net.maizegenetics.plugindef.ParameterCache Maven / Gradle / Ivy
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TASSEL 6 is a software package to evaluate traits association. Feature Tables are at the heart of the package where, a feature is a range of positions or a single position. Row in the that table are taxon.
package net.maizegenetics.plugindef;
import net.maizegenetics.util.Utils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import java.io.BufferedReader;
import java.util.Enumeration;
import java.util.Optional;
import java.util.Properties;
/**
* This class is for storing a cache of parameters retrieved from a {@link java.util.Properties}
* file that is available to all plugins on the command line.
* This is used when run_pipeline.pl -configParameters config.txt... is used.
*
* config.txt example entries as follow... First five are using by GetDBConnectionPlugin -config config.txt
* but that should be refactored to individual PluginParameters.
* Then entry example would be GetDBConnectionPlugin.DBType=sqlite
* KinshipPlugin.method=TYPE is the standard. PLUGIN_NAME.COMMAND_LINE_NAME=VALUE
*
* host=localHost
* user=sqlite
* password=sqlite
* DB=/tempFileDir/outputDir/phgTestDB.db
* DBtype=sqlite
* KinshipPlugin.method=Normalized_IBS
*
* @author Terry Casstevens
* Created January 05, 2018
*/
public class ParameterCache {
private static final Logger myLogger = LogManager.getLogger(ParameterCache.class);
private static Properties CACHE = null;
private ParameterCache() {
}
/**
* Loads the parameter cache with the values in the given {@link java.util.Properties} file.
*
* @param filename file name
*/
public static void load(String filename) {
if (filename == null || filename.trim().isEmpty()) {
CACHE = null;
return;
}
myLogger.info("load: loading parameter cache with: " + filename);
CACHE = new Properties();
try (BufferedReader reader = Utils.getBufferedReader(filename)) {
CACHE.load(reader);
} catch (Exception e) {
CACHE = null;
myLogger.debug(e.getMessage(), e);
throw new IllegalArgumentException("ParameterCache: load: problem reading properties file: " + filename);
}
for (String key : CACHE.stringPropertyNames()) {
myLogger.info("ParameterCache: key: " + key + " value: " + CACHE.getProperty(key));
}
}
/**
* Returns the value if any for the given plugin and parameter. Value for PluginClassName.parameter will
* be returned if it exists. If not, value for parameter will be returned. Otherwise, an empty optional.
*
* @param plugin plugin
* @param parameter parameter
*
* @return value if exists
*/
public static Optional value(Plugin plugin, String parameter) {
if (CACHE == null) {
return Optional.empty();
}
String value = CACHE.getProperty(Utils.getBasename(plugin.getClass().getName()) + "." + parameter);
if (value != null) {
return Optional.of(value);
}
value = CACHE.getProperty(parameter);
return Optional.ofNullable(value);
}
/**
* Returns the value if any for the given key.
*
* @param key key
*
* @return value if exists
*/
public static Optional value(String key) {
if (CACHE == null) {
return Optional.empty();
}
return Optional.ofNullable(CACHE.getProperty(key));
}
/**
* Returns true if this cache has been loaded with values.
*
* @return true if this cache has been loaded with values.
*/
public static boolean hasValues() {
return CACHE != null;
}
public static Enumeration keys() {
if (CACHE == null) {
return null;
}
return CACHE.propertyNames();
}
}