SE-137 AggregateFunction: moved to shared.basic.dto, more functions added

SVN: 12523

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowerToolBar.java

@@ -46,8 +46,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceColumnDefinition;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
 
 /**
  * @author Franz-Josef Elmer

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java

@@ -42,9 +42,9 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKin
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.columns.InternalAbundanceColumnDefinition;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.columns.ProteinColDefKind;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceColumnDefinition;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.Treatment;
 

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListProteinByExperimentCriteria.java

@@ -20,6 +20,7 @@ import com.google.gwt.user.client.rpc.IsSerializable;
 
 import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
 import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
 
 /**

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinOriginalDataProvider.java

@@ -21,8 +21,8 @@ import java.util.List;
 import ch.systemsx.cisd.common.exceptions.UserFailureException;
 import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.IOriginalDataProvider;
 import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
 
 /**

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java

@@ -32,7 +32,6 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
 import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientService;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentAndReferenceCriteria;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinSequenceCriteria;
@@ -40,6 +39,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListSam
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ResourceNames;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceColumnDefinition;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.DataSetProtein;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java

@@ -38,7 +38,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
 import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
 import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyPE;
 import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTranslator;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.AccessionNumberBuilder;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IAbundanceColumnDefinitionTable;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IBusinessObjectFactory;
@@ -52,6 +51,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQue
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ResourceNames;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceColumnDefinition;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.DataSetProtein;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerLogger.java

@@ -24,9 +24,9 @@ import ch.systemsx.cisd.openbis.generic.server.AbstractServerLogger;
 import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
 import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceColumnDefinition;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.DataSetProtein;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IProteinInfoTable.java

@@ -19,8 +19,8 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business;
 import java.util.List;
 
 import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceColumnDefinition;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
 
 /**

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinInfoTable.java

@@ -28,10 +28,10 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
 import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
 import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
 import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IPhosphoNetXDAOFactory;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQueryDAO;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceColumnDefinition;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinWithAbundances;

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IPhosphoNetXServer.java

@@ -28,8 +28,8 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAll
 import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
 import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceColumnDefinition;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.DataSetProtein;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/AggregateFunction.java → rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AggregateFunction.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto;
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
 
 import java.util.Arrays;
 
@@ -28,6 +28,24 @@ import com.google.gwt.user.client.rpc.IsSerializable;
 public enum AggregateFunction implements IsSerializable
 {
     MEAN("mean")
+    {
+        @Override
+        public double aggregate(double[] values)
+        {
+            return SUM.aggregate(values) / values.length;
+        }
+    },
+    MEDIAN("median")
+    {
+        @Override
+        public double aggregate(double[] values)
+        {
+            Arrays.sort(values);
+            int i = values.length / 2;
+            return values.length % 2 == 0 ? (values[i - 1] + values[i]) / 2 : values[i];
+        }
+    },
+    SUM("sum")
     {
         @Override
         public double aggregate(double[] values)
@@ -37,17 +55,33 @@ public enum AggregateFunction implements IsSerializable
             {
                 sum += value;
             }
-            return sum / values.length;
+            return sum;
         }
     },
-    MEDIAN("median")
+    MIN("minimum")
     {
         @Override
         public double aggregate(double[] values)
         {
-            Arrays.sort(values);
-            int i = values.length / 2;
-            return values.length % 2 == 0 ? (values[i - 1] + values[i]) / 2 : values[i];
+            double min = Double.MAX_VALUE;
+            for (double value : values)
+            {
+                min = Math.min(min, value);
+            }
+            return min;
+        }
+    },
+    MAX("maximum")
+    {
+        @Override
+        public double aggregate(double[] values)
+        {
+            double max = -Double.MAX_VALUE;
+            for (double value : values)
+            {
+                max = Math.max(max, value);
+            }
+            return max;
         }
     },
     COUNT("count")

rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinInfoTableTest.java

@@ -29,11 +29,11 @@ import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
 import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
 import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
 import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.MockDataSet;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IPhosphoNetXDAOFactory;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQueryDAO;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceColumnDefinition;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProbabilityFDRMapping;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;

rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/AggregateFunctionTest.java → rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AggregateFunctionTest.java

@@ -14,11 +14,13 @@
  * limitations under the License.
  */
 
-package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto;
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
 
 import org.testng.AssertJUnit;
 import org.testng.annotations.Test;
 
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
+
 /**
  * 
  *
@@ -43,6 +45,27 @@ public class AggregateFunctionTest extends AssertJUnit
         assertEquals(46.5, AggregateFunction.MEDIAN.aggregate(new double[] {42, 43, 50, 59}));
     }
     
+    @Test
+    public void testSum()
+    {
+        assertEquals(42.0, AggregateFunction.SUM.aggregate(new double[] {42}));
+        assertEquals(85.0, AggregateFunction.SUM.aggregate(new double[] {42, 43}));
+    }
+    
+    @Test
+    public void testMin()
+    {
+        assertEquals(42.0, AggregateFunction.MIN.aggregate(new double[] {42}));
+        assertEquals(42.0, AggregateFunction.MIN.aggregate(new double[] {42, 43}));
+    }
+    
+    @Test
+    public void testMax()
+    {
+        assertEquals(42.0, AggregateFunction.MAX.aggregate(new double[] {42}));
+        assertEquals(43.0, AggregateFunction.MAX.aggregate(new double[] {42, 43}));
+    }
+    
     @Test
     public void testCount()
     {