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