diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
index 3d2c1a1d332a4949e8326038606c1181efe1578e..663bcbaebaa1541211f21506e2df75f760013278 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
@@ -18,7 +18,9 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.server;
import java.util.ArrayList;
import java.util.Collection;
+import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Map;
import javax.annotation.Resource;
@@ -43,6 +45,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IDataSetProte
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IProteinDetailsBO;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IProteinSequenceTable;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IProteinWithAbundancesTable;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.ISampleIDProvider;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.ISampleTable;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.TreatmentFinder;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IPhosphoNetXDAOFactory;
@@ -56,7 +59,6 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSeque
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.SampleWithPropertiesAndAbundance;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinWithAbundances;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.SimpleSample;
/**
* @author Franz-Josef Elmer
@@ -98,31 +100,35 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
public List<AbundanceColumnDefinition> getAbundanceColumnDefinitionsForProteinByExperiment(
String sessionToken, TechId experimentID) throws UserFailureException
{
- getSessionManager().getSession(sessionToken);
+ Session session = getSessionManager().getSession(sessionToken);
String experimentPermID = getExperimentPermIDFor(experimentID);
IProteinQueryDAO dao = specificDAOFactory.getProteinQueryDAO();
- DataSet<SimpleSample> samples = dao.listAbundanceRelatedSamplesByExperiment(experimentPermID);
+ DataSet<String> samplePermIDs =
+ dao.listAbundanceRelatedSamplePermIDsByExperiment(experimentPermID);
try
{
- List<AbundanceColumnDefinition> columnDefinitions = new ArrayList<AbundanceColumnDefinition>();
- for (SimpleSample simpleSample : samples)
+ Map<Long, AbundanceColumnDefinition> columnDefinitions =
+ new LinkedHashMap<Long, AbundanceColumnDefinition>();
+ ISampleIDProvider idProvider = specificBOFactory.createSampleIDProvider(session);
+ for (String samplePermID : samplePermIDs)
{
- AbundanceColumnDefinition columnDefinition = new AbundanceColumnDefinition();
- columnDefinition.setSampleID(simpleSample.getId());
- String samplePermID = simpleSample.getSamplePermID();
- SamplePE sample = getDAOFactory().getSampleDAO().tryToFindByPermID(samplePermID);
- if (sample == null)
+ long sampleID = idProvider.getSampleIDOrParentSampleID(samplePermID);
+ AbundanceColumnDefinition columnDefinition = columnDefinitions.get(sampleID);
+ if (columnDefinition == null)
{
- throw new UserFailureException("No sample found for perm ID " + samplePermID);
+ columnDefinition = new AbundanceColumnDefinition();
+ columnDefinition.setSampleID(sampleID);
+ SamplePE sample =
+ getDAOFactory().getSampleDAO().getByTechId(new TechId(sampleID));
+ columnDefinition.setSampleCode(sample.getCode());
+ columnDefinition.setTreatments(treatmentFinder.findTreatmentsOf(sample));
+ columnDefinitions.put(sampleID, columnDefinition);
}
- columnDefinition.setSampleCode(sample.getCode());
- columnDefinition.setTreatments(treatmentFinder.findTreatmentsOf(sample));
- columnDefinitions.add(columnDefinition);
}
- return columnDefinitions;
+ return new ArrayList<AbundanceColumnDefinition>(columnDefinitions.values());
} finally
{
- samples.close();
+ samplePermIDs.close();
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManager.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManager.java
index 015aea99500d62b0d80f0ea711c2f2acd27e1699..df7c4fd37a3be54df7037739d807c3dd36332058 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManager.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManager.java
@@ -22,6 +22,7 @@ import java.util.LinkedHashSet;
import java.util.Map;
import java.util.Set;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinWithAbundances;
@@ -33,19 +34,33 @@ class AbundanceManager
private final Map<String, ProteinWithAbundances> proteins =
new LinkedHashMap<String, ProteinWithAbundances>();
+ private final ISampleIDProvider sampleIDProvider;
+
private final Set<Long> sampleIDs = new LinkedHashSet<Long>();
+ AbundanceManager(ISampleDAO sampleDAO)
+ {
+ this(new SampleIDProvider(sampleDAO));
+ }
+
+ AbundanceManager(ISampleIDProvider sampleIDProvider)
+ {
+ this.sampleIDProvider = sampleIDProvider;
+
+ }
+
public void handle(ProteinReferenceWithProbability proteinReference)
{
ProteinWithAbundances protein = getOrCreateProtein(proteinReference);
- Long sampleID = proteinReference.getSampleID();
- if (sampleID != null)
+ String samplePermID = proteinReference.getSamplePermID();
+ if (samplePermID != null)
{
+ long sampleID = sampleIDProvider.getSampleIDOrParentSampleID(samplePermID);
sampleIDs.add(sampleID);
protein.addAbundanceFor(sampleID, proteinReference.getAbundance());
}
}
-
+
private ProteinWithAbundances getOrCreateProtein(ProteinReferenceWithProbability proteinReference)
{
String accessionNumber = proteinReference.getAccessionNumber();
@@ -66,7 +81,7 @@ class AbundanceManager
return proteins.values();
}
- public final Set<Long> getSampleIDs()
+ public final Collection<Long> getSampleIDs()
{
return sampleIDs;
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
index 0cf6f83ccd79ffa00b57b841fc2a7a087c47b4d6..7706d2acce24c217d2d6daf47335768a36692ae8 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
@@ -61,4 +61,9 @@ public class BusinessObjectFactory implements IBusinessObjectFactory
return new SampleTable(daoFactory, specificDAOFactory, session);
}
+ public ISampleIDProvider createSampleIDProvider(Session session)
+ {
+ return new SampleIDProvider(daoFactory.getSampleDAO());
+ }
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java
index 26caab4125ee9a22686c8b62d03433ee24004bd8..ae828695b5510271fdd8701f3b35fef0408ea6a3 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java
@@ -34,4 +34,6 @@ public interface IBusinessObjectFactory
public IProteinDetailsBO createProteinDetailsBO(Session session);
public ISampleTable createSampleTable(Session session);
+
+ public ISampleIDProvider createSampleIDProvider(Session session);
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IProteinWithAbundancesTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IProteinWithAbundancesTable.java
index a4559040d722dea16bc99d9bcdf80b5670ef2683..7e40d2eb4443726b00e5629513a4dc21a4192fc5 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IProteinWithAbundancesTable.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IProteinWithAbundancesTable.java
@@ -17,7 +17,6 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business;
import java.util.Collection;
-import java.util.Set;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinWithAbundances;
@@ -36,6 +35,6 @@ public interface IProteinWithAbundancesTable
public Collection<ProteinWithAbundances> getProteinsWithAbundances();
- public Set<Long> getSampleIDs();
+ public Collection<Long> getSampleIDs();
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/SimpleSample.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ISampleIDProvider.java
similarity index 59%
rename from rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/SimpleSample.java
rename to rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ISampleIDProvider.java
index 99905077d2e00f03b84dcc539a10fd5880fd131c..a1a7b7205a8ca24076d71ec4020d2da333ffcd32 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/SimpleSample.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ISampleIDProvider.java
@@ -14,29 +14,22 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto;
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business;
-import net.lemnik.eodsql.ResultColumn;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
/**
- *
+ * Provides the ID of a sample or its parent.
*
* @author Franz-Josef Elmer
*/
-public class SimpleSample extends AbstractDTOWithID
+public interface ISampleIDProvider
{
-
- @ResultColumn("perm_id")
- private String samplePermID;
-
- public final String getSamplePermID()
- {
- return samplePermID;
- }
-
- public final void setSamplePermID(String samplePermID)
- {
- this.samplePermID = samplePermID;
- }
+ /**
+ * Returns the ID of the specified sample or the ID of its parent if it exist.
+ *
+ * @throws UserFailureException if no sample could be found.
+ */
+ public long getSampleIDOrParentSampleID(String samplePermID);
}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinWithAbundancesTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinWithAbundancesTable.java
index 0788af1d9bad71f8bc2d517f2886e1a050c4c080..bac44d1b9f53c9e095b5159a521a664a76adcb80 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinWithAbundancesTable.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinWithAbundancesTable.java
@@ -18,7 +18,6 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business;
import java.util.ArrayList;
import java.util.Collection;
-import java.util.Set;
import net.lemnik.eodsql.DataSet;
@@ -38,7 +37,7 @@ class ProteinWithAbundancesTable extends AbstractBusinessObject implements
IProteinWithAbundancesTable
{
private Collection<ProteinWithAbundances> proteins;
- private Set<Long> sampleIDs;
+ private Collection<Long> sampleIDs;
ProteinWithAbundancesTable(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory,
Session session)
@@ -57,7 +56,7 @@ class ProteinWithAbundancesTable extends AbstractBusinessObject implements
public void load(String experimentPermID, double falseDiscoveryRate)
{
- AbundanceManager abundanceManager = new AbundanceManager();
+ AbundanceManager abundanceManager = new AbundanceManager(getDaoFactory().getSampleDAO());
proteins = new ArrayList<ProteinWithAbundances>();
IProteinQueryDAO dao = getSpecificDAOFactory().getProteinQueryDAO();
ErrorModel errorModel = new ErrorModel(getSpecificDAOFactory());
@@ -80,7 +79,7 @@ class ProteinWithAbundancesTable extends AbstractBusinessObject implements
}
}
- public Set<Long> getSampleIDs()
+ public Collection<Long> getSampleIDs()
{
if (sampleIDs == null)
{
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleIDProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleIDProvider.java
new file mode 100644
index 0000000000000000000000000000000000000000..5a8a2f9d2a747349643be5f125101f231b963aea
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleIDProvider.java
@@ -0,0 +1,63 @@
+/*
+ * 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.plugin.phosphonetx.server.business;
+
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
+
+/**
+ * Implementation based on {@link ISampleDAO}.
+ *
+ * @author Franz-Josef Elmer
+ */
+class SampleIDProvider implements ISampleIDProvider
+{
+ private final ISampleDAO sampleDAO;
+ private final Map<String, Long> sampleIDs = new LinkedHashMap<String, Long>();
+
+ SampleIDProvider(ISampleDAO sampleDAO)
+ {
+ this.sampleDAO = sampleDAO;
+ }
+
+ public long getSampleIDOrParentSampleID(String samplePermID)
+ {
+ Long sampleID = sampleIDs.get(samplePermID);
+ if (sampleID == null)
+ {
+ SamplePE sample = sampleDAO.tryToFindByPermID(samplePermID);
+ if (sample == null)
+ {
+ throw new UserFailureException("No sample found for permID " + samplePermID);
+ }
+ sampleID = sample.getId();
+ SamplePE parentSample = sample.getGeneratedFrom();
+ if (parentSample != null)
+ {
+ sampleID = HibernateUtils.getId(parentSample);
+ }
+ sampleIDs.put(samplePermID, sampleID);
+ }
+ return sampleID;
+
+ }
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java
index c6e6a58983d4167f4210d825dfd356f7cee4882b..5c73ea7bf195f1f10a838615d89223cc418fa68a 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java
@@ -27,7 +27,6 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.SampleAbundance;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.Sequence;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.SimpleSample;
/**
*
@@ -40,7 +39,7 @@ public interface IProteinQueryDAO extends BaseQuery
public DataSet<ProbabilityFDRMapping> getProbabilityFDRMapping(long dataSetID);
@Select("select pr.id, pr.accession_number, pr.description, d.id as data_set_id, p.probability, "
- + " a.value as abundance, samples.id as sample_id "
+ + " a.value as abundance, samples.perm_id as sample_perm_id "
+ "from identified_proteins as ip left join proteins as p on ip.prot_id = p.id "
+ "left join data_sets as d on p.dase_id = d.id "
+ "left join experiments as e on d.expe_id = e.id "
@@ -48,16 +47,16 @@ public interface IProteinQueryDAO extends BaseQuery
+ "left join protein_references as pr on s.prre_id = pr.id "
+ "left join abundances as a on p.id = a.prot_id "
+ "left join samples on a.samp_id = samples.id "
- + "where e.perm_id = ?{1} order by pr.accession_number, samples.id")
+ + "where e.perm_id = ?{1} order by pr.accession_number, samples.perm_id")
public DataSet<ProteinReferenceWithProbability> listProteinsByExperiment(String experimentPermID);
- @Select("select distinct s.id, s.perm_id "
+ @Select("select distinct s.perm_id "
+ "from abundances as a left join proteins as p on a.prot_id = p.id "
+ " left join data_sets as d on p.dase_id = d.id "
+ " left join experiments as e on d.expe_id = e.id "
+ " left join samples as s on a.samp_id = s.id "
+ "where e.perm_id = ?{1}")
- public DataSet<SimpleSample> listAbundanceRelatedSamplesByExperiment(String experimentPermID);
+ public DataSet<String> listAbundanceRelatedSamplePermIDsByExperiment(String experimentPermID);
@Select("select * from protein_references where id = ?{1}")
public ProteinReference tryToGetProteinReference(long proteinReferenceID);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProbability.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProbability.java
index 030e8b8e0a304b5f99d978b81e1fad1f737c0952..73bd90d1b340ec940bcfd2a6fb0f947d057764c3 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProbability.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProbability.java
@@ -34,8 +34,8 @@ public class ProteinReferenceWithProbability extends ProteinReference
@ResultColumn("abundance")
private Double abundance;
- @ResultColumn("sample_id")
- private Long sampleID;
+ @ResultColumn("sample_perm_id")
+ private String samplePermID;
public final long getDataSetID()
{
@@ -67,14 +67,14 @@ public class ProteinReferenceWithProbability extends ProteinReference
this.abundance = abundance;
}
- public final Long getSampleID()
+ public final String getSamplePermID()
{
- return sampleID;
+ return samplePermID;
}
- public final void setSampleID(Long sampleID)
+ public final void setSamplePermID(String samplePermID)
{
- this.sampleID = sampleID;
+ this.samplePermID = samplePermID;
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/SampleAbundance.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/SampleAbundance.java
index ff2e8d0a59b5c25ba93d1edb601b6fb32b1fa9b2..6fd3bedfeee9641a4d209a86edf9ce54f09a0c74 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/SampleAbundance.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/SampleAbundance.java
@@ -24,8 +24,11 @@ import net.lemnik.eodsql.ResultColumn;
*
* @author Franz-Josef Elmer
*/
-public class SampleAbundance extends SimpleSample
+public class SampleAbundance extends AbstractDTOWithID
{
+ @ResultColumn("perm_id")
+ private String samplePermID;
+
@ResultColumn("value")
private double abundance;
@@ -39,4 +42,14 @@ public class SampleAbundance extends SimpleSample
this.abundance = abundance;
}
+ public final String getSamplePermID()
+ {
+ return samplePermID;
+ }
+
+ public final void setSamplePermID(String samplePermID)
+ {
+ this.samplePermID = samplePermID;
+ }
+
}
diff --git a/rtd_phosphonetx/source/sql/postgresql/001/schema-001.png b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.png
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..84c5a177c879021beacb52d4070ae887bcb89a7c 100644
Binary files a/rtd_phosphonetx/source/sql/postgresql/001/schema-001.png and b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.png differ
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerTest.java
index 678756e6dcb709b66b2c9b1de84490752470d4b8..1a01c15b0d7522d3019d44b8c6b9de84964457a6 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerTest.java
@@ -25,7 +25,6 @@ import org.jmock.Expectations;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.plugin.IDataSetTypeSlaveServerPlugin;
import ch.systemsx.cisd.openbis.generic.server.plugin.ISampleTypeSlaveServerPlugin;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
@@ -39,10 +38,10 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyTermPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityDataType;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.ISampleIDProvider;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IPhosphoNetXDAOFactory;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQueryDAO;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceColumnDefinition;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.SimpleSample;
/**
*
@@ -53,8 +52,8 @@ public class PhosphoNetXServerTest extends AbstractServerTestCase
{
private static final TechId EXPERIMENT_ID = new TechId(42L);
private static final String EXPERIMENT_PERM_ID = "e123-45";
- private static final long SAMPLE_ID = 4711;
private static final String SAMPLE_PERM_ID = "s34-56";
+ private static final long SAMPLE_ID = 4711;
private static final String SAMPLE_CODE = "S42";
private IPhosphoNetXDAOFactory phosphoNetXDAOFactory;
@@ -63,6 +62,7 @@ public class PhosphoNetXServerTest extends AbstractServerTestCase
private IDataSetTypeSlaveServerPlugin dataSetTypeSlaveServerPlugin;
private IProteinQueryDAO proteinDAO;
private PhosphoNetXServer server;
+ private ISampleIDProvider sampleIDProvider;
@Override
@BeforeMethod
@@ -71,6 +71,7 @@ public class PhosphoNetXServerTest extends AbstractServerTestCase
super.setUp();
phosphoNetXDAOFactory = context.mock(IPhosphoNetXDAOFactory.class);
boFactory = context.mock(IBusinessObjectFactory.class);
+ sampleIDProvider = context.mock(ISampleIDProvider.class);
sampleTypeSlaveServerPlugin = context.mock(ISampleTypeSlaveServerPlugin.class);
dataSetTypeSlaveServerPlugin = context.mock(IDataSetTypeSlaveServerPlugin.class);
proteinDAO = context.mock(IProteinQueryDAO.class);
@@ -88,84 +89,75 @@ public class PhosphoNetXServerTest extends AbstractServerTestCase
}
@Test
- public void testGetAbundanceColumnDefinitionsForUnkownSample()
+ public void testGetNoAbundanceColumnDefinitions()
{
prepareGetSession();
prepareGetExperimentPermID();
- MockDataSet<SimpleSample> mockDataSet = new MockDataSet<SimpleSample>();
- SimpleSample s = new SimpleSample();
- s.setId(SAMPLE_ID);
- s.setSamplePermID(SAMPLE_PERM_ID);
- mockDataSet.add(s);
+ MockDataSet<String> mockDataSet = new MockDataSet<String>();
prepareListAbundanceRelatedSamples(mockDataSet);
- prepareFindSample(null);
-
- try
- {
+
+ List<AbundanceColumnDefinition> definitions =
server.getAbundanceColumnDefinitionsForProteinByExperiment(SESSION_TOKEN,
EXPERIMENT_ID);
- fail("UserFailureException expected");
- } catch (UserFailureException e)
- {
- assertEquals("No sample found for perm ID " + SAMPLE_PERM_ID, e.getMessage());
- }
-
+ assertEquals(0, definitions.size());
assertEquals(true, mockDataSet.hasCloseBeenInvoked());
context.assertIsSatisfied();
}
-
+
@Test
- public void testGetNoAbundanceColumnDefinitions()
+ public void testGetOneAbundanceColumnDefinitionWithoutTreatments()
{
prepareGetSession();
prepareGetExperimentPermID();
- MockDataSet<SimpleSample> mockDataSet = new MockDataSet<SimpleSample>();
+ MockDataSet<String> mockDataSet = new MockDataSet<String>();
+ mockDataSet.add(SAMPLE_PERM_ID);
prepareListAbundanceRelatedSamples(mockDataSet);
+ prepareFindSample(createSample());
List<AbundanceColumnDefinition> definitions =
server.getAbundanceColumnDefinitionsForProteinByExperiment(SESSION_TOKEN,
EXPERIMENT_ID);
- assertEquals(0, definitions.size());
+ assertEquals(1, definitions.size());
+ assertEquals(SAMPLE_CODE, definitions.get(0).getSampleCode());
+ assertEquals(0, definitions.get(0).getTreatments().size());
+
assertEquals(true, mockDataSet.hasCloseBeenInvoked());
context.assertIsSatisfied();
}
@Test
- public void testGetOneAbundanceColumnDefinitionWithoutTreatments()
+ public void testGetOneAbundanceColumnDefinitionWithOneTreatment()
{
prepareGetSession();
prepareGetExperimentPermID();
- MockDataSet<SimpleSample> mockDataSet = new MockDataSet<SimpleSample>();
- SimpleSample s = new SimpleSample();
- s.setId(SAMPLE_ID);
- s.setSamplePermID(SAMPLE_PERM_ID);
- mockDataSet.add(s);
+ MockDataSet<String> mockDataSet = new MockDataSet<String>();
+ mockDataSet.add(SAMPLE_PERM_ID);
prepareListAbundanceRelatedSamples(mockDataSet);
- prepareFindSample(createSample());
+ final SamplePE samplePE = createSample();
+ addTreatment(samplePE, "", "abc");
+ prepareFindSample(samplePE);
List<AbundanceColumnDefinition> definitions =
server.getAbundanceColumnDefinitionsForProteinByExperiment(SESSION_TOKEN,
EXPERIMENT_ID);
assertEquals(1, definitions.size());
- assertEquals(SAMPLE_ID, definitions.get(0).getSampleID());
assertEquals(SAMPLE_CODE, definitions.get(0).getSampleCode());
- assertEquals(0, definitions.get(0).getTreatments().size());
+ assertEquals(1, definitions.get(0).getTreatments().size());
+ assertEquals("abc", definitions.get(0).getTreatments().get(0).getValue());
+ assertEquals("PH", definitions.get(0).getTreatments().get(0).getType());
assertEquals(true, mockDataSet.hasCloseBeenInvoked());
context.assertIsSatisfied();
}
-
@Test
- public void testGetOneAbundanceColumnDefinitionWithOneTreatment()
+ public void testGetAbundanceColumnDefinitionForTwoSamplesWithSameParent()
{
prepareGetSession();
prepareGetExperimentPermID();
- MockDataSet<SimpleSample> mockDataSet = new MockDataSet<SimpleSample>();
- SimpleSample s = new SimpleSample();
- s.setId(SAMPLE_ID);
- s.setSamplePermID(SAMPLE_PERM_ID);
- mockDataSet.add(s);
+ MockDataSet<String> mockDataSet = new MockDataSet<String>();
+ mockDataSet.add(SAMPLE_PERM_ID);
+ mockDataSet.add(SAMPLE_PERM_ID + "a");
prepareListAbundanceRelatedSamples(mockDataSet);
final SamplePE samplePE = createSample();
addTreatment(samplePE, "", "abc");
@@ -175,7 +167,6 @@ public class PhosphoNetXServerTest extends AbstractServerTestCase
server.getAbundanceColumnDefinitionsForProteinByExperiment(SESSION_TOKEN,
EXPERIMENT_ID);
assertEquals(1, definitions.size());
- assertEquals(SAMPLE_ID, definitions.get(0).getSampleID());
assertEquals(SAMPLE_CODE, definitions.get(0).getSampleCode());
assertEquals(1, definitions.get(0).getTreatments().size());
assertEquals("abc", definitions.get(0).getTreatments().get(0).getValue());
@@ -190,19 +181,28 @@ public class PhosphoNetXServerTest extends AbstractServerTestCase
context.checking(new Expectations()
{
{
- one(sampleDAO).tryToFindByPermID(SAMPLE_PERM_ID);
+ one(sampleDAO).getByTechId(new TechId(SAMPLE_ID));
will(returnValue(samplePE));
}
});
}
- private void prepareListAbundanceRelatedSamples(final MockDataSet<SimpleSample> mockDataSet)
+ private void prepareListAbundanceRelatedSamples(final MockDataSet<String> mockDataSet)
{
context.checking(new Expectations()
{
{
- one(proteinDAO).listAbundanceRelatedSamplesByExperiment(EXPERIMENT_PERM_ID);
+ one(proteinDAO).listAbundanceRelatedSamplePermIDsByExperiment(EXPERIMENT_PERM_ID);
will(returnValue(mockDataSet));
+
+ one(boFactory).createSampleIDProvider(SESSION);
+ will(returnValue(sampleIDProvider));
+
+ for (String samplePermID : mockDataSet)
+ {
+ one(sampleIDProvider).getSampleIDOrParentSampleID(samplePermID);
+ will(returnValue(SAMPLE_ID));
+ }
}
});
}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManagerTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManagerTest.java
index 9d7b516b549d5512da47db7217a562ff102d3f0c..ccba48f2df6dafad324729a115a19201727fa4d0 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManagerTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManagerTest.java
@@ -19,9 +19,11 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business;
import java.util.Collection;
import java.util.Iterator;
-import org.testng.AssertJUnit;
+import org.jmock.Expectations;
+import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinWithAbundances;
@@ -30,13 +32,29 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinWithAbundan
*
* @author Franz-Josef Elmer
*/
-public class AbundanceManagerTest extends AssertJUnit
+public class AbundanceManagerTest extends AbstractServerTestCase
{
+ private static final String PERM_ID1 = "s101";
+ private static final String PERM_ID2 = "s102";
+ private static final long SAMPLE_ID_A = 42;
+ private static final long SAMPLE_ID_B = 4711;
+
+ private AbundanceManager abundanceManager;
+ private ISampleIDProvider sampleIDProvider;
+
+ @Override
+ @BeforeMethod
+ public void setUp()
+ {
+ super.setUp();
+
+ sampleIDProvider = context.mock(ISampleIDProvider.class);
+ abundanceManager = new AbundanceManager(sampleIDProvider);
+ }
@Test
public void testNoProteinReferenceHandled()
{
- AbundanceManager abundanceManager = new AbundanceManager();
assertEquals(0, abundanceManager.getSampleIDs().size());
assertEquals(0, abundanceManager.getProteinsWithAbundances().size());
}
@@ -44,12 +62,12 @@ public class AbundanceManagerTest extends AssertJUnit
@Test
public void testHandleTwoProteinReferencesButOnlyOneHasAnAbundance()
{
- AbundanceManager abundanceManager = new AbundanceManager();
+ prepareSampleIDProvider();
ProteinReferenceWithProbability protein1 = new ProteinReferenceWithProbability();
protein1.setId(1);
protein1.setAccessionNumber("abc1");
protein1.setDescription("abc one");
- protein1.setSampleID(101L);
+ protein1.setSamplePermID(PERM_ID1);
protein1.setAbundance(1.5);
abundanceManager.handle(protein1);
ProteinReferenceWithProbability protein2 = new ProteinReferenceWithProbability();
@@ -67,26 +85,28 @@ public class AbundanceManagerTest extends AssertJUnit
assertEquals("abc one", p1.getDescription());
assertEquals("abc1", p1.getAccessionNumber());
assertEquals(1, p1.getSampleIDs().size());
- assertEquals(101, p1.getSampleIDs().iterator().next().longValue());
+ assertEquals(SAMPLE_ID_A, p1.getSampleIDs().iterator().next().longValue());
assertEquals(0, p1.getAbundancesForSample(12345678).length);
- assertEquals(1, p1.getAbundancesForSample(101).length);
- assertEquals(1.5, p1.getAbundancesForSample(101)[0]);
+ assertEquals(1, p1.getAbundancesForSample(SAMPLE_ID_A).length);
+ assertEquals(1.5, p1.getAbundancesForSample(SAMPLE_ID_A)[0]);
ProteinWithAbundances p2 = iterator.next();
assertEquals(2, p2.getId());
assertEquals("abc two", p2.getDescription());
assertEquals("abc2", p2.getAccessionNumber());
assertEquals(0, p2.getSampleIDs().size());
+
+ context.assertIsSatisfied();
}
@Test
public void testHandleProteinReferencesWithManyAbundancesForTwoSamples()
{
- AbundanceManager abundanceManager = new AbundanceManager();
- abundanceManager.handle(createProteinReference(101, 1.5));
- abundanceManager.handle(createProteinReference(101, 2.25));
- abundanceManager.handle(createProteinReference(102, 42));
- abundanceManager.handle(createProteinReference(102, 4.75));
- abundanceManager.handle(createProteinReference(102, 7.5));
+ prepareSampleIDProvider();
+ abundanceManager.handle(createProteinReference(PERM_ID1, 1.5));
+ abundanceManager.handle(createProteinReference(PERM_ID1, 2.25));
+ abundanceManager.handle(createProteinReference(PERM_ID2, 42));
+ abundanceManager.handle(createProteinReference(PERM_ID2, 4.75));
+ abundanceManager.handle(createProteinReference(PERM_ID2, 7.5));
assertEquals(2, abundanceManager.getSampleIDs().size());
Collection<ProteinWithAbundances> proteinsWithAbundances = abundanceManager.getProteinsWithAbundances();
@@ -97,24 +117,39 @@ public class AbundanceManagerTest extends AssertJUnit
assertEquals("abc1", protein.getAccessionNumber());
assertEquals(2, protein.getSampleIDs().size());
Iterator<Long> iterator = protein.getSampleIDs().iterator();
- assertEquals(101, iterator.next().longValue());
- assertEquals(102, iterator.next().longValue());
- assertEquals(2, protein.getAbundancesForSample(101).length);
- assertEquals(1.5, protein.getAbundancesForSample(101)[0]);
- assertEquals(2.25, protein.getAbundancesForSample(101)[1]);
- assertEquals(3, protein.getAbundancesForSample(102).length);
- assertEquals(42.0, protein.getAbundancesForSample(102)[0]);
- assertEquals(4.75, protein.getAbundancesForSample(102)[1]);
- assertEquals(7.5, protein.getAbundancesForSample(102)[2]);
+ assertEquals(SAMPLE_ID_A, iterator.next().longValue());
+ assertEquals(SAMPLE_ID_B, iterator.next().longValue());
+ assertEquals(2, protein.getAbundancesForSample(SAMPLE_ID_A).length);
+ assertEquals(1.5, protein.getAbundancesForSample(SAMPLE_ID_A)[0]);
+ assertEquals(2.25, protein.getAbundancesForSample(SAMPLE_ID_A)[1]);
+ assertEquals(3, protein.getAbundancesForSample(SAMPLE_ID_B).length);
+ assertEquals(42.0, protein.getAbundancesForSample(SAMPLE_ID_B)[0]);
+ assertEquals(4.75, protein.getAbundancesForSample(SAMPLE_ID_B)[1]);
+ assertEquals(7.5, protein.getAbundancesForSample(SAMPLE_ID_B)[2]);
+
+ context.assertIsSatisfied();
+ }
+
+ private void prepareSampleIDProvider()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ allowing(sampleIDProvider).getSampleIDOrParentSampleID(PERM_ID1);
+ will(returnValue(SAMPLE_ID_A));
+ allowing(sampleIDProvider).getSampleIDOrParentSampleID(PERM_ID2);
+ will(returnValue(SAMPLE_ID_B));
+ }
+ });
}
- private ProteinReferenceWithProbability createProteinReference(long sampleID, double abundance)
+ private ProteinReferenceWithProbability createProteinReference(String samplePermID, double abundance)
{
ProteinReferenceWithProbability protein1 = new ProteinReferenceWithProbability();
protein1.setId(1);
protein1.setAccessionNumber("abc1");
protein1.setDescription("abc one");
- protein1.setSampleID(sampleID);
+ protein1.setSamplePermID(samplePermID);
protein1.setAbundance(abundance);
return protein1;
}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinWithAbundancesTableTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinWithAbundancesTableTest.java
index 85e6cf920f8ec3dc1df65501dea9d0e74c5daa38..7dc51258fe0c55a4e310d787945c1118753ef2b6 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinWithAbundancesTableTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinWithAbundancesTableTest.java
@@ -17,13 +17,13 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business;
import java.util.Collection;
-import java.util.Set;
import org.jmock.Expectations;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.MockDataSet;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IPhosphoNetXDAOFactory;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQueryDAO;
@@ -40,7 +40,8 @@ public class ProteinWithAbundancesTableTest extends AbstractServerTestCase
{
private static final Double ABUNDANCE = new Double(47.11);
private static final long PROTEIN_ID = 41L;
- private static final long SAMPLE_ID = 4711L;
+ private static final String SAMPLE_PERM_ID = "s47-11";
+ private static final long SAMPLE_ID = 4711;
private static final long DATA_SET_ID = 42L;
private static final String EXPERIMENT_ID = "abc-234";
private static final double FALSE_DISCOVERY_RATE = 0.25;
@@ -96,7 +97,7 @@ public class ProteinWithAbundancesTableTest extends AbstractServerTestCase
new MockDataSet<ProteinReferenceWithProbability>();
ProteinReferenceWithProbability proteinReference = new ProteinReferenceWithProbability();
proteinReference.setDataSetID(DATA_SET_ID);
- proteinReference.setSampleID(SAMPLE_ID);
+ proteinReference.setSamplePermID(SAMPLE_PERM_ID);
proteinReference.setAccessionNumber(ACCESSION_NUMBER);
proteinReference.setId(PROTEIN_ID);
proteinReference.setAbundance(ABUNDANCE);
@@ -112,19 +113,24 @@ public class ProteinWithAbundancesTableTest extends AbstractServerTestCase
mapping.setFalseDiscoveryRate(1);
mappings.add(mapping);
context.checking(new Expectations()
- {
{
- one(proteinDAO).listProteinsByExperiment(EXPERIMENT_ID);
- will(returnValue(dataSet));
-
- one(proteinDAO).getProbabilityFDRMapping(DATA_SET_ID);
- will(returnValue(mappings));
- }
- });
+ {
+ one(proteinDAO).listProteinsByExperiment(EXPERIMENT_ID);
+ will(returnValue(dataSet));
+
+ one(proteinDAO).getProbabilityFDRMapping(DATA_SET_ID);
+ will(returnValue(mappings));
+
+ one(sampleDAO).tryToFindByPermID(SAMPLE_PERM_ID);
+ SamplePE samplePE = new SamplePE();
+ samplePE.setId(SAMPLE_ID);
+ will(returnValue(samplePE));
+ }
+ });
table.load(EXPERIMENT_ID, FALSE_DISCOVERY_RATE);
- Set<Long> sampleIDs = table.getSampleIDs();
+ Collection<Long> sampleIDs = table.getSampleIDs();
assertEquals(1, sampleIDs.size());
Long sampleID = sampleIDs.iterator().next();
assertEquals(SAMPLE_ID, sampleID.longValue());