Changeset 1930

Timestamp:

Apr 16, 2013, 9:28:14 AM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #472 and #473. Use 'ng/ml' in Qubit files since that is what is shown in the display on the Qubit. The importer converts to 'ng/µl'.

Location:

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

Files:

• plugins/QubitSampleNameExporter.java (modified) (1 diff)
• servlet/LibPrepServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/QubitSampleNameExporter.java

@@ -287 +287 @@
     tw.setEncoder(new CsvEncoderDecoder());
     
-    tw.tablePrintData("# Enter concentration measurements in nanogram/microliter");
-    tw.tablePrintData("# All extracts should have an 'Original conc.' value");
+    tw.tablePrintData("# Enter concentration measurements in nanogram/milliliter");
+    tw.tablePrintData("# All extracts should have an 'Qubit ng/ml' value");
     tw.tablePrintData("# Extracts that have been SpeedVac:ed should have ");
     tw.tablePrintData("# a second measurement made after the SpeedVac");
     tw.tablePrintData("#");
-    tw.tablePrintData("Well", "Library name", "Original conc.", "SpeedVac conc.");
+    tw.tablePrintData("Well", "Library name", "Qubit ng/ml", "After SpeedVac");
     Iterator<BioWell> it = query.iterate(dc);
     int lastCol = -1;

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

@@ -629 +629 @@
     // Parse the Qubit file and store concentration before and after speedvac in two maps
     FlatFileParser ffp = new FlatFileParser();
-    ffp.setDataHeaderRegexp(Pattern.compile("Well\\tLibrary name\\tOriginal conc\\.\\tSpeedVac conc\\..*"));
+    ffp.setDataHeaderRegexp(Pattern.compile("Well\\tLibrary name\\tQubit ng/ml\\tAfter SpeedVac.*"));
     ffp.setIgnoreRegexp(Pattern.compile("^#.*")); // Ignore all lines starting with '#'
     ffp.setDataSplitterRegexp(Pattern.compile("\t")); // Split on tab
@@ -640 +640 @@
 
     Mapper nameMapper = ffp.getMapper("\\Library name\\");
-    Mapper originalConcMapper = ffp.getMapper("\\Original conc.\\");
-    Mapper speedVacConcMapper = ffp.getMapper("\\SpeedVac conc.\\");
-
-    Map<String, String> originalConc = new HashMap<String, String>();
-    Map<String, String> speedVacConc = new HashMap<String, String>();
+    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, originalConcMapper.getValue(data));
-      speedVacConc.put(libName, speedVacConcMapper.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, String> originalConcLookup = new LookupConverter<String, String>(originalConc, 
+    LookupConverter<String, Float> originalConcLookup = new LookupConverter<String, Float>(originalConc, 
       "Could not find original concentration for extract '{KEY}'"
       );
-    LookupConverter<String, String> speedVacConcLookup = new LookupConverter<String, String>(speedVacConc, null);
+    LookupConverter<String, Float> speedVacConcLookup = new LookupConverter<String, Float>(speedVacConc, null);
 
     cpi.addExternalLookup(originalConcLookup, originalConcType);
     cpi.addExternalLookup(speedVacConcLookup, speedVacConcType);
   }
+  
+  private Float checkQubitConcentration(Float value, int lineNo)
+  {
+    return value == null ? null : value / 1000;
+  }
 }