Changeset 1938

Timestamp:

Apr 17, 2013, 2:50:51 PM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #424: Select RNA items for library preparation

Add support for selecting 'Stratagene' when designing a new mRNA plate.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/libprep/assign_barcode.jsp (modified) (2 diffs)
• resources/libprep/mrna_protocol2.jsp (modified) (2 diffs)
• resources/libprep/select_rna.jsp (modified) (10 diffs)
• resources/reggie.js (modified) (1 diff)
• src/net/sf/basedb/reggie/dao/Rna.java (modified) (3 diffs)
• src/net/sf/basedb/reggie/servlet/MRnaServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/libprep/assign_barcode.jsp

@@ -224 +224 @@
 {
   // Set the 'stratagene'/'external' flag
-  cdna.stratagene = cdna.name.indexOf(STRATAGENE_NAME) == 0;
+  cdna.stratagene = cdna.name.indexOf(GENERIC_STRATAGENE_NAME) == 0;
   cdna.external = cdna.name.indexOf(EXTERNAL_RNA_NAME) == 0;
 }
@@ -602 +602 @@
 {
   background-image: url('../images/mrnaqc.png');
-  background-position: 95% 5%;
+  background-position: 95% 25%;
   background-repeat: no-repeat;
 }

extensions/net.sf.basedb.reggie/trunk/resources/libprep/mrna_protocol2.jsp

@@ -140 +140 @@
     var rna = mrna.rna;
     // Set the 'stratagene' flag
-    rna.stratagene = rna.name == STRATAGENE_NAME;
+    rna.stratagene = rna.name.indexOf(GENERIC_STRATAGENE_NAME) == 0;
     rna.external = rna.name == EXTERNAL_RNA_NAME;
     
@@ -466 +466 @@
   {
     background-image: url('../images/mrnaqc.png');
-    background-position: 95% 5%;
+    background-position: 95% 25%;
     background-repeat: no-repeat;
   }

extensions/net.sf.basedb.reggie/trunk/resources/libprep/select_rna.jsp

@@ -56 +56 @@
     var tmp = {};
     tmp.name = name;
-    tmp.stratagene = name == STRATAGENE_NAME;
+    tmp.stratagene = name.indexOf(GENERIC_STRATAGENE_NAME) == 0;
     tmp.external = name == EXTERNAL_RNA_NAME;
     tmp.info = rna.infoByName(name);
@@ -70 +70 @@
     var tmp = {};
     tmp.name = info.name;
-    tmp.stratagene = tmp.name == STRATAGENE_NAME;
+    tmp.stratagene = tmp.name.indexOf(GENERIC_STRATAGENE_NAME) == 0;
     tmp.external = tmp.name == EXTERNAL_RNA_NAME;
     tmp.id = info.id;
@@ -185 +185 @@
       
       var warningMsg = null;
+      if (info.bioWell)
+      {
+        var rnaWell = info.bioWell;
+        text += '<div class="location">'+rnaWell.bioPlate.name+'['+rnaWell.location+']</div>';
+      }
+      else if (!rna.stratagene && !rna.external)
+      {
+        if (!warningMsg) warningMsg = 'No location';
+      }
+
       if (info && info.id && !rna.stratagene && !rna.external)
       {
@@ -190 +200 @@
         var use = Math.ceil(quantity/info.NDConc);
         var water = Math.round(50-use);
-        if (info.bioWell)
-        {
-          var rnaWell = info.bioWell;
-          text += '<div class="location">'+rnaWell.bioPlate.name+'['+WELL_ALPHA[rnaWell.row]+(rnaWell.column+1)+']</div>';
-        }
-        else
-        {
-          if (!warningMsg) warningMsg = 'No location';
-        }
         if (info.remainingQuantity)
         {
@@ -227 +228 @@
           if (!warningMsg) warningMsg = 'No NDConc value';
         }
-        if (warningMsg)
-        {
-          well.setWarning(warningMsg);
-        }
       }
       else if (!rna.id)
@@ -240 +237 @@
         text += '<div class="comment">'+Main.encodeTags(rna.comment)+'</div>';
       }
+      if (warningMsg)
+      {
+        well.setWarning(warningMsg);
+      }
     }
     else if (well.copyText)
@@ -257 +258 @@
 function init()
 {
+  loadStratagene();
+  
   keepSessionAlive('<%=ID%>', debug, '../');
   
@@ -274 +277 @@
   Plate.name = findNextMRnaPlateName();
   setInnerHTML('plateName', Plate.name);
+}
+
+function loadStratagene()
+{
+  var request = Ajax.getXmlHttpRequest();
+  var url = '../MRna.servlet?ID=<%=ID%>&cmd=GetStratagene'; 
+  if (debug) Main.debug(url);
+  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;
+  }
+  
+  var stratagene = response.stratagene;
+  
+  var frm = document.forms['reggie'];
+
+  for (var i = 0; i < stratagene.length; i++)
+  {
+    var s = stratagene[i];
+    var name = s.name;
+    if (s.bioWell)
+    {
+      name += ' -- ' + s.bioWell.bioPlate.name + ' ('+s.bioWell.location + ')';
+    }
+    frm.stratagene[frm.stratagene.length] = new Option(name, s.name);
+  }
+  
 }
 
@@ -374 +410 @@
 function setToStratagene()
 {
-  setToSpecial(STRATAGENE_NAME, true);
+  var frm = document.forms['reggie'];
+  setToSpecial(frm.stratagene.value, true);
 }
 
@@ -1509 +1546 @@
       </tr>
       <tr valign="top">
+        <td class="prompt">Stratagene to use</td>
+        <td class="input">
+          <select name="stratagene" style="width: 25em;"></select>
+        </td>
+        <td class="help">
+          Select the Stratagene tube to use. If not known, the
+          generic <b>Stratagene.r</b> (last in the list) should be used.
+        </td>
+      </tr>
+      <tr valign="top">
         <td class="prompt">Preliminary pool layout</td>
         <td class="input">
-          <select name="pool_schema" onchange="poolSchemaOnChange()"></select>
+          <select name="pool_schema" onchange="poolSchemaOnChange()" style="width: 25em;"></select>
         </td>
         <td class="help">Preliminary pool layout (can be changed later).</td>

extensions/net.sf.basedb.reggie/trunk/resources/reggie.js

@@ -2 +2 @@
 var WELL_ALPHA = [ 'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z'];
 
-var STRATAGENE_NAME = 'Stratagene.r';
+var GENERIC_STRATAGENE_NAME = 'Stratagene.r';
 var EXTERNAL_RNA_NAME = 'External.r';
 

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

@@ -63 +63 @@
   
   /**
-    The name of the RNA item in BASE that represents Stratagene.
+    The name of the RNA item in BASE that represents Generic Stratagene.
+    Tracked Stratagene should use the pattern 'Stratagene.rNNN' where
+    'NNN' is a number.
     @since 2.12
   */
@@ -73 +75 @@
   */
   public static final String EXTERNAL = "External.r";
+  
+  /**
+    Checks if an item with the given name is a Stratagene RNA or a 
+    derivative from a Stratagene RNA.
+    @since 2.12
+  */
+  public static boolean isStratagene(String name)
+  {
+    return name.startsWith(STRATAGENE);
+  }
   
   /**
@@ -109 +121 @@
     // Filter on id not equal to any that has a RNAQC child
     query.restrict(Restrictions.neq(Hql.property("id"), Expressions.all(subquery)));
-    // Filter on creation date (eg. to get rid of 'Stratagene')
+    // Filter on creation date==null and parent != null (eg. to get rid of 'Stratagene')
     query.join(Hql.innerJoin("creationEvent", "ce"));
     query.restrict(Restrictions.neq(Hql.property("ce", "eventDate"), null));
+    query.restrict(Restrictions.neq(Hql.property("parent"), null));
     
     query.order(Orders.asc(Hql.property("id")));
+    
+    return toRna(query.list(dc));
+  }
+  
+  /**
+    Find all Stratagene RNA that is available for selection in the
+    mRNA wizards. This should include all 'Stratagene.rNNN' where
+    'NNN' is a number that has a registered location on a bioplate, and
+    the generic 'Stratagene.r' extract.
+  */
+  public static List<Rna> findStratagene(DbControl dc)
+  {
+    ItemQuery<Extract> query = Extract.getQuery();
+    query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+    // Join bioplate
+    query.join(Hql.leftJoin(null, "bioWell", "bw", null, true));
+    query.join(Hql.leftJoin("bw", "bioPlate", "bp", null, true));
+    
+    // Filter on RNA subtype
+    Subtype.RNA.addFilter(dc, query);
+    
+    // Filter on name='Stratagene.r' OR name ~ 'Stratagene.rNNN'
+    query.restrict(
+      Restrictions.or(
+        Restrictions.eq(Hql.property("name"), Expressions.string(Rna.STRATAGENE)),
+        Restrictions.and(
+          Restrictions.rlike(Hql.property("name"), Expressions.string("^"+ Rna.STRATAGENE + "[0-9]+$")),
+          Restrictions.neq(Hql.property("bioWell"), null)
+        )
+      )
+    );
+
+    // Sort by bioplate position -- those without plate are sorted last by name
+    query.order(Orders.asc(Hql.expression("coalesce(bp.name, 'zzzz')", null)));
+    query.order(Orders.asc(Hql.property("bw", "row")));
+    query.order(Orders.asc(Hql.property("bw", "column")));
+    query.order(Orders.asc(Hql.property("name")));
     
     return toRna(query.list(dc));

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

@@ -94 +94 @@
         json.put("name", bioPlateType.generateNextName(dc, 1));
       }
+      else if ("GetStratagene".equals(cmd))
+      {
+        dc = sc.newDbControl();
+        List<Rna> stratagene = Rna.findStratagene(dc);
+        
+        JSONArray jsonStratagene = new JSONArray();
+        for (Rna s : stratagene)
+        {
+          s.loadBioPlateLocation();
+          jsonStratagene.add(s.asJSONObject());
+        }
+        json.put("stratagene", jsonStratagene);
+        
+      }
       else if ("GetUnprocessedPlates".equals(cmd))
       {
@@ -143 +157 @@
         query.join(Hql.innerJoin("creationEvent", "ce"));
         query.restrict(Restrictions.neq(Hql.property("ce", "eventDate"), null));
+        // Filter on parent != null (to get rid of 'Stratagene'
+        query.restrict(Restrictions.neq(Hql.property("parent"), null));
         
         // Join AUTO_PROCESSING annotation