From abcbf3b5842516aff255e0729128680c1ea647a5 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Wed, 9 Sep 2009 06:55:11 +0000
Subject: [PATCH] SE-137 bugs in protein viewer fixed
SVN: 12526
---
.../client/application/ProteinSamplesSection.java | 8 +++++---
.../client/web/client/application/ProteinViewer.java | 12 +++++++-----
.../application/SampleAbundanceBrowserGrid.java | 3 ++-
.../dto/ListSampleAbundanceByProteinCriteria.java | 11 +++++++++++
.../web/server/ListSampleAbundanceDataProvider.java | 7 +++++--
.../client/web/server/PhosphoNetXClientService.java | 2 +-
.../plugin/phosphonetx/server/PhosphoNetXServer.java | 5 +++--
.../phosphonetx/server/PhosphoNetXServerLogger.java | 7 ++++---
.../phosphonetx/server/business/ISampleTable.java | 2 +-
.../phosphonetx/server/business/SampleTable.java | 8 +++++---
.../server/dataaccess/IProteinQueryDAO.java | 9 ++++++---
.../phosphonetx/shared/IPhosphoNetXServer.java | 3 ++-
12 files changed, 52 insertions(+), 25 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 6330f85a981..a18c1ec9ae9 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
@@ -22,6 +22,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.SingleSect
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.IDatabaseModificationObserver;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
/**
@@ -38,12 +39,13 @@ public class ProteinSamplesSection extends SingleSectionPanel
private IDisposableComponent sampleDisposableGrid;
public ProteinSamplesSection(final IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- final TechId proteinReferenceID)
+ final TechId proteinReferenceID, Experiment experimentOrNull)
{
super("Samples");
+ Long experimentID = experimentOrNull == null ? null : experimentOrNull.getId();
sampleDisposableGrid =
- SampleAbundanceBrowserGrid.createGridForProteinSamples(viewContext, proteinReferenceID,
- createGridId(proteinReferenceID));
+ SampleAbundanceBrowserGrid.createGridForProteinSamples(viewContext,
+ proteinReferenceID, experimentID, createGridId(proteinReferenceID));
add(sampleDisposableGrid.getComponent());
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java
index c0d92e92e88..77d8904cde8 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java
@@ -77,7 +77,7 @@ public class ProteinViewer extends
{
public String getId()
{
- return createWidgetID(proteinInfo.getId());
+ return createWidgetID(experimentOrNull, proteinInfo.getId());
}
public ITabItem create()
@@ -106,9 +106,10 @@ public class ProteinViewer extends
return StringUtils.abbreviate(info, 30);
}
- static String createWidgetID(TechId proteinReferenceID)
+ static String createWidgetID(Experiment experimentOrNull, TechId proteinReferenceID)
{
- return ID_PREFIX + proteinReferenceID.getId();
+ Long experimentID = experimentOrNull == null ? null : experimentOrNull.getId();
+ return ID_PREFIX + experimentID + "_" + proteinReferenceID.getId();
}
private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
@@ -122,7 +123,7 @@ public class ProteinViewer extends
private ProteinViewer(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
Experiment experimentOrNull, TechId proteinReferenceID)
{
- super(viewContext, "", createWidgetID(proteinReferenceID), false);
+ super(viewContext, "", createWidgetID(experimentOrNull, proteinReferenceID), false);
this.viewContext = viewContext;
this.experimentOrNull = experimentOrNull;
this.proteinReferenceID = proteinReferenceID;
@@ -151,7 +152,8 @@ public class ProteinViewer extends
} else
{
add(propertyPanel, createBorderLayoutData(LayoutRegion.CENTER));
- proteinSamplesSection = new ProteinSamplesSection(viewContext, proteinReferenceID);
+ proteinSamplesSection =
+ new ProteinSamplesSection(viewContext, proteinReferenceID, experimentOrNull);
add(proteinSamplesSection, createBorderLayoutData(LayoutRegion.SOUTH));
layout();
}
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 053d69249d7..83a9df3cd3f 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
@@ -87,11 +87,12 @@ public class SampleAbundanceBrowserGrid
public static IDisposableComponent createGridForProteinSamples(
final IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- final TechId proteinReferenceID, final String gridId)
+ final TechId proteinReferenceID, Long experimentIDOrNull, final String gridId)
{
final ListSampleAbundanceByProteinCriteria criteria =
new ListSampleAbundanceByProteinCriteria();
criteria.setProteinReferenceID(proteinReferenceID);
+ criteria.setExperimentID(experimentIDOrNull);
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 6eefaa1677b..9cf36395a4a 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
@@ -30,8 +30,19 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.SampleWithPr
public class ListSampleAbundanceByProteinCriteria extends
DefaultResultSetConfig<String, SampleWithPropertiesAndAbundance> implements IsSerializable
{
+ private TechId experimentID;
private TechId proteinReferenceID;
+ public final TechId getExperimentID()
+ {
+ return experimentID;
+ }
+
+ public final void setExperimentID(Long experimentID)
+ {
+ this.experimentID = experimentID == null ? null : new TechId(experimentID);
+ }
+
public final TechId getProteinReferenceID()
{
return 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 13350d8a519..c7ce947019b 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
@@ -35,20 +35,23 @@ class ListSampleAbundanceDataProvider implements IOriginalDataProvider<SampleWit
private final String sessionToken;
+ private final TechId experimentID;
+
private final TechId proteinReferenceID;
ListSampleAbundanceDataProvider(IPhosphoNetXServer server, String sessionToken,
- TechId proteinReferenceID)
+ TechId experimentID, TechId proteinReferenceID)
{
this.server = server;
this.sessionToken = sessionToken;
+ this.experimentID = experimentID;
this.proteinReferenceID = proteinReferenceID;
}
public List<SampleWithPropertiesAndAbundance> getOriginalData() throws UserFailureException
{
- return server.listSamplesWithAbundanceByProtein(sessionToken, proteinReferenceID);
+ return server.listSamplesWithAbundanceByProtein(sessionToken, experimentID, 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 cbc836978be..96a748d55f2 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
@@ -154,7 +154,7 @@ public class PhosphoNetXClientService extends AbstractClientService implements
{
final String sessionToken = getSessionToken();
return listEntities(criteria, new ListSampleAbundanceDataProvider(server, sessionToken,
- criteria.getProteinReferenceID()));
+ criteria.getExperimentID(), 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 e12e5502dc6..dd798d11f4b 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
@@ -182,11 +182,12 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
}
public List<SampleWithPropertiesAndAbundance> listSamplesWithAbundanceByProtein(
- String sessionToken, TechId proteinReferenceID) throws UserFailureException
+ String sessionToken, TechId experimentID, TechId proteinReferenceID)
+ throws UserFailureException
{
final Session session = getSessionManager().getSession(sessionToken);
ISampleTable sampleTable = specificBOFactory.createSampleTable(session);
- sampleTable.loadSamplesWithAbundance(proteinReferenceID);
+ sampleTable.loadSamplesWithAbundance(experimentID, 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 a4bc062abe4..4222fd2b29f 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
@@ -96,10 +96,11 @@ public class PhosphoNetXServerLogger extends AbstractServerLogger implements IPh
}
public List<SampleWithPropertiesAndAbundance> listSamplesWithAbundanceByProtein(
- String sessionToken, TechId proteinReferenceID) throws UserFailureException
+ String sessionToken, TechId experimentID, TechId proteinReferenceID)
+ throws UserFailureException
{
- logAccess(sessionToken, "list_samples_with_abundance_by_protein", "PROTEIN_REFERENCE_ID(%s)",
- proteinReferenceID);
+ logAccess(sessionToken, "list_samples_with_abundance_by_protein",
+ "EXPERIMENT_ID(%s) PROTEIN_REFERENCE_ID(%s)", experimentID, 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 63e7d88cf96..f7006ad7ec9 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 proteinReferenceID);
+ public void loadSamplesWithAbundance(TechId experimentID, 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 85e07e332e3..898e5efbda3 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
@@ -59,15 +59,17 @@ class SampleTable extends AbstractBusinessObject implements ISampleTable
return samples;
}
- public void loadSamplesWithAbundance(TechId proteinReferenceID)
+ public void loadSamplesWithAbundance(TechId experimentID, TechId proteinReferenceID)
{
samples = new ArrayList<SampleWithPropertiesAndAbundance>();
IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO();
- ISampleDAO sampleDAO = getDaoFactory().getSampleDAO();
+ IDAOFactory daoFactory = getDaoFactory();
+ String experimentPermID = daoFactory.getExperimentDAO().getByTechId(experimentID).getPermId();
DataSet<SampleAbundance> sampleAbundances =
- proteinQueryDAO.listSampleAbundanceByProtein(proteinReferenceID.getId());
+ proteinQueryDAO.listSampleAbundanceByProtein(experimentPermID, proteinReferenceID.getId());
try
{
+ ISampleDAO sampleDAO = daoFactory.getSampleDAO();
for (SampleAbundance sampleAbundance : sampleAbundances)
{
SampleWithPropertiesAndAbundance sample = new SampleWithPropertiesAndAbundance();
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 6061c44940e..39bd86b6d41 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
@@ -83,12 +83,15 @@ public interface IProteinQueryDAO extends BaseQuery
@Select("select * from peptides where prot_id = ?{1}")
public DataSet<IdentifiedPeptide> listIdentifiedPeptidesByProtein(long proteinID);
- @Select("select distinct a.id, perm_id, value "
+ @Select("select distinct a.id, samples.perm_id, value "
+ "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 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);
+ + "where e.perm_id = ?{1} and s.prre_id = ?{2}")
+ public DataSet<SampleAbundance> listSampleAbundanceByProtein(String experimentPermID,
+ 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 ab481b78388..ce73f84b4ce 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
@@ -81,6 +81,7 @@ public interface IPhosphoNetXServer extends IServer
@Transactional
@RolesAllowed(RoleSet.OBSERVER)
public List<SampleWithPropertiesAndAbundance> listSamplesWithAbundanceByProtein(
- String sessionToken, TechId proteinReferenceID) throws UserFailureException;
+ String sessionToken, TechId experimentID, TechId proteinReferenceID)
+ throws UserFailureException;
}
--
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