1 /* Copyright (c) 2010 Peter Troshin
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3 * Amino Acid Conservation Web Service client @version: 1.0
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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.OutputStream;
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34 import java.net.MalformedURLException;
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35 import java.net.URL;
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36 import java.util.HashSet;
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37 import java.util.List;
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38 import java.util.Map;
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39 import java.util.Set;
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40 import java.util.logging.Level;
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41 import java.util.logging.Logger;
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43 import javax.xml.namespace.QName;
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44 import javax.xml.ws.Service;
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45 import javax.xml.ws.WebServiceException;
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47 import compbio.data.msa.SequenceAnnotation;
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48 import compbio.data.sequence.FastaSequence;
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49 import compbio.data.sequence.Score;
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50 import compbio.data.sequence.SequenceUtil;
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51 import compbio.data.sequence.UnknownFileFormatException;
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52 import compbio.metadata.JobSubmissionException;
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53 import compbio.metadata.Option;
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54 import compbio.metadata.Preset;
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55 import compbio.metadata.ResultNotAvailableException;
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56 import compbio.metadata.WrongParameterException;
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57 import compbio.ws.server.AAConWS;
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60 * A command line client for AACon web service
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65 public class AAConClient {
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68 * Use java.util.Logger instead of log4j logger to reduce the size of the
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71 private static final Logger log = Logger.getLogger(AAConClient.class
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72 .getCanonicalName());
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75 * The fully qualified web service namespace
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77 static final String QUALIFIED_SERVICE_NAME = "http://msa.data.compbio/01/12/2010/";
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82 static final String hostname = "http://www.compbio.dundee.ac.uk/aacon";
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83 // static final String hostname = "http://localhost:8080/jabaws";
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88 static final String serviceName = "AAConWS";
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91 * Connects to the service and do the job as requested, if something goes
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92 * wrong reports or/and prints usage help.
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95 * command line options
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96 * @throws IOException
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97 * if the system cannot read/write from/into the file system
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99 @SuppressWarnings("unchecked")
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100 AAConClient(String[] cmd) throws IOException {
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102 File inputFile = IOHelper.getFile(cmd, inputkey, true);
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103 File outFile = IOHelper.getFile(cmd, outputkey, false);
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104 File parametersFile = IOHelper.getFile(cmd, paramFile, true);
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105 String presetName = CmdHelper.getPresetName(cmd);
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107 SequenceAnnotation<AAConWS> msaws = connect();
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108 Preset<AAConWS> preset = null;
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109 if (presetName != null) {
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110 preset = MetadataHelper.getPreset(msaws, presetName);
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112 List<Option<AAConWS>> customOptions = null;
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113 if (parametersFile != null) {
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114 List<String> prms = IOHelper.loadParameters(parametersFile);
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115 customOptions = MetadataHelper.processParameters(prms,
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116 msaws.getRunnerOptions());
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118 Map<String, HashSet<Score>> result = null;
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119 if (inputFile != null) {
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120 System.out.println("Calculating conservation...");
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121 result = analize(inputFile, msaws, preset, customOptions);
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122 OutputStream outStream = null;
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123 if (outFile != null) {
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124 outStream = IOHelper.getOutStream(outFile);
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126 // this stream is going to be closed later which is fine as
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127 // std.out will not be
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128 outStream = System.out;
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130 writeOut(outStream, result);
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131 // stream is closed in the method no need to close it here
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134 boolean listParameters = CmdHelper.listParameters(cmd);
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135 if (listParameters) {
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136 System.out.println(MetadataHelper.getParametersList(msaws));
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138 boolean listPreset = CmdHelper.listPresets(cmd);
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140 System.out.println(MetadataHelper.getPresetList(msaws));
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142 boolean listLimits = CmdHelper.listLimits(cmd);
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144 System.out.println(MetadataHelper.getLimits(msaws));
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146 log.fine("Disconnecting...");
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147 ((Closeable) msaws).close();
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148 log.fine("Disconnected successfully!");
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152 * Outputs AAcon results into the file represented by the outStream
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156 * the AACon scores to output
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158 static void writeOut(OutputStream outStream,
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159 Map<String, HashSet<Score>> result) {
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161 for (Map.Entry<String, ? extends Set<Score>> entry : result
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163 System.out.println(">" + entry.getKey());
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164 Score.write(entry.getValue(), outStream);
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166 } catch (IOException e) {
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168 .println("Problems writing output file! Stack trace is below: ");
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169 e.printStackTrace();
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171 if (outStream != null) {
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174 } catch (IOException ignored) {
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175 // e.printStackTrace();
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182 * Connects to a AACon web service by the host and the service name
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185 * @return {@link AlignmentAnnotation}
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186 * @throws WebServiceException
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187 * if cannot connect to a web service
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189 public static SequenceAnnotation<AAConWS> connect()
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190 throws WebServiceException {
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192 log.log(Level.FINE, "Attempting to connect...");
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194 url = new URL(hostname + "/" + "AAConWS" + "?wsdl");
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195 } catch (MalformedURLException e) {
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196 e.printStackTrace();
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197 // ignore as the host name is already verified
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199 QName qname = new QName(QUALIFIED_SERVICE_NAME, "AAConWS");
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200 Service serv = Service.create(url, qname);
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201 QName portName = new QName(QUALIFIED_SERVICE_NAME, "AAConWS" + "Port");
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203 @SuppressWarnings("unchecked")
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204 SequenceAnnotation<AAConWS> serviceIF = serv.getPort(portName,
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205 SequenceAnnotation.class);
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207 log.log(Level.FINE, "Connected successfully!");
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212 * Calculate conservation for sequences loaded from the file
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215 * a web service proxy
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217 * the file to read the results from
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219 * Preset to use optional
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220 * @param customOptions
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221 * the list of options
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222 * @return Set<Score> the conservation scores
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223 * @throws UnknownFileFormatException
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225 static Map<String, HashSet<Score>> analize(File file,
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226 SequenceAnnotation<AAConWS> wsproxy, Preset<AAConWS> preset,
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227 List<Option<AAConWS>> customOptions) {
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229 List<FastaSequence> fastalist = null;
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230 Map<String, HashSet<Score>> scores = null;
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232 fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());
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234 String jobId = null;
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235 if (customOptions != null && preset != null) {
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237 .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");
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239 if (customOptions != null) {
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240 jobId = wsproxy.customAnalize(fastalist, customOptions);
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241 } else if (preset != null) {
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242 jobId = wsproxy.presetAnalize(fastalist, preset);
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244 jobId = wsproxy.analize(fastalist);
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246 Thread.sleep(1000);
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247 scores = wsproxy.getAnnotation(jobId);
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249 } catch (IOException e) {
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251 .println("Exception while reading the input file. "
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252 + "Check that the input file contains a list of fasta formatted sequences! "
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253 + "Exception details are below:");
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254 e.printStackTrace();
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255 } catch (JobSubmissionException e) {
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257 .println("Exception while submitting job to a web server. "
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258 + "Exception details are below:");
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259 e.printStackTrace();
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260 } catch (ResultNotAvailableException e) {
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261 System.err.println("Exception while waiting for results. "
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262 + "Exception details are below:");
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263 e.printStackTrace();
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264 } catch (InterruptedException ignored) {
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265 // ignore and propagate an interruption
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266 Thread.currentThread().interrupt();
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267 } catch (WrongParameterException e) {
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269 .println("Exception while parsing the web method input parameters. "
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270 + "Exception details are below:");
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271 e.printStackTrace();
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272 } catch (UnknownFileFormatException e) {
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274 .println("Exception while attempting to read the input file "
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275 + "Exception details are below:");
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276 System.out.println(e.getMessage());
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277 e.printStackTrace();
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283 * Prints AAConClient usage information to standard out
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285 * @param exitStatus
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287 static void printUsage(int exitStatus) {
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288 System.out.println();
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289 System.out.println("Usage: <Class or Jar file name> "
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290 + " ACTION [OPTIONS] ");
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291 System.out.println();
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292 System.out.println("ACTIONS: ");
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296 + "<inputFile> - full path to fasta or Clustal formatted alignment file ");
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297 System.out.println(paramList
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298 + " - lists parameters supported by web service");
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299 System.out.println(presetList
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300 + " - lists presets supported by web service");
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301 System.out.println(limitList + " - lists web services limits");
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303 .println("Please note that if input file is specified other actions are ignored");
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305 System.out.println();
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306 System.out.println("OPTIONS (only for use with -i action):");
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308 System.out.println(presetkey + pseparator
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309 + "<presetName> - name of the preset to use");
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313 + "<outputFile> - full path to the file where to write the result");
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315 .println("-f=<parameterInputFile> - the name of the file with the list of parameters to use.");
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317 .println("Please note that -r and -f options cannot be used together. "
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318 + "Conservation is calculated with either a preset or "
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319 + "the parameters from the file, but not both!");
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321 System.exit(exitStatus);
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325 * Starts command line client, if no parameters are supplied prints help.
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328 * Usage: <Class or Jar file name> ACTION [OPTIONS]
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330 * -i=<inputFile> - full path to fasta or Clustal formatted
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333 * -parameters - lists parameters supported by web service
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335 * -presets - lists presets supported by web service
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337 * -limits - lists web services limits. Please note that if input
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338 * file is specified other actions are ignored
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340 * OPTIONS: (only for use with -i action):
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342 * -r=<presetName> - name of the preset to use
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344 * -o=<outputFile> - full path to the file where to write results
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345 * -f=<parameterInputFile> - the name of the file with the list
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346 * of parameters to use. Please note that -r and -f options
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347 * cannot be used together. Conservation is calculated with
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348 * either a preset or parameters from the file, but not both!
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351 public static void main(String[] args) {
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353 if (args == null) {
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356 if (args.length < 1) {
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357 System.out.println("No options is specified! ");
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362 new AAConClient(args);
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363 } catch (IOException e) {
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364 log.log(Level.SEVERE, "IOException in client! " + e.getMessage(),
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366 System.err.println("Cannot write output file! Stack trace: ");
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367 e.printStackTrace();
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