GATK ConfigFactory类介绍

ConfigFactory 是 GATK（Genome Analysis Toolkit）中用于管理和加载配置文件的类。虽然在 GATK 的不同版本中可能有不同的实现方式，但 ConfigFactory 通常是一个用于加载、解析和提供配置信息的实用工具类。以下是对 ConfigFactory 类的详细介绍：

功能概述

1. 配置文件加载:

   • ConfigFactory 主要负责从配置文件（例如 .properties 文件、JSON 文件或 YAML 文件）中读取配置信息。通过这种方式，程序可以灵活地管理各种参数和设置，而不需要硬编码到程序中。

2. 配置缓存:

   • 配置信息通常在程序启动时加载并缓存，避免在每次需要访问配置时重新加载文件。ConfigFactory可能会提供静态方法或单例模式来确保配置文件只加载一次，并在整个应用程序中共享。

3. 提供默认值:

   • 在配置文件中可能缺少某些参数时，ConfigFactory 可以提供默认值，确保程序的健壮性。

4. 环境变量支持:

   • 一些版本的 ConfigFactory 可能会支持从环境变量中加载配置，这样可以根据部署环境动态调整配置。

5. 类型转换:

   • ConfigFactory 通常会包含类型转换功能，将字符串形式的配置值转换为适当的数据类型，例如整数、布尔值或列表。

ConfigFactor源码

package org.broadinstitute.hellbender.utils.config;

import com.google.common.annotations.VisibleForTesting;
import htsjdk.samtools.util.Log;
import org.aeonbits.owner.Config;
import org.aeonbits.owner.ConfigCache;
import org.aeonbits.owner.Factory;
import org.apache.logging.log4j.Level;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.broadinstitute.hellbender.exceptions.GATKException;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.utils.ClassUtils;
import org.broadinstitute.hellbender.utils.LoggingUtils;
import org.broadinstitute.hellbender.utils.Utils;

import java.io.OutputStream;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.StandardOpenOption;
import java.text.SimpleDateFormat;
import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

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

    private static final Logger logger = LogManager.getLogger(ConfigFactory.class);

    //=======================================
    // Singleton members / methods:
    private static final ConfigFactory instance;

    static {
        instance = new ConfigFactory();
    }

    /**
     * @return An instance of this {@link ConfigFactory}, which can be used to create a configuration.
     */
    public static ConfigFactory getInstance() {
        return instance;
    }

    // This class is a singleton, so no public construction.
    private ConfigFactory() {}

    //=======================================

    /**
     * A regex to use to look for variables in the Sources annotation
     */
    private static final Pattern sourcesAnnotationPathVariablePattern = Pattern.compile("\\$\\{(.*)}");

    /**
     * Value to set each variable for configuration file paths when the variable
     * has not been set in either Java System properties or environment properties.
     */
    @VisibleForTesting
    static final String NO_PATH_VARIABLE_VALUE = "/dev/null";

    /**
     * A set to keep track of the classes we've already resolved for configuration path purposes:
     */
    private final Set<Class<? extends Config>> alreadyResolvedPathVariables = new HashSet<>();

    // =================================================================================================================

    /**
     * Checks each of the given {@code filenameProperties} for if they are defined in system {@link System#getProperties()}
     * or environment {@link System#getenv()} properties.  If they are not, this method will set them in the
     * {@link org.aeonbits.owner.ConfigFactory} to an empty file path so the {@link org.aeonbits.owner.ConfigFactory} will know to try to resolve them as
     * variables at load-time (and not as raw paths).
     * @param filenameProperties A {@link List} of filename properties as specified in {@link Config} {@link org.aeonbits.owner.Config.Sources} annotations to check for existence in system and environment properties.
     */
    @VisibleForTesting
    void checkFileNamePropertyExistenceAndSetConfigFactoryProperties(final List<String> filenameProperties) {
        // Grab the system properties:
        final Properties systemProperties = System.getProperties();

        // Grab the environment properties:
        final Map<String, String> environmentProperties = System.getenv();

        // Make sure that if our property isn't in the system, environment, and ConfigFactory
        // properties, that we set it to a neutral value that will not contain
        // anything (so that the property will fall back into the next value).
        for (final String property : filenameProperties) {

            if ( environmentProperties.containsKey(property) ) {
                logger.debug("Config path variable found in Environment Properties: " + property + "=" + environmentProperties.get(property) + " - will search for config here.");
            }
            else if ( systemProperties.containsKey(property) ) {
                logger.debug("Config path variable found in System Properties: " + property + "=" + systemProperties.get(property) + " - will search for config here.");
            }
            else if ( org.aeonbits.owner.ConfigFactory.getProperties().containsKey(property) ) {
                logger.debug("Config path variable found in Config Factory Properties(probably from the command-line): " + property + "=" + org.aeonbits.owner.ConfigFactory.getProperty(property) + " - will search for config here.");
            }
            else {
                logger.debug("Config path variable not found: " + property +
                        " - setting value to default empty variable: " + (NO_PATH_VARIABLE_VALUE == null ? "null" : String.valueOf(NO_PATH_VARIABLE_VALUE)) );
                org.aeonbits.owner.ConfigFactory.setProperty(property, NO_PATH_VARIABLE_VALUE);
            }
        }
    }

    /**
     * Get a list of the config file variables from the given {@link Config} classes.
     * @param configurationClasses A list of configuration classes from which to extract variable names in their {@link org.aeonbits.owner.Config.Sources}.
     * @return A list of variables in the {@link org.aeonbits.owner.Config.Sources} of the given {@code configurationClasses}
     */
    @VisibleForTesting
    List<String> getConfigPathVariableNamesFromConfigClasses(final List<Class<?>> configurationClasses) {

        final List<String> configPathVariableNames = new ArrayList<>();

        // Loop through our classes and grab any sources with variables in there:
        for ( final Class<?> clazz : ClassUtils.getClassesOfType(Config.class, configurationClasses) ) {
            @SuppressWarnings("unchecked")
            final Class<? extends Config> castedClass = (Class<? extends Config>) clazz;
            configPathVariableNames.addAll( getSourcesAnnotationPathVariables(castedClass));
        }

        return configPathVariableNames;
    }

    /**
     * Get a list of the config file variables from the given {@link Config} class.
     * @param configClass A configuration class from which to extract variable names in its {@link org.aeonbits.owner.Config.Sources}.
     * @return A list of variables in the {@link org.aeonbits.owner.Config.Sources} of the given {