SE-163 ProteinSummaryTableTest added

SVN: 13489

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

@@ -39,7 +39,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWi
  */
 class ProteinSummaryTable extends AbstractBusinessObject implements IProteinSummaryTable
 {
-    private static final double[] FDR_LEVELS = new double[] {0, 0.01, 0.025, 0.05, 0.1};
+    static final double[] FDR_LEVELS = new double[] {0, 0.01, 0.025, 0.05, 0.1};
     
     private static final class Counter
     {
@@ -92,7 +92,8 @@ class ProteinSummaryTable extends AbstractBusinessObject implements IProteinSumm
         String permID = experimentDAO.getByTechId(experimentID).getPermId();
         IProteinQueryDAO dao = getSpecificDAOFactory().getProteinQueryDAO();
         ErrorModel errorModel = new ErrorModel(getSpecificDAOFactory());
-        DataSet<ProteinReferenceWithProbabilityAndPeptide> resultSet = dao.listProteinsWithProbabilityAndPeptidesByExperiment(permID);
+        DataSet<ProteinReferenceWithProbabilityAndPeptide> resultSet =
+                dao.listProteinsWithProbabilityAndPeptidesByExperiment(permID);
         List<Counter> counters = new ArrayList<Counter>(FDR_LEVELS.length);
         for (double fdrLevel : FDR_LEVELS)
         {

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

+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business;
+
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.ProteinSummaryTable.FDR_LEVELS;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.jmock.Expectations;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+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.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.ProteinSummary;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProbabilityFDRMapping;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbabilityAndPeptide;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class ProteinSummaryTableTest extends AbstractServerTestCase
+{
+    private static final TechId EXPERIMENT_ID = new TechId(234L);
+
+    private static final String EXPERIMENT_PERM_ID = "abc-234";
+
+    private static final long DATA_SET_ID = 42L;
+
+    private IPhosphoNetXDAOFactory specificDAOFactory;
+
+    private IProteinQueryDAO proteinDAO;
+
+    private ProteinSummaryTable table;
+
+    @Override
+    @BeforeMethod
+    public void setUp()
+    {
+        super.setUp();
+        specificDAOFactory = context.mock(IPhosphoNetXDAOFactory.class);
+        proteinDAO = context.mock(IProteinQueryDAO.class);
+        context.checking(new Expectations()
+            {
+                {
+                    allowing(specificDAOFactory).getProteinQueryDAO();
+                    will(returnValue(proteinDAO));
+                }
+            });
+        table = new ProteinSummaryTable(daoFactory, specificDAOFactory, SESSION);
+    }
+
+    @Test
+    public void testLoadEmptyData()
+    {
+        prepare();
+
+        table.load(EXPERIMENT_ID);
+
+        List<ProteinSummary> summaries = table.getProteinSummaries();
+        for (ProteinSummary proteinSummary : summaries)
+        {
+            assertEquals(0, proteinSummary.getProteinCount());
+            assertEquals(0, proteinSummary.getPeptideCount());
+        }
+        assertEquals(FDR_LEVELS.length, summaries.size());
+        context.assertIsSatisfied();
+    }
+
+    @Test
+    public void testLoadData()
+    {
+        ProteinReferenceWithProbabilityAndPeptide i1 = createItem(0.5, 123, "ABCD");
+        ProteinReferenceWithProbabilityAndPeptide i2 = createItem(0.5, 123, "DEF");
+        ProteinReferenceWithProbabilityAndPeptide i3 = createItem(0.75, 123, "DEF");
+        ProteinReferenceWithProbabilityAndPeptide i4 = createItem(0.75, 456, "ABC");
+        ProteinReferenceWithProbabilityAndPeptide i5 = createItem(1, 456, "DEF");
+        ProteinReferenceWithProbabilityAndPeptide i6 = createItem(1, 456, "XYZ");
+        prepare(i1, i2, i3, i4, i5, i6);
+        context.checking(new Expectations()
+            {
+                {
+                    allowing(proteinDAO).getProbabilityFDRMapping(DATA_SET_ID);
+                    MockDataSet<ProbabilityFDRMapping> dataSet =
+                            new MockDataSet<ProbabilityFDRMapping>();
+                    dataSet.add(createMappingItem(0.5, FDR_LEVELS[3]));
+                    dataSet.add(createMappingItem(0.75, FDR_LEVELS[2]));
+                    dataSet.add(createMappingItem(1, FDR_LEVELS[0]));
+                    will(returnValue(dataSet));
+                }
+
+            });
+        table.load(EXPERIMENT_ID);
+
+        List<ProteinSummary> summaries = table.getProteinSummaries();
+        assertSummary(0, 1, 2, summaries);
+        assertSummary(1, 1, 2, summaries);
+        assertSummary(2, 2, 3, summaries);
+        assertSummary(3, 2, 4, summaries);
+        assertSummary(4, 2, 4, summaries);
+        assertEquals(FDR_LEVELS.length, summaries.size());
+        context.assertIsSatisfied();
+    }
+
+    private void assertSummary(int index, int expectedProteinCount, int expectedPeptideCount,
+            List<ProteinSummary> summaries)
+    {
+        ProteinSummary proteinSummary = summaries.get(index);
+        assertEquals(FDR_LEVELS[index], proteinSummary.getFDR(), 1e-6);
+        assertEquals(expectedProteinCount, proteinSummary.getProteinCount());
+        assertEquals(expectedPeptideCount, proteinSummary.getPeptideCount());
+    }
+
+    private ProbabilityFDRMapping createMappingItem(double probability, double falseDiscoveryRate)
+    {
+        ProbabilityFDRMapping m1 = new ProbabilityFDRMapping();
+        m1.setProbability(probability);
+        m1.setFalseDiscoveryRate(falseDiscoveryRate);
+        return m1;
+    }
+
+    private void prepare(final ProteinReferenceWithProbabilityAndPeptide... items)
+    {
+        context.checking(new Expectations()
+            {
+                {
+                    one(experimentDAO).getByTechId(EXPERIMENT_ID);
+                    ExperimentPE experimentPE = new ExperimentPE();
+                    experimentPE.setPermId(EXPERIMENT_PERM_ID);
+                    will(returnValue(experimentPE));
+
+                    one(proteinDAO).listProteinsWithProbabilityAndPeptidesByExperiment(
+                            EXPERIMENT_PERM_ID);
+                    MockDataSet<ProteinReferenceWithProbabilityAndPeptide> dataSet =
+                            new MockDataSet<ProteinReferenceWithProbabilityAndPeptide>();
+                    dataSet.addAll(Arrays.asList(items));
+                    will(returnValue(dataSet));
+                }
+            });
+    }
+
+    private ProteinReferenceWithProbabilityAndPeptide createItem(double probability, long id,
+            String peptideSequence)
+    {
+        ProteinReferenceWithProbabilityAndPeptide item =
+                new ProteinReferenceWithProbabilityAndPeptide();
+        item.setDataSetID(DATA_SET_ID);
+        item.setProbability(probability);
+        item.setId(id);
+        item.setPeptideSequence(peptideSequence);
+        return item;
+    }
+
+}