src/jalview/ws/MsaWSClient.java

   1 /*\r
   2 * Jalview - A Sequence Alignment Editor and Viewer\r
   3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4 *\r
   5 * This program is free software; you can redistribute it and/or\r
   6 * modify it under the terms of the GNU General Public License\r
   7 * as published by the Free Software Foundation; either version 2\r
   8 * of the License, or (at your option) any later version.\r
   9 *\r
  10 * This program is distributed in the hope that it will be useful,\r
  11 * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13 * GNU General Public License for more details.\r
  14 *\r
  15 * You should have received a copy of the GNU General Public License\r
  16 * along with this program; if not, write to the Free Software\r
  17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18 */\r
  19 package jalview.ws;\r
  20 \r
  21 import ext.vamsas.*;\r
  22 \r
  23 import jalview.analysis.AlignSeq;\r
  24 \r
  25 import jalview.datamodel.*;\r
  26 \r
  27 import jalview.gui.*;\r
  28 \r
  29 import java.util.*;\r
  30 \r
  31 import javax.swing.*;\r
  32 \r
  33 \r
  34 /**\r
  35  * DOCUMENT ME!\r
  36  *\r
  37  * @author $author$\r
  38  * @version $Revision$\r
  39  */\r
  40 public class MsaWSClient extends WSClient\r
  41 {\r
  42     /**\r
  43     * server is a WSDL2Java generated stub for an archetypal MsaWSI service.\r
  44     */\r
  45     ext.vamsas.MuscleWS server;\r
  46 \r
  47     /**\r
  48      * Creates a new MsaWSClient object.\r
  49      *\r
  50      * @param MsaWSName DOCUMENT ME!\r
  51      * @param altitle DOCUMENT ME!\r
  52      * @param msa DOCUMENT ME!\r
  53      * @param submitGaps DOCUMENT ME!\r
  54      * @param preserveOrder DOCUMENT ME!\r
  55      */\r
  56     public MsaWSClient(String MsaWSName, String altitle, SequenceI[] msa,\r
  57         boolean submitGaps, boolean preserveOrder)\r
  58     {\r
  59         if (setWebService(MsaWSName) == false)\r
  60         {\r
  61             JOptionPane.showMessageDialog(Desktop.desktop,\r
  62                 "The Multiple Sequence Alignment Service named " + MsaWSName +\r
  63                 " is unknown", "Internal Jalview Error",\r
  64                 JOptionPane.WARNING_MESSAGE);\r
  65 \r
  66             return;\r
  67         }\r
  68 \r
  69         wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle,\r
  70                 WebServiceReference);\r
  71 \r
  72         if (!locateWebService())\r
  73         {\r
  74             return;\r
  75         }\r
  76 \r
  77         wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment") +\r
  78             " of " + altitle + "\nJob details\n");\r
  79 \r
  80         MsaWSThread musclethread = new MsaWSThread(WebServiceName +\r
  81                 " alignment of " + altitle, msa, submitGaps, preserveOrder);\r
  82         wsInfo.setthisService(musclethread);\r
  83         musclethread.start();\r
  84     }\r
  85 \r
  86     // JBPNote Nasty object-global state setting methods shouldn't be allowed\r
  87     private boolean setWebService(String MsaWSName)\r
  88     {\r
  89         if (MsaWServices.info.containsKey(MsaWSName))\r
  90         {\r
  91             WebServiceName = MsaWSName;\r
  92 \r
  93             String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName);\r
  94             WsURL = wsinfo[0];\r
  95             WebServiceJobTitle = wsinfo[1];\r
  96             WebServiceReference = wsinfo[2];\r
  97 \r
  98             return true;\r
  99         }\r
 100         else\r
 101         {\r
 102             return false;\r
 103         }\r
 104     }\r
 105 \r
 106     /**\r
 107      * DOCUMENT ME!\r
 108      *\r
 109      * @return DOCUMENT ME!\r
 110      */\r
 111     private boolean locateWebService()\r
 112     {\r
 113         // TODO: MuscleWS transmuted to generic MsaWS client\r
 114         MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default\r
 115 \r
 116         try\r
 117         {\r
 118             this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));\r
 119             ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute timeout\r
 120         }\r
 121         catch (Exception ex)\r
 122         {\r
 123             wsInfo.setProgressText("Serious! " + WebServiceName +\r
 124                 " Service location failed\nfor URL :" + WsURL + "\n" +\r
 125                 ex.getMessage());\r
 126             wsInfo.setStatus(wsInfo.ERROR);\r
 127             ex.printStackTrace();\r
 128 \r
 129             return false;\r
 130         }\r
 131 \r
 132         loc.getEngine().setOption("axis", "1");\r
 133 \r
 134         return true;\r
 135     }\r
 136 \r
 137     protected class MsaWSThread extends Thread implements WSClientI\r
 138     {\r
 139         String ServiceName = WebServiceName;\r
 140         String OutputHeader;\r
 141         vamsas.objects.simple.MsaResult result = null;\r
 142         vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();\r
 143         Hashtable SeqNames = null;\r
 144         boolean submitGaps = false; // and always store and recover sequence order\r
 145         boolean preserveOrder = true; // and always store and recover sequence order\r
 146         String jobId;\r
 147         String alTitle; // name which will be used to form new alignment window.\r
 148         int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
 149         boolean jobComplete = false;\r
 150 \r
 151         MsaWSThread(String title, SequenceI[] msa, boolean subgaps,\r
 152             boolean presorder)\r
 153         {\r
 154             alTitle = title;\r
 155             submitGaps = subgaps;\r
 156             preserveOrder = presorder;\r
 157 \r
 158             OutputHeader = wsInfo.getProgressText();\r
 159             SeqNames = new Hashtable();\r
 160 \r
 161             vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.Sequence[msa.length];\r
 162 \r
 163             for (int i = 0; i < msa.length; i++)\r
 164             {\r
 165                 String newname = jalview.analysis.SeqsetUtils.unique_name(i);\r
 166 \r
 167                 // uniquify as we go\r
 168                 // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation\r
 169                 SeqNames.put(newname,\r
 170                     jalview.analysis.SeqsetUtils.SeqCharacterHash(msa[i]));\r
 171                 seqarray[i] = new vamsas.objects.simple.Sequence();\r
 172                 seqarray[i].setId(newname);\r
 173                 seqarray[i].setSeq((submitGaps) ? msa[i].getSequence()\r
 174                                                 : AlignSeq.extractGaps(\r
 175                         jalview.util.Comparison.GapChars, msa[i].getSequence()));\r
 176             }\r
 177 \r
 178             this.seqs = new vamsas.objects.simple.SequenceSet();\r
 179             this.seqs.setSeqs(seqarray);\r
 180         }\r
 181 \r
 182         public boolean isCancellable()\r
 183         {\r
 184             return true;\r
 185         }\r
 186 \r
 187         public void cancelJob()\r
 188         {\r
 189             if ((jobId != null) && !jobId.equals("") && !jobComplete)\r
 190             {\r
 191                 String cancelledMessage = "";\r
 192 \r
 193                 try\r
 194                 {\r
 195                     vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);\r
 196 \r
 197                     if (cancelledJob.getStatus() == 2)\r
 198                     {\r
 199                         // CANCELLED_JOB\r
 200                         cancelledMessage = "Job cancelled.";\r
 201                         wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);\r
 202                         jobComplete = true;\r
 203                         jobsRunning--;\r
 204                         result = null;\r
 205                     }\r
 206                     else if (cancelledJob.getStatus() == 3)\r
 207                     {\r
 208                         // VALID UNSTOPPABLE JOB\r
 209                         cancelledMessage += "Server cannot cancel this job. just close the window.\n";\r
 210                     }\r
 211 \r
 212                     if (cancelledJob.getJobId() != null)\r
 213                     {\r
 214                         cancelledMessage += ("[" + cancelledJob.getJobId() +\r
 215                         "]");\r
 216                     }\r
 217 \r
 218                     cancelledMessage += "\n";\r
 219                 }\r
 220                 catch (Exception exc)\r
 221                 {\r
 222                     cancelledMessage += ("\nProblems cancelling the job : Exception received...\n" +\r
 223                     exc + "\n");\r
 224                     exc.printStackTrace();\r
 225                 }\r
 226 \r
 227                 wsInfo.setProgressText(OutputHeader + cancelledMessage + "\n");\r
 228             }\r
 229             else\r
 230             {\r
 231                 if (!jobComplete)\r
 232                 {\r
 233                     wsInfo.setProgressText(OutputHeader +\r
 234                         "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");\r
 235                 }\r
 236             }\r
 237         }\r
 238 \r
 239         public void run()\r
 240         {\r
 241             StartJob();\r
 242 \r
 243             while (!jobComplete && (allowedServerExceptions > 0))\r
 244             {\r
 245                 try\r
 246                 {\r
 247                     if ((result = server.getResult(jobId)) == null)\r
 248                     {\r
 249                         throw (new Exception(\r
 250                             "Timed out when communicating with server\nTry again later.\n"));\r
 251                     }\r
 252 \r
 253                     if (result.isRunning())\r
 254                     {\r
 255                         wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
 256                     }\r
 257                     else if (result.isQueued())\r
 258                     {\r
 259                         wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
 260                     }\r
 261 \r
 262                     if (result.isFinished())\r
 263                     {\r
 264                         parseResult();\r
 265                         jobComplete = true;\r
 266                         jobsRunning--;\r
 267                     }\r
 268                     else\r
 269                     {\r
 270                         if (result.getStatus() != null)\r
 271                         {\r
 272                             wsInfo.setProgressText(OutputHeader + "\n" +\r
 273                                 result.getStatus());\r
 274                         }\r
 275 \r
 276                         if (!(result.isJobFailed() || result.isServerError()))\r
 277                         {\r
 278                             Thread.sleep(5000);\r
 279 \r
 280                             //  System.out.println("I'm alive "+seqid+" "+jobid);\r
 281                         }\r
 282                         else\r
 283                         {\r
 284                             break;\r
 285                         }\r
 286                     }\r
 287                 }\r
 288                 catch (Exception ex)\r
 289                 {\r
 290                     allowedServerExceptions--;\r
 291                     wsInfo.appendProgressText("\n" + ServiceName +\r
 292                         " Server exception!\n" + ex.getMessage());\r
 293                     System.err.println(ServiceName + " Server exception: " +\r
 294                         ex.getMessage());\r
 295 \r
 296                     //          ex.printStackTrace(); JBPNote Debug\r
 297                     try\r
 298                     {\r
 299                         if (allowedServerExceptions > 0)\r
 300                         {\r
 301                             Thread.sleep(5000);\r
 302                         }\r
 303                     }\r
 304                     catch (InterruptedException ex1)\r
 305                     {\r
 306                     }\r
 307                 }\r
 308             }\r
 309 \r
 310             if (allowedServerExceptions == 0)\r
 311             {\r
 312                 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
 313             }\r
 314             else\r
 315             {\r
 316                 if (!((result != null) &&\r
 317                         (result.isJobFailed() || result.isServerError())))\r
 318                 {\r
 319                     wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
 320                 }\r
 321                 else\r
 322                 {\r
 323                     if (result.isFailed())\r
 324                     {\r
 325                         wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
 326                     }\r
 327 \r
 328                     if (result.isServerError())\r
 329                     {\r
 330                         wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
 331                     }\r
 332                 }\r
 333             }\r
 334         }\r
 335 \r
 336         void StartJob()\r
 337         {\r
 338             try\r
 339             {\r
 340                 vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);\r
 341 \r
 342                 if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))\r
 343                 {\r
 344                     jobId = jobsubmit.getJobId();\r
 345                     System.out.println(WsURL + " Job Id '" + jobId + "'");\r
 346                 }\r
 347                 else\r
 348                 {\r
 349                     if (jobsubmit == null)\r
 350                     {\r
 351                         throw new Exception("Server at " + WsURL +\r
 352                             " returned null object, it probably cannot be contacted. Try again later ?");\r
 353                     }\r
 354 \r
 355                     throw new Exception(jobsubmit.getJobId());\r
 356                 }\r
 357             }\r
 358             catch (Exception e)\r
 359             {\r
 360                 // TODO: JBPNote catch timeout or other fault types explicitly\r
 361                 // For unexpected errors\r
 362                 System.err.println(WebServiceName +\r
 363                     "Client: Failed to submit the sequences for alignment (probably a server side problem)\n" +\r
 364                     "When contacting Server:" + WsURL + "\n" + e.toString() +\r
 365                     "\n");\r
 366                 this.allowedServerExceptions = 0;\r
 367                 wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
 368                 wsInfo.appendProgressText(\r
 369                     "Failed to submit sequences for alignment.\n" +\r
 370                     "It is most likely that there is a problem with the server.\n" +\r
 371                     "Just close the window\n");\r
 372 \r
 373                 // e.printStackTrace(); // TODO: JBPNote DEBUG\r
 374             }\r
 375         }\r
 376 \r
 377         private void addFloatAnnotations(Alignment al, int[] gapmap,\r
 378             Vector values, String Symname, String Visname, float min,\r
 379             float max, int winLength)\r
 380         {\r
 381             Annotation[] annotations = new Annotation[al.getWidth()];\r
 382 \r
 383             for (int j = 0; j < values.size(); j++)\r
 384             {\r
 385                 float value = Float.parseFloat(values.get(j).toString());\r
 386                 annotations[gapmap[j]] = new Annotation("", value + "", ' ',\r
 387                         value);\r
 388             }\r
 389 \r
 390             al.addAnnotation(new AlignmentAnnotation(Symname, Visname,\r
 391                     annotations, min, max, winLength));\r
 392         }\r
 393 \r
 394         private jalview.datamodel.Sequence[] getVamsasAlignment(\r
 395             vamsas.objects.simple.Alignment valign)\r
 396         {\r
 397             vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();\r
 398             jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];\r
 399 \r
 400             for (int i = 0, j = seqs.length; i < j; i++)\r
 401                 msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),\r
 402                         seqs[i].getSeq());\r
 403 \r
 404             return msa;\r
 405         }\r
 406 \r
 407         void parseResult()\r
 408         {\r
 409             SequenceI[] seqs = null;\r
 410 \r
 411             try\r
 412             {\r
 413                 // OutputHeader = output.getText();\r
 414                 if (result.isFailed())\r
 415                 {\r
 416                     OutputHeader += "Job failed.\n";\r
 417                 }\r
 418 \r
 419                 if (result.getStatus() != null)\r
 420                 {\r
 421                     OutputHeader += ("\n" + result.getStatus());\r
 422                 }\r
 423 \r
 424                 if (result.getMsa() != null)\r
 425                 {\r
 426                     OutputHeader += "\nAlignment Object Method Notes\n";\r
 427 \r
 428                     String[] lines = result.getMsa().getMethod();\r
 429 \r
 430                     for (int line = 0; line < lines.length; line++)\r
 431                         OutputHeader += (lines[line] + "\n");\r
 432 \r
 433                     // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data\r
 434                     seqs = getVamsasAlignment(result.getMsa());\r
 435                 }\r
 436 \r
 437                 wsInfo.setProgressText(OutputHeader);\r
 438 \r
 439                 if (seqs != null)\r
 440                 {\r
 441                     AlignmentOrder msaorder = new AlignmentOrder(seqs);\r
 442 \r
 443                     if (preserveOrder)\r
 444                     {\r
 445                         jalview.analysis.AlignmentSorter.recoverOrder(seqs);\r
 446                     }\r
 447 \r
 448                     jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);\r
 449 \r
 450                     Alignment al = new Alignment(seqs);\r
 451 \r
 452                     // TODO: JBPNote Should also rename the query sequence sometime...\r
 453                     AlignFrame af = new AlignFrame(al);\r
 454                     af.addSortByOrderMenuItem(ServiceName + " Ordering",\r
 455                         msaorder);\r
 456 \r
 457                     Desktop.addInternalFrame(af, alTitle,\r
 458                         AlignFrame.NEW_WINDOW_WIDTH,\r
 459                         AlignFrame.NEW_WINDOW_HEIGHT);\r
 460                 }\r
 461             }\r
 462             catch (Exception ex)\r
 463             {\r
 464                 ex.printStackTrace();\r
 465             }\r
 466         }\r
 467     }\r
 468 }\r