Changeset 3107

Timestamp:

Feb 6, 2007, 3:26:22 PM (16 years ago)

Author:

Johan Enell

Message:

Fixes #439

File:

• trunk/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java (modified) (18 diffs)

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

@@ -26 +26 @@
 
 import net.sf.basedb.core.AnnotationType;
-import net.sf.basedb.core.AnyToAny;
 import net.sf.basedb.core.BaseException;
 import net.sf.basedb.core.BioAssay;
@@ -65 +64 @@
 import net.sf.basedb.core.plugin.Request;
 import net.sf.basedb.core.plugin.Response;
-import net.sf.basedb.core.query.Aggregations;
 import net.sf.basedb.core.query.Dynamic;
-import net.sf.basedb.core.query.Expression;
-import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.Hql;
 import net.sf.basedb.core.query.JoinType;
@@ -113 +109 @@
 {
 
-  public BioAssaySetExporter()
-  {
-  }
-
-
   public void configure(GuiContext context, Request request, Response response)
   {
@@ -194 +185 @@
 
   
-  void exportBaseFileMatrix(BioAssaySet bas, File file, Map<String, String> parameters, 
+  public void exportBaseFileMatrix(BioAssaySet bas, File file, Map<String, String> parameters, 
     List<String> reporterFields, List<String> spotFields, Boolean mergeReporters)
     throws IOException, SQLException
@@ -200 +191 @@
     DbControl dc = bas.getDbControl();
     PrintWriter out = new PrintWriter(file.getUploadStream(false));
-    Map<String, QueryItem> qis = getBaseFileQIMap(dc, bas);
-
-    exportBaseFileSectionHead(out, parameters);
-    exportBaseFileSectionAssays(out, dc, bas);
-
-    DynamicSpotQuery query = bas.getSpotData();
-    for (String field : reporterFields)
-    {
-      QueryItem qi = qis.get(field);
-      query.select(Selects.expression(BioAssaySetUtil.createJepExpression(dc, bas, qi.getJep(), true), field));
-    }
-    for (String field : spotFields)
-    {
-      QueryItem qi = qis.get(field);
-      query.select(Selects.expression(BioAssaySetUtil.createJepExpression(dc, bas, qi.getJep(), true), field));
-    }
-    if (mergeReporters)
-    {
-      // not implemented
-    }   
-    exportBaseFileSectionSpots(out, dc, bas, query, reporterFields, spotFields, bas.getBioAssays().list(dc));
-  }
-  
-  
-  private void exportBaseFileSectionHead(PrintWriter out, Map<String, String> parameters)
-  {
-    out.println("BASEfile");
-    if (!parameters.isEmpty())
-    {
-      for (String key : parameters.keySet())
-      {
-        out.println(key+"\t"+parameters.get(key));
-      }
-      out.println("%");
-      out.println();
+    try
+    {
+      Map<String, QueryItem> qis = getBaseFileQIMap(dc, bas);
+  
+      exportBaseFileSectionHead(out, parameters);
+      exportBaseFileSectionAssays(out, dc, bas);
+  
+      DynamicSpotQuery query = bas.getSpotData();
+      for (String field : reporterFields)
+      {
+        QueryItem qi = qis.get(field);
+        if (qi == null)
+        {
+          throw new BaseException("Unknown field in reporter fields: "+field);
+        }
+        query.select(Selects.expression(BioAssaySetUtil.createJepExpression(dc, bas, qi.getJep(), true), field));
+      }
+      for (String field : spotFields)
+      {
+        QueryItem qi = qis.get(field);
+        if (qi == null)
+        {
+          throw new BaseException("Unknown field in spot fields: "+field);
+        }
+        query.select(Selects.expression(BioAssaySetUtil.createJepExpression(dc, bas, qi.getJep(), true), field));
+      }
+      if (mergeReporters)
+      {
+        throw new BaseException("'Merge on reporter' not implemented");
+      }   
+      exportBaseFileSectionSpots(out, dc, bas, query, reporterFields, spotFields, bas.getBioAssays().list(dc));
+    }
+    finally
+    {
+      if (out != null) out.close();
     }
   }
@@ -264 +255 @@
     out.println();
   }
-
-  
+  
+  
+  private void exportBaseFileSectionHead(PrintWriter out, Map<String, String> parameters)
+  {
+    out.println("BASEfile");
+    if (!parameters.isEmpty())
+    {
+      for (String key : parameters.keySet())
+      {
+        out.println(key+"\t"+parameters.get(key));
+      }
+      out.println("%");
+      out.println();
+    }
+  }
+  
+  
+  public void exportBaseFileSerial(BioAssaySet bas, File file, Map<String, String> parameters, 
+    List<String> reporterFields, List<String> spotFields, Boolean mergeReporters)
+    throws IOException, SQLException
+  {
+    DbControl dc = bas.getDbControl();
+    PrintWriter out = new PrintWriter(file.getUploadStream(false));
+    try
+    {
+      Map<String, QueryItem> qis = getBaseFileQIMap(dc, bas);
+  
+      exportBaseFileSectionHead(out, parameters);
+      exportBaseFileSectionAssays(out, dc, bas);
+      
+      for (BioAssay ba : bas.getBioAssays().list(dc))
+      {
+        DynamicSpotQuery query = ba.getSpotData();
+        for (String field : reporterFields)
+        {
+          QueryItem qi = qis.get(field);
+          query.select(Selects.expression(BioAssaySetUtil.createJepExpression(dc, bas, qi.getJep(), true), field));
+        }
+        for (String field : spotFields)
+        {
+          QueryItem qi = qis.get(field);
+          query.select(Selects.expression(BioAssaySetUtil.createJepExpression(dc, bas, qi.getJep(), true), field));
+        }
+        if (mergeReporters)
+        {
+          throw new BaseException("'Merge on reporter' not implemented");
+        }
+  
+        exportBaseFileSectionSpots(out, dc, bas, query, reporterFields, spotFields, Collections.singletonList(ba));
+        
+        out.println();
+      }
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+      if (out != null) out.close();
+    }
+  }
+
+
   private void exportBaseFileSectionSpots(PrintWriter out, DbControl dc, BioAssaySet bas, DynamicSpotQuery query,
     List<String> reporterFields, List<String> spotFields, List<BioAssay> assays)
@@ -287 +337 @@
     }
     out.println("\tassayData");
-    out.print("assays\t");
+    out.print("assays");
     for (BioAssay ba : assays)
     {
-      out.print(ba.getId());
+      out.print("\t" + ba.getId());
     }
     out.println();
@@ -378 +428 @@
   
   
-  void exportBaseFileSerial(BioAssaySet bioAssaySet, File file, Map<String, String> parameters, 
-    List<String> reporterFields, List<String> spotFields, Boolean mergeReporters)
-    throws IOException, SQLException
-  {
-    DbControl dc = sc.newDbControl();
-    BioAssaySet bas = BioAssaySet.getById(dc, bioAssaySet.getId());
-    PrintWriter out = new PrintWriter(file.getUploadStream(false));
-    Map<String, QueryItem> qis = getBaseFileQIMap(dc, bas);
-
-    exportBaseFileSectionHead(out, parameters);
-    exportBaseFileSectionAssays(out, dc, bas);
-    
-    for (BioAssay ba : bas.getBioAssays().list(dc))
-    {
-      DynamicSpotQuery query = ba.getSpotData();
-      for (String field : reporterFields)
-      {
-        QueryItem qi = qis.get(field);
-        query.select(Selects.expression(BioAssaySetUtil.createJepExpression(dc, bas, qi.getJep(), true), field));
-      }
-      for (String field : spotFields)
-      {
-        QueryItem qi = qis.get(field);
-        query.select(Selects.expression(BioAssaySetUtil.createJepExpression(dc, bas, qi.getJep(), true), field));
-      }
-      if (mergeReporters)
-      {
-        // not implemented
-      }
-
-      exportBaseFileSectionSpots(out, dc, bas, query, reporterFields, spotFields, Collections.singletonList(ba));
-      
-      out.println();
-    }
-  }
-
-
   public void exportMeV(BioAssaySet bioassayset, OutputStream to,
                          ProgressReporter progress)
@@ -572 +585 @@
 
 
+  public About getAbout()
+  {
+    return about;
+  }
+  
+  
+  private List<QueryItem> getBaseFileExtraQI(DbControl dc, BioAssaySet bas)
+  {
+    List<QueryItem> items = new ArrayList<QueryItem>();
+    ItemQuery<ExtraValue> query = bas.getExtraValues();
+    query.order(Orders.asc(Hql.property("extraValueType.name")));
+    for (ExtraValue ev : query.list(dc))
+    {
+      ExtraValueType evt = ev.getExtraValueType();
+      items.add(new QueryItem("_xc_"+evt.getExternalId(), "[Extra] "+evt.getName(), "xtra('" + evt.getExternalId() + "')"));
+    }
+    Collections.sort(items, new QueryItemTitleComparator());
+    return items;
+  }
+  
+  
+  private List<QueryItem> getBaseFileFormulaQI(DbControl dc, BioAssaySet bas)
+  {
+    List<QueryItem> items = new ArrayList<QueryItem>();
+    ItemQuery<Formula> queryFormula = Formula.getQuery(Formula.Type.COLUMN_EXPRESSION, bas.getRawDataType());
+    queryFormula.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);
+    queryFormula.order(Orders.asc(Hql.property("name")));
+    for (Formula f : queryFormula.list(dc))
+    {
+      items.add(new QueryItem(f.getName(), "[Formula] "+f.getName(), f.getFormula(0)));
+    }
+    Collections.sort(items, new QueryItemTitleComparator());
+    return items;
+  }
+  
+  
+  private Map<String, QueryItem> getBaseFileQIMap(DbControl dc, BioAssaySet bas)
+  {
+    Map<String, QueryItem> items = new HashMap<String, QueryItem>();
+    for (QueryItem qi : getBaseFileExtraQI(dc, bas)) items.put(qi.getName(), qi);
+    for (QueryItem qi : getBaseFileFormulaQI(dc, bas)) items.put(qi.getName(), qi);
+    for (QueryItem qi : getBaseFileRawQI(bas)) items.put(qi.getName(), qi);
+    for (QueryItem qi : getBaseFileReporterQI()) items.put(qi.getName(), qi);
+    for (QueryItem qi : getBaseFileSpotQI(bas)) items.put(qi.getName(), qi);
+    return items;
+  }
+  
+  
+  private List<QueryItem> getBaseFileRawQI(BioAssaySet bas)
+  {
+    List<QueryItem> items = new ArrayList<QueryItem>();
+    items.add(new QueryItem("rawPosition", "[Raw] Position", "raw('position')"));
+    items.add(new QueryItem("block", "[Raw] Array block", "raw('block')"));
+    items.add(new QueryItem("metaGridX", "[Raw] Meta grid X", "raw('metaGridX')"));
+    items.add(new QueryItem("metaGridY", "[Raw] Meta grid Y", "raw('metaGridY')"));
+    items.add(new QueryItem("numRow", "[Raw] Row in block", "raw('row')"));
+    items.add(new QueryItem("numCol", "[Raw] Column in block", "raw('column')"));
+    items.add(new QueryItem("x", "[Raw] X coordinate", "raw('x')"));
+    items.add(new QueryItem("y", "[Raw] Y coordinate", "raw('y')"));
+    for (RawDataProperty rdp : bas.getRawDataType().getProperties())
+    {
+      items.add(new QueryItem(rdp.getName(), "[Raw] "+rdp.getTitle(), "raw('"+rdp.getName()+"')"));
+    }
+    Collections.sort(items, new QueryItemTitleComparator());
+    return items;
+  }
+  
+  
+  private List<QueryItem> getBaseFileReporterQI()
+  {
+    List<QueryItem> items = new ArrayList<QueryItem>();
+    items.add(new QueryItem("reporter", "Reporter (internal id)", "rep('id')"));
+    items.add(new QueryItem("reporterName", "Reporter Name", "rep('name')"));
+    items.add(new QueryItem("reporterId", "Reporter ID", "rep('externalId')"));
+    items.add(new QueryItem("geneSymbol", "Gene symbol", "rep('symbol')"));
+    items.add(new QueryItem("description", "Description", "rep('description')"));
+    items.add(new QueryItem("lastUpdate", "Last updated", "rep('lastUpdate')"));
+    for (ExtendedProperty ep : ExtendedProperties.getProperties(ReporterData.class.toString()))
+    {
+      items.add(new QueryItem(ep.getName(), ep.getTitle(), "rep('"+ep.getName()+"')"));
+    }
+    Collections.sort(items, new QueryItemTitleComparator());
+    return items;
+  } 
+  
+  
+  private List<QueryItem> getBaseFileSpotQI(BioAssaySet bas)
+  {
+    List<QueryItem> items = new ArrayList<QueryItem>();
+    items.add(new QueryItem("position", "Position", "pos()"));
+    int channels = bas.getRawDataType().getChannels(); 
+    for (int channel = 1; channel <= channels; ++channel)
+    {
+      items.add(new QueryItem("intensity"+channel, "Int ch"+channel, "ch("+channel+")"));
+    }
+    Collections.sort(items, new QueryItemTitleComparator());
+    return items;
+  }
+
+  
+  private RequestInformation getConfigureBasefileParameters(GuiContext context)
+  {
+    if (configureJobBasefile == null)
+    {
+      DbControl dc = null;
+      try
+      {
+        dc = sc.newDbControl();
+        List<PluginParameter<?>> parameters = new ArrayList<PluginParameter<?>>();
+        geneAveragesParameter = new PluginParameter<Boolean>
+          ( "geneAverages",
+            "Average on reporters",
+            "Average on reporters within each assay.",
+            new BooleanParameterType(false, true));
+        
+        Enumeration<Boolean, String> serialFormat = new Enumeration<Boolean, String>();
+        serialFormat.add(false, "Normal BASEfile (one big matrix)");
+        serialFormat.add(true, "Serial BASEfile (one section per assay)");
+        serialFormatParameter = new PluginParameter<Boolean>
+          ( "serialFormat",
+            "Export as matrix or serial basefile.",
+            "The data can be exported as a matrix with all data in the same section or in a " +
+            "serial format where the data is separated for each assay.",
+            new BooleanParameterType(false, true, 1, serialFormat));
+        
+        Enumeration<String, String> fields = new Enumeration<String, String>();
+        BioAssaySet bas = (BioAssaySet) job.getValue(bioAssaySetParameter.getName());
+        for (QueryItem qi : getBaseFileSpotQI(bas))
+        {
+          fields.add(qi.getName(), qi.getTitle());
+        }
+        for (QueryItem qi : getBaseFileFormulaQI(dc, bas))
+        {
+          fields.add(qi.getName(), qi.getTitle());
+        }
+        for (QueryItem qi : getBaseFileExtraQI(dc, bas))
+        {
+          fields.add(qi.getName(), qi.getTitle());
+        }
+        for (QueryItem qi : getBaseFileRawQI(bas))
+        {
+          fields.add(qi.getName(), qi.getTitle());
+        }
+        //Limsfields???
+        usedFieldsParameter = new PluginParameter<String>(
+          "usedFields",
+          "Fields",
+          "The spot information that is exporter. The position is allways exported when avarage on reporter is false.",
+          new StringParameterType(null, null, true, 0, 0, 0, fields));
+
+        Enumeration<String, String> columns = new Enumeration<String, String>();
+        for (QueryItem qi : getBaseFileReporterQI())
+        {
+          columns.add(qi.getName(), qi.getTitle());
+        }
+        usedColumnsParameter = new PluginParameter<String>(
+          "usedColumns",
+          "Reporter",
+          "The reporter information that is exported. An internal reporter id is allways exported.",
+          new StringParameterType(null, null, false, 0, 0, 0, columns));
+        
+        parameters.add(geneAveragesParameter);
+        parameters.add(serialFormatParameter);
+        parameters.add(usedFieldsParameter);
+        parameters.add(usedColumnsParameter);
+  
+        configureJobBasefile = new RequestInformation
+          ( COMMAND_CONFIGURE_BASEFILE,
+            "Configure BASEfile export.",
+            "Here you configure the parameter for the BASEfile format.",
+            parameters );
+      }
+      finally
+      {
+        if (dc != null)
+        {
+          dc.close();
+        }
+      }
+    }
+    return configureJobBasefile;
+  }
+
+
+  
   private RequestInformation getConfigureJobParameters(GuiContext context)
   {
@@ -620 +818 @@
   
   
-  private RequestInformation getConfigureBasefileParameters(GuiContext context)
-  {
-    if (configureJobBasefile == null)
-    {
-      DbControl dc = null;
-      try
-      {
-        dc = sc.newDbControl();
-        List<PluginParameter<?>> parameters = new ArrayList<PluginParameter<?>>();
-        geneAveragesParameter = new PluginParameter<Boolean>
-          ( "geneAverages",
-            "Average on reporters",
-            "Average on reporters within each assay.",
-            new BooleanParameterType(false, true));
-        
-        Enumeration<Boolean, String> serialFormat = new Enumeration<Boolean, String>();
-        serialFormat.add(false, "Normal BASEfile (one big matrix)");
-        serialFormat.add(true, "Serial BASEfile (one section per assay)");
-        serialFormatParameter = new PluginParameter<Boolean>
-          ( "serialFormat",
-            "Export as matrix or serial basefile.",
-            "The data can be exported as a matrix with all data in the same section or in a " +
-            "serial format where the data is separated for each assay.",
-            new BooleanParameterType(false, true, 1, serialFormat));
-        
-        Enumeration<String, String> fields = new Enumeration<String, String>();
-        BioAssaySet bas = (BioAssaySet) job.getValue(bioAssaySetParameter.getName());
-        for (QueryItem qi : getBaseFileSpotQI(bas))
-        {
-          fields.add(qi.getName(), qi.getTitle());
-        }
-        for (QueryItem qi : getBaseFileFormulaQI(dc, bas))
-        {
-          fields.add(qi.getName(), qi.getTitle());
-        }
-        for (QueryItem qi : getBaseFileExtraQI(dc, bas))
-        {
-          fields.add(qi.getName(), qi.getTitle());
-        }
-        for (QueryItem qi : getBaseFileRawQI(bas))
-        {
-          fields.add(qi.getName(), qi.getTitle());
-        }
-        //Limsfields???
-        usedFieldsParameter = new PluginParameter<String>(
-          "usedFields",
-          "Fields",
-          "The spot information that is exporter. The position is allways exported when avarage on reporter is false.",
-          new StringParameterType(null, null, true, 0, 0, 0, fields));
-
-        Enumeration<String, String> columns = new Enumeration<String, String>();
-        for (QueryItem qi : getBaseFileReporterQI())
-        {
-          columns.add(qi.getName(), qi.getTitle());
-        }
-        usedColumnsParameter = new PluginParameter<String>(
-          "usedColumns",
-          "Reporter",
-          "The reporter information that is exported. An internal reporter id is allways exported.",
-          new StringParameterType(null, null, false, 0, 0, 0, columns));
-        
-        parameters.add(geneAveragesParameter);
-        parameters.add(serialFormatParameter);
-        parameters.add(usedFieldsParameter);
-        parameters.add(usedColumnsParameter);
-  
-        configureJobBasefile = new RequestInformation
-          ( COMMAND_CONFIGURE_BASEFILE,
-            "Configure BASEfile export.",
-            "Here you configure the parameter for the BASEfile format.",
-            parameters );
-      }
-      finally
-      {
-        if (dc != null)
-        {
-          dc.close();
-        }
-      }
-    }
-    return configureJobBasefile;
-  }
-
-
-  public About getAbout()
-  {
-    return about;
-  }
-  
-  
-  private List<QueryItem> getBaseFileExtraQI(DbControl dc, BioAssaySet bas)
-  {
-    List<QueryItem> items = new ArrayList<QueryItem>();
-    ItemQuery<ExtraValue> query = bas.getExtraValues();
-    query.order(Orders.asc(Hql.property("extraValueType.name")));
-    for (ExtraValue ev : query.list(dc))
-    {
-      ExtraValueType evt = ev.getExtraValueType();
-      items.add(new QueryItem("_xc_"+evt.getExternalId(), "[Extra] "+evt.getName(), "xtra('" + evt.getExternalId() + "')"));
-    }
-    Collections.sort(items, new QueryItemTitleComparator());
-    return items;
-  }
-  
-  
-  private List<QueryItem> getBaseFileFormulaQI(DbControl dc, BioAssaySet bas)
-  {
-    List<QueryItem> items = new ArrayList<QueryItem>();
-    ItemQuery<Formula> queryFormula = Formula.getQuery(Formula.Type.COLUMN_EXPRESSION, bas.getRawDataType());
-    queryFormula.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);
-    queryFormula.order(Orders.asc(Hql.property("name")));
-    for (Formula f : queryFormula.list(dc))
-    {
-      items.add(new QueryItem(f.getName(), "[Formula] "+f.getName(), f.getFormula(0)));
-    }
-    Collections.sort(items, new QueryItemTitleComparator());
-    return items;
-  }
-  
-  
-  private List<QueryItem> getBaseFileSpotQI(BioAssaySet bas)
-  {
-    List<QueryItem> items = new ArrayList<QueryItem>();
-    items.add(new QueryItem("position", "Position", "pos()"));
-    int channels = bas.getRawDataType().getChannels(); 
-    for (int channel = 1; channel <= channels; ++channel)
-    {
-      items.add(new QueryItem("intensity"+channel, "Int ch"+channel, "ch("+channel+")"));
-    }
-    Collections.sort(items, new QueryItemTitleComparator());
-    return items;
-  }
-  
-  
-  private Map<String, QueryItem> getBaseFileQIMap(DbControl dc, BioAssaySet bas)
-  {
-    Map<String, QueryItem> items = new HashMap<String, QueryItem>();
-    for (QueryItem qi : getBaseFileExtraQI(dc, bas)) items.put(qi.getName(), qi);
-    for (QueryItem qi : getBaseFileFormulaQI(dc, bas)) items.put(qi.getName(), qi);
-    for (QueryItem qi : getBaseFileRawQI(bas)) items.put(qi.getName(), qi);
-    for (QueryItem qi : getBaseFileReporterQI()) items.put(qi.getName(), qi);
-    for (QueryItem qi : getBaseFileSpotQI(bas)) items.put(qi.getName(), qi);
-    return items;
-  }
-  
-  private List<QueryItem> getBaseFileRawQI(BioAssaySet bas)
-  {
-    List<QueryItem> items = new ArrayList<QueryItem>();
-    items.add(new QueryItem("rawPosition", "[Raw] Position", "raw('position')"));
-    items.add(new QueryItem("block", "[Raw] Array block", "raw('block')"));
-    items.add(new QueryItem("metaGridX", "[Raw] Meta grid X", "raw('metaGridX')"));
-    items.add(new QueryItem("metaGridY", "[Raw] Meta grid Y", "raw('metaGridY')"));
-    items.add(new QueryItem("numRow", "[Raw] Row in block", "raw('row')"));
-    items.add(new QueryItem("numCol", "[Raw] Column in block", "raw('column')"));
-    items.add(new QueryItem("x", "[Raw] X coordinate", "raw('x')"));
-    items.add(new QueryItem("y", "[Raw] Y coordinate", "raw('y')"));
-    for (RawDataProperty rdp : bas.getRawDataType().getProperties())
-    {
-      items.add(new QueryItem(rdp.getName(), "[Raw] "+rdp.getTitle(), "raw('"+rdp.getName()+"')"));
-    }
-    Collections.sort(items, new QueryItemTitleComparator());
-    return items;
-  }
-  
-  
-  private List<QueryItem> getBaseFileReporterQI()
-  {
-    List<QueryItem> items = new ArrayList<QueryItem>();
-    items.add(new QueryItem("reporter", "Reporter (internal id)", "rep('id')"));
-    items.add(new QueryItem("reporterName", "Reporter Name", "rep('name')"));
-    items.add(new QueryItem("reporterId", "Reporter ID", "rep('externalId')"));
-    items.add(new QueryItem("geneSymbol", "Gene symbol", "rep('symbol')"));
-    items.add(new QueryItem("description", "Description", "rep('description')"));
-    items.add(new QueryItem("lastUpdate", "Last updated", "rep('lastUpdate')"));
-    for (ExtendedProperty ep : ExtendedProperties.getProperties(ReporterData.class.toString()))
-    {
-      items.add(new QueryItem(ep.getName(), ep.getTitle(), "rep('"+ep.getName()+"')"));
-    }
-    Collections.sort(items, new QueryItemTitleComparator());
-    return items;
-  }
-  
-
   public List<AnnotationType> getExperimentalFactors(DbControl dc, BioAssaySet bas)
   {
@@ -810 +825 @@
     return query.list(dc);
   }
-  
-
+
+  
   public Set<GuiContext> getGuiContexts()
   {
@@ -843 +858 @@
   }
 
-
+  
   public RequestInformation getRequestInformation(GuiContext context, String command)
     throws BaseException
@@ -859 +874 @@
   }
 
-
+  
   public String isInContext(GuiContext context, Object item)
   {
@@ -874 +889 @@
   }
 
-
+  
   @Override
   public boolean requiresConfiguration()
@@ -881 +896 @@
   }
 
-
+  
   @SuppressWarnings("unchecked")
   public void run(Request request, Response response, ProgressReporter progress)
@@ -948 +963 @@
   }
 
-
+  
   @Override
   public boolean supportsConfigurations()
@@ -955 +970 @@
   }
 
-
+  
   private static final About about =
     new AboutImpl
@@ -994 +1009 @@
   private static final String FORMAT_MEV = "MeV";
   
-  
 
   public class QueryItem