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Commit 39e47700 authored by tpylak's avatar tpylak
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SE-124 phosphonetx: fix unit tests 

SVN: 12077
parent b32d61fb
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rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
+ 90
− 60
View file @ 39e47700
......@@ -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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