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.IOException;\r
  29 import java.io.PrintWriter;\r
  30 import java.io.Writer;\r
  31 import java.net.ConnectException;\r
  32 import java.net.MalformedURLException;\r
  33 import java.net.URL;\r
  34 import java.util.Arrays;\r
  35 import java.util.Collections;\r
  36 import java.util.List;\r
  37 import java.util.Set;\r
  38 import java.util.logging.Level;\r
  39 import java.util.logging.Logger;\r
  40 \r
  41 import javax.xml.namespace.QName;\r
  42 import javax.xml.ws.Service;\r
  43 import javax.xml.ws.WebServiceException;\r
  44 \r
  45 import compbio.data.msa.JABAService;\r
  46 import compbio.data.msa.Metadata;\r
  47 import compbio.data.msa.MsaWS;\r
  48 import compbio.data.msa.RegistryWS;\r
  49 import compbio.data.msa.SequenceAnnotation;\r
  50 import compbio.data.sequence.Alignment;\r
  51 import compbio.data.sequence.FastaSequence;\r
  52 import compbio.data.sequence.ScoreManager;\r
  53 import compbio.data.sequence.SequenceUtil;\r
  54 import compbio.data.sequence.UnknownFileFormatException;\r
  55 import compbio.metadata.JobSubmissionException;\r
  56 import compbio.metadata.Option;\r
  57 import compbio.metadata.Preset;\r
  58 import compbio.metadata.ResultNotAvailableException;\r
  59 import compbio.metadata.WrongParameterException;\r
  60 import compbio.util.FileUtil;\r
  61 \r
  62 /**\r
  63  * A command line client for JAva Bioinformatics Analysis Web Services\r
  64  * \r
  65  * @author pvtroshin\r
  66  * @version 1.0\r
  67  */\r
  68 public class Jws2Client {\r
  69 \r
  70         /*\r
  71          * Use java.util.Logger instead of log4j logger to reduce the size of the client package\r
  72          */\r
  73         private static final Logger log = Logger.getLogger(Jws2Client.class.getCanonicalName());\r
  74 \r
  75         /**\r
  76          * Attempt to construct the URL object from the string\r
  77          * \r
  78          * @param urlstr\r
  79          * @return true if it succeed false otherwise\r
  80          */\r
  81         public static boolean validURL(String urlstr) {\r
  82                 try {\r
  83                         if (urlstr == null || urlstr.trim().length() == 0) {\r
  84                                 return false;\r
  85                         }\r
  86                         new URL(urlstr);\r
  87                 } catch (MalformedURLException e) {\r
  88                         return false;\r
  89                 }\r
  90                 return true;\r
  91         }\r
  92 \r
  93         /**\r
  94          * Connects to the service and do the job as requested, if something goes\r
  95          * wrong reports or/and prints usage help.\r
  96          * \r
  97          * @param <T>\r
  98          *            web service type\r
  99          * @param cmd\r
 100          *            command line options\r
 101          * @throws IOException\r
 102          */\r
 103         <T> Jws2Client(String[] cmd) throws IOException {\r
 104                 \r
 105 \r
 106                 String hostname = CmdHelper.getHost(cmd);\r
 107                 if (hostname == null) {\r
 108                         System.err.println("Host name is not provided!");\r
 109                         System.out.println(Constraints.help_text);\r
 110                         System.exit(1);\r
 111                 }\r
 112 \r
 113                 if (!validURL(hostname)) {\r
 114                         System.err.println("Host name is not valid!");\r
 115                         System.out.println(Constraints.help_text);\r
 116                         System.exit(1);\r
 117                 }\r
 118 \r
 119                 boolean listServices = CmdHelper.listServices(cmd);\r
 120                 if (listServices) {\r
 121                         listAllServices(hostname);\r
 122                         System.exit(0);\r
 123                 }\r
 124 \r
 125                 String serviceName = CmdHelper.getServiceName(cmd);\r
 126                 if (serviceName == null) {\r
 127                         System.err.println("Service name is no provided!");\r
 128                         System.out.println(Constraints.help_text);\r
 129                         System.exit(1);\r
 130                 }\r
 131 \r
 132                 Services service = Services.getService(serviceName);\r
 133                 if (service == null) {\r
 134                         String mess = "Service " + serviceName + " is no available! Valid values are: ";\r
 135                         System.err.println(mess + Arrays.toString(Services.values()));\r
 136                         System.out.println(Constraints.help_text);\r
 137                         System.exit(1);\r
 138                 }\r
 139 \r
 140                 if (CmdHelper.testService(cmd)) {\r
 141                         testService(hostname, service, new PrintWriter(System.out, true));\r
 142                         System.exit(0);\r
 143                 }\r
 144 \r
 145                 Metadata<T> thews = (Metadata<T>) connect(hostname, service);\r
 146                 Preset<T> preset = null;\r
 147                 if (null != CmdHelper.getPresetName(cmd)) {\r
 148                         preset = MetadataHelper.getPreset(thews, CmdHelper.getPresetName(cmd));\r
 149                 }\r
 150 \r
 151                 List<Option<T>> customOptions = null;\r
 152                 if (null != IOHelper.getFile(cmd, paramFile, true)) {\r
 153                         List<String> prms = IOHelper.loadParameters(IOHelper.getFile(cmd, paramFile, true));\r
 154                         customOptions = MetadataHelper.processParameters(prms, thews.getRunnerOptions());\r
 155                 }\r
 156 \r
 157                 if (null != IOHelper.getFile(cmd, inputkey, true)) {\r
 158                         File infile = IOHelper.getFile(cmd, inputkey, true);\r
 159                         File outfile = IOHelper.getFile(cmd, outputkey, false);\r
 160                         Writer writer = null;\r
 161                         if (outfile != null) {\r
 162                                 writer = IOHelper.getWriter(outfile);\r
 163                         } else {\r
 164                                 // this stream is going to be closed later which is fine as std.out will not be\r
 165                                 writer = new PrintWriter(System.out, true);\r
 166                         }\r
 167                         if (service.getServiceType() == SequenceAnnotation.class) {\r
 168                                 ScoreManager result = analize(infile, ((SequenceAnnotation<T>) thews), preset, customOptions);\r
 169                                 IOHelper.writeOut(writer, result);\r
 170                         } else if (service.getServiceType() == MsaWS.class) {\r
 171                                 Alignment alignment = align(infile, (MsaWS<T>) thews, preset, customOptions);\r
 172                                 IOHelper.writeOut(writer, alignment);\r
 173                         }\r
 174                         writer.close();\r
 175                 }\r
 176 \r
 177                 if (CmdHelper.listParameters(cmd)) {\r
 178                         System.out.println(MetadataHelper.getParametersList(thews));\r
 179                 }\r
 180                 if (CmdHelper.listPresets(cmd)) {\r
 181                         System.out.println(MetadataHelper.getPresetList(thews));\r
 182                 }\r
 183                 if (CmdHelper.listLimits(cmd)) {\r
 184                         System.out.println(MetadataHelper.getLimits(thews));\r
 185                 }\r
 186                 log.fine("Disconnecting...");\r
 187                 ((Closeable) thews).close();\r
 188                 log.fine("Disconnected successfully!");\r
 189         }\r
 190 \r
 191         /**\r
 192          * Connects to a web service by the host and the service name web service type\r
 193          * \r
 194          * @param host\r
 195          *            the fully qualified name of JABAWS server including JABAWS\r
 196          *            context name e.g\r
 197          *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 198          * @param service\r
 199          *            the name of the JABAWS service to connect to\r
 200          * @return JABAService<T>\r
 201          * @throws WebServiceException\r
 202          * @throws ConnectException\r
 203          *             if fails to connect to the service on the host\r
 204          */\r
 205         public static JABAService connect(String host, Services service)\r
 206                         throws WebServiceException, ConnectException {\r
 207                 URL url = null;\r
 208                 log.log(Level.FINE, "Attempting to connect with " + service.toString() + "...");\r
 209                 System.out.println ("Attempting to connect with " + service.toString() + "...");\r
 210                 try {\r
 211                         url = new URL(host + "/" + service.toString() + "?wsdl");\r
 212                 } catch (MalformedURLException e) {\r
 213                         e.printStackTrace();\r
 214                         // ignore as the host name is already verified\r
 215                 }\r
 216                 Service serv = null;\r
 217                 try {\r
 218                         serv = service.getService(url, service.getServiceNamespace());\r
 219                 } catch (WebServiceException wse) {\r
 220                         wse.printStackTrace();\r
 221                 }\r
 222                 if (serv == null) {\r
 223                         throw new ConnectException("Could not connect to " + url + ". Is the server down?");\r
 224                 }\r
 225                 JABAService serviceIF = service.getInterface(serv);\r
 226                 log.log(Level.INFO, "Connected successfully!");\r
 227 \r
 228                 return serviceIF;\r
 229         }\r
 230 \r
 231         /**\r
 232          * Get a connection of JABAWS registry\r
 233          * \r
 234          * @param host\r
 235          *            the fully qualified name of JABAWS server including JABAWS\r
 236          *            context name e.g\r
 237          *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 238          * @return compbio.data.msa.RegistryWS - instance of a RegistryWS web\r
 239          *         service\r
 240          * @throws WebServiceException\r
 241          * @throws ConnectException\r
 242          */\r
 243         public static compbio.data.msa.RegistryWS connectToRegistry(String host)\r
 244                         throws WebServiceException, ConnectException {\r
 245                 URL url = null;\r
 246                 String service = "RegistryWS";\r
 247                 log.log(Level.FINE, "Attempting to connect...");\r
 248 \r
 249                 try {\r
 250                         url = new URL(host + "/" + service + "?wsdl");\r
 251                 } catch (MalformedURLException e) {\r
 252                         e.printStackTrace();\r
 253                         // ignore as the host name is already verified\r
 254                 }\r
 255                 QName qname = new QName(JABAService.V2_SERVICE_NAMESPACE, service);\r
 256                 Service serv = Service.create(url, qname);\r
 257 \r
 258                 if (serv == null) {\r
 259                         throw new ConnectException("Could not connect to " + url + ". Is the server down?");\r
 260                 }\r
 261 \r
 262                 QName portName = new QName(serv.getServiceName().getNamespaceURI(), service + "Port");\r
 263                 compbio.data.msa.RegistryWS serviceIF = serv.getPort(portName, compbio.data.msa.RegistryWS.class);\r
 264                 log.log(Level.INFO, "Connected to " + service + " successfully!");\r
 265 \r
 266                 return serviceIF;\r
 267         }\r
 268 \r
 269         /**\r
 270          * Asks registry to test the service on the host hostname\r
 271          * \r
 272          * @param hostname\r
 273          * @param service\r
 274          * @param writer\r
 275          * @throws ConnectException\r
 276          * @throws WebServiceException\r
 277          */\r
 278         public static void testService(String hostname, Services service, PrintWriter writer)\r
 279                         throws ConnectException, WebServiceException {\r
 280                 RegistryWS registry = connectToRegistry(hostname);\r
 281                 if (registry != null) {\r
 282                         String message = registry.testService(service);\r
 283                         writer.println("Service " + service + " testing results: ");\r
 284                         writer.println(message);\r
 285                         FileUtil.closeSilently(((Closeable) registry));\r
 286                 }\r
 287                 writer.flush();\r
 288         }\r
 289 \r
 290         private static void listAllServices(String hostname) throws WebServiceException, IOException {\r
 291                 RegistryWS registry = connectToRegistry(hostname);\r
 292                 Set<Services> func_services = Collections.EMPTY_SET;\r
 293                 Set<Services> nonfunc_services = Collections.EMPTY_SET;\r
 294                 if (registry != null) {\r
 295                         func_services = registry.getSupportedServices();\r
 296                         nonfunc_services = registry.getNonoperatedServices();\r
 297                         FileUtil.closeSilently(((Closeable) registry));\r
 298                 } else {\r
 299                         System.out.println("Failed to connect to the registry! ");\r
 300                         return;\r
 301                 }\r
 302                 if (!func_services.isEmpty()) {\r
 303                         String mess = "\n\rAvailable services: ";\r
 304                         System.out.println(mess + Services.toString(func_services));\r
 305                 }\r
 306                 if (!nonfunc_services.isEmpty()) {\r
 307                         String mess = "Non-available services (internal tests failed): ";\r
 308                         System.out.println(mess + Services.toString(nonfunc_services));\r
 309                 }\r
 310         }\r
 311 \r
 312         /**\r
 313          * Calculate conservation for sequences loaded from a FASTA record list structure \r
 314          * \r
 315          * @param fastalist\r
 316          *            the list of FASTA records\r
 317          * @param wsproxy\r
 318          *            a web service proxy\r
 319          * @param preset\r
 320          *            Preset to use optional\r
 321          * @param customOptions\r
 322          *            the list of options\r
 323          * @return Set<Score> the conservation scores\r
 324          * @throws UnknownFileFormatException\r
 325          */\r
 326         static <T> ScoreManager analize(List<FastaSequence> fastalist, SequenceAnnotation<T> wsproxy, Preset<T> preset, List<Option<T>> customOptions) {\r
 327                 ScoreManager scores = null;\r
 328                 try {\r
 329                         String jobId = null;\r
 330                         if (customOptions != null && preset != null) {\r
 331                                 System.out.println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 332                         }\r
 333                         if (customOptions != null) {\r
 334                                 jobId = wsproxy.customAnalize(fastalist, customOptions);\r
 335                         } else if (preset != null) {\r
 336                                 jobId = wsproxy.presetAnalize(fastalist, preset);\r
 337                         } else {\r
 338                                 jobId = wsproxy.analize(fastalist);\r
 339                         }\r
 340                         System.out.println("\n\rcalling predictor.........");\r
 341                         Thread.sleep(100);\r
 342                         scores = wsproxy.getAnnotation(jobId);\r
 343                 } catch (JobSubmissionException e) {\r
 344                         System.err.println("Exception while submitting job to a web server. Exception details are below:");\r
 345                         e.printStackTrace();\r
 346                 } catch (ResultNotAvailableException e) {\r
 347                         System.err.println("Exception while waiting for results. Exception details are below:");\r
 348                         e.printStackTrace();\r
 349                 } catch (InterruptedException e) {\r
 350                         Thread.currentThread().interrupt();\r
 351                         System.err.println("Exception while waiting for results. Exception details are below:");\r
 352                         e.printStackTrace();\r
 353                 } catch (WrongParameterException e) {\r
 354                         String mess = "Parsing the web method input parameters failed Exception details are below:";\r
 355                         System.err.println(mess);\r
 356                         e.printStackTrace();\r
 357                 }\r
 358                 return scores;\r
 359 \r
 360         }\r
 361 \r
 362         /**\r
 363          * Calculate conservation for sequences loaded from the file\r
 364          * \r
 365          * @param wsproxy\r
 366          *            a web service proxy\r
 367          * @param file\r
 368          *            the file to read the results from\r
 369          * @param preset\r
 370          *            Preset to use optional\r
 371          * @param customOptions\r
 372          *            the list of options\r
 373          * @return Set<Score> the conservation scores\r
 374          * @throws IOException\r
 375          * @throws UnknownFileFormatException\r
 376          */\r
 377         static <T> ScoreManager analize(File file, SequenceAnnotation<T> wsproxy, Preset<T> preset, List<Option<T>> customOptions) {\r
 378                 List<FastaSequence> fastalist = null;\r
 379                 try {\r
 380                         fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
 381                         assert !fastalist.isEmpty() : "Input is empty!";\r
 382                 } catch (IOException e) {\r
 383                         String mess = "Reading the input file failed. Check that the file contains a list of FASTA records!\n";\r
 384                         System.err.println(mess + "Exception details are below:");\r
 385                         e.printStackTrace();\r
 386                 } catch (UnknownFileFormatException e) {\r
 387                         String mess = "Reading the input file failed. Exception details are below:";\r
 388                         System.err.println(mess);\r
 389                         System.out.println(e.getMessage());\r
 390                         e.printStackTrace();\r
 391                 }\r
 392                 return analize(fastalist, wsproxy, preset, customOptions);\r
 393         }\r
 394 \r
 395         /**\r
 396          * Align sequences from the file using MsaWS\r
 397          * \r
 398          * @param <T>\r
 399          *            web service type e.g. Clustal\r
 400          * @param file\r
 401          *            to write the resulting alignment to\r
 402          * @param msaws\r
 403          *            MsaWS required\r
 404          * @param preset\r
 405          *            Preset to use optional\r
 406          * @param customOptions\r
 407          *            file which contains new line separated list of options\r
 408          * @return Alignment\r
 409          */\r
 410         static <T> Alignment align(File file, MsaWS<T> msaws, Preset<T> preset,\r
 411                         List<Option<T>> customOptions) {\r
 412                 FileInputStream instream = null;\r
 413                 List<FastaSequence> fastalist = null;\r
 414                 Alignment alignment = null;\r
 415                 try {\r
 416                         instream = new FileInputStream(file);\r
 417                         fastalist = SequenceUtil.readFasta(instream);\r
 418                         instream.close();\r
 419                         String jobId = null;\r
 420                         if (customOptions != null && preset != null) {\r
 421                                 System.out.println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
 422                         }\r
 423                         if (customOptions != null) {\r
 424                                 jobId = msaws.customAlign(fastalist, customOptions);\r
 425                         } else if (preset != null) {\r
 426                                 jobId = msaws.presetAlign(fastalist, preset);\r
 427                         } else {\r
 428                                 jobId = msaws.align(fastalist);\r
 429                         }\r
 430                         System.out.println("\ncalling aligner.........");\r
 431                         Thread.sleep(1000);\r
 432                         alignment = msaws.getResult(jobId);\r
 433 \r
 434                 } catch (IOException e) {\r
 435                         System.err.println("Exception while reading the input file. "\r
 436                                                 + "Check that the input file contains a list of fasta formatted sequences! "\r
 437                                                 + "Exception details are below:");\r
 438                         e.printStackTrace();\r
 439                 } catch (JobSubmissionException e) {\r
 440                         System.err.println("Exception while submitting job to a web server. "\r
 441                                                 + "Exception details are below:");\r
 442                         e.printStackTrace();\r
 443                 } catch (ResultNotAvailableException e) {\r
 444                         System.err.println("Exception while waiting for results. "\r
 445                                         + "Exception details are below:");\r
 446                         e.printStackTrace();\r
 447                 } catch (InterruptedException ignored) {\r
 448                         // ignore and propagate an interruption\r
 449                         Thread.currentThread().interrupt();\r
 450                 } catch (WrongParameterException e) {\r
 451                         e.printStackTrace();\r
 452                 } finally {\r
 453                         if (instream != null) {\r
 454                                 try {\r
 455                                         instream.close();\r
 456                                 } catch (IOException ignored) {\r
 457                                         // ignore\r
 458                                 }\r
 459                         }\r
 460                 }\r
 461                 return alignment;\r
 462         }\r
 463         \r
 464         /**\r
 465          * Starts command line client, if no parameter are supported print help. Two\r
 466          * parameters are required for successful call the JWS2 host name and a\r
 467          * service name.\r
 468          * \r
 469          * @param args\r
 470          *            Usage: <Class or Jar file name> -h=host_and_context\r
 471          *            -s=serviceName ACTION [OPTIONS]\r
 472          * \r
 473          *            -h=<host_and_context> - a full URL to the JWS2 web server\r
 474          *            including context path e.g. http://10.31.1.159:8080/ws\r
 475          * \r
 476          *            -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,\r
 477          *            TcoffeeWS, ProbconsWS] ACTIONS:\r
 478          * \r
 479          *            -i=<inputFile> - full path to fasta formatted sequence file,\r
 480          *            from which to align sequences\r
 481          * \r
 482          *            -parameters - lists parameters supported by web service\r
 483          * \r
 484          *            -presets - lists presets supported by web service\r
 485          * \r
 486          *            -limits - lists web services limits Please note that if input\r
 487          *            file is specified other actions are ignored\r
 488          * \r
 489          *            OPTIONS: (only for use with -i action):\r
 490          * \r
 491          *            -r=<presetName> - name of the preset to use\r
 492          * \r
 493          *            -o=<outputFile> - full path to the file where to write an\r
 494          *            alignment -f=<parameterInputFile> - the name of the file with\r
 495          *            the list of parameters to use. Please note that -r and -f\r
 496          *            options cannot be used together. Alignment is done with either\r
 497          *            preset or a parameters from the file, but not both!\r
 498          * \r
 499          */\r
 500         public static void main(String[] args) {\r
 501 \r
 502                 if (args == null) {\r
 503                         System.out.println(Constraints.help_text);\r
 504                         System.exit(1);\r
 505                 }\r
 506                 if (args.length < 2) {\r
 507                         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
 508                         System.out.println(Constraints.help_text);\r
 509                         System.exit(1);\r
 510                 }\r
 511 \r
 512                 try {\r
 513                         new Jws2Client(args);\r
 514                 } catch (IOException e) {\r
 515                         log.log(Level.SEVERE, "IOException in client! " + e.getMessage(), e.getCause());\r
 516                         System.err.println("Cannot write output file! Stack trace: ");\r
 517                         e.printStackTrace();\r
 518                 }\r
 519         }\r
 520 }\r