X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fbin%2FCache.java;h=1abb1711df86e47d18ffdbd1dbc8dd27a4e7fdcc;hb=a0770a417ea5add70c3075b9ae9218a58533ef13;hp=1a4f3418168d75b6e5f16152c2c603126e40dc88;hpb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 1a4f341..1abb171 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -24,7 +24,9 @@ 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;
@@ -34,23 +36,27 @@ 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 java.util.regex.Pattern;
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.JLogger;
import jalview.log.JLoggerLog4j;
import jalview.schemes.ColourSchemeLoader;
import jalview.schemes.ColourSchemes;
@@ -59,7 +65,6 @@ import jalview.structure.StructureImportSettings;
import jalview.urls.IdOrgSettings;
import jalview.util.ChannelProperties;
import jalview.util.ColorUtils;
-import jalview.util.Log4j;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.sifts.SiftsSettings;
@@ -124,7 +129,7 @@ import jalview.ws.sifts.SiftsSettings;
* service
*
QUESTIONNAIRE last questionnaire:responder id string from questionnaire
* service
- * USAGESTATS (false - user prompted) Enable google analytics tracker for
+ * USAGESTATS (false - user prompted) Enable analytics tracker for
* collecting usage statistics
* SHOW_OVERVIEW boolean for overview window display
* ANTI_ALIAS boolean for smooth fonts
@@ -136,6 +141,10 @@ import jalview.ws.sifts.SiftsSettings;
* WRAP_ALIGNMENT
* EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
* style check
+ * BITMAP_SCALE - scale factor for PNG export - default 0.0 - native
+ * resolution
+ * BITMAP_HEIGHT - height bound for PNG export or 0 for unbound
+ * BITMAP_WIDTH - width bound for PNG export or 0 for unbound
* SORT_ALIGNMENT (No sort|Id|Pairwise Identity)
* SEQUENCE_LINKS list of name|URL pairs for opening a url with
* $SEQUENCE_ID$
@@ -173,6 +182,8 @@ import jalview.ws.sifts.SiftsSettings;
* FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
* respond to selections made in other alignments containing the same sequences.
*
+ * SHOW_JWS2_SERVICES (true) when set to false, jalview will not
+ * auto-discover JABAWS services
* JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services
* SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
* warning dialog box is displayed.
@@ -200,7 +211,13 @@ import jalview.ws.sifts.SiftsSettings;
* CHIMERA_PATH specify full path to Chimera program (if non-standard)
* ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
*
- *
+ * NONEWS - when set disables Jalview News from automatically appearing
+ * NOHTMLTEMPLATES - when set, the
+ * https://github.com/jalview/exporter-templates/tree/master/biojs repository is
+ * not downloaded automatically
+ * NOIDENTIFIERSSERVICE - when set, jalview won't automatically download
+ * available URL linkouts via www.jalview.org/services/identifiers
+ *
*
* Deprecated settings:
*
@@ -235,6 +252,9 @@ public class Cache
*/
public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
+ // for tests
+ public static final String BOOTSTRAP_TEST = "BOOTSTRAP_TEST";
+
/**
* Sifts settings
*/
@@ -276,8 +296,6 @@ public class Cache
public final static String JALVIEW_LOGGER_NAME = "JalviewLogger";
- public static JLoggerLog4j log;
-
// save the proxy properties set at startup
public final static String[] startupProxyProperties = {
System.getProperty("http.proxyHost"),
@@ -300,6 +318,24 @@ public class Cache
// 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 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()
{
@@ -317,64 +353,21 @@ public class Cache
/** Default file is ~/.jalview_properties */
static String propertiesFile;
- private static boolean propsAreReadOnly = Platform.isJS();
-
- private final static String JS_PROPERTY_PREFIX = "jalview_";
+ private static final String fallbackPropertiesFile = ".jalview_properties";
- public final static String LOGGING_TEST_MESSAGE = "Logging to STDERR";
+ private static boolean propsAreReadOnly = Platform.isJS();
- public static JLogger.LogLevel getCachedLogLevel()
+ public static boolean isPropsAreReadOnly()
{
- return getCachedLogLevel(JALVIEWLOGLEVEL);
+ return propsAreReadOnly;
}
- public static JLogger.LogLevel getCachedLogLevel(String key)
+ public static void setPropsAreReadOnly(boolean propsAreReadOnly)
{
- return JLogger.toLevel(Cache.getDefault(key, "INFO"));
+ Cache.propsAreReadOnly = propsAreReadOnly;
}
- public static boolean initLogger()
- {
- if (log != null)
- {
- return true;
- }
- try
- {
- JLogger.LogLevel cachedLevel = getCachedLogLevel();
- if (!Platform.isJS())
- {
- Log4j.init(cachedLevel);
- }
- // log output
- // is laxis used? Does getLogger do anything without a Logger object?
- // Logger laxis = Log4j.getLogger("org.apache.axis", myLevel);
- JLoggerLog4j.getLogger("org.apache.axis", cachedLevel);
-
- // The main application logger
- log = JLoggerLog4j.getLogger(JALVIEW_LOGGER_NAME, cachedLevel);
- } catch (NoClassDefFoundError e)
- {
- System.err.println("Could not initialise the logger framework");
- e.printStackTrace();
- }
-
- // Test message
- if (log != null)
- {
- // Logging test message should got through the logger object
- if (log.loggerExists())
- log.debug(LOGGING_TEST_MESSAGE);
- // Tell the user that debug is enabled
- Cache.debug(ChannelProperties.getProperty("app_name")
- + " Debugging Output Follows.");
- return true;
- }
- else
- {
- return false;
- }
- }
+ private final static String JS_PROPERTY_PREFIX = "jalview_";
/**
* Loads properties from the given properties file. Any existing properties
@@ -389,7 +382,7 @@ public class Cache
{
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")
@@ -416,10 +409,13 @@ public class Cache
{
// 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)
{
@@ -447,7 +443,9 @@ public class Cache
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);
}
}
@@ -486,7 +484,7 @@ public class Cache
default:
String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
+ proxyType;
- Cache.warn(message);
+ Console.warn(message);
}
// LOAD THE AUTHORS FROM THE authors.props file
@@ -503,7 +501,9 @@ public class Cache
}
} 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)
@@ -566,29 +566,36 @@ public class Cache
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(remoteBuildPropertiesUrl);
+ try
+ {
+ System.setProperty("sun.net.client.defaultConnectTimeout",
+ "5000");
- BufferedReader in = new BufferedReader(
- new InputStreamReader(url.openStream()));
+ URL url = new URL(remoteBuildPropertiesUrl);
- Properties remoteBuildProperties = new Properties();
- remoteBuildProperties.load(in);
- remoteVersion = remoteBuildProperties.getProperty("VERSION");
- } catch (Exception ex)
- {
- System.out
- .println("Non-fatal exception when checking version at "
- + remoteBuildPropertiesUrl + ":");
- System.out.println(ex);
- remoteVersion = getProperty("VERSION");
+ BufferedReader in = new BufferedReader(
+ new InputStreamReader(url.openStream()));
+
+ Properties remoteBuildProperties = new Properties();
+ remoteBuildProperties.load(in);
+ remoteVersion = remoteBuildProperties.getProperty("VERSION");
+ } catch (Exception ex)
+ {
+ if (!Jalview.quiet())
+ {
+ jalview.bin.Console.errPrintln(
+ "Non-fatal exception when checking version at "
+ + remoteBuildPropertiesUrl + ":");
+ jalview.bin.Console.printStackTrace(ex);
+ }
+ remoteVersion = getProperty("VERSION");
+ }
}
System.setProperty("sun.net.client.defaultConnectTimeout",
orgtimeout);
@@ -635,8 +642,8 @@ 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
@@ -678,9 +685,16 @@ public class Cache
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");
@@ -700,8 +714,9 @@ 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);
}
}
@@ -727,7 +742,21 @@ public class Cache
*/
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()
@@ -762,8 +791,28 @@ public class Cache
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 + "'");
}
}
@@ -796,16 +845,25 @@ public class Cache
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;
}
@@ -835,7 +893,8 @@ public class Cache
out.close();
} catch (Exception ex)
{
- System.out.println("Error saving properties: " + ex);
+ if (!Jalview.quiet())
+ jalview.bin.Console.errPrintln("Error saving properties: " + ex);
}
}
}
@@ -859,11 +918,13 @@ public class Cache
if (jalview.jbgui.GDesktop.class.getClassLoader()
.loadClass("uk.ac.vamsas.client.VorbaId") != null)
{
- debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+ Console.debug(
+ "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
vamsasJarsArePresent = 1;
JLoggerLog4j lvclient = JLoggerLog4j.getLogger("uk.ac.vamsas",
- getCachedLogLevel("logs.Vamsas.Level"));
- JLoggerLog4j.addAppender(lvclient, log, JALVIEW_LOGGER_NAME);
+ Console.getCachedLogLevel("logs.Vamsas.Level"));
+ JLoggerLog4j.addAppender(lvclient, Console.log,
+ JALVIEW_LOGGER_NAME);
// Tell the user that debug is enabled
lvclient.debug(ChannelProperties.getProperty("app_name")
+ " Vamsas Client Debugging Output Follows.");
@@ -871,7 +932,7 @@ public class Cache
} catch (Exception e)
{
vamsasJarsArePresent = 0;
- debug("Vamsas Classes are not present");
+ Console.debug("Vamsas Classes are not present");
}
}
return (vamsasJarsArePresent > 0);
@@ -896,11 +957,13 @@ public class Cache
if (Cache.class.getClassLoader()
.loadClass("groovy.lang.GroovyObject") != null)
{
- debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
+ Console.debug(
+ "Found Groovy (groovy.lang.GroovyObject can be loaded)");
groovyJarsArePresent = 1;
JLoggerLog4j lgclient = JLoggerLog4j.getLogger("groovy",
- getCachedLogLevel("logs.Groovy.Level"));
- JLoggerLog4j.addAppender(lgclient, log, JALVIEW_LOGGER_NAME);
+ Console.getCachedLogLevel("logs.Groovy.Level"));
+ JLoggerLog4j.addAppender(lgclient, Console.log,
+ JALVIEW_LOGGER_NAME);
// Tell the user that debug is enabled
lgclient.debug(ChannelProperties.getProperty("app_name")
+ " Groovy Client Debugging Output Follows.");
@@ -908,107 +971,53 @@ public class Cache
} catch (Error e)
{
groovyJarsArePresent = 0;
- debug("Groovy Classes are not present", e);
+ Console.debug("Groovy Classes are not present", e);
} catch (Exception e)
{
groovyJarsArePresent = 0;
- 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)
+ 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)
- {
- 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)
- {
- debug("Caught runtime exception in googletracker init:", re);
- }
- if (ex != null)
- {
- warn("Failed to initialise GoogleTracker for Jalview Desktop with version "
- + vrs, ex);
- }
- if (err != null)
- {
- error("Whilst initing GoogleTracker for Jalview Desktop version "
- + vrs, err);
- }
- }
- else
- {
- 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 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
*
@@ -1026,7 +1035,8 @@ public class Cache
Color col = ColorUtils.parseColourString(colprop);
if (col == null)
{
- warn("Couldn't parse '" + colprop + "' as a colour for " + property);
+ Console.warn("Couldn't parse '" + colprop + "' as a colour for "
+ + property);
}
return (col == null) ? defcolour : col;
}
@@ -1074,8 +1084,9 @@ 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;
@@ -1098,8 +1109,8 @@ 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;
@@ -1162,7 +1173,9 @@ public class Cache
}
} 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()))
@@ -1194,8 +1207,11 @@ public class Cache
{
return;
}
- String line = prefix + (value != null ? value : defaultValue) + suffix;
- sb.append(line);
+ if (prefix != null)
+ sb.append(prefix);
+ sb.append(value == null ? defaultValue : value);
+ if (suffix != null)
+ sb.append(suffix);
}
/**
@@ -1219,6 +1235,7 @@ public class Cache
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"));
@@ -1239,17 +1256,19 @@ public class Cache
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]*$",
- Cache.getDefault("VERSION", "TEST")))
+ appendIfNotNull(sb, "Channel: ",
+ ChannelProperties.getProperty("channel"), "\n", null);
+ if (Console.isDebugEnabled()
+ || !"release".equals(ChannelProperties.getProperty("channel")))
{
appendIfNotNull(sb, "Getdown appdir: ",
- System.getProperty("getdownappdir"), "\n", null);
+ System.getProperty("getdowninstanceappdir"), "\n", null);
appendIfNotNull(sb, "Getdown appbase: ",
- System.getProperty("getdownappbase"), "\n", null);
+ 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();
}
@@ -1306,7 +1325,7 @@ public class Cache
? " [" + startupProxyProperties[6] + "]"
: "");
- Cache.debug(sb.toString());
+ Console.debug(sb.toString());
}
public static void setProxyPropertiesFromPreferences()
@@ -1332,7 +1351,7 @@ public class Cache
case Cache.PROXYTYPE_NONE:
if (!previousProxyType.equals(proxyType))
{
- Cache.info("Setting no proxy settings");
+ Console.info("Setting no proxy settings");
Cache.setProxyProperties(null, null, null, null, null, null, null,
null, null);
}
@@ -1340,7 +1359,7 @@ public class Cache
case Cache.PROXYTYPE_CUSTOM:
// always re-set a custom proxy -- it might have changed, particularly
// password
- Cache.info("Setting custom proxy settings");
+ 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),
@@ -1354,7 +1373,7 @@ public class Cache
proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost");
break;
default: // system proxy settings by default
- Cache.info("Setting system proxy settings");
+ Console.info("Setting system proxy settings");
Cache.resetProxyProperties();
}
}
@@ -1406,8 +1425,10 @@ public class Cache
char[] displayHttpPw = new char[httpPassword == null ? 0
: httpPassword.length];
Arrays.fill(displayHttpPw, '*');
- Cache.debug("CACHE Proxy: setting new Authenticator with httpUser='"
- + httpUser + "' httpPassword='" + displayHttpPw + "'");
+ Console.debug(
+ "CACHE Proxy: setting new Authenticator with httpUser='"
+ + httpUser + "' httpPassword='" + displayHttpPw
+ + "'");
if (!Platform.isJS())
/* *
* java.net.Authenticator not implemented in SwingJS yet
@@ -1428,10 +1449,11 @@ 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
@@ -1456,7 +1478,7 @@ public class Cache
&& getRequestingPort() == Integer
.valueOf(httpPort))
{
- Cache.debug(
+ Console.debug(
"AUTHENTICATOR returning PasswordAuthentication(\""
+ httpUser + "\", '"
+ new String(displayHttpPw) + "')");
@@ -1471,7 +1493,7 @@ public class Cache
{
char[] displayHttpsPw = new char[httpPassword.length];
Arrays.fill(displayHttpsPw, '*');
- Cache.debug(
+ Console.debug(
"AUTHENTICATOR returning PasswordAuthentication(\""
+ httpsUser + "\", '" + displayHttpsPw
+ "'");
@@ -1480,15 +1502,15 @@ public class Cache
}
} catch (NumberFormatException e)
{
- Cache.error("Problem with proxy port values [http:"
+ Console.error("Problem with proxy port values [http:"
+ httpPort + ", https:" + httpsPort + "]");
}
- Cache.debug(
+ Console.debug(
"AUTHENTICATOR after trying to get PasswordAuthentication");
}
}
// non proxy request
- Cache.debug("AUTHENTICATOR returning null");
+ Console.debug("AUTHENTICATOR returning null");
return null;
}
});
@@ -1496,13 +1518,13 @@ public class Cache
// required to re-enable basic authentication (should be okay for a
// local proxy)
- Cache.debug(
+ Console.debug(
"AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\"");
System.setProperty("jdk.http.auth.tunneling.disabledSchemes", "");
} catch (SecurityException e)
{
- Cache.error("Could not set default Authenticator");
- Cache.debug(getStackTraceString(e));
+ Console.error("Could not set default Authenticator");
+ Console.debug(getStackTraceString(e));
}
}
else
@@ -1520,14 +1542,16 @@ public class Cache
*
*/
{
- Cache.debug("AUTHENTICATOR setting default Authenticator to null");
+ Console.debug(
+ "AUTHENTICATOR setting default Authenticator to null");
Authenticator.setDefault(null);
}
}
// nonProxyHosts not currently configurable in Preferences
- Cache.debug("AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
- + nonProxyHosts + "\"");
+ Console.debug(
+ "AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
+ + nonProxyHosts + "\"");
setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts);
}
@@ -1553,176 +1577,6 @@ public class Cache
}
}
- public static void trace(String message)
- {
- if (initLogger())
- {
- log.trace(message, null);
- }
- else
- {
- System.out.println(message);
- }
- }
-
- public static void trace(String message, Throwable t)
- {
- if (initLogger())
- {
- log.trace(message, t);
- }
- else
- {
- System.out.println(message);
- t.printStackTrace();
- }
- }
-
- public static void debug(String message)
- {
- if (initLogger())
- {
- log.debug(message, null);
- }
- else
- {
- System.out.println(message);
- }
-
- }
-
- public static void debug(String message, Throwable t)
- {
- if (initLogger())
- {
- log.debug(message, t);
- }
- else
- {
- System.out.println(message);
- t.printStackTrace();
- }
-
- }
-
- public static void info(String message)
- {
- if (initLogger())
- {
- log.info(message, null);
- }
- else
- {
- System.out.println(message);
- }
-
- }
-
- public static void info(String message, Throwable t)
- {
- if (initLogger())
- {
- log.info(message, t);
- }
- else
- {
- System.out.println(message);
- t.printStackTrace();
- }
-
- }
-
- public static void warn(String message)
- {
- if (initLogger())
- {
- log.warn(message, null);
- }
- else
- {
- System.out.println(message);
- }
-
- }
-
- public static void warn(String message, Throwable t)
- {
- if (initLogger())
- {
- log.warn(message, t);
- }
- else
- {
- System.out.println(message);
- t.printStackTrace();
- }
-
- }
-
- public static void error(String message)
- {
- if (initLogger())
- {
- log.error(message, null);
- }
- else
- {
- System.err.println(message);
- }
-
- }
-
- public static void error(String message, Throwable t)
- {
- if (initLogger())
- {
- log.error(message, t);
- }
- else
- {
- System.err.println(message);
- t.printStackTrace(System.err);
- }
-
- }
-
- public static void fatal(String message)
- {
- if (initLogger())
- {
- log.fatal(message, null);
- }
- else
- {
- System.err.println(message);
- }
-
- }
-
- public static void fatal(String message, Throwable t)
- {
- if (initLogger())
- {
- log.fatal(message, t);
- }
- else
- {
- System.err.println(message);
- t.printStackTrace(System.err);
- }
-
- }
-
- public static boolean isDebugEnabled()
- {
- return log == null ? false : log.isDebugEnabled();
- }
-
- public static boolean isTraceEnabled()
- {
- return log == null ? false : log.isTraceEnabled();
- }
-
/**
* Getdown appbase methods
*/
@@ -1795,4 +1649,78 @@ public class Cache
String appbase = getGetdownAppbase();
return appbase + "/" + getdownDistDir + "/build_properties";
}
+
+ private static final Collection 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())
+ {
+ String channelPrefsFilename = ChannelProperties
+ .getProperty("preferences.filename");
+ String propertiesFilename = System.getProperty("user.home")
+ + File.separatorChar + channelPrefsFilename;
+ file = new File(propertiesFilename);
+ }
+ if (file == null || !file.exists())
+ {
+ String releasePrefsFilename = fallbackPropertiesFile;
+ String releasePropertiesFilename = System.getProperty("user.home")
+ + File.separatorChar + releasePrefsFilename;
+ file = new File(releasePropertiesFilename);
+ }
+
+ if (filename == null)
+ return null;
+ if (!file.exists())
+ {
+ jalview.bin.Console
+ .errPrintln("Could not load bootstrap preferences file '"
+ + filename + "'");
+ 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);
+ }
}