webservices/compbio/ws/client/Jws2Client.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \r
   4  * \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
   7  * \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
  11  * \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
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 \r
  19 package compbio.ws.client;\r
  20 \r
  21 import static compbio.ws.client.Constraints.inputkey;\r
  22 import static compbio.ws.client.Constraints.outputkey;\r
  23 import static compbio.ws.client.Constraints.paramFile;\r
  24 \r
  25 import java.io.Closeable;\r
  26 import java.io.File;\r
  27 import java.io.FileInputStream;\r
  28 import java.io.FileOutputStream;\r
  29 import java.io.IOException;\r
  30 import java.io.OutputStream;\r
  31 import java.io.PrintWriter;\r
  32 import java.io.Writer;\r
  33 import java.net.ConnectException;\r
  34 import java.net.MalformedURLException;\r
  35 import java.net.URL;\r
  36 import java.util.Arrays;\r
  37 import java.util.Collections;\r
  38 import java.util.List;\r
  39 import java.util.Set;\r
  40 import java.util.logging.Level;\r
  41 import java.util.logging.Logger;\r
  42 \r
  43 import javax.xml.namespace.QName;\r
  44 import javax.xml.ws.Service;\r
  45 import javax.xml.ws.WebServiceException;\r
  46 \r
  47 import compbio.data.msa.JABAService;\r
  48 import compbio.data.msa.Metadata;\r
  49 import compbio.data.msa.MsaWS;\r
  50 import compbio.data.msa.RegistryWS;\r
  51 import compbio.data.msa.SequenceAnnotation;\r
  52 import compbio.data.sequence.Alignment;\r
  53 import compbio.data.sequence.AlignmentMetadata;\r
  54 import compbio.data.sequence.JpredAlignment;\r
  55 import compbio.data.sequence.FastaSequence;\r
  56 import compbio.data.sequence.ScoreManager;\r
  57 import compbio.data.sequence.SequenceUtil;\r
  58 import compbio.data.sequence.UnknownFileFormatException;\r
  59 import compbio.metadata.JobSubmissionException;\r
  60 import compbio.metadata.Option;\r
  61 import compbio.metadata.Preset;\r
  62 import compbio.metadata.ResultNotAvailableException;\r
  63 import compbio.metadata.WrongParameterException;\r
  64 import compbio.util.FileUtil;\r
  65 \r
  66 /**\r
  67  * A command line client for JAva Bioinformatics Analysis Web Services\r
  68  * \r
  69  * @author pvtroshin\r
  70  * @version 1.0\r
  71  */\r
  72 public class Jws2Client {\r
  73 \r
  74         /**\r
  75          * Use java.util.Logger instead of log4j logger to reduce the size of the client package\r
  76          */\r
  77         private static final Logger log = Logger.getLogger(Jws2Client.class.getCanonicalName());\r
  78 \r
  79         /**\r
  80          * Attempt to construct the URL object from the string\r
  81          * \r
  82          * @param urlstr\r
  83          * @return true if it succeed false otherwise\r
  84          */\r
  85         public static boolean validURL(String urlstr) {\r
  86                 try {\r
  87                         if (urlstr == null || urlstr.trim().length() == 0) {\r
  88                                 return false;\r
  89                         }\r
  90                         new URL(urlstr);\r
  91                 } catch (MalformedURLException e) {\r
  92                         return false;\r
  93                 }\r
  94                 return true;\r
  95         }\r
  96 \r
  97         /**\r
  98          * Connects to the service and do the job as requested, if something goes\r
  99          * wrong reports or/and prints usage help.\r
 100          * \r
 101          * @param <T>\r
 102          *            web service type\r
 103          * @param cmd\r
 104          *            command line options\r
 105          * @throws IOException\r
 106          */\r
 107         @SuppressWarnings("unchecked")\r
 108         <T> Jws2Client(String[] cmd) throws IOException {\r
 109                 \r
 110 \r
 111                 String hostname = CmdHelper.getHost(cmd);\r
 112                 if (hostname == null) {\r
 113                         System.err.println("Host name is not provided!");\r
 114                         System.out.println(Constraints.help_text);\r
 115                         System.exit(1);\r
 116                 }\r
 117 \r
 118                 if (!validURL(hostname)) {\r
 119                         System.err.println("Host name is not valid!");\r
 120                         System.out.println(Constraints.help_text);\r
 121                         System.exit(1);\r
 122                 }\r
 123 \r
 124                 boolean listServices = CmdHelper.listServices(cmd);\r
 125                 if (listServices) {\r
 126                         listAllServices(hostname);\r
 127                         System.exit(0);\r
 128                 }\r
 129 \r
 130                 String serviceName = CmdHelper.getServiceName(cmd);\r
 131                 if (serviceName == null) {\r
 132                         System.err.println("Service name is no provided!");\r
 133                         System.out.println(Constraints.help_text);\r
 134                         System.exit(1);\r
 135                 }\r
 136 \r
 137                 Services service = Services.getService(serviceName);\r
 138                 if (service == null) {\r
 139                         String mess = "Service " + serviceName + " is no available! Valid values are: ";\r
 140                         System.err.println(mess + Arrays.toString(Services.values()));\r
 141                         System.out.println(Constraints.help_text);\r
 142                         System.exit(1);\r
 143                 }\r
 144 \r
 145                 if (CmdHelper.testService(cmd)) {\r
 146                         testService(hostname, service, new PrintWriter(System.out, true));\r
 147                         System.exit(0);\r
 148                 }\r
 149 \r
 150                 Metadata<T> thews = (Metadata<T>) connect(hostname, service);\r
 151                 Preset<T> preset = null;\r
 152                 if (null != CmdHelper.getPresetName(cmd)) {\r
 153                         preset = MetadataHelper.getPreset(thews, CmdHelper.getPresetName(cmd));\r
 154                 }\r
 155 \r
 156                 List<Option<T>> customOptions = null;\r
 157                 if (null != IOHelper.getFile(cmd, paramFile, true)) {\r
 158                         List<String> prms = IOHelper.loadParameters(IOHelper.getFile(cmd, paramFile, true));\r
 159                         customOptions = MetadataHelper.processParameters(prms, thews.getRunnerOptions());\r
 160                 }\r
 161 \r
 162                 if (null != IOHelper.getFile(cmd, inputkey, true)) {\r
 163                         File infile = IOHelper.getFile(cmd, inputkey, true);\r
 164                         File outfile = IOHelper.getFile(cmd, outputkey, false);\r
 165                         Writer writer = null;\r
 166                         if (outfile != null) {\r
 167                                 writer = IOHelper.getWriter(outfile);\r
 168                         } else {\r
 169                                 writer = new PrintWriter(System.out, true);\r
 170                         }\r
 171                         if (service.getServiceType() == SequenceAnnotation.class) {\r
 172                                 ScoreManager result = analize(infile, ((SequenceAnnotation<T>) thews), preset, customOptions);\r
 173                                 IOHelper.writeOut(writer, result);\r
 174                                 writer.close();\r
 175                         } else if (service.getServiceType() == MsaWS.class) {\r
 176                                 Alignment alignment = align(infile, (MsaWS<T>) thews, preset, customOptions);\r
 177                                 if (serviceName.equalsIgnoreCase("JpredWS")) {\r
 178                                         writer.close();\r
 179                                         JpredAlignment jpred = (JpredAlignment)alignment;\r
 180                                         if (outfile != null) {\r
 181                                                 FileOutputStream fout = new FileOutputStream(outfile);\r
 182                                                 SequenceUtil.writeFastaKeepTheStream(fout, jpred.getJpredSequences(), 60);\r
 183                                                 fout.close();\r
 184                                         } else {\r
 185                                                 SequenceUtil.writeFasta(System.out, jpred.getJpredSequences());\r
 186                                         }\r
 187                                 } else {\r
 188                                         IOHelper.writeOut(writer, alignment);\r
 189                                         writer.close();\r
 190                                 }\r
 191                         }\r
 192                 }\r
 193 \r
 194                 if (CmdHelper.listParameters(cmd)) {\r
 195                         System.out.println(MetadataHelper.getParametersList(thews));\r
 196                 }\r
 197                 if (CmdHelper.listPresets(cmd)) {\r
 198                         System.out.println(MetadataHelper.getPresetList(thews));\r
 199                 }\r
 200                 if (CmdHelper.listLimits(cmd)) {\r
 201                         System.out.println(MetadataHelper.getLimits(thews));\r
 202                 }\r
 203                 log.fine("Disconnecting...");\r
 204                 ((Closeable) thews).close();\r
 205                 log.fine("Disconnected successfully!");\r
 206         }\r
 207 \r
 208         /**\r
 209          * Connects to a web service by the host and the service name web service type\r
 210          * \r
 211          * @param host\r
 212          *            the fully qualified name of JABAWS server including JABAWS\r
 213          *            context name e.g\r
 214          *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 215          * @param service\r
 216          *            the name of the JABAWS service to connect to\r
 217          * @return JABAService<T>\r
 218          * @throws WebServiceException\r
 219          * @throws ConnectException\r
 220          *             if fails to connect to the service on the host\r
 221          */\r
 222         public static JABAService connect(String host, Services service)\r
 223                         throws WebServiceException, ConnectException {\r
 224                 URL url = null;\r
 225                 log.log(Level.FINE, "Attempting to connect with " + service.toString() + "...");\r
 226                 System.out.println ("Attempting to connect with " + service.toString() + "...");\r
 227                 try {\r
 228                         url = new URL(host + "/" + service.toString() + "?wsdl");\r
 229                 } catch (MalformedURLException e) {\r
 230                         e.printStackTrace();\r
 231                         // ignore as the host name is already verified\r
 232                 }\r
 233                 Service serv = null;\r
 234                 try {\r
 235                         serv = service.getService(url, service.getServiceNamespace());\r
 236                 } catch (WebServiceException wse) {\r
 237                         wse.printStackTrace();\r
 238                 }\r
 239                 if (serv == null) {\r
 240                         throw new ConnectException("Could not connect to " + url + ". Is the server down?");\r
 241                 }\r
 242                 JABAService serviceIF = service.getInterface(serv);\r
 243                 log.log(Level.INFO, "Connected successfully!");\r
 244 \r
 245                 return serviceIF;\r
 246         }\r
 247 \r
 248         /**\r
 249          * Get a connection of JABAWS registry\r
 250          * \r
 251          * @param host\r
 252          *            the fully qualified name of JABAWS server including JABAWS\r
 253          *            context name e.g\r
 254          *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 255          * @return compbio.data.msa.RegistryWS - instance of a RegistryWS web\r
 256          *         service\r
 257          * @throws WebServiceException\r
 258          * @throws ConnectException\r
 259          */\r
 260         public static compbio.data.msa.RegistryWS connectToRegistry(String host)\r
 261                         throws WebServiceException, ConnectException {\r
 262                 URL url = null;\r
 263                 String service = "RegistryWS";\r
 264                 log.log(Level.FINE, "Attempting to connect...");\r
 265 \r
 266                 try {\r
 267                         url = new URL(host + "/" + service + "?wsdl");\r
 268                 } catch (MalformedURLException e) {\r
 269                         e.printStackTrace();\r
 270                         // ignore as the host name is already verified\r
 271                 }\r
 272                 QName qname = new QName(JABAService.V2_SERVICE_NAMESPACE, service);\r
 273                 Service serv = Service.create(url, qname);\r
 274 \r
 275                 if (serv == null) {\r
 276                         throw new ConnectException("Could not connect to " + url + ". Is the server down?");\r
 277                 }\r
 278 \r
 279                 QName portName = new QName(serv.getServiceName().getNamespaceURI(), service + "Port");\r
 280                 compbio.data.msa.RegistryWS serviceIF = serv.getPort(portName, compbio.data.msa.RegistryWS.class);\r
 281                 log.log(Level.INFO, "Connected to " + service + " successfully!");\r
 282 \r
 283                 return serviceIF;\r
 284         }\r
 285 \r
 286         /**\r
 287          * Asks registry to test the service on the host hostname\r
 288          * \r
 289          * @param hostname\r
 290          * @param service\r
 291          * @param writer\r
 292          * @throws ConnectException\r
 293          * @throws WebServiceException\r
 294          */\r
 295         public static void testService(String hostname, Services service, PrintWriter writer)\r
 296                         throws ConnectException, WebServiceException {\r
 297                 RegistryWS registry = connectToRegistry(hostname);\r
 298                 if (registry != null) {\r
 299                         String message = registry.testService(service);\r
 300                         writer.println("Service " + service + " testing results: ");\r
 301                         writer.println(message);\r
 302                         FileUtil.closeSilently(((Closeable) registry));\r
 303                 }\r
 304                 writer.flush();\r
 305         }\r
 306 \r
 307         private static void listAllServices(String hostname) throws WebServiceException, IOException {\r
 308                 RegistryWS registry = connectToRegistry(hostname);\r
 309                 Set<Services> func_services = Collections.EMPTY_SET;\r
 310                 Set<Services> nonfunc_services = Collections.EMPTY_SET;\r
 311                 if (registry != null) {\r
 312                         func_services = registry.getSupportedServices();\r
 313                         nonfunc_services = registry.getNonoperatedServices();\r
 314                         FileUtil.closeSilently(((Closeable) registry));\r
 315                 } else {\r
 316                         System.out.println("Failed to connect to the registry! ");\r
 317                         return;\r
 318                 }\r
 319                 if (!func_services.isEmpty()) {\r
 320                         System.out.println("There are " + func_services.size() + " services at " + hostname + ":");\r
 321                         String mess = "\n\rThe list:\n";\r
 322                         System.out.println(mess + Services.toString(func_services));\r
 323                 }\r
 324                 if (!nonfunc_services.isEmpty()) {\r
 325                         System.out.println("There are " + nonfunc_services.size() + " non-available services at " + hostname + ":");\r
 326                         String mess = "The list (internal tests failed): ";\r
 327                         System.out.println(mess + Services.toString(nonfunc_services));\r
 328                 }\r
 329         }\r
 330 \r
 331         /**\r
 332          * Calculate conservation for sequences loaded from a FASTA record list structure \r
 333          * \r
 334          * @param fastalist\r
 335          *            the list of FASTA records\r
 336          * @param wsproxy\r
 337          *            a web service proxy\r
 338          * @param preset\r
 339          *            Preset to use optional\r
 340          * @param customOptions\r
 341          *            the list of options\r
 342          * @return Set<Score> the conservation scores\r
 343          * @throws UnknownFileFormatException\r
 344          */\r
 345         static <T> ScoreManager analize(List<FastaSequence> fastalist, SequenceAnnotation<T> wsproxy, Preset<T> preset, List<Option<T>> customOptions) {\r
 346                 ScoreManager scores = null;\r
 347                 try {\r
 348                         String jobId = null;\r
 349                         if (customOptions != null && preset != null) {\r
 350                                 System.out.println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 351                         }\r
 352                         if (customOptions != null) {\r
 353                                 jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 354                         } else if (preset != null) {\r
 355                                 jobId = wsproxy.presetAnalize(fastalist, preset);\r
 356                         } else {\r
 357                                 jobId = wsproxy.analize(fastalist);\r
 358                         }\r
 359                         System.out.println("\n\rcalling predictor.........");\r
 360                         Thread.sleep(100);\r
 361                         scores = wsproxy.getAnnotation(jobId);\r
 362                 } catch (JobSubmissionException e) {\r
 363                         System.err.println("Exception while submitting job to a web server. Exception details are below:");\r
 364                         e.printStackTrace();\r
 365                 } catch (ResultNotAvailableException e) {\r
 366                         System.err.println("Exception while waiting for results. Exception details are below:");\r
 367                         e.printStackTrace();\r
 368                 } catch (InterruptedException e) {\r
 369                         Thread.currentThread().interrupt();\r
 370                         System.err.println("Exception while waiting for results. Exception details are below:");\r
 371                         e.printStackTrace();\r
 372                 } catch (WrongParameterException e) {\r
 373                         String mess = "Parsing the web method input parameters failed Exception details are below:";\r
 374                         System.err.println(mess);\r
 375                         e.printStackTrace();\r
 376                 }\r
 377                 return scores;\r
 378 \r
 379         }\r
 380 \r
 381         /**\r
 382          * Calculate conservation for sequences loaded from the file\r
 383          * \r
 384          * @param wsproxy\r
 385          *            a web service proxy\r
 386          * @param file\r
 387          *            the file to read the results from\r
 388          * @param preset\r
 389          *            Preset to use optional\r
 390          * @param customOptions\r
 391          *            the list of options\r
 392          * @return Set<Score> the conservation scores\r
 393          * @throws IOException\r
 394          * @throws UnknownFileFormatException\r
 395          */\r
 396         static <T> ScoreManager analize(File file, SequenceAnnotation<T> wsproxy, Preset<T> preset, List<Option<T>> customOptions) {\r
 397                 List<FastaSequence> fastalist = null;\r
 398                 try {\r
 399                         fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
 400                         assert !fastalist.isEmpty() : "Input is empty!";\r
 401                 } catch (IOException e) {\r
 402                         String mess = "Reading the input file failed. Check that the file contains a list of FASTA records!\n";\r
 403                         System.err.println(mess + "Exception details are below:");\r
 404                         e.printStackTrace();\r
 405                 } catch (UnknownFileFormatException e) {\r
 406                         String mess = "Reading the input file failed. Exception details are below:";\r
 407                         System.err.println(mess);\r
 408                         System.out.println(e.getMessage());\r
 409                         e.printStackTrace();\r
 410                 }\r
 411                 return analize(fastalist, wsproxy, preset, customOptions);\r
 412         }\r
 413 \r
 414         /**\r
 415          * Align sequences from the file using MsaWS\r
 416          * \r
 417          * @param <T>\r
 418          *            web service type e.g. Clustal\r
 419          * @param file\r
 420          *            to write the resulting alignment to\r
 421          * @param msaws\r
 422          *            MsaWS required\r
 423          * @param preset\r
 424          *            Preset to use optional\r
 425          * @param customOptions\r
 426          *            file which contains new line separated list of options\r
 427          * @return Alignment\r
 428          */\r
 429         static <T> Alignment align(File file, MsaWS<T> msaws, Preset<T> preset,\r
 430                         List<Option<T>> customOptions) {\r
 431                 FileInputStream instream = null;\r
 432                 Alignment alignment = null;\r
 433                 try {\r
 434                         instream = new FileInputStream(file);\r
 435                         List<FastaSequence> fastalist = SequenceUtil.readFasta(instream);\r
 436                         instream.close();\r
 437                         String jobId = null;\r
 438                         if (customOptions != null && preset != null) {\r
 439                                 System.out.println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 440                         }\r
 441                         if (customOptions != null) {\r
 442                                 jobId = msaws.customAlign(fastalist, customOptions);\r
 443                         } else if (preset != null) {\r
 444                                 jobId = msaws.presetAlign(fastalist, preset);\r
 445                         } else {\r
 446                                 jobId = msaws.align(fastalist);\r
 447                         }\r
 448                         System.out.println("\ncalling program.........");\r
 449                         Thread.sleep(100);\r
 450                         alignment = msaws.getResult(jobId);\r
 451                 } catch (IOException e) {\r
 452                         System.err.println("Exception while reading the input file. Check that the input file is a FASTA file! "\r
 453                                                 + "Exception details are below:");\r
 454                         e.printStackTrace();\r
 455                 } catch (JobSubmissionException e) {\r
 456                         System.err.println("Exception while submitting job to a web server. Exception details are below:");\r
 457                         e.printStackTrace();\r
 458                 } catch (ResultNotAvailableException e) {\r
 459                         System.err.println("Exception while waiting for results. Exception details are below:");\r
 460                         e.printStackTrace();\r
 461                 } catch (InterruptedException ignored) {\r
 462                         // ignore and propagate an interruption\r
 463                         Thread.currentThread().interrupt();\r
 464                 } catch (WrongParameterException e) {\r
 465                         e.printStackTrace();\r
 466                 } finally {\r
 467                         if (instream != null) {\r
 468                                 try {\r
 469                                         instream.close();\r
 470                                 } catch (IOException ignored) {\r
 471                                         // ignore\r
 472                                 }\r
 473                         }\r
 474                 }\r
 475                 return alignment;\r
 476         }\r
 477         \r
 478         /**\r
 479          * Starts command line client, if no parameter are supported print help. Two\r
 480          * parameters are required for successful call the JWS2 host name and a\r
 481          * service name.\r
 482          * \r
 483          * @param args\r
 484          *            Usage: <Class or Jar file name> -h=host_and_context\r
 485          *            -s=serviceName ACTION [OPTIONS]\r
 486          * \r
 487          *            -h=<host_and_context> - a full URL to the JWS2 web server\r
 488          *            including context path e.g. http://10.31.1.159:8080/ws\r
 489          * \r
 490          *            -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,\r
 491          *            TcoffeeWS, ProbconsWS] ACTIONS:\r
 492          * \r
 493          *            -i=<inputFile> - full path to fasta formatted sequence file,\r
 494          *            from which to align sequences\r
 495          * \r
 496          *            -parameters - lists parameters supported by web service\r
 497          * \r
 498          *            -presets - lists presets supported by web service\r
 499          * \r
 500          *            -limits - lists web services limits Please note that if input\r
 501          *            file is specified other actions are ignored\r
 502          * \r
 503          *            OPTIONS: (only for use with -i action):\r
 504          * \r
 505          *            -r=<presetName> - name of the preset to use\r
 506          * \r
 507          *            -o=<outputFile> - full path to the file where to write an\r
 508          *            alignment -f=<parameterInputFile> - the name of the file with\r
 509          *            the list of parameters to use. Please note that -r and -f\r
 510          *            options cannot be used together. Alignment is done with either\r
 511          *            preset or a parameters from the file, but not both!\r
 512          * \r
 513          */\r
 514         public static void main(String[] args) {\r
 515 \r
 516                 if (args == null) {\r
 517                         System.out.println(Constraints.help_text);\r
 518                         System.exit(1);\r
 519                 }\r
 520                 if (args.length < 2) {\r
 521                         System.err.println("Host (-h=<host>, e.g. -h=http://www.compbio.dundee.ac.uk/jabaws) and service (-s=<ServiceName>, e.g. -s=Jpred) are required!");\r
 522                         System.out.println(Constraints.help_text);\r
 523                         System.exit(1);\r
 524                 }\r
 525 \r
 526                 try {\r
 527                         new Jws2Client(args);\r
 528                 } catch (IOException e) {\r
 529                         log.log(Level.SEVERE, "IOException in client! " + e.getMessage(), e.getCause());\r
 530                         System.err.println("Cannot write output file! Stack trace: ");\r
 531                         e.printStackTrace();\r
 532                 }\r
 533         }\r
 534 }\r