Changeset 1968

Timestamp:

May 8, 2013, 11:10:06 AM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #473: Register library processing results

Swithced order of file selection so that the Qubit file is selected first. This makes it possible to validate that file at the same time the Caliper Well Table file is validated.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/libprep/lib_registration.jsp (modified) (5 diffs)
• src/net/sf/basedb/reggie/servlet/LibPrepServlet.java (modified) (3 diffs)

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

@@ -258 +258 @@
   {
     qubitCsvFileOnChange();
-    frm.libProtocol.focus();
   }
   else
@@ -310 +309 @@
   Main.addClass(document.body, 'please-wait');
   setInputStatus('welltable', 'Checking...', 'checking');
-  var url = '../LibPrep.servlet?ID=<%=ID%>&cmd=PreValidateCaliperWellTable&csv='+csvId+'&bioplate='+frm.bioplate.value;
+  var qubitCsv = frm['qubitcsv.id'].value;
+  var url = '../LibPrep.servlet?ID=<%=ID%>&cmd=PreValidateCaliperWellTable&csv='+csvId+'&bioplate='+frm.bioplate.value+'&qubit='+qubitCsv;
   
   var request = Ajax.getXmlHttpRequest();
@@ -633 +633 @@
         <td class="input">
           <input type="text" class="required" name="libDate" value="" size="12" maxlength="10"
-            onblur="libDateOnChange()" onkeypress="focusOnEnter(event, 'welltable.path')">
+            onblur="libDateOnChange()" onkeypress="focusOnEnter(event, 'qubitcsv.path')">
         </td>
         <td class="status" id="libDate.status"></td>
@@ -641 +641 @@
       </tr>
       <tbody id="filesSection">
+      <tr>
+        <td class="prompt">Qubit files</td>
+        <td class="input"></td>
+        <td class="status"></td>
+        <td class="help"></td>
+      </tr>
+      <tr valign="top">
+        <td class="subprompt">Conc. CSV</td>
+        <td class="input">
+          <input type="hidden" name="qubitcsv.id" value="">
+          <table>
+          <tr>
+          <td><input class="text required" type="text" 
+            name="qubitcsv.path" value=""
+            size="50" onkeypress="doOnEnter(event, function(){document.getElementById('btnQubitCsv').click()})"
+            onblur="qubitCsvFileOnChange()"
+            ></td>
+          <td style="padding-left: 4px;"><base:button 
+              title="Browse&hellip;"
+              onclick="browseOnClick('qubitcsv', 'csv')"
+              id="btnQubitCsv"
+              />
+          </td>
+          </tr>
+          </table>
+        </td>
+        <td class="status" id="qubitcsv.status"></td>
+        <td class="help"><span id="qubitcsv.message" class="message" style="display: none;"></span>
+          Select the <b>Qubit CSV</b> file that contains the table with concentration
+          measurements.
+        </td>
+      </tr>
       <tr>
         <td class="prompt">Caliper files</td>
@@ -722 +754 @@
         </td>
       </tr>
-      <tr>
-        <td class="prompt">Qubit files</td>
-        <td class="input"></td>
-        <td class="status"></td>
-        <td class="help"></td>
-      </tr>
-      <tr valign="top">
-        <td class="subprompt">Conc. CSV</td>
-        <td class="input">
-          <input type="hidden" name="qubitcsv.id" value="">
-          <table>
-          <tr>
-          <td><input class="text required" type="text" 
-            name="qubitcsv.path" value=""
-            size="50" onkeypress="doOnEnter(event, function(){document.getElementById('btnQubitCsv').click()})"
-            onblur="qubitCsvFileOnChange()"
-            ></td>
-          <td style="padding-left: 4px;"><base:button 
-              title="Browse&hellip;"
-              onclick="browseOnClick('qubitcsv', 'csv')"
-              id="btnQubitCsv"
-              />
-          </td>
-          </tr>
-          </table>
-        </td>
-        <td class="status" id="qubitcsv.status"></td>
-        <td class="help"><span id="qubitcsv.message" class="message" style="display: none;"></span>
-          Select the <b>Qubit CSV</b> file that contains the table with concentration
-          measurements.
-        </td>
-      </tr>
       </tbody>
       <tr valign="top">

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

@@ -411 +411 @@
         int csvId = Values.getInt(req.getParameter("csv"));
         int libPlateId = Values.getInt(req.getParameter("bioplate"));
+        int qubitId = Values.getInt(req.getParameter("qubit"));
         
         dc = sc.newDbControl();
@@ -420 +421 @@
         cpi.setBioPlate(BioPlate.getById(dc, libPlateId));
         cpi.setAllowMatchAgainstLocation(true); // Allow a few lines to have location coordinates instead of lib name
+        
+        if (qubitId != 0)
+        {
+          AnnotationType qubitConcType = Annotationtype.QUBIT_CONC.load(dc);
+          AnnotationType speedVacConcType = Annotationtype.QUBIT_CONC_AFTER_SPEEDVAC.load(dc);
+          File qubitCsv = File.getById(dc, qubitId);
+          addQubitFileLookups(cpi, qubitCsv, qubitConcType, speedVacConcType);
+        }
+        
         if (cpi.doImport(dc, csv.getDownloadStream(0), true))
         {
@@ -631 +641 @@
   // Parse the Qubit file and return a map extract name -> concentration
   private void addQubitFileLookups(CaliperPlateImporter cpi, File qubitCsv, AnnotationType originalConcType, AnnotationType speedVacConcType)
-    throws IOException
   {
-    // Parse the Qubit file and store concentration before and after speedvac in two maps
-    FlatFileParser ffp = new FlatFileParser();
-    ffp.setDataHeaderRegexp(Pattern.compile(".*Well.*Library name.*Qubit ng/ml.*After SpeedVac.*"));
-    ffp.setIgnoreRegexp(Pattern.compile("^\\\"?#.*")); // Ignore all lines starting with '#' ( or "#)
-    ffp.setDataSplitterRegexp(Pattern.compile("\t|,")); // Split on tab or comma
-    ffp.setInputStream(qubitCsv.getDownloadStream(0), "UTF-8");
-    ffp.setTrimQuotes(true);
-    if (ffp.parseHeaders() != LineType.DATA_HEADER)
-    {
-      throw new InvalidDataException("File '" + qubitCsv.getName() + "': Could not find header line starting with 'Well{tab}Library name{tab}Qubit ng/ml...'");
-    }
-
-    Mapper nameMapper = ffp.getMapper("\\Library name\\");
-    Mapper originalConcMapper = ffp.getMapper("\\Qubit ng/ml\\");
-    Mapper speedVacConcMapper = ffp.getMapper("\\After SpeedVac\\");
-
-    Map<String, Float> originalConc = new HashMap<String, Float>();
-    Map<String, Float> speedVacConc = new HashMap<String, Float>();
-    while (ffp.hasMoreData())
-    {
-      int lineNo = ffp.getParsedLines();
-      FlatFileParser.Data data = ffp.nextData();
-      String libName = nameMapper.getValue(data);
-      originalConc.put(libName, checkQubitConcentration(originalConcMapper.getFloat(data), lineNo));
-      speedVacConc.put(libName, checkQubitConcentration(speedVacConcMapper.getFloat(data), lineNo));
-    }
-    
-    // An original concentration is required, but SpeedVac concentration is optional
-    LookupConverter<String, Float> originalConcLookup = new LookupConverter<String, Float>(originalConc, 
-      "Could not find original concentration for extract '{KEY}'"
-      );
-    LookupConverter<String, Float> speedVacConcLookup = new LookupConverter<String, Float>(speedVacConc, null);
-
-    cpi.addExternalLookup(originalConcLookup, originalConcType);
-    cpi.addExternalLookup(speedVacConcLookup, speedVacConcType);
+    try
+    {
+      // Parse the Qubit file and store concentration before and after speedvac in two maps
+      FlatFileParser ffp = new FlatFileParser();
+      ffp.setDataHeaderRegexp(Pattern.compile(".*Well.*Library name.*Qubit ng/ml.*After SpeedVac.*"));
+      ffp.setIgnoreRegexp(Pattern.compile("^\\\"?#.*")); // Ignore all lines starting with '#' ( or "#)
+      ffp.setDataSplitterRegexp(Pattern.compile("\t|,")); // Split on tab or comma
+      ffp.setInputStream(qubitCsv.getDownloadStream(0), "UTF-8");
+      ffp.setTrimQuotes(true);
+      if (ffp.parseHeaders() != LineType.DATA_HEADER)
+      {
+        throw new InvalidDataException("Could not find header line starting with 'Well{tab}Library name{tab}Qubit ng/ml...'");
+      }
+  
+      Mapper nameMapper = ffp.getMapper("\\Library name\\");
+      Mapper originalConcMapper = ffp.getMapper("\\Qubit ng/ml\\");
+      Mapper speedVacConcMapper = ffp.getMapper("\\After SpeedVac\\");
+  
+      Map<String, Float> originalConc = new HashMap<String, Float>();
+      Map<String, Float> speedVacConc = new HashMap<String, Float>();
+      while (ffp.hasMoreData())
+      {
+        int lineNo = ffp.getParsedLines();
+        FlatFileParser.Data data = ffp.nextData();
+        String libName = nameMapper.getValue(data);
+        originalConc.put(libName, checkQubitConcentration(originalConcMapper.getFloat(data), lineNo));
+        speedVacConc.put(libName, checkQubitConcentration(speedVacConcMapper.getFloat(data), lineNo));
+      }
+      
+      // An original concentration is required, but SpeedVac concentration is optional
+      LookupConverter<String, Float> originalConcLookup = new LookupConverter<String, Float>(originalConc, 
+        "Could not find Qubit concentration for extract '{KEY}' in file: " + qubitCsv.getName()
+        );
+      LookupConverter<String, Float> speedVacConcLookup = new LookupConverter<String, Float>(speedVacConc, null);
+  
+      cpi.addExternalLookup(originalConcLookup, originalConcType);
+      cpi.addExternalLookup(speedVacConcLookup, speedVacConcType);
+    }
+    catch (Exception ex)
+    {
+      throw new RuntimeException("File '" + qubitCsv.getName() + "': " + ex.getMessage(), ex);
+    }
   }