public static Config getDefaultMiscellaneous() {
Config.Builder cb = Config.newBuilder();
cb.put(Keys.verbose(), Defaults.verbose());
cb.put(Keys.schedulerService(), Defaults.schedulerService());
return cb.build();
}
public static Config getSandboxBinaries() {
Config.Builder cb = Config.newBuilder();
cb.put(Keys.executorSandboxBinary(), Defaults.executorSandboxBinary());
cb.put(Keys.stmgrSandboxBinary(), Defaults.stmgrSandboxBinary());
cb.put(Keys.tmasterSandboxBinary(), Defaults.tmasterSandboxBinary());
cb.put(Keys.shellSandboxBinary(), Defaults.shellSandboxBinary());
return cb.build();
}
public static Config getDefaultResources() {
Config.Builder cb = Config.newBuilder();
cb.put(Keys.stmgrRam(), Defaults.stmgrRam());
cb.put(Keys.instanceCpu(), Defaults.instanceCpu());
cb.put(Keys.instanceRam(), Defaults.instanceRam());
cb.put(Keys.instanceDisk(), Defaults.instanceDisk());
return cb.build();
}
public static Config getSandboxHome() {
Config.Builder cb = Config.newBuilder();
cb.put(Keys.heronSandboxHome(), Defaults.heronSandboxHome());
cb.put(Keys.heronSandboxBin(), Defaults.heronSandboxBin());
cb.put(Keys.heronSandboxConf(), Defaults.heronSandboxConf());
cb.put(Keys.heronSandboxLib(), Defaults.heronSandboxLib());
cb.put(Keys.javaSandboxHome(), Defaults.javaSandboxHome());
return cb.build();
}
/**
* Creates DirectoryValidator to ensure directories read from user (if any - default otherwise)
* settings via keys:
*
* <ul>
* <li>{@link DeploymentConfiguration#KEY_USER_CACHE_DIR}
* <li>{@link DeploymentConfiguration#KEY_USER_PERSISTENCE_CACHE_DIR}
* <li>{@link DeploymentConfiguration#KEY_SYSTEM_CACHE_DIR}
* <li>{@link DeploymentConfiguration#KEY_USER_LOG_DIR}
* <li>{@link DeploymentConfiguration#KEY_USER_TMP_DIR}
* <li>{@link DeploymentConfiguration#KEY_USER_LOCKS_DIR}
* </ul>
*/
public DirectoryValidator() {
dirsToCheck = new ArrayList<File>(6);
DeploymentConfiguration dc = JNLPRuntime.getConfiguration();
String[] keys =
new String[] {
DeploymentConfiguration.KEY_USER_CACHE_DIR,
DeploymentConfiguration.KEY_USER_PERSISTENCE_CACHE_DIR,
DeploymentConfiguration.KEY_SYSTEM_CACHE_DIR,
DeploymentConfiguration.KEY_USER_LOG_DIR,
DeploymentConfiguration.KEY_USER_TMP_DIR,
DeploymentConfiguration.KEY_USER_LOCKS_DIR
};
for (String key : keys) {
String value = dc.getProperty(key);
if (value == null) {
OutputController.getLogger()
.log(
OutputController.Level.MESSAGE_DEBUG,
"WARNING: key " + key + " has no value, setting to default value");
value = Defaults.getDefaults().get(key).getValue();
}
if (value == null) {
if (JNLPRuntime.isDebug()) {
OutputController.getLogger()
.log(
OutputController.Level.MESSAGE_DEBUG,
"WARNING: key " + key + " has no value, skipping");
}
continue;
}
File f = new File(value);
dirsToCheck.add(f);
}
}
public void l(int level, String str, boolean sysOnly) {
synchronized (MyLog.class) {
str = str.trim();
// Messages of this severity are handled specially
if (level == Log.ERROR || level == Log.WARN) {
Globals.setLastError(str);
}
if (level >= Defaults.getConsoleLogLevel()) {
Log.println(level, tag, str);
}
if (!sysOnly) { // some messages only go to the Android log
if (level >= Defaults.getUiLogLevel()) {
FTPServerService.log(level, str);
}
}
}
}
public static Config getSandboxDefaultFiles() {
Config.Builder cb = Config.newBuilder();
cb.put(Keys.clusterSandboxFile(), Defaults.clusterSandboxFile());
cb.put(Keys.defaultsSandboxFile(), Defaults.defaultsSandboxFile());
cb.put(Keys.metricsSinksSandboxFile(), Defaults.metricsSinksSandboxFile());
cb.put(Keys.packingSandboxFile(), Defaults.packingSandboxFile());
cb.put(Keys.schedulerSandboxFile(), Defaults.schedulerSandboxFile());
cb.put(Keys.stateManagerSandboxFile(), Defaults.stateManagerSandboxFile());
cb.put(Keys.systemSandboxFile(), Defaults.systemSandboxFile());
cb.put(Keys.uploaderSandboxFile(), Defaults.uploaderSandboxFile());
return cb.build();
}
public static Config getDefaultHome() {
Config.Builder cb = Config.newBuilder();
cb.put(Keys.heronHome(), Defaults.heronHome());
cb.put(Keys.heronBin(), Defaults.heronBin());
cb.put(Keys.heronConf(), Defaults.heronConf());
cb.put(Keys.heronDist(), Defaults.heronDist());
cb.put(Keys.heronEtc(), Defaults.heronEtc());
cb.put(Keys.heronLib(), Defaults.heronLib());
cb.put(Keys.javaHome(), Defaults.javaHome());
return cb.build();
}
/**
* Returns the caller UserDTO. If the caller is not set, the default for unauthenticated calls is
* returned instead.
*/
public static UserDTO get() {
if (caller.get() == null) {
// no caller set, try to get default username and password
Defaults defaults = (Defaults) Context.getBean(Context.Name.WEB_SERVICES_CALLER_DEFAULTS);
if (defaults.getUsername() != null && defaults.getPassword() != null) {
IUserSessionBean userSession =
(IUserSessionBean) Context.getBean(Context.Name.USER_SESSION);
UserDTO user =
userSession.webServicesAuthenticate(defaults.getUsername(), defaults.getPassword());
if (user != null) {
LOG.info("Using default username and password for " + "unauthenticated API call/s.");
set(user);
} else {
throw new SecurityException("Invalid default " + "username/password");
}
} else {
throw new SecurityException("No caller set.");
}
}
return caller.get();
}
public static Config getDefaultFilesAndPaths() {
Config.Builder cb = Config.newBuilder();
cb.put(Keys.corePackageUri(), Defaults.corePackageUri());
// cb.put(Keys.logDirectory(), Defaults.logDirectory());
cb.put(Keys.instanceClassPath(), Defaults.instanceClassPath());
cb.put(Keys.metricsManagerClassPath(), Defaults.metricsManagerClassPath());
cb.put(Keys.packingClassPath(), Defaults.packingClassPath());
cb.put(Keys.schedulerClassPath(), Defaults.schedulerClassPath());
cb.put(Keys.stateManagerClassPath(), Defaults.stateManagerClassPath());
cb.put(Keys.uploaderClassPath(), Defaults.uploaderClassPath());
return cb.build();
}
public static Config getSandboxFilesAndPaths() {
Config.Builder cb = Config.newBuilder();
cb.put(Keys.instanceSandboxClassPath(), Defaults.instanceSandboxClassPath());
cb.put(Keys.metricsManagerSandboxClassPath(), Defaults.metricsManagerSandboxClassPath());
cb.put(Keys.packingSandboxClassPath(), Defaults.packingSandboxClassPath());
cb.put(Keys.schedulerSandboxClassPath(), Defaults.schedulerSandboxClassPath());
cb.put(Keys.stateManagerSandboxClassPath(), Defaults.stateManagerSandboxClassPath());
cb.put(Keys.uploaderSandboxClassPath(), Defaults.uploaderSandboxClassPath());
return cb.build();
}
/**
* this is what a Mapper does
*
* @param valuein @return iterator over mapped key values
*/
@Override
public Iterable<KeyValueObject<PeakMZKey, ICluster>> mapValues(final ICluster valuein) {
double precursorMZ = valuein.getPrecursorMz();
List<KeyValueObject<PeakMZKey, ICluster>> ret =
new ArrayList<KeyValueObject<PeakMZKey, ICluster>>();
List<ISpectrum> clusteredSpectra = valuein.getClusteredSpectra();
if (!clusteredSpectra.isEmpty() && precursorMZ < MZIntensityUtilities.HIGHEST_USABLE_MZ) {
for (ISpectrum match : clusteredSpectra) {
ICluster cluster = ClusterUtilities.asCluster(match);
for (int peakMz : match.asMajorPeakMZs(Defaults.getMajorPeakCount())) {
PeakMZKey mzKey = new PeakMZKey(peakMz, precursorMZ);
ret.add(new KeyValueObject<PeakMZKey, ICluster>(mzKey, cluster));
}
}
}
return ret;
}
/** Create a default instance of F10. */
public F10() {
this(Defaults.getRandomizer(F10.class));
}
public static Config getSandboxJars() {
Config.Builder cb = Config.newBuilder();
cb.put(Keys.schedulerSandboxJar(), Defaults.schedulerSandboxJar());
return cb.build();
}
private EquatableArray(String serialized) {
this(Defaults.deserialize(serialized));
}
@Override
public String toString() {
return Defaults.serialize(content);
}
/** Create a default instance of F6. */
public F6() {
this(Defaults.getRandomizer(F6.class));
}