import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
+import org.apache.log4j.builders.appender.ConsoleAppenderBuilder;
+import org.apache.logging.log4j.core.config.Configurator;
+import org.apache.logging.log4j.core.config.builder.api.AppenderComponentBuilder;
+import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilder;
+import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilderFactory;
+import org.apache.logging.log4j.core.config.builder.impl.BuiltConfiguration;
import jalview.datamodel.PDBEntry;
import jalview.gui.Preferences;
* 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>
}
};
+ /* build Properties (not all saved to .jalview_properties) */
+ public static Properties buildProperties = new Properties();
+
/** Default file is ~/.jalview_properties */
static String propertiesFile;
}
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
+ // configure the root logger to stderr
+ ConfigurationBuilder<BuiltConfiguration> builder = ConfigurationBuilderFactory.newConfigurationBuilder();
+ AppenderComponentBuilder consoleApp = builder.newAppender("stderr", "Console");
+ builder.add(consoleApp);
+ Configurator.initialize(builder.build());
// log output
Logger laxis = Logger.getLogger("org.apache.axis");
Logger lcastor = Logger.getLogger("org.exolab.castor");
}
/**
- * Loads properties from the given properties file. Any existing properties
- * are first cleared.
+ * 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 = ".jalview_properties";
propertiesFile = System.getProperty("user.home") + File.separatorChar
- + ".jalview_properties";
+ + channelPrefsFilename;
+ releasePropertiesFile = System.getProperty("user.home")
+ + File.separatorChar + releasePrefsFilename;
+ defaultProperties = true;
}
else
{
InputStream fis;
try
{
+ // 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.");
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);
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
@Override
public void run()
{
- String buildPropertiesUrl = Cache.getAppbaseBuildProperties();
+ String remoteBuildPropertiesUrl = Cache
+ .getAppbaseBuildProperties();
String orgtimeout = System
.getProperty("sun.net.client.defaultConnectTimeout");
{
System.setProperty("sun.net.client.defaultConnectTimeout",
"5000");
- java.net.URL url = new java.net.URL(buildPropertiesUrl);
+ java.net.URL url = new java.net.URL(remoteBuildPropertiesUrl);
BufferedReader in = new BufferedReader(
new InputStreamReader(url.openStream()));
{
System.out
.println("Non-fatal exception when checking version at "
- + buildPropertiesUrl + ":");
+ + remoteBuildPropertiesUrl + ":");
System.out.println(ex);
remoteVersion = getProperty("VERSION");
}
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"));
+ }
} catch (Exception ex)
{
System.out.println("Error reading build details: " + ex);
}
/**
- * Gets Jalview application property of given key. Returns null if key not
- * found
+ * Gets Jalview application property of given key. Returns null if key not found
*
* @param key
- * Name of property
+ * Name of property
*
* @return Property value
*/
}
/**
- * These methods are used when checking if the saved preference is different
- * to the default setting
+ * These methods are used when checking if the saved preference is different to
+ * the default setting
*/
public static boolean getDefault(String property, boolean def)
}
/**
- * Answers the value of the given property, or the supplied default value if
- * the property is not set
+ * Answers the value of the given property, or the supplied default value if the
+ * property is not set
*/
public static String getDefault(String property, String def)
{
* Stores property in the file "HOME_DIR/.jalview_properties"
*
* @param key
- * Name of object
+ * Name of object
* @param obj
- * String value of property
+ * String value of property
*
* @return previous value of property (or null)
*/
* Loads in user colour schemes from files.
*
* @param files
- * a '|'-delimited list of file paths
+ * a '|'-delimited list of file paths
*/
public static void initUserColourSchemes(String files)
{
// open Preferences -> Connections
String message = MessageManager
.getString("label.proxy_password_required");
- Preferences.openPreferences(Preferences.CONNECTIONS_TAB,
- message);
+ Preferences.openPreferences(
+ Preferences.TabRef.CONNECTIONS_TAB, message);
Preferences.getInstance()
.proxyAuthPasswordCheckHighlight(true, true);
}
static
{
- 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";
+ 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
String distDir = System.getProperty("getdowndistdir");
if (appbase == null)
{
+ appbase = buildProperties.getProperty("GETDOWNAPPBASE");
+ distDir = buildProperties.getProperty("GETDOWNAPPDISTDIR");
+ }
+ if (appbase == null)
+ {
appbase = releaseAppbase;
distDir = "release";
}
getdownDistDir = distDir;
}
- private static String getGetdownAppbase()
+ public static String getGetdownAppbase()
{
setGetdownAppbase();
return getdownAppbase;
}
- private static String getAppbaseBuildProperties()
+ public static String getAppbaseBuildProperties()
{
String appbase = getGetdownAppbase();
return appbase + "/" + getdownDistDir + "/build_properties";
git://source.jalview.org / jalview.git / blobdiff