1 /* Copyright (c) 2011 Peter Troshin
\r
3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0
\r
5 * This library is free software; you can redistribute it and/or modify it under the terms of the
\r
6 * Apache License version 2 as published by the Apache Software Foundation
\r
8 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
\r
9 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
\r
10 * License for more details.
\r
12 * A copy of the license is in apache_license.txt. It is also available here:
\r
13 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
\r
15 * Any republication or derived work distributed in source code form
\r
16 * must include this copyright and license notice.
\r
19 package compbio.ws.client;
\r
21 import static compbio.ws.client.Constraints.inputkey;
\r
22 import static compbio.ws.client.Constraints.limitList;
\r
23 import static compbio.ws.client.Constraints.outputkey;
\r
24 import static compbio.ws.client.Constraints.paramFile;
\r
25 import static compbio.ws.client.Constraints.paramList;
\r
26 import static compbio.ws.client.Constraints.presetList;
\r
27 import static compbio.ws.client.Constraints.presetkey;
\r
28 import static compbio.ws.client.Constraints.pseparator;
\r
30 import java.io.Closeable;
\r
31 import java.io.File;
\r
32 import java.io.IOException;
\r
33 import java.io.PrintWriter;
\r
34 import java.io.Writer;
\r
35 import java.net.MalformedURLException;
\r
36 import java.net.URL;
\r
37 import java.util.List;
\r
38 import java.util.logging.Level;
\r
39 import java.util.logging.Logger;
\r
41 import javax.xml.namespace.QName;
\r
42 import javax.xml.ws.Service;
\r
43 import javax.xml.ws.WebServiceException;
\r
45 import compbio.data.msa.SequenceAnnotation;
\r
46 import compbio.data.sequence.FastaSequence;
\r
47 import compbio.data.sequence.ScoreManager;
\r
48 import compbio.data.sequence.SequenceUtil;
\r
49 import compbio.data.sequence.UnknownFileFormatException;
\r
50 import compbio.metadata.JobSubmissionException;
\r
51 import compbio.metadata.Option;
\r
52 import compbio.metadata.Preset;
\r
53 import compbio.metadata.ResultNotAvailableException;
\r
54 import compbio.metadata.WrongParameterException;
\r
55 import compbio.ws.server.AAConWS;
\r
58 * A command line client for AACon web service
\r
63 public class AAConClient {
\r
66 * Use java.util.Logger instead of log4j logger to reduce the size of the
\r
69 private static final Logger log = Logger.getLogger(AAConClient.class
\r
70 .getCanonicalName());
\r
73 * The fully qualified web service namespace
\r
75 static final String QUALIFIED_SERVICE_NAME = "http://msa.data.compbio/01/12/2010/";
\r
80 static final String hostname = "http://www.compbio.dundee.ac.uk/aacon";
\r
81 // static final String hostname = "http://localhost:8080/jabaws";
\r
86 static final String serviceName = "AAConWS";
\r
89 * Connects to the service and do the job as requested, if something goes
\r
90 * wrong reports or/and prints usage help.
\r
93 * command line options
\r
94 * @throws IOException
\r
95 * if the system cannot read/write from/into the file system
\r
97 @SuppressWarnings("unchecked")
\r
98 AAConClient(String[] cmd) throws IOException {
\r
100 File inputFile = IOHelper.getFile(cmd, inputkey, true);
\r
101 File outFile = IOHelper.getFile(cmd, outputkey, false);
\r
102 File parametersFile = IOHelper.getFile(cmd, paramFile, true);
\r
103 String presetName = CmdHelper.getPresetName(cmd);
\r
105 SequenceAnnotation<AAConWS> msaws = connect();
\r
106 Preset<AAConWS> preset = null;
\r
107 if (presetName != null) {
\r
108 preset = MetadataHelper.getPreset(msaws, presetName);
\r
110 List<Option<AAConWS>> customOptions = null;
\r
111 if (parametersFile != null) {
\r
112 List<String> prms = IOHelper.loadParameters(parametersFile);
\r
113 customOptions = MetadataHelper.processParameters(prms,
\r
114 msaws.getRunnerOptions());
\r
116 ScoreManager result = null;
\r
117 if (inputFile != null) {
\r
118 System.out.println("Calculating conservation...");
\r
119 result = analize(inputFile, msaws, preset, customOptions);
\r
120 Writer outStream = null;
\r
121 if (outFile != null) {
\r
122 outStream = IOHelper.getWriter(outFile);
\r
124 // this stream is going to be closed later which is fine as
\r
125 // std.out will not be
\r
126 outStream = new PrintWriter(System.out, true);
\r
128 writeOut(outStream, result);
\r
129 // stream is closed in the method no need to close it here
\r
132 boolean listParameters = CmdHelper.listParameters(cmd);
\r
133 if (listParameters) {
\r
134 System.out.println(MetadataHelper.getParametersList(msaws));
\r
136 boolean listPreset = CmdHelper.listPresets(cmd);
\r
138 System.out.println(MetadataHelper.getPresetList(msaws));
\r
140 boolean listLimits = CmdHelper.listLimits(cmd);
\r
142 System.out.println(MetadataHelper.getLimits(msaws));
\r
144 log.fine("Disconnecting...");
\r
145 ((Closeable) msaws).close();
\r
146 log.fine("Disconnected successfully!");
\r
150 * Outputs AAcon results into the file represented by the outStream
\r
154 * the AACon scores to output
\r
156 static void writeOut(Writer writer, ScoreManager result) {
\r
158 result.writeOut(writer);
\r
159 } catch (IOException e) {
\r
161 .println("Problems writing output file! Stack trace is below: ");
\r
162 e.printStackTrace();
\r
164 if (writer != null) {
\r
167 } catch (IOException ignored) {
\r
168 // e.printStackTrace();
\r
175 * Connects to a AACon web service by the host and the service name
\r
178 * @return {@link AlignmentAnnotation}
\r
179 * @throws WebServiceException
\r
180 * if cannot connect to a web service
\r
182 public static SequenceAnnotation<AAConWS> connect()
\r
183 throws WebServiceException {
\r
185 log.log(Level.FINE, "Attempting to connect...");
\r
187 url = new URL(hostname + "/" + "AAConWS" + "?wsdl");
\r
188 } catch (MalformedURLException e) {
\r
189 e.printStackTrace();
\r
190 // ignore as the host name is already verified
\r
192 QName qname = new QName(QUALIFIED_SERVICE_NAME, "AAConWS");
\r
193 Service serv = Service.create(url, qname);
\r
194 QName portName = new QName(QUALIFIED_SERVICE_NAME, "AAConWS" + "Port");
\r
196 @SuppressWarnings("unchecked")
\r
197 SequenceAnnotation<AAConWS> serviceIF = serv.getPort(portName,
\r
198 SequenceAnnotation.class);
\r
200 log.log(Level.FINE, "Connected successfully!");
\r
205 * Calculate conservation for sequences loaded from the file
\r
208 * a web service proxy
\r
210 * the file to read the results from
\r
212 * Preset to use optional
\r
213 * @param customOptions
\r
214 * the list of options
\r
215 * @return Set<Score> the conservation scores
\r
216 * @throws UnknownFileFormatException
\r
218 static ScoreManager analize(File file, SequenceAnnotation<AAConWS> wsproxy,
\r
219 Preset<AAConWS> preset, List<Option<AAConWS>> customOptions) {
\r
221 List<FastaSequence> fastalist = null;
\r
222 ScoreManager scores = null;
\r
224 fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());
\r
226 String jobId = null;
\r
227 if (customOptions != null && preset != null) {
\r
229 .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");
\r
231 if (customOptions != null) {
\r
232 jobId = wsproxy.customAnalize(fastalist, customOptions);
\r
233 } else if (preset != null) {
\r
234 jobId = wsproxy.presetAnalize(fastalist, preset);
\r
236 jobId = wsproxy.analize(fastalist);
\r
238 Thread.sleep(1000);
\r
239 scores = wsproxy.getAnnotation(jobId);
\r
241 } catch (IOException e) {
\r
243 .println("Exception while reading the input file. "
\r
244 + "Check that the input file contains a list of fasta formatted sequences! "
\r
245 + "Exception details are below:");
\r
246 e.printStackTrace();
\r
247 } catch (JobSubmissionException e) {
\r
249 .println("Exception while submitting job to a web server. "
\r
250 + "Exception details are below:");
\r
251 e.printStackTrace();
\r
252 } catch (ResultNotAvailableException e) {
\r
253 System.err.println("Exception while waiting for results. "
\r
254 + "Exception details are below:");
\r
255 e.printStackTrace();
\r
256 } catch (InterruptedException ignored) {
\r
257 // ignore and propagate an interruption
\r
258 Thread.currentThread().interrupt();
\r
259 } catch (WrongParameterException e) {
\r
261 .println("Exception while parsing the web method input parameters. "
\r
262 + "Exception details are below:");
\r
263 e.printStackTrace();
\r
264 } catch (UnknownFileFormatException e) {
\r
266 .println("Exception while attempting to read the input file "
\r
267 + "Exception details are below:");
\r
268 System.out.println(e.getMessage());
\r
269 e.printStackTrace();
\r
275 * Prints AAConClient usage information to standard out
\r
277 * @param exitStatus
\r
279 static void printUsage(int exitStatus) {
\r
280 System.out.println();
\r
281 System.out.println("Usage: <Class or Jar file name> "
\r
282 + " ACTION [OPTIONS] ");
\r
283 System.out.println();
\r
284 System.out.println("ACTIONS: ");
\r
288 + "<inputFile> - full path to fasta or Clustal formatted alignment file ");
\r
289 System.out.println(paramList
\r
290 + " - lists parameters supported by web service");
\r
291 System.out.println(presetList
\r
292 + " - lists presets supported by web service");
\r
293 System.out.println(limitList + " - lists web services limits");
\r
295 .println("Please note that if input file is specified other actions are ignored");
\r
297 System.out.println();
\r
298 System.out.println("OPTIONS (only for use with -i action):");
\r
300 System.out.println(presetkey + pseparator
\r
301 + "<presetName> - name of the preset to use");
\r
305 + "<outputFile> - full path to the file where to write the result");
\r
307 .println("-f=<parameterInputFile> - the name of the file with the list of parameters to use.");
\r
309 .println("Please note that -r and -f options cannot be used together. "
\r
310 + "Conservation is calculated with either a preset or "
\r
311 + "the parameters from the file, but not both!");
\r
313 System.exit(exitStatus);
\r
317 * Starts command line client, if no parameters are supplied prints help.
\r
320 * Usage: <Class or Jar file name> ACTION [OPTIONS]
\r
322 * -i=<inputFile> - full path to fasta or Clustal formatted
\r
325 * -parameters - lists parameters supported by web service
\r
327 * -presets - lists presets supported by web service
\r
329 * -limits - lists web services limits. Please note that if input
\r
330 * file is specified other actions are ignored
\r
332 * OPTIONS: (only for use with -i action):
\r
334 * -r=<presetName> - name of the preset to use
\r
336 * -o=<outputFile> - full path to the file where to write results
\r
337 * -f=<parameterInputFile> - the name of the file with the list
\r
338 * of parameters to use. Please note that -r and -f options
\r
339 * cannot be used together. Conservation is calculated with
\r
340 * either a preset or parameters from the file, but not both!
\r
343 public static void main(String[] args) {
\r
345 if (args == null) {
\r
348 if (args.length < 1) {
\r
349 System.out.println("No options is specified! ");
\r
354 new AAConClient(args);
\r
355 } catch (IOException e) {
\r
356 log.log(Level.SEVERE, "IOException in client! " + e.getMessage(),
\r
358 System.err.println("Cannot write output file! Stack trace: ");
\r
359 e.printStackTrace();
\r