Changeset 2961

Timestamp:

Nov 27, 2006, 2:32:05 PM (16 years ago)

Author:

Johan Enell

Message:

References #429

File:

• branches/2.1/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java (modified) (7 diffs)

branches/2.1/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java

@@ -69 +69 @@
 import net.sf.basedb.core.query.JoinType;
 import net.sf.basedb.core.query.Orders;
+import net.sf.basedb.core.query.Selects;
 import net.sf.basedb.core.query.SqlResult;
 import net.sf.basedb.util.BioAssaySetUtil;
@@ -186 +187 @@
 
   
-  private void exportBASE(BioAssaySet bas, File file, Map<String, String> parameters, List<String> reporterFields, List<String> spotFields)
+  private void exportBASE(BioAssaySet bas, File file, Map<String, String> parameters, List<String> reporterFields, List<String> spotFields, Boolean serialFormat, Boolean mergeReporters)
+    throws IOException, SQLException
   {
     DbControl dc = bas.getDbControl();
@@ -205 +207 @@
     // assay section    
     out.println("section\tassays");
-    
+    out.println("count\t" + bas.getBioAssays().count(dc));
+    String annotationString = "";
+    for (AnnotationType at : getExperimentalFactors(dc, bas))
+    {
+      annotationString += "\t" + at.getName();
+    }
+    out.println("columns\tid\tname" + annotationString);
+    out.println("annotationColumns" + annotationString);
     out.println("%");
     for (BioAssay ba : bas.getBioAssays().list(dc))
@@ -214 +223 @@
         out.print("\t");
         Set<Object> values = BioAssaySetUtil.getAnnotationValues(dc, ba, at);
-        for (Object v : values) out.print("\t"+v);
+        if (!values.isEmpty()) out.print(values.iterator().next());
       }
     }
@@ -220 +229 @@
     
     // spot section(s)
-    out.println("section\tspots");
-    out.println("%");
-    out.println();
+    String fieldString = spotFields.toString().substring(1, spotFields.toString().length() - 1).replace(", ", "\t");
+    String columnString = reporterFields.toString().substring(1, reporterFields.toString().length() - 1).replace(", ", "\t") + "\tassayData";
+
+    if (serialFormat)
+    {
+      for (BioAssay ba : bas.getBioAssays().list(dc))
+      {
+        out.println("section\tspots");
+        out.println("channels\t" + bas.getRawDataType().getChannels());
+        out.println("assayFields\t" + fieldString);
+        out.println("columns\t" + columnString);
+        out.println("assays\t" + ba.getId());
+        out.println("count\t" + ba.getNumSpots());
+        out.println("%");
+        
+        DynamicSpotQuery query = ba.getSpotData();
+        for (String field : reporterFields)
+        {
+          query.select(Selects.expression(BioAssaySetUtil.createJepExpression(dc, bas, field), field));
+        }
+        for (String field : spotFields)
+        {
+          query.select(Selects.expression(BioAssaySetUtil.createJepExpression(dc, bas, field), field));
+        }
+        if (mergeReporters)
+        {
+          // not implemented
+        }
+        DynamicResultIterator result = query.iterate(dc);
+        
+        List<Integer> reporterIndex = new ArrayList<Integer>(reporterFields.size());
+        List<Integer> spotIndex = new ArrayList<Integer>(spotFields.size());
+        for (String column : reporterFields)
+        {
+          reporterIndex.add(result.getIndex(column));
+        }
+        for (String field : spotFields)
+        {
+          spotIndex.add(result.getIndex(field));
+        }
+
+        while (result.hasNext())
+        {
+          SqlResult r = result.next();
+          boolean del = false;
+          for (Integer column : reporterIndex)
+          {
+            if (del)
+            {
+              out.print("\t");
+            }
+            out.print(r.getString(column) != null ? r.getString(column) : "");
+            del = true;
+          }
+          for (Integer field : spotIndex)
+          {
+            out.print("\t");
+            out.print(r.getString(field) != null ? r.getString(field) : "");
+          }
+          out.println();
+        }
+        
+        out.println();
+      }
+    }
+    else
+    {
+      
+    }
+    
   }
   
@@ -644 +720 @@
 
 
+  @SuppressWarnings("unchecked")
   public void run(Request request, Response response, ProgressReporter progress)
   {
@@ -671 +748 @@
         List<String> spotFields = new ArrayList<String>((List<String>) job.getValues(usedFieldsParameter.getName()));
         
-        exportBASE(bioassayset, file, null, reporterFields, spotFields);
+        boolean serialFormat = (Boolean) job.getValue(serialFormatParameter.getName());
+        boolean geneAverage = (Boolean) job.getValue(geneAveragesParameter.getName());
+        
+        exportBASE(bioassayset, file, null, reporterFields, spotFields, serialFormat, geneAverage);
       }
       else