From 39e4770041a2732f00b65c20956ff0711e9f4646 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Wed, 12 Aug 2009 12:45:25 +0000
Subject: [PATCH] SE-124 phosphonetx: fix unit tests
SVN: 12077
---
.../ResultDataSetUploaderTest.java | 150 +++++++++++-------
1 file changed, 90 insertions(+), 60 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 7006bbd2366..0df36c7b680 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
@@ -32,6 +32,7 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.test.AssertionUtil;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.AminoAcidMass;
@@ -61,42 +62,68 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class ResultDataSetUploaderTest extends AssertJUnit
{
private static final long MOD_PEPTIDE_ID = 101L;
+
private static final long PEPTIDE_ID = 99L;
+
private static final long CELL_LYSATE_ID1 = 88L;
+
private static final String CELL_LYSATE1 = "cell_lysate1";
+
private static final String CELL_LYSATE_PERM_ID1 = "c1";
+
private static final long SEQUENCE_ID = 77L;
+
private static final long PROTEIN_REFERENCE_ID = 66L;
+
private static final String UNIPROT_ID1 = "unipr1";
+
private static final String PROTEIN_NAME1 = "my protein";
+
private static final String SEQUENCE1 = "seq";
+
private static final String UNIPROT_ID2 = "unipr2";
+
private static final String PROTEIN_NAME2 = "my 2. protein";
+
private static final String SEQUENCE2 = "seqe";
+
private static final long PROTEIN1_ID = 55L;
+
private static final long DATA_SET_ID = 42L;
+
private static final String DATA_SET_CODE = "ds1";
+
private static final long DATABASE_ID = 33l;
+
private static final String NAME_AND_VERSION = "uniprot.HUMAN.v123.fasta";
+
private static final String REFERENCE_DATABASE = "/here/and/there/" + NAME_AND_VERSION;
+
private static final long EXPERIMENT_ID = 11l;
+
private static final String EXPERIMENT_PERM_ID = "e1234";
+
private static final long SAMPLE_ID = 22l;
+
private static final String SAMPLE_PERM_ID = "s1234";
+
private static final String DB_INSTANCE = "DB";
+
private static final String GROUP_CODE = "G1";
-
+
private Mockery context;
+
private Connection connection;
+
private IEncapsulatedOpenBISService service;
+
private IProtDAO dao;
+
private ResultDataSetUploader uploader;
@BeforeMethod
@@ -106,10 +133,10 @@ public class ResultDataSetUploaderTest extends AssertJUnit
connection = context.mock(Connection.class);
dao = context.mock(IProtDAO.class);
service = context.mock(IEncapsulatedOpenBISService.class);
-
+
uploader = new ResultDataSetUploader(dao, connection, service);
}
-
+
@AfterMethod
public void afterMethod()
{
@@ -150,9 +177,9 @@ public class ResultDataSetUploaderTest extends AssertJUnit
}
});
prepareForCommit();
-
+
uploader.upload(createDataSetInfo(), createProteinSummary());
-
+
context.assertIsSatisfied();
}
@@ -161,25 +188,25 @@ public class ResultDataSetUploaderTest extends AssertJUnit
{
prepareForCreatingExperimentSampleDatabaseAndDataSet();
prepareForCommit();
-
+
uploader.upload(createDataSetInfo(), createProteinSummary());
-
+
context.assertIsSatisfied();
}
-
+
@Test
public void testEmptyProteinGroup()
{
prepareForCreatingExperimentSampleDatabaseAndDataSet();
prepareForCommit();
-
+
ProteinSummary summary = createProteinSummary();
summary.getProteinGroups().add(createProteinGroup());
uploader.upload(createDataSetInfo(), summary);
-
+
context.assertIsSatisfied();
}
-
+
@Test
public void testProteinGroupWithTwoProteins()
{
@@ -191,14 +218,14 @@ public class ResultDataSetUploaderTest extends AssertJUnit
ProteinAnnotation a2 = createAnnotation(UNIPROT_ID2, PROTEIN_NAME2, SEQUENCE2);
prepareForCreatingIdentifiedProtein(a2, true);
prepareForCommit();
-
+
ProteinSummary summary = createProteinSummary();
Protein p1 = createProtein(probability, a1, a2);
- p1.setPeptides(Collections.<Peptide>emptyList());
+ p1.setPeptides(Collections.<Peptide> emptyList());
summary.getProteinGroups().add(createProteinGroup(p1, new Protein()));
-
+
uploader.upload(createDataSetInfo(), summary);
-
+
context.assertIsSatisfied();
}
@@ -230,12 +257,12 @@ public class ResultDataSetUploaderTest extends AssertJUnit
will(returnValue(null));
one(dao).createSample(EXPERIMENT_ID, CELL_LYSATE_PERM_ID1);
will(returnValue(CELL_LYSATE_ID1));
-
+
one(dao).createAbundance(PROTEIN1_ID, CELL_LYSATE_ID1, 2.5);
}
});
p1.setPeptides(Collections.<Peptide> emptyList());
-
+
prepareForCreatingProtein(probability);
summary.getProteinGroups().add(createProteinGroup(p1));
ProteinAnnotation a2 = createAnnotation(UNIPROT_ID2, PROTEIN_NAME2, SEQUENCE2);
@@ -244,11 +271,11 @@ public class ResultDataSetUploaderTest extends AssertJUnit
p2.setName(PROTEIN_NAME1);
p2.getParameters().add(createAbundance(CELL_LYSATE1, 42.5));
context.checking(new Expectations()
- {
{
- one(dao).createAbundance(PROTEIN1_ID, CELL_LYSATE_ID1, 42.5);
- }
- });
+ {
+ one(dao).createAbundance(PROTEIN1_ID, CELL_LYSATE_ID1, 42.5);
+ }
+ });
p2.setPeptides(Collections.<Peptide> emptyList());
summary.getProteinGroups().add(createProteinGroup(p2));
prepareForCommit();
@@ -257,7 +284,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
context.assertIsSatisfied();
}
-
+
@Test
public void testAbundancesForNonExistingSample()
{
@@ -270,8 +297,8 @@ public class ResultDataSetUploaderTest extends AssertJUnit
p1.getParameters().add(createAbundance(CELL_LYSATE1, 2.5));
p1.getParameters().add(new Parameter());
final SampleIdentifier sampleIdentifier =
- new SampleIdentifier(new GroupIdentifier(DB_INSTANCE, GROUP_CODE), CELL_LYSATE1
- .toUpperCase());
+ new SampleIdentifier(new GroupIdentifier(DB_INSTANCE, GROUP_CODE), CELL_LYSATE1
+ .toUpperCase());
context.checking(new Expectations()
{
{
@@ -282,21 +309,21 @@ public class ResultDataSetUploaderTest extends AssertJUnit
p1.setPeptides(Collections.<Peptide> emptyList());
summary.getProteinGroups().add(createProteinGroup(p1));
prepareForRollback();
-
+
try
{
uploader.upload(createDataSetInfo(), summary);
fail("UserFailureException expected");
} catch (UserFailureException ex)
{
- assertEquals("Protein '" + PROTEIN_NAME1
+ AssertionUtil.assertContains("Protein '" + PROTEIN_NAME1
+ "' has an abundance value for a non-existing sample: " + sampleIdentifier, ex
.getMessage());
}
-
+
context.assertIsSatisfied();
}
-
+
@Test
public void testProteinWithUnmodifiedPeptide()
{
@@ -306,7 +333,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
ProteinAnnotation a1 = createAnnotation(UNIPROT_ID1, PROTEIN_NAME1, SEQUENCE1);
prepareForCreatingIdentifiedProtein(a1, false);
prepareForCommit();
-
+
ProteinSummary summary = createProteinSummary();
Protein p1 = createProtein(probability, a1);
final Peptide peptide = new Peptide();
@@ -321,9 +348,9 @@ public class ResultDataSetUploaderTest extends AssertJUnit
will(returnValue(PEPTIDE_ID));
}
});
-
+
uploader.upload(createDataSetInfo(), summary);
-
+
context.assertIsSatisfied();
}
@@ -357,11 +384,11 @@ public class ResultDataSetUploaderTest extends AssertJUnit
{
one(dao).createPeptide(PROTEIN1_ID, peptide.getSequence(), peptide.getCharge());
will(returnValue(PEPTIDE_ID));
-
+
one(dao).createModifiedPeptide(PEPTIDE_ID, modification.getNTermMass(),
modification.getCTermMass());
will(returnValue(MOD_PEPTIDE_ID));
-
+
one(dao).createModification(MOD_PEPTIDE_ID, mass.getPosition(), mass.getMass());
}
});
@@ -370,7 +397,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
context.assertIsSatisfied();
}
-
+
private Parameter createAbundance(String sampleCode, double value)
{
Parameter parameter = new Parameter();
@@ -379,7 +406,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
parameter.setType(ResultDataSetUploader.PARAMETER_TYPE_ABUNDANCE);
return parameter;
}
-
+
private Protein createProtein(double probability, ProteinAnnotation... annotations)
{
Protein protein = new Protein();
@@ -398,7 +425,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
protein.setIndistinguishableProteins(indistinguishableProteins);
return protein;
}
-
+
private ProteinAnnotation createAnnotation(String uniprotID, String description, String sequence)
{
ProteinAnnotation proteinAnnotation = new ProteinAnnotation();
@@ -416,7 +443,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
proteinGroup.setProteins(Arrays.asList(proteins));
return proteinGroup;
}
-
+
private void prepareForCreatingProtein(final double probability)
{
context.checking(new Expectations()
@@ -427,7 +454,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
}
});
}
-
+
private void prepareForCreatingIdentifiedProtein(ProteinAnnotation annotation,
final boolean referenceExist)
{
@@ -442,7 +469,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
if (referenceExist == false)
{
will(returnValue(null));
-
+
one(dao).createProteinReference(uniprotID, description);
will(returnValue(PROTEIN_REFERENCE_ID));
} else
@@ -450,11 +477,13 @@ public class ResultDataSetUploaderTest extends AssertJUnit
ProteinReference proteinReference = new ProteinReference();
proteinReference.setId(PROTEIN_REFERENCE_ID);
will(returnValue(proteinReference));
-
- one(dao).updateProteinReferenceDescription(PROTEIN_REFERENCE_ID, description);
+
+ one(dao).updateProteinReferenceDescription(PROTEIN_REFERENCE_ID,
+ description);
}
-
- one(dao).tryToGetSequencesByReferenceAndDatabase(PROTEIN_REFERENCE_ID, DATABASE_ID);
+
+ one(dao).tryToGetSequencesByReferenceAndDatabase(PROTEIN_REFERENCE_ID,
+ DATABASE_ID);
Sequence seq = new Sequence(sequence);
seq.setId(SEQUENCE_ID);
if (referenceExist == false)
@@ -467,9 +496,9 @@ public class ResultDataSetUploaderTest extends AssertJUnit
will(returnValue(SEQUENCE_ID));
} else
{
- will(returnValue(seq));
+ will(returnValue(Arrays.asList(seq)));
}
-
+
one(dao).createIdentifiedProtein(PROTEIN1_ID, SEQUENCE_ID);
}
});
@@ -518,23 +547,23 @@ public class ResultDataSetUploaderTest extends AssertJUnit
}
});
}
-
+
private void prepareForRollback()
{
context.checking(new Expectations()
- {
{
- try
- {
- one(connection).rollback();
- } catch (SQLException ex)
{
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ try
+ {
+ one(connection).rollback();
+ } catch (SQLException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
}
- }
- });
+ });
}
-
+
private DataSetInformation createDataSetInfo()
{
DataSetInformation info = new DataSetInformation();
@@ -553,7 +582,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
info.setSample(sample);
return info;
}
-
+
private ProteinSummary createProteinSummary(ProteinSummaryDataFilter... dataFilters)
{
ProteinSummary proteinSummary = new ProteinSummary();
@@ -562,11 +591,12 @@ public class ResultDataSetUploaderTest extends AssertJUnit
ProgramDetails programDetails = new ProgramDetails();
ProteinProphetDetails proteinProphetDetails = new ProteinProphetDetails();
proteinProphetDetails.setDataFilters(Arrays.asList(dataFilters));
- programDetails.setSummary(new Object[] {proteinProphetDetails});
+ programDetails.setSummary(new Object[]
+ { proteinProphetDetails });
proteinSummaryHeader.setProgramDetails(programDetails);
proteinSummary.setSummaryHeader(proteinSummaryHeader);
proteinSummary.setProteinGroups(new ArrayList<ProteinGroup>());
return proteinSummary;
}
-
+
}
--
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