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 org.apache.axis.client.*;\r
  30 \r
  31 import vamsas.objects.*;\r
  32 \r
  33 import java.awt.*;\r
  34 \r
  35 import java.util.*;\r
  36 \r
  37 import javax.swing.*;\r
  38 \r
  39 import javax.xml.namespace.QName;\r
  40 \r
  41 \r
  42 public class MsaWSClient extends WSClient {\r
  43     /**\r
  44  * server is a WSDL2Java generated stub for an archetypal MsaWSI service.\r
  45  */\r
  46     ext.vamsas.MuscleWS server;\r
  47 \r
  48     public MsaWSClient(String MsaWSName, String altitle, SequenceI[] msa,\r
  49         boolean submitGaps, boolean preserveOrder) {\r
  50         if (setWebService(MsaWSName) == false) {\r
  51             JOptionPane.showMessageDialog(Desktop.desktop,\r
  52                 "The Multiple Sequence Alignment Service named " + MsaWSName +\r
  53                 " is unknown", "Internal Jalview Error",\r
  54                 JOptionPane.WARNING_MESSAGE);\r
  55 \r
  56             return;\r
  57         }\r
  58 \r
  59         wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle,\r
  60                 WebServiceReference);\r
  61 \r
  62         if (!locateWebService()) {\r
  63             return;\r
  64         }\r
  65 \r
  66         wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment") +\r
  67             " of " + altitle + "\nJob details\n");\r
  68 \r
  69         MsaWSThread musclethread = new MsaWSThread(WebServiceName +\r
  70                 " alignment of " + altitle, msa, submitGaps, preserveOrder);\r
  71         wsInfo.setthisService(musclethread);\r
  72         musclethread.start();\r
  73     }\r
  74 \r
  75     // JBPNote Nasty object-global state setting methods shouldn't be allowed\r
  76     private boolean setWebService(String MsaWSName) {\r
  77         if (MsaWServices.info.containsKey(MsaWSName)) {\r
  78             WebServiceName = MsaWSName;\r
  79 \r
  80             String[] wsinfo = (String[]) MsaWServices.info.get(MsaWSName);\r
  81             WsURL = wsinfo[0];\r
  82             WebServiceJobTitle = wsinfo[1];\r
  83             WebServiceReference = wsinfo[2];\r
  84 \r
  85             return true;\r
  86         } else {\r
  87             return false;\r
  88         }\r
  89     }\r
  90 \r
  91     private boolean locateWebService() {\r
  92         // TODO: MuscleWS transmuted to generic MsaWS client\r
  93         MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default\r
  94 \r
  95         try {\r
  96             this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));\r
  97             ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute timeout\r
  98         } catch (Exception ex) {\r
  99             wsInfo.setProgressText("Serious! " + WebServiceName +\r
 100                 " Service location failed\nfor URL :" + WsURL + "\n" +\r
 101                 ex.getMessage());\r
 102             wsInfo.setStatus(wsInfo.ERROR);\r
 103             ex.printStackTrace();\r
 104 \r
 105             return false;\r
 106         }\r
 107 \r
 108         loc.getEngine().setOption("axis", "1");\r
 109 \r
 110         return true;\r
 111     }\r
 112 \r
 113     protected class MsaWSThread extends Thread implements WSClientI {\r
 114         String ServiceName = WebServiceName;\r
 115         String OutputHeader;\r
 116         vamsas.objects.simple.MsaResult result = null;\r
 117         vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();\r
 118         Hashtable SeqNames = null;\r
 119         boolean submitGaps = false; // and always store and recover sequence order\r
 120         boolean preserveOrder = true; // and always store and recover sequence order\r
 121         String jobId;\r
 122         String alTitle; // name which will be used to form new alignment window.\r
 123         int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
 124         boolean jobComplete = false;\r
 125 \r
 126         MsaWSThread(String title, SequenceI[] msa, boolean subgaps,\r
 127             boolean presorder) {\r
 128             alTitle = title;\r
 129             submitGaps = subgaps;\r
 130             preserveOrder = presorder;\r
 131 \r
 132             OutputHeader = wsInfo.getProgressText();\r
 133             SeqNames = new Hashtable();\r
 134 \r
 135             vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.Sequence[msa.length];\r
 136 \r
 137             for (int i = 0; i < msa.length; i++) {\r
 138                 String newname = jalview.analysis.SeqsetUtils.unique_name(i);\r
 139 \r
 140                 // uniquify as we go\r
 141                 // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation\r
 142                 SeqNames.put(newname,\r
 143                     jalview.analysis.SeqsetUtils.SeqCharacterHash(msa[i]));\r
 144                 seqarray[i] = new vamsas.objects.simple.Sequence();\r
 145                 seqarray[i].setId(newname);\r
 146                 seqarray[i].setSeq((submitGaps) ? msa[i].getSequence()\r
 147                                                 : AlignSeq.extractGaps(\r
 148                         jalview.util.Comparison.GapChars, msa[i].getSequence()));\r
 149             }\r
 150 \r
 151             this.seqs = new vamsas.objects.simple.SequenceSet();\r
 152             this.seqs.setSeqs(seqarray);\r
 153         }\r
 154 \r
 155         public boolean isCancellable() {\r
 156             return true;\r
 157         }\r
 158 \r
 159         public void cancelJob() {\r
 160             if ((jobId != null) && !jobId.equals("") && !jobComplete) {\r
 161                 String cancelledMessage = "";\r
 162 \r
 163                 try {\r
 164                     vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);\r
 165 \r
 166                     if (cancelledJob.getStatus() == 2) {\r
 167                         // CANCELLED_JOB\r
 168                         cancelledMessage = "Job cancelled.";\r
 169                         wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);\r
 170                         jobComplete = true;\r
 171                         jobsRunning--;\r
 172                         result = null;\r
 173                     } else if (cancelledJob.getStatus() == 3) {\r
 174                         // VALID UNSTOPPABLE JOB\r
 175                         cancelledMessage += "Server cannot cancel this job. just close the window.\n";\r
 176                     }\r
 177 \r
 178                     if (cancelledJob.getJobId() != null) {\r
 179                         cancelledMessage += ("[" + cancelledJob.getJobId() +\r
 180                         "]");\r
 181                     }\r
 182 \r
 183                     cancelledMessage += "\n";\r
 184                 } catch (Exception exc) {\r
 185                     cancelledMessage += ("\nProblems cancelling the job : Exception received...\n" +\r
 186                     exc + "\n");\r
 187                     exc.printStackTrace();\r
 188                 }\r
 189 \r
 190                 wsInfo.setProgressText(OutputHeader + cancelledMessage + "\n");\r
 191             } else {\r
 192                 if (!jobComplete) {\r
 193                     wsInfo.setProgressText(OutputHeader +\r
 194                         "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");\r
 195                 }\r
 196             }\r
 197         }\r
 198 \r
 199         public void run() {\r
 200             StartJob();\r
 201 \r
 202             while (!jobComplete && (allowedServerExceptions > 0)) {\r
 203                 try {\r
 204                     if ((result = server.getResult(jobId)) == null) {\r
 205                         throw (new Exception(\r
 206                             "Timed out when communicating with server\nTry again later.\n"));\r
 207                     }\r
 208 \r
 209                     if (result.isRunning()) {\r
 210                         wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
 211                     } else if (result.isQueued()) {\r
 212                         wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
 213                     }\r
 214 \r
 215                     if (result.isFinished()) {\r
 216                         parseResult();\r
 217                         jobComplete = true;\r
 218                         jobsRunning--;\r
 219                     } else {\r
 220                         if (result.getStatus() != null) {\r
 221                             wsInfo.setProgressText(OutputHeader + "\n" +\r
 222                                 result.getStatus());\r
 223                         }\r
 224 \r
 225                         if (!(result.isJobFailed() || result.isServerError())) {\r
 226                             Thread.sleep(5000);\r
 227 \r
 228                             //  System.out.println("I'm alive "+seqid+" "+jobid);\r
 229                         } else {\r
 230                             break;\r
 231                         }\r
 232                     }\r
 233                 } catch (Exception ex) {\r
 234                     allowedServerExceptions--;\r
 235                     wsInfo.appendProgressText("\n" + ServiceName +\r
 236                         " Server exception!\n" + ex.getMessage());\r
 237                     System.err.println(ServiceName + " Server exception: " +\r
 238                         ex.getMessage());\r
 239 \r
 240                     //          ex.printStackTrace(); JBPNote Debug\r
 241                     try {\r
 242                         if (allowedServerExceptions > 0) {\r
 243                             Thread.sleep(5000);\r
 244                         }\r
 245                     } catch (InterruptedException ex1) {\r
 246                     }\r
 247                 }\r
 248             }\r
 249 \r
 250             if (allowedServerExceptions == 0) {\r
 251                 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
 252             } else {\r
 253                 if (!((result != null) &&\r
 254                         (result.isJobFailed() || result.isServerError()))) {\r
 255                     wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
 256                 } else {\r
 257                     if (result.isFailed()) {\r
 258                         wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
 259                     }\r
 260 \r
 261                     if (result.isServerError()) {\r
 262                         wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
 263                     }\r
 264                 }\r
 265             }\r
 266         }\r
 267 \r
 268         void StartJob() {\r
 269             try {\r
 270                 vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);\r
 271 \r
 272                 if ((jobsubmit != null) && (jobsubmit.getStatus() == 1)) {\r
 273                     jobId = jobsubmit.getJobId();\r
 274                     System.out.println(WsURL + " Job Id '" + jobId + "'");\r
 275                 } else {\r
 276                     if (jobsubmit == null) {\r
 277                         throw new Exception("Server at " + WsURL +\r
 278                             " returned null object, it probably cannot be contacted. Try again later ?");\r
 279                     }\r
 280 \r
 281                     throw new Exception(jobsubmit.getJobId());\r
 282                 }\r
 283             } catch (Exception e) {\r
 284                 // TODO: JBPNote catch timeout or other fault types explicitly\r
 285                 // For unexpected errors\r
 286                 System.err.println(WebServiceName +\r
 287                     "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"\r
 288                     + "When contacting Server:"+WsURL + "\n" + e.toString() + "\n");\r
 289                 this.allowedServerExceptions = 0;\r
 290                 wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
 291                 wsInfo.appendProgressText("Failed to submit sequences for alignment.\n"\r
 292                     + "It is most likely that there is a problem with the server.\n"\r
 293                     + "Just close the window\n");\r
 294 \r
 295                 // e.printStackTrace(); // TODO: JBPNote DEBUG\r
 296             }\r
 297         }\r
 298 \r
 299         private void addFloatAnnotations(Alignment al, int[] gapmap,\r
 300             Vector values, String Symname, String Visname, float min,\r
 301             float max, int winLength) {\r
 302             Annotation[] annotations = new Annotation[al.getWidth()];\r
 303 \r
 304             for (int j = 0; j < values.size(); j++) {\r
 305                 float value = Float.parseFloat(values.get(j).toString());\r
 306                 annotations[gapmap[j]] = new Annotation("", value + "", ' ',\r
 307                         value);\r
 308             }\r
 309 \r
 310             al.addAnnotation(new AlignmentAnnotation(Symname, Visname,\r
 311                     annotations, min, max, winLength));\r
 312         }\r
 313 \r
 314         private jalview.datamodel.Sequence[] getVamsasAlignment(\r
 315             vamsas.objects.simple.Alignment valign) {\r
 316             vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();\r
 317             jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];\r
 318 \r
 319             for (int i = 0, j = seqs.length; i < j; i++)\r
 320                 msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),\r
 321                         seqs[i].getSeq());\r
 322 \r
 323             return msa;\r
 324         }\r
 325 \r
 326         void parseResult() {\r
 327             SequenceI[] seqs = null;\r
 328 \r
 329             try {\r
 330                 // OutputHeader = output.getText();\r
 331                 if (result.isFailed()) {\r
 332                     OutputHeader += "Job failed.\n";\r
 333                 }\r
 334 \r
 335                 if (result.getStatus() != null) {\r
 336                     OutputHeader += ("\n" + result.getStatus());\r
 337                 }\r
 338 \r
 339                 if (result.getMsa() != null) {\r
 340                     OutputHeader += "\nAlignment Object Method Notes\n";\r
 341 \r
 342                     String[] lines = result.getMsa().getMethod();\r
 343 \r
 344                     for (int line = 0; line < lines.length; line++)\r
 345                         OutputHeader += (lines[line] + "\n");\r
 346 \r
 347                     // 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
 348                     seqs = getVamsasAlignment(result.getMsa());\r
 349                 }\r
 350 \r
 351                 wsInfo.setProgressText(OutputHeader);\r
 352 \r
 353                 if (seqs != null) {\r
 354                     AlignmentOrder msaorder = new AlignmentOrder(seqs);\r
 355 \r
 356                     if (preserveOrder) {\r
 357                         jalview.analysis.AlignmentSorter.recoverOrder(seqs);\r
 358                     }\r
 359 \r
 360                     jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);\r
 361 \r
 362                     Alignment al = new Alignment(seqs);\r
 363 \r
 364                     // TODO: JBPNote Should also rename the query sequence sometime...\r
 365                     AlignFrame af = new AlignFrame(al);\r
 366                     af.addSortByOrderMenuItem(ServiceName + " Ordering",\r
 367                         msaorder);\r
 368 \r
 369                     Desktop.addInternalFrame(af, alTitle,\r
 370                         AlignFrame.NEW_WINDOW_WIDTH,\r
 371                         AlignFrame.NEW_WINDOW_HEIGHT);\r
 372                 }\r
 373             } catch (Exception ex) {\r
 374                 ex.printStackTrace();\r
 375             }\r
 376         }\r
 377     }\r
 378 }\r