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/* Copyright (c) 2009 Peter Troshin
*
* JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
*
* This library is free software; you can redistribute it and/or modify it under the terms of the
* Apache License version 2 as published by the Apache Software Foundation
*
* This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
* even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
* License for more details.
*
* A copy of the license is in apache_license.txt. It is also available here:
* @see: http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Any republication or derived work distributed in source code form
* must include this copyright and license notice.
*/
package compbio.metadata;
import java.util.List;
import javax.xml.bind.ValidationException;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlRootElement;
import compbio.util.Util;
/**
* Collection of presets and methods to manipulate them @see {@link Preset}
*
* @author pvtroshin
*
* @version 1.0 December 2009
* @param <T>
* type of executable.
*/
@XmlRootElement(name = "presets")
@XmlAccessorType(XmlAccessType.FIELD)
public class PresetManager<T> {
@XmlElement(required = true)
String runnerClassName;
@XmlElement(required = true)
List<Preset<T>> preset;
public static final String LOCAL_ENGINE_LIMIT_PRESET = "# LocalEngineExecutionLimit #";
public List<Preset<T>> getPresets() {
return preset;
}
public void setPresets(List<Preset<T>> presets) {
this.preset = presets;
}
/**
*
* @return fully qualified class name of type T
*/
public String getRunnerClassName() {
return runnerClassName;
}
public void setRunnerClassName(String runnerClassName) {
this.runnerClassName = runnerClassName;
}
/**
*
* @param presetName
* @return preset by its name, null if no preset found
*/
public Preset<T> getPresetByName(String presetName) {
for (Preset<T> p : preset) {
if (p.getName().equalsIgnoreCase(presetName)) {
return p;
}
}
return null;
}
boolean isComposite(String value) {
assert value != null;
return value.contains(" ");
}
boolean containsValue(List<String> values, String value) {
assert !Util.isEmpty(value);
for (String v : values) {
if (v.equals(value)) {
return true;
}
}
return false;
}
boolean isNumeric(String value) {
assert value != null;
try {
Double.parseDouble(value);
return true;
} catch (NumberFormatException e) {
// ignore
return false;
}
}
/**
* Checks whether preset option and parameter are defined in RunnerConfig
* object.
*
* TODO handle parameters with values properly!
*
* @throws ValidationException
* if preset is found to be invalid.
*
*/
public void validate(RunnerConfig<T> options) throws ValidationException {
for (Preset<T> p : preset) {
if (Util.isEmpty(p.name)) {
throw new ValidationException("Preset name must not be empty!");
}
List<String> optionNames = p.getOptions();
if (optionNames == null || optionNames.size() == 0) {
throw new ValidationException(
"At lease one option must be defined for a preset!");
}
for (String oName : optionNames) {
if (isComposite(oName)) {
String name = oName.split(" ")[0];
Argument<T> arg = getArgument(options, name);
String value = oName.split(" ")[1];
// Ignore numeric values
if (!isNumeric(value)
&& !containsValue(arg.getPossibleValues(), value)) {
throw new ValidationException("Value " + value
+ " is not found in the option " + name);
}
} else {
getArgument(options, oName);
}
}
}
}
Argument<T> getArgument(RunnerConfig<T> options, String optionName)
throws ValidationException {
Argument<T> arg = options.getArgumentByOptionName(optionName);
if (arg == null) {
throw new ValidationException(
"Option "
+ optionName
+ " is not found in the option list (<RunnerName>Parameter.xml file)");
}
return arg;
}
@Override
public String toString() {
String value = "Runner: " + this.runnerClassName + "\n";
for (Preset<T> p : preset) {
value += "##############################################################################\n" + p.toString() + "\n";
}
return value;
}
}
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