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.FileOutputStream;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.net.URL;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Collections;
* service</li>
* <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
* collecting usage statistics</li>
- * <li>DAS_LOCAL_SOURCE list of local das sources</li>
* <li>SHOW_OVERVIEW boolean for overview window display</li>
* <li>ANTI_ALIAS boolean for smooth fonts</li>
* <li>RIGHT_ALIGN_IDS boolean</li>
* sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
* <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
* jalview.utils.GroupURLLink for more info</li>
- * <li>DAS_REGISTRY_URL the registry to query</li>
* <li>DEFAULT_BROWSER for unix</li>
- * <li>DAS_ACTIVE_SOURCE list of active sources</li>
* <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
* (false)</li>
* <li>VERSION_CHECK (true) check for the latest release version from
*/
public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
- public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
-
- public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
-
- public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
-
/**
* Sifts settings
*/
/** Default file is ~/.jalview_properties */
static String propertiesFile;
- private static boolean propsAreReadOnly = /** @j2sNative true || */
- false;
+ private static boolean propsAreReadOnly = Platform.isJS();
+
+ private final static String JS_PROPERTY_PREFIX = "jalview_";
public static void initLogger()
{
public static void loadProperties(String propsFile)
{
propertiesFile = propsFile;
- if (propsFile == null)
+ if (propsFile == null && !propsAreReadOnly)
{
propertiesFile = System.getProperty("user.home") + File.separatorChar
+ ".jalview_properties";
propsAreReadOnly = true;
}
- try
+ if (propertiesFile == null)
+ { // BH 2019
+ Platform.readInfoProperties(JS_PROPERTY_PREFIX,
+ applicationProperties);
+ }
+ 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.");
- propsAreReadOnly = true;
+ 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.");
+ propsAreReadOnly = true;
+
+ } catch (Exception ex)
+ {
+ fis = null;
+ }
+ if (fis == null)
+ {
+ fis = new FileInputStream(propertiesFile);
+ }
+ applicationProperties.clear();
+ applicationProperties.load(fis);
+ // remove any old build properties
+
+ deleteBuildProperties();
+ fis.close();
} catch (Exception ex)
{
- fis = null;
- }
- if (fis == null)
- {
- fis = new FileInputStream(propertiesFile);
+ System.out.println("Error reading properties file: " + ex);
}
- applicationProperties.clear();
- applicationProperties.load(fis);
-
- // remove any old build properties
-
- deleteBuildProperties();
- fis.close();
- } catch (Exception ex)
- {
- System.out.println("Error reading properties file: " + ex);
}
-
if (getDefault("USE_PROXY", false))
{
String proxyServer = getDefault("PROXY_SERVER", ""),
}
// LOAD THE AUTHORS FROM THE authors.props file
+ String authorDetails = resolveResourceURLFor("/authors.props");
+
try
{
- String authorDetails = /** @j2sNative "xxx" || */
- "jar:"
- .concat(Cache.class.getProtectionDomain().getCodeSource()
- .getLocation().toString().concat("!/authors.props"));
-
- java.net.URL localJarFileURL = new java.net.URL(authorDetails);
-
- InputStream in = localJarFileURL.openStream();
- applicationProperties.load(in);
- in.close();
+ if (authorDetails != null)
+ {
+ 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);
- applicationProperties.remove("AUTHORS");
- applicationProperties.remove("AUTHORFNAMES");
- applicationProperties.remove("YEAR");
+ authorDetails = null;
}
-
- // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
- // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
- // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
- try
+ if (authorDetails == null)
{
- String buildDetails = /** @j2sNative "xxx" || */
- "jar:".concat(Cache.class.getProtectionDomain()
- .getCodeSource().getLocation().toString()
- .concat("!/.build_properties"));
-
- java.net.URL localJarFileURL = new java.net.URL(buildDetails);
-
- InputStream in = localJarFileURL.openStream();
- applicationProperties.load(in);
- in.close();
- } catch (Exception ex)
- {
- System.out.println("Error reading build details: " + ex);
- applicationProperties.remove("VERSION");
+ applicationProperties.remove("AUTHORS");
+ applicationProperties.remove("AUTHORFNAMES");
+ applicationProperties.remove("YEAR");
}
- String jnlpVersion = System.getProperty("jalview.version");
- String codeVersion = getProperty("VERSION");
- String codeInstallation = getProperty("INSTALLATION");
- if (codeVersion == null)
- {
- // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
- codeVersion = "Test";
- jnlpVersion = "Test";
- codeInstallation = "";
- }
- else
- {
- codeInstallation = " (" + codeInstallation + ")";
- }
- new BuildDetails(codeVersion, null, codeInstallation);
+ loadBuildProperties(false);
SiftsSettings
.setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
"http://www.jalview.org/services/identifiers"));
IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
- System.out
- .println("Jalview Version: " + codeVersion + codeInstallation);
-
StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
.getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
StructureImportSettings
// StructureImportSettings
// .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
// "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
- // jnlpVersion will be null if we're using InstallAnywhere
+
+ String jnlpVersion = System.getProperty("jalview.version");
+
+ // 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")))
{
-
- class VersionChecker extends Thread
+ new Thread()
{
@Override
public void run()
setProperty("LATEST_VERSION", remoteVersion);
}
- }
-
- VersionChecker vc = new VersionChecker();
- vc.start();
+ }.start();
}
else
{
}
}
- setProperty("VERSION", codeVersion);
-
// LOAD USERDEFINED COLOURS
- jalview.bin.Cache
- .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
+ Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
false);
}
+ /**
+ * construct a resource URL for the given absolute resource pathname
+ *
+ * @param resourcePath
+ * @return
+ */
+ private static String resolveResourceURLFor(String resourcePath)
+ {
+ String url = null;
+ if (Platform.isJS() || !Cache.class.getProtectionDomain()
+ .getCodeSource().getLocation().toString().endsWith(".jar"))
+ {
+ try
+ {
+ url = Cache.class.getResource(resourcePath).toString();
+ } catch (Exception ex)
+ {
+ System.err.println("Failed to resolve resource " + resourcePath + ": "
+ + ex.getMessage());
+ }
+ }
+ else
+ {
+ url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource()
+ .getLocation().toString().concat("!" + resourcePath));
+ }
+ return url;
+ }
+
+ public static void loadBuildProperties(boolean reportVersion)
+ {
+ String codeInstallation = getProperty("INSTALLATION");
+ boolean printVersion = codeInstallation == null;
+
+ /*
+ * read build properties - from the Jalview jar for a Java distribution,
+ * or from codebase file in test or JalviewJS context
+ */
+ try
+ {
+ String buildDetails = resolveResourceURLFor("/.build_properties");
+ URL localJarFileURL = new URL(buildDetails);
+ InputStream in = localJarFileURL.openStream();
+ applicationProperties.load(in);
+ in.close();
+ } catch (Exception ex)
+ {
+ System.out.println("Error reading build details: " + ex);
+ applicationProperties.remove("VERSION");
+ }
+ String codeVersion = getProperty("VERSION");
+ codeInstallation = getProperty("INSTALLATION");
+
+ if (codeVersion == null)
+ {
+ // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
+ codeVersion = "Test";
+ codeInstallation = "";
+ }
+ else
+ {
+ codeInstallation = " (" + codeInstallation + ")";
+ }
+ setProperty("VERSION", codeVersion);
+ new BuildDetails(codeVersion, null, codeInstallation);
+ if (printVersion && reportVersion)
+ {
+ System.out
+ .println("Jalview Version: " + codeVersion + codeInstallation);
+ }
+ }
+
private static void deleteBuildProperties()
{
applicationProperties.remove("LATEST_VERSION");
*/
public static String getProperty(String key)
{
- return applicationProperties.getProperty(key);
+ String prop = applicationProperties.getProperty(key);
+ if (prop == null && Platform.isJS())
+ {
+ prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
+ + "_" + JS_PROPERTY_PREFIX + key);
+ }
+ return prop;
}
/**
return def;
}
- /**
- * These methods are used when checking if the saved preference is different
- * to the default setting
- */
- public static String getDefault(String property, String def)
+ public static int getDefault(String property, int def)
{
String string = getProperty(property);
if (string != null)
{
- return string;
+ try
+ {
+ def = Integer.parseInt(string);
+ } catch (NumberFormatException e)
+ {
+ System.out.println("Error parsing int property '" + property
+ + "' with value '" + string + "'");
+ }
}
return def;
}
/**
+ * 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)
+ {
+ String value = getProperty(property);
+ return value == null ? def : value;
+ }
+
+ /**
* Stores property in the file "HOME_DIR/.jalview_properties"
*
* @param key
try
{
oldValue = applicationProperties.setProperty(key, obj);
- if (!propsAreReadOnly)
+ if (propertiesFile != null && !propsAreReadOnly)
{
FileOutputStream out = new FileOutputStream(propertiesFile);
applicationProperties.store(out, "---JalviewX Properties File---");
}
}
}
+
+ /**
+ * 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;
+ }
+ String line = prefix + (value != null ? value : defaultValue) + suffix;
+ sb.append(line);
+ }
+
+ /**
+ *
+ * @return Jalview version, build details and JVM platform version for console
+ */
+ public static String getVersionDetailsForConsole()
+ {
+ StringBuilder sb = new StringBuilder();
+ sb.append("Jalview Version: " + jalview.bin.Cache.getDefault("VERSION", "TEST"));
+ sb.append("\n");
+ sb.append("Jalview Installation: "
+ + jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
+ sb.append("\n");
+ sb.append("Build Date: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+ sb.append("\n");
+ sb.append("Java version: " + System.getProperty("java.version"));
+ sb.append("\n");
+ sb.append(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + 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);
+ if (jalview.bin.Cache.getDefault("VERSION", "TEST").equals("DEVELOPMENT")) {
+ appendIfNotNull(sb, "Getdown appdir: ",
+ System.getProperty("getdownappdir"), "\n", null);
+ appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
+ "\n", "unknown");
+ }
+ return sb.toString();
+ }
+
+ /**
+ *
+ * @return build details as reported in splashscreen
+ */
+ public static String getBuildDetailsForSplash()
+ {
+ // consider returning more human friendly info
+ // eg 'built from Source' or update channel
+ return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
+ }
}
git://source.jalview.org / jalview.git / blobdiff