Changeset 2931

Timestamp:

Nov 17, 2006, 11:23:10 AM (16 years ago)

Author:

Johan Enell

Message:

References #439
Added job configuration for basefile
Added method to get Expermental Factors from a bioassayset

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

@@ -25 +25 @@
 package net.sf.basedb.plugins;
 
+import net.sf.basedb.core.AnnotationType;
 import net.sf.basedb.core.BaseException;
 import net.sf.basedb.core.BioAssay;
@@ -69 +70 @@
 import net.sf.basedb.core.query.Orders;
 import net.sf.basedb.core.query.SqlResult;
+import net.sf.basedb.util.BioAssaySetUtil;
 import net.sf.basedb.util.Enumeration;
 
 import java.io.IOException;
-import java.io.OutputStreamWriter;
-import java.io.Writer;
+import java.io.PrintWriter;
 import java.sql.SQLException;
 import java.util.ArrayList;
@@ -83 +84 @@
 import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
@@ -162 +164 @@
   }
 
+  
+  private void exportBASE(BioAssaySet bas, File file, Map<String, String> parameters, List<String> reporterFields, List<String> spotFields)
+  {
+    DbControl dc = bas.getDbControl();
+    PrintWriter out = new PrintWriter(file.getUploadStream(false));
+
+    // header and parameter section
+    out.println("BASEfile");
+    if (parameters != null)
+    {
+      for (String key : parameters.keySet())
+      {
+        out.println(key+"/t"+parameters.get(key));
+      }
+      out.println("%");
+    }
+    out.println();
+    
+    // assay section    
+    out.println("section/tassays");
+    
+    out.println("%");
+    for (BioAssay ba : bas.getBioAssays().list(dc))
+    {
+      out.print(ba.getId() + "\t" + ba.getName());
+      for (AnnotationType at : getExperimentalFactors(dc, bas))
+      {
+        out.print("\t");
+        Set<Object> values = BioAssaySetUtil.getAnnotationValues(dc, ba, at);
+        for (Object v : values) out.print("/t"+v);
+      }
+    }
+    out.println();
+    
+    // spot section(s)
+    out.println("section/tspots");
+    out.println("%");
+    out.println();
+  }
+  
 
   private void exportMeV(BioAssaySet bioassayset, File file)
@@ -167 +209 @@
   {
     DbControl dc=bioassayset.getDbControl();
-    Writer out = new OutputStreamWriter(file.getUploadStream(false));
+    PrintWriter out = new PrintWriter(file.getUploadStream(false));
 
     // comment header
@@ -443 +485 @@
 
 
+  public List<AnnotationType> getExperimentalFactors(DbControl dc, BioAssaySet bas)
+  {
+    ItemQuery<AnnotationType> query = bas.getExperiment().getExperimentalFactors();
+    query.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);
+    query.order(Orders.asc(Hql.property("name")));
+    return query.list(dc);
+  }
+  
+
   public Set<GuiContext> getGuiContexts()
   {
@@ -551 +602 @@
 
       // Add other export formats here
-      exportMeV(bioassayset,file);
-
+      String format = (String) job.getValue(formatParameter.getName());
+      if (format.equals(FORMAT_MEV)) exportMeV(bioassayset,file);
+      else if (format.equals(FORMAT_BASEFILE)) 
+      {
+        List<String> reporterFields = new ArrayList<String>((List<String>) job.getValues(usedColumnsParameter.getName()));
+        List<String> spotFields = new ArrayList<String>((List<String>) job.getValues(usedFieldsParameter.getName()));
+        
+        exportBASE(bioassayset, file, null, reporterFields, spotFields);
+      }
+      else
+      {
+        throw new BaseException("Unknown format. "+format);
+      }
+      
       dc.commit();
       response.setDone("Bioassay set '" + bioassayset.getName() +