From 2a4edc0fe97b697db7dc38128d7e3c9cf838963d Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Wed, 15 Jul 2009 06:26:10 +0000
Subject: [PATCH] LMS-1028 Unit tests for uploading.
SVN: 11755
---
.../phosphonetx/ProteinDescription.java | 74 +++
.../phosphonetx/ResultDataSetUploader.java | 60 +-
.../etlserver/phosphonetx/dto/Sequence.java | 23 +-
.../ResultDataSetUploaderTest.java | 582 ++++++++++++++++++
4 files changed, 685 insertions(+), 54 deletions(-)
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinDescription.java
create mode 100644 rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinDescription.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinDescription.java
new file mode 100644
index 00000000000..3e88488ebc4
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinDescription.java
@@ -0,0 +1,74 @@
+/*
+ * 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.etlserver.phosphonetx;
+
+final class ProteinDescription
+{
+ static final String DESCRIPTION_KEY = "DE";
+ static final String SEQUENCE_KEY = "SEQ";
+
+ static String createKeyValuePair(String key, String value)
+ {
+ return "\\" + key + "=" + value;
+ }
+
+ private final String uniprotID;
+ private final String description;
+ private final String sequence;
+
+ public ProteinDescription(String proteinDescription)
+ {
+ String[] items = proteinDescription.split("\\\\");
+ uniprotID = tryToGetUniprotID(items);
+ description = tryToGetValue(items, DESCRIPTION_KEY);
+ sequence = tryToGetValue(items, SEQUENCE_KEY);
+ }
+
+ public final String getUniprotID()
+ {
+ return uniprotID;
+ }
+
+ public final String getDescription()
+ {
+ return description;
+ }
+
+ public final String getSequence()
+ {
+ return sequence;
+ }
+
+ private String tryToGetUniprotID(String[] items)
+ {
+ return items == null || items.length == 0 ? null : items[0].trim();
+ }
+
+ private String tryToGetValue(String[] items, String key)
+ {
+ for (String item : items)
+ {
+ int indexOfEqualSign = item.indexOf('=');
+ if (indexOfEqualSign > 0
+ && item.substring(0, indexOfEqualSign).trim().equalsIgnoreCase(key))
+ {
+ return item.substring(indexOfEqualSign + 1).trim();
+ }
+ }
+ return null;
+ }
+}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
index 9aa9abeda71..673e01ef366 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
@@ -53,63 +53,19 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
*/
class ResultDataSetUploader extends AbstractHandler
{
- private static final String PARAMETER_TYPE_ABUNDANCE = "abundance";
-
- private static final class ProteinDescription
- {
- private final String uniprotID;
- private final String description;
- private final String sequence;
-
- public ProteinDescription(String proteinDescription)
- {
- String[] items = proteinDescription.split("\\\\");
- uniprotID = tryToGetUniprotID(items);
- description = tryToGetValue(items, "DE");
- sequence = tryToGetValue(items, "SEQ");
- }
-
- public final String getUniprotID()
- {
- return uniprotID;
- }
-
- public final String getDescription()
- {
- return description;
- }
-
- public final String getSequence()
- {
- return sequence;
- }
-
- private String tryToGetUniprotID(String[] items)
- {
- return items == null || items.length == 0 ? null : items[0].trim();
- }
-
- private String tryToGetValue(String[] items, String key)
- {
- for (String item : items)
- {
- int indexOfEqualSign = item.indexOf('=');
- if (indexOfEqualSign > 0
- && item.substring(0, indexOfEqualSign).trim().equalsIgnoreCase(key))
- {
- return item.substring(indexOfEqualSign + 1).trim();
- }
- }
- return null;
- }
- }
+ static final String PARAMETER_TYPE_ABUNDANCE = "abundance";
private final Connection connection;
private final IEncapsulatedOpenBISService openbisService;
ResultDataSetUploader(Connection connection, IEncapsulatedOpenBISService openbisService)
{
- super(QueryTool.getQuery(connection, IProtDAO.class));
+ this(QueryTool.getQuery(connection, IProtDAO.class), connection, openbisService);
+ }
+
+ ResultDataSetUploader(IProtDAO dao, Connection connection, IEncapsulatedOpenBISService openbisService)
+ {
+ super(dao);
this.connection = connection;
this.openbisService = openbisService;
}
@@ -260,8 +216,6 @@ class ResultDataSetUploader extends AbstractHandler
if (proteinReference == null)
{
proteinReference = new ProteinReference();
- proteinReference.setUniprotID(uniprotID);
- proteinReference.setDescription(description);
proteinReference.setId(dao.createProteinReference(uniprotID, description));
} else if (description.equals(proteinReference.getDescription()) == false)
{
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/Sequence.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/Sequence.java
index cb861ba3d7c..f78c65bda20 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/Sequence.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/Sequence.java
@@ -96,10 +96,31 @@ public class Sequence extends AbstractDTOWithID
this.checksum = checksum;
}
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof Sequence == false)
+ {
+ return false;
+ }
+ return ((Sequence) obj).toString().equals(toString());
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return toString().hashCode();
+ }
+
@Override
public String toString()
{
- return getId() + ":" + sequence + "[" + checksum + "]";
+ return getDatabaseID() + "-" + getProteinReferenceID() + ":" + sequence
+ + "[" + checksum + "]";
}
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
new file mode 100644
index 00000000000..69240f603bc
--- /dev/null
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
@@ -0,0 +1,582 @@
+/*
+ * 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.etlserver.phosphonetx;
+
+import java.sql.Connection;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+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;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.AnnotatedProtein;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.DataSet;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Database;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Experiment;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ModificationType;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Parameter;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Peptide;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.PeptideModification;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProgramDetails;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Protein;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinAnnotation;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinGroup;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinProphetDetails;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinReference;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummary;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummaryDataFilter;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummaryHeader;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sample;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sequence;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.MockDataSet;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ResultDataSetUploaderTest extends AssertJUnit
+{
+ 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 static final long MODIFICATION_TYPE_ID = 1L;
+
+ private Mockery context;
+ private Connection connection;
+ private IEncapsulatedOpenBISService service;
+ private IProtDAO dao;
+ private ResultDataSetUploader uploader;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ context = new Mockery();
+ connection = context.mock(Connection.class);
+ dao = context.mock(IProtDAO.class);
+ service = context.mock(IEncapsulatedOpenBISService.class);
+ context.checking(new Expectations()
+ {
+ {
+ one(dao).listModificationTypes();
+ MockDataSet<ModificationType> types = new MockDataSet<ModificationType>();
+ ModificationType modificationType = new ModificationType();
+ modificationType.setId(MODIFICATION_TYPE_ID);
+ modificationType.setMass(0);
+ modificationType.setMassTolerance(1e5);
+ types.add(modificationType);
+ will(returnValue(types));
+ }
+ });
+
+ uploader = new ResultDataSetUploader(dao, connection, service);
+ }
+
+ @AfterMethod
+ public void afterMethod()
+ {
+ // To following line of code should also be called at the end of each test method.
+ // Otherwise one do not known which test failed.
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testNoProteinsGetExperimentSampleDatabaseAndDataSet()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(dao).tryToGetExperimentByPermID(EXPERIMENT_PERM_ID);
+ Experiment experiment = new Experiment();
+ experiment.setPermID(EXPERIMENT_PERM_ID);
+ experiment.setId(EXPERIMENT_ID);
+ will(returnValue(experiment));
+
+ one(dao).tryToGetSampleByPermID(SAMPLE_PERM_ID);
+ Sample sample = new Sample();
+ sample.setPermID(SAMPLE_PERM_ID);
+ sample.setId(SAMPLE_ID);
+ will(returnValue(sample));
+
+ one(dao).tryToGetDatabaseByName(NAME_AND_VERSION);
+ Database database = new Database();
+ database.setNameAndVersion(NAME_AND_VERSION);
+ database.setId(DATABASE_ID);
+ will(returnValue(database));
+
+ one(dao).tryToGetDataSetByPermID(DATA_SET_CODE);
+ DataSet dataSet = new DataSet();
+ dataSet.setId(DATA_SET_ID);
+ dataSet.setDatabaseID(DATABASE_ID);
+ will(returnValue(dataSet));
+ }
+ });
+ prepareForCommit();
+
+ uploader.upload(createDataSetInfo(), createProteinSummary());
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testNoProteinsCreateExperimentSampleDatabaseAndDataSet()
+ {
+ prepareForCreatingExperimentSampleDatabaseAndDataSet();
+ prepareForCommit();
+
+ uploader.upload(createDataSetInfo(), createProteinSummary());
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testEmptyProteinGroup()
+ {
+ prepareForCreatingExperimentSampleDatabaseAndDataSet();
+ prepareForCommit();
+
+ ProteinSummary summary = createProteinSummary();
+ summary.getProteinGroups().add(createProteinGroup(1.0));
+ uploader.upload(createDataSetInfo(), summary);
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testProteinGroupWithTwoProteins()
+ {
+ prepareForCreatingExperimentSampleDatabaseAndDataSet();
+ double probability = 1.0;
+ prepareForCreatingProtein(probability);
+ ProteinAnnotation a1 = createAnnotation(UNIPROT_ID1, PROTEIN_NAME1, SEQUENCE1);
+ prepareForCreatingIdentifiedProtein(a1, false);
+ ProteinAnnotation a2 = createAnnotation(UNIPROT_ID2, PROTEIN_NAME2, SEQUENCE2);
+ prepareForCreatingIdentifiedProtein(a2, true);
+ prepareForCommit();
+
+ ProteinSummary summary = createProteinSummary();
+ Protein p1 = createProtein(a1, a2);
+ p1.setPeptides(Collections.<Peptide>emptyList());
+ summary.getProteinGroups().add(createProteinGroup(probability, p1, new Protein()));
+
+ uploader.upload(createDataSetInfo(), summary);
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testAbundancesForSameSampleInTwoDifferentProteins()
+ {
+ prepareForCreatingExperimentSampleDatabaseAndDataSet();
+ double probability = 0.75;
+ ProteinSummary summary = createProteinSummary();
+ prepareForCreatingProtein(probability);
+ ProteinAnnotation a1 = createAnnotation(UNIPROT_ID1, PROTEIN_NAME1, SEQUENCE1);
+ prepareForCreatingIdentifiedProtein(a1, false);
+ Protein p1 = createProtein(a1);
+ p1.setName(PROTEIN_NAME1);
+ 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());
+ context.checking(new Expectations()
+ {
+ {
+ one(service).tryGetSampleWithExperiment(sampleIdentifier);
+ SamplePE samplePE = new SamplePE();
+ samplePE.setPermId(CELL_LYSATE_PERM_ID1);
+ will(returnValue(samplePE));
+
+ one(dao).tryToGetSampleByPermID(CELL_LYSATE_PERM_ID1);
+ 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(probability, p1));
+ ProteinAnnotation a2 = createAnnotation(UNIPROT_ID2, PROTEIN_NAME2, SEQUENCE2);
+ prepareForCreatingIdentifiedProtein(a2, false);
+ Protein p2 = createProtein(a2);
+ 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);
+ }
+ });
+ p2.setPeptides(Collections.<Peptide> emptyList());
+ summary.getProteinGroups().add(createProteinGroup(probability, p2));
+ prepareForCommit();
+
+ uploader.upload(createDataSetInfo(), summary);
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testAbundancesForNonExistingSample()
+ {
+ prepareForCreatingExperimentSampleDatabaseAndDataSet();
+ double probability = 0.75;
+ prepareForCreatingProtein(probability);
+ ProteinSummary summary = createProteinSummary();
+ Protein p1 = createProtein();
+ p1.setName(PROTEIN_NAME1);
+ 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());
+ context.checking(new Expectations()
+ {
+ {
+ one(service).tryGetSampleWithExperiment(sampleIdentifier);
+ will(returnValue(null));
+ }
+ });
+ p1.setPeptides(Collections.<Peptide> emptyList());
+ summary.getProteinGroups().add(createProteinGroup(probability, p1));
+ prepareForRollback();
+
+ try
+ {
+ uploader.upload(createDataSetInfo(), summary);
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ assertEquals("Protein '" + PROTEIN_NAME1
+ + "' has an abundance value for a non-existing sample: " + sampleIdentifier, ex
+ .getMessage());
+ }
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testProteinWithUnmodifiedPeptide()
+ {
+ prepareForCreatingExperimentSampleDatabaseAndDataSet();
+ double probability = 1.0;
+ prepareForCreatingProtein(probability);
+ ProteinAnnotation a1 = createAnnotation(UNIPROT_ID1, PROTEIN_NAME1, SEQUENCE1);
+ prepareForCreatingIdentifiedProtein(a1, false);
+ prepareForCommit();
+
+ ProteinSummary summary = createProteinSummary();
+ Protein p1 = createProtein(a1);
+ final Peptide peptide = new Peptide();
+ peptide.setSequence("abcd");
+ peptide.setCharge(3);
+ p1.setPeptides(Arrays.asList(peptide));
+ summary.getProteinGroups().add(createProteinGroup(probability, p1));
+ context.checking(new Expectations()
+ {
+ {
+ one(dao).createPeptide(PROTEIN1_ID, peptide.getSequence(), peptide.getCharge());
+ will(returnValue(PEPTIDE_ID));
+ }
+ });
+
+ uploader.upload(createDataSetInfo(), summary);
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testProteinWithModifiedPeptide()
+ {
+ prepareForCreatingExperimentSampleDatabaseAndDataSet();
+ double probability = 1.0;
+ prepareForCreatingProtein(probability);
+ ProteinAnnotation a1 = createAnnotation(UNIPROT_ID1, PROTEIN_NAME1, SEQUENCE1);
+ prepareForCreatingIdentifiedProtein(a1, false);
+ prepareForCommit();
+
+ ProteinSummary summary = createProteinSummary();
+ Protein p1 = createProtein(a1);
+ final Peptide peptide = new Peptide();
+ peptide.setSequence("abcd");
+ peptide.setCharge(3);
+ PeptideModification peptideModification = new PeptideModification();
+ final AminoAcidMass mass = new AminoAcidMass();
+ mass.setMass(123);
+ mass.setPosition(1);
+ peptideModification.setAminoAcidMasses(Arrays.asList(mass));
+ peptide.getModifications().add(peptideModification);
+ p1.setPeptides(Arrays.asList(peptide));
+ summary.getProteinGroups().add(createProteinGroup(probability, p1));
+ context.checking(new Expectations()
+ {
+ {
+ one(dao).createPeptide(PROTEIN1_ID, peptide.getSequence(), peptide.getCharge());
+ will(returnValue(PEPTIDE_ID));
+
+ one(dao).createModification(PEPTIDE_ID, MODIFICATION_TYPE_ID,
+ mass.getPosition(), mass.getMass());
+ }
+ });
+
+ uploader.upload(createDataSetInfo(), summary);
+
+ context.assertIsSatisfied();
+ }
+
+ private Parameter createAbundance(String sampleCode, double value)
+ {
+ Parameter parameter = new Parameter();
+ parameter.setName(sampleCode);
+ parameter.setValue(Double.toString(value));
+ parameter.setType(ResultDataSetUploader.PARAMETER_TYPE_ABUNDANCE);
+ return parameter;
+ }
+
+ private Protein createProtein(ProteinAnnotation... annotations)
+ {
+ Protein protein = new Protein();
+ if (annotations.length > 0)
+ {
+ protein.setAnnotation(annotations[0]);
+ }
+ List<AnnotatedProtein> indistinguishableProteins = new ArrayList<AnnotatedProtein>();
+ for (int i = 1; i < annotations.length; i++)
+ {
+ AnnotatedProtein annotatedProtein = new AnnotatedProtein();
+ annotatedProtein.setAnnotation(annotations[i]);
+ indistinguishableProteins.add(annotatedProtein);
+ }
+ protein.setIndistinguishableProteins(indistinguishableProteins);
+ return protein;
+ }
+
+ private ProteinAnnotation createAnnotation(String uniprotID, String description, String sequence)
+ {
+ ProteinAnnotation proteinAnnotation = new ProteinAnnotation();
+ proteinAnnotation.setDescription(uniprotID
+ + " "
+ + ProteinDescription.createKeyValuePair(ProteinDescription.DESCRIPTION_KEY,
+ description) + " "
+ + ProteinDescription.createKeyValuePair(ProteinDescription.SEQUENCE_KEY, sequence));
+ return proteinAnnotation;
+ }
+
+ private ProteinGroup createProteinGroup(double probability, Protein... proteins)
+ {
+ ProteinGroup proteinGroup = new ProteinGroup();
+ proteinGroup.setProbability(probability);
+ proteinGroup.setProteins(Arrays.asList(proteins));
+ return proteinGroup;
+ }
+
+ private void prepareForCreatingProtein(final double probability)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(dao).createProtein(DATA_SET_ID, probability);
+ will(returnValue(PROTEIN1_ID));
+ }
+ });
+ }
+
+ private void prepareForCreatingIdentifiedProtein(ProteinAnnotation annotation,
+ final boolean referenceExist)
+ {
+ ProteinDescription proteinDescription = new ProteinDescription(annotation.getDescription());
+ final String uniprotID = proteinDescription.getUniprotID();
+ final String description = proteinDescription.getDescription();
+ final String sequence = proteinDescription.getSequence();
+ context.checking(new Expectations()
+ {
+ {
+ one(dao).tryToGetProteinReference(uniprotID);
+ if (referenceExist == false)
+ {
+ will(returnValue(null));
+
+ one(dao).createProteinReference(uniprotID, description);
+ will(returnValue(PROTEIN_REFERENCE_ID));
+ } else
+ {
+ ProteinReference proteinReference = new ProteinReference();
+ proteinReference.setId(PROTEIN_REFERENCE_ID);
+ will(returnValue(proteinReference));
+
+ one(dao).updateProteinReferenceDescription(PROTEIN_REFERENCE_ID, description);
+ }
+
+ one(dao).tryToGetSequenceByReferenceAndDatabase(PROTEIN_REFERENCE_ID, DATABASE_ID);
+ Sequence seq = new Sequence(sequence);
+ seq.setId(SEQUENCE_ID);
+ if (referenceExist == false)
+ {
+ will(returnValue(null));
+
+ seq.setDatabaseID(DATABASE_ID);
+ seq.setProteinReferenceID(PROTEIN_REFERENCE_ID);
+ one(dao).createSequence(seq);
+ will(returnValue(SEQUENCE_ID));
+ } else
+ {
+ will(returnValue(seq));
+ }
+
+ one(dao).createIdentifiedProtein(PROTEIN1_ID, SEQUENCE_ID);
+ }
+ });
+ }
+
+ private void prepareForCreatingExperimentSampleDatabaseAndDataSet()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(dao).tryToGetExperimentByPermID(EXPERIMENT_PERM_ID);
+ will(returnValue(null));
+ one(dao).createExperiment(EXPERIMENT_PERM_ID);
+ will(returnValue(EXPERIMENT_ID));
+
+ one(dao).tryToGetSampleByPermID(SAMPLE_PERM_ID);
+ will(returnValue(null));
+ one(dao).createSample(EXPERIMENT_ID, SAMPLE_PERM_ID);
+ will(returnValue(SAMPLE_ID));
+
+ one(dao).tryToGetDatabaseByName(NAME_AND_VERSION);
+ will(returnValue(null));
+ one(dao).createDatabase(NAME_AND_VERSION);
+ will(returnValue(DATABASE_ID));
+
+ one(dao).tryToGetDataSetByPermID(DATA_SET_CODE);
+ will(returnValue(null));
+ one(dao).createDataSet(EXPERIMENT_ID, SAMPLE_ID, DATA_SET_CODE, DATABASE_ID);
+ will(returnValue(DATA_SET_ID));
+ }
+ });
+ }
+
+ private void prepareForCommit()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ try
+ {
+ one(connection).commit();
+ } catch (SQLException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+ });
+ }
+
+ private void prepareForRollback()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ try
+ {
+ one(connection).rollback();
+ } catch (SQLException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+ });
+ }
+
+ private DataSetInformation createDataSetInfo()
+ {
+ DataSetInformation info = new DataSetInformation();
+ info.setDataSetCode(DATA_SET_CODE);
+ SamplePE sample = new SamplePE();
+ sample.setPermId(SAMPLE_PERM_ID);
+ ExperimentPE experiment = new ExperimentPE();
+ experiment.setPermId(EXPERIMENT_PERM_ID);
+ sample.setExperiment(experiment);
+ GroupPE group = new GroupPE();
+ DatabaseInstancePE databaseInstance = new DatabaseInstancePE();
+ databaseInstance.setCode(DB_INSTANCE);
+ group.setDatabaseInstance(databaseInstance);
+ group.setCode(GROUP_CODE);
+ sample.setGroup(group);
+ info.setSample(sample);
+ return info;
+ }
+
+ private ProteinSummary createProteinSummary(ProteinSummaryDataFilter... dataFilters)
+ {
+ ProteinSummary proteinSummary = new ProteinSummary();
+ ProteinSummaryHeader proteinSummaryHeader = new ProteinSummaryHeader();
+ proteinSummaryHeader.setReferenceDatabase(REFERENCE_DATABASE);
+ ProgramDetails programDetails = new ProgramDetails();
+ ProteinProphetDetails proteinProphetDetails = new ProteinProphetDetails();
+ proteinProphetDetails.setDataFilters(Arrays.asList(dataFilters));
+ programDetails.setSummary(new Object[] {proteinProphetDetails});
+ proteinSummaryHeader.setProgramDetails(programDetails);
+ proteinSummary.setSummaryHeader(proteinSummaryHeader);
+ proteinSummary.setProteinGroups(new ArrayList<ProteinGroup>());
+ return proteinSummary;
+ }
+
+}
--
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