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/* Copyright (c) 2011 Peter Troshin
*
* JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0
*
* 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.ws.client;
import static compbio.ws.client.Constraints.pseparator;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.net.MalformedURLException;
import java.net.URL;
import compbio.data.msa.Metadata;
import compbio.metadata.Limit;
import compbio.metadata.LimitsManager;
import compbio.metadata.Option;
import compbio.metadata.Preset;
import compbio.metadata.PresetManager;
import compbio.metadata.RunnerConfig;
import compbio.metadata.WrongParameterException;
public class MetadataHelper {
/**
* Returns a list of options supported by web service
*
* @param <T>
* web service type
* @param msaws
* web service proxy
* @return List of options supported by a web service
*/
static <T> List<Option<T>> getParametersList(Metadata<T> msaws) {
assert msaws != null;
RunnerConfig<T> config = msaws.getRunnerOptions();
if (config == null) {
return Collections.emptyList();
}
return config.getArguments();
}
/**
* Returns a list of options supported by web service
*
* @param <T>
* web service type
* @param msaws
* web service proxy
* @param host
* the server URL, as a string
* @return List of options supported by a web service
*/
static <T> List<Option<T>> getParametersList(Metadata<T> msaws, String host) throws MalformedURLException {
assert msaws != null;
RunnerConfig<T> config = msaws.getRunnerOptions();
if (config == null) {
return Collections.emptyList();
}
List<Option<T>> opts = config.getArguments();
for (Option<T> o : opts) {
o.setBasicURL(new URL(host + "/"));
}
return opts;
}
/**
* Returns an objects from which the list of presets supported by web
* service <T> can be obtained
*
* @param <T>
* web service type
* @param msaws
* web service proxy
* @return PresetManager, object which operates on presets
*/
static <T> PresetManager<T> getPresetList(Metadata<T> msaws) {
assert msaws != null;
PresetManager<T> presetman = msaws.getPresets();
return presetman;
}
/**
* Returns a list of limits supported by web service Each limit correspond
* to a particular preset.
*
* @param <T>
* web service type
* @param msaws
* web service proxy
* @return List of limits supported by a web service
*/
static <T> List<Limit<T>> getLimits(Metadata<T> msaws) {
assert msaws != null;
LimitsManager<T> lmanger = msaws.getLimits();
return lmanger != null ? lmanger.getLimits() : null;
}
/**
* Returns {@code Preset} by its name
*
* @see Preset
* @param <T>
* @param msaws
* @param presetName
* @return Return a Preset by its optionName
*/
static <T> Preset<T> getPreset(Metadata<T> msaws, String presetName) {
assert presetName != null;
PresetManager<T> presets = MetadataHelper.getPresetList(msaws);
if (presets == null) {
System.out.println("No presets are supported by the service! Ignoring -r directive!");
return null;
}
Preset<T> pre = presets.getPresetByName(presetName);
if (pre == null) {
System.out.println("Cannot find preset: " + presetName + " WARN: ignoring -r directive!");
}
return pre;
}
/**
* Converts options supplied via parameters file into {@code Option} objects
*
* @param <T>
* web service type
* @param params
* @param options
* @return List of Options of type T
*/
static <T> List<Option<T>> processParameters(List<String> params,
RunnerConfig<T> options) {
List<Option<T>> chosenOptions = new ArrayList<Option<T>>();
for (String param : params) {
String oname = null;
if (isParameter(param)) {
oname = getParamName(param);
} else {
oname = param;
}
Option<T> o = options.getArgumentByOptionName(oname);
if (o == null) {
System.out.println("WARN ignoring unsuppoted parameter: " + oname);
continue;
}
if (isParameter(param)) {
try {
o.setValue(getParamValue(param));
} catch (WrongParameterException e) {
System.out.println("Problem setting value for the parameter: " + param);
e.printStackTrace();
}
}
chosenOptions.add(o);
}
return chosenOptions;
}
static String getParamName(String fullName) {
assert isParameter(fullName);
return fullName.substring(0, fullName.indexOf(pseparator));
}
static String getParamValue(String fullName) {
assert isParameter(fullName);
return fullName.substring(fullName.indexOf(pseparator) + 1);
}
static boolean isParameter(String param) {
return param.contains(pseparator);
}
}
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