X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=4a83b35c81d95e0b2443caebabe91f514f7da569;hp=76fdb695563a70fd462064dc84b35f37157ecb02;hb=5d501d5230ad1c42f1e17a485cb86a04ba8b538a;hpb=e8ab1b32267d78c12e9ec2db2a65cf1b472fe1d0 diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 76fdb69..4a83b35 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -20,12 +20,6 @@ */ package jalview.bin; -import jalview.datamodel.PDBEntry; -import jalview.structure.StructureImportSettings; -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; @@ -33,20 +27,45 @@ 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.Authenticator; +import java.net.PasswordAuthentication; +import java.net.URL; import java.text.DateFormat; import java.text.SimpleDateFormat; +import java.util.Arrays; import java.util.Collections; import java.util.Date; import java.util.Enumeration; 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.Preferences; +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.ChannelProperties; +import jalview.util.ColorUtils; +import jalview.util.MessageManager; +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 @@ -70,7 +89,8 @@ import org.apache.log4j.SimpleLayout; *
  • SHOW_FULLSCREEN boolean
    • *
  • FONT_NAME java font name for alignment text display
    • *
  • FONT_SIZE size of displayed alignment text
    • - *
  • FONT_STYLE style of font displayed (sequence labels are always italic)
    • + *
  • FONT_STYLE style of font displayed (sequence labels are always + * italic)
    • *
  • GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')
    • *
  • LAST_DIRECTORY last directory for browsing alignment
    • *
  • USER_DEFINED_COLOURS list of user defined colour scheme files
    • @@ -108,7 +128,6 @@ 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
    • @@ -122,11 +141,13 @@ import org.apache.log4j.SimpleLayout; *
  • SORT_ALIGNMENT (No sort|Id|Pairwise Identity)
    • *
  • SEQUENCE_LINKS list of name|URL pairs for opening a url with * $SEQUENCE_ID$
    • + *
  • STORED_LINKS list of name|url pairs which user has entered but are not + * currently used + *
  • DEFAULT_LINK name of single url to be used when user double clicks a + * 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 @@ -179,6 +200,8 @@ import org.apache.log4j.SimpleLayout; *
  • STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure * display
    • *
  • CHIMERA_PATH specify full path to Chimera program (if non-standard)
    • + *
  • ID_ORG_HOSTURL location of jalview service providing identifiers.org urls + *
    • * * * Deprecated settings: @@ -214,25 +237,27 @@ 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 + .getProperty("user.home") + File.separatorChar + ".sifts_downloads" + File.separatorChar; private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2"; private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30"; - + + /** + * Identifiers.org download settings + */ + private static final String ID_ORG_FILE = System.getProperty("user.home") + + File.separatorChar + ".identifiers.org.ids.json"; + /** * Allowed values are PDB or mmCIF */ - private final static String DEFAULT_STRUCTURE_FORMAT = PDBEntry.Type.MMCIF + private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF .toString(); private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER @@ -244,14 +269,36 @@ public class Cache * even if the user changes their locale setting */ private static final DateFormat date_format = SimpleDateFormat - .getDateTimeInstance(SimpleDateFormat.LONG, - SimpleDateFormat.LONG, Locale.UK); + .getDateTimeInstance(SimpleDateFormat.MEDIUM, + SimpleDateFormat.MEDIUM, Locale.UK); /** * Initialises the Jalview Application Log */ public static Logger log; + // save the proxy properties set at startup + public final static String[] startupProxyProperties = { + System.getProperty("http.proxyHost"), + System.getProperty("http.proxyPort"), + System.getProperty("https.proxyHost"), + System.getProperty("https.proxyPort"), + System.getProperty("http.proxyUser"), + System.getProperty("http.proxyPassword"), + System.getProperty("https.proxyUser"), + System.getProperty("https.proxyPassword"), + System.getProperty("http.nonProxyHosts") }; + + public final static String PROXYTYPE_NONE = "none"; + + // "false" and "true" for backward compatibility + public final static String PROXYTYPE_SYSTEM = "false"; + + public final static String PROXYTYPE_CUSTOM = "true"; + + // in-memory only storage of proxy password, safer to use char array + public static char[] proxyAuthPassword = null; + /** Jalview Properties */ public static Properties applicationProperties = new Properties() { @@ -259,14 +306,19 @@ public class Cache @Override public synchronized Enumeration keys() { - return Collections.enumeration(new TreeSet(super.keySet())); + return Collections.enumeration(new TreeSet<>(super.keySet())); } }; + /* build Properties (not all saved to .jalview_properties) */ + public static Properties buildProperties = new Properties(); + /** 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() { @@ -288,8 +340,8 @@ public class Cache Logger lcastor = Logger.getLogger("org.exolab.castor"); jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview"); - laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level", - Level.INFO.toString()))); + laxis.setLevel(Level.toLevel( + Cache.getDefault("logs.Axis.Level", Level.INFO.toString()))); lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", Level.INFO.toString()))); lcastor = Logger.getLogger("org.exolab.castor.xml"); @@ -298,13 +350,18 @@ public class Cache // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller"); // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", // Level.INFO.toString()))); - jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault( - "logs.Jalview.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); // lcastor.addAppender(ap); // jalview.bin.Cache.log.addAppender(ap); // Tell the user that debug is enabled - jalview.bin.Cache.log.debug("Jalview Debugging Output Follows."); + jalview.bin.Cache.log.debug(ChannelProperties.getProperty("app_name") + + " Debugging Output Follows."); } catch (Exception ex) { System.err.println("Problems initializing the log4j system\n"); @@ -312,11 +369,14 @@ 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; - if (propsFile == null) + if (propsFile == null && !propsAreReadOnly) { propertiesFile = System.getProperty("user.home") + File.separatorChar + ".jalview_properties"; @@ -327,141 +387,156 @@ 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 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.load(fis); - - // remove any old build properties - - deleteBuildProperties(); - fis.close(); - } catch (Exception ex) - { - System.out.println("Error reading properties file: " + ex); } + /* TO BE REPLACED WITH PROXY_TYPE SETTINGS if (getDefault("USE_PROXY", false)) { - String proxyServer = getDefault("PROXY_SERVER", ""), proxyPort = getDefault( - "PROXY_PORT", "8080"); - - System.out.println("Using proxyServer: " + proxyServer - + " proxyPort: " + proxyPort); + String proxyServer = getDefault("PROXY_SERVER", ""), + proxyPort = getDefault("PROXY_PORT", "8080"); + } + */ - System.setProperty("http.proxyHost", proxyServer); - System.setProperty("http.proxyPort", proxyPort); + // PROXY TYPE settings (now three options "none", "false", "true", but using + // backward compatible strings) + String proxyType = getDefault("USE_PROXY", PROXYTYPE_SYSTEM); + // default to upgrading old settings + switch (proxyType) + { + case PROXYTYPE_NONE: + clearProxyProperties(); + break; + case PROXYTYPE_SYSTEM: // use system settings + resetProxyProperties(); + break; + case PROXYTYPE_CUSTOM: // use specified proxy settings + String httpHost = getDefault("PROXY_SERVER", ""); + String httpPort = getDefault("PROXY_PORT", "8080"); + String httpsHost = getDefault("PROXY_SERVER_HTTPS", httpHost); + String httpsPort = getDefault("PROXY_PORT_HTTPS", httpPort); + String httpUser = getDefault("PROXY_AUTH_USER", null); + // https.proxyUser and https.proxyPassword are not able to be + // independently set in Preferences yet (or http.nonProxyHosts) + String httpsUser = getDefault("PROXY_AUTH_USER_HTTPS", httpUser); + setProxyProperties(httpHost, httpPort, httpsHost, httpsPort, httpUser, + proxyAuthPassword, httpsUser, proxyAuthPassword, "localhost"); + break; + default: + String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): " + + proxyType; + Cache.warn(message); } // 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)); - SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault( - "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR)); + SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache + .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR)); - SiftsSettings.setFailSafePIDThreshold(jalview.bin.Cache.getDefault( - "sifts_fail_safe_pid_threshold", - DEFAULT_FAIL_SAFE_PID_THRESHOLD)); + SiftsSettings.setFailSafePIDThreshold( + jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold", + DEFAULT_FAIL_SAFE_PID_THRESHOLD)); - SiftsSettings.setCacheThresholdInDays(jalview.bin.Cache.getDefault( - "sifts_cache_threshold_in_days", - DEFAULT_CACHE_THRESHOLD_IN_DAYS)); + SiftsSettings.setCacheThresholdInDays( + jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days", + DEFAULT_CACHE_THRESHOLD_IN_DAYS)); - System.out - .println("Jalview Version: " + codeVersion + codeInstallation); + IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL", + "http://www.jalview.org/services/identifiers")); + IdOrgSettings.setDownloadLocation(ID_ORG_FILE); StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache - .getDefault( - "DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT)); + .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT)); StructureImportSettings - .setDefaultPDBFileParser(jalview.bin.Cache.getDefault( - "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER)); - // jnlpVersion will be null if we're using InstallAnywhere + .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER); + // StructureImportSettings + // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault( + // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER)); + + 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) + + if (jnlpVersion == null && getDefault("VERSION_CHECK", true) && (System.getProperty("java.awt.headless") == null || System .getProperty("java.awt.headless").equals("false"))) { class VersionChecker extends Thread { + @Override public void run() { + String remoteBuildPropertiesUrl = Cache + .getAppbaseBuildProperties(); + String orgtimeout = System .getProperty("sun.net.client.defaultConnectTimeout"); if (orgtimeout == null) @@ -475,28 +550,19 @@ 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"); - BufferedReader in = new BufferedReader(new InputStreamReader( - url.openStream())); - String line = null; - while ((line = in.readLine()) != null) - { - if (line.indexOf("jalview.version") == -1) - { - continue; - } + java.net.URL url = new java.net.URL(remoteBuildPropertiesUrl); - line = line.substring(line.indexOf("value=") + 7); - line = line.substring(0, line.lastIndexOf("\"")); - remoteVersion = line; - break; - } + BufferedReader in = new BufferedReader( + new InputStreamReader(url.openStream())); + + 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 :"); + .println("Non-fatal exception when checking version at " + + remoteBuildPropertiesUrl + ":"); System.out.println(ex); remoteVersion = getProperty("VERSION"); } @@ -522,15 +588,99 @@ public class Cache } } - setProperty("VERSION", codeVersion); - // LOAD USERDEFINED COLOURS - jalview.gui.UserDefinedColours - .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(); + buildProperties.load(in); + in.close(); + if (buildProperties.getProperty("BUILD_DATE", null) != null) + { + applicationProperties.put("BUILD_DATE", + buildProperties.getProperty("BUILD_DATE")); + } + if (buildProperties.getProperty("INSTALLATION", null) != null) + { + applicationProperties.put("INSTALLATION", + buildProperties.getProperty("INSTALLATION")); + } + if (buildProperties.getProperty("VERSION", null) != null) + { + applicationProperties.put("VERSION", + buildProperties.getProperty("VERSION")); + } + } 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(ChannelProperties.getProperty("app_name") + + " Version: " + codeVersion + codeInstallation); + } + } + private static void deleteBuildProperties() { applicationProperties.remove("LATEST_VERSION"); @@ -553,7 +703,13 @@ public class Cache */ 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; } /** @@ -572,22 +728,35 @@ 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 @@ -595,15 +764,15 @@ 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---"); @@ -611,10 +780,10 @@ public class Cache } } catch (Exception ex) { - System.out.println("Error setting property: " + key + " " + obj - + "\n" + ex); + System.out.println( + "Error setting property: " + key + " " + obj + "\n" + ex); } - return obj; + return oldValue; } /** @@ -663,19 +832,20 @@ public class Cache { try { - if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass( - "uk.ac.vamsas.client.VorbaId") != null) + if (jalview.jbgui.GDesktop.class.getClassLoader() + .loadClass("uk.ac.vamsas.client.VorbaId") != null) { - jalview.bin.Cache.log - .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)"); + jalview.bin.Cache.log.debug( + "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)"); vamsasJarsArePresent = 1; Logger lvclient = Logger.getLogger("uk.ac.vamsas"); - lvclient.setLevel(Level.toLevel(Cache.getDefault( - "logs.Vamsas.Level", Level.INFO.toString()))); + lvclient.setLevel(Level.toLevel(Cache + .getDefault("logs.Vamsas.Level", Level.INFO.toString()))); lvclient.addAppender(log.getAppender("JalviewLogger")); // Tell the user that debug is enabled - lvclient.debug("Jalview Vamsas Client Debugging Output Follows."); + lvclient.debug(ChannelProperties.getProperty("app_name") + + " Vamsas Client Debugging Output Follows."); } } catch (Exception e) { @@ -702,19 +872,20 @@ public class Cache { try { - if (Cache.class.getClassLoader().loadClass( - "groovy.lang.GroovyObject") != null) + if (Cache.class.getClassLoader() + .loadClass("groovy.lang.GroovyObject") != null) { - jalview.bin.Cache.log - .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)"); + jalview.bin.Cache.log.debug( + "Found Groovy (groovy.lang.GroovyObject can be loaded)"); groovyJarsArePresent = 1; Logger lgclient = Logger.getLogger("groovy"); - lgclient.setLevel(Level.toLevel(Cache.getDefault( - "logs.Groovy.Level", Level.INFO.toString()))); + lgclient.setLevel(Level.toLevel(Cache + .getDefault("logs.Groovy.Level", Level.INFO.toString()))); lgclient.addAppender(log.getAppender("JalviewLogger")); // Tell the user that debug is enabled - lgclient.debug("Jalview Groovy Client Debugging Output Follows."); + lgclient.debug(ChannelProperties.getProperty("app_name") + + " Groovy Client Debugging Output Follows."); } } catch (Error e) { @@ -751,15 +922,14 @@ public class Cache // try to get the tracker class try { - jgoogleanalyticstracker = Cache.class - .getClassLoader() - .loadClass( - "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker"); - trackerfocus = Cache.class.getClassLoader().loadClass( - "com.boxysystems.jgoogleanalytics.FocusPoint"); + jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass( + "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker"); + trackerfocus = Cache.class.getClassLoader() + .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint"); } catch (Exception e) { - log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled."); + log.debug( + "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled."); tracker = null; jgoogleanalyticstracker = null; trackerfocus = null; @@ -773,22 +943,22 @@ public class Cache try { // Google analytics tracking code for Library Finder - tracker = jgoogleanalyticstracker.getConstructor( - new Class[] { String.class, String.class, String.class }) - .newInstance( - new Object[] { - "Jalview Desktop", - (vrs = jalview.bin.Cache.getProperty("VERSION") - + "_" - + jalview.bin.Cache.getDefault( - "BUILD_DATE", "unknown")), - "UA-9060947-1" }); - jgoogleanalyticstracker.getMethod("trackAsynchronously", - new Class[] { trackerfocus }).invoke( - tracker, - new Object[] { trackerfocus.getConstructor( - new Class[] { String.class }).newInstance( - new Object[] { "Application Started." }) }); + tracker = jgoogleanalyticstracker + .getConstructor(new Class[] + { String.class, String.class, String.class }) + .newInstance(new Object[] + { ChannelProperties.getProperty("app_name") + " Desktop", + (vrs = jalview.bin.Cache.getProperty("VERSION") + "_" + + jalview.bin.Cache.getDefault("BUILD_DATE", + "unknown")), + "UA-9060947-1" }); + jgoogleanalyticstracker + .getMethod("trackAsynchronously", new Class[] + { trackerfocus }) + .invoke(tracker, new Object[] + { trackerfocus.getConstructor(new Class[] { String.class }) + .newInstance(new Object[] + { "Application Started." }) }); } catch (RuntimeException e) { re = e; @@ -805,42 +975,45 @@ public class Cache { if (re != null) { - log.debug("Caught runtime exception in googletracker init:", re); + log.debug("Caught runtime exception in googletracker init:", + re); } if (ex != null) { log.warn( "Failed to initialise GoogleTracker for Jalview Desktop with version " - + vrs, ex); + + vrs, + ex); } if (err != null) { log.error( "Whilst initing GoogleTracker for Jalview Desktop version " - + vrs, err); + + vrs, + err); } } else { if (re != null) { - System.err - .println("Debug: Caught runtime exception in googletracker init:" + System.err.println( + "Debug: Caught runtime exception in googletracker init:" + vrs); re.printStackTrace(); } if (ex != null) { - System.err - .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version " + System.err.println( + "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version " + vrs); ex.printStackTrace(); } if (err != null) { - System.err - .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version " + System.err.println( + "ERROR: Whilst initing GoogleTracker for Jalview Desktop version " + vrs); err.printStackTrace(); } @@ -867,19 +1040,11 @@ public class Cache { return defcolour; } - Color col = jalview.schemes.ColourSchemeProperty - .getAWTColorFromName(colprop); + Color col = ColorUtils.parseColourString(colprop); if (col == null) { - try - { - col = new jalview.schemes.UserColourScheme(colprop).findColour('A'); - } catch (Exception ex) - { - log.warn("Couldn't parse '" + colprop + "' as a colour for " - + property); - col = null; - } + log.warn("Couldn't parse '" + colprop + "' as a colour for " + + property); } return (col == null) ? defcolour : col; } @@ -894,7 +1059,7 @@ public class Cache { setProperty(property, jalview.util.Format.getHexString(colour)); } - + /** * Stores a formatted date in a jalview property, using a fixed locale. * @@ -958,42 +1123,593 @@ public class Cache return null; } - private static DasSourceRegistryI sourceRegistry = null; + /** + * Set the specified value, or remove it if null or empty. Does not save the + * properties file. + * + * @param propName + * @param value + */ + public static void setOrRemove(String propName, String value) + { + if (propName == null) + { + return; + } + if (value == null || value.trim().length() < 1) + { + Cache.applicationProperties.remove(propName); + } + else + { + Cache.applicationProperties.setProperty(propName, value); + } + } /** - * initialise and .. + * Loads in user colour schemes from files. * - * @return instance of the das source registry + * @param files + * a '|'-delimited list of file paths */ - public static DasSourceRegistryI getDasSourceRegistry() + public static void initUserColourSchemes(String files) { - if (sourceRegistry == null) + if (files == null || files.length() == 0) + { + return; + } + + // In case colours can't be loaded, we'll remove them + // from the default list here. + StringBuffer coloursFound = new StringBuffer(); + StringTokenizer st = new StringTokenizer(files, "|"); + while (st.hasMoreElements()) + { + String file = st.nextToken(); + try + { + UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file); + if (ucs != null) + { + if (coloursFound.length() > 0) + { + coloursFound.append("|"); + } + coloursFound.append(file); + ColourSchemes.getInstance().registerColourScheme(ucs); + } + } catch (Exception ex) + { + System.out.println("Error loading User ColourFile\n" + ex); + } + } + if (!files.equals(coloursFound.toString())) { - sourceRegistry = new DasSourceRegistry(); + if (coloursFound.toString().length() > 1) + { + setProperty(UserDefinedColours.USER_DEFINED_COLOURS, + coloursFound.toString()); + } + else + { + applicationProperties + .remove(UserDefinedColours.USER_DEFINED_COLOURS); + } } - return sourceRegistry; } /** - * Set the specified value, or remove it if null or empty. Does not save the - * properties file. + * Initial logging information helper for various versions output * - * @param propName + * @param prefix * @param value + * @param defaultValue */ - public static void setOrRemove(String propName, String value) + private static void appendIfNotNull(StringBuilder sb, String prefix, + String value, String suffix, String defaultValue) { - if (propName == null) + if (value == null && defaultValue == null) { return; } - if (value == null || value.trim().length() < 1) + 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(ChannelProperties.getProperty("app_name")) + .append(" Version: "); + sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST")); + sb.append("\n"); + sb.append(ChannelProperties.getProperty("app_name")) + .append(" 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"))) { - Cache.applicationProperties.remove(propName); + 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(); + } + + // proxy properties methods + public static void clearProxyProperties() + { + setProxyProperties(null, null, null, null, null, null, null, null, + null); + } + + public static void resetProxyProperties() + { + setProxyProperties(startupProxyProperties[0], startupProxyProperties[1], + startupProxyProperties[2], startupProxyProperties[3], + startupProxyProperties[4], + startupProxyProperties[5] == null ? null + : startupProxyProperties[5].toCharArray(), + startupProxyProperties[6], + startupProxyProperties[7] == null ? null + : startupProxyProperties[7].toCharArray(), + startupProxyProperties[8]); + StringBuilder sb = new StringBuilder(); + sb.append("Setting proxy properties to: http.proxyHost=") + .append(startupProxyProperties[0]).append(", http.proxyPort=") + .append(startupProxyProperties[1]) + .append(startupProxyProperties[4] != null + && !startupProxyProperties[4].isEmpty() + ? " [" + startupProxyProperties[4] + "]" + : "") + .append(", https.proxyHost=").append(startupProxyProperties[2]) + .append(", https.proxyPort=").append(startupProxyProperties[3]) + .append(startupProxyProperties[6] != null + && !startupProxyProperties[6].isEmpty() + ? " [" + startupProxyProperties[6] + "]" + : ""); + + Cache.debug(sb.toString()); + } + + public static void setProxyPropertiesFromPreferences() + { + setProxyPropertiesFromPreferences(Cache.PROXYTYPE_SYSTEM); + } + + public static void setProxyPropertiesFromPreferences( + String previousProxyType) + { + String proxyType = Cache.getDefault("USE_PROXY", + Cache.PROXYTYPE_SYSTEM); + if (previousProxyType != null + && !proxyType.equals(Cache.PROXYTYPE_CUSTOM) // always apply + // customProxy + && proxyType.equals(previousProxyType)) + { + // no change + return; + } + switch (proxyType) + { + case Cache.PROXYTYPE_NONE: + if (!previousProxyType.equals(proxyType)) + { + Cache.log.info("Setting no proxy settings"); + Cache.setProxyProperties(null, null, null, null, null, null, null, + null, null); + } + break; + case Cache.PROXYTYPE_CUSTOM: + // always re-set a custom proxy -- it might have changed, particularly + // password + Cache.log.info("Setting custom proxy settings"); + boolean proxyAuthSet = Cache.getDefault("PROXY_AUTH", false); + Cache.setProxyProperties(Cache.getDefault("PROXY_SERVER", null), + Cache.getDefault("PROXY_PORT", null), + Cache.getDefault("PROXY_SERVER_HTTPS", null), + Cache.getDefault("PROXY_PORT_HTTPS", null), + proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "") + : null, + proxyAuthSet ? Cache.proxyAuthPassword : null, + proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "") + : null, + proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost"); + break; + default: // system proxy settings by default + Cache.log.info("Setting system proxy settings"); + Cache.resetProxyProperties(); + } + } + + public static void setProxyProperties(String httpHost, String httpPort, + String httpsHost, String httpsPort, String httpUser, + char[] httpPassword, String httpsUser, char[] httpsPassword, + String nonProxyHosts) + { + setOrClearSystemProperty("http.proxyHost", httpHost); + setOrClearSystemProperty("http.proxyPort", httpPort); + setOrClearSystemProperty("https.proxyHost", httpsHost); + setOrClearSystemProperty("https.proxyPort", httpsPort); + setOrClearSystemProperty("http.proxyUser", httpUser); + setOrClearSystemProperty("https.proxyUser", httpsUser); + // note: passwords for http.proxyPassword and https.proxyPassword are sent + // via the Authenticator, properties do not need to be set + + // are we using a custom proxy (password prompt might be required)? + boolean customProxySet = getDefault("USE_PROXY", PROXYTYPE_SYSTEM) + .equals(PROXYTYPE_CUSTOM); + + /* + * A bug in Java means the AuthCache does not get reset, so once it has working credentials, + * it never asks for more, so changing the Authenticator has no effect (as getPasswordAuthentication() + * is not re-called). + * This could lead to password leak to a hostile proxy server, so I'm putting in a hack to clear + * the AuthCache. + * see https://www.generacodice.com/en/articolo/154918/Reset-the-Authenticator-credentials + * ... + * Turns out this is only accessible in Java 8, and not in Java 9 onwards, so commenting out + */ + /* + try + { + sun.net.www.protocol.http.AuthCacheValue + .setAuthCache(new sun.net.www.protocol.http.AuthCacheImpl()); + } catch (Throwable t) + { + Cache.error(t.getMessage()); + Cache.debug(getStackTraceString(t)); + } + */ + + if (httpUser != null || httpsUser != null) + { + try + { + char[] displayHttpPw = new char[httpPassword == null ? 0 + : httpPassword.length]; + Arrays.fill(displayHttpPw, '*'); + Cache.debug("CACHE Proxy: setting new Authenticator with httpUser='" + + httpUser + "' httpPassword='" + displayHttpPw + "'"); + if (!Platform.isJS()) + /* * + * java.net.Authenticator not implemented in SwingJS yet + * + * @j2sIgnore + * + */ + { + Authenticator.setDefault(new Authenticator() + { + @Override + protected PasswordAuthentication getPasswordAuthentication() + { + if (getRequestorType() == RequestorType.PROXY) + { + String protocol = getRequestingProtocol(); + boolean needProxyPasswordSet = false; + if (customProxySet && + // we have a username but no password for the scheme being + // requested + (protocol.equalsIgnoreCase("http") + && (httpUser != null && httpUser.length() > 0 + && (httpPassword == null + || httpPassword.length == 0))) + || (protocol.equalsIgnoreCase("https") + && (httpsUser != null + && httpsUser.length() > 0 + && (httpsPassword == null + || httpsPassword.length == 0)))) + { + // open Preferences -> Connections + String message = MessageManager + .getString("label.proxy_password_required"); + Preferences.openPreferences(Preferences.CONNECTIONS_TAB, + message); + Preferences.getInstance() + .proxyAuthPasswordCheckHighlight(true, true); + } + else + { + try + { + if (protocol.equalsIgnoreCase("http") + && getRequestingHost() + .equalsIgnoreCase(httpHost) + && getRequestingPort() == Integer + .valueOf(httpPort)) + { + Cache.debug( + "AUTHENTICATOR returning PasswordAuthentication(\"" + + httpUser + "\", '" + + new String(displayHttpPw) + "')"); + return new PasswordAuthentication(httpUser, + httpPassword); + } + if (protocol.equalsIgnoreCase("https") + && getRequestingHost() + .equalsIgnoreCase(httpsHost) + && getRequestingPort() == Integer + .valueOf(httpsPort)) + { + char[] displayHttpsPw = new char[httpPassword.length]; + Arrays.fill(displayHttpsPw, '*'); + Cache.debug( + "AUTHENTICATOR returning PasswordAuthentication(\"" + + httpsUser + "\", '" + displayHttpsPw + + "'"); + return new PasswordAuthentication(httpsUser, + httpsPassword); + } + } catch (NumberFormatException e) + { + Cache.error("Problem with proxy port values [http:" + + httpPort + ", https:" + httpsPort + "]"); + } + Cache.debug( + "AUTHENTICATOR after trying to get PasswordAuthentication"); + } + } + // non proxy request + Cache.debug("AUTHENTICATOR returning null"); + return null; + } + }); + } // end of j2sIgnore for java.net.Authenticator + + // required to re-enable basic authentication (should be okay for a + // local proxy) + Cache.debug( + "AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\""); + System.setProperty("jdk.http.auth.tunneling.disabledSchemes", ""); + } catch (SecurityException e) + { + Cache.error("Could not set default Authenticator"); + Cache.debug(getStackTraceString(e)); + } } else { - Cache.applicationProperties.setProperty(propName, value); + // reset the Authenticator to protect http.proxyUser and + // http.proxyPassword Just In Case + /* as noted above, due to bug in java this doesn't work if the sun.net.www.protocol.http.AuthCache + * has working credentials. No workaround for Java 11. + */ + if (!Platform.isJS()) + /* * + * java.net.Authenticator not implemented in SwingJS yet + * + * @j2sIgnore + * + */ + { + Cache.debug("AUTHENTICATOR setting default Authenticator to null"); + Authenticator.setDefault(null); + } + } + + // nonProxyHosts not currently configurable in Preferences + Cache.debug("AUTHENTICATOR setting property 'http.nonProxyHosts' to \"" + + nonProxyHosts + "\""); + setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts); + } + + public static void setOrClearSystemProperty(String key, char[] value) + { + setOrClearSystemProperty(key, + (value == null) ? null : new String(value)); + } + + public static void setOrClearSystemProperty(String key, String value) + { + if (key == null) + { + return; + } + if (value == null) + { + System.clearProperty(key); + } + else + { + System.setProperty(key, value); + } + } + + public final static int TRACE = 10; + + public final static int DEBUG = 20; + + public final static int INFO = 30; + + public final static int WARN = 40; + + public final static int ERROR = 50; + + public static boolean println(int level, String message) + { + if (Cache.log == null) + { + if (level >= WARN) + System.err.println(message); + else if (level >= INFO) + System.out.println(message); + // not printing debug or trace messages + return false; + } + if (level >= ERROR) + { + Cache.log.error(message); + } + else if (level >= WARN) + { + Cache.log.warn(message); } + else if (level >= INFO) + { + Cache.log.info(message); + } + else if (level >= DEBUG) + { + Cache.log.debug(message); + } + else + { + Cache.log.trace(message); + } + return true; + } + + public static void trace(String message) + { + println(TRACE, message); + } + + public static void debug(String message) + { + println(DEBUG, message); + } + + public static void info(String message) + { + println(INFO, message); + } + + public static void warn(String message) + { + println(WARN, message); + } + + public static void error(String message) + { + println(ERROR, message); + } + + /** + * Getdown appbase methods + */ + + private static final String releaseAppbase; + + private static String getdownAppbase; + + private static String getdownDistDir; + + static + { + if (!Platform.isJS()) + { + 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"; + } + else + { + // this value currenly made up, can be changed to URL that will be + // "https://www.jalview.org/jalview-js/swingjs/j2s/build_properties" + releaseAppbase = "https://www.jalview.org/jalview-js"; + getdownAppbase = releaseAppbase; + getdownDistDir = "/swingjs/j2s"; + } + } + + // 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 = buildProperties.getProperty("GETDOWNAPPBASE"); + distDir = buildProperties.getProperty("GETDOWNAPPDISTDIR"); + } + 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"; } }