X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=600d19c3f48bc14e5d820770c6d2578b6c76300d;hb=48040645e199f64d0bd396cc3a6137035a697737;hp=aa156bf243d8d35ae717d2e81967aeda621c81d0;hpb=1aa00eba1b3b8a8cfed866141d5f83bf56ee06e7;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index aa156bf..600d19c 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -20,16 +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.sifts.SiftsSettings; - import java.awt.Color; import java.io.BufferedReader; import java.io.File; @@ -37,6 +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; @@ -46,12 +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 @@ -114,7 +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
    • @@ -134,9 +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 @@ -171,8 +174,8 @@ import org.apache.log4j.SimpleLayout; * when shading by annotation
    • *
  • ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation * when shading by annotation
    • - *
  • www.jalview.org (http://www.jalview.org) a property enabling all HTTP - * requests to be redirected to a mirror of http://www.jalview.org
    • + *
  • www.jalview.org (https://www.jalview.org) a property enabling all HTTP + * requests to be redirected to a mirror of https://www.jalview.org
    • *
  • FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported * alignment figure to accommodate even the longest sequence ID or annotation * label.
    • @@ -226,12 +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 */ @@ -318,6 +315,10 @@ public class Cache // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller"); // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", // Level.INFO.toString()))); + // we shouldn't need to do this + org.apache.log4j.Logger.getRootLogger() + .setLevel(org.apache.log4j.Level.INFO); + jalview.bin.Cache.log.setLevel(Level.toLevel(Cache .getDefault("logs.Jalview.level", Level.INFO.toString()))); // laxis.addAppender(ap); @@ -414,41 +415,7 @@ 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)); @@ -465,12 +432,9 @@ public class Cache 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); - System.out - .println("Jalview Version: " + codeVersion + codeInstallation); - StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT)); StructureImportSettings @@ -478,8 +442,13 @@ 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"))) @@ -487,9 +456,12 @@ public class Cache class VersionChecker extends Thread { + @Override public void run() { + String buildPropertiesUrl = Cache.getAppbaseBuildProperties(); + String orgtimeout = System .getProperty("sun.net.client.defaultConnectTimeout"); if (orgtimeout == null) @@ -503,28 +475,19 @@ public class Cache { 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"); + java.net.URL url = new java.net.URL(buildPropertiesUrl); + BufferedReader in = new BufferedReader( new InputStreamReader(url.openStream())); - String line = null; - while ((line = in.readLine()) != null) - { - if (line.indexOf("jalview.version") == -1) - { - continue; - } - - line = line.substring(line.indexOf("value=") + 7); - line = line.substring(0, line.lastIndexOf("\"")); - remoteVersion = line; - break; - } + + Properties remoteBuildProperties = new Properties(); + remoteBuildProperties.load(in); + remoteVersion = remoteBuildProperties.getProperty("VERSION"); } catch (Exception ex) { - System.out.println( - "Non-fatal exception when checking version at www.jalview.org :"); + System.out + .println("Non-fatal exception when checking version at " + + buildPropertiesUrl + ":"); System.out.println(ex); remoteVersion = getProperty("VERSION"); } @@ -550,8 +513,6 @@ public class Cache } } - setProperty("VERSION", codeVersion); - // LOAD USERDEFINED COLOURS jalview.bin.Cache .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS")); @@ -559,6 +520,50 @@ 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"); @@ -649,7 +654,7 @@ public class Cache try { oldValue = applicationProperties.setProperty(key, obj); - if (!propsAreReadOnly) + if (propertiesFile != null && !propsAreReadOnly) { FileOutputStream out = new FileOutputStream(propertiesFile); applicationProperties.store(out, "---JalviewX Properties File---"); @@ -1072,4 +1077,152 @@ 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, "Getdown appbase: ", + System.getProperty("getdownappbase"), "\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(); + } + + /** + * Getdown appbase methods + */ + + private static final String releaseAppbase; + + private static String getdownAppbase; + + private static String getdownDistDir; + + 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"; + } + + // 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 = 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"; + } }