1 /* Copyright (c) 2011 Peter Troshin
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3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0
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5 * This library is free software; you can redistribute it and/or modify it under the terms of the
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6 * Apache License version 2 as published by the Apache Software Foundation
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8 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
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9 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
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10 * License for more details.
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12 * A copy of the license is in apache_license.txt. It is also available here:
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13 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
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15 * Any republication or derived work distributed in source code form
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16 * must include this copyright and license notice.
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19 package compbio.ws.client;
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21 import static compbio.ws.client.Constraints.inputkey;
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22 import static compbio.ws.client.Constraints.limitList;
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23 import static compbio.ws.client.Constraints.outputkey;
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24 import static compbio.ws.client.Constraints.paramFile;
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25 import static compbio.ws.client.Constraints.paramList;
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26 import static compbio.ws.client.Constraints.presetList;
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27 import static compbio.ws.client.Constraints.presetkey;
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28 import static compbio.ws.client.Constraints.pseparator;
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30 import java.io.Closeable;
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31 import java.io.File;
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32 import java.io.IOException;
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33 import java.io.PrintWriter;
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34 import java.io.Writer;
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35 import java.net.MalformedURLException;
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36 import java.net.URL;
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37 import java.util.List;
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38 import java.util.logging.Level;
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39 import java.util.logging.Logger;
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41 import javax.xml.namespace.QName;
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42 import javax.xml.ws.Service;
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43 import javax.xml.ws.WebServiceException;
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45 import compbio.data.msa.SequenceAnnotation;
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46 import compbio.data.sequence.FastaSequence;
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47 import compbio.data.sequence.ScoreManager;
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48 import compbio.data.sequence.SequenceUtil;
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49 import compbio.data.sequence.UnknownFileFormatException;
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50 import compbio.metadata.JobSubmissionException;
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51 import compbio.metadata.Option;
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52 import compbio.metadata.Preset;
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53 import compbio.metadata.ResultNotAvailableException;
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54 import compbio.metadata.WrongParameterException;
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55 import compbio.ws.server.AAConWS;
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58 * A command line client for AACon web service
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63 public class AAConClient {
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66 * Use java.util.Logger instead of log4j logger to reduce the size of the
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69 private static final Logger log = Logger.getLogger(AAConClient.class.getCanonicalName());
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72 * The fully qualified web service namespace
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74 static final String QUALIFIED_SERVICE_NAME = "http://msa.data.compbio/01/12/2010/";
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79 static final String hostname = "http://www.compbio.dundee.ac.uk/aacon";
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84 static final String serviceName = "AAConWS";
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87 * Connects to the service and do the job as requested, if something goes
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88 * wrong reports or/and prints usage help.
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91 * command line options
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92 * @throws IOException
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93 * if the system cannot read/write from/into the file system
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95 @SuppressWarnings("unchecked")
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96 AAConClient(String[] cmd) throws IOException {
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97 File inputFile = IOHelper.getFile(cmd, inputkey, true);
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98 File outFile = IOHelper.getFile(cmd, outputkey, false);
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99 File parametersFile = IOHelper.getFile(cmd, paramFile, true);
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100 String presetName = CmdHelper.getPresetName(cmd);
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102 SequenceAnnotation<AAConWS> msaws = connect();
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103 Preset<AAConWS> preset = null;
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104 if (presetName != null) {
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105 preset = MetadataHelper.getPreset(msaws, presetName);
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107 List<Option<AAConWS>> customOptions = null;
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108 if (parametersFile != null) {
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109 List<String> prms = IOHelper.loadParameters(parametersFile);
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110 customOptions = MetadataHelper.processParameters(prms, msaws.getRunnerOptions());
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112 ScoreManager result = null;
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113 if (inputFile != null) {
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114 System.out.println("Calculating conservation...");
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115 result = analize(inputFile, msaws, preset, customOptions);
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116 Writer outStream = null;
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117 if (outFile != null) {
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118 outStream = IOHelper.getWriter(outFile);
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120 // this stream is going to be closed later which is fine as
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121 // std.out will not be
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122 outStream = new PrintWriter(System.out, true);
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124 writeOut(outStream, result);
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125 // stream is closed in the method no need to close it here
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128 boolean listParameters = CmdHelper.listParameters(cmd);
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129 if (listParameters) {
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130 System.out.println(MetadataHelper.getParametersList(msaws));
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132 boolean listPreset = CmdHelper.listPresets(cmd);
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134 System.out.println(MetadataHelper.getPresetList(msaws));
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136 boolean listLimits = CmdHelper.listLimits(cmd);
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138 System.out.println(MetadataHelper.getLimits(msaws));
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140 log.fine("Disconnecting...");
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141 ((Closeable) msaws).close();
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142 log.fine("Disconnected successfully!");
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146 * Outputs AAcon results into the file represented by the outStream
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150 * the AACon scores to output
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152 static void writeOut(Writer writer, ScoreManager result) {
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154 result.writeOut(writer);
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155 } catch (IOException e) {
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156 System.err.println("Problems writing output file! Stack trace is below: ");
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157 e.printStackTrace();
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159 if (writer != null) {
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162 } catch (IOException ignored) {
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163 // e.printStackTrace();
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170 * Connects to a AACon web service by the host and the service name
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173 * @return {@link AlignmentAnnotation}
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174 * @throws WebServiceException
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175 * if cannot connect to a web service
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177 public static SequenceAnnotation<AAConWS> connect()
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178 throws WebServiceException {
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180 log.log(Level.FINE, "Attempting to connect...");
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182 url = new URL(hostname + "/" + "AAConWS" + "?wsdl");
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183 } catch (MalformedURLException e) {
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184 e.printStackTrace();
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185 // ignore as the host name is already verified
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187 QName qname = new QName(QUALIFIED_SERVICE_NAME, "AAConWS");
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188 Service serv = Service.create(url, qname);
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189 QName portName = new QName(QUALIFIED_SERVICE_NAME, "AAConWS" + "Port");
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191 @SuppressWarnings("unchecked")
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192 SequenceAnnotation<AAConWS> serviceIF = serv.getPort(portName, SequenceAnnotation.class);
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194 log.log(Level.FINE, "Connected successfully!");
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199 * Calculate conservation for sequences loaded from the file
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202 * a web service proxy
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204 * the file to read the results from
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206 * Preset to use optional
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207 * @param customOptions
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208 * the list of options
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209 * @return Set<Score> the conservation scores
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210 * @throws UnknownFileFormatException
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212 static ScoreManager analize(File file, SequenceAnnotation<AAConWS> wsproxy,
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213 Preset<AAConWS> preset, List<Option<AAConWS>> customOptions) {
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215 List<FastaSequence> fastalist = null;
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216 ScoreManager scores = null;
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218 fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());
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220 String jobId = null;
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221 if (customOptions != null && preset != null) {
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222 System.out.println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");
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224 if (customOptions != null) {
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225 jobId = wsproxy.customAnalize(fastalist, customOptions);
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226 } else if (preset != null) {
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227 jobId = wsproxy.presetAnalize(fastalist, preset);
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229 jobId = wsproxy.analize(fastalist);
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231 Thread.sleep(1000);
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232 scores = wsproxy.getAnnotation(jobId);
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234 } catch (IOException e) {
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235 System.err.println("Exception while reading the input file. "
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236 + "Check that the input file contains a list of fasta formatted sequences! "
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237 + "Exception details are below:");
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238 e.printStackTrace();
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239 } catch (JobSubmissionException e) {
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240 System.err.println("Exception while submitting job to a web server. "
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241 + "Exception details are below:");
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242 e.printStackTrace();
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243 } catch (ResultNotAvailableException e) {
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244 System.err.println("Exception while waiting for results. "
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245 + "Exception details are below:");
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246 e.printStackTrace();
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247 } catch (InterruptedException ignored) {
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248 // ignore and propagate an interruption
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249 Thread.currentThread().interrupt();
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250 } catch (WrongParameterException e) {
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251 System.err.println("Exception while parsing the web method input parameters. "
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252 + "Exception details are below:");
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253 e.printStackTrace();
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254 } catch (UnknownFileFormatException e) {
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255 System.err.println("Exception while attempting to read the input file "
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256 + "Exception details are below:");
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257 System.out.println(e.getMessage());
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258 e.printStackTrace();
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264 * Prints AAConClient usage information to standard out
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266 * @param exitStatus
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268 static void printUsage(int exitStatus) {
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269 System.out.println();
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270 System.out.println("Usage: <Class or Jar file name> ACTION [OPTIONS] ");
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271 System.out.println();
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272 System.out.println("ACTIONS: ");
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273 System.out.println(inputkey + pseparator + "<inputFile> - full path to fasta or Clustal formatted alignment file ");
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274 System.out.println(paramList + " - lists parameters supported by web service");
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275 System.out.println(presetList + " - lists presets supported by web service");
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276 System.out.println(limitList + " - lists web services limits");
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277 System.out.println("Please note that if input file is specified other actions are ignored\n");
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278 System.out.println("OPTIONS (only for use with -i action):");
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279 System.out.println(presetkey + pseparator + "<presetName> - name of the preset to use");
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280 System.out.println(outputkey + pseparator + "<outputFile> - full path to the file where to write the result");
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281 System.out.println("-f=<parameterInputFile> - the name of the file with the list of parameters to use.");
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282 System.out.println("Please note that -r and -f options cannot be used together. "
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283 + "Conservation is calculated with either a preset or parameters from the file, but not both!");
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284 System.exit(exitStatus);
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288 * Starts command line client, if no parameters are supplied prints help.
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291 * Usage: <Class or Jar file name> ACTION [OPTIONS]
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293 * -i=<inputFile> - full path to fasta or Clustal formatted
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296 * -parameters - lists parameters supported by web service
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298 * -presets - lists presets supported by web service
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300 * -limits - lists web services limits. Please note that if input
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301 * file is specified other actions are ignored
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303 * OPTIONS: (only for use with -i action):
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305 * -r=<presetName> - name of the preset to use
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307 * -o=<outputFile> - full path to the file where to write results
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308 * -f=<parameterInputFile> - the name of the file with the list
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309 * of parameters to use. Please note that -r and -f options
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310 * cannot be used together. Conservation is calculated with
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311 * either a preset or parameters from the file, but not both!
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314 public static void main(String[] args) {
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316 if (args == null) {
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319 if (args.length < 1) {
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320 System.out.println("No options is specified! ");
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325 new AAConClient(args);
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326 } catch (IOException e) {
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327 log.log(Level.SEVERE, "IOException in client! " + e.getMessage(), e.getCause());
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328 System.err.println("Cannot write output file! Stack trace: ");
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329 e.printStackTrace();
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