X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=6e44b0c44671cfaed65cb5773dffb322211b5c70;hb=af259f508805faf2da90585ee9a67cd7853bf5aa;hp=dc5084347e9bc01cab00b33cf6a8a44479085053;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index dc50843..6e44b0c 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -20,18 +20,6 @@
*/
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.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
-import jalview.ws.sifts.SiftsSettings;
-
import java.awt.Color;
import java.io.BufferedReader;
import java.io.File;
@@ -39,6 +27,8 @@ import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.io.StringWriter;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Collections;
@@ -48,12 +38,26 @@ import java.util.Locale;
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 org.apache.log4j.ConsoleAppender;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
+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.ws.sifts.SiftsSettings;
+
/**
* Stores and retrieves Jalview Application Properties Lists and fields within
* list entries are separated by '|' symbols unless otherwise stated (|) clauses
@@ -116,7 +120,6 @@ import org.apache.log4j.SimpleLayout;
* service
*
USAGESTATS (false - user prompted) Enable google analytics tracker for
* collecting usage statistics
- * DAS_LOCAL_SOURCE list of local das sources
* SHOW_OVERVIEW boolean for overview window display
* ANTI_ALIAS boolean for smooth fonts
* RIGHT_ALIGN_IDS boolean
@@ -136,9 +139,7 @@ import org.apache.log4j.SimpleLayout;
* sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
* GROUP_LINKS list of name|URL[|<separator>] tuples - see
* jalview.utils.GroupURLLink for more info
- * DAS_REGISTRY_URL the registry to query
* DEFAULT_BROWSER for unix
- * DAS_ACTIVE_SOURCE list of active sources
* SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
* (false)
* VERSION_CHECK (true) check for the latest release version from
@@ -228,12 +229,6 @@ public class Cache
*/
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
*/
@@ -281,7 +276,7 @@ public class Cache
@Override
public synchronized Enumeration keys()
{
- return Collections.enumeration(new TreeSet(super.keySet()));
+ return Collections.enumeration(new TreeSet<>(super.keySet()));
}
};
@@ -334,7 +329,10 @@ public class Cache
}
}
- /** Called when Jalview is started */
+ /**
+ * Loads properties from the given properties file. Any existing properties
+ * are first cleared.
+ */
public static void loadProperties(String propsFile)
{
propertiesFile = propsFile;
@@ -369,6 +367,7 @@ public class Cache
{
fis = new FileInputStream(propertiesFile);
}
+ applicationProperties.clear();
applicationProperties.load(fis);
// remove any old build properties
@@ -412,41 +411,7 @@ public class Cache
applicationProperties.remove("YEAR");
}
- // 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
- {
- String buildDetails = "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");
- }
-
- 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));
@@ -466,9 +431,6 @@ public class Cache
"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
@@ -476,8 +438,13 @@ public class Cache
// 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")))
@@ -548,8 +515,6 @@ public class Cache
}
}
- setProperty("VERSION", codeVersion);
-
// LOAD USERDEFINED COLOURS
jalview.bin.Cache
.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
@@ -557,6 +522,50 @@ public class Cache
false);
}
+ public static void loadBuildProperties(boolean reportVersion)
+ {
+ String codeInstallation = getProperty("INSTALLATION");
+ boolean printV = codeInstallation == null;
+
+ // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
+ try
+ {
+ String buildDetails = "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");
+ }
+ 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 (printV && reportVersion)
+ {
+ System.out.println(
+ "Jalview Version: " + codeVersion + codeInstallation);
+ }
+ }
+
private static void deleteBuildProperties()
{
applicationProperties.remove("LATEST_VERSION");
@@ -598,6 +607,24 @@ public class Cache
return def;
}
+ public static int getDefault(String property, int def)
+ {
+ String string = getProperty(property);
+ if (string != null)
+ {
+ try
+ {
+ def = Integer.parseInt(string);
+ } catch (NumberFormatException e)
+ {
+ System.out.println("Error parsing int property '" + property
+ + "' with value '" + string + "'");
+ }
+ }
+
+ return def;
+ }
+
/**
* These methods are used when checking if the saved preference is different
* to the default setting
@@ -621,15 +648,15 @@ public class Cache
* @param obj
* String value of property
*
- * @return String value of property
+ * @return previous value of property (or null)
*/
- public static String setProperty(String key, String obj)
+ public static Object setProperty(String key, String obj)
{
-
+ Object oldValue = null;
try
{
- applicationProperties.setProperty(key, obj);
- if (!propsAreReadOnly)
+ oldValue = applicationProperties.setProperty(key, obj);
+ if (propertiesFile != null && !propsAreReadOnly)
{
FileOutputStream out = new FileOutputStream(propertiesFile);
applicationProperties.store(out, "---JalviewX Properties File---");
@@ -640,7 +667,7 @@ public class Cache
System.out.println(
"Error setting property: " + key + " " + obj + "\n" + ex);
}
- return obj;
+ return oldValue;
}
/**
@@ -978,22 +1005,6 @@ public class Cache
return null;
}
- private static DasSourceRegistryI sourceRegistry = null;
-
- /**
- * initialise and ..
- *
- * @return instance of the das source registry
- */
- public static DasSourceRegistryI getDasSourceRegistry()
- {
- if (sourceRegistry == null)
- {
- sourceRegistry = new DasSourceRegistry();
- }
- return sourceRegistry;
- }
-
/**
* Set the specified value, or remove it if null or empty. Does not save the
* properties file.
@@ -1068,4 +1079,93 @@ public class Cache
}
}
}
+
+ /**
+ * 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: ");
+ sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST"));
+ sb.append("\n");
+ sb.append("Jalview Installation: ");
+ sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
+ sb.append("\n");
+ sb.append("Build Date: ");
+ sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+ sb.append("\n");
+ sb.append("Java version: ");
+ sb.append(System.getProperty("java.version"));
+ sb.append("\n");
+ 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");
+ // Not displayed in release version ( determined by possible version number
+ // regex 9[9.]*9[.-_a9]* )
+ if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
+ jalview.bin.Cache.getDefault("VERSION", "TEST")))
+ {
+ 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");
+ }
+
+ public static String getStackTraceString(Throwable t)
+ {
+ StringWriter sw = new StringWriter();
+ PrintWriter pw = new PrintWriter(sw);
+ t.printStackTrace(pw);
+ return sw.toString();
+ }
}