Changeset 4092

Timestamp:

Jan 18, 2008, 2:34:10 PM (16 years ago)

Author:

Johan Enell

Message:

Merged from 2.5.1 Correct

File:

• trunk/src/plugins/core/net/sf/basedb/plugins/IlluminaRawDataImporter.java (modified) (11 diffs)

trunk/src/plugins/core/net/sf/basedb/plugins/IlluminaRawDataImporter.java

@@ -38 +38 @@
 
 
+import net.sf.basedb.core.ArrayDesign;
 import net.sf.basedb.core.BaseException;
 import net.sf.basedb.core.BasicItem;
@@ -93 +94 @@
   to an experiment.
   <p>
-  Since the data files doesn't have any coordinate information, the plug-in create
-  fake coordinates like this: block=1, column=1, row=linenumber in file.
-  The linenmbers start with 1 at the first data line, ie. header lines are not counted.
+  Since the data files doesn't have any coordinate information the importer will 
+  use one of the following methods.
+  
+  <ul>
+  <li>
+    If no array design has been selected or if the array design is using the
+    {@link FeatureIdentificationMethod#COORDINATES} method for identifying features:
+    The plug-in create fake coordinates like this: block=1, column=1, row=linenumber in file.
+    The linenmbers start with 1 at the first data line, ie. header lines are not counted.
+
+  <li>
+    If the array design uses the {@link FeatureIdentificationMethod#POSITION}
+    method for identiyfing features: The plug-in sets the position=line number in file.
+    The linenmbers start with 1 at the first data line, ie. header lines are not counted.
+    
+  <li>
+    If the array design uses the {@link FeatureIdentificationMethod#FEATURE_ID}
+    method for identifying features. The plug-in assumes that the feature ID is the
+    same as the reporter ID.
+  </ul>
+  
+  <p>
+  NOTE! Since the methods are not conflicting with each other, there will not
+  be an actual check which method to use by this plug-in. We will simple set all
+  values as specified above and let the BASE core handle the identification.
 
   @author nicklas
@@ -129 +152 @@
     ));
   
+  private static final PluginParameter<String> featureIdentificationParameter = 
+    new PluginParameter<String>(
+      "featureIdentification",
+      "Identify features by",
+      "Choose which method to use for identifying features. If no value " +
+      "is selected the identification method used on the array design is used: \n\n" +
+      "* COORDINATES: Use auto-generated coordinates (block = 1, column = 1, row = line number in file)\n" +
+      "* POSITION: Use auto-generated position = line number in file\n" +
+      "* FEATURE_ID: Use TargetID (requires that each Target ID only appears once in the file)\n\n" +
+      "NOTE! This parameter has no meaning unless an array design is selected",
+      new StringParameterType(255, null, false, 1, 0, 0, 
+        Arrays.asList(new String[] {"COORDINATE", "POSITION", "FEATURE_ID" } ))
+    );
+
+  
   
   private static final PluginParameter<String> invalidColumnsErrorParameter = new PluginParameter<String>(
@@ -257 +295 @@
         // Associations
         storeValue(job, request, ri.getParameter("experiment"));
+        storeValue(job, request, ri.getParameter("arrayDesign"));
+        storeValue(job, request, featureIdentificationParameter);
         storeValue(job, request, ri.getParameter("scan"));
         storeValue(job, request, ri.getParameter("protocol"));
@@ -286 +326 @@
   private DbControl dc;
   private Experiment experiment;
+  private ArrayDesign design;
   private Scan scan;
   private Software software;
   private Protocol protocol;
+  private FeatureIdentificationMethod fiMethod;
   private List<RawBioAssay> rawBioAssays;
   private List<BatchAndMapHolder> holders;
@@ -371 +413 @@
     this.headerLines = new LinkedList<Line>();
     this.experiment = (Experiment)job.getValue("experiment");
+    this.design = (ArrayDesign)job.getValue("arrayDesign");
     this.scan = (Scan)job.getValue("scan");
     this.protocol = (Protocol)job.getValue("protocol");
     this.software = (Software)job.getValue("software");
     
+    // Feature identification
+    try
+    {
+      String fiTemp = (String)job.getValue("featureIdentification");
+      fiMethod = FeatureIdentificationMethod.valueOf(fiTemp);
+    }
+    catch (Exception ex)
+    {
+      fiMethod = null;
+    }
     // Setup error handling
     this.nullIfException = "null".equals(getErrorOption("numberFormatError"));
@@ -431 +484 @@
       // Need to reload raw bioassay with current DbControl
       rba = RawBioAssay.getById(dc, rba.getId());
-      RawDataBatcher batcher = rba.getRawDataBatcher();
+      RawDataBatcher batcher = rba.getRawDataBatcher(fiMethod);
       batcher.useNullIfReporterNotFound(nullIfMissingReporter);
       holders.add(new BatchAndMapHolder(batcher, illumina, ffp));
@@ -566 +619 @@
             RawBioAssay rba = RawBioAssay.getNew(dc, generic, illumina);
             rba.setName(arrayName);
+            if (design != null) rba.setArrayDesign(design);
             if (scan != null) rba.setScan(scan);
             if (protocol != null) rba.setProtocol(protocol);
@@ -619 +673 @@
         parameters.add(getDecimalSeparatorParameter(null, null, (String)job.getValue(DECIMAL_SEPARATOR)));
   
-        // parameters for scan, protocol and software
+        // parameters for scan, protocol, software and array design
         dc = sc.newDbControl();
         List<Scan> scans = getItems(dc, Scan.getQuery());
@@ -634 +688 @@
             )
           );
+        List<ArrayDesign> designs = getItems(dc, ArrayDesign.getQuery(),
+          Restrictions.gt(
+              Hql.property("numDbFeatures"), 
+              Expressions.integer(0)
+            )
+          );
         
         boolean hasAssociations = 
           context.getItem() == Item.EXPERIMENT || scans.size() > 0 || 
-          protocols.size() > 0 || software.size() > 0;
+          protocols.size() > 0 || software.size() > 0 || designs.size() > 0;
         
         if (hasAssociations)
@@ -651 +711 @@
                 new ItemParameterType<Experiment>(Experiment.class, null, true, 1, null)
               ));
+          }
+          if (!designs.isEmpty())
+          {
+            parameters.add(new PluginParameter<ArrayDesign>(
+              "arrayDesign",
+              "Array design",
+              "The imported raw bioassays will be linked to the selected array design.",
+              new ItemParameterType<ArrayDesign>(ArrayDesign.class, null, false, 1, designs)
+            ));
+            parameters.add(featureIdentificationParameter);
           }
           if (!scans.isEmpty())