From e37ac3a35ab493114f9030583eba84f48ef0ccb7 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 1 Sep 2009 06:14:45 +0000
Subject: [PATCH] SE-127 ProteinWithAbundancesTableTest and
AbundanceManagerTest added
SVN: 12340
---
.../business/IProteinWithAbundancesTable.java | 6 +-
.../business/ProteinWithAbundancesTable.java | 2 +-
.../shared/dto/ProteinWithAbundances.java | 4 +-
.../server/business/AbundanceManagerTest.java | 121 +++++++++++++++
.../ProteinWithAbundancesTableTest.java | 146 ++++++++++++++++++
5 files changed, 275 insertions(+), 4 deletions(-)
create mode 100644 rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManagerTest.java
create mode 100644 rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinWithAbundancesTableTest.java
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IProteinWithAbundancesTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IProteinWithAbundancesTable.java
index cc91c22fc72..a4559040d72 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IProteinWithAbundancesTable.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IProteinWithAbundancesTable.java
@@ -22,12 +22,16 @@ import java.util.Set;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinWithAbundances;
/**
- *
+ * Business object for loading proteins together with their abundances.
*
* @author Franz-Josef Elmer
*/
public interface IProteinWithAbundancesTable
{
+ /**
+ * Loads proteins of all data sets registered for the specified experiment. All proteins
+ * are filtered out if their false discovery rate is larger then the specifie one.
+ */
public void load(String experimentPermID, double falseDiscoveryRate);
public Collection<ProteinWithAbundances> getProteinsWithAbundances();
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinWithAbundancesTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinWithAbundancesTable.java
index 2507732e0d6..0788af1d9ba 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinWithAbundancesTable.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinWithAbundancesTable.java
@@ -30,7 +30,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWi
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinWithAbundances;
/**
- *
+ * Implementation based of {@link IDAOFactory} and {@link IPhosphoNetXDAOFactory}.
*
* @author Franz-Josef Elmer
*/
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinWithAbundances.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinWithAbundances.java
index be627d6a6c1..b6701cddc76 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinWithAbundances.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinWithAbundances.java
@@ -16,7 +16,7 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto;
-import java.util.HashMap;
+import java.util.LinkedHashMap;
import java.util.Map;
import java.util.Set;
@@ -29,7 +29,7 @@ public class ProteinWithAbundances extends ProteinReference
{
private static final double[] EMPTY_ARRAY = new double[0];
- private final Map<Long, double[]> abundances = new HashMap<Long, double[]>();
+ private final Map<Long, double[]> abundances = new LinkedHashMap<Long, double[]>();
public void addAbundanceFor(long sampleID, double abundance)
{
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManagerTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManagerTest.java
new file mode 100644
index 00000000000..9d7b516b549
--- /dev/null
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManagerTest.java
@@ -0,0 +1,121 @@
+/*
+ * 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 java.util.Collection;
+import java.util.Iterator;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinWithAbundances;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class AbundanceManagerTest extends AssertJUnit
+{
+
+ @Test
+ public void testNoProteinReferenceHandled()
+ {
+ AbundanceManager abundanceManager = new AbundanceManager();
+ assertEquals(0, abundanceManager.getSampleIDs().size());
+ assertEquals(0, abundanceManager.getProteinsWithAbundances().size());
+ }
+
+ @Test
+ public void testHandleTwoProteinReferencesButOnlyOneHasAnAbundance()
+ {
+ AbundanceManager abundanceManager = new AbundanceManager();
+ ProteinReferenceWithProbability protein1 = new ProteinReferenceWithProbability();
+ protein1.setId(1);
+ protein1.setAccessionNumber("abc1");
+ protein1.setDescription("abc one");
+ protein1.setSampleID(101L);
+ protein1.setAbundance(1.5);
+ abundanceManager.handle(protein1);
+ ProteinReferenceWithProbability protein2 = new ProteinReferenceWithProbability();
+ protein2.setId(2);
+ protein2.setAccessionNumber("abc2");
+ protein2.setDescription("abc two");
+ abundanceManager.handle(protein2);
+
+ assertEquals(1, abundanceManager.getSampleIDs().size());
+ Collection<ProteinWithAbundances> proteinsWithAbundances = abundanceManager.getProteinsWithAbundances();
+ assertEquals(2, proteinsWithAbundances.size());
+ Iterator<ProteinWithAbundances> iterator = proteinsWithAbundances.iterator();
+ ProteinWithAbundances p1 = iterator.next();
+ assertEquals(1, p1.getId());
+ assertEquals("abc one", p1.getDescription());
+ assertEquals("abc1", p1.getAccessionNumber());
+ assertEquals(1, p1.getSampleIDs().size());
+ assertEquals(101, p1.getSampleIDs().iterator().next().longValue());
+ assertEquals(0, p1.getAbundancesForSample(12345678).length);
+ assertEquals(1, p1.getAbundancesForSample(101).length);
+ assertEquals(1.5, p1.getAbundancesForSample(101)[0]);
+ ProteinWithAbundances p2 = iterator.next();
+ assertEquals(2, p2.getId());
+ assertEquals("abc two", p2.getDescription());
+ assertEquals("abc2", p2.getAccessionNumber());
+ assertEquals(0, p2.getSampleIDs().size());
+ }
+
+ @Test
+ public void testHandleProteinReferencesWithManyAbundancesForTwoSamples()
+ {
+ AbundanceManager abundanceManager = new AbundanceManager();
+ abundanceManager.handle(createProteinReference(101, 1.5));
+ abundanceManager.handle(createProteinReference(101, 2.25));
+ abundanceManager.handle(createProteinReference(102, 42));
+ abundanceManager.handle(createProteinReference(102, 4.75));
+ abundanceManager.handle(createProteinReference(102, 7.5));
+
+ assertEquals(2, abundanceManager.getSampleIDs().size());
+ Collection<ProteinWithAbundances> proteinsWithAbundances = abundanceManager.getProteinsWithAbundances();
+ assertEquals(1, proteinsWithAbundances.size());
+ ProteinWithAbundances protein = proteinsWithAbundances.iterator().next();
+ assertEquals(1, protein.getId());
+ assertEquals("abc one", protein.getDescription());
+ assertEquals("abc1", protein.getAccessionNumber());
+ assertEquals(2, protein.getSampleIDs().size());
+ Iterator<Long> iterator = protein.getSampleIDs().iterator();
+ assertEquals(101, iterator.next().longValue());
+ assertEquals(102, iterator.next().longValue());
+ assertEquals(2, protein.getAbundancesForSample(101).length);
+ assertEquals(1.5, protein.getAbundancesForSample(101)[0]);
+ assertEquals(2.25, protein.getAbundancesForSample(101)[1]);
+ assertEquals(3, protein.getAbundancesForSample(102).length);
+ assertEquals(42.0, protein.getAbundancesForSample(102)[0]);
+ assertEquals(4.75, protein.getAbundancesForSample(102)[1]);
+ assertEquals(7.5, protein.getAbundancesForSample(102)[2]);
+ }
+
+ private ProteinReferenceWithProbability createProteinReference(long sampleID, double abundance)
+ {
+ ProteinReferenceWithProbability protein1 = new ProteinReferenceWithProbability();
+ protein1.setId(1);
+ protein1.setAccessionNumber("abc1");
+ protein1.setDescription("abc one");
+ protein1.setSampleID(sampleID);
+ protein1.setAbundance(abundance);
+ return protein1;
+ }
+}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinWithAbundancesTableTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinWithAbundancesTableTest.java
new file mode 100644
index 00000000000..85e6cf920f8
--- /dev/null
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinWithAbundancesTableTest.java
@@ -0,0 +1,146 @@
+/*
+ * 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 java.util.Collection;
+import java.util.Set;
+
+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.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.dto.ProbabilityFDRMapping;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinWithAbundances;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ProteinWithAbundancesTableTest extends AbstractServerTestCase
+{
+ private static final Double ABUNDANCE = new Double(47.11);
+ private static final long PROTEIN_ID = 41L;
+ private static final long SAMPLE_ID = 4711L;
+ private static final long DATA_SET_ID = 42L;
+ private static final String EXPERIMENT_ID = "abc-234";
+ private static final double FALSE_DISCOVERY_RATE = 0.25;
+ private static final String ACCESSION_NUMBER = "ABC123";
+
+ private IPhosphoNetXDAOFactory specificDAOFactory;
+ private IProteinQueryDAO proteinDAO;
+ private ProteinWithAbundancesTable 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 ProteinWithAbundancesTable(daoFactory, specificDAOFactory, SESSION);
+ }
+
+ @Test
+ public void testLoadLeadingToAnEmptyTable()
+ {
+ final MockDataSet<ProteinReferenceWithProbability> dataSet =
+ new MockDataSet<ProteinReferenceWithProbability>();
+ context.checking(new Expectations()
+ {
+ {
+ one(proteinDAO).listProteinsByExperiment(EXPERIMENT_ID);
+ will(returnValue(dataSet));
+ }
+ });
+
+ table.load(EXPERIMENT_ID, FALSE_DISCOVERY_RATE);
+
+ assertEquals(0, table.getSampleIDs().size());
+ assertEquals(0, table.getProteinsWithAbundances().size());
+
+ assertEquals(true, dataSet.hasCloseBeenInvoked());
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testLoad()
+ {
+ final MockDataSet<ProteinReferenceWithProbability> dataSet =
+ new MockDataSet<ProteinReferenceWithProbability>();
+ ProteinReferenceWithProbability proteinReference = new ProteinReferenceWithProbability();
+ proteinReference.setDataSetID(DATA_SET_ID);
+ proteinReference.setSampleID(SAMPLE_ID);
+ proteinReference.setAccessionNumber(ACCESSION_NUMBER);
+ proteinReference.setId(PROTEIN_ID);
+ proteinReference.setAbundance(ABUNDANCE);
+ dataSet.add(proteinReference);
+ proteinReference = new ProteinReferenceWithProbability();
+ proteinReference.setProbability(1);
+ proteinReference.setDataSetID(DATA_SET_ID);
+ dataSet.add(proteinReference);
+ final MockDataSet<ProbabilityFDRMapping> mappings = new MockDataSet<ProbabilityFDRMapping>();
+ mappings.add(new ProbabilityFDRMapping());
+ ProbabilityFDRMapping mapping = new ProbabilityFDRMapping();
+ mapping.setProbability(1);
+ mapping.setFalseDiscoveryRate(1);
+ mappings.add(mapping);
+ context.checking(new Expectations()
+ {
+ {
+ one(proteinDAO).listProteinsByExperiment(EXPERIMENT_ID);
+ will(returnValue(dataSet));
+
+ one(proteinDAO).getProbabilityFDRMapping(DATA_SET_ID);
+ will(returnValue(mappings));
+ }
+ });
+
+ table.load(EXPERIMENT_ID, FALSE_DISCOVERY_RATE);
+
+ Set<Long> sampleIDs = table.getSampleIDs();
+ assertEquals(1, sampleIDs.size());
+ Long sampleID = sampleIDs.iterator().next();
+ assertEquals(SAMPLE_ID, sampleID.longValue());
+ Collection<ProteinWithAbundances> proteins = table.getProteinsWithAbundances();
+ assertEquals(1, proteins.size());
+ ProteinWithAbundances protein = proteins.iterator().next();
+ assertEquals(PROTEIN_ID, protein.getId());
+ assertEquals(ACCESSION_NUMBER, protein.getAccessionNumber());
+ assertEquals(sampleIDs, protein.getSampleIDs());
+ double[] abundances = protein.getAbundancesForSample(sampleID);
+ assertEquals(1, abundances.length);
+ assertEquals(ABUNDANCE, abundances[0]);
+
+ assertEquals(true, dataSet.hasCloseBeenInvoked());
+ assertEquals(true, mappings.hasCloseBeenInvoked());
+ context.assertIsSatisfied();
+ }
+
+}
--
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