From 6c65a35922e03f1148a2226c8f304e7f2fbb9bee Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Mon, 29 Mar 2010 14:15:03 +0000
Subject: [PATCH] SE-229 tests fixed
SVN: 15307
---
.../ResultDataSetUploaderTest.java | 2 ++
.../server/business/ProteinInfoTableTest.java | 27 +++----------------
2 files changed, 5 insertions(+), 24 deletions(-)
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
index 45abce45274..b786b17e346 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
@@ -547,6 +547,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
try
{
one(connection).commit();
+ one(connection).close();
} catch (SQLException ex)
{
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
@@ -563,6 +564,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
try
{
one(connection).rollback();
+ one(connection).close();
} catch (SQLException ex)
{
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinInfoTableTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinInfoTableTest.java
index a1227f6dba3..8fb2b940c65 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinInfoTableTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinInfoTableTest.java
@@ -36,7 +36,6 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceCol
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.ProteinReferenceWithPeptideSequence;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;
/**
@@ -46,13 +45,13 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWi
*/
public class ProteinInfoTableTest extends AbstractServerTestCase
{
+ private static final double COVERAGE = 0.5;
private static final String PERM_ID_PREFIX = "abc-";
private static final long SAMPLE_ID_3 = 211L;
private static final long SAMPLE_ID_2 = 102L;
private static final long SAMPLE_ID_1 = 101L;
private static final Double ABUNDANCE = new Double(47.11);
private static final long PROTEIN_ID = 41L;
- private static final long SEQUENCE_ID = 4142L;
private static final String SAMPLE_PERM_ID = "s47-11";
private static final long SAMPLE_ID = 4711;
private static final long DATA_SET_ID = 42L;
@@ -221,7 +220,7 @@ public class ProteinInfoTableTest extends AbstractServerTestCase
assertEquals(2, abundances.size());
assertEquals(expectedAbundance, abundances.get(SAMPLE_ID_1 * 37 + SAMPLE_ID_2).doubleValue());
assertEquals(20.0, abundances.get(SAMPLE_ID_3).doubleValue());
- assertEquals(50.0, protein.getCoverage());
+ assertEquals(100 * COVERAGE, protein.getCoverage());
assertEquals(true, dataSet.hasCloseBeenInvoked());
assertEquals(true, mappings.hasCloseBeenInvoked());
@@ -240,27 +239,6 @@ public class ProteinInfoTableTest extends AbstractServerTestCase
one(proteinDAO).listProteinsByExperiment(EXPERIMENT_PERM_ID);
will(returnValue(dataSet));
-
- one(proteinDAO).listProteinsWithSequencesByExperiment(EXPERIMENT_PERM_ID);
- MockDataSet<ProteinReferenceWithPeptideSequence> dataSet1 =
- new MockDataSet<ProteinReferenceWithPeptideSequence>();
- ProteinReferenceWithPeptideSequence protein1 =
- new ProteinReferenceWithPeptideSequence();
- protein1.setId(PROTEIN_ID);
- protein1.setSequenceID(SEQUENCE_ID);
- protein1.setProteinSequence("ABCDEFblabla");
- dataSet1.add(protein1);
- will(returnValue(dataSet1));
-
- one(proteinDAO).listProteinsWithPeptidesByExperiment(EXPERIMENT_PERM_ID);
- MockDataSet<ProteinReferenceWithPeptideSequence> dataSet2 =
- new MockDataSet<ProteinReferenceWithPeptideSequence>();
- ProteinReferenceWithPeptideSequence protein2 = new ProteinReferenceWithPeptideSequence();
- protein2.setId(PROTEIN_ID);
- protein2.setSequenceID(SEQUENCE_ID);
- protein2.setPeptideSequence("ABCDEF");
- dataSet2.add(protein2);
- will(returnValue(dataSet2));
}
});
}
@@ -273,6 +251,7 @@ public class ProteinInfoTableTest extends AbstractServerTestCase
proteinReference.setAccessionNumber(ACCESSION_NUMBER);
proteinReference.setId(PROTEIN_ID);
proteinReference.setAbundance(abundance);
+ proteinReference.setCoverage(COVERAGE);
return proteinReference;
}
--
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