org.broadinstitute.hellbender.utils.config

Class ConfigFactory

java.lang.Object

org.broadinstitute.hellbender.utils.config.ConfigFactory

public final class ConfigFactory
extends java.lang.Object

A singleton class to act as a user interface for loading configuration files from org.aeonbits.owner. This class wraps functionality in the org.aeonbits.owner configuration utilities to be a more GATK-specific interface. Created by jonn on 7/19/17.

Method Summary

Modifier and Type	Method and Description
<T extends org.aeonbits.owner.Config> T	create(java.lang.Class<? extends T> clazz, java.util.Map<?,?>... imports) Wrapper around ConfigFactory.create(Class, Map[]) which will ensure that path variables specified in Config.Sources annotations are resolved prior to creation.
static <T extends org.aeonbits.owner.Config> void	dumpConfigSettings(T config, java.nio.file.Path outFilePath) Dump the configuration to a file that can be easily read into Properties.
<T extends org.aeonbits.owner.Config> T	get(java.lang.Object key) Wrapper around ConfigCache.get(Object).
static java.lang.String	getConfigFilenameFromArgs(java.lang.String[] args, java.lang.String configFileOption) Get the configuration file name from the given arguments.
GATKConfig	getGATKConfig() Quick way to get the GATK configuration.
static ConfigFactory	getInstance()
<T extends org.aeonbits.owner.Config> T	getOrCreate(java.lang.Class<? extends T> clazz, java.util.Map<?,?>... imports) Wrapper around ConfigCache.getOrCreate(Class, Map[]) which will ensure that path variables specified in Config.Sources annotations are resolved prior to creation.
<T extends org.aeonbits.owner.Config> T	getOrCreate(org.aeonbits.owner.Factory factory, java.lang.Class<? extends T> clazz, java.util.Map<?,?>... imports) Wrapper around ConfigCache.getOrCreate(Factory, Class, Map[]) which will ensure that path variables specified in Config.Sources annotations are resolved prior to creation.
<T extends org.aeonbits.owner.Config> T	getOrCreate(org.aeonbits.owner.Factory factory, java.lang.Object key, java.lang.Class<? extends T> clazz, java.util.Map<?,?>... imports) Wrapper around ConfigCache.getOrCreate(Factory, Object, Class, Map[]) which will ensure that path variables specified in Config.Sources annotations are resolved prior to creation.
<T extends org.aeonbits.owner.Config> T	getOrCreate(java.lang.Object key, java.lang.Class<? extends T> clazz, java.util.Map<?,?>... imports) Wrapper around ConfigCache.getOrCreate(Object, Class, Map[]) which will ensure that path variables specified in Config.Sources annotations are resolved prior to creation.
void	initializeConfigurationsFromCommandLineArgs(java.lang.String[] argList, java.lang.String configFileOption) Get the configuration filename from the command-line (if it exists) and create a configuration for it.
<T extends org.aeonbits.owner.Config> void	initializeConfigurationsFromCommandLineArgs(java.lang.String[] argList, java.lang.String configFileOption, java.lang.Class<? extends T> configClass) Get the configuration from filename the command-line (if it exists) and create a configuration for it of the given type.
<T extends org.aeonbits.owner.Config> void	injectSystemPropertiesFromConfig(T config) Injects system properties from the given configuration file.
static <T extends org.aeonbits.owner.Config> void	logConfigFields(T config) Logs all the parameters in the given Config object at Level.DEBUG
static <T extends org.aeonbits.owner.Config> void	logConfigFields(T config, htsjdk.samtools.util.Log.LogLevel logLevel) Logs all the parameters in the given Config object at the given Log.LogLevel

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getInstance

public static ConfigFactory getInstance()

Returns:

An instance of this ConfigFactory, which can be used to create a configuration.

getGATKConfig

public GATKConfig getGATKConfig()

Quick way to get the GATK configuration.

Returns:

The GATK Configuration.

dumpConfigSettings

public static <T extends org.aeonbits.owner.Config> void dumpConfigSettings(T config,
                                                                            java.nio.file.Path outFilePath)

Dump the configuration to a file that can be easily read into Properties.

Type Parameters:

T - Some configuration class that extends Config.

Parameters:

config - Configuration instance to dump.

outFilePath - Path to output location.

create

public <T extends org.aeonbits.owner.Config> T create(java.lang.Class<? extends T> clazz,
                                                      java.util.Map<?,?>... imports)

Wrapper around ConfigFactory.create(Class, Map[]) which will ensure that path variables specified in Config.Sources annotations are resolved prior to creation. Creates a Config instance from the specified interface

Type Parameters:

T - type of the interface.

Parameters:

clazz - the interface extending from Config that you want to instantiate.

imports - additional variables to be used to resolve the properties.

Returns:

an object implementing the given interface, which maps methods to property values.

getOrCreate

public <T extends org.aeonbits.owner.Config> T getOrCreate(java.lang.Class<? extends T> clazz,
                                                           java.util.Map<?,?>... imports)

Wrapper around ConfigCache.getOrCreate(Class, Map[]) which will ensure that path variables specified in Config.Sources annotations are resolved prior to creation. Gets from the cache or create, an instance of the given class using the given imports. The factory used to create new instances is the static ConfigFactory.INSTANCE.

Type Parameters:

T - type of the interface.

Parameters:

clazz - the interface extending from Config that you want to instantiate.

imports - additional variables to be used to resolve the properties.

Returns:

an object implementing the given interface, that can be taken from the cache, which maps methods to property values.

getOrCreate

public <T extends org.aeonbits.owner.Config> T getOrCreate(org.aeonbits.owner.Factory factory,
                                                           java.lang.Class<? extends T> clazz,
                                                           java.util.Map<?,?>... imports)

Wrapper around ConfigCache.getOrCreate(Factory, Class, Map[]) which will ensure that path variables specified in Config.Sources annotations are resolved prior to creation. Gets from the cache or create, an instance of the given class using the given imports.

Type Parameters:

T - type of the interface.

Parameters:

factory - the factory to use to eventually create the instance.

clazz - the interface extending from Config that you want to instantiate.

imports - additional variables to be used to resolve the properties.

Returns:

an object implementing the given interface, that can be taken from the cache, which maps methods to property values.

getOrCreate

public <T extends org.aeonbits.owner.Config> T getOrCreate(java.lang.Object key,
                                                           java.lang.Class<? extends T> clazz,
                                                           java.util.Map<?,?>... imports)

Wrapper around ConfigCache.getOrCreate(Object, Class, Map[]) which will ensure that path variables specified in Config.Sources annotations are resolved prior to creation. Gets from the cache or create, an instance of the given class using the given imports. The factory used to create new instances is the static ConfigFactory.INSTANCE.

Type Parameters:

T - type of the interface.

Parameters:

key - the key object to be used to identify the instance in the cache.

clazz - the interface extending from Config that you want to instantiate.

imports - additional variables to be used to resolve the properties.

Returns:

an object implementing the given interface, that can be taken from the cache, which maps methods to property values.

getOrCreate

public <T extends org.aeonbits.owner.Config> T getOrCreate(org.aeonbits.owner.Factory factory,
                                                           java.lang.Object key,
                                                           java.lang.Class<? extends T> clazz,
                                                           java.util.Map<?,?>... imports)

Wrapper around ConfigCache.getOrCreate(Factory, Object, Class, Map[]) which will ensure that path variables specified in Config.Sources annotations are resolved prior to creation.

Type Parameters:

T - type of the interface.

Parameters:

factory - the factory to use to eventually create the instance.

key - the key object to be used to identify the instance in the cache.

clazz - the interface extending from Config that you want to instantiate.

imports - additional variables to be used to resolve the properties.

Returns:

an object implementing the given interface, that can be taken from the cache, which maps methods to property values.

get

public <T extends org.aeonbits.owner.Config> T get(java.lang.Object key)

Wrapper around ConfigCache.get(Object). This method is here to complete the interface for getting Config objects. Gets from the cache the Config instance identified by the given key.

Type Parameters:

T - type of the interface.

Parameters:

key - the key object to be used to identify the instance in the cache.

Returns:

the Config object from the cache if exists, or null if it doesn't.

getConfigFilenameFromArgs

public static java.lang.String getConfigFilenameFromArgs(java.lang.String[] args,
                                                         java.lang.String configFileOption)

Get the configuration file name from the given arguments. NOTE: Does NOT validate that the resulting string is a valid configuration file.

Parameters:

args - Command-line arguments passed to this program.

configFileOption - The command-line option indicating that the config file is next

Returns:

The name of the configuration file for this program or null.

initializeConfigurationsFromCommandLineArgs

public void initializeConfigurationsFromCommandLineArgs(java.lang.String[] argList,
                                                        java.lang.String configFileOption)

Get the configuration filename from the command-line (if it exists) and create a configuration for it. Configuration type defaults to GATKConfig Also sets system-level properties from the system config file.

Parameters:

argList - The list of arguments from which to read the config file.

configFileOption - The command-line option specifying the main configuration file.

initializeConfigurationsFromCommandLineArgs

public <T extends org.aeonbits.owner.Config> void initializeConfigurationsFromCommandLineArgs(java.lang.String[] argList,
                                                                                              java.lang.String configFileOption,
                                                                                              java.lang.Class<? extends T> configClass)

Get the configuration from filename the command-line (if it exists) and create a configuration for it of the given type. Also sets system-level properties from the system config file.

Parameters:

argList - The list of arguments from which to read the config file.

configFileOption - The command-line option specifying the main configuration file.

configClass - The class of the configuration file to instantiate.

injectSystemPropertiesFromConfig

public <T extends org.aeonbits.owner.Config> void injectSystemPropertiesFromConfig(T config)

Injects system properties from the given configuration file. System properties are specified by the presence of the SystemProperty annotation. This will NOT override properties that already exist in the system.

Parameters:

config - The GATKConfig object from which to inject system properties.

logConfigFields

public static <T extends org.aeonbits.owner.Config> void logConfigFields(T config)

Logs all the parameters in the given Config object at Level.DEBUG

Type Parameters:

T - any Config type to use to log all configuration information.

Parameters:

config - A Config object from which to log all parameters and values.

logConfigFields

public static <T extends org.aeonbits.owner.Config> void logConfigFields(T config,
                                                                         htsjdk.samtools.util.Log.LogLevel logLevel)

Logs all the parameters in the given Config object at the given Log.LogLevel

Type Parameters:

T - any Config type to use to log all configuration information.

Parameters:

config - A Config object from which to log all parameters and values.

logLevel - The log Log.LogLevel at which to log the data in config