Changeset 2088

Timestamp:

Oct 18, 2013, 2:29:03 PM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #499: Export sample sheet for flow cell

Added ReadString as a parameter to the sample sheet exporter.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• META-INF/plugin-configurations.xml (modified) (1 diff)
• src/net/sf/basedb/reggie/plugins/FlowCellSampleSheetExporter.java (modified) (9 diffs)

extensions/net.sf.basedb.reggie/trunk/META-INF/plugin-configurations.xml

@@ -129 +129 @@
     <configname>SCAN-B</configname>
     <description>Configuration for the default SCAN-B setup.</description>
+   <parameter>
+      <name>ReadString</name>
+      <label>Read string</label>
+      <description>Pattern describing how each sequencing cycle is used.
+
+Y = the cycle should be used as part of an insert read
+N = the cycle should be skipped
+I = the cycle should be used as part of the index (barcode)
+J = the cycle is part of the index but should not be used in demultiplexing
+
+A number means repeat the preceeding letter this many times.</description>
+      <class>java.lang.String</class>
+      <value>Y54N1I6J1Y53N1</value>
+    </parameter>
     <parameter>
       <name>SequencingCenter</name>

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

@@ -66 +66 @@
     The deault read string pattern.
   */
-  public static final String DEFAULT_READ_STRING = "Y100N1I6J1Y100N1";
+  public static final String DEFAULT_READ_STRING = "Y54N1I6J1Y53N1";
   
   public static final String DEFAULT_PROJECT_NAME = "scanb";
@@ -165 +165 @@
           return;
         }
-
+        String readString = (String)request.getParameterValue("ReadString");
+        if (!isValidReadString(readString))
+        {
+          response.setError("Not a valid ReadString: '"+readString + "'", null);
+          return;
+        }
+
+        storeValue(configuration, request, ri.getParameter("ReadString"));
         storeValue(configuration, request, ri.getParameter("Project"));
         storeValue(configuration, request, ri.getParameter("SequencingCenter"));
@@ -181 +188 @@
           response.setError(errors.size() + " invalid parameters were found in the request",errors);
           return;
-        }       
+        }
+        
+        String readString = (String)request.getParameterValue("ReadString");
+        if (!isValidReadString(readString))
+        {
+          response.setError("Not a valid ReadString: '"+readString + "'", null);
+          return;
+        }
 
         storeValue(job, request, ri.getParameter("flowCell"));
+        storeValue(job, request, ri.getParameter("ReadString"));
         storeValue(job, request, ri.getParameter("Project"));
         storeValue(job, request, ri.getParameter("SequencingCenter"));
@@ -277 +292 @@
     {
       dc = sc.newDbControl();
+      parameters.add(getReadStringParameter(null));
       parameters.add(getProjectParameter(dc));
       parameters.add(getSequencingCenterParameter());
@@ -304 +320 @@
         
         PhysicalBioAssay currentBioAssay = null;
+        String currentSequencingCycles = null;
         int currentBioAssayId = sc.getCurrentContext(Item.PHYSICALBIOASSAY).getId();
         if (currentBioAssayId != 0)
         {
           currentBioAssay = PhysicalBioAssay.getById(dc, currentBioAssayId);
+          currentSequencingCycles = (String)Annotationtype.SEQUENCING_CYCLES.getAnnotationValue(dc, currentBioAssay);
         }
         
@@ -330 +348 @@
         parameters.add(new PluginParameter<String>(null, "Sample sheet options", 
           "The options for the entire sample sheet are defined in the plug-in configuration but can be modified here.", null));
+        parameters.add(getReadStringParameter(currentSequencingCycles));
         parameters.add(getProjectParameter(dc));
         parameters.add(getSequencingCenterParameter());
@@ -396 +415 @@
     // Some info is global on the flow cell
     info[0] = Annotationtype.FLOWCELL_ID.getAnnotationValue(dc, flowCell); // Flow cell ID
-    info[2] = Annotationtype.READ_STRING.getAnnotationValue(dc, flowCell); // Read string
+    info[2] = getParameter(parameters, "ReadString", DEFAULT_READ_STRING); // Read string
     info[3] = getParameter(parameters, "Project", projectName); // Project name
     info[9] = getParameter(parameters, "Width", DEFAULT_LIBRARY_WIDTH); // Width
@@ -511 +530 @@
   
   /**
+    Check that the value is a sequence of Y, N, I, J followed by a number
+  */
+  private boolean isValidReadString(String value)
+  {
+    return value != null && value.matches("([YNIJ]\\d+)+");
+  }
+
+  
+  /**
     Convert to lower case and remove all characters not in [a-z0-9_]
   */
@@ -518 +546 @@
   }
 
+  private PluginParameter<String> getReadStringParameter(String sequencingCycles)
+  {
+    
+    PluginParameter<String> parameter = new PluginParameter<String>("ReadString", "Read string",
+      (sequencingCycles != null ? "<b>SequencingCycles for this flow cell: <i>" + sequencingCycles + "</i></b>\n\n" : "") + 
+      "Pattern describing how each sequencing cycle is used.\n\n"+
+      "Y = the cycle should be used as part of an insert read\n"+
+      "N = the cycle should be skipped\n"+
+      "I = the cycle should be used as part of the index (barcode)\n"+
+      "J = the cycle is part of the index but should not be used in demultiplexing\n\n"+
+      "A number means repeat the preceeding letter this many times.",
+      new StringParameterType(255, DEFAULT_READ_STRING, true)
+      );
+    return parameter;
+  }
+
+  
   private PluginParameter<String> getProjectParameter(DbControl dc)
   {