ httpPassword);
+ }
+ if (protocol.equalsIgnoreCase("https")
+ && getRequestingHost()
+ .equalsIgnoreCase(httpsHost)
+ && getRequestingPort() == Integer
+ .valueOf(httpsPort))
+ {
+ char[] displayHttpsPw = new char[httpPassword.length];
+ Arrays.fill(displayHttpsPw, '*');
+ Console.debug(
+ "AUTHENTICATOR returning PasswordAuthentication(\""
+ + httpsUser + "\", '" + displayHttpsPw
+ + "'");
+ return new PasswordAuthentication(httpsUser,
+ httpsPassword);
+ }
+ } catch (NumberFormatException e)
+ {
+ Console.error("Problem with proxy port values [http:"
+ + httpPort + ", https:" + httpsPort + "]");
+ }
+ Console.debug(
+ "AUTHENTICATOR after trying to get PasswordAuthentication");
+ }
+ }
+ // non proxy request
+ Console.debug("AUTHENTICATOR returning null");
+ return null;
+ }
+ });
+ } // end of j2sIgnore for java.net.Authenticator
+
+ // required to re-enable basic authentication (should be okay for a
+ // local proxy)
+ Console.debug(
+ "AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\"");
+ System.setProperty("jdk.http.auth.tunneling.disabledSchemes", "");
+ } catch (SecurityException e)
+ {
+ Console.error("Could not set default Authenticator");
+ Console.debug(getStackTraceString(e));
+ }
+ }
+ else
+ {
+ // reset the Authenticator to protect http.proxyUser and
+ // http.proxyPassword Just In Case
+ /* as noted above, due to bug in java this doesn't work if the sun.net.www.protocol.http.AuthCache
+ * has working credentials. No workaround for Java 11.
+ */
+ if (!Platform.isJS())
+ /* *
+ * java.net.Authenticator not implemented in SwingJS yet
+ *
+ * @j2sIgnore
+ *
+ */
+ {
+ Console.debug(
+ "AUTHENTICATOR setting default Authenticator to null");
+ Authenticator.setDefault(null);
+ }
+ }
+
+ // nonProxyHosts not currently configurable in Preferences
+ Console.debug(
+ "AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
+ + nonProxyHosts + "\"");
+ setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts);
+ }
+
+ public static void setOrClearSystemProperty(String key, char[] value)
+ {
+ setOrClearSystemProperty(key,
+ (value == null) ? null : new String(value));
+ }
+
+ public static void setOrClearSystemProperty(String key, String value)
+ {
+ if (key == null)
+ {
+ return;
+ }
+ if (value == null)
+ {
+ System.clearProperty(key);
+ }
+ else
+ {
+ System.setProperty(key, value);
+ }
+ }
+
+ /**
+ * Getdown appbase methods
+ */
+
+ private static final String releaseAppbase;
+
+ private static String getdownAppbase;
+
+ private static String getdownDistDir;
+
+ static
+ {
+ if (!Platform.isJS())
+ {
+ 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";
+ }
+ else
+ {
+ // this value currenly made up, can be changed to URL that will be
+ // "https://www.jalview.org/jalview-js/swingjs/j2s/build_properties"
+ releaseAppbase = "https://www.jalview.org/jalview-js";
+ getdownAppbase = releaseAppbase;
+ getdownDistDir = "/swingjs/j2s";
+ }
+ }
+
+ // 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 = buildProperties.getProperty("GETDOWNAPPBASE");
+ distDir = buildProperties.getProperty("GETDOWNAPPDISTDIR");
+ }
+ 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";
+ }
+
+ 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