// // Getdown - application installer, patcher and launcher // Copyright (C) 2004-2018 Getdown authors // https://github.com/threerings/getdown/blob/master/LICENSE package com.threerings.getdown.data; import java.io.*; import java.lang.reflect.Method; import java.net.MalformedURLException; import java.net.Proxy; import java.net.URI; import java.net.URISyntaxException; import java.net.URL; import java.net.URLClassLoader; import java.net.URLConnection; import java.net.URLDecoder; import java.net.URLEncoder; import java.nio.channels.FileChannel; import java.nio.channels.FileLock; import java.nio.channels.OverlappingFileLockException; import java.security.*; import java.security.cert.Certificate; import java.util.*; import java.util.concurrent.*; import java.util.regex.Matcher; import java.util.regex.Pattern; import java.util.zip.GZIPInputStream; import jalview.bin.HiDPISetting; import jalview.bin.MemorySetting; //import com.install4j.api.launcher.Variables; import com.threerings.getdown.util.*; // avoid ambiguity with java.util.Base64 which we can't use as it's 1.8+ import com.threerings.getdown.util.Base64; import com.threerings.getdown.data.EnvConfig; import com.threerings.getdown.data.EnvConfig.Note; import static com.threerings.getdown.Log.log; import static java.nio.charset.StandardCharsets.UTF_8; /** * Parses and provide access to the information contained in the getdown.txt * configuration file. */ public class Application { /** The name of our configuration file. */ public static final String CONFIG_FILE = "getdown.txt"; /** Dir where a backup config file might reside */ public static final String BACKUP_CONFIG_DIR = "install"; /** The name of our target version file. */ public static final String VERSION_FILE = "version.txt"; /** System properties that are prefixed with this string will be passed through to our * application (minus this prefix). */ public static final String PROP_PASSTHROUGH_PREFIX = "app."; /** Suffix used for control file signatures. */ public static final String SIGNATURE_SUFFIX = ".sig"; /** A special classname that means 'use -jar code.jar' instead of a classname. */ public static final String MANIFEST_CLASS = "manifest"; /** Used to communicate information about the UI displayed when updating the application. */ public static final class UpdateInterface { /** * The major steps involved in updating, along with some arbitrary percentages * assigned to them, to mark global progress. */ public enum Step { //UPDATE_JAVA(10), UPDATE_JAVA(20), //VERIFY_METADATA(15, 65, 95), VERIFY_METADATA(15, 45, 90), DOWNLOAD(60), PATCH(60), //VERIFY_RESOURCES(70, 97), VERIFY_RESOURCES(40, 90), //REDOWNLOAD_RESOURCES(90), REDOWNLOAD_RESOURCES(80), //UNPACK(98), UNPACK(95), //LAUNCH(99); LAUNCH(100); /** What is the final percent value for this step? */ public final List defaultPercents; /** Enum constructor. */ Step (int... percents) { this.defaultPercents = intsToList(percents); } } /** The human readable name of this application. */ public final String name; /** A background color, just in case. */ public final int background; /** Background image specifiers for `RotatingBackgrounds`. */ public final List rotatingBackgrounds; /** The error background image for `RotatingBackgrounds`. */ public final String errorBackground; /** The paths (relative to the appdir) of images for the window icon. */ public final List iconImages; /** The path (relative to the appdir) to a single background image to appear first. */ public final String instantBackgroundImage; /** The path (relative to the appdir) to a single background image. */ public final String backgroundImage; /** The path (relative to the appdir) to the progress bar image. */ public final String progressImage; /** The dimensions of the progress bar. */ public final Rectangle progress; /** The color of the progress text. */ public final int progressText; /** The color of the progress bar. */ public final int progressBar; /** The dimensions of the status display. */ public final Rectangle status; /** The color of the status text. */ public final int statusText; /** The color of the text shadow. */ public final int textShadow; /** Where to point the user for help with install errors. */ public final String installError; /** The dimensions of the patch notes button. */ public final Rectangle patchNotes; /** The patch notes URL. */ public final String patchNotesUrl; /** Whether window decorations are hidden for the UI. */ public final boolean hideDecorations; /** Whether progress text should be hidden or not. */ public final boolean hideProgressText; /** Whether the splash screen should update non-asynchronously before being shown. */ public final boolean progressSync; /** Whether the splash screen should update non-asynchronously after being shown. */ public final boolean progressSyncAfterShown; /** Whether the splash screen should retain focus. */ public final boolean keepOnTop; /** Whether to display the appbase. */ public final boolean displayAppbase; /** Whether to display the version. */ public final boolean displayVersion; /** The minimum number of seconds to display the GUI. This is to prevent the GUI from * flashing up on the screen and immediately disappearing, which can be confusing to the * user. */ public final int minShowSeconds; /** The global percentages for each step. A step may have more than one, and * the lowest reasonable one is used if a step is revisited. */ public final Map> stepPercentages; /** Generates a string representation of this instance. */ @Override public String toString () { return "[name=" + name + ", bg=" + background + ", bg=" + backgroundImage + ", instant_bg=" + instantBackgroundImage + ", pi=" + progressImage + ", prect=" + progress + ", pt=" + progressText + ", pb=" + progressBar + ", srect=" + status + ", st=" + statusText + ", shadow=" + textShadow + ", err=" + installError + ", nrect=" + patchNotes + ", notes=" + patchNotesUrl + ", stepPercentages=" + stepPercentages + ", hideProgressText=" + hideProgressText + ", keepOnTop=" + keepOnTop + ", progressSync=" + progressSync + ", progressSyncAfterShown=" + progressSyncAfterShown + ", minShow=" + minShowSeconds + ", displayAppbase=" + displayAppbase + ", displayVersion=" + displayVersion + "]"; } public UpdateInterface (Config config) { this.name = config.getString("ui.name"); this.progress = config.getRect("ui.progress", new Rectangle(5, 5, 300, 15)); this.progressText = config.getColor("ui.progress_text", Color.BLACK); this.hideProgressText = config.getBoolean("ui.hide_progress_text"); this.progressSync = config.getBoolean("ui.progress_sync_before_shown"); this.progressSyncAfterShown = config.getBoolean("ui.progress_sync_after_shown"); this.keepOnTop = config.getBoolean("ui.keep_on_top"); this.displayAppbase = config.getBoolean("ui.display_appbase"); this.displayVersion = config.getBoolean("ui.display_version"); this.minShowSeconds = config.getInt("ui.min_show_seconds", 5); this.progressBar = config.getColor("ui.progress_bar", 0x6699CC); this.status = config.getRect("ui.status", new Rectangle(5, 25, 500, 100)); this.statusText = config.getColor("ui.status_text", Color.BLACK); this.textShadow = config.getColor("ui.text_shadow", Color.CLEAR); this.hideDecorations = config.getBoolean("ui.hide_decorations"); this.backgroundImage = config.getString("ui.background_image"); this.instantBackgroundImage = config.getString("ui.instant_background_image"); // default to black or white bg color, depending on the brightness of the progressText int defaultBackground = (0.5f < Color.brightness(this.progressText)) ? Color.BLACK : Color.WHITE; this.background = config.getColor("ui.background", defaultBackground); this.progressImage = config.getString("ui.progress_image"); this.rotatingBackgrounds = stringsToList( config.getMultiValue("ui.rotating_background")); this.iconImages = stringsToList(config.getMultiValue("ui.icon")); this.errorBackground = config.getString("ui.error_background"); // On an installation error, where do we point the user. String installError = config.getUrl("ui.install_error", null); this.installError = (installError == null) ? "m.default_install_error" : MessageUtil.taint(installError); // the patch notes bits this.patchNotes = config.getRect("ui.patch_notes", new Rectangle(5, 50, 112, 26)); this.patchNotesUrl = config.getUrl("ui.patch_notes_url", null); // step progress percentage (defaults and then customized values) EnumMap> stepPercentages = new EnumMap<>(Step.class); for (Step step : Step.values()) { stepPercentages.put(step, step.defaultPercents); } for (UpdateInterface.Step step : UpdateInterface.Step.values()) { String spec = config.getString("ui.percents." + step.name()); if (spec != null) { try { stepPercentages.put(step, intsToList(StringUtil.parseIntArray(spec))); } catch (Exception e) { log.warning("Failed to parse percentages for " + step + ": " + spec); } } } this.stepPercentages = Collections.unmodifiableMap(stepPercentages); } } /** * Used by {@link #verifyMetadata} to communicate status in circumstances where it needs to * take network actions. */ public static interface StatusDisplay { /** Requests that the specified status message be displayed. */ public void updateStatus (String message); } /** * Contains metadata for an auxiliary resource group. */ public static class AuxGroup { public final String name; public final List codes; public final List rsrcs; public AuxGroup (String name, List codes, List rsrcs) { this.name = name; this.codes = Collections.unmodifiableList(codes); this.rsrcs = Collections.unmodifiableList(rsrcs); } } /** The proxy that should be used to do HTTP downloads. This must be configured prior to using * the application instance. Yes this is a public mutable field, no I'm not going to create a * getter and setter just to pretend like that's not the case. */ public Proxy proxy = Proxy.NO_PROXY; /** * Creates an application instance which records the location of the getdown.txt * configuration file from the supplied application directory. * */ public Application (EnvConfig envc) { _envc = envc; _config = getLocalPath(envc.appDir, CONFIG_FILE); _backupConfig = getLocalPath(envc.appDir, BACKUP_CONFIG_DIR+File.separator+CONFIG_FILE); } /** * Returns the configured application directory. */ public File getAppDir () { return _envc.appDir; } /** * Returns whether the application should cache code resources prior to launching the * application. */ public boolean useCodeCache () { return _useCodeCache; } /** * Returns the number of days a cached code resource is allowed to stay unused before it * becomes eligible for deletion. */ public int getCodeCacheRetentionDays () { return _codeCacheRetentionDays; } /** * Returns the configured maximum concurrent downloads. Used to cap simultaneous downloads of * app files from its hosting server. */ public int maxConcurrentDownloads () { return _maxConcDownloads; } /** * Returns a resource that refers to the application configuration file itself. */ public Resource getConfigResource () { try { return createResource(CONFIG_FILE, Resource.NORMAL); } catch (Exception e) { throw new RuntimeException("Invalid appbase '" + _vappbase + "'.", e); } } /** * Returns a list of the code {@link Resource} objects used by this application. */ public List getCodeResources () { return _codes; } /** * Returns a list of the non-code {@link Resource} objects used by this application. */ public List getResources () { return _resources; } public List getDigestOnly () { return _digestonly; } /** * Returns the digest of the given {@code resource}. */ public String getDigest (Resource resource) { return _digest.getDigest(resource); } /** * Returns a list of all the active {@link Resource} objects used by this application (code and * non-code). */ public List getAllActiveResources () { List allResources = new ArrayList<>(); allResources.addAll(getActiveCodeResources()); allResources.addAll(getActiveResources()); return allResources; } /** * Returns the auxiliary resource group with the specified name, or null. */ public AuxGroup getAuxGroup (String name) { return _auxgroups.get(name); } /** * Returns the set of all auxiliary resource groups defined by the application. An auxiliary * resource group is a collection of resource files that are not downloaded unless a group * token file is present in the application directory. */ public Iterable getAuxGroups () { return _auxgroups.values(); } /** * Returns true if the specified auxgroup has been "activated", false if not. Non-activated * groups should be ignored, activated groups should be downloaded and patched along with the * main resources. */ public boolean isAuxGroupActive (String auxgroup) { Boolean active = _auxactive.get(auxgroup); if (active == null) { // TODO: compare the contents with the MD5 hash of the auxgroup name and the client's // machine ident active = getLocalPath(auxgroup + ".dat").exists(); _auxactive.put(auxgroup, active); } return active; } /** * Returns all main code resources and all code resources from active auxiliary resource groups. */ public List getActiveCodeResources () { ArrayList codes = new ArrayList<>(); codes.addAll(getCodeResources()); for (AuxGroup aux : getAuxGroups()) { if (isAuxGroupActive(aux.name)) { codes.addAll(aux.codes); } } return codes; } /** * Returns all resources indicated to contain native library files (.dll, .so, etc.). */ public List getNativeResources () { List natives = new ArrayList<>(); for (Resource resource: _resources) { if (resource.isNative()) { natives.add(resource); } } return natives; } /** * Returns all non-code resources and all resources from active auxiliary resource groups. */ public List getActiveResources () { ArrayList rsrcs = new ArrayList<>(); rsrcs.addAll(getResources()); for (AuxGroup aux : getAuxGroups()) { if (isAuxGroupActive(aux.name)) { rsrcs.addAll(aux.rsrcs); } } return rsrcs; } /** * Returns a resource that can be used to download a patch file that will bring this * application from its current version to the target version. * * @param auxgroup the auxiliary resource group for which a patch resource is desired or null * for the main application patch resource. */ public Resource getPatchResource (String auxgroup) { if (_targetVersion <= _version) { log.warning("Requested patch resource for up-to-date or non-versioned application", "cvers", _version, "tvers", _targetVersion); return null; } String infix = (auxgroup == null) ? "" : ("-" + auxgroup); String pfile = "patch" + infix + _version + ".dat"; try { URL remote = new URL(createVAppBase(_targetVersion), encodePath(pfile)); return new Resource(pfile, remote, getLocalPath(pfile), Resource.NORMAL); } catch (Exception e) { log.warning("Failed to create patch resource path", "pfile", pfile, "appbase", _appbase, "tvers", _targetVersion, "error", e); return null; } } /** * Returns a resource for a zip file containing a Java VM that can be downloaded to use in * place of the installed VM (in the case where the VM that launched Getdown does not meet the * application's version requirements) or null if no VM is available for this platform. */ public Resource getJavaVMResource () { if (StringUtil.isBlank(_javaLocation)) { return null; } String extension = (_javaLocation.endsWith(".tgz"))?".tgz":".jar"; String vmfile = LaunchUtil.LOCAL_JAVA_DIR + extension; log.info("vmfile is '"+vmfile+"'"); System.out.println("vmfile is '"+vmfile+"'"); try { URL remote = new URL(createVAppBase(_targetVersion), encodePath(_javaLocation)); log.info("Attempting to fetch jvm at "+remote.toString()); System.out.println("Attempting to fetch jvm at "+remote.toString()); return new Resource(vmfile, remote, getLocalPath(vmfile), EnumSet.of(Resource.Attr.UNPACK, Resource.Attr.CLEAN)); } catch (Exception e) { log.warning("Failed to create VM resource", "vmfile", vmfile, "appbase", _appbase, "tvers", _targetVersion, "javaloc", _javaLocation, "error", e); System.out.println("Failed to create VM resource: vmfile="+vmfile+", appbase="+_appbase+ ", tvers="+_targetVersion+", javaloc="+_javaLocation+", error="+e); return null; } } /** * Returns a resource that can be used to download an archive containing all files belonging to * the application. */ public Resource getFullResource () { String file = "full"; try { URL remote = new URL(createVAppBase(_targetVersion), encodePath(file)); return new Resource(file, remote, getLocalPath(file), Resource.NORMAL); } catch (Exception e) { log.warning("Failed to create full resource path", "file", file, "appbase", _appbase, "tvers", _targetVersion, "error", e); return null; } } /** * Returns the URL to use to report an initial download event. Returns null if no tracking * start URL was configured for this application. * * @param event the event to be reported: start, jvm_start, jvm_complete, complete. */ public URL getTrackingURL (String event) { try { String suffix = _trackingURLSuffix == null ? "" : _trackingURLSuffix; String ga = getGATrackingCode(); return _trackingURL == null ? null : HostWhitelist.verify(new URL(_trackingURL + encodePath(event + suffix + ga))); } catch (MalformedURLException mue) { log.warning("Invalid tracking URL", "path", _trackingURL, "event", event, "error", mue); return null; } } /** * Returns the URL to request to report that we have reached the specified percentage of our * initial download. Returns null if no tracking request was configured for the specified * percentage. */ public URL getTrackingProgressURL (int percent) { if (_trackingPcts == null || !_trackingPcts.contains(percent)) { return null; } return getTrackingURL("pct" + percent); } /** * Returns the name of our tracking cookie or null if it was not set. */ public String getTrackingCookieName () { return _trackingCookieName; } /** * Returns the name of our tracking cookie system property or null if it was not set. */ public String getTrackingCookieProperty () { return _trackingCookieProperty; } /** * Instructs the application to parse its {@code getdown.txt} configuration and prepare itself * for operation. The application base URL will be parsed first so that if there are errors * discovered later, the caller can use the application base to download a new {@code * getdown.txt} file and try again. * * @return a {@code Config} instance that contains information from the config file. * * @exception IOException thrown if there is an error reading the file or an error encountered * during its parsing. */ public Config init (boolean checkPlatform) throws IOException { if (_initialised && _initialisedConfig != null) { return _initialisedConfig; } try { Application.i4jVersion = com.install4j.api.launcher.Variables.getCompilerVariable("sys.install4jVersion"); } catch (IOException e) { System.err.println("install4j version not available"); } catch (NoClassDefFoundError e) { log.warning("Starting without install4j classes"); } catch (Throwable t) { System.err.println("install4j not available"); t.printStackTrace(); } Config config = null; File cfgfile = _config; Config.ParseOpts opts = Config.createOpts(checkPlatform); try { // if we have a configuration file, read the data from it if (cfgfile.exists()) { config = Config.parseConfig(_config, opts); } // otherwise, try reading data from our backup config file; thanks to funny windows // bullshit, we have to do this backup file fiddling in case we got screwed while // updating getdown.txt during normal operation else if ((cfgfile = getLocalPath(CONFIG_FILE + "_old")).exists()) { config = Config.parseConfig(cfgfile, opts); } // otherwise, issue a warning that we found no getdown file else { log.info("Found no getdown.txt file", "appdir", getAppDir()); } } catch (Exception e) { log.warning("Failure reading config file", "file", _config, e); } if (config == null || config.getString("appbase") == null || config.getString("appbase").isEmpty()) { try { Config backupConfig = Config.parseConfig(_backupConfig, opts); config = backupConfig; log.warning("Using backup config file", "appdir", getAppDir(), "backupConfig", _backupConfig.getAbsoluteFile()); } catch (Exception e) { log.warning("Failure reading backup config file", "file", _backupConfig, e); } } // see if there's an override config from locator file Config locatorConfig = createLocatorConfig(opts); // merge the locator file config into config (or replace config with) if (locatorConfig != null) { if (config == null || locatorConfig.getBoolean(LOCATOR_FILE_EXTENSION+"_replace")) { config = locatorConfig; } else { config.mergeConfig(locatorConfig, locatorConfig.getBoolean(LOCATOR_FILE_EXTENSION+"_merge")); } } // if we failed to read our config file, check for an appbase specified via a system // property; we can use that to bootstrap ourselves back into operation if (config == null) { String appbase = _envc.appBase; log.info("Using 'appbase' from bootstrap config", "appbase", appbase); Map cdata = new HashMap<>(); cdata.put("appbase", appbase); config = new Config(cdata); } // first determine our application base, this way if anything goes wrong later in the // process, our caller can use the appbase to download a new configuration file _appbase = config.getString("appbase"); // see if locatorConfig override if (locatorConfig != null && !StringUtil.isBlank(locatorConfig.getString("appbase"))) { _appbase = locatorConfig.getString("appbase"); } if (_appbase == null) { throw new RuntimeException("m.missing_appbase"); } // check if we're overriding the domain in the appbase _appbase = SysProps.overrideAppbase(_appbase); // make sure there's a trailing slash if (!_appbase.endsWith("/")) { _appbase = _appbase + "/"; } // extract our version information _version = config.getLong("version", -1L); // if we are a versioned deployment, create a versioned appbase try { _vappbase = createVAppBase(_version); } catch (MalformedURLException mue) { String err = MessageUtil.tcompose("m.invalid_appbase", _appbase); throw (IOException) new IOException(err).initCause(mue); } // check for a latest config URL String latest = config.getString("latest"); if (latest != null) { if (latest.startsWith(_appbase)) { latest = _appbase + latest.substring(_appbase.length()); } else { latest = SysProps.replaceDomain(latest); } try { _latest = HostWhitelist.verify(new URL(latest)); } catch (MalformedURLException mue) { log.warning("Invalid URL for latest attribute.", mue); } } String appPrefix = _envc.appId == null ? "" : (_envc.appId + "."); // determine our application class name (use app-specific class _if_ one is provided) _class = config.getString("class"); if (appPrefix.length() > 0) { _class = config.getString(appPrefix + "class", _class); } if (_class == null) { throw new IOException("m.missing_class"); } // determine whether we want strict comments _strictComments = config.getBoolean("strict_comments"); // check to see if we're using a custom java.version property and regex _javaVersionProp = config.getString("java_version_prop", _javaVersionProp); _javaVersionRegex = config.getString("java_version_regex", _javaVersionRegex); // check to see if we require a particular JVM version and have a supplied JVM _javaMinVersion = config.getLong("java_version", _javaMinVersion); // we support java_min_version as an alias of java_version; it better expresses the check // that's going on and better mirrors java_max_version _javaMinVersion = config.getLong("java_min_version", _javaMinVersion); // check to see if we require a particular max JVM version and have a supplied JVM _javaMaxVersion = config.getLong("java_max_version", _javaMaxVersion); // check to see if we require a particular JVM version and have a supplied JVM _javaExactVersionRequired = config.getBoolean("java_exact_version_required"); // this is a little weird, but when we're run from the digester, we see a String[] which // contains java locations for all platforms which we can't grok, but the digester doesn't // need to know about that; when we're run in a real application there will be only one! Object javaloc = config.getRaw("java_location"); if (javaloc instanceof String) { _javaLocation = (String)javaloc; } // determine whether we have any tracking configuration _trackingURL = config.getString("tracking_url"); // check for tracking progress percent configuration String trackPcts = config.getString("tracking_percents"); if (!StringUtil.isBlank(trackPcts)) { _trackingPcts = new HashSet<>(); for (int pct : StringUtil.parseIntArray(trackPcts)) { _trackingPcts.add(pct); } } else if (!StringUtil.isBlank(_trackingURL)) { _trackingPcts = new HashSet<>(); _trackingPcts.add(50); } // Check for tracking cookie configuration _trackingCookieName = config.getString("tracking_cookie_name"); _trackingCookieProperty = config.getString("tracking_cookie_property"); // Some app may need an extra suffix added to the tracking URL _trackingURLSuffix = config.getString("tracking_url_suffix"); // Some app may need to generate google analytics code _trackingGAHash = config.getString("tracking_ga_hash"); // clear our arrays as we may be reinitializing _codes.clear(); _resources.clear(); _digestonly.clear(); _auxgroups.clear(); _jvmargs.clear(); _appargs.clear(); _txtJvmArgs.clear(); // parse our code resources if (config.getMultiValue("code") == null && config.getMultiValue("ucode") == null) { throw new IOException("m.missing_code"); } parseResources(config, "code", Resource.NORMAL, _codes); parseResources(config, "ucode", Resource.UNPACK, _codes); // parse our non-code resources parseResources(config, "resource", Resource.NORMAL, _resources); parseResources(config, "uresource", Resource.UNPACK, _resources); parseResources(config, "xresource", Resource.EXEC, _resources); parseResources(config, "presource", Resource.PRELOAD, _resources); parseResources(config, "nresource", Resource.NATIVE, _resources); parseResources(config, "digestonly", Resource.NORMAL, _digestonly); // parse our auxiliary resource groups for (String auxgroup : config.getList("auxgroups")) { ArrayList codes = new ArrayList<>(); parseResources(config, auxgroup + ".code", Resource.NORMAL, codes); parseResources(config, auxgroup + ".ucode", Resource.UNPACK, codes); ArrayList rsrcs = new ArrayList<>(); parseResources(config, auxgroup + ".resource", Resource.NORMAL, rsrcs); parseResources(config, auxgroup + ".xresource", Resource.EXEC, rsrcs); parseResources(config, auxgroup + ".uresource", Resource.UNPACK, rsrcs); parseResources(config, auxgroup + ".presource", Resource.PRELOAD, rsrcs); parseResources(config, auxgroup + ".nresource", Resource.NATIVE, rsrcs); _auxgroups.put(auxgroup, new AuxGroup(auxgroup, codes, rsrcs)); } // transfer our JVM arguments (we include both "global" args and app_id-prefixed args) String[] jvmargs = config.getMultiValue("jvmarg"); addAll(jvmargs, _jvmargs); if (appPrefix.length() > 0) { jvmargs = config.getMultiValue(appPrefix + "jvmarg"); addAll(jvmargs, _jvmargs); } // see if a percentage of physical memory, or max heap size options exist jvmmempc = config.getString("jvmmempc", null); jvmmemmax = config.getString("jvmmemmax", null); // app_id prefixed setting overrides if (appPrefix.length() > 0) { jvmmempc = config.getString(appPrefix + "jvmmempc", jvmmempc); jvmmemmax = config.getString(appPrefix + "jvmmemmax", jvmmemmax); } // get the set of optimum JVM arguments _optimumJvmArgs = config.getMultiValue("optimum_jvmarg"); // transfer our application arguments String[] appargs = config.getMultiValue(appPrefix + "apparg"); addAll(appargs, _appargs); // add the launch specific application arguments _appargs.addAll(_envc.appArgs); // look for custom arguments fillAssignmentListFromPairs("extra.txt", _txtJvmArgs); // determine whether we want to allow offline operation (defaults to false) _allowOffline = config.getBoolean("allow_offline"); // look for a debug.txt file which causes us to run in java.exe on Windows so that we can // obtain a thread dump of the running JVM _windebug = getLocalPath("debug.txt").exists(); // whether to cache code resources and launch from cache _useCodeCache = config.getBoolean("use_code_cache"); _codeCacheRetentionDays = config.getInt("code_cache_retention_days", 7); // maximum simultaneous downloads _maxConcDownloads = Math.max(1, config.getInt("max_concurrent_downloads", SysProps.threadPoolSize())); // extract some info used to configure our child process on macOS _dockName = config.getString("ui.name"); _dockIconPath = config.getString("ui.mac_dock_icon", "../desktop.icns"); _initialised = true; _initialisedConfig = config; return config; } /** * Adds strings of the form pair0=pair1 to collector for each pair parsed out of pairLocation. */ protected void fillAssignmentListFromPairs (String pairLocation, List collector) { File pairFile = getLocalPath(pairLocation); if (pairFile.exists()) { try { List args = Config.parsePairs(pairFile, Config.createOpts(false)); for (String[] pair : args) { if (pair[1].length() == 0) { collector.add(pair[0]); } else { collector.add(pair[0] + "=" + pair[1]); } } } catch (Throwable t) { log.warning("Failed to parse '" + pairFile + "': " + t); } } } /** * Returns a URL from which the specified path can be fetched. Our application base URL is * properly versioned and combined with the supplied path. */ public URL getRemoteURL (String path) throws MalformedURLException { return new URL(_vappbase, encodePath(path)); } /** * Returns the local path to the specified resource. */ public File getLocalPath (String path) { return getLocalPath(getAppDir(), path); } /** * Returns true if we either have no version requirement, are running in a JVM that meets our * version requirements or have what appears to be a version of the JVM that meets our * requirements. */ public boolean haveValidJavaVersion () { // if we're doing no version checking, then yay! if (_javaMinVersion == 0 && _javaMaxVersion == 0) return true; try { // parse the version out of the java.version (or custom) system property long version = SysProps.parseJavaVersion(_javaVersionProp, _javaVersionRegex); log.info("Checking Java version", "current", version, "wantMin", _javaMinVersion, "wantMax", _javaMaxVersion); // if we have an unpacked VM, check the 'release' file for its version Resource vmjar = getJavaVMResource(); if (vmjar != null && vmjar.isMarkedValid()) { File vmdir = new File(getAppDir(), LaunchUtil.LOCAL_JAVA_DIR); File relfile = new File(vmdir, "release"); if (!relfile.exists()) { log.warning("Unpacked JVM missing 'release' file. Assuming valid version."); return true; } long vmvers = VersionUtil.readReleaseVersion(relfile, _javaVersionRegex); if (vmvers == 0L) { log.warning("Unable to read version from 'release' file. Assuming valid."); return true; } version = vmvers; log.info("Checking version of unpacked JVM [vers=" + version + "]."); } if (_javaExactVersionRequired) { if (version == _javaMinVersion) return true; else { log.warning("An exact Java VM version is required.", "current", version, "required", _javaMinVersion); return false; } } boolean minVersionOK = (_javaMinVersion == 0) || (version >= _javaMinVersion); boolean maxVersionOK = (_javaMaxVersion == 0) || (version <= _javaMaxVersion); return minVersionOK && maxVersionOK; } catch (RuntimeException re) { // if we can't parse the java version we're in weird land and should probably just try // our luck with what we've got rather than try to download a new jvm log.warning("Unable to parse VM version, hoping for the best", "error", re, "needed", _javaMinVersion); return true; } } /** * Checks whether the app has a set of "optimum" JVM args that we wish to try first, detecting * whether the launch is successful and, if necessary, trying again without the optimum * arguments. */ public boolean hasOptimumJvmArgs () { return _optimumJvmArgs != null; } /** * Returns true if the app should attempt to run even if we have no Internet connection. */ public boolean allowOffline () { return _allowOffline; } /** * Attempts to redownload the getdown.txt file based on information parsed from a * previous call to {@link #init}. */ public void attemptRecovery (StatusDisplay status) throws IOException { status.updateStatus("m.updating_metadata"); downloadConfigFile(); } /** * Downloads and replaces the getdown.txt and digest.txt files with * those for the target version of our application. */ public void updateMetadata () throws IOException { try { // update our versioned application base with the target version _vappbase = createVAppBase(_targetVersion); } catch (MalformedURLException mue) { String err = MessageUtil.tcompose("m.invalid_appbase", _appbase); throw (IOException) new IOException(err).initCause(mue); } try { // now re-download our control files; we download the digest first so that if it fails, // our config file will still reference the old version and re-running the updater will // start the whole process over again downloadDigestFiles(); downloadConfigFile(); } catch (IOException ex) { // if we are allowing offline execution, we want to allow the application to run in its // current form rather than aborting the entire process; to do this, we delete the // version.txt file and "trick" Getdown into thinking that it just needs to validate // the application as is; next time the app runs when connected to the internet, it // will have to rediscover that it needs updating and reattempt to update itself if (_allowOffline) { log.warning("Failed to update digest files. Attempting offline operaton.", ex); if (!FileUtil.deleteHarder(getLocalPath(VERSION_FILE))) { log.warning("Deleting version.txt failed. This probably isn't going to work."); } } else { throw ex; } } } /** * Invokes the process associated with this application definition. * * @param optimum whether or not to include the set of optimum arguments (as opposed to falling * back). */ public Process createProcess (boolean optimum) throws IOException { ArrayList args = new ArrayList<>(); // reconstruct the path to the JVM args.add(LaunchUtil.getJVMPath(getAppDir(), _windebug || optimum)); // check whether we're using -jar mode or -classpath mode boolean dashJarMode = MANIFEST_CLASS.equals(_class); // add the -classpath arguments if we're not in -jar mode ClassPath classPath = PathBuilder.buildClassPath(this); if (!dashJarMode) { args.add("-classpath"); args.add(classPath.asArgumentString()); } // we love our Mac users, so we do nice things to preserve our application identity if (LaunchUtil.isMacOS()) { args.add("-Xdock:icon=" + getLocalPath(_dockIconPath).getAbsolutePath()); args.add("-Xdock:name=" + _dockName); } // pass along our proxy settings String proxyHost; if ((proxyHost = System.getProperty("http.proxyHost")) != null) { args.add("-Dhttp.proxyHost=" + proxyHost); args.add("-Dhttp.proxyPort=" + System.getProperty("http.proxyPort")); args.add("-Dhttps.proxyHost=" + proxyHost); args.add("-Dhttps.proxyPort=" + System.getProperty("http.proxyPort")); } // add the marker indicating the app is running in getdown args.add("-D" + Properties.GETDOWN + "=true"); args.add("-Dsys.install4jVersion=" + Application.i4jVersion); args.add("-Dinstaller_template_version=" + System.getProperty("installer_template_version")); args.add("-Dlauncher_version=" + Build.version()); // set HiDPI property if wanted String scalePropertyArg = HiDPISetting.getScalePropertyArg(); if (scalePropertyArg != null) { args.add(scalePropertyArg); } // set the native library path if we have native resources // @TODO optional getdown.txt parameter to set addCurrentLibraryPath to true or false? ClassPath javaLibPath = PathBuilder.buildLibsPath(this, true); if (javaLibPath != null) { args.add("-Djava.library.path=" + javaLibPath.asArgumentString()); } // pass along any pass-through arguments for (Map.Entry entry : System.getProperties().entrySet()) { String key = (String)entry.getKey(); if (key.startsWith(PROP_PASSTHROUGH_PREFIX)) { key = key.substring(PROP_PASSTHROUGH_PREFIX.length()); args.add("-D" + key + "=" + entry.getValue()); } } // test for jalview/s URL. Insert startupNotification URI into start of _appargs if (! StringUtil.isBlank(_jalviewUri)) { _appargs.add(0, _jalviewUri); } if (_appargs.size() > 0) { String uri = _appargs.get(0); try { log.info("TRYING TO PARSE URL '"+uri+"'"); URI jalviewUri = new URI(uri); if (jalviewUri != null) { String scheme = jalviewUri.getScheme(); if (scheme != null && (scheme.equals("jalview") || scheme.equals("jalviews"))) { boolean https = jalviewUri.getScheme().equals("jalviews"); String host = jalviewUri.getHost(); int port = jalviewUri.getPort(); String file = jalviewUri.getPath(); String ref = jalviewUri.getFragment(); String query = jalviewUri.getQuery(); _appargs.clear(); _appargs.add("-open"); if (host != null && host.length() > 0) { URL newUrl = new URL( (https?"https":"http") + "://" + host + (port > -1? String.valueOf(port) : "") + jalviewUri.getRawPath() + (query != null && query.length() > 0 ? "?" + jalviewUri.getRawQuery() : "") ); _appargs.add(newUrl.toString()); } else { _appargs.add(file); } if (ref != null && ref.length() > 0) { String[] refArgs = ref.split("&"); for (String refArg : refArgs) { if (refArg.startsWith("jvmmempc=")) { jvmmempc = refArg.substring(9); continue; } if (refArg.startsWith("jvmmemmax=")) { jvmmemmax = refArg.substring(10); continue; } _appargs.add(URLDecoder.decode(refArg, "UTF-8")); } } } } } catch (URISyntaxException e) { log.error("Malformed jalview URI", uri); } } for (String argString: _appargs) { if (argString.startsWith("-jvmmempc=")) { jvmmempc = argString.substring(10); continue; } if (argString.startsWith("-jvmmemmax=")) { jvmmemmax = argString.substring(11); continue; } } // add the memory setting from jvmmempc and jvmmemmax long maxMemLong = -1; maxMemLong = MemorySetting.getMemorySetting(jvmmemmax, jvmmempc); if (maxMemLong > 0) { String[] maxMemHeapArg = new String[]{"-Xmx"+Long.toString(maxMemLong)}; // remove other max heap size arg ARG: for (int i = 0; i < _jvmargs.size(); i++) { if (_jvmargs.get(i) instanceof java.lang.String && _jvmargs.get(i).startsWith("-Xmx")) { _jvmargs.remove(i); break ARG; } } addAll(maxMemHeapArg, _jvmargs); } // add the JVM arguments for (String string : _jvmargs) { args.add(processArg(string)); } // add the optimum arguments if requested and available if (optimum && _optimumJvmArgs != null) { for (String string : _optimumJvmArgs) { args.add(processArg(string)); } } // add the arguments from extra.txt (after the optimum ones, in case they override them) for (String string : _txtJvmArgs) { args.add(processArg(string)); } // if we're in -jar mode add those arguments, otherwise add the app class name if (dashJarMode) { args.add("-jar"); args.add(classPath.asArgumentString()); } else { args.add(_class); } // almost finally check the startup file arguments for (File f : _startupFiles) { _appargs.add(f.getAbsolutePath()); break; // Only add one file to open } // check if one arg with recognised extension if ( _appargs.size() == 1 && _appargs.get(0) != null ) { String filename = _appargs.get(0); String ext = null; int j = filename.lastIndexOf('.'); if (j > -1) { ext = filename.substring(j+1); } if (ext != null && LOCATOR_FILE_EXTENSION.equals(ext.toLowerCase())) { // this file extension should have been dealt with in Getdown class } else { _appargs.add(0, "-open"); } } // finally add the application arguments for (String string : _appargs) { args.add(processArg(string)); } String[] envp = createEnvironment(); String[] sargs = args.toArray(new String[args.size()]); log.info("Running " + StringUtil.join(sargs, "\n ")); return Runtime.getRuntime().exec(sargs, envp, getAppDir()); } /** * If the application provided environment variables, combine those with the current * environment and return that in a style usable for {@link Runtime#exec(String, String[])}. * If the application didn't provide any environment variables, null is returned to just use * the existing environment. */ protected String[] createEnvironment () { List envvar = new ArrayList<>(); fillAssignmentListFromPairs("env.txt", envvar); if (envvar.isEmpty()) { log.info("Didn't find any custom environment variables, not setting any."); return null; } List envAssignments = new ArrayList<>(); for (String assignment : envvar) { envAssignments.add(processArg(assignment)); } for (Map.Entry environmentEntry : System.getenv().entrySet()) { envAssignments.add(environmentEntry.getKey() + "=" + environmentEntry.getValue()); } String[] envp = envAssignments.toArray(new String[envAssignments.size()]); log.info("Environment " + StringUtil.join(envp, "\n ")); return envp; } /** * Runs this application directly in the current VM. */ public void invokeDirect () throws IOException { ClassPath classPath = PathBuilder.buildClassPath(this); URL[] jarUrls = classPath.asUrls(); // create custom class loader URLClassLoader loader = new URLClassLoader(jarUrls, ClassLoader.getSystemClassLoader()) { @Override protected PermissionCollection getPermissions (CodeSource code) { Permissions perms = new Permissions(); perms.add(new AllPermission()); return perms; } }; Thread.currentThread().setContextClassLoader(loader); log.info("Configured URL class loader:"); for (URL url : jarUrls) log.info(" " + url); // configure any system properties that we can for (String jvmarg : _jvmargs) { if (jvmarg.startsWith("-D")) { jvmarg = processArg(jvmarg.substring(2)); int eqidx = jvmarg.indexOf("="); if (eqidx == -1) { log.warning("Bogus system property: '" + jvmarg + "'?"); } else { System.setProperty(jvmarg.substring(0, eqidx), jvmarg.substring(eqidx+1)); } } } // pass along any pass-through arguments Map passProps = new HashMap<>(); for (Map.Entry entry : System.getProperties().entrySet()) { String key = (String)entry.getKey(); if (key.startsWith(PROP_PASSTHROUGH_PREFIX)) { key = key.substring(PROP_PASSTHROUGH_PREFIX.length()); passProps.put(key, (String)entry.getValue()); } } // we can't set these in the above loop lest we get a ConcurrentModificationException for (Map.Entry entry : passProps.entrySet()) { System.setProperty(entry.getKey(), entry.getValue()); } // prepare our app arguments String[] args = new String[_appargs.size()]; for (int ii = 0; ii < args.length; ii++) args[ii] = processArg(_appargs.get(ii)); try { log.info("Loading " + _class); Class appclass = loader.loadClass(_class); Method main = appclass.getMethod("main", EMPTY_STRING_ARRAY.getClass()); log.info("Invoking main({" + StringUtil.join(args, ", ") + "})"); main.invoke(null, new Object[] { args }); } catch (Exception e) { log.warning("Failure invoking app main", e); } } /** Replaces the application directory and version in any argument. */ protected String processArg (String arg) { arg = arg.replace("%APPDIR%", getAppDir().getAbsolutePath()); arg = arg.replace("%VERSION%", String.valueOf(_version)); // if this argument contains %ENV.FOO% replace those with the associated values looked up // from the environment if (arg.contains(ENV_VAR_PREFIX)) { StringBuffer sb = new StringBuffer(); Matcher matcher = ENV_VAR_PATTERN.matcher(arg); while (matcher.find()) { String varName = matcher.group(1), varValue = System.getenv(varName); String repValue = varValue == null ? "MISSING:"+varName : varValue; matcher.appendReplacement(sb, Matcher.quoteReplacement(repValue)); } matcher.appendTail(sb); arg = sb.toString(); } return arg; } /** * Loads the digest.txt file and verifies the contents of both that file and the * getdown.text file. Then it loads the version.txt and decides * whether or not the application needs to be updated or whether we can proceed to verification * and execution. * * @return true if the application needs to be updated, false if it is up to date and can be * verified and executed. * * @exception IOException thrown if we encounter an unrecoverable error while verifying the * metadata. */ public boolean verifyMetadata (StatusDisplay status) throws IOException { log.info("Verifying application: " + _vappbase); log.info("Version: " + _version); log.info("Class: " + _class); // this will read in the contents of the digest file and validate itself try { _digest = new Digest(getAppDir(), _strictComments); } catch (IOException ioe) { log.info("Failed to load digest: " + ioe.getMessage() + ". Attempting recovery..."); } // if we have no version, then we are running in unversioned mode so we need to download // our digest.txt file on every invocation if (_version == -1) { // make a note of the old meta-digest, if this changes we need to revalidate all of our // resources as one or more of them have also changed String olddig = (_digest == null) ? "" : _digest.getMetaDigest(); try { status.updateStatus("m.checking"); downloadDigestFiles(); _digest = new Digest(getAppDir(), _strictComments); if (!olddig.equals(_digest.getMetaDigest())) { log.info("Unversioned digest changed. Revalidating..."); status.updateStatus("m.validating"); clearValidationMarkers(); } } catch (IOException ioe) { log.warning("Failed to refresh non-versioned digest: " + ioe.getMessage() + ". Proceeding..."); } } // regardless of whether we're versioned, if we failed to read the digest from disk, try to // redownload the digest file and give it another good college try; this time we allow // exceptions to propagate up to the caller as there is nothing else we can do if (_digest == null) { status.updateStatus("m.updating_metadata"); downloadDigestFiles(); _digest = new Digest(getAppDir(), _strictComments); } // now verify the contents of our main config file Resource crsrc = getConfigResource(); if (!_digest.validateResource(crsrc, null)) { status.updateStatus("m.updating_metadata"); // attempt to redownload both of our metadata files; again we pass errors up to our // caller because there's nothing we can do to automatically recover downloadConfigFile(); downloadDigestFiles(); _digest = new Digest(getAppDir(), _strictComments); // revalidate everything if we end up downloading new metadata clearValidationMarkers(); // if the new copy validates, reinitialize ourselves; otherwise report baffling hoseage if (_digest.validateResource(crsrc, null)) { // unset _initialisedConfig so new file is initialised _initialisedConfig = null; init(true); } else { log.warning(CONFIG_FILE + " failed to validate even after redownloading. " + "Blindly forging onward."); } } // start by assuming we are happy with our version _targetVersion = _version; // if we are a versioned application, read in the contents of the version.txt file // and/or check the latest config URL for a newer version if (_version != -1) { File vfile = getLocalPath(VERSION_FILE); long fileVersion = VersionUtil.readVersion(vfile); if (fileVersion != -1) { _targetVersion = fileVersion; } if (_latest != null) { try (InputStream in = ConnectionUtil.open(proxy, _latest, 0, 0).getInputStream(); InputStreamReader reader = new InputStreamReader(in, UTF_8); BufferedReader bin = new BufferedReader(reader)) { for (String[] pair : Config.parsePairs(bin, Config.createOpts(false))) { if (pair[0].equals("version")) { _targetVersion = Math.max(Long.parseLong(pair[1]), _targetVersion); if (fileVersion != -1 && _targetVersion > fileVersion) { // replace the file with the newest version try (FileOutputStream fos = new FileOutputStream(vfile); PrintStream out = new PrintStream(fos)) { out.println(_targetVersion); } } break; } } } catch (Exception e) { log.warning("Unable to retrieve version from latest config file.", e); } } } // finally let the caller know if we need an update return _version != _targetVersion; } /** * Verifies the code and media resources associated with this application. A list of resources * that do not exist or fail the verification process will be returned. If all resources are * ready to go, null will be returned and the application is considered ready to run. * * @param obs a progress observer that will be notified of verification progress. NOTE: this * observer may be called from arbitrary threads, so if you update a UI based on calls to it, * you have to take care to get back to your UI thread. * @param alreadyValid if non-null a 1 element array that will have the number of "already * validated" resources filled in. * @param unpacked a set to populate with unpacked resources. * @param toInstall a list into which to add resources that need to be installed. * @param toDownload a list into which to add resources that need to be downloaded. */ public void verifyResources ( ProgressObserver obs, int[] alreadyValid, Set unpacked, Set toInstall, Set toDownload) throws InterruptedException { // resources are verified on background threads supplied by the thread pool, and progress // is reported by posting runnable actions to the actions queue which is processed by the // main (UI) thread ExecutorService exec = Executors.newFixedThreadPool(SysProps.threadPoolSize()); final BlockingQueue actions = new LinkedBlockingQueue(); final int[] completed = new int[1]; long start = System.currentTimeMillis(); // obtain the sizes of the resources to validate List rsrcs = getAllActiveResources(); long[] sizes = new long[rsrcs.size()]; long totalSize = 0; for (int ii = 0; ii < sizes.length; ii++) { totalSize += sizes[ii] = rsrcs.get(ii).getLocal().length(); } final ProgressObserver fobs = obs; // as long as we forward aggregated progress updates to the UI thread, having multiple // threads update a progress aggregator is "mostly" thread-safe final ProgressAggregator pagg = new ProgressAggregator(new ProgressObserver() { public void progress (final int percent) { actions.add(new Runnable() { public void run () { fobs.progress(percent); } }); } }, sizes); final int[] fAlreadyValid = alreadyValid; final Set toInstallAsync = new ConcurrentSkipListSet<>(toInstall); final Set toDownloadAsync = new ConcurrentSkipListSet<>(); final Set unpackedAsync = new ConcurrentSkipListSet<>(); for (int ii = 0; ii < sizes.length; ii++) { final Resource rsrc = rsrcs.get(ii); final int index = ii; exec.execute(new Runnable() { public void run () { verifyResource(rsrc, pagg.startElement(index), fAlreadyValid, unpackedAsync, toInstallAsync, toDownloadAsync); actions.add(new Runnable() { public void run () { completed[0] += 1; } }); } }); } while (completed[0] < rsrcs.size()) { // we should be getting progress completion updates WAY more often than one every // minute, so if things freeze up for 60 seconds, abandon ship Runnable action = actions.poll(60, TimeUnit.SECONDS); action.run(); } exec.shutdown(); toInstall.addAll(toInstallAsync); toDownload.addAll(toDownloadAsync); unpacked.addAll(unpackedAsync); long complete = System.currentTimeMillis(); log.info("Verified resources", "count", rsrcs.size(), "size", (totalSize/1024) + "k", "duration", (complete-start) + "ms"); } private void verifyResource (Resource rsrc, ProgressObserver obs, int[] alreadyValid, Set unpacked, Set toInstall, Set toDownload) { if (rsrc.isMarkedValid()) { if (alreadyValid != null) { alreadyValid[0]++; } obs.progress(100); return; } try { if (_digest.validateResource(rsrc, obs)) { // if the resource has a _new file, add it to to-install list if (rsrc.getLocalNew().exists()) { toInstall.add(rsrc); return; } rsrc.applyAttrs(); unpacked.add(rsrc); rsrc.markAsValid(); return; } } catch (Exception e) { log.info("Failure verifying resource. Requesting redownload...", "rsrc", rsrc, "error", e); } finally { obs.progress(100); } toDownload.add(rsrc); } /** * Unpacks the resources that require it (we know that they're valid). * * @param unpacked a set of resources to skip because they're already unpacked. */ public void unpackResources (ProgressObserver obs, Set unpacked) throws InterruptedException { List rsrcs = getActiveResources(); // remove resources that we don't want to unpack for (Iterator it = rsrcs.iterator(); it.hasNext(); ) { Resource rsrc = it.next(); if (!rsrc.shouldUnpack() || unpacked.contains(rsrc)) { it.remove(); } } // obtain the sizes of the resources to unpack long[] sizes = new long[rsrcs.size()]; for (int ii = 0; ii < sizes.length; ii++) { sizes[ii] = rsrcs.get(ii).getLocal().length(); } ProgressAggregator pagg = new ProgressAggregator(obs, sizes); for (int ii = 0; ii < sizes.length; ii++) { Resource rsrc = rsrcs.get(ii); ProgressObserver pobs = pagg.startElement(ii); try { rsrc.unpack(); } catch (IOException ioe) { log.warning("Failure unpacking resource", "rsrc", rsrc, ioe); } pobs.progress(100); } } /** * Clears all validation marker files. */ public void clearValidationMarkers () { clearValidationMarkers(getAllActiveResources().iterator()); } /** * Returns the version number for the application. Should only be called after successful * return of verifyMetadata. */ public long getVersion () { return _version; } /** * Creates a versioned application base URL for the specified version. */ protected URL createVAppBase (long version) throws MalformedURLException { String url = version < 0 ? _appbase : _appbase.replace("%VERSION%", "" + version); return HostWhitelist.verify(new URL(url)); } /** * Clears all validation marker files for the resources in the supplied iterator. */ protected void clearValidationMarkers (Iterator iter) { while (iter.hasNext()) { iter.next().clearMarker(); } } /** * Downloads a new copy of CONFIG_FILE. */ protected void downloadConfigFile () throws IOException { downloadControlFile(CONFIG_FILE, 0); } /** * @return true if gettingdown.lock was unlocked, already locked by this application or if * we're not locking at all. */ public synchronized boolean lockForUpdates () { if (_lock != null && _lock.isValid()) { return true; } try { _lockChannel = new RandomAccessFile(getLocalPath("gettingdown.lock"), "rw").getChannel(); } catch (FileNotFoundException e) { log.warning("Unable to create lock file", "message", e.getMessage(), e); return false; } try { _lock = _lockChannel.tryLock(); } catch (IOException e) { log.warning("Unable to create lock", "message", e.getMessage(), e); return false; } catch (OverlappingFileLockException e) { log.warning("The lock is held elsewhere in this JVM", e); return false; } log.info("Able to lock for updates: " + (_lock != null)); return _lock != null; } /** * Release gettingdown.lock */ public synchronized void releaseLock () { if (_lock != null) { log.info("Releasing lock"); try { _lock.release(); } catch (IOException e) { log.warning("Unable to release lock", "message", e.getMessage(), e); } try { _lockChannel.close(); } catch (IOException e) { log.warning("Unable to close lock channel", "message", e.getMessage(), e); } _lockChannel = null; _lock = null; } } /** * Downloads the digest files and validates their signature. * @throws IOException */ protected void downloadDigestFiles () throws IOException { for (int version = 1; version <= Digest.VERSION; version++) { downloadControlFile(Digest.digestFile(version), version); } } /** * Downloads a new copy of the specified control file, optionally validating its signature. * If the download is successful, moves it over the old file on the filesystem. * *

TODO: Switch to PKCS #7 or CMS. * * @param sigVersion if {@code 0} no validation will be performed, if {@code > 0} then this * should indicate the version of the digest file being validated which indicates which * algorithm to use to verify the signature. See {@link Digest#VERSION}. */ protected void downloadControlFile (String path, int sigVersion) throws IOException { File target = downloadFile(path); if (sigVersion > 0) { if (_envc.certs.isEmpty()) { log.info("No signing certs, not verifying digest.txt", "path", path); } else { File signatureFile = downloadFile(path + SIGNATURE_SUFFIX); byte[] signature = null; try (FileInputStream signatureStream = new FileInputStream(signatureFile)) { signature = StreamUtil.toByteArray(signatureStream); } finally { FileUtil.deleteHarder(signatureFile); // delete the file regardless } byte[] buffer = new byte[8192]; int length, validated = 0; for (Certificate cert : _envc.certs) { try (FileInputStream dataInput = new FileInputStream(target)) { Signature sig = Signature.getInstance(Digest.sigAlgorithm(sigVersion)); sig.initVerify(cert); while ((length = dataInput.read(buffer)) != -1) { sig.update(buffer, 0, length); } if (!sig.verify(Base64.decode(signature, Base64.DEFAULT))) { log.info("Signature does not match", "cert", cert.getPublicKey()); continue; } else { log.info("Signature matches", "cert", cert.getPublicKey()); validated++; } } catch (IOException ioe) { log.warning("Failure validating signature of " + target + ": " + ioe); } catch (GeneralSecurityException gse) { // no problem! } } // if we couldn't find a key that validates our digest, we are the hosed! if (validated == 0) { // delete the temporary digest file as we know it is invalid FileUtil.deleteHarder(target); throw new IOException("m.corrupt_digest_signature_error"); } } } // now move the temporary file over the original File original = getLocalPath(path); if (!FileUtil.renameTo(target, original)) { throw new IOException("Failed to rename(" + target + ", " + original + ")"); } } /** * Download a path to a temporary file, returning a {@link File} instance with the path * contents. */ protected File downloadFile (String path) throws IOException { File target = getLocalPath(path + "_new"); URL targetURL = null; try { targetURL = getRemoteURL(path); } catch (Exception e) { log.warning("Requested to download invalid control file", "appbase", _vappbase, "path", path, "error", e); throw (IOException) new IOException("Invalid path '" + path + "'.").initCause(e); } log.info("Attempting to refetch '" + path + "' from '" + targetURL + "'."); // stream the URL into our temporary file URLConnection uconn = ConnectionUtil.open(proxy, targetURL, 0, 0); // we have to tell Java not to use caches here, otherwise it will cache any request for // same URL for the lifetime of this JVM (based on the URL string, not the URL object); // if the getdown.txt file, for example, changes in the meanwhile, we would never hear // about it; turning off caches is not a performance concern, because when Getdown asks // to download a file, it expects it to come over the wire, not from a cache uconn.setUseCaches(false); uconn.setRequestProperty("Accept-Encoding", "gzip"); try (InputStream fin = uconn.getInputStream()) { String encoding = uconn.getContentEncoding(); boolean gzip = "gzip".equalsIgnoreCase(encoding); try (InputStream fin2 = (gzip ? new GZIPInputStream(fin) : fin)) { try (FileOutputStream fout = new FileOutputStream(target)) { StreamUtil.copy(fin2, fout); } } } return target; } /** Helper function for creating {@link Resource} instances. */ protected Resource createResource (String path, EnumSet attrs) throws MalformedURLException { return new Resource(path, getRemoteURL(path), getLocalPath(path), attrs); } /** Helper function to add all values in {@code values} (if non-null) to {@code target}. */ protected static void addAll (String[] values, List target) { if (values != null) { for (String value : values) { target.add(value); } } } /** * Make an immutable List from the specified int array. */ public static List intsToList (int[] values) { List list = new ArrayList<>(values.length); for (int val : values) { list.add(val); } return Collections.unmodifiableList(list); } /** * Make an immutable List from the specified String array. */ public static List stringsToList (String[] values) { return values == null ? null : Collections.unmodifiableList(Arrays.asList(values)); } /** Used to parse resources with the specified name. */ protected void parseResources (Config config, String name, EnumSet attrs, List list) { String[] rsrcs = config.getMultiValue(name); if (rsrcs == null) { return; } for (String rsrc : rsrcs) { try { list.add(createResource(rsrc, attrs)); } catch (Exception e) { log.warning("Invalid resource '" + rsrc + "'. " + e); } } } /** Possibly generates and returns a google analytics tracking cookie. */ protected String getGATrackingCode () { if (_trackingGAHash == null) { return ""; } long time = System.currentTimeMillis() / 1000; if (_trackingStart == 0) { _trackingStart = time; } if (_trackingId == 0) { int low = 100000000, high = 1000000000; _trackingId = low + _rando.nextInt(high-low); } StringBuilder cookie = new StringBuilder("&utmcc=__utma%3D").append(_trackingGAHash); cookie.append(".").append(_trackingId); cookie.append(".").append(_trackingStart).append(".").append(_trackingStart); cookie.append(".").append(time).append(".1%3B%2B"); cookie.append("__utmz%3D").append(_trackingGAHash).append("."); cookie.append(_trackingStart).append(".1.1."); cookie.append("utmcsr%3D(direct)%7Cutmccn%3D(direct)%7Cutmcmd%3D(none)%3B"); int low = 1000000000, high = 2000000000; cookie.append("&utmn=").append(_rando.nextInt(high-low)); return cookie.toString(); } /** * Encodes a path for use in a URL. */ protected static String encodePath (String path) { try { // we want to keep slashes because we're encoding an entire path; also we need to turn // + into %20 because web servers don't like + in paths or file names, blah return URLEncoder.encode(path, "UTF-8").replace("%2F", "/").replace("+", "%20"); } catch (UnsupportedEncodingException ue) { log.warning("Failed to URL encode " + path + ": " + ue); return path; } } protected File getLocalPath (File appdir, String path) { return new File(appdir, path); } public static void setStartupFilesFromParameterString(String p) { // multiple files *might* be passed in as space separated quoted filenames String q = "\""; if (!StringUtil.isBlank(p)) { String[] filenames; // split quoted params or treat as single string array if (p.startsWith(q) && p.endsWith(q)) { // this fails if, e.g. // p=q("stupidfilename\" " "otherfilename") // let's hope no-one ever ends a filename with '" ' filenames = p.substring(q.length(),p.length()-q.length()).split(q+" "+q); } else { // single unquoted filename filenames = new String[]{p}; } // check for locator file. Only allow one locator file to be double clicked (if multiple files opened, ignore locator files) String locatorFilename = filenames.length >= 1 ? filenames[0] : null; if ( !StringUtil.isBlank(locatorFilename) && locatorFilename.toLowerCase().endsWith("."+Application.LOCATOR_FILE_EXTENSION) ) { setLocatorFile(locatorFilename); // remove the locator filename from the filenames array String[] otherFilenames = new String[filenames.length - 1]; System.arraycopy(filenames, 1, otherFilenames, 0, otherFilenames.length); filenames = otherFilenames; } for (int i = 0; i < filenames.length; i++) { String filename = filenames[i]; // skip any other locator files in a multiple file list if (filename.startsWith("jalview://") || filename.startsWith("jalviews://")) { setJalviewUri(filename); } else if (! filename.toLowerCase().endsWith("."+Application.LOCATOR_FILE_EXTENSION)) { addStartupFile(filename); } } } } public static void setLocatorFile(String filename) { _locatorFile = new File(filename); } public static void addStartupFile(String filename) { _startupFiles.add(new File(filename)); } public static void setJalviewUri(String uri) { _jalviewUri = uri; } private Config createLocatorConfig(Config.ParseOpts opts) { if (_locatorFile == null) { return null; } Config locatorConfig = null; try { Config tmpConfig = null; Map tmpData = new HashMap<>(); if (_locatorFile.exists()) { tmpConfig = Config.parseConfig(_locatorFile, opts); // appbase is sanitised in HostWhitelist Map tmpConfigData = tmpConfig.getData(); if (tmpConfig != null) { for (Map.Entry entry : tmpConfigData.entrySet()) { String key = entry.getKey(); Object value = entry.getValue(); String mkey = key.indexOf('.') > -1 ? key.substring(key.indexOf('.') + 1) : key; if (Config.allowedReplaceKeys.contains(mkey) || Config.allowedMergeKeys.contains(mkey)) { tmpData.put(key, value); } } } else { log.warning("Error occurred reading config file", "file", _locatorFile); } } else { log.warning("Given locator file does not exist", "file", _locatorFile); } locatorConfig = new Config(tmpData); } catch (Exception e) { log.warning("Failure reading locator file", "file", _locatorFile, e); } return locatorConfig; } public String getAppbase() { return _appbase; } protected final EnvConfig _envc; protected File _config; protected File _backupConfig; protected Digest _digest; protected long _version = -1; protected long _targetVersion = -1; protected String _appbase; protected URL _vappbase; protected URL _latest; protected String _class; protected String _dockName; protected String _dockIconPath; protected boolean _strictComments; protected boolean _windebug; protected boolean _allowOffline; protected int _maxConcDownloads; protected String _trackingURL; protected Set _trackingPcts; protected String _trackingCookieName; protected String _trackingCookieProperty; protected String _trackingURLSuffix; protected String _trackingGAHash; protected long _trackingStart; protected int _trackingId; protected String _javaVersionProp = "java.version"; protected String _javaVersionRegex = "(\\d+)(?:\\.(\\d+)(?:\\.(\\d+)(_\\d+)?)?)?"; protected long _javaMinVersion, _javaMaxVersion; protected boolean _javaExactVersionRequired; protected String _javaLocation; protected List _codes = new ArrayList<>(); protected List _resources = new ArrayList<>(); protected List _digestonly = new ArrayList<>(); protected boolean _useCodeCache; protected int _codeCacheRetentionDays; protected Map _auxgroups = new HashMap<>(); protected Map _auxactive = new HashMap<>(); protected List _jvmargs = new ArrayList<>(); protected List _appargs = new ArrayList<>(); protected String[] _optimumJvmArgs; protected List _txtJvmArgs = new ArrayList<>(); /** If a warning has been issued about not being able to set modtimes. */ protected boolean _warnedAboutSetLastModified; /** Locks gettingdown.lock in the app dir. Held the entire time updating is going on.*/ protected FileLock _lock; /** Channel to the file underlying _lock. Kept around solely so the lock doesn't close. */ protected FileChannel _lockChannel; protected Random _rando = new Random(); protected static final String[] EMPTY_STRING_ARRAY = new String[0]; protected static final String ENV_VAR_PREFIX = "%ENV."; protected static final Pattern ENV_VAR_PATTERN = Pattern.compile("%ENV\\.(.*?)%"); protected static File _locatorFile; protected static List _startupFiles = new ArrayList<>(); protected static String _jalviewUri; public static final String LOCATOR_FILE_EXTENSION = "jvl"; private boolean _initialised = false; private Config _initialisedConfig = null; public static String i4jVersion = null; private String jvmmempc = null; private String jvmmemmax = null; }