Changeset 2202


Ignore:
Timestamp:
Jan 20, 2014, 12:43:51 PM (9 years ago)
Author:
Nicklas Nordborg
Message:

References #562: Re-design clustering and sequencing startup wizards

Started to split the "Register clustering and sequencing startup" wizard. The existing registration has been modified to only register clustering information. It has support for registering 1 or 2 flow cells at the same time, but if not the date, operator is the same each flow cell must be separately registered.

Location:
extensions/net.sf.basedb.reggie/trunk
Files:
3 edited

Legend:

Unmodified
Added
Removed

  • extensions/net.sf.basedb.reggie/trunk/resources/index.jsp

    r2201 r2202  
    216216      url = 'FlowCell.servlet?ID=<%=ID%>&cmd=CountUnprocessedFlowCells';
    217217    }
     218    else if (what == 'clustered-flow-cells')
     219    {
     220      url = 'FlowCell.servlet?ID=<%=ID%>&cmd=CountClusteredFlowCells';
     221    }
    218222    else if (what == 'active-sequencing-runs')
    219223    {
    … …  
    368372    else if (currentCount == 'unregistered-flow-cells')
    369373    {
    370       var msg = error || 'Number of flow cells waiting for sequencing';
     374      var msg = error || 'Number of flow cells waiting for clustering';
    371375      var count = error ? -1 : response.count;
    372376      setCount('count.flow-cells.1', count, 'flow cells', msg);
    373377      setCount('count.flow-cells.2', count, 'flow cells', msg);
     378      startCounting('clustered-flow-cells');
     379    }
     380    else if (currentCount == 'clustered-flow-cells')
     381    {
     382      var msg = error || 'Number of flow cells waiting for sequencing';
     383      var count = error ? -1 : response.count;
     384      setCount('count.flow-cells.3', count, 'flow cells', msg);
    374385      startCounting('active-sequencing-runs');
    375386    }
    … …  
    652663         
    653664          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/flowcell_registration.jsp?ID=<%=ID%>"
    654             >Register clustering and sequencing startup</span> <span class="counter" id="count.flow-cells.2" title="Counting..."><img src="images/loading-small.gif"></span>
     665            >Register clustering</span> <span class="counter" id="count.flow-cells.2" title="Counting..."><img src="images/loading-small.gif"></span>
     666
     667          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/sequencing_started.jsp?ID=<%=ID%>"
     668            >Register sequencing started</span> <span class="counter" id="count.flow-cells.3" title="Counting..."><img src="images/loading-small.gif"></span>
    655669
    656670          <li><span class="require-permission" data-role="LibPrep" data-link="libprep/sequencing_ended.jsp?ID=<%=ID%>"

  • extensions/net.sf.basedb.reggie/trunk/resources/libprep/flowcell_registration.jsp

    r2107 r2202  
    3737var dateIsValid = [];
    3838var flowCellIdIsValid = [];
    39 var sequencingCyclesIsValid = [];
    4039
    4140function init()
    … …  
    113112    if (step1IsValid()) gotoStep2();
    114113  }
    115   else if (currentStep == 2)
    116   {
    117     if (step2IsValid()) gotoStep3();
    118   }
    119   setCurrentStep(currentStep);
    120114}
    121115
    … …  
    153147  var failed = frm.outcome[1].checked;
    154148  if (failed && !frm.verifyFailure.checked) return false;
     149 
     150  if (!dateIsValid['clusterDate']) return false;
    155151 
    156152  var index = 0;
    … …  
    161157      var fc = frm.flowcells[i].flowCell;
    162158      if (flowCellIdIsValid['fc-'+index+'.externalId'] != true) return false;
    163       if (dateIsValid['fc-'+index+'.clusterDate'] != true) return false;
    164159      if (commentsIsValid['fc-'+index+'.comments'] != true) return false;
    165160      index++;
    … …  
    177172}
    178173
    179 function step3IsValid()
    180 {
    181   if (dateIsValid['sequencingStartDate'] != true) return false;
    182  
    183   var frm = document.forms['reggie'];
    184   var index = 0;
    185   for (var i = 0; i < frm.flowcells.length; i++)
    186   {
    187     if (frm.flowcells[i].selected)
    188     {
    189       var fc = frm.flowcells[i].flowCell;
    190       if (sequencingCyclesIsValid['fc-'+index+'.sequencingCycles'] != true) return false;
    191       index++;
    192     }
    193   }
    194  
    195   return true;
    196 }
    197174
    198175function getFlowCells()
    … …  
    236213  currentStep = 2;
    237214  Main.show('step.2.section');
    238   Main.hide('step.1.section');
    239215  Main.addClass(document.getElementById('step.1.section'), 'disabled');
    240216  Main.show('gocancel');
     217 
     218  Main.hide('gonext');
     219  Main.show('goregister');
     220 
    241221  if (failed)
    242222  {
    243     Main.hide('gonext');
    244     Main.show('goregister');
    245    
    246223    setInnerHTML('gonext.message', '<input type="checkbox" name="verifyFailure" onclick="verifyFailureOnClick()"> Check to verify registration of failure');
    247224    Main.addClass(document.getElementById('goregister'), 'disabled');
    … …  
    266243  {
    267244    var cbot = cbots[i];
    268     frm['fc-0.cBot'][frm['fc-0.cBot'].length] = new Option(cbot.name, cbot.id, cbot.isDefault);
    269     frm['fc-1.cBot'][frm['fc-1.cBot'].length] = new Option(cbot.name, cbot.id, cbot.isDefault);
    270     setInputStatus('fc-0.cBot', '', 'valid');
    271     setInputStatus('fc-1.cBot', '', 'valid');
     245    frm.cBot[frm.cBot.length] = new Option(cbot.name, cbot.id, cbot.isDefault);
     246    setInputStatus('cBot', '', 'valid');
    272247  }
    273248  if (cbots.length == 0)
    274249  {
    275     frm['fc-0.cBot'][0] = new Option('- none -', '');
    276     frm['fc-1.cBot'][0] = new Option('- none -', '');
     250    frm.cBot[0] = new Option('- none -', '');
    277251  }
    278252
    … …  
    299273    Main.addClass(document.getElementById('step.2.section'), 'hide-fc-1');
    300274  }
    301 
    302  
    303   frm['fc-0.externalId'].focus();
     275 
     276  frm.clusterDate.focus();
    304277}
    305278
    … …  
    309282  // Disable controls
    310283  frm.clusterProtocol.disabled = true;
     284  frm.clusterDate.disabled = true;
     285  frm.clusterOperator.disabled = true;
     286  frm.cBot.disabled = true;
    311287  frm['fc-0.externalId'].disabled = true;
    312   frm['fc-0.clusterDate'].disabled = true;
    313   frm['fc-0.clusterOperator'].disabled = true;
    314   frm['fc-0.cBot'].disabled = true;
    315288  frm['fc-0.comments'].disabled = true;
    316289  frm['fc-1.externalId'].disabled = true;
    317   frm['fc-1.clusterDate'].disabled = true;
    318   frm['fc-1.clusterOperator'].disabled = true;
    319   frm['fc-1.cBot'].disabled = true;
    320290  frm['fc-1.comments'].disabled = true;
    321 
    322291  Main.addClass(document.getElementById('step.2.section'), 'disabled');
    323292}
    324293
    325 function gotoStep3()
    326 {
    327   var frm = document.forms['reggie'];
    328  
    329   disableStep2();
    330   Main.hide('step.2.section');
    331   Main.show('step.3.section');
    332   Main.hide('gonext');
    333   Main.show('goregister');
    334   currentStep = 3;
    335 
    336   // Load sequencing protocols
    337   var protocols = getProtocols('SEQUENCING_PROTOCOL');
    338   for (var i = 0; i < protocols.length; i++)
    339   {
    340     var protocol = protocols[i];
    341     frm.sequencingProtocol[frm.sequencingProtocol.length] = new Option(protocol.name, protocol.id, protocol.isDefault);
    342     setInputStatus('sequencingProtocol', '', 'valid');
    343   }
    344   if (frm.sequencingProtocol.length == 0)
    345   {
    346     frm.sequencingProtocol[0] = new Option('- none -', '');
    347   }
    348 
    349   // Load sequencing machines
    350   var sequencers = getHardware('SEQUENCER');
    351   for (var i = 0; i < sequencers.length; i++)
    352   {
    353     var sequencer = sequencers[i];
    354     frm.sequencer[frm.sequencer.length] = new Option(sequencer.name, sequencer.id, sequencer.isDefault);
    355     setInputStatus('sequencer', '', 'valid');
    356   }
    357   if (frm.sequencer.length == 0)
    358   {
    359     frm.sequencer[0] = new Option('- none -', '');
    360   }
    361  
    362   var index = 0;
    363   for (var i = 0; i < frm.flowcells.length && index < 2; i++)
    364   {
    365     if (frm.flowcells[i].selected)
    366     {
    367       var fc = frm.flowcells[i].flowCell;
    368       var prefix = 'fc-'+index;
    369       setInnerHTML(prefix+'.externalId', frm[prefix+'.externalId'].value);
    370       document.getElementById(prefix+'.externalId').title = fc.name;
    371       frm[prefix+'.sequencingCycles'].value = fc.SequencingCycles;
    372       sequencingCyclesOnBlur(prefix+'.sequencingCycles');
    373       index++;
    374     }
    375   }
    376 
    377   if (index == 1)
    378   {
    379     // Only one flow cell selected
    380     Main.addClass(document.getElementById('step.3.section'), 'hide-fc-1');
    381   }
    382    
    383   frm.sequencingStartDate.focus();
    384 }
    385294
    386295function getProtocols(subtype)
    … …  
    441350  Main.addOrRemoveClass(frm['fc-0.comments'], 'required', failed);
    442351  Main.addOrRemoveClass(frm['fc-1.comments'], 'required', failed);
    443   if (failed)
    444   {
    445     Main.hide('step.3.box');
    446   }
    447   else
    448   {
    449     Main.showInline('step.3.box');
    450   }
    451352}
    452353
    … …  
    541442}
    542443
    543 function sequencingCyclesOnBlur(sequencingCyclesField)
    544 {
    545   var frm = document.forms['reggie'];
    546  
    547   setInputStatus(sequencingCyclesField, '', '');
    548   sequencingCyclesIsValid[sequencingCyclesField] = false;
    549  
    550   var sequencingCycles = frm[sequencingCyclesField].value;
    551   if (sequencingCycles == '')
    552   {
    553     setInputStatus(sequencingCyclesField, 'Sequencing cycles is a required value', 'invalid');
    554     return;
    555   }
    556   if (!sequencingCycles.match(/^\d+\-\d+\-\d+$/))
    557   {
    558     setInputStatus(sequencingCyclesField, 'Not a valid Sequencing cycles value', 'invalid');
    559     return;
    560   }
    561  
    562   sequencingCyclesIsValid[sequencingCyclesField] = true;
    563   setInputStatus(sequencingCyclesField, '', 'valid');
    564 }
    565444
    566445
    … …  
    569448  var failed = document.getElementById('outcomeFailed').checked;
    570449  var frm = document.forms['reggie'];
    571   if (failed)
    572   {
    573     if (!step2IsValid()) return;
    574     disableStep2();
    575   }
    576   else
    577   {
    578     if (!step3IsValid()) return;
    579     Main.addClass(document.getElementById('step.3.section'), 'disabled');
    580     frm.sequencingStartDate.disabled = true;
    581     frm.sequencingOperator.disabled = true;
    582     frm.sequencingProtocol.disabled = true;
    583     frm.sequencer.disabled = true;
    584     frm.sequencingComments.disabled = true;
    585   }
     450
     451  if (!step2IsValid()) return;
     452  disableStep2();
    586453 
    587454  Main.hide('goregister');
    … …  
    592459  submitInfo.failed = failed;
    593460 
    594   // Cluster fields
    595   submitInfo.clusterProtocol = parseInt(frm.clusterProtocol.value, 10);
    596  
    597   if (!failed)
    598   {
    599     // Sequence start fields
    600     submitInfo.sequencingStartDate = frm.sequencingStartDate.value;
    601     submitInfo.sequencingOperator = frm.sequencingOperator.value;
    602     submitInfo.sequencingProtocol = parseInt(frm.sequencingProtocol.value, 10);
    603     submitInfo.sequencer = parseInt(frm.sequencer.value, 10);
    604     submitInfo.sequencingComments = frm.sequencingComments.value;
    605   }
    606 
    607461  submitInfo.flowCells = [];
    608462  var index = 0;
    … …  
    612466    {
    613467      var fc = frm.flowcells[i].flowCell;
    614       frm['fc-'+index+'.sequencingCycles'].disabled = true;
    615468      fc.externalId = frm['fc-'+index+'.externalId'].value;
    616       fc.clusterDate = frm['fc-'+index+'.clusterDate'].value;
    617       fc.clusterOperator = frm['fc-'+index+'.clusterOperator'].value;
    618       fc.cBot = parseInt(frm['fc-'+index+'.cBot'].value, 10);
     469      fc.clusterDate = frm.clusterDate.value;
     470      fc.clusterOperator = frm.clusterOperator.value;
     471      fc.cBot = parseInt(frm.cBot.value, 10);
     472      fc.clusterProtocol = parseInt(frm.clusterProtocol.value, 10);
    619473      fc.comments = frm['fc-'+index+'.comments'].value;
    620       if (!failed)
    621       {
    622         fc.SequencingCycles = frm['fc-'+index+'.sequencingCycles'].value;
    623         fc.HiSeqPosition = Forms.getCheckedRadio(frm['fc-'+index+'.pos']).value;
    624       }
    625474      submitInfo.flowCells[submitInfo.flowCells.length] = fc;
    626475      index++;
    … …  
    676525}
    677526
    678 function hiseqPosOnClick(index)
    679 {
    680   var frm = document.forms['reggie'];
    681 
    682   var clicked = frm['fc-'+index+'.pos'];
    683   var other = frm['fc-'+(1-index)+'.pos'];
    684  
    685   other[0].checked = clicked[1].checked;
    686   other[1].checked = clicked[0].checked;
    687  
    688 }
    689 
    690527</script>
    691528<style>
    … …  
    706543  <p:path><p:pathelement
    707544    title="Reggie" href="<%="../index.jsp?ID="+ID%>"
    708     /><p:pathelement title="Register clustering and sequencing startup"
     545    /><p:pathelement title="Register clustering"
    709546    /></p:path>
    710547
    … …  
    722559  %>
    723560
    724   <div class="allsteps">
    725     <div class="step current" id="step.1">1</div>
    726     ›
    727     <div class="step future" id="step.2">2</div>
    728     <span id="step.3.box">
    729     ›
    730     <div class="step future" id="step.3">3</div>
    731     </span>
    732   </div>
    733 
    734561
    735562  <form name="reggie" onsubmit="return false;">
    736  
    737563  <div id="step.1.section">
    738564  <table class="stepform">
    … …  
    756582      </tr>
    757583      <tr valign="top">
     584        <td colspan="2">
     585          <div class="messagecontainer note">
     586            <b>Note!</b>
     587            Register each flow cell separately if the outcome, cluster date, operator, etc. is different.
     588          </div>
     589           
     590        </td>
     591        <td class="status" ></td>
     592        <td class="help">
     593        </td>
     594      </tr>
     595      <tr valign="top">
    758596        <td class="prompt">Outcome</td>
    759597        <td class="input">
    760598          <input type="radio" name="outcome" id="outcomeSuccess"
    761             onchange="outcomeOnChange()" checked><label for="outcomeSuccess">Success</label> - sequencing has started<br>
     599            onchange="outcomeOnChange()" checked><label for="outcomeSuccess">Success</label> - continue with sequencing<br>
    762600          <input type="radio" name="outcome" id="outcomeFailed"
    763601            onchange="outcomeOnChange()"><label for="outcomeFailed">Failure</label> - no sequencing
    … …  
    765603        <td class="status"></td>
    766604        <td class="help">
    767           Select the <b>Success</b> option if sequencing has been started.
     605          Select the <b>Success</b> option if the flow cell is ready for sequencing.
    768606          Select the <b>Failure</b> option if it was not poosible to start sequencing
    769607          the flow cells.
    … …  
    786624      <table style="border-collapse: collapse;">
    787625      <tr valign="top">
     626        <td class="prompt">Start date</td>
     627        <td class="input">
     628          <input type="text" class="required" name="clusterDate" value="" size="12" maxlength="10"
     629            onblur="dateOnChange(this.name)" onkeypress="focusOnEnter(event, 'clusterOperator')">
     630            <base:icon
     631              onclick="Dates.selectDate('Cluster date', 'reggie', 'clusterDate', 'setDate', 'yyyyMMdd')"
     632              image="calendar.png"
     633              tooltip="Select a date from a calendar"
     634              tabindex="-1"
     635            />
     636        </td>
     637        <td class="status" id="clusterDate.status"></td>
     638        <td class="help">
     639          <span id="clusterDate.message" class="message" style="display: none;"></span>Date the clustering was started (YYYYMMDD or MMDD)
     640        </td>
     641      </tr>
     642      <tr valign="top">
     643        <td class="prompt">Operator</td>
     644        <td class="input">
     645          <input type="text" name="clusterOperator" value="<%=HTML.encodeTags(user.getName()) %>"
     646            style="width: 90%;" maxlength="255" onkeypress="focusOnEnter(event, 'cBot')">
     647        </td>
     648        <td class="status" id="clusterOperator.status"></td>
     649        <td class="help">
     650          <span id="clusterOperator.message" class="message" style="display: none;"></span>
     651        </td>
     652      </tr>
     653      <tr valign="top">
     654        <td class="prompt">cBot</td>
     655        <td class="input"><select style="width:90%" name="cBot" 
     656          onkeypress="focusOnEnter(event, 'clusterProtocol')"></select></td>
     657        <td class="status" id="cBot.status"></td>
     658        <td class="help"><span id="cBot.message" class="message" style="display: none;"></span>
     659          Select the cBot which was used in the clustering.
     660        </td>
     661      </tr>
     662      <tr valign="top">
    788663        <td class="prompt">Protocol</td>
    789664        <td class="input"><select style="width:90%" name="clusterProtocol" id="clusterProtocol"
    … …  
    794669        </td>
    795670      </tr>
     671
    796672      <tbody class="fc-0">
    797673      <tr valign="top" style="background-color: #E8E8E8;">
    … …  
    803679      <tr valign="top">
    804680        <td class="subprompt">ID</td>
    805         <td class="input"><input type="text" class="required" name="fc-0.externalId" onblur="flowCellIdOnBlur(this.name)" onkeypress="focusOnEnter(event, 'fc-0.clusterDate')"></td>
     681        <td class="input"><input type="text" class="required" name="fc-0.externalId" onblur="flowCellIdOnBlur(this.name)" onkeypress="focusOnEnter(event, 'fc-0.comments')"></td>
    806682        <td class="status" id="fc-0.externalId.status"></td>
    807         <td class="help"><span id="fc-0.externalId.message" class="message"></span></td>
    808       </tr>
    809       <tr valign="top">
    810         <td class="subprompt">Start date</td>
    811         <td class="input">
    812           <input type="text" class="required" name="fc-0.clusterDate" value="" size="12" maxlength="10"
    813             onblur="dateOnChange(this.name)" onkeypress="focusOnEnter(event, 'fc-0.clusterOperator')">
    814             <base:icon
    815               onclick="Dates.selectDate('Cluster date', 'reggie', 'fc-0.clusterDate', 'setDate', 'yyyyMMdd')"
    816               image="calendar.png"
    817               tooltip="Select a date from a calendar"
    818               tabindex="-1"
    819             />
    820         </td>
    821         <td class="status" id="fc-0.clusterDate.status"></td>
    822         <td class="help">
    823           <span id="fc-0.clusterDate.message" class="message" style="display: none;"></span>Date the clustering was started (YYYYMMDD or MMDD)
    824         </td>
    825       </tr>
    826       <tr valign="top">
    827         <td class="subprompt">Operator</td>
    828         <td class="input">
    829           <input type="text" name="fc-0.clusterOperator" value="<%=HTML.encodeTags(user.getName()) %>"
    830             style="width: 90%;" maxlength="255" onkeypress="focusOnEnter(event, 'fc-0.cBot')">
    831         </td>
    832         <td class="status" id="fc-0.clusterOperator.status"></td>
    833         <td class="help">
    834           <span id="fc-0.clusterOperator.message" class="message" style="display: none;"></span>
    835         </td>
    836       </tr>
    837       <tr valign="top">
    838         <td class="subprompt">cBot</td>
    839         <td class="input"><select style="width:90%" name="fc-0.cBot" 
    840           onkeypress="focusOnEnter(event, 'fc-0.comments')"></select></td>
    841         <td class="status" id="fc-0.cBot.status"></td>
    842         <td class="help"><span id="fc-0.cBot.message" class="message" style="display: none;"></span>
    843           Select the cBot which was used in the clustering.
     683        <td class="help"><span id="fc-0.externalId.message" class="message"></span>
     684          The barcode of the flow cell.
    844685        </td>
    845686      </tr>
    … …  
    862703      <tr valign="top">
    863704        <td class="subprompt">ID</td>
    864         <td class="input"><input type="text" class="required" name="fc-1.externalId" onblur="flowCellIdOnBlur(this.name)" onkeypress="focusOnEnter(event, 'fc-1.clusterDate')"></td>
     705        <td class="input"><input type="text" class="required" name="fc-1.externalId" onblur="flowCellIdOnBlur(this.name)" onkeypress="focusOnEnter(event, 'fc-1.comments')"></td>
    865706        <td class="status" id="fc-1.externalId.status"></td>
    866         <td class="help"><span id="fc-1.externalId.message" class="message"></span></td>
    867       </tr>
    868       <tr valign="top">
    869         <td class="subprompt">Start date</td>
    870         <td class="input">
    871           <input type="text" class="required" name="fc-1.clusterDate" value="" size="12" maxlength="10"
    872             onblur="dateOnChange(this.name)" onkeypress="focusOnEnter(event, 'fc-1.clusterOperator')">
    873             <base:icon
    874               onclick="Dates.selectDate('Cluster date', 'reggie', 'fc-1.clusterDate', 'setDate', 'yyyyMMdd')"
    875               image="calendar.png"
    876               tooltip="Select a date from a calendar"
    877               tabindex="-1"
    878             />
    879         </td>
    880         <td class="status" id="fc-1.clusterDate.status"></td>
    881         <td class="help">
    882           <span id="fc-1.clusterDate.message" class="message" style="display: none;"></span>Date the clustering was started (YYYYMMDD or MMDD)
    883         </td>
    884       </tr>
    885       <tr valign="top">
    886         <td class="subprompt">Operator</td>
    887         <td class="input">
    888           <input type="text" name="fc-1.clusterOperator" value="<%=HTML.encodeTags(user.getName()) %>"
    889             style="width: 90%;" maxlength="255" onkeypress="focusOnEnter(event, 'fc-1.cBot')">
    890         </td>
    891         <td class="status" id="fc-1.clusterOperator.status"></td>
    892         <td class="help">
    893           <span id="fc-1.clusterOperator.message" class="message" style="display: none;"></span>
    894         </td>
    895       </tr>
    896       <tr valign="top">
    897         <td class="subprompt">cBot</td>
    898         <td class="input"><select style="width:90%" name="fc-1.cBot" 
    899           onkeypress="focusOnEnter(event, 'fc-1.comments')"></select></td>
    900         <td class="status" id="fc-1.cBot.status"></td>
    901         <td class="help"><span id="fc-1.cBot.message" class="message" style="display: none;"></span>
    902           Select the cBot which was used in the clustering.
     707        <td class="help"><span id="fc-1.externalId.message" class="message"></span>
     708          The barcode of the flow cell.
    903709        </td>
    904710      </tr>
    … …  
    918724  </div>
    919725 
    920  
    921   <div id="step.3.section" style="display: none;">
    922   <table class="stepform">
    923   <tr>
    924     <td rowspan="3" class="stepno">3</td>
    925     <td class="steptitle">Sequencing startup information</td>
    926   </tr>
    927   <tr>
    928     <td class="stepfields">
    929       <table style="border-collapse: collapse;">
    930       <tr>
    931         <td class="prompt">Sequencing start date</td>
    932         <td class="input" colspan="2">
    933           <input type="text" class="required" name="sequencingStartDate" maxlength="10" style="width: 8em;"
    934             onblur="dateOnChange('sequencingStartDate')" onkeypress="focusOnEnter(event, 'sequencingOperator')">
    935             <base:icon
    936               onclick="Dates.selectDate('Sequence start date', 'reggie', 'sequencingStartDate', 'setDate', 'yyyyMMdd')"
    937               image="calendar.png"
    938               tooltip="Select a date from a calendar"
    939               tabindex="-1"
    940             />
    941         </td>
    942         <td class="status" id="sequencingStartDate.status"></td>
    943         <td class="help">
    944           <span id="sequencingStartDate.message" class="message" style="display: none;"></span>(YYYYMMDD or MMDD)
    945         </td>
    946       </tr>
    947       <tr valign="top">
    948         <td class="prompt">Operator</td>
    949         <td class="input" colspan="2">
    950           <input type="text" name="sequencingOperator" value="<%=HTML.encodeTags(user.getName()) %>"
    951             style="width: 90%;" maxlength="255" onkeypress="focusOnEnter(event, 'sequencingProtocol')">
    952         </td>
    953         <td class="status" id="sequencingOperator.status"></td>
    954         <td class="help">
    955           <span id="sequencingOperator.message" class="message" style="display: none;"></span>
    956         </td>
    957       </tr>
    958       <tr valign="top">
    959         <td class="prompt">Protocol</td>
    960         <td class="input" colspan="2"><select style="width:90%" name="sequencingProtocol" id="sequencingProtocol"
    961           onkeypress="focusOnEnter(event, 'sequencer')"></select></td>
    962         <td class="status" id="sequencingProtocol.status"></td>
    963         <td class="help"><span id="sequencingProtocol.message" class="message" style="display: none;"></span>
    964           Select the protocol for the sequencing.
    965         </td>
    966       </tr>
    967       <tr valign="top">
    968         <td class="prompt">Sequencing machine</td>
    969         <td class="input" colspan="2"><select style="width:90%" name="sequencer" id="sequencer"
    970           onkeypress="focusOnEnter(event, 'sequencingComments')"></select></td>
    971         <td class="status" id="sequencer.status"></td>
    972         <td class="help"><span id="sequencer.message" class="message" style="display: none;"></span>
    973           Select the HiSeq machine which is used for sequencing.
    974         </td>
    975       </tr>
    976      
    977       <tr valign="top" style="border-top: 1em solid transparent;">
    978         <td class="prompt"></td>
    979         <td style="font-weight: bold;">HiSeq position</td>
    980         <td style="font-weight: bold;">Sequencing cycles</td>
    981         <td class="status"></td>
    982         <td class="help"></td>
    983       </tr>
    984       <tr valign="top">
    985         <td class="prompt"></td>
    986         <td></td>
    987         <td style="font-style: italic;">(Read 1 - Index - Read 2)</td>
    988         <td class="status"></td>
    989         <td class="help"></td>
    990       </tr>
    991       <tr valign="top" class="fc-0">
    992         <td class="subprompt"><span id="fc-0.externalId"></span></td>
    993         <td>&nbsp;
    994           <label><input type="radio" name="fc-0.pos" value="A" onclick="hiseqPosOnClick(0)" checked>A</label>
    995           &nbsp;
    996           <label><input type="radio" name="fc-0.pos" value="B" onclick="hiseqPosOnClick(0)">B</label>
    997         </td>
    998         <td><input type="text" class="required" name="fc-0.sequencingCycles" onblur="sequencingCyclesOnBlur(this.name)"></td>
    999         <td class="status" id="fc-0.sequencingCycles.status"></td>
    1000         <td class="help"><span id="fc-0.sequencingCycles.message" class="message"></span></td>
    1001       </tr>
    1002       <tr valign="top" class="fc-1">
    1003         <td class="subprompt"><span id="fc-1.externalId"></span></td>
    1004         <td>&nbsp;
    1005           <label><input type="radio" name="fc-1.pos" value="A" onclick="hiseqPosOnClick(1)">A</label>
    1006           &nbsp;
    1007           <label><input type="radio" name="fc-1.pos" value="B" onclick="hiseqPosOnClick(1)" checked>B</label>
    1008         </td>
    1009         <td><input type="text" class="required" name="fc-1.sequencingCycles" onblur="sequencingCyclesOnBlur(this.name)"></td>
    1010         <td class="status" id="fc-1.sequencingCycles.status"></td>
    1011         <td class="help"><span id="fc-1.sequencingCycles.message" class="message"></span></td>
    1012       </tr>
    1013 
    1014 
    1015       <tr valign="top" style="border-top: 1em solid transparent;">
    1016         <td class="prompt">Comments</td>
    1017         <td class="input" colspan="2"><textarea rows="4" cols="50" style="width: 90%;" name="sequencingComments" value=""></textarea></td>
    1018         <td class="status" id="sequencingComments.status"></td>
    1019         <td class="help"><span id="sequencingComments.message" class="message" style="display: none;"></span>Comments about the sequencing startup.</td>
    1020       </tr>
    1021       </table>
    1022     </td>
    1023   </tr>
    1024   </table>
    1025   </div>
    1026726 
    1027727  <div class="loading" id="loading" style="display: none;"><table><tr><td><img src="../images/loading.gif"></td><td id="loading.msg">Please wait...</td></tr></table></div>

  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/FlowCellServlet.java

    r2196 r2202  
    4646import net.sf.basedb.reggie.dao.ReactionPlate;
    4747import net.sf.basedb.reggie.dao.ReggieRole;
    48 import net.sf.basedb.reggie.dao.SequencingRun;
    4948import net.sf.basedb.reggie.dao.Subtype;
    5049import net.sf.basedb.util.Values;
    … …  
    223222        json.put("flowCellInfo", jsonFlowCellInfo);
    224223      }
    225       else if ("CountSequencingFlowCells".equals(cmd))
    226       {
    227         dc = sc.newDbControl();
    228         ItemQuery<DerivedBioAssay> query = DerivedBioAssay.getQuery();
     224      else if ("CountClusteredFlowCells".equals(cmd))
     225      {
     226        dc = sc.newDbControl();
     227        ItemQuery<PhysicalBioAssay> query = PhysicalBioAssay.getQuery();
    229228        query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
    230         Subtype.SEQUENCING_RUN.addFilter(dc, query);
    231         // Must have a SEQUENCING_START annotation
    232         query.join(Annotations.leftJoin(null, Annotationtype.SEQUENCING_START.load(dc), "sst"));
    233         query.restrict(Restrictions.neq(Hql.alias("sst"), null));
    234         // Must NOT have a SEQUENCING_END annotation
    235         query.join(Annotations.leftJoin(null, Annotationtype.SEQUENCING_END.load(dc), "sse"));
    236         query.restrict(Restrictions.eq(Hql.alias("sse"), null));
     229        Subtype.FLOW_CELL.addFilter(dc, query);
     230        // Must have a creation date
     231        query.join(Hql.innerJoin("creationEvent", "ce"));
     232        query.restrict(Restrictions.neq(Hql.property("ce", "eventDate"), null));
     233        // and have a PLATE_PROCESS_RESULT=Success
     234        query.join(Annotations.leftJoin(null, Annotationtype.PLATE_PROCESS_RESULT.load(dc), "ppr"));
     235        query.restrict(Restrictions.eq(Hql.alias("ppr"), Expressions.string(ReactionPlate.PROCESS_SUCCESSFUL)));
     236        // but no child SequencingRun items
     237        query.join(Hql.leftJoin("derivedBioAssays", "ssr"));
     238        query.restrict(Restrictions.eq(Hql.alias("ssr"), null));
     239       
    237240        long count = query.count(dc);
    238241        json.put("count", count);
    … …  
    395398          pools = new HashSet<Extract>();
    396399        }
    397         else
    398         {
    399           Number sequencerId = (Number)jsonReq.get("sequencer");
    400           Hardware sequencer = sequencerId == null ? null : Hardware.getById(dc, sequencerId.intValue());
    401          
    402           Number sequencingProtocolId = (Number)jsonReq.get("sequencingProtocol");
    403           Protocol sequencingProtocol = sequencingProtocolId == null ? null : Protocol.getById(dc, sequencingProtocolId.intValue());
    404 
    405           String sequencingComments = Values.getStringOrNull((String)jsonReq.get("sequencingComments"));
    406           Date sequencingStartDate = Reggie.CONVERTER_STRING_TO_DATE.convert((String)jsonReq.get("sequencingStartDate"));
    407           String sequencingOperator = Values.getStringOrNull((String)jsonReq.get("sequencingOperator"));
    408          
    409           sequenceRun = DerivedBioAssay.getNew(dc, true, null);
    410           sequenceRun.setItemSubtype(Subtype.SEQUENCING_RUN.get(dc));
    411           sequenceRun.setName(SequencingRun.generateNamesForBatch(dc, 1, 1).get(0));
    412           sequenceRun.setDescription(sequencingComments);
    413           sequenceRun.setHardware(sequencer);
    414           dc.saveItem(sequenceRun);
    415          
    416           Annotationtype.SEQUENCING_START.setAnnotationValue(dc, sequenceRun, sequencingStartDate);
    417           Annotationtype.SEQUENCING_OPERATOR.setAnnotationValue(dc, sequenceRun, sequencingOperator);
    418          
    419           jsonMessages.add("Created '" + sequenceRun.getName()+"'.");
    420         }
    421        
    422400       
    423401        // Clustering information
    424         Number clusterProtocolId = (Number)jsonReq.get("clusterProtocol");     
    425         Protocol clusterProtocol = clusterProtocolId == null ? null : Protocol.getById(dc, clusterProtocolId.intValue());
    426 
    427402        for (int fcNo = 0; fcNo < jsonFlowCells.size(); ++fcNo)
    428403        {
    … …  
    433408          Hardware cBot = cBotId == null ? null : Hardware.getById(dc, cBotId.intValue());
    434409
     410          Number clusterProtocolId = (Number)jsonFlowCell.get("clusterProtocol");     
     411          Protocol clusterProtocol = clusterProtocolId == null ? null : Protocol.getById(dc, clusterProtocolId.intValue());
     412         
    435413          Date clusterDate = Reggie.CONVERTER_STRING_TO_DATE.convert((String)jsonFlowCell.get("clusterDate"));
    436414          String clusterOperator = Values.getStringOrNull((String)jsonFlowCell.get("clusterOperator"));
    … …  
    481459          else
    482460          {
    483             sequenceRun.addPhysicalBioAssay(flowCell);
    484             Annotationtype.SEQUENCING_CYCLES.setAnnotationValue(dc, flowCell, jsonFlowCell.get("SequencingCycles"));
    485             Annotationtype.HISEQ_POSITION.setAnnotationValue(dc, flowCell, jsonFlowCell.get("HiSeqPosition"));
    486            
    487461            Annotationtype.PLATE_PROCESS_RESULT.setAnnotationValue(dc, flowCell, ReactionPlate.PROCESS_SUCCESSFUL);
    488             jsonMessages.add("Sequencing started for flow cell '" + flowCell.getName() + "'.");
     462            jsonMessages.add("Flow cell '" + flowCell.getName() + "' registered with status: " + (ReactionPlate.PROCESS_SUCCESSFUL));
    489463          }
    490464        }
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