X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=40fccb0e61bd06e4d4100a6207544c4501a4c315;hb=b9bf3044b32b62771648842169f79ca8e7050c7f;hp=9dcc949ee84d8b111e81d0964b0496d31d9f4aca;hpb=8fa69554edf6aeb278b4a4afd8e2b60264fdccd8;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 9dcc949..40fccb0 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -20,17 +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.util.Platform; -import jalview.ws.sifts.SiftsSettings; - import java.awt.Color; import java.io.BufferedReader; import java.io.File; @@ -38,6 +27,9 @@ 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.net.URL; import java.text.DateFormat; import java.text.SimpleDateFormat; import java.util.Collections; @@ -47,12 +39,27 @@ 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.util.Platform; +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 @@ -312,6 +319,10 @@ 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); @@ -356,7 +367,7 @@ public class Cache InputStream fis; try { - fis = new java.net.URL(propertiesFile).openStream(); + fis = new URL(propertiesFile).openStream(); System.out.println( "Loading jalview properties from : " + propertiesFile); System.out.println( @@ -396,16 +407,13 @@ public class Cache } // LOAD THE AUTHORS FROM THE authors.props file - String authorDetails = (Platform.isJS() ? null - : "jar:".concat(Cache.class.getProtectionDomain() - .getCodeSource().getLocation().toString() - .concat("!/authors.props"))); + String authorDetails = resolveResourceURLFor("/authors.props"); try { if (authorDetails != null) { - java.net.URL localJarFileURL = new java.net.URL(authorDetails); + URL localJarFileURL = new URL(authorDetails); InputStream in = localJarFileURL.openStream(); applicationProperties.load(in); in.close(); @@ -417,51 +425,12 @@ public class Cache } if (authorDetails == null) { - applicationProperties.remove("AUTHORS"); - applicationProperties.remove("AUTHORFNAMES"); - applicationProperties.remove("YEAR"); + applicationProperties.remove("AUTHORS"); + applicationProperties.remove("AUTHORFNAMES"); + 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 - String buildDetails = (Platform.isJS() ? null - : "jar:".concat(Cache.class.getProtectionDomain() - .getCodeSource().getLocation().toString() - .concat("!/.build_properties"))); - if (buildDetails != null) - { - try - { - 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); - buildDetails = null; - } - } - if (buildDetails == null) - { - 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)); @@ -481,9 +450,6 @@ 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 @@ -491,8 +457,13 @@ 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"))) @@ -563,15 +534,83 @@ public class Cache } } - 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() { @@ -664,7 +703,7 @@ 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---"); @@ -1088,18 +1127,92 @@ public class Cache } } - /** - * Add a known domain that implements access-control-allow-origin:* bh 2018 - * - * @param defaultUniprotDomain - */ - public static void addJ2SDirectDatabaseCall(String domain) - { - - /** - * @j2sNative - * - * J2S.addDirectDatabaseCall(domain); - */ - } + /** + * 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(); + } }