Changeset 24 for trunk/grails-app/domain

Timestamp:

Mar 23, 2011, 1:24:24 PM (11 years ago)

Author:

robert@…

Message:

Improved export of fasta files and added properties to assaysamples

File:

• trunk/grails-app/domain/nl/tno/metagenomics/AssaySample.groovy (modified) (4 diffs)

trunk/grails-app/domain/nl/tno/metagenomics/AssaySample.groovy

@@ -15 +15 @@
         Integer numUniqueSequences      // Number of unique sequences / OTUs. Is only available after preprocessing
 
-        String oligoNumber              // Oligonumber used to identify the sample
-        String tagSequence              // Tag originally used to identify the sample
-        String tagName                  // Tag name
+        String fwOligo
+        String fwMidName
+        String fwTotalSeq
+        String fwMidSeq
+        String fwPrimerSeq
+        
+        String revOligo
+        String revMidName
+        String revTotalSeq
+        String revMidSeq
+        String revPrimerSeq
 
         static belongsTo  = [ assay: Assay, sample: Sample, run: Run ]
@@ -24 +32 @@
         static constraints = {
                 numUniqueSequences(nullable: true)
-                oligoNumber(nullable: true)
-                
-                /*
-                , validator: { value, obj, errors ->
-                        // When one oligoNumber is used in different assaysamples,
-                        // they must also have the same tagSequences and tagNames
-                        
-                        // Check whether this oligoNumber exists in the database
-                        def otherAssaySamples = AssaySample.findAllByOligoNumber( value )
-                        if( !otherAssaySamples || otherAssaySamples.size() == 0 ) {
-                                return true;
-                        }
-                        
-                        // Loop through the other assaysamples with this oligonumber
-                        otherAssaySamples.each { otherAS ->
-                                // Only check other objects, don't compare with itself (because that
-                                // way it wouldn't be possible anymore to edit an object)
-                                if( otherAS.id != obj.id ) {
-                                        if( otherAS.tagSequence != obj.tagSequence || otherAS.tagName != obj.tagName ) {
-                                                return false;
-                                        }
-                                }
-                        }
-                        
-                        return true
-                } 
-                 */
-                tagSequence(nullable: true)
-                tagName(nullable:true)
+                fwOligo(nullable: true)
+                fwMidName(nullable: true)
+                fwTotalSeq(nullable:true)
+                fwMidSeq(nullable:true)
+                fwPrimerSeq(nullable:true)
+                revOligo(nullable: true)
+                revMidName(nullable: true)
+                revTotalSeq(nullable:true)
+                revMidSeq(nullable:true)
+                revPrimerSeq(nullable:true)
                 run(nullable: true);
         }
@@ -201 +190 @@
          */
         public boolean containsData() {
-                return tagSequence || tagName || oligoNumber || numFiles() > 0;
+                return  fwOligo || fwMidName || fwTotalSeq || fwMidSeq || fwPrimerSeq ||
+                                revOligo || revMidName || revTotalSeq || revMidSeq || revPrimerSeq ||
+                                numFiles() > 0;
         }
         
@@ -213 +204 @@
         public void moveValuableDataTo( AssaySample otherAssaySample ) {
                 // Copy properties
-                otherAssaySample.tagSequence = tagSequence;
-                otherAssaySample.oligoNumber = oligoNumber;
-                otherAssaySample.tagName         = tagName;
+                otherAssaySample.fwOligo                = fwOligo;
+                otherAssaySample.fwMidName              = fwMidName;
+                otherAssaySample.fwTotalSeq     = fwTotalSeq;
+                otherAssaySample.fwMidSeq               = fwMidSeq;
+                otherAssaySample.fwPrimerSeq    = fwPrimerSeq;
                 
+                otherAssaySample.revOligo               = revOligo;
+                otherAssaySample.revMidName             = revMidName;
+                otherAssaySample.revTotalSeq    = revTotalSeq;
+                otherAssaySample.revMidSeq              = revMidSeq;
+                otherAssaySample.revPrimerSeq   = revPrimerSeq;
+
                 // Move attached data
                 def dataList = [] + sequenceData?.toList()