Changeset 1379

Timestamp:

Jun 27, 2011, 3:58:52 PM (12 years ago)

Author:

Martin Svensson

Message:

References #317. Added a section to fill in information for each individual specimen tube in a case. Also began to build the finishing create-process, which will create or update the items BASE

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/specimentube.jsp (modified) (18 diffs)
• src/net/sf/basedb/reggie/Reggie.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/dao/SpecimenTube.java (modified) (4 diffs)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/SpecimenTubeServlet.java (modified) (7 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/specimentube.jsp

@@ -30 +30 @@
 var nofDeliveredTubesIsValid = true;
 var nofTubesIsValid = false;
+var lateralityIsValid = false;
 var debug = false;
 var currentStep = 1;
 
 var caseInfo = null;
-var specimenTubeInfo = null;
+var boxInfo = null;
 
 function init()
@@ -42 +43 @@
 }
 
-function goNext(manual)
+function goNext()
 {
   setInnerHTML('gonext.message', '');
   if (currentStep == 1)
-  {
-    if(step1IsValid())
-    {
-      gotoStep2();
-    }
-  }
-  if (currentStep == 2)
-  {
-    gotoStep3();
-  }
+  {   
+    gotoStep2();
+  }
+  else if (currentStep == 2)
+  {
+    if (step2IsValid()) gotoStep3();
+  }
+}
+
+function step2IsValid()
+{
+  var frm = document.forms['reggie']; 
+  if (!nofTubesIsValid) frm.nofTubes.focus();
+  else if (lateralityIsValid) return true;
 }
 
@@ -61 +66 @@
 {
   var frm = document.forms['reggie'];
-  frm.caseName.disabled = true;
-  currentStep = 2;
+  var caseName = frm.caseName.value;
+  if (caseName == '')
+  {
+    setInputStatus('case', 'Missing', 'invalid');
+    return;
+  }
+  setInputStatus('case', '', 'valid');
+  
+  getCaseInfo();
+  
   var hasSpecimen = caseInfo.specimen && caseInfo.specimen.length > 0;
   var hasLeftSpecimen = false;
@@ -74 +87 @@
   var thisPad = null;
 
+  frm.caseName.disabled = true;
+    
   Main.show('gocancel');
   Main.show('caseSection');
-
+  
+  frm.nofTubes.focus();
+  currentStep = 2;
+      
+  // Load annotations from the actual case
+  if (hasSpecimen)
+  {
+    frm.nofTubes.value = thisNumberOfTubes;
+    frm.nofTubes.disabled = true;
+    frm.arrivalDate.focus();
+    for (var i=0; i < caseInfo.specimen.length; i++)
+    {
+      var specimen = caseInfo.specimen[i];        
+      if (specimen.pad && !thisPad)
+      {         
+        thisPad = specimen.pad;
+      }
+      if(specimen.arrivalDate && !thisArrivalDate)
+      { 
+        thisArrivalDate = specimen.arrivalDate;
+      }
+      if (specimen.nofTubes && !thisNumberOfTubes)
+      {
+        thisNumberOfTubes = specimen.nofTubes;
+      }
+      if (specimen.samplingDate && !thisCaseSamplingDate) 
+      {
+        thisCaseSamplingDate = specimen.samplingDate;         
+      }
+      if (specimen.rnaLaterDate && !thisCaseRNALaterDate) 
+      {
+        thisCaseRNALaterDate = specimen.rnaLaterDate;
+      }
+      if (specimen.laterality && !thisCaseLaterality) 
+      {
+        if (specimen.laterality == 'LEFT') hasLeftSpecimen = true;
+        if (specimen.laterality == 'RIGHT') hasRightSpecimen = true;
+        thisCaseLaterality = specimen.laterality;
+      }
+      else if(!thisCaseLaterality)
+      {
+        hasUnknownSpecimen = true;        
+      }
+    }
+    // If the number of tubes not is set - use the current number of specimen tubes.
+    if (!thisNumberOfTubes) thisNumberOfTubes = caseInfo.specimen.length;
+          
+    // Check that all specimen tubes have the same laterality
+    var numLateralities = 0;
+    if (hasLeftSpecimen) numLateralities++;
+    if (hasRightSpecimen) numLateralities++;
+    if (hasUnknownSpecimen) numLateralities++;      
+    if (numLateralities > 1)
+    {
+      setInputStatus('laterality', 'Specimen tubes with different laterality', 'warning');
+      thisCaseLaterality = null;
+      Forms.checkRadio(frm.laterality, thisCaseLaterality);       
+    }     
+    Forms.checkRadio(frm.laterality, thisCaseLaterality);
+    lateralityOnChange();
+    
+    if (thisPad != null)
+    {
+      frm.pad.value = thisPad;
+      padOnChange();
+    }
+    if (thisArrivalDate != null)
+    {
+      frm.arrivalDate.value = thisArrivalDate;
+    }
+    if (thisNumberOfTubes != null)
+    {
+      frm.nofTubes.value = thisNumberOfTubes;
+      nofTubesOnChange();
+    }
+    if (thisCaseSamplingDate != null)
+    {
+      frm.samplingDate.value = thisCaseSamplingDate.substring(0, 8);
+      frm.samplingTime.value = thisCaseSamplingDate.substring(9, 13);
+      samplingDateTimeOnChange();
+    }
+    if (thisCaseRNALaterDate != null)
+    {
+      frm.rnaLaterDate.value = thisCaseRNALaterDate.substring(0, 8);
+      frm.rnaLaterTime.value = thisCaseRNALaterDate.substring(9, 13);
+      rnaLaterDateTimeOnChange();
+    }
+  }
+
+  var hasLeftCase = false;
+  var hasRightCase = false;
+  var hasUnknownCase = false;
   if (caseInfo.id)
   {
     setInnerHTML('step2.title', 'Update Case Information');
-    if (caseInfo.pad)
+    if (caseInfo.pad && !thisPad)     
     {     
-      frm.pad.value = caseInfo.pad;
+      thisPad = caseInfo.pad;     
     }
     if (caseInfo.laterality)
     {
-      if(caseInfo.laterality == 'LEFT') hasLeftSpecimen = true;
-      if(caseInfo.laterality == 'RIGHT') hasRightSpecimen = true;
-      thisCaseLaterality = caseInfo.laterality;
-      Forms.checkRadio(frm.laterality, thisCaseLaterality);
+      var lateralityInput = '';
+      lateralityInput += '<input type="radio" name="laterality" value="LEFT" ';
+      if (caseInfo.laterality == 'LEFT') lateralityInput += 'checked';
+      lateralityInput += ' onChange="lateralityOnChange()">LEFT';
+      lateralityInput += '<br>';
+      lateralityInput += '<input type="radio" name="laterality" value="RIGHT" ';
+      if (caseInfo.laterality == 'RIGHT') lateralityInput += 'checked';
+      lateralityInput += ' onChange="lateralityOnChange()">RIGHT';
+      setInnerHTML('laterality.input', lateralityInput);
       lateralityOnChange();
-    }
-    // Load annotations from the actual case
-    if (hasSpecimen)
-    {
-      frm.nofTubes.value = thisNumberOfTubes;
-      frm.nofTubes.disabled = true;
-      for (var i=0; i < caseInfo.specimen.length; i++)
-      {
-        var specimen = caseInfo.specimen[i];        
-        if (specimen.pad && !thisPad)
-        {         
-          thisPad = specimen.pad;
-        }
-        if(specimen.arrivalDate && !thisArrivalDate)
-        { 
-          thisArrivalDate = specimen.arrivalDate;
-        }
-        if (specimen.nofTubes && !thisNumberOfTubes)
-        {
-          thisNumberOfTubes = specimen.nofTubes;
-        }
-        if (specimen.samplingDate && !thisCaseSamplingDate) 
-        {
-          thisCaseSamplingDate = specimen.samplingDate;         
-        }
-        if (specimen.rnaLaterDate && !thisCaseRNALaterDate) 
-        {
-          thisCaseRNALaterDate = specimen.rnaLaterDate;
-        }
-        if (specimen.laterality) 
-        {
-          if (specimen.laterality == 'LEFT') hasLeftSpecimen = true;
-          if (specimen.laterality == 'RIGHT') hasRightSpecimen = true;
-          if (!thisCaseLaterality) thisCaseLaterality = specimen.laterality;
-        }
-        else
-        {
-          hasUnknownSpecimen = true;        
-        }
-      }
-      // If the number of tubes not is set - use the current number of specimen tubes.
-      if (!thisNumberOfTubes) thisNumberOfTubes = caseInfo.specimen.length;
-      frm.nofTubes.value = thisNumberOfTubes;
-      // Check that all specimen tubes have the same laterality
-      var numLateralities = 0;
-      if (hasLeftSpecimen) numLateralities++;
-      if (hasRightSpecimen) numLateralities++;
-      if (hasUnknownSpecimen) numLateralities++;      
-      if (numLateralities > 1)
-      {
-        setInputStatus('laterality', 'Specimen tubes with different laterality', 'warning');
-        thisCaseLaterality = null;
-        Forms.checkRadio(frm.laterality, thisCaseLaterality);       
-      }     
-      Forms.checkRadio(frm.laterality, thisCaseLaterality);
-      lateralityOnChange();
-      
-      if (thisPad != null)
-      {
-        frm.pad.value = thisPad;
-      }
-      if (thisArrivalDate != null)
-      {
-        frm.arrivalDate.value = thisArrivalDate;
-      }
-      if (thisNumberOfTubes != null)
-      {
-        frm.nofTubes.value = thisNumberOfTubes;
-      }
-      if (thisCaseSamplingDate != null)
-      {
-        frm.samplingDate.value = thisCaseSamplingDate.substring(0, 8);
-        frm.samplingTime.value = thisCaseSamplingDate.substring(9, 13);
-        samplingDateTimeOnChange();
-      }
-      if (thisCaseRNALaterDate != null)
-      {
-        frm.rnaLaterDate.value = thisCaseRNALaterDate.substring(0, 8);
-        frm.rnaLaterTime.value = thisCaseRNALaterDate.substring(9, 13);
-        rnaLaterDateTimeOnChange();
-      }
     }
   } 
@@ -193 +223 @@
   frm.rnaLaterTime.disabled = true;
   frm.samplingTime.disabled = true;
-  frm.pathNote.disabled = true; 
+  frm.pathNote.disabled = true;
   
   for (var i=0;i<nofTubes;i++)
   {
     var specimen = null;
+    var boxValue = '';
+    var rowValue = '';
+    var columnValue = '';
     if (caseInfo.specimen && caseInfo.specimen.length>0 && i<caseInfo.specimen.length)
     {
       specimen = caseInfo.specimen[i];
+      boxValue = specimen.box;
+      rowValue = specimen.row;
+      columnValue = specimen.column;
     }
     inputTubeHtml += '<tr>';
@@ -209 +245 @@
     inputTubeHtml += '<tr>';
     inputTubeHtml += '<td class="subprompt">Box</td>';
-    inputTubeHtml += '<td class="input"><input type="text" name='+box+' value="" size="12" maxlength="10"></td>';
+    inputTubeHtml += '<td class="input"><input type="text" name='+box+' value="' + boxValue + '" size="18" maxlength="12" onBlur="boxOnChange('+i+')"></td>';
     inputTubeHtml += '<td class="status" id="'+box+'.status"></td>';
     inputTubeHtml += '<td class="help"><span id="'+box+'.message" class="message" style="display: none;"></span>Box the specimen tube is located in.</td>';   
-    inputTubeHtml += '</tr>';
+    inputTubeHtml += '</tr>';       
 
     var row = 'row'+i;
@@ -218 +254 @@
     inputTubeHtml += '<tr>';
     inputTubeHtml += '<td class="subprompt">Row</td>';
-    inputTubeHtml += '<td class="input"><input type="text" name='+row+' value="" size="3" maxlength="3">';
-    inputTubeHtml += '&nbsp;Column<input type="text" name='+column+' value="" size="3" maxlength="3">';
+    inputTubeHtml += '<td class="input"><input type="text" name='+row+' value="' + rowValue + '" size="3" maxlength="3"';
+    inputTubeHtml += boxValue != '' ? '' : ' disabled';
+    inputTubeHtml += ' onBlur="wellOnChange('+i+')">';
+    inputTubeHtml += '&nbsp;Column<input type="text" name='+column+' value="'+ columnValue + '" size="3" maxlength="3"';
+    inputTubeHtml += boxValue != '' ? '' : ' disabled';
+    inputTubeHtml += ' onBlur="wellOnChange('+i+')">';
     inputTubeHtml += '</td>';
     inputTubeHtml += '<td class="status" id="rowColumn'+i+'.status"></td>';
-    inputTubeHtml += '<td class="help"><span id="rowColumn'+i+'.message" class="message" style="display: none;"></span>Row and column the specimen tube is located at.</td>';   
+    inputTubeHtml += '<td class="help"><span id="rowColumn'+i+'.message" class="message" style="display: none;"></span></td>';    
     inputTubeHtml += '</tr>';
     
@@ -252 +292 @@
     inputTubeHtml += '<tr>';
     inputTubeHtml += '<td class="subprompt">Operator comment</td>';
-    inputTubeHtml += '<td class="input"><input type="text" name='+deliveryComment+' value="" size="12" maxlength="10"></td>';
+    inputTubeHtml += '<td class="input"><textarea rows="3" cols="30" name='+deliveryComment+' value=""></textarea></td>';
     inputTubeHtml += '<td class="status" id="'+deliveryComment+'.status"></td>';
     inputTubeHtml += '<td class="help"><span id="'+deliveryComment+'.message" class="message" style="display: none;"></span>Operator delivery comment</td>';    
     inputTubeHtml += '</tr>';
   }
-
   setInnerHTML('tubeInputs', inputTubeHtml);
-  Main.show('tubeSection');
+  boxInfo = Array();
+  currentStep = 3;
+  Main.show('tubeSection'); 
   Main.hide('gonext');
-  Main.show('gocreate');
-  
+  Main.show('gocreate');  
+  frm.box0.focus();
 }
 
@@ -300 +341 @@
 }
 
+function boxOnChange(tubeIndex)
+{
+  var frm = document.forms['reggie'];
+  var boxName = 'box'+tubeIndex;
+  var rowName = 'row'+tubeIndex;
+  var columnName = 'column'+tubeIndex;  
+  var boxValue = frm.elements[boxName].value; 
+  
+  if (frm.elements[boxName].value == '')
+  {
+    frm.elements[rowName].disabled = true;
+    frm.elements[rowName].value = '';
+    frm.elements[columnName].disabled = true;
+    frm.elements[columnName].value = '';
+    frm.elements['his'+tubeIndex].focus();
+    setInputStatus(boxName, '', '');  
+    setInputStatus('rowColumn'+tubeIndex, '', '');        
+    return false;
+  }
+    
+  var request = Ajax.getXmlHttpRequest();
+  var url = 'SpecimenTubeRegistration.servlet?ID=<%=ID%>&cmd=GetBoxInfo';
+  url += '&boxName=' + boxValue;  
+  request.open("GET", url, false);
+  request.send(null);
+
+  if (debug) Main.debug(request.responseText);
+
+  var response = JSON.parse(request.responseText);
+  if (response.status != 'ok')
+  {
+    setFatalError(response.message);
+    return false;
+  } 
+  if (!response.boxInfo)
+  {
+    setInputStatus(boxName, response.message, 'invalid');
+    frm.elements[rowName].value = '';
+    frm.elements[columnName].value = '';
+    frm.elements[rowName].disabled = true;
+    frm.elements[columnName].disabled = true;
+    return false;
+  }   
+  else
+  { 
+    boxInfo[tubeIndex] = response.boxInfo;  
+    frm.elements[rowName].disabled = false;
+    frm.elements[columnName].disabled = false;
+    frm.elements[rowName].value = '';
+    setInputStatus('rowColumn'+tubeIndex,'Row[A-'+response.rows+'], Columns[1-'+response.columns+']','');   
+    frm.elements[columnName].disabled = '';
+    setInputStatus(boxName, '', 'valid');   
+    frm.elements[rowName].focus();    
+  }   
+}
+
+function wellOnChange(tubeIndex)
+{
+  var frm = document.forms['reggie'];
+  var boxName = 'box'+tubeIndex;
+  var rowName = 'row'+tubeIndex;
+  var columnName = 'column'+tubeIndex;
+  var rowValue = frm.elements[rowName].value;
+  var columnValue = frm.elements[columnName].value
+  var boxValue = frm.elements[boxName].value; 
+  var nofTubes = frm.nofTubes.value;
+  
+  if (boxValue != '' && 
+      (rowValue == '' || columnValue == ''))
+  {
+    setInputStatus('rowColumn'+tubeIndex, 'Row or column cannot be empty when the box is specified.', 'invalid');
+    return false;
+  }
+  
+  var request = Ajax.getXmlHttpRequest();
+  var url = 'SpecimenTubeRegistration.servlet?ID=<%=ID%>&cmd=ValidateWell';
+  url += '&boxId=' + boxInfo[tubeIndex];  
+  url += '&row=' + rowValue;
+  url += '&column=' + columnValue;
+  request.open("GET", url, false);
+  request.send(null);
+
+  if (debug) Main.debug(request.responseText);
+
+  var response = JSON.parse(request.responseText);
+  if (response.status != 'ok')
+  {
+    setFatalError(response.message);
+    return false;
+  }
+  if (response.message)
+  {
+    setInputStatus('rowColumn'+tubeIndex, response.message, 'invalid')
+    return false;
+  }
+  for (var i=0;i<nofTubes;i++)
+  {
+    if (i != tubeIndex && frm.elements['box'+i].value == boxValue)
+    {
+      if (rowValue == frm.elements['row'+i].value && 
+          columnValue == frm.elements['column'+i].value)
+      {
+        setInputStatus('rowColumn'+tubeIndex, 'The row and column are already used once in this wizard','invalid');       
+        return false;
+      }
+    }
+  }
+  setInputStatus('rowColumn'+tubeIndex, '', 'valid');
+}
+
 function rnaLaterDateTimeOnChange()
 {
@@ -372 +523 @@
 }
 
-function nofTubesOnBlur()
+function nofTubesOnChange()
 {
   var frm = document.forms['reggie'];
@@ -382 +533 @@
     return;
   }
-  setInputStatus('nofTubes','', 'valid'); 
-}
-
-function caseNameOnBlur()
-{
-  var frm = document.forms['reggie'];
-  var caseName = frm.caseName.value;
-  if (caseName == '')
-  {
-    setInputStatus('case', 'Missing', 'invalid');
-    return;
-  }
-  setInputStatus('case', '', 'valid');
-  caseIsValid = true;
-
-  getCaseInfo();
+  setInputStatus('nofTubes','', 'valid');
+  nofTubesIsValid = true; 
 }
 
@@ -428 +565 @@
     return;
   }
+  setInputStatus('laterality', '', 'valid');
+  lateralityIsValid = true;
   var laterality = selectedLaterality.value;  
+  
   // No specimen tubes?
   if (!caseInfo.specimen || caseInfo.specimen.length == 0) return;
@@ -447 +587 @@
       return;
     }
+  } 
+}
+
+function step3IsValid()
+{
+  return false;
+}
+
+function goCreate()
+{
+  if (!step3IsValid()) return;
+
+  Main.hide('gocancel');
+  Main.hide('gocreate');
+  var frm = document.forms['reggie'];
+
+  caseInfo.laterality = Forms.getCheckedRadio(frm.laterality).value;
+  caseInfo.pad = frm.pad.value;
+  caseInfo.samplingDate = Main.trimString(frm.samplingDate.value + ' ' + frm.samplingTime.value);
+  caseInfo.rnaLaterDate = Main.trimString(frm.rnaLaterDate.value + ' ' + frm.rnaLaterTime.value);
+  caseInfo.pathNote = frm.pathNote.value;
+
+  var nofTubes = frm.nofTubes.value;
+  for (var i=0; i<nofTubes; i++)
+  {
+    var specimenTube = new Object();    
+    if (caseInfo.specimen[i]) specimenTube = caseInfo.specimen[i];
+    specimenTube.name = caseInfo.name+'.'+i; 
+
+    caseInfo.specimen[i] = specimenTube;
+  }
+
+  var submitInfo = new Object();
+  submitInfo.caseInfo = caseInfo;
+
+  if (debug) Main.debug(JSON.stringify(submitInfo));
+  
+  var request = Ajax.getXmlHttpRequest();
+  var url = 'SpecimenTubeRegistration.servlet?ID=<%=ID%>&cmd=';
+  url += 'CreateSpecimenTubes';
+  request.open("POST", url, false);
+  request.setRequestHeader("Content-Type", "application/json");
+  request.send(JSON.stringify(submitInfo));
+
+  if (debug) Main.debug(request.responseText);
+
+  var response = JSON.parse(request.responseText);
+  if (response.status != 'ok')
+  {
+    setFatalError(response.message);
+    return false;
   } 
 }
@@ -468 +659 @@
     return false;
   }
-
   caseInfo = response.caseInfo;
-  if (caseInfo)
-  {
-    gotoStep2();
-  }
-}
-
+}
 </script>
 
@@ -511 +696 @@
         <td class="prompt">Case name</td>
         <td class="input"><input type="text" name="caseName" 
-          size="18" maxlength="12" onblur="caseNameOnBlur()"></td>
+          size="18" maxlength="12" onkeypress="doOnTabOrEnter(event, goNext)"></td>
         <td class="status" id="case.status"></td>
         <td class="help"><span id="case.message" class="message" style="display: none;"></span>The case (barcode) associated with this specimen tube.</td>
@@ -533 +718 @@
       <td class="prompt">Number of tubes</td>
       <td class="input"><input type="text" name="nofTubes"
-        value="" size="12" maxlength="10" onblur="nofTubesOnBlur()"></td>
+        value="" size="12" maxlength="10" onblur='nofTubesOnChange()'></td>
       <td class="status" id="nofTubes.status"></td>
       <td class="help"><span id="nofTubes.message" class="message" style="display:none"></span>Number of tubes in this case.</td>
@@ -575 +760 @@
         <input type="radio" name="laterality" value="LEFT" onclick="lateralityOnChange()">LEFT<br>
         <input type="radio" name="laterality" value="RIGHT" onclick="lateralityOnChange()">RIGHT<br>
-        <input type="radio" name="laterality" value="" onclick="lateralityOnChange()"><i>unknown</i>
+        <input type="radio" name="laterality" value="" checked onclick="lateralityOnChange()"><i>unknown</i>
       </td>
       <td class="status" id="laterality.status"></td>
@@ -582 +767 @@
     <tr>
       <td class="prompt" id="pathNote.prompt">Path note</td>
-      <td class="input" id="pathNote.input"><textarea rows="3" cols="30" name="pathNote" value=""></textarea></td>
+      <td class="input" id="pathNote.input"><textarea rows="3" cols="30" 
+        name="pathNote" value="" onkeypress="doOnTabOrEnter(event, goNext)"></textarea></td>
       <td class="status" id="pathNote.status"></td>
       <td class="help"><span id="pathNote.message" class="message" style="display: none;"></span></td>

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/Reggie.java

@@ -91 +91 @@
   */
   public static final String ANNOTATION_PAD_CASE = "PADcase";
+  
+  /**
+    The name of the "PathNote" annotation type, 
+    used for samples (Case). It is a string annotation type.
+  */
+  public static final String ANNOTATION_PATH_NOTE = "PathNote";
 
   /**
@@ -135 +141 @@
   */
   public static final String GROUP_PATIENT_CURATOR = "PatientCurator";
+
+  /**
+    The name of the "OperatorComment" annotation type, used
+    for samples (Specimen tube). It is a String annotation type.
+  */
+  public static final String ANNOTATION_OPERATOR_COMMENT = "OperatorComment";
   
   /**

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/SpecimenTube.java

@@ -4 +4 @@
 import java.util.List;
 
+import org.json.simple.JSONObject;
+
+import net.sf.basedb.core.BioPlate;
+import net.sf.basedb.core.BioWell;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Include;
@@ -63 +67 @@
     List<SpecimenTube> tubes = new ArrayList<SpecimenTube>();
     for (Sample s : specimenQuery.list(dc))
-    {
+    {   
       tubes.add(new SpecimenTube(s));
     }
@@ -93 +97 @@
   }
   
+  private final String box;
+  private final Integer row;
+  private final Integer column;
+  
   private SpecimenTube(Sample sample)
   {
     super(sample);
-  }
+    if (sample.getBioWell() != null)
+    {
+      BioWell well = sample.getBioWell();
+      box = well.getPlate().getName();
+      row = well.getRow();
+      column = well.getColumn();
+    }
+    else
+    {
+      box = null;
+      row = null;
+      column = null;
+    }
+  } 
+  
   
   /**
@@ -106 +128 @@
   }
 
+  /**
+    Get the box where this specimen tube is located  
+   */
+  public String getBox()
+  {
+    return this.box;
+  }
+
+  /**
+    Get the row index in the box, where this specimen tube can be found. 
+  */
+  public Integer getRow() 
+  {
+    return row;
+  }
+
+  /**
+    Get the column index in the box, where this specimen tube can be found.
+  */
+  public Integer getColumn() 
+  {
+    return column;
+  }
   
+  @SuppressWarnings("unchecked")
+  @Override
+  protected void initJSON(JSONObject json)
+  {
+    json.put("box", box);
+    json.put("row", row);
+    json.put("column", column);
+  }
 }

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

@@ -129 +129 @@
         jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_NOF_DELIVERED_TUBES, Item.SAMPLE, Type.INT, 1, 
             null, effectiveOptions, createIfMissing));
+        jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_OPERATOR_COMMENT, Item.SAMPLE, Type.STRING, 1, 
+            null, effectiveOptions, createIfMissing));
+        jsonChecks.add(checkAnnotationType(dc, Reggie.ANNOTATION_PATH_NOTE, Item.SAMPLE, Type.STRING, 1, 
+            null, effectiveOptions, createIfMissing));
         
         json.put("checks", jsonChecks);

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/SpecimenTubeServlet.java

@@ -11 +11 @@
 import javax.servlet.http.HttpServletResponse;
 
-import net.sf.basedb.core.AnnotationSet;
 import net.sf.basedb.core.AnnotationType;
 import net.sf.basedb.core.Application;
+import net.sf.basedb.core.BioPlate;
+import net.sf.basedb.core.BioWell;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.InvalidDataException;
 import net.sf.basedb.core.Item;
+import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.Sample;
 import net.sf.basedb.core.SessionControl;
+import net.sf.basedb.core.Type;
+import net.sf.basedb.core.query.Expression;
+import net.sf.basedb.core.query.Expressions;
+import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.reggie.Reggie;
 import net.sf.basedb.reggie.converter.DateToStringConverter;
@@ -25 +33 @@
 import net.sf.basedb.util.Values;
 import net.sf.basedb.util.error.ThrowableUtil;
+import net.sf.basedb.util.formatter.WellCoordinateFormatter;
 
 import org.json.simple.JSONArray;
@@ -95 +104 @@
           AnnotationType arrivalDateType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_ARRIVAL_DATE, true);
           AnnotationType nofDeliveredTubesType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_NOF_DELIVERED_TUBES, true);
+          AnnotationType operatorCommentType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_OPERATOR_COMMENT, true);
           
           DateToStringConverter dateTimeConverter = new DateToStringConverter(new SimpleDateFormat("yyyyMMdd HHmm"));
@@ -106 +116 @@
             tube.loadAnnotations("arrivalDate", arrivalDateType, dateConverter);
             tube.loadAnnotations("nofTubes", nofDeliveredTubesType, null);
+            tube.loadAnnotations("operatorComment", operatorCommentType, null);
             
             jsonTubes.add(tube.asJSONObject());
@@ -113 +124 @@
         
         json.put("caseInfo", jsonCase);
+      }
+      else if ("GetBoxInfo".equals(cmd))
+      {
+        dc = sc.newDbControl();
+        
+        String boxName = req.getParameter("boxName");
+        ItemQuery<BioPlate> boxQuery = BioPlate.getQuery();
+        boxQuery.restrict(Restrictions.eq(Hql.property("name"), Expressions.string(boxName)));
+        List<BioPlate> boxes = boxQuery.list(dc);
+        
+        if (boxes.size() == 0)
+        {
+          json.put("message", "Box does not exist.");         
+        }
+        else if (boxes.size() > 1)
+        {
+          json.put("message", "More then one box were found.");
+        }
+        else
+        {         
+          WellCoordinateFormatter wcfRow = new WellCoordinateFormatter(true);
+          
+          json.put("boxInfo", boxes.get(0).getId());
+          json.put("rows", wcfRow.format(boxes.get(0).getRows()-1));
+          json.put("columns", boxes.get(0).getColumns());
+        }
+        
+      }
+      else if ("ValidateWell".equals(cmd))
+      {
+        dc = sc.newDbControl();
+        
+        int boxId = Integer.parseInt(req.getParameter("boxId"));
+        BioPlate plate = BioPlate.getById(dc, boxId);
+        
+        WellCoordinateFormatter wcfRow = new WellCoordinateFormatter(true);       
+        String rowString = req.getParameter("row");
+        int rowNumber = wcfRow.parseString(rowString);
+                
+        Integer columnIndex = Integer.parseInt(req.getParameter("column")) - 1;
+        WellCoordinateFormatter wcfColumn = new WellCoordinateFormatter(false);
+        
+        String msg = null;
+        if (rowNumber < 1 || rowNumber > plate.getRows()) 
+        {
+          msg = "The row must be between "+ wcfRow.format(0) +" and " + wcfRow.format(plate.getRows()-1);
+        }
+        else if (columnIndex < 0 || columnIndex > plate.getColumns())
+        {
+          msg = "The column must be between " +  1 + " and " + plate.getColumns();
+        }
+        else if (!plate.getBioWell(rowNumber-1, columnIndex).isEmpty())
+        {
+          msg = "Specified row:column("+rowString+":"+wcfColumn.format(columnIndex)+") is already taken.";
+        }
+        json.put("message", msg);       
       }
     }
@@ -144 +211 @@
     
     JSONArray jsonMessages = new JSONArray();
-    
     final SessionControl sc = Application.getSessionControl(ID, req.getRemoteAddr());
     DbControl dc = null;
@@ -150 +216 @@
     try
     {
-      if ("CreateSpecimenTube".equals(cmd))
-      {
-        
+      if ("CreateSpecimenTubes".equals(cmd))
+      {
+        dc = sc.newDbControl();
+        
+        JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader());       
+        JSONObject jsonCase = (JSONObject)jsonReq.get("caseInfo");
+        Number caseId = (Number)jsonCase.get("id");
+        Sample theCase = null;
+        
+        if (caseId != null)
+        {
+          theCase = Sample.getById(dc, caseId.intValue());
+        }
+        else
+        {
+          theCase = Sample.getNew(dc);
+          theCase.setName((String)jsonCase.get("name"));
+          
+          dc.saveItem(theCase);
+        }
+          
+        String laterality = Values.getStringOrNull((String)jsonCase.get("laterality"));
+        String padCase = Values.getStringOrNull((String)jsonCase.get("pad"));
+        String pathNote = Values.getStringOrNull((String)jsonCase.get("pathNote"));
+        StringToDateConverter dateTimeConverter = new StringToDateConverter(new SimpleDateFormat("yyyyMMdd HHmm"));
+        StringToDateConverter dateConverter = new StringToDateConverter(new SimpleDateFormat("yyyyMMdd"));        
+        Date samplingDate = dateTimeConverter.convert((String)jsonCase.get("samplingDate"));
+        Date rnaLaterDate = dateTimeConverter.convert((String)jsonCase.get("rnaLaterDate"));
+        Date arrivalDate = dateConverter.convert((String)jsonCase.get("arrivalDate"));
+        
+        AnnotationType padCaseType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_PAD_CASE, true);
+        AnnotationType lateralityType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_LATERALITY, true);
+//        AnnotationType pathNoteType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_PATH_NOTE, true);
+        AnnotationType samplingDateType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_SAMPLING_DATETIME, true);
+        AnnotationType rnaLaterDateType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_RNALATER_DATETIME, true);
+        AnnotationType arrivalDateType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_ARRIVAL_DATE, true);
+        
+        Reggie.setAnnotationValue(theCase, lateralityType, laterality);
+        Reggie.setAnnotationValue(theCase, arrivalDateType, arrivalDate);
+//        Reggie.setAnnotationValue(theCase, pathNoteType, pathNote);
+        
+        if (padCase != null) Reggie.appendAnnotationValueIfUnique(theCase, padCaseType, padCase);
         
         dc.commit();