SE-137 Abundance columns sorted: Improve comparison, sorting moved to TreatmentFinder

SVN: 12496

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

@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business;
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -53,7 +54,9 @@ public class TreatmentFinder
     {
         Map<String, Treatment> treatments = new LinkedHashMap<String, Treatment>();
         findAndAddTreatments(treatments, sample);
-        return new ArrayList<Treatment>(treatments.values());
+        List<Treatment> treatmentList = new ArrayList<Treatment>(treatments.values());
+        Collections.sort(treatmentList);
+        return treatmentList;
     }
     
     private void findAndAddTreatments(Map<String, Treatment> treatments, SamplePE sampleOrNull)

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AbundanceColumnDefinition.java

@@ -17,7 +17,6 @@
 package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
 
 import java.io.Serializable;
-import java.util.Collections;
 import java.util.List;
 
 import com.google.gwt.user.client.rpc.IsSerializable;
@@ -73,14 +72,7 @@ public class AbundanceColumnDefinition implements Serializable, IsSerializable,
     {
         if (this.treatments != null && that.treatments != null)
         {
-            int sizeDiff = this.treatments.size() - that.treatments.size();
-            if (sizeDiff != 0)
-            {
-                return sizeDiff;
-            }
-            Collections.sort(this.treatments);
-            Collections.sort(that.treatments);
-            for (int i = 0, n = treatments.size(); i < n; i++)
+            for (int i = 0, n = Math.min(this.treatments.size(), that.treatments.size()); i < n; i++)
             {
                 Treatment thisTreatment = this.treatments.get(i);
                 Treatment thatTreatment = that.treatments.get(i);
@@ -90,6 +82,11 @@ public class AbundanceColumnDefinition implements Serializable, IsSerializable,
                     return diff;
                 }
             }
+            int sizeDiff = this.treatments.size() - that.treatments.size();
+            if (sizeDiff != 0)
+            {
+                return sizeDiff;
+            }
         }
         if (this.sampleCode != null && that.sampleCode != null)
         {

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/Treatment.java

@@ -74,9 +74,10 @@ public class Treatment implements Serializable, IsSerializable, Comparable<Treat
 
     public int compareTo(Treatment that)
     {
-        if (this.type.compareTo(that.type) != 0)
+        int typeComparisonResult = this.type.toLowerCase().compareTo(that.type.toLowerCase());
+        if (typeComparisonResult != 0)
         {
-            return this.type.compareTo(that.type);
+            return typeComparisonResult;
         }
         double thisNumber = convert(this.value);
         double thatNumber = convert(that.value);

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

@@ -19,7 +19,6 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business;
 import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.TreatmentFinder.TREATMENT_TYPE_CODE;
 import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.TreatmentFinder.TREATMENT_VALUE_CODE;
 
-import java.util.HashMap;
 import java.util.List;
 
 import org.testng.AssertJUnit;
@@ -56,14 +55,9 @@ public class TreatmentFinderTest extends AssertJUnit
         List<Treatment> treatments = new TreatmentFinder().findTreatmentsOf(sample);
         
         assertEquals(3, treatments.size());
-        HashMap<String, Treatment> map = new HashMap<String, Treatment>();
-        for (Treatment treatment : treatments)
-        {
-            map.put(treatment.getType(), treatment);
-        }
-        assertTreatment("7", "pH", map.get("pH"));
-        assertTreatment("20", "PLASMA", map.get("PLASMA"));
-        assertTreatment("HIV", "VIRUS", EntityDataType.MATERIAL, map.get("VIRUS"));
+        assertTreatment("7", "pH", treatments.get(0));
+        assertTreatment("20", "PLASMA", treatments.get(1));
+        assertTreatment("HIV", "VIRUS", EntityDataType.MATERIAL, treatments.get(2));
     }
 
     @Test
@@ -82,8 +76,8 @@ public class TreatmentFinderTest extends AssertJUnit
         List<Treatment> treatments = new TreatmentFinder().findTreatmentsOf(sample);
         
         assertEquals(2, treatments.size());
-        assertTreatment("20", "PLASMA", treatments.get(0));
-        assertTreatment("7", "pH", treatments.get(1));
+        assertTreatment("7", "pH", treatments.get(0));
+        assertTreatment("20", "PLASMA", treatments.get(1));
     }
     
     @Test
@@ -135,10 +129,12 @@ public class TreatmentFinderTest extends AssertJUnit
     private void assertTreatment(String expectedValue, String expectedType,
             EntityDataType expectedDataType, Treatment treatment)
     {
-        assertEquals(expectedValue, treatment.getValue());
-        assertEquals(expectedDataType.toString(), treatment.getValueType());
-        assertEquals(expectedType, treatment.getType());
-        assertEquals(expectedValue + " " + expectedType, treatment.getLabel());
+        assertEquals("Actual treatment: " + treatment, expectedValue, treatment.getValue());
+        assertEquals("Actual treatment: " + treatment, expectedDataType.toString(), treatment
+                .getValueType());
+        assertEquals("Actual treatment: " + treatment, expectedType, treatment.getType());
+        assertEquals("Actual treatment: " + treatment, expectedValue + " " + expectedType,
+                treatment.getLabel());
     }
     
     private void addTreatment(SamplePE sample, String treatmentCodePostfix, String treatmentType,

rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AbundanceColumnDefinitionTest.java

@@ -77,7 +77,7 @@ public class AbundanceColumnDefinitionTest extends AssertJUnit
     @Test
     public void testCompareTwoDefinitonsWithOneNumericalTreatment()
     {
-        AbundanceColumnDefinition d1 = create("abc", treatment("pH", "7.5"));
+        AbundanceColumnDefinition d1 = create("abc", treatment("pH", "7.5"), treatment("T", "yes"));
         AbundanceColumnDefinition d2 = create("abc", treatment("pH", "9e-1"));
         
         assertEquals(true, d1.compareTo(d2) > 0);