From 76b1846a62fd7f7fc53cfef716ec0e16dd5c0672 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Wed, 2 Sep 2009 07:12:38 +0000
Subject: [PATCH] SE-127 some bugs (but not all) in samples table of protein
details view fixed
SVN: 12357
---
.../application/ProteinSamplesSection.java | 6 ++--
.../SampleAbundanceBrowserGrid.java | 6 ++--
.../ListSampleAbundanceByProteinCriteria.java | 10 +++---
.../ListSampleAbundanceDataProvider.java | 9 +++---
.../web/server/PhosphoNetXClientService.java | 2 +-
.../phosphonetx/server/PhosphoNetXServer.java | 4 +--
.../server/PhosphoNetXServerLogger.java | 6 ++--
.../server/business/ISampleTable.java | 2 +-
.../server/business/SampleTable.java | 32 +++++--------------
.../server/dataaccess/IProteinQueryDAO.java | 10 ++++--
.../shared/IPhosphoNetXServer.java | 2 +-
11 files changed, 39 insertions(+), 50 deletions(-)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinSamplesSection.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinSamplesSection.java
index 0d7b2f5c3e3..6330f85a981 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinSamplesSection.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinSamplesSection.java
@@ -38,12 +38,12 @@ public class ProteinSamplesSection extends SingleSectionPanel
private IDisposableComponent sampleDisposableGrid;
public ProteinSamplesSection(final IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- final TechId proteinID)
+ final TechId proteinReferenceID)
{
super("Samples");
sampleDisposableGrid =
- SampleAbundanceBrowserGrid.createGridForProteinSamples(viewContext, proteinID,
- createGridId(proteinID));
+ SampleAbundanceBrowserGrid.createGridForProteinSamples(viewContext, proteinReferenceID,
+ createGridId(proteinReferenceID));
add(sampleDisposableGrid.getComponent());
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/SampleAbundanceBrowserGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/SampleAbundanceBrowserGrid.java
index b4701b88583..053d69249d7 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/SampleAbundanceBrowserGrid.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/SampleAbundanceBrowserGrid.java
@@ -86,12 +86,12 @@ public class SampleAbundanceBrowserGrid
private final IViewContext<IPhosphoNetXClientServiceAsync> phosphoViewContext;
public static IDisposableComponent createGridForProteinSamples(
- final IViewContext<IPhosphoNetXClientServiceAsync> viewContext, final TechId proteinID,
- final String gridId)
+ final IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
+ final TechId proteinReferenceID, final String gridId)
{
final ListSampleAbundanceByProteinCriteria criteria =
new ListSampleAbundanceByProteinCriteria();
- criteria.setProteinID(proteinID);
+ criteria.setProteinReferenceID(proteinReferenceID);
ISampleAbundanceCriteriaProvider criteriaProvider =
new SampleAbundanceCriteriaProvider(viewContext, criteria);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListSampleAbundanceByProteinCriteria.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListSampleAbundanceByProteinCriteria.java
index 592ec020411..6eefaa1677b 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListSampleAbundanceByProteinCriteria.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListSampleAbundanceByProteinCriteria.java
@@ -30,15 +30,15 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.SampleWithPr
public class ListSampleAbundanceByProteinCriteria extends
DefaultResultSetConfig<String, SampleWithPropertiesAndAbundance> implements IsSerializable
{
- private TechId proteinID;
+ private TechId proteinReferenceID;
- public final TechId getProteinID()
+ public final TechId getProteinReferenceID()
{
- return proteinID;
+ return proteinReferenceID;
}
- public final void setProteinID(TechId proteinID)
+ public final void setProteinReferenceID(TechId proteinReferenceID)
{
- this.proteinID = proteinID;
+ this.proteinReferenceID = proteinReferenceID;
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListSampleAbundanceDataProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListSampleAbundanceDataProvider.java
index e8701aec368..13350d8a519 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListSampleAbundanceDataProvider.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListSampleAbundanceDataProvider.java
@@ -35,19 +35,20 @@ class ListSampleAbundanceDataProvider implements IOriginalDataProvider<SampleWit
private final String sessionToken;
- private final TechId proteinID;
+ private final TechId proteinReferenceID;
- ListSampleAbundanceDataProvider(IPhosphoNetXServer server, String sessionToken, TechId proteinID)
+ ListSampleAbundanceDataProvider(IPhosphoNetXServer server, String sessionToken,
+ TechId proteinReferenceID)
{
this.server = server;
this.sessionToken = sessionToken;
- this.proteinID = proteinID;
+ this.proteinReferenceID = proteinReferenceID;
}
public List<SampleWithPropertiesAndAbundance> getOriginalData() throws UserFailureException
{
- return server.listSamplesWithAbundanceByProtein(sessionToken, proteinID);
+ return server.listSamplesWithAbundanceByProtein(sessionToken, proteinReferenceID);
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
index b2696ff2588..a605154b033 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
@@ -144,7 +144,7 @@ public class PhosphoNetXClientService extends AbstractClientService implements
{
final String sessionToken = getSessionToken();
return listEntities(criteria, new ListSampleAbundanceDataProvider(server, sessionToken,
- criteria.getProteinID()));
+ criteria.getProteinReferenceID()));
}
public String prepareExportSamplesWithAbundance(
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 663bcbaebaa..0f964cb130b 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
@@ -187,11 +187,11 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
}
public List<SampleWithPropertiesAndAbundance> listSamplesWithAbundanceByProtein(
- String sessionToken, TechId proteinID) throws UserFailureException
+ String sessionToken, TechId proteinReferenceID) throws UserFailureException
{
final Session session = getSessionManager().getSession(sessionToken);
ISampleTable sampleTable = specificBOFactory.createSampleTable(session);
- sampleTable.loadSamplesWithAbundance(proteinID);
+ sampleTable.loadSamplesWithAbundance(proteinReferenceID);
return sampleTable.getSamples();
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerLogger.java
index 025e9d0e986..a3e35f953f3 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerLogger.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerLogger.java
@@ -83,10 +83,10 @@ public class PhosphoNetXServerLogger extends AbstractServerLogger implements IPh
}
public List<SampleWithPropertiesAndAbundance> listSamplesWithAbundanceByProtein(
- String sessionToken, TechId proteinID) throws UserFailureException
+ String sessionToken, TechId proteinReferenceID) throws UserFailureException
{
- logAccess(sessionToken, "list_samples_with_abundance_by_protein", "PROTEIN_ID(%s)",
- proteinID);
+ logAccess(sessionToken, "list_samples_with_abundance_by_protein", "PROTEIN_REFERENCE_ID(%s)",
+ proteinReferenceID);
return null;
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ISampleTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ISampleTable.java
index cbf5d9da684..63e7d88cf96 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ISampleTable.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ISampleTable.java
@@ -29,7 +29,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.SampleWithPr
public interface ISampleTable
{
- public void loadSamplesWithAbundance(TechId proteinID);
+ public void loadSamplesWithAbundance(TechId proteinReferenceID);
public List<SampleWithPropertiesAndAbundance> getSamples();
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleTable.java
index 4db06a266bf..85e07e332e3 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleTable.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleTable.java
@@ -27,7 +27,6 @@ import org.apache.commons.lang.StringEscapeUtils;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
@@ -47,10 +46,12 @@ class SampleTable extends AbstractBusinessObject implements ISampleTable
{
private List<SampleWithPropertiesAndAbundance> samples =
new ArrayList<SampleWithPropertiesAndAbundance>();
+ private SampleIDProvider sampleIDProvider;
SampleTable(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory, Session session)
{
super(daoFactory, specificDAOFactory, session);
+ sampleIDProvider = new SampleIDProvider(daoFactory.getSampleDAO());
}
public List<SampleWithPropertiesAndAbundance> getSamples()
@@ -58,13 +59,13 @@ class SampleTable extends AbstractBusinessObject implements ISampleTable
return samples;
}
- public void loadSamplesWithAbundance(TechId proteinID)
+ public void loadSamplesWithAbundance(TechId proteinReferenceID)
{
samples = new ArrayList<SampleWithPropertiesAndAbundance>();
IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO();
ISampleDAO sampleDAO = getDaoFactory().getSampleDAO();
DataSet<SampleAbundance> sampleAbundances =
- proteinQueryDAO.listSampleAbundanceByProtein(proteinID.getId());
+ proteinQueryDAO.listSampleAbundanceByProtein(proteinReferenceID.getId());
try
{
for (SampleAbundance sampleAbundance : sampleAbundances)
@@ -72,12 +73,8 @@ class SampleTable extends AbstractBusinessObject implements ISampleTable
SampleWithPropertiesAndAbundance sample = new SampleWithPropertiesAndAbundance();
sample.setAbundance(sampleAbundance.getAbundance());
String samplePermID = sampleAbundance.getSamplePermID();
- SamplePE samplePE = sampleDAO.tryToFindByPermID(samplePermID);
- if (samplePE == null)
- {
- throw new IllegalStateException("No sample with following permanent ID found: "
- + samplePermID);
- }
+ long sampleID = sampleIDProvider.getSampleIDOrParentSampleID(samplePermID);
+ SamplePE samplePE = sampleDAO.getByTechId(new TechId(sampleID));
fillSampleData(sample, samplePE);
samples.add(sample);
}
@@ -95,20 +92,7 @@ class SampleTable extends AbstractBusinessObject implements ISampleTable
result.setIdentifier(StringEscapeUtils.escapeHtml(samplePE.getIdentifier()));
result.setSampleType(SampleTypeTranslator.translate(samplePE.getSampleType(),
new HashMap<PropertyTypePE, PropertyType>()));
- setProperties(result, samplePE);
- }
-
- private static void setProperties(final SampleWithPropertiesAndAbundance result,
- final SamplePE samplePE)
- {
- if (samplePE.isPropertiesInitialized())
- {
- result.setProperties(EntityPropertyTranslator.translate(samplePE.getProperties(),
- new HashMap<PropertyTypePE, PropertyType>()));
- } else
- {
- result.setProperties(new ArrayList<IEntityProperty>());
- }
+ result.setProperties(EntityPropertyTranslator.translate(samplePE.getProperties(),
+ new HashMap<PropertyTypePE, PropertyType>()));
}
-
}
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 5c73ea7bf19..232314502d4 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
@@ -83,8 +83,12 @@ public interface IProteinQueryDAO extends BaseQuery
@Select("select * from peptides where prot_id = ?{1}")
public DataSet<IdentifiedPeptide> listIdentifiedPeptidesByProtein(long proteinID);
- @Select("select a.id, perm_id, value from abundances as a join samples as s on a.samp_id = s.id "
- + "where a.prot_id = ?{1}")
- public DataSet<SampleAbundance> listSampleAbundanceByProtein(long proteinID);
+ @Select("select distinct a.id, perm_id, value "
+ + "from abundances as a left join proteins as p on a.prot_id = p.id "
+ + " left join identified_proteins as i on i.prot_id = p.id "
+ + " left join sequences as s on i.sequ_id = s.id "
+ + " left join samples on a.samp_id = samples.id "
+ + "where s.prre_id = ?{1}")
+ public DataSet<SampleAbundance> listSampleAbundanceByProtein(long proteinReferenceID);
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IPhosphoNetXServer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IPhosphoNetXServer.java
index 732f465312b..342e5af0953 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IPhosphoNetXServer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IPhosphoNetXServer.java
@@ -74,6 +74,6 @@ public interface IPhosphoNetXServer extends IServer
@Transactional
@RolesAllowed(RoleSet.OBSERVER)
public List<SampleWithPropertiesAndAbundance> listSamplesWithAbundanceByProtein(
- String sessionToken, TechId proteinID) throws UserFailureException;
+ String sessionToken, TechId proteinReferenceID) throws UserFailureException;
}
--
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