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 45abce452741618481e135fd594feeb9780e0506..b786b17e3467d1388115c14ed293013dc9038039 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 a1227f6dba3e9c83387bbe8e77086aa20cab592a..8fb2b940c65986d9d295fde6e87273f427ee58a8 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; }