Package uk.ac.bbsrc.tgac.miso.core.data.impl.solid

Examples of uk.ac.bbsrc.tgac.miso.core.data.impl.solid.SolidRun

121
122
123
124
125
126
127
128
129
130
131
        try {
          if (attemptRunPopulation) {
            if (r == null) {
              log.debug("Saving new run and status: " + is.getRunName());
              r = new SolidRun(xml);
              r.getStatus().setHealth(ht);
              if (run.has("fullPath")) {
                r.setFilePath(run.getString("fullPath"));
              }
View Full Code Here
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
  }

  public JSONObject changeSolidContainer(HttpSession session, JSONObject json) {
    int numContainers = json.getInt("numContainers");
    StringBuilder b = new StringBuilder();
    SolidRun run = (SolidRun) session.getAttribute("run_" + json.getString("run_cId"));
    run.getSequencerPartitionContainers().clear();

    for (int i = 0; i < numContainers; i++) {
      b.append("<h2>Container " + (i + 1) + "</h2>");
      b.append("<table class='in'>");
      b.append("<tr><td>ID:</td><td><button onclick='Run.container.lookupContainer(this, " + i + ");' type='button' class='right-button ui-state-default ui-corner-all'>Lookup</button><div style='overflow:hidden'><input type='text' id='sequencerPartitionContainers[" + i + "].identificationBarcode' name='sequencerPartitionContainers[" + i + "].identificationBarcode'/></div></td></tr>");
      b.append("<tr><td>Location:</td><td><input type='text' id='sequencerPartitionContainers[" + i + "].locationBarcode' name='sequencerPartitionContainers[" + i + "].locationBarcode'/></td></tr>");
      b.append("<tr><td>Paired:</td><td><input type='checkbox' id='sequencerPartitionContainers[" + i + "].paired' name='sequencerPartitionContainers[" + i + "].paired'/></td></tr>");
      b.append("</table>");
      b.append("<div id='partitionErrorDiv'> </div>");
      b.append("<div id='partitionDiv'>");
      if ("AB SOLiD 5500xl".equals(run.getSequencerReference().getPlatform().getInstrumentModel())) {
        b.append("<table class='in'>");
        b.append("<th>Chamber No.</th>");
        b.append("<th>Pool</th>");

        b.append("<tr><td>1 </td><td width='90%'><div id='p_div_" + i + "-0' class='elementListDroppableDiv'><ul class='runPartitionDroppable' bind='sequencerPartitionContainers[" + i + "].partitions[0].pool' partition='" + i + "_0'></ul></div></td></tr>");
        b.append("<tr><td>2 </td><td width='90%'><div id='p_div_" + i + "-1' class='elementListDroppableDiv'><ul class='runPartitionDroppable' bind='sequencerPartitionContainers[" + i + "].partitions[1].pool' partition='" + i + "_1'></ul></div></td></tr>");
        b.append("<tr><td>3 </td><td width='90%'><div id='p_div_" + i + "-2' class='elementListDroppableDiv'><ul class='runPartitionDroppable' bind='sequencerPartitionContainers[" + i + "].partitions[2].pool' partition='" + i + "_2'></ul></div></td></tr>");
        b.append("<tr><td>4 </td><td width='90%'><div id='p_div_" + i + "-3' class='elementListDroppableDiv'><ul class='runPartitionDroppable' bind='sequencerPartitionContainers[" + i + "].partitions[3].pool' partition='" + i + "_3'></ul></div></td></tr>");
        b.append("<tr><td>5 </td><td width='90%'><div id='p_div_" + i + "-4' class='elementListDroppableDiv'><ul class='runPartitionDroppable' bind='sequencerPartitionContainers[" + i + "].partitions[4].pool' partition='" + i + "_4'></ul></div></td></tr>");
        b.append("<tr><td>6 </td><td width='90%'><div id='p_div_" + i + "-5' class='elementListDroppableDiv'><ul class='runPartitionDroppable' bind='sequencerPartitionContainers[" + i + "].partitions[5].pool' partition='" + i + "_5'></ul></div></td></tr>");
        b.append("</table>");
      }
      else {
        b.append("<input id='chamber1' name='container" + i + "Select' onchange='Run.ui.changeSolidChamber(this, " + i + ");' type='radio' value='1'/>1 ");
        b.append("<input id='chamber4' name='container" + i + "Select' onchange='Run.ui.changeSolidChamber(this, " + i + ");' type='radio' value='4'/>4 ");
        b.append("<input id='chamber8' name='container" + i + "Select' onchange='Run.ui.changeSolidChamber(this, " + i + ");' type='radio' value='8'/>8 ");
        b.append("<input id='chamber16' name='container" + i + "Select' onchange='Run.ui.changeSolidChamber(this, " + i + ");' type='radio' value='16'/>16<br/>");
      }
      b.append("<div id='containerdiv" + i + "'> </div>");
      b.append("</div>");
      SequencerPartitionContainer<SequencerPoolPartition> f = dataObjectFactory.getSequencerPartitionContainer();
      run.addSequencerPartitionContainer(f);
    }
    return JSONUtils.SimpleJSONResponse(b.toString());
  }
View Full Code Here
427
428
429
430
431
432
433
434
435
436
437
438
  public JSONObject changeSolidChamber(HttpSession session, JSONObject json) {
    int numChambers = json.getInt("numChambers");
    int container = json.getInt("container");

    SolidRun run = (SolidRun) session.getAttribute("run_" + json.getString("run_cId"));
    SequencerPartitionContainer<SequencerPoolPartition> f = run.getSequencerPartitionContainers().get(container);
    f.setPartitionLimit(numChambers);
    f.initEmptyPartitions();

    StringBuilder b = new StringBuilder();
    b.append("<table class='in'>");
View Full Code Here
338
339
340
341
342
343
344
      throw new SecurityException();
    }
  }

  public Run getSolidRun() {
    return new SolidRun();
  }
View Full Code Here
342
343
344
345
346
347
348
  public Run getSolidRun() {
    return new SolidRun();
  }

  public Run getSolidRun(User user) {
    return new SolidRun(user);
  }
View Full Code Here
347
348
349
350
351
352
353
354
355
356
357
    return new SolidRun(user);
  }

  public Run getSolidRun(Experiment experiment, User user) {
    if (experiment.userCanWrite(user)) {
      return new SolidRun(user);

    }
    else {
      throw new SecurityException();
    }
View Full Code Here
TOP

Related Classes of uk.ac.bbsrc.tgac.miso.core.data.impl.solid.SolidRun

  • com.eaglegenomics.simlims.core.SecurityProfile
  • uk.ac.bbsrc.tgac.miso.core.data.impl.StatusImpl
  • uk.ac.bbsrc.tgac.miso.core.factory.TgacDataObjectFactory
  • uk.ac.bbsrc.tgac.miso.core.util.UnicodeReader
  • uk.ac.bbsrc.tgac.miso.notification.consumer.service.mechanism.SolidNotificationMessageConsumerMechanism
  • uk.ac.bbsrc.tgac.miso.spring.ajax.RunControllerHelperService
  • java.util.regex.Pattern
  • org.w3c.dom.Document
  • java.util.regex.Matcher
  • org.w3c.dom.Element
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.