Changeset 2014

Timestamp:

Aug 2, 2013, 1:54:32 PM (9 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #475: Improve box placement suggestion in specimen tube registration

The wizard now uses a single call to get information about as many wells as are needed immediately when entering step 3. If the user makes changes, no additional suggestions are made, only validation to check if the changed position exists and is emtpy.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/sampleproc/specimentube.jsp (modified) (20 diffs)
• src/net/sf/basedb/reggie/dao/StoragePlate.java (modified) (3 diffs)
• src/net/sf/basedb/reggie/servlet/SpecimenTubeServlet.java (modified) (8 diffs)

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

@@ -26 +26 @@
   dc = sc.newDbControl();
   final User user = User.getById(dc, sc.getLoggedInUserId());
-  final ItemContext cc = Base.getAndSetCurrentContext(sc, Item.SAMPLE, null, null);
-  final List<BioPlate> recentBoxes = (List<BioPlate>)cc.getRecent(dc, Item.BIOPLATE, "reggie_specimentube");
-  BioPlate recentBox = null;
-  String recentBoxName = "";  
-  int recentBoxId = 0;
-  if (recentBoxes.size() > 0)
-  {
-    recentBox = recentBoxes.get(0);
-    int lastRow = recentBox.getRows()-1;
-    int lastColumn = recentBox.getColumns()-1;
-    // Move on to next box in order if the last position isn't empty.
-    if (!recentBox.getBioWell(lastRow, lastColumn).isEmpty())
-    {
-      Integer currentBoxNumber = Values.getInteger(recentBox.getName().substring(2), null);
-      if (currentBoxNumber != null)
-      {
-        currentBoxNumber++;
-        String nameString = ""+currentBoxNumber;        
-        while(nameString.length() < 3)
-        {
-          nameString = "0"+nameString;
-        }
-        recentBoxName = "Sp"+nameString;
-      }     
-    }
-    else
-    {
-      recentBoxName = recentBox.getName();
-      recentBoxId = recentBox.getId();
-    }
-  }
 %>
 <base:page type="default" >
@@ -205 +174 @@
   var frm = document.forms['reggie'];
   var inputTubeHtml = '';
-  var nofTubes = frm.nofTubes.value;
-  boxInfo = Array(nofTubes);
+  var nofTubes = parseInt(frm.nofTubes.value);
+  boxInfo = new Array(nofTubes);
+  
+  var freeWells = findStoragePositions(nofTubes);
   
   frm.arrivalDate.disabled = true;
@@ -223 +194 @@
   frm.biopsyType.disabled = true;
   
+  boxesAreValid = new Array(nofTubes);
+  wellsAreValid = new Array(nofTubes);
+  
   for (var i=0;i<nofTubes;i++)
   {
     var specimen = null;
-    var boxValue = '<%=recentBoxName %>';
-    var rowValue = '';
-    var columnValue = '';
+    
+    var freeWell = freeWells.length > i ? freeWells[i] : null;
+    var boxValue = freeWell == null ? '' : freeWell.bioPlate.name;
+    var rowValue = freeWell == null ? '' : WELL_ALPHA[freeWell.row];
+    var columnValue = freeWell == null ? '' : freeWell.column+1;
+    boxInfo[i] = freeWell == null ? '' : freeWell.bioPlate.id;
+    boxesAreValid[i] = freeWell != null;
+    wellsAreValid[i] = freeWell != null;
     var spWeightValue = '';
     var hisWeightValue = '';
     var allPrepWeightValue = '';
-
-    boxInfo[i] = <%=recentBoxId == 0 ? "null" : recentBoxId %>;
-    var boxDisabled = '';
     
     inputTubeHtml += '<tr>';
@@ -247 +223 @@
     inputTubeHtml += '<td class="subprompt">Box</td>';
     inputTubeHtml += '<td class="input">';
-    inputTubeHtml += '<input type="text" onkeypress="focusOnEnter(event, \''+row+'\')" name='+box+' value="' + boxValue + '" '+ boxDisabled +' size="12" maxlength="12" onKeyUp="boxOnKeyUp('+i+')" onBlur="boxOnChange('+i+')"></td>';
-    inputTubeHtml += '<td class="status" id="'+box+'.status"></td>';
+    inputTubeHtml += '<input type="text" onkeypress="focusOnEnter(event, \''+row+'\')" name='+box+' value="' + boxValue + '" size="12" maxlength="12" onKeyUp="boxOnKeyUp('+i+')" onBlur="boxOnChange('+i+')"></td>';
+    inputTubeHtml += '<td class="status ' + (boxesAreValid[i] ? 'valid' : '') + '" id="'+box+'.status"></td>';
     inputTubeHtml += '<td class="help"><span id="'+box+'.message" class="message" style="display: none;"></span>Box-number where the specimen tube is located in.</td>';    
     inputTubeHtml += '</tr>';       
     
-    var wellDisabled = rowValue != '' || boxValue == '' ? 'disabled' : '';
     inputTubeHtml += '<tr>';
     inputTubeHtml += '<td class="subprompt">Row</td>';
-    inputTubeHtml += '<td class="input"><input style="text-transform:uppercase;" type="text"  onkeypress="focusOnEnter(event, \''+column+'\')" name='+row+' value="' + rowValue + '" size="3" maxlength="2" ' + wellDisabled;
+    inputTubeHtml += '<td class="input"><input style="text-transform:uppercase;" type="text"  onkeypress="focusOnEnter(event, \''+column+'\')" name='+row+' value="' + rowValue + '" size="3" maxlength="2" ';
     inputTubeHtml += ' onBlur="wellOnChange('+i+')">';
-    inputTubeHtml += '&nbsp;Column<input type="text" onkeypress="focusOnEnter(event, \''+operatorComment+'\')" name='+column+' value="'+ columnValue + '" size="3" maxlength="3" ' + wellDisabled;
+    inputTubeHtml += '&nbsp;Column<input type="text" onkeypress="focusOnEnter(event, \''+operatorComment+'\');  return true || Numbers.integerOnly(event);" name='+column+' value="'+ columnValue + '" size="3" maxlength="3" ';
     inputTubeHtml += ' onBlur="wellOnChange('+i+')">';
-    inputTubeHtml += '&nbsp;<a href="javascript:suggestWellOnClick('+i+')" disabled>Suggest</a>'
     inputTubeHtml += '</td>';
-    inputTubeHtml += '<td class="status" id="rowColumn'+i+'.status"></td>';
+    inputTubeHtml += '<td class="status ' + (wellsAreValid[i] ? 'valid' : '') + '" id="rowColumn'+i+'.status"></td>';
     inputTubeHtml += '<td class="help"><span id="rowColumn'+i+'.message" class="message" style="display: none;"></span></td>';    
     inputTubeHtml += '</tr>';
@@ -274 +248 @@
   }
   setInnerHTML('tubeInputs', inputTubeHtml);  
-  boxesAreValid = Array(nofTubes);
-  wellsAreValid = Array(nofTubes);
   currentStep = 3;
   Main.show('tubeSection'); 
@@ -285 +257 @@
   frm.box0.focus();
   frm.box0.setSelectionRange(textLength,textLength);
-}
+  
+}
+
+function findStoragePositions(nofTubes)
+{
+  var frm = document.forms['reggie']; 
+  
+  var request = Ajax.getXmlHttpRequest();
+  try
+  {
+    showLoadingAnimation('Loading Lysate extracts...');
+    var url = '../SpecimenTubeRegistration.servlet?ID=<%=ID%>&cmd=FindStoragePositions';  
+    url += '&nofTubes='+nofTubes;
+    request.open("GET", url, false);  
+    request.send(null);
+  }
+  finally
+  {
+    hideLoadingAnimation();
+  }
+  
+  if (debug) Main.debug(request.responseText);
+  var response = JSON.parse(request.responseText);  
+  if (response.status != 'ok')
+  {
+    setFatalError(response.message);
+    return false;
+  }
+  return response.wells;
+}
+
 
 function samplingDateTimeOnChange()
@@ -345 +347 @@
   var frm = document.forms['reggie'];
   var boxName = 'box'+tubeIndex;
-  var rowName = 'row'+tubeIndex;
-  var columnName = 'column'+tubeIndex;  
   var boxValue = frm.elements[boxName].value; 
-  var nofTubes = frm.nofTubes.value;
   
   boxValue = boxValue.substring(2); 
@@ -360 +359 @@
   } 
   frm.elements[boxName].value = boxValue;
-  
-  wellsAreValid[tubeIndex] = false;
-  
-  if (frm.elements[boxName].value == 'Sp' || frm.elements[boxName].value == '')
-  {
-    boxesAreValid[tubeIndex] = true;
-    wellsAreValid[tubeIndex] = true;
-    frm.elements[rowName].disabled = true;
-    frm.elements[rowName].value = '';
-    frm.elements[columnName].disabled = true;
-    frm.elements[columnName].value = '';    
-    setInputStatus(boxName, '', '');  
-    setInputStatus('rowColumn'+tubeIndex, '', '');        
-    return false;
-  }
     
   var request = Ajax.getXmlHttpRequest();
   var url = '../SpecimenTubeRegistration.servlet?ID=<%=ID%>&cmd=GetBoxInfo';
-  url += '&boxName=' + boxValue;  
-  url += '&nofTubes=' + nofTubes;
+  url += '&boxName=' + boxValue;
   request.open("GET", url, false);
   request.send(null);
@@ -395 +378 @@
   {
     boxesAreValid[tubeIndex] = false;
-    setInputStatus(boxName, response.message, 'invalid');   
-    frm.elements[rowName].value = '';
-    frm.elements[columnName].value = '';
-    frm.elements[rowName].disabled = true;
-    frm.elements[columnName].disabled = true;
+    setInputStatus(boxName, response.message, 'invalid');
     return false;
   }   
@@ -407 +386 @@
     boxesAreValid[tubeIndex] = true;
     boxInfo[tubeIndex] = response.boxInfo;  
-    frm.elements[rowName].disabled = false;
-    frm.elements[columnName].disabled = false;
-    
-    var nextWellRow = '';
-    var nextWellColumn = '';
     
     if (tubeIndex==0)
@@ -421 +395 @@
     {     
       setInputStatus(boxName, 'More then one box is used','warning');
-      frm.elements[rowName].focus();
       return;
     }
-    
-    if (response.freeRow != null && response.freeColumn != null)
-    {
-      nextWellRow = response.freeRow;
-      nextWellColumn = parseInt(response.freeColumn, 10)+1;   
-      
-      nextWellColumn = nextWellColumn + tubeIndex;
-      
-      if (frm.elements[rowName].value == '' && 
-          frm.elements[columnName].value == '')
-      {
-        frm.elements[rowName].value = nextWellRow;    
-        frm.elements[columnName].value = nextWellColumn;
-      }
-    }         
     setInputStatus('rowColumn'+tubeIndex,'Row[A-'+response.rows+'], Columns[1-'+response.columns+']','');
     if (response.message && "Warning:" == response.message.substring(0,8))
@@ -447 +405 @@
     {
       setInputStatus(boxName, '', 'valid');
-    }       
-    frm.elements[rowName].focus();    
+    }
   }   
 }
@@ -463 +420 @@
   var nofTubes = frm.nofTubes.value;
   
+  wellsAreValid[tubeIndex] = false;
+  
   if (boxValue != '' && 
       (rowValue == '' || columnValue == ''))
   {
-    wellsAreValid[tubeIndex] = false;
     setInputStatus('rowColumn'+tubeIndex, 'Row or column cannot be empty when the box is specified.', 'invalid');
     return false;
@@ -490 +448 @@
   if (response.status != 'ok')
   {
-    wellsAreValid[tubeIndex] = false;
-    setFatalError(response.message);
+    setInputStatus('rowColumn'+tubeIndex, response.message, 'invalid');
     return false;
   }
@@ -502 +459 @@
     else
     {
-      wellsAreValid[tubeIndex] = false;
       setInputStatus('rowColumn'+tubeIndex, response.message, 'invalid')
       return false;
@@ -514 +470 @@
           columnValue == frm.elements['column'+i].value)
       {
-        wellsAreValid[tubeIndex] = false;
         setInputStatus('rowColumn'+tubeIndex, 'The row and column are already used once in this wizard','invalid');       
         return false;
@@ -522 +477 @@
   wellsAreValid[tubeIndex] = true;
   setInputStatus('rowColumn'+tubeIndex, '', 'valid');
-}
-
-function suggestWellOnClick(tubeIndex)
-{
-  var frm = document.forms['reggie'];
-  var boxName = 'box'+tubeIndex;
-  var boxValue = frm.elements[boxName].value;
-  var rowName = 'row'+tubeIndex;
-  var columnName = 'column'+tubeIndex;
-  var nextWellRow = '';
-  var nextWellColumn = '';
-  var nofTubes = frm.nofTubes.value;
-  
-  if (boxValue && boxValue != 'Sp')
-  {
-    var request = Ajax.getXmlHttpRequest();
-    var url = '../SpecimenTubeRegistration.servlet?ID=<%=ID%>&cmd=GetBoxInfo';
-    url += '&boxName=' + boxValue;  
-    url += '&nofTubes=' + nofTubes;
-    request.open("GET", url, false);
-    request.send(null);
-
-    if (debug) Main.debug(request.responseText);
-
-    var response = JSON.parse(request.responseText);
-    if (response.status != 'ok')
-    {
-      boxesAreValid[tubeIndex] = false;   
-      setFatalError(response.message);
-      return false;
-    }
-    if (response.boxInfo)
-    {
-      boxInfo[tubeIndex] = response.boxInfo;
-      if (response.freeRow && response.freeColumn)
-      {
-        nextWellRow = response.freeRow;
-        nextWellColumn = parseInt(response.freeColumn, 10)+1;
-        if( (nextWellColumn + tubeIndex) > response.columns)
-        {
-          nextWellColumn = 0;
-          nextWellRow = '';
-        }
-        else
-        {
-          nextWellColumn = nextWellColumn + tubeIndex;
-        }
-        frm.elements[rowName].value = nextWellRow;    
-        frm.elements[columnName].value = nextWellColumn;
-      }     
-    }
-    wellOnChange(tubeIndex);
-    frm.elements['operatorComment'+tubeIndex].focus();
-  }
 }
 
@@ -766 +667 @@
   var i=0;
   var bioWellsAreValid = true;
-  
   while (i<boxesAreValid.length && bioWellsAreValid)
   {
@@ -772 +672 @@
     {
       bioWellsAreValid = false;
-    }     
+    }
     i++;
   }
@@ -939 +839 @@
       <td class="prompt">Number of tubes</td>
       <td class="input"><input type="text" name="nofTubes"
-        onkeypress="focusOnEnter(event, 'arrivalDate')" value="1" size="12" maxlength="10" onblur='nofTubesOnChange()'></td>
+        onkeypress="focusOnEnter(event, 'arrivalDate'); return Numbers.integerOnly(event);" value="1" 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>

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

@@ -11 +11 @@
 import net.sf.basedb.core.BioWell;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.Item;
 import net.sf.basedb.core.ItemNotFoundException;
 import net.sf.basedb.core.ItemQuery;
@@ -150 +151 @@
     PlateGeometry geometry = plate.getPlateGeometry();
     ItemSubtype bioMaterialSubtype = plateType.getItemSubtype();
+    Item bioMaterialType = plateType.getBioMaterialType();
     
     json.put("freeWells", plate.getFreeWells());
@@ -157 +159 @@
     JSONObject jsonBioPlateType = new JSONObject();
     jsonBioPlateType.put("id", plateType.getId());
-    jsonBioPlateType.put("bioMaterialType", plateType.getBioMaterialType().name());
+    jsonBioPlateType.put("name", plateType.getName());
+    if (bioMaterialType != null)
+    {
+      jsonBioPlateType.put("bioMaterialType", bioMaterialType.name());
+    }
     json.put("bioPlateType", jsonBioPlateType);
     

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

@@ -24 +24 @@
 import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.core.query.Orders;
 import net.sf.basedb.core.query.Restrictions;
+import net.sf.basedb.reggie.JsonUtil;
 import net.sf.basedb.reggie.Site;
 import net.sf.basedb.reggie.converter.StringToDateConverter;
@@ -118 +120 @@
         json.put("caseInfo", jsonCase);
       }
+      else if ("FindStoragePositions".equals(cmd))
+      {
+        // Find a given number of storage positions. The process
+        // is complicated by the fact that "old" boxes still may have empty
+        // locations so we need to find the first 'Sp*' box that has
+        // I9 empty.
+        Integer nofTubes = Values.getInt(req.getParameter("nofTubes"), 1);
+        dc = sc.newDbControl();
+        
+        ItemQuery<BioPlate> spBoxQuery = BioPlate.getQuery();
+        spBoxQuery.join(Hql.innerJoin("bioWells", "bw"));
+        spBoxQuery.join(Hql.leftJoin("bw", "bioMaterial", "bm", null, false));
+        spBoxQuery.restrict(Restrictions.like(Hql.property("name"), Expressions.string("Sp%")));
+        spBoxQuery.restrict(Restrictions.eq(Hql.property("bw", "row"), Expressions.integer(8)));
+        spBoxQuery.restrict(Restrictions.eq(Hql.property("bw", "column"), Expressions.integer(8)));
+        spBoxQuery.restrict(Restrictions.eq(Hql.alias("bm"), null));
+        
+        spBoxQuery.order(Orders.asc(Hql.property("name")));
+        List<BioPlate> spBoxes = spBoxQuery.list(dc);
+        
+        JSONArray jsonWells = new JSONArray();
+        for (BioPlate box : spBoxes)
+        {
+          BioWell free = getFirstFreeWell(box, 1);
+          while (free != null)
+          {
+            jsonWells.add(JsonUtil.getBioWellAsJSON(free));
+            if (jsonWells.size() == nofTubes) break;
+            free = getNextFreeWell(free);
+          }
+          if (jsonWells.size() == nofTubes) break;
+        }
+        
+        json.put("wells", jsonWells);
+      }
       else if ("GetBoxInfo".equals(cmd))
       {
@@ -124 +161 @@
         // Get spBox
         String boxName = req.getParameter("boxName");       
-        Integer spaceReq = Values.getInt(req.getParameter("nofTubes"), 1);
         ItemQuery<BioPlate> spBoxQuery = BioPlate.getQuery();
         spBoxQuery.restrict(Restrictions.eq(Hql.property("name"), Expressions.string(boxName)));
@@ -146 +182 @@
           else if (lysBoxes.size() > 1)
           {
-            json.put("message", "Warning:More then one lys-box were found.");
-          }
-          else
-          {
-            // Search for empty position in corresponding lys-box.
-            emptyWell = getFirstFreeWell(lysBoxes.get(0),spaceReq);
-          } 
-          
-          // No empty position were found in lys-box. Search for empty position in Sp-box.
-          if (emptyWell == null)
-          {
-            emptyWell = getFirstFreeWell(box, spaceReq);
-          }
-          else
-          {
-            // else control that same position is free in Sp-box or look in Sp-box.
-            if (!box.getBioWell(emptyWell.getRow(), emptyWell.getColumn()).isEmpty())
-            {
-              emptyWell = getFirstFreeWell(box, spaceReq);              
-            }
-          }
-          
-          if (emptyWell == null)
-          {
-            json.put("message", "Warning:An empty position can not be suggested.");
-          }
-          
+            json.put("message", "Warning:More then one Lys-box were found.");
+          }
           WellCoordinateFormatter wcfRow = new WellCoordinateFormatter(true);
           json.put("boxInfo", spBoxes.get(0).getId());
           json.put("rows", wcfRow.format(spBoxes.get(0).getRows()-1));
           json.put("columns", spBoxes.get(0).getColumns());
-          if (emptyWell != null)
-          {
-            json.put("freeColumn", emptyWell.getColumn());
-            json.put("freeRow", wcfRow.format(emptyWell.getRow()));
-          }                   
+            
         }
         else if (spBoxes.size()==0)
@@ -218 +225 @@
         else if (!plate.getBioWell(rowNumber-1, columnIndex).isEmpty() )
         {
-          msg = "Specified row:column("+rowString+":"+wcfColumn.format(columnIndex)+") is already taken.";
+          msg = "Location '"+rowString+wcfColumn.format(columnIndex)+"' is already used.";
         }
         json.put("message", msg);       
@@ -260 +267 @@
       {
         dc = sc.newDbControl();
-        ItemContext cc = sc.getCurrentContext(Item.SAMPLE);
         JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader());       
         JSONObject jsonCase = (JSONObject)jsonReq.get("caseInfo");
@@ -333 +339 @@
               if (well != null)
               {
-                specimen.setBioWell(well);
-                cc.setRecent(well.getPlate(), "reggie_specimentube", 1);                
+                specimen.setBioWell(well);              
               }
             }           
@@ -405 +410 @@
     return firstFreeWell;
   }
+  
+  private BioWell getNextFreeWell(BioWell well)
+  {
+    BioWell nextFree = null;
+    BioPlate plate = well.getPlate();
+    int numColumns = plate.getColumns();
+    
+    int nextPos = well.getRow() * numColumns + well.getColumn()+1;
+    int nextCol = nextPos % numColumns;
+    int nextRow = nextPos / numColumns;
+    nextFree = plate.getBioWell(nextRow, nextCol);
+    
+    return nextFree;
+  }
+
 }