From 4d83bd425521cd07068480c73536814fc0d0bb86 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 24 Nov 2009 12:18:58 +0000
Subject: [PATCH] SE-163 ProteinSummaryTableTest added
SVN: 13489
---
.../server/business/ProteinSummaryTable.java | 5 +-
.../business/ProteinSummaryTableTest.java | 173 ++++++++++++++++++
2 files changed, 176 insertions(+), 2 deletions(-)
create mode 100644 rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTableTest.java
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTable.java
index c891781b433..f15ea14ce74 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTable.java
+++ b/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)
{
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTableTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTableTest.java
new file mode 100644
index 00000000000..fd86e373abf
--- /dev/null
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTableTest.java
@@ -0,0 +1,173 @@
+/*
+ * 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;
+ }
+
+}
--
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