diff --git a/rtd_phosphonetx/build/build.xml b/rtd_phosphonetx/build/build.xml
index 934cd0a46f0665fd91df9a4a1fef23db31c826ae..55eb3d6f6523678b5000bff8158039daa9848aae 100644
--- a/rtd_phosphonetx/build/build.xml
+++ b/rtd_phosphonetx/build/build.xml
@@ -33,6 +33,9 @@
<include name="ch/systemsx/cisd/openbis/plugin/proteomics/shared/**/*.class" />
<include name="${proteomics-build.info.filename}" />
</fileset>
+ <fileset dir="../rtd_phosphonetx/source">
+ <include name="**/*.sql" />
+ </fileset>
<manifest>
<attribute name="Version" value="${version.number}" />
<attribute name="Build-Number"
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DatabaseVersionHolder.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DatabaseVersionHolder.java
new file mode 100644
index 0000000000000000000000000000000000000000..34de34da5f90afbce8ff1a544392c1aff998379a
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DatabaseVersionHolder.java
@@ -0,0 +1,33 @@
+/*
+ * Copyright 2012 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.proteomics;
+
+import ch.systemsx.cisd.openbis.dss.generic.shared.IDatabaseVersionHolder;
+
+/**
+ * Holds the version of the proteomics database.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class DatabaseVersionHolder implements IDatabaseVersionHolder
+{
+ public String getDatabaseVersion()
+ {
+ return "005"; // changed in S124
+ }
+}
+
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinSequenceGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinSequenceGrid.java
index 070bc0682ddd334294611f2dceac53cead3ce483..cca90bf4c7bb01b7903caec4e75e6bd2fdec695f 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinSequenceGrid.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinSequenceGrid.java
@@ -29,6 +29,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteri
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.IPhosphoNetXClientServiceAsync;
import ch.systemsx.cisd.openbis.plugin.proteomics.client.web.client.dto.ListProteinSequenceCriteria;
@@ -46,9 +47,9 @@ public class ProteinSequenceGrid extends TypedTableGrid<ProteinSequence>
public static final String GRID_ID = PREFIX + TypedTableGrid.GRID_POSTFIX;
static IDisposableComponent create(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- TechId proteinReferenceID)
+ Experiment experimentOrNull, TechId proteinReferenceID)
{
- return new ProteinSequenceGrid(viewContext, proteinReferenceID)
+ return new ProteinSequenceGrid(viewContext, experimentOrNull, proteinReferenceID)
.asDisposableWithoutToolbar();
}
@@ -57,12 +58,16 @@ public class ProteinSequenceGrid extends TypedTableGrid<ProteinSequence>
private ListProteinSequenceCriteria criteria;
private ProteinSequenceGrid(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- TechId proteinReferenceID)
+ Experiment experimentOrNull, TechId proteinReferenceID)
{
super(viewContext.getCommonViewContext(), BROWSER_ID + proteinReferenceID, true,
PhosphoNetXDisplayTypeIDGenerator.PROTEIN_SEQUENCE_BROWSER_GRID);
specificViewContext = viewContext;
criteria = new ListProteinSequenceCriteria();
+ if (experimentOrNull != null)
+ {
+ criteria.setExperimentID(new TechId(experimentOrNull.getId()));
+ }
criteria.setProteinReferenceID(proteinReferenceID);
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinViewer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinViewer.java
index 92fb27a5eff2ef927df3c55a86df8d9f4004af80..f16523ef81d9a67b62a973d3d84ac345014aadb4 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinViewer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/application/ProteinViewer.java
@@ -260,7 +260,7 @@ public class ProteinViewer extends AbstractViewerWithVerticalSplit<IEntityInform
protected IDisposableComponent createDisposableContent()
{
return ProteinSequenceGrid.create(ProteinViewer.this.getViewContext(),
- proteinReferenceID);
+ experimentOrNull, proteinReferenceID);
}
};
add(sequencesSection, createRightBorderLayoutData());
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListProteinSequenceCriteria.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListProteinSequenceCriteria.java
index 62bf4d4de048eb5ea540f288434cde8ca037502d..a06dea8c7821b0061d12bd613e63656ed11c17de 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListProteinSequenceCriteria.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/client/dto/ListProteinSequenceCriteria.java
@@ -33,6 +33,7 @@ public class ListProteinSequenceCriteria extends
IsSerializable
{
private TechId proteinReferenceID;
+ private TechId experimentID;
public final TechId getProteinReferenceID()
{
@@ -43,4 +44,15 @@ public class ListProteinSequenceCriteria extends
{
this.proteinReferenceID = proteinReferenceID;
}
+
+ public void setExperimentID(TechId experimentID)
+ {
+ this.experimentID = experimentID;
+ }
+
+ public TechId getExperimentID()
+ {
+ return experimentID;
+ }
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/PhosphoNetXClientService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/PhosphoNetXClientService.java
index b0ceedfcaccefab3aa29e413106ff0b4fbb92ca2..0a4dca52a9446723c80df91fdb90ec879ea62486 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/PhosphoNetXClientService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/PhosphoNetXClientService.java
@@ -310,7 +310,7 @@ public class PhosphoNetXClientService extends AbstractClientService implements
{
final String sessionToken = getSessionToken();
return listEntities(
- new ProteinSequenceProvider(server, sessionToken, criteria.getProteinReferenceID()),
+ new ProteinSequenceProvider(server, sessionToken, criteria.getExperimentID(), criteria.getProteinReferenceID()),
criteria);
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSequenceProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSequenceProvider.java
index 03390de6b095abb246f3c96c1b98dea3b4817400..1192d15682a9255761d58eb039893d4de4634396 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSequenceProvider.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSequenceProvider.java
@@ -38,13 +38,15 @@ public class ProteinSequenceProvider extends AbstractTableModelProvider<ProteinS
{
private final IPhosphoNetXServer server;
private final String sessionToken;
+ private final TechId experimentID;
private final TechId proteinReferenceID;
public ProteinSequenceProvider(IPhosphoNetXServer server, String sessionToken,
- TechId proteinReferenceID)
+ TechId experimentID, TechId proteinReferenceID)
{
this.server = server;
this.sessionToken = sessionToken;
+ this.experimentID = experimentID;
this.proteinReferenceID = proteinReferenceID;
}
@@ -52,7 +54,7 @@ public class ProteinSequenceProvider extends AbstractTableModelProvider<ProteinS
protected TypedTableModel<ProteinSequence> createTableModel()
{
List<ProteinSequence> sequences =
- server.listProteinSequencesByProteinReference(sessionToken, proteinReferenceID);
+ server.listProteinSequencesByProteinReference(sessionToken, experimentID, proteinReferenceID);
TypedTableModelBuilder<ProteinSequence> builder =
new TypedTableModelBuilder<ProteinSequence>();
builder.addColumn(SEQUENCE_SHORT_NAME).withDefaultWidth(20);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServer.java
index ae1701df3052313a5e684540c3b37ca940d0089a..843c343143b3e6222d8474ce92b60ab169de63a0 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServer.java
@@ -123,7 +123,7 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
ISampleProvider sampleProvider, TechId experimentID, String treatmentTypeOrNull)
{
String experimentPermID = getExperimentPermIDFor(experimentID);
- IProteinQueryDAO dao = specificDAOFactory.getProteinQueryDAO();
+ IProteinQueryDAO dao = specificDAOFactory.getProteinQueryDAO(experimentID);
DataSet<String> samplePermIDs =
dao.listAbundanceRelatedSamplePermIDsByExperiment(experimentPermID);
try
@@ -169,7 +169,7 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
TechId proteinReferenceID) throws UserFailureException
{
Session session = getSession(sessionToken);
- IProteinQueryDAO proteinQueryDAO = specificDAOFactory.getProteinQueryDAO();
+ IProteinQueryDAO proteinQueryDAO = specificDAOFactory.getProteinQueryDAO(experimentID);
ProteinByExperiment proteinByExperiment = new ProteinByExperiment();
ProteinReference proteinReference =
proteinQueryDAO.tryToGetProteinReference(proteinReferenceID.getId());
@@ -190,11 +190,11 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
}
public List<ProteinSequence> listProteinSequencesByProteinReference(String sessionToken,
- TechId proteinReferenceID) throws UserFailureException
+ TechId experimentID, TechId proteinReferenceID) throws UserFailureException
{
final Session session = getSession(sessionToken);
IProteinSequenceTable sequenceTable = specificBOFactory.createProteinSequenceTable(session);
- sequenceTable.loadByReference(proteinReferenceID);
+ sequenceTable.loadByReference(experimentID, proteinReferenceID);
return sequenceTable.getSequences();
}
@@ -203,7 +203,7 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
{
final Session session = getSession(sessionToken);
IProteinSequenceTable sequenceTable = specificBOFactory.createProteinSequenceTable(session);
- sequenceTable.loadByReference(proteinReferenceID);
+ sequenceTable.loadByReference(experimentId, proteinReferenceID);
IDataSetProteinTable dataSetProteinTable = specificBOFactory.createDataSetProteinTable(session);
dataSetProteinTable.load(getExperimentPermIDFor(experimentId), proteinReferenceID, sequenceTable);
return dataSetProteinTable.getDataSetProteins();
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServerLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServerLogger.java
index ccf44388000c4d397eb584051a331d073690b843..f710f694f02d5650cfa00f11caf6a0e423115d38 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServerLogger.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServerLogger.java
@@ -90,10 +90,10 @@ public class PhosphoNetXServerLogger extends AbstractServerLogger implements IPh
}
public List<ProteinSequence> listProteinSequencesByProteinReference(String sessionToken,
- TechId proteinReferenceID) throws UserFailureException
+ TechId experimentID, TechId proteinReferenceID) throws UserFailureException
{
logAccess(sessionToken, "list_protein_sequences_by_reference",
- "PROTEIN_REFERENCE_ID(%s)", proteinReferenceID);
+ "EXPERIMENT_ID(%s) PROTEIN_REFERENCE_ID(%s)", experimentID, proteinReferenceID);
return null;
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/DataSetProteinTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/DataSetProteinTable.java
index 8a6643aaa14b486f07a337ec07bfa5f8b4b3bdf9..c11bc4522c90ad3dc9aad239daf1377d5a82fd2a 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/DataSetProteinTable.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/DataSetProteinTable.java
@@ -50,8 +50,8 @@ class DataSetProteinTable extends AbstractBusinessObject implements IDataSetProt
public void load(String experimentPermID, TechId proteinReferenceID,
IProteinSequenceTable sequenceTable)
{
- IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO();
- ErrorModel errorModel = new ErrorModel(getSpecificDAOFactory());
+ IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO(experimentPermID);
+ ErrorModel errorModel = new ErrorModel(proteinQueryDAO);
DataSet<IdentifiedProtein> proteins =
proteinQueryDAO.listProteinsByProteinReferenceAndExperiment(experimentPermID,
proteinReferenceID.getId());
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ErrorModel.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ErrorModel.java
index 80e8f3986a5a97dc49f50ff9ee6475081bee51e2..dcf16b6e031976c65b6793e2c603bbd2a62b6c30 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ErrorModel.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ErrorModel.java
@@ -21,7 +21,6 @@ import java.util.Map;
import net.lemnik.eodsql.DataSet;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQueryDAO;
import ch.systemsx.cisd.openbis.plugin.proteomics.shared.ProbabilityToFDRCalculator;
import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.IdentifiedProtein;
@@ -35,12 +34,11 @@ class ErrorModel
{
private final Map<Long, ProbabilityToFDRCalculator> calculators =
new HashMap<Long, ProbabilityToFDRCalculator>();
+ private final IProteinQueryDAO dao;
- private final IPhosphoNetXDAOFactory specificDAOFactory;
-
- ErrorModel(IPhosphoNetXDAOFactory specificDAOFactory)
+ ErrorModel(IProteinQueryDAO dao)
{
- this.specificDAOFactory = specificDAOFactory;
+ this.dao = dao;
}
boolean passProtein(ProteinReferenceWithProtein protein, double falseDiscoveryRate)
@@ -69,7 +67,6 @@ class ErrorModel
if (calculator == null)
{
calculator = new ProbabilityToFDRCalculator();
- IProteinQueryDAO dao = specificDAOFactory.getProteinQueryDAO();
DataSet<ProbabilityFDRMapping> mappings = dao.getProbabilityFDRMapping(dataSetID);
for (ProbabilityFDRMapping probabilityFDRMapping : mappings)
{
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinSequenceTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinSequenceTable.java
index 45ab1915a503f72c891e3b22bb2c1f591a3cd484..f0bd8e7fd00d956d79b4fe0b6b04e94892c6f30b 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinSequenceTable.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/IProteinSequenceTable.java
@@ -29,7 +29,7 @@ import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.dto.ProteinSequen
public interface IProteinSequenceTable
{
- public void loadByReference(TechId proteinReferenceID);
+ public void loadByReference(TechId experimentID, TechId proteinReferenceID);
public List<ProteinSequence> getSequences();
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinDetailsBO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinDetailsBO.java
index 57a67ff776ae59e0486fcb5405b41eb29aae3435..004b2d70f1c42e97dddd730314afc92791088654 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinDetailsBO.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinDetailsBO.java
@@ -61,7 +61,7 @@ class ProteinDetailsBO extends AbstractBusinessObject implements IProteinDetails
public void loadByExperimentAndReference(TechId experimentID, TechId proteinReferenceID)
{
String experimentPermID = getExperimentPermIDFor(experimentID);
- IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO();
+ IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO(experimentID);
DataSet<IdentifiedProtein> proteins =
proteinQueryDAO.listProteinsByProteinReferenceAndExperiment(experimentPermID,
proteinReferenceID.getId());
@@ -69,7 +69,7 @@ class ProteinDetailsBO extends AbstractBusinessObject implements IProteinDetails
{
if (proteins.size() == 1)
{
- ErrorModel errorModel = new ErrorModel(getSpecificDAOFactory());
+ ErrorModel errorModel = new ErrorModel(proteinQueryDAO);
IdentifiedProtein protein = proteins.get(0);
errorModel.setFalseDiscoveryRateFor(protein);
details = new ProteinDetails();
@@ -86,10 +86,10 @@ class ProteinDetailsBO extends AbstractBusinessObject implements IProteinDetails
details.setDataSetTechID(ds.getId());
details.setDataSetTypeCode(ds.getDataSetType().getCode());
}
- details.setPeptides(loadPeptides(protein));
+ details.setPeptides(loadPeptides(proteinQueryDAO, protein));
long proteinID = protein.getProteinID();
details.setProteinID(new TechId(proteinID));
- details.setIndistinguishableProteinInfos(loadIndistinguishableProteinInfos(proteinID));
+ details.setIndistinguishableProteinInfos(loadIndistinguishableProteinInfos(proteinQueryDAO, proteinID));
}
} finally
{
@@ -97,9 +97,8 @@ class ProteinDetailsBO extends AbstractBusinessObject implements IProteinDetails
}
}
- private List<IndistinguishableProteinInfo> loadIndistinguishableProteinInfos(long proteinID)
+ private List<IndistinguishableProteinInfo> loadIndistinguishableProteinInfos(IProteinQueryDAO proteinQueryDAO, long proteinID)
{
- IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO();
DataSet<IndistinguishableProtein> proteins =
proteinQueryDAO.listIndistinguishableProteinsByProteinID(proteinID);
try
@@ -125,9 +124,8 @@ class ProteinDetailsBO extends AbstractBusinessObject implements IProteinDetails
}
}
- private List<Peptide> loadPeptides(IdentifiedProtein protein)
+ private List<Peptide> loadPeptides(IProteinQueryDAO proteinQueryDAO, IdentifiedProtein protein)
{
- IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO();
DataSet<PeptideWithModification> identifiedPeptides =
proteinQueryDAO.listIdentifiedPeptidesByProtein(protein.getProteinID());
try
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinInfoTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinInfoTable.java
index d2d620583e65380c0aeefca2f035c61823141aed..c5c08fbeb245dd5fd784d456b6641c7695c5c97a 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinInfoTable.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinInfoTable.java
@@ -131,7 +131,7 @@ class ProteinInfoTable extends AbstractBusinessObject implements IProteinInfoTab
{
AbundanceManager abundanceManager = new AbundanceManager(sampleProvider);
IPhosphoNetXDAOFactory specificDAOFactory = getSpecificDAOFactory();
- IProteinQueryDAO dao = specificDAOFactory.getProteinQueryDAO();
+ IProteinQueryDAO dao = specificDAOFactory.getProteinQueryDAO(experimentPermID);
long time = System.currentTimeMillis();
DataSet<ProteinReferenceWithProtein> dataSet =
dao.listProteinReferencesByExperiment(experimentPermID);
@@ -149,8 +149,8 @@ class ProteinInfoTable extends AbstractBusinessObject implements IProteinInfoTab
dataSet.close();
}
operationLog.info("(" + (System.currentTimeMillis() - time) + "ms) for listProteinReferencesByExperiment");
- Map<Long, List<ProteinAbundance>> abundancesPerProtein = getAbudancesPerProtein(proteinIDs);
- ErrorModel errorModel = new ErrorModel(specificDAOFactory);
+ Map<Long, List<ProteinAbundance>> abundancesPerProtein = getAbudancesPerProtein(dao, proteinIDs);
+ ErrorModel errorModel = new ErrorModel(dao);
for (ProteinReferenceWithProtein protein : proteins)
{
if (errorModel.passProtein(protein, falseDiscoveryRate))
@@ -162,9 +162,8 @@ class ProteinInfoTable extends AbstractBusinessObject implements IProteinInfoTab
return abundanceManager;
}
- private Map<Long, List<ProteinAbundance>> getAbudancesPerProtein(LongOpenHashSet proteinIDs)
+ private Map<Long, List<ProteinAbundance>> getAbudancesPerProtein(IProteinQueryDAO dao, LongOpenHashSet proteinIDs)
{
- IProteinQueryDAO dao = getSpecificDAOFactory().getProteinQueryDAO();
long time = System.currentTimeMillis();
DataSet<ProteinAbundance> dataSet = dao.listProteinWithAbundanceByExperiment(proteinIDs);
List<ProteinAbundance> proteinAbundances = new ArrayList<ProteinAbundance>();
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinRelatedSampleTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinRelatedSampleTable.java
index 946ad65d4009a1ef642014072973cced0ddc0731..1b10940300a7b1c2eeaa19d70dbf181186806ecd 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinRelatedSampleTable.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinRelatedSampleTable.java
@@ -69,7 +69,7 @@ class ProteinRelatedSampleTable implements IProteinRelatedSampleTable
{
String experimentPermID =
daoFactory.getExperimentDAO().getByTechId(experimentID).getPermId();
- IProteinQueryDAO proteinQueryDAO = specificDAOFactory.getProteinQueryDAO();
+ IProteinQueryDAO proteinQueryDAO = specificDAOFactory.getProteinQueryDAO(experimentID);
Map<String, List<SampleAbundance>> sampleAbundanceMap =
createSampleMap(proteinQueryDAO.listSampleAbundanceByProtein(experimentPermID,
proteinReferenceID.getId()));
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSequenceTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSequenceTable.java
index 3fa864fc93ff5b633bcd548431fefca63fe7e18d..2ab3e6d555686508a841a39befa26ab384265934 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSequenceTable.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSequenceTable.java
@@ -70,9 +70,9 @@ class ProteinSequenceTable extends AbstractBusinessObject implements IProteinSeq
return shortName;
}
- public void loadByReference(TechId proteinReferenceID)
+ public void loadByReference(TechId experimentID, TechId proteinReferenceID)
{
- IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO();
+ IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO(experimentID);
DataSet<Sequence> sequences =
proteinQueryDAO.listProteinSequencesByProteinReference(proteinReferenceID.getId());
proteinSequences = new ArrayList<ProteinSequence>(sequences.size());
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSummaryTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSummaryTable.java
index c8bd95e4610b70c8bfeee0175a1efbaaf017a8ba..ac8528e517cfcd02c10e8790fbb1e551d9c4f498 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSummaryTable.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSummaryTable.java
@@ -107,8 +107,8 @@ class ProteinSummaryTable extends AbstractBusinessObject implements IProteinSumm
{
IExperimentDAO experimentDAO = getDaoFactory().getExperimentDAO();
String permID = experimentDAO.getByTechId(experimentID).getPermId();
- IProteinQueryDAO dao = getSpecificDAOFactory().getProteinQueryDAO();
- ErrorModel errorModel = new ErrorModel(getSpecificDAOFactory());
+ IProteinQueryDAO dao = getSpecificDAOFactory().getProteinQueryDAO(experimentID);
+ ErrorModel errorModel = new ErrorModel(dao);
DataSet<ProteinReferenceWithProbabilityAndPeptide> resultSet =
dao.listProteinsWithProbabilityAndPeptidesByExperiment(permID);
List<Counter> counters = new ArrayList<Counter>(FDR_LEVELS.length);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleTable.java
index 2d92850ca72e6ecb8c6cc4dc53c6a164e30f8c58..b2cc41cc2c8baaed6e4b9c9f4030795b227b2f55 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleTable.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/SampleTable.java
@@ -61,7 +61,7 @@ class SampleTable extends AbstractBusinessObject implements ISampleTable
public void loadSamplesWithAbundance(TechId experimentID, TechId proteinReferenceID)
{
samples = new ArrayList<SampleWithPropertiesAndAbundance>();
- IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO();
+ IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO(experimentID);
IDAOFactory daoFactory = getDaoFactory();
String experimentPermID =
daoFactory.getExperimentDAO().getByTechId(experimentID).getPermId();
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/IPhosphoNetXDAOFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/IPhosphoNetXDAOFactory.java
index f5629915e7d22c8066892bda1699652936bccda4..c063b1bb1224c2bd0927ab1a64b6225862c8e1df 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/IPhosphoNetXDAOFactory.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/IPhosphoNetXDAOFactory.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+
/**
* A factory for PhosphoNetX specific DAOs.
@@ -24,5 +26,7 @@ package ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess;
*/
public interface IPhosphoNetXDAOFactory
{
- public IProteinQueryDAO getProteinQueryDAO();
+ public IProteinQueryDAO getProteinQueryDAO(TechId experimentID);
+
+ public IProteinQueryDAO getProteinQueryDAO(String experimentPermID);
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/db/PhosphoNetXDAOFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/db/PhosphoNetXDAOFactory.java
index dd45f366288c352cb303db797298699b2d101938..ed1cc9c4f2683260981f518639ac58d3535b3387 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/db/PhosphoNetXDAOFactory.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/dataaccess/db/PhosphoNetXDAOFactory.java
@@ -16,14 +16,27 @@
package ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.db;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.sql.DataSource;
+
import net.lemnik.eodsql.QueryTool;
import org.apache.log4j.Logger;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.dbmigration.DBMigrationEngine;
-import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataSourceProvider;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQueryDAO;
@@ -32,26 +45,84 @@ import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQuer
*/
public class PhosphoNetXDAOFactory implements IPhosphoNetXDAOFactory
{
- /** Current version of the database. */
- public static final String DATABASE_VERSION = "005";
-
private static final Logger operationLog =
LogFactory.getLogger(LogCategory.OPERATION, PhosphoNetXDAOFactory.class);
+
+ private final Map<DataSource, IProteinQueryDAO> daos = new HashMap<DataSource, IProteinQueryDAO>();
- private final IProteinQueryDAO proteinQueryDAO;
+ private final IDAOFactory daoFactory;
- public PhosphoNetXDAOFactory(DatabaseConfigurationContext context)
+ private final IDataSourceProvider dataSourceProvider;
+
+ public PhosphoNetXDAOFactory(IDataSourceProvider dataSourceProvider, IDAOFactory daoFactory)
{
- DBMigrationEngine.createOrMigrateDatabaseAndGetScriptProvider(context, DATABASE_VERSION);
- proteinQueryDAO = QueryTool.getQuery(context.getDataSource(), IProteinQueryDAO.class);
+ this.dataSourceProvider = dataSourceProvider;
+ this.daoFactory = daoFactory;
if (operationLog.isInfoEnabled())
{
operationLog.info("DAO factory for proteomics created.");
}
}
- public IProteinQueryDAO getProteinQueryDAO()
+ public IProteinQueryDAO getProteinQueryDAO(String experimentPermID)
+ {
+ ExperimentPE experiment = daoFactory.getExperimentDAO().tryGetByPermID(experimentPermID);
+ if (experiment == null)
+ {
+ throw new UserFailureException("No experiment with following perm ID found: "
+ + experimentPermID);
+ }
+ return getProteinQueryDAO(experiment);
+ }
+
+ public IProteinQueryDAO getProteinQueryDAO(TechId experimentID)
{
- return proteinQueryDAO;
+ ExperimentPE experiment = daoFactory.getExperimentDAO().tryGetByTechId(experimentID);
+ if (experiment == null)
+ {
+ throw new UserFailureException("No experiment with following technical ID found: "
+ + experimentID);
+ }
+ return getProteinQueryDAO(experiment);
}
+
+ public IProteinQueryDAO getProteinQueryDAO(ExperimentPE experiment)
+ {
+ DataSource dataSource = getDataSource(experiment);
+ IProteinQueryDAO dao = daos.get(dataSource);
+ if (dao == null)
+ {
+ dao = QueryTool.getQuery(dataSource, IProteinQueryDAO.class);
+ daos.put(dataSource, dao);
+ }
+ return dao;
+ }
+
+ private DataSource getDataSource(ExperimentPE experiment)
+ {
+ IDataDAO dataDAO = daoFactory.getDataDAO();
+
+ List<DataPE> dataSets = dataDAO.listDataSets(experiment);
+ Set<String> dataStores = new HashSet<String>();
+ for (DataPE data : dataSets)
+ {
+ dataStores.add(data.getDataStore().getCode());
+ }
+ if (dataStores.isEmpty())
+ {
+ throw new UserFailureException("Experiment with " + experiment.getIdentifier()
+ + " has no data sets.");
+ }
+ if (dataStores.size() > 1)
+ {
+ throw new UserFailureException("Experiment with " + experiment.getIdentifier()
+ + " has data sets from more than one store. The stores are the following: "
+ + dataStores);
+ }
+ DataSource dataSource =
+ dataSourceProvider.getDataSourceByDataStoreServerCode(dataStores.iterator()
+ .next(), "proteomics");
+ return dataSource;
+ }
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/IPhosphoNetXServer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/IPhosphoNetXServer.java
index 3fc47cfda959d61720a33ff2cf5268f444dde8e0..283ca2b1b07655f6446b469d125aca7b7986a014 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/IPhosphoNetXServer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/shared/IPhosphoNetXServer.java
@@ -81,7 +81,7 @@ public interface IPhosphoNetXServer extends IServer
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<ProteinSequence> listProteinSequencesByProteinReference(String sessionToken,
- TechId proteinReferenceID) throws UserFailureException;
+ TechId experimentID, TechId proteinReferenceID) throws UserFailureException;
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
diff --git a/rtd_phosphonetx/source/java/proteomics-plugin-applicationContext.xml b/rtd_phosphonetx/source/java/proteomics-plugin-applicationContext.xml
index 6834762327ba0cd0238c980d3b90be324a2a3cf1..59a6dcaf5320bc073c9eb81ddcc17d5e059d485e 100644
--- a/rtd_phosphonetx/source/java/proteomics-plugin-applicationContext.xml
+++ b/rtd_phosphonetx/source/java/proteomics-plugin-applicationContext.xml
@@ -7,29 +7,15 @@
http://www.springframework.org/schema/tx
http://www.springframework.org/schema/tx/spring-tx-2.5.xsd">
- <bean id="proteomics-db-configuration-context"
- class="ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext">
- <property name="basicDatabaseName" value="${proteomics.database.basic-name}" />
- <property name="createFromScratch" value="${proteomics.database.create-from-scratch}" />
- <property name="scriptSingleStepMode" value="${proteomics.database.script-single-step-mode}" />
- <property name="sequenceNameMapper">
- <bean class="ch.systemsx.cisd.openbis.generic.server.dataaccess.db.SequenceNameMapper" />
- </property>
- <property name="urlHostPart" value="${proteomics.database.url-host-part}" />
- <property name="adminUser" value="${proteomics.database.admin-user}" />
- <property name="owner" value="${proteomics.database.owner}" />
- <property name="readOnlyGroup" value="phosphonetx_readonly" />
- <property name="password" value="${proteomics.database.owner-password}" />
- <property name="adminPassword" value="${proteomics.database.admin-password}" />
- <property name="databaseKind" value="${proteomics.database.kind}" />
- <property name="databaseEngineCode" value="${proteomics.database.engine}" />
- <property name="scriptFolder" value="${proteomics.script-folder}" />
- <property name="databaseInstance" value="${proteomics.database-instance}" />
+ <bean id="dss-based-data-source-provider" class="ch.systemsx.cisd.openbis.generic.server.dataaccess.DataStoreServerBasedDataSourceProvider">
+ <constructor-arg ref="dao-factory"/>
</bean>
+
<bean id="proteomics-dao-factory"
class="ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.db.PhosphoNetXDAOFactory">
- <constructor-arg ref="proteomics-db-configuration-context"/>
+ <constructor-arg ref="dss-based-data-source-provider"/>
+ <constructor-arg ref="dao-factory"/>
</bean>
<bean id="proteomics-bo-factory"
diff --git a/rtd_phosphonetx/source/java/service.properties b/rtd_phosphonetx/source/java/service.properties
index e465bbd10f2d0e2ab438c5cf50ba021fc3326b5e..5eeac2a677bbf7461e58e53d814f8d9ceb24c4b2 100644
--- a/rtd_phosphonetx/source/java/service.properties
+++ b/rtd_phosphonetx/source/java/service.properties
@@ -25,18 +25,6 @@ database.owner-password =
database.admin-user =
database.admin-password =
-proteomics.database.engine = postgresql
-proteomics.database.create-from-scratch = false
-proteomics.database.script-single-step-mode = false
-proteomics.database.url-host-part =
-proteomics.database.basic-name = phosphonetx
-proteomics.database.kind = dev
-proteomics.database.owner =
-proteomics.database.owner-password =
-proteomics.database.admin-user =
-proteomics.database.admin-password =
-proteomics.script-folder = source/sql/proteomics
-
crowd.service.host = crowd.systemsx.ch
crowd.service.port = 8443
crowd.application.name = lims
@@ -64,6 +52,11 @@ hibernate.search.maxResults = 100000
web-client-configuration-file = etc/web-client.properties
+dss-based-data-source-provider.data-store-servers = DSS1
+dss-based-data-source-provider.DSS1.database-driver = org.postgresql.Driver
+dss-based-data-source-provider.DSS1.database-url = jdbc:postgresql://localhost/proteomics_dev
+
+
# Database Configurations for Query module
query-databases = 1, 2
@@ -77,4 +70,4 @@ query-databases = 1, 2
2.label = Protein Data
2.creator-minimal-role = SPACE_USER
2.database-driver = org.postgresql.Driver
-2.database-url = jdbc:postgresql://localhost/phosphonetx_${proteomics.database.kind}
+2.database-url = ${dss-based-data-source-provider.DSS1.database-url}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSequenceProviderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSequenceProviderTest.java
index 32bce8d1949989dea12aa0473b9ac2aeff7c095f..a08b7602edd125f207fd5dd093a697076ff77b9a 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSequenceProviderTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/client/web/server/resultset/ProteinSequenceProviderTest.java
@@ -46,12 +46,12 @@ public class ProteinSequenceProviderTest extends AbstractProviderTest
context.checking(new Expectations()
{
{
- one(phosphonetxServer).listProteinSequencesByProteinReference(SESSION_TOKEN, new TechId(42));
+ one(phosphonetxServer).listProteinSequencesByProteinReference(SESSION_TOKEN, new TechId(42), new TechId(43));
will(returnValue(Arrays.asList(ps)));
}
});
ProteinSequenceProvider provider =
- new ProteinSequenceProvider(phosphonetxServer, SESSION_TOKEN, new TechId(42));
+ new ProteinSequenceProvider(phosphonetxServer, SESSION_TOKEN, new TechId(42), new TechId(43));
TypedTableModel<ProteinSequence> model = provider.createTableModel();
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServerTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServerTest.java
index db8c6772e1251054112ea74108a2f618db86dd23..05d74ca9b1307b7e7a5a5337e964dfb91fad5723 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServerTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/PhosphoNetXServerTest.java
@@ -85,9 +85,6 @@ public class PhosphoNetXServerTest extends AbstractServerTestCase
context.checking(new Expectations()
{
{
- allowing(phosphoNetXDAOFactory).getProteinQueryDAO();
- will(returnValue(proteinDAO));
-
allowing(boFactory).createProteinDetailsBO(SESSION);
will(returnValue(proteinDetailsBO));
@@ -112,6 +109,9 @@ public class PhosphoNetXServerTest extends AbstractServerTestCase
experimentPE.setPermId(EXPERIMENT_PERM_ID);
will(returnValue(experimentPE));
+ allowing(phosphoNetXDAOFactory).getProteinQueryDAO(EXPERIMENT_ID);
+ will(returnValue(proteinDAO));
+
one(proteinDAO).listAbundanceRelatedSamplePermIDsByExperiment(EXPERIMENT_PERM_ID);
will(returnValue(mockDataSet));
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbstractBOTestCase.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbstractBOTestCase.java
index 20771d7999e3d94c22c5cba8ac251585c5de58f4..3f8c5e9d52a9a9cd5bcd97a9eeef92df38962954 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbstractBOTestCase.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/AbstractBOTestCase.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.plugin.proteomics.server.business;
-import org.jmock.Expectations;
import org.testng.annotations.BeforeMethod;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
@@ -40,13 +39,6 @@ public abstract class AbstractBOTestCase extends AbstractServerTestCase
super.setUp();
specificDAOFactory = context.mock(IPhosphoNetXDAOFactory.class);
proteinDAO = context.mock(IProteinQueryDAO.class);
- context.checking(new Expectations()
- {
- {
- allowing(specificDAOFactory).getProteinQueryDAO();
- will(returnValue(proteinDAO));
- }
- });
}
}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ErrorModelTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ErrorModelTest.java
index 1e6ae7ebb69e969218e50cdb552cc96bf43b4d35..fdde68882d8cbd1e81e2ddb608b75b6c5a66392e 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ErrorModelTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ErrorModelTest.java
@@ -24,8 +24,6 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.common.eodsql.MockDataSet;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.ErrorModel;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IPhosphoNetXDAOFactory;
import ch.systemsx.cisd.openbis.plugin.proteomics.server.dataaccess.IProteinQueryDAO;
import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.IdentifiedProtein;
import ch.systemsx.cisd.openbis.plugin.proteomics.shared.dto.ProbabilityFDRMapping;
@@ -44,7 +42,6 @@ public class ErrorModelTest extends AssertJUnit
private static final long DATA_SET3_ID = 44;
private Mockery context;
- private IPhosphoNetXDAOFactory specificDAOFactory;
private IProteinQueryDAO proteinQueryDAO;
private ErrorModel errorModel;
@@ -52,14 +49,11 @@ public class ErrorModelTest extends AssertJUnit
public void beforeMethod()
{
context = new Mockery();
- specificDAOFactory = context.mock(IPhosphoNetXDAOFactory.class);
proteinQueryDAO = context.mock(IProteinQueryDAO.class);
- errorModel = new ErrorModel(specificDAOFactory);
+ errorModel = new ErrorModel(proteinQueryDAO);
context.checking(new Expectations()
{
{
- allowing(specificDAOFactory).getProteinQueryDAO();
- will(returnValue(proteinQueryDAO));
atMost(1).of(proteinQueryDAO).getProbabilityFDRMapping(DATA_SET1_ID);
MockDataSet<ProbabilityFDRMapping> dataSet1 = new MockDataSet<ProbabilityFDRMapping>();
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinInfoTableTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinInfoTableTest.java
index c9d1d92a2f983c63639ba001c6a6aa62d19900c5..00702afb6343b18c4c624bce8aab20b2fc212e57 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinInfoTableTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinInfoTableTest.java
@@ -95,6 +95,7 @@ public class ProteinInfoTableTest extends AbstractBOTestCase
@Test
public void testLoadLeadingToAnEmptyTable()
{
+ prepareGetProteinQueryDAO(EXPERIMENT_PERM_ID);
MockDataSet<ProteinReferenceWithProtein> proteinReferences = new MockDataSet<ProteinReferenceWithProtein>();
MockDataSet<ProteinAbundance> proteinAbundances = new MockDataSet<ProteinAbundance>();
prepareLoadDataSet(proteinReferences, proteinAbundances);
@@ -112,6 +113,7 @@ public class ProteinInfoTableTest extends AbstractBOTestCase
@Test
public void testSimpleLoad()
{
+ prepareGetProteinQueryDAO(EXPERIMENT_PERM_ID);
MockDataSet<ProteinReferenceWithProtein> proteinReferences =
new MockDataSet<ProteinReferenceWithProtein>();
MockDataSet<ProteinAbundance> abundances = new MockDataSet<ProteinAbundance>();
@@ -182,6 +184,7 @@ public class ProteinInfoTableTest extends AbstractBOTestCase
private void checkAggregationType(double expectedAbundance, boolean aggregateOriginal)
{
+ prepareGetProteinQueryDAO(EXPERIMENT_PERM_ID);
final MockDataSet<ProteinReferenceWithProtein> proteinReferences =
new MockDataSet<ProteinReferenceWithProtein>();
ProteinReferenceWithProtein proteinReference = new ProteinReferenceWithProtein();
@@ -238,6 +241,17 @@ public class ProteinInfoTableTest extends AbstractBOTestCase
context.assertIsSatisfied();
}
+ private void prepareGetProteinQueryDAO(final String experimentPermID)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(specificDAOFactory).getProteinQueryDAO(experimentPermID);
+ will(returnValue(proteinDAO));
+ }
+ });
+ }
+
private void prepareLoadDataSet(
final MockDataSet<ProteinReferenceWithProtein> proteinReferences,
final DataSet<ProteinAbundance> proteinAbundances)
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinRelatedSampleTableTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinRelatedSampleTableTest.java
index f257e456f7f297491bee005b2318b36fa633765c..e32ad6a91cd9f8682c8d2abb0dd531cc157b8d64 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinRelatedSampleTableTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinRelatedSampleTableTest.java
@@ -92,6 +92,9 @@ public class ProteinRelatedSampleTableTest extends AbstractBOTestCase
context.checking(new Expectations()
{
{
+ one(specificDAOFactory).getProteinQueryDAO(experimentID);
+ will(returnValue(proteinDAO));
+
one(experimentDAO).getByTechId(experimentID);
ExperimentPE experiment = new ExperimentPE();
experiment.setPermId("exp-1");
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSummaryTableTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSummaryTableTest.java
index 96a8e791d62bc18f443eefc1e32ecc00f1cd4b98..8bba9b0753f2aed1a87e7289c423a209fdb4fe5d 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSummaryTableTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ProteinSummaryTableTest.java
@@ -60,13 +60,6 @@ public class ProteinSummaryTableTest extends AbstractServerTestCase
super.setUp();
specificDAOFactory = context.mock(IPhosphoNetXDAOFactory.class);
proteinDAO = context.mock(IProteinQueryDAO.class);
- context.checking(new Expectations()
- {
- {
- allowing(specificDAOFactory).getProteinQueryDAO();
- will(returnValue(proteinDAO));
- }
- });
table = new ProteinSummaryTable(daoFactory, specificDAOFactory, SESSION);
}
@@ -180,6 +173,9 @@ public class ProteinSummaryTableTest extends AbstractServerTestCase
context.checking(new Expectations()
{
{
+ allowing(specificDAOFactory).getProteinQueryDAO(EXPERIMENT_ID);
+ will(returnValue(proteinDAO));
+
one(experimentDAO).getByTechId(EXPERIMENT_ID);
ExperimentPE experimentPE = new ExperimentPE();
experimentPE.setPermId(EXPERIMENT_PERM_ID);