Changeset 3587

Timestamp:

Jul 20, 2007, 3:45:13 PM (16 years ago)

Author:

Martin Svensson

Message:

References #686 Two more coreplugins are updated
AbstractAnalysisPlugin? got a method to set restriction on using selected bioassays

Location:

trunk/src

Files:

• core/net/sf/basedb/core/plugin/AbstractAnalysisPlugin.java (modified) (3 diffs)
• plugins/core/net/sf/basedb/plugins/JepExtraValueCalculator.java (modified) (3 diffs)
• plugins/core/net/sf/basedb/plugins/JepIntensityTransformer.java (modified) (8 diffs)

trunk/src/core/net/sf/basedb/core/plugin/AbstractAnalysisPlugin.java

@@ -31 +31 @@
 import net.sf.basedb.core.BioAssaySet;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.DynamicSpotQuery;
 import net.sf.basedb.core.Experiment;
 import net.sf.basedb.core.Item;
@@ -40 +41 @@
 import net.sf.basedb.core.StringParameterType;
 import net.sf.basedb.core.Transformation;
+import net.sf.basedb.core.VirtualColumn;
+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.Restrictions;
 
 /**
@@ -414 +420 @@
   }
 
-  
+  /**
+    Restricts a query to only include values from listed bioassays
+      @param query The query to set restriction on
+      @param bioAssays A list with bioassays the restriction should include
+      @return A DynamicSpotQuery object. The query parameter is restricted if bioAssays holds item(s), 
+        otherwise it will it will be the same 
+      @since 2.4
+  */
+  protected DynamicSpotQuery restrictSource(DynamicSpotQuery query, List<BioAssay> bioAssays)
+  {
+    if ( (bioAssays != null) && !bioAssays.isEmpty() )
+    {
+      Expression[] selectedColumns = new Expression[bioAssays.size()];
+      for (int i=0; i<selectedColumns.length; i++)
+      {
+        BioAssay ba = bioAssays.get(i);
+        selectedColumns[i] = Expressions.integer(ba.getDataCubeColumnNo());
+      }       
+      query.restrict(Restrictions.in(
+          Dynamic.column(VirtualColumn.COLUMN), 
+          selectedColumns));
+    }
+    return query;
+  }
 }

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

@@ -23 +23 @@
 */
 package net.sf.basedb.plugins;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.EnumSet;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
 
 import net.sf.basedb.core.BaseException;
@@ -60 +51 @@
 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.Orders;
-import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.core.query.Selects;
 import net.sf.basedb.util.BioAssaySetUtil;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.EnumSet;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
 
 /**
@@ -169 +167 @@
       Expression extraExpression = BioAssaySetUtil.createJepExpression(dc, source, expression, false);
       query.select(Selects.expression(extraExpression, "xtra"));
-      // If one or more bioassays are selected-restrict to them.
-      if (bioAssays != null && !bioAssays.isEmpty())
-      {
-        Expression[] selectedColumns = new Expression[bioAssays.size()];
-        for (int i=0; i<selectedColumns.length; i++)
-        {
-          BioAssay ba = bioAssays.get(i);
-          selectedColumns[i] = Expressions.integer(ba.getDataCubeColumnNo());
-        }       
-        query.restrict(Restrictions.in(
-            Dynamic.column(VirtualColumn.COLUMN), 
-            selectedColumns));
-      }
+      // Restrict to selected bioassays if there are any
+      query = restrictSource(query, bioAssays);
 
       if (progress != null) progress.display(10, "Calculating extra value ("+source.getNumSpots()+" total)...");

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

@@ -27 +27 @@
 import java.util.Arrays;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.EnumSet;
 import java.util.HashSet;
@@ -33 +34 @@
 
 import net.sf.basedb.core.BaseException;
+import net.sf.basedb.core.BioAssay;
 import net.sf.basedb.core.BioAssaySet;
 import net.sf.basedb.core.DbControl;
@@ -92 +94 @@
 
   private static final Set<Permissions> permissions = new HashSet<Permissions>();
+  private static final Set<GuiContext> guiContexts = Collections.unmodifiableSet(
+      new HashSet<GuiContext>(Arrays.asList(CONTEXT_BIOASSAYSET, CONTEXT_BIOASSAYS)));
 
   private RequestInformation configureJob;
@@ -139 +143 @@
       // Get all parameters
       BioAssaySet source = getSourceBioAssaySet(dc);
+      List<BioAssay> bioAssays = getSourceBioAssays(dc);
       String childName = Values.getString((String)job.getValue(CHILD_NAME), source.getName());
       String childDescription = (String)job.getValue(CHILD_DESCRIPTION);
@@ -163 +168 @@
       query.select(Dynamic.select(VirtualColumn.COLUMN));
       query.select(Dynamic.select(VirtualColumn.POSITION));
+      
+      // Restrict to selected bioassays
+      restrictSource(query, bioAssays);
 
       // Transformation expressions
@@ -208 +216 @@
     -------------------------------------------
   */
+  @Override
+  public Set<GuiContext> getGuiContexts()
+  {
+    return guiContexts;
+  }
+  
   public RequestInformation getRequestInformation(GuiContext context, String command) 
     throws BaseException
@@ -235 +249 @@
         // Source bioassay set
         storeValue(job, request, ri.getParameter(SOURCE_BIOASSAYSET));
+        
+        // Selected bioassays
+        storeValue(job, request, ri.getParameter(SOURCE_BIOASSAYS));
         
         // Child name, description and transformation
@@ -275 +292 @@
         // Source and child bioassay set parameters
         parameters.add(getSourceBioAssaySetParameter(null, null));
+        parameters.add(getSourceBioAssaysParameter(null, null));
         parameters.add(getChildNameParameter(null, null, bas.getName()));
         parameters.add(getChildDescriptionParameter(null, null, null));