X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=09004f4cb2ebefb6204020e041953e9ffc6a61a5;hb=48e68905336d8ee17ee6b3903d80b36bac8c56cf;hp=fcc4f6db56e87c1365b12524291e20182fba2b94;hpb=13e054c5117102197ee0b22073603a6a38962865;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index fcc4f6d..09004f4 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -20,25 +20,13 @@ */ 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; import java.io.FileInputStream; 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; @@ -54,6 +42,18 @@ import org.apache.log4j.Level; import org.apache.log4j.Logger; import org.apache.log4j.SimpleLayout; +import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; +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 @@ -116,7 +116,6 @@ 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 +135,7 @@ 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 @@ -178,7 +175,7 @@ import org.apache.log4j.SimpleLayout; *
  • FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported * alignment figure to accommodate even the longest sequence ID or annotation * label.
    • - *
  • FIGURE_USERIDWIDTH Specifies the width to use for the left-hand column + *
  • FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true * will override this).
    • *
  • STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB @@ -211,8 +208,26 @@ import org.apache.log4j.SimpleLayout; * @author $author$ * @version $Revision$ */ -public class Cache +public class Cache implements ApplicationSingletonI { + + private Cache() + { + // private singleton + } + + /** + * In Java, this will be a static field instance, which will be + * application-specific; in JavaScript it will be an applet-specific instance + * tied to the applet's ThreadGroup. + * + * @return + */ + public static Cache getInstance() + { + return (Cache) ApplicationSingletonProvider.getInstance(Cache.class); + } + /** * property giving log4j level for CASTOR loggers */ @@ -228,19 +243,11 @@ 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 */ - public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System - .getProperty("user.home") + File.separatorChar - + ".sifts_downloads" + File.separatorChar; - + public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = Platform.getUserPath(".sifts_downloads/"); + private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2"; private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30"; @@ -248,8 +255,7 @@ public class Cache /** * Identifiers.org download settings */ - private static final String ID_ORG_FILE = System.getProperty("user.home") - + File.separatorChar + ".identifiers.org.ids.json"; + private static final String ID_ORG_FILE = Platform.getUserPath(".identifiers.org.ids.json"); /** * Allowed values are PDB or mmCIF @@ -275,7 +281,7 @@ public class Cache public static Logger log; /** Jalview Properties */ - public static Properties applicationProperties = new Properties() + private Properties applicationProperties = new Properties() { // override results in properties output in alphabetical order @Override @@ -288,7 +294,9 @@ public class Cache /** Default file is ~/.jalview_properties */ static String propertiesFile; - private static boolean propsAreReadOnly = false; + private static boolean propsAreReadOnly = Platform.isJS(); + + private final static String JS_PROPERTY_PREFIX = "jalview_"; public static void initLogger() { @@ -340,11 +348,18 @@ public class Cache */ public static void loadProperties(String propsFile) { + + getInstance().loadPropertiesImpl(propsFile); + + } + + private void loadPropertiesImpl(String propsFile) + { + propertiesFile = propsFile; - if (propsFile == null) + if (propsFile == null && !propsAreReadOnly) { - propertiesFile = System.getProperty("user.home") + File.separatorChar - + ".jalview_properties"; + propertiesFile = Platform.getUserPath(".jalview_properties"); } else { @@ -352,38 +367,45 @@ public class Cache 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; + System.out.println("Error reading properties file: " + ex); } - if (fis == null) - { - fis = new FileInputStream(propertiesFile); - } - 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", ""), @@ -397,60 +419,30 @@ public class Cache } // LOAD THE AUTHORS FROM THE authors.props file + String authorDetails = resolveResourceURLFor("/authors.props"); + try { - String authorDetails = "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); + authorDetails = null; + } + if (authorDetails == null) + { 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 - 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)); @@ -470,9 +462,6 @@ 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 @@ -480,14 +469,19 @@ 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"))) { - - class VersionChecker extends Thread + new Thread() { @Override public void run() @@ -535,10 +529,7 @@ public class Cache setProperty("LATEST_VERSION", remoteVersion); } - } - - VersionChecker vc = new VersionChecker(); - vc.start(); + }.start(); } else { @@ -552,16 +543,85 @@ 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); } - private static void deleteBuildProperties() + /** + * 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 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 void deleteBuildProperties() { applicationProperties.remove("LATEST_VERSION"); applicationProperties.remove("VERSION"); @@ -583,7 +643,13 @@ public class Cache */ public static String getProperty(String key) { - return applicationProperties.getProperty(key); + String prop = getInstance().applicationProperties.getProperty(key); + // if (prop == null && Platform.isJS()) + // { + // prop = applicationProperties.getProperty(Platform.getUniqueAppletID() + // + "_" + JS_PROPERTY_PREFIX + key); + // } + return prop; } /** @@ -602,22 +668,35 @@ public class Cache 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 @@ -629,33 +708,48 @@ public class Cache */ public static Object setProperty(String key, String obj) { - Object oldValue = null; - try - { - oldValue = applicationProperties.setProperty(key, obj); - if (!propsAreReadOnly) - { - FileOutputStream out = new FileOutputStream(propertiesFile); - applicationProperties.store(out, "---JalviewX Properties File---"); - out.close(); - } - } catch (Exception ex) - { - System.out.println( - "Error setting property: " + key + " " + obj + "\n" + ex); - } - return oldValue; + return getInstance().setPropertyImpl(key, obj, true); } /** - * remove the specified property from the jalview properties file + * Removes the specified property from the jalview properties file * - * @param string + * @param key */ - public static void removeProperty(String string) + public static void removeProperty(String key) { - applicationProperties.remove(string); - saveProperties(); + getInstance().removePropertyImpl(key, true); + } + + /** + * Removes the named property for the running application, without saving the + * properties file + * + * BH noting that ColourMenuHelper calls this. If the intent is to save, then + * simply chanet that call to removeProperty(key). + * + * @param key + */ + public static void removePropertyNoSave(String key) + { + + getInstance(). + + removePropertyImpl(key, false); + } + + /** + * Removes the named property, and optionally saves the current properties to + * file + * + * @param key + * @param andSave + */ + private void removePropertyImpl(String key, boolean andSave) + { + applicationProperties.remove(key); + if (andSave) + saveProperties(); } /** @@ -663,6 +757,15 @@ public class Cache */ public static void saveProperties() { + getInstance().savePropertiesImpl(); + } + + /** + * save the properties to the jalview properties path + */ + private void savePropertiesImpl() + + { if (!propsAreReadOnly) { try @@ -914,9 +1017,9 @@ public class Cache * @param property * @param colour */ - public static void setColourProperty(String property, Color colour) + public static void setColourPropertyNoSave(String property, Color colour) { - setProperty(property, jalview.util.Format.getHexString(colour)); + setPropertyNoSave(property, jalview.util.Format.getHexString(colour)); } /** @@ -944,11 +1047,16 @@ public class Cache public static Date getDateProperty(String propertyName) { String val = getProperty(propertyName); + if (val != null) { try { - return date_format.parse(val); + if ((val = val.trim()).indexOf(",") < 0 && val.indexOf("-") >= 0 && val.indexOf(" ") == val.lastIndexOf(" ")) { + val = val.replace(" ",", ").replace('-',' '); + } + Date date = date_format.parse(val); + return date; } catch (Exception ex) { System.err.println("Invalid or corrupt date in property '" @@ -982,22 +1090,6 @@ 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. @@ -1013,11 +1105,11 @@ public class Cache } if (value == null || value.trim().length() < 1) { - Cache.applicationProperties.remove(propName); + getInstance().applicationProperties.remove(propName); } else { - Cache.applicationProperties.setProperty(propName, value); + getInstance().applicationProperties.setProperty(propName, value); } } @@ -1067,9 +1159,124 @@ public class Cache } else { - applicationProperties + getInstance().applicationProperties .remove(UserDefinedColours.USER_DEFINED_COLOURS); } } } + + /** + * 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"); + } + + /** + * + * For AppletParams and Preferences ok_actionPerformed and + * startupFileTextfield_mouseClicked + * + * Sets a property value for the running application, without saving it to the + * properties file + * + * @param key + * @param obj + */ + public static void setPropertyNoSave(String key, String obj) + { + getInstance().setPropertyImpl(key, obj, false); + } + + /** + * Sets a property value, and optionally also saves the current properties to + * file + * + * @param key + * @param obj + * @param andSave + * @return + */ + private Object setPropertyImpl( + String key, String obj, boolean andSave) + { + Object oldValue = null; + try + { + oldValue = applicationProperties.setProperty(key, obj); + if (andSave && !propsAreReadOnly && propertiesFile != null) + { + FileOutputStream out = new FileOutputStream(propertiesFile); + applicationProperties.store(out, "---JalviewX Properties File---"); + out.close(); + } + } catch (Exception ex) + { + System.out.println( + "Error setting property: " + key + " " + obj + "\n" + ex); + } + return oldValue; + } + }