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