diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java
index c5ac2124a1751ea2fd46126917ced10b80a5fb31..d2e243a164a0a4353af6d9de8f9f033fc8997cb0 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java
@@ -38,10 +38,16 @@ class AbundanceHandler extends AbstractHandler
{
@Private static final String MZXML_FILENAME = "MZXML_FILENAME";
+ private static final class SampleOrError
+ {
+ Sample sample;
+ String error;
+ }
+
private final IEncapsulatedOpenBISService openbisService;
private final GroupIdentifier groupIdentifier;
private final Experiment experiment;
- private final Map<String, Sample> samples = new HashMap<String, Sample>();
+ private final Map<String, SampleOrError> samplesOrErrors = new HashMap<String, SampleOrError>();
AbundanceHandler(IEncapsulatedOpenBISService openbisService, IProtDAO dao,
GroupIdentifier groupIdentifier, Experiment experiment)
@@ -68,16 +74,16 @@ class AbundanceHandler extends AbstractHandler
private Sample getOrCreateSample(String parameterName, String proteinName)
{
- Sample sample = samples.get(parameterName);
- if (sample == null)
+ SampleOrError sampleOrError = samplesOrErrors.get(parameterName);
+ if (sampleOrError == null)
{
SampleIdentifier sampleIdentifier =
new SampleIdentifier(groupIdentifier, parameterName);
SamplePE samplePE = openbisService.tryGetSampleWithExperiment(sampleIdentifier);
- String permID;
+ sampleOrError = new SampleOrError();
if (samplePE != null)
{
- permID = samplePE.getPermId();
+ sampleOrError.sample = getOrCreateSample(experiment, samplePE.getPermId());
} else
{
List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample> list =
@@ -87,21 +93,22 @@ class AbundanceHandler extends AbstractHandler
.getGroupCode(), null));
if (list == null || list.size() == 0)
{
- throw new UserFailureException("Protein '" + proteinName
- + "' has an abundance value for an unidentified samples: "
- + parameterName);
- }
- if (list.size() > 1)
+ sampleOrError.error = "an unidentified sample: " + parameterName;
+ } else if (list.size() > 1)
{
- throw new UserFailureException("Protein '" + proteinName
- + "' has an abundance value for which " + list.size()
- + " samples are found: " + parameterName);
+ sampleOrError.error = list.size() + " samples are found: " + parameterName;
+ } else
+ {
+ sampleOrError.sample = getOrCreateSample(experiment, list.get(0).getPermId());
}
- permID = list.get(0).getPermId();
}
- sample = getOrCreateSample(experiment, permID);
- samples.put(parameterName, sample);
+ samplesOrErrors.put(parameterName, sampleOrError);
+ }
+ if (sampleOrError.error != null)
+ {
+ throw new UserFailureException("Protein '" + proteinName
+ + "' has an abundance value for " + sampleOrError.error);
}
- return sample;
+ return sampleOrError.sample;
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java
index a1b0361b19b893f6505f225514ceea0edfa3194b..d42359319d28347ee5b92e24ff1d56370751b7d9 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java
@@ -18,7 +18,6 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.applicatio
import java.util.ArrayList;
import java.util.List;
-import java.util.Map;
import java.util.Set;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
@@ -27,7 +26,6 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewConte
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DispatcherHelper;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.BaseEntityModel;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.renderer.LinkRenderer;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.AbstractColumnDefinition;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.IColumnDefinitionKind;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.IColumnDefinitionUI;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.AbstractSimpleBrowserGrid;
@@ -42,6 +40,7 @@ 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.DatabaseModificationKind.ObjectKind;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.columns.InternalAbundanceColumnDefinition;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.columns.ProteinColDefKind;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.AggregateFunction;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
@@ -134,29 +133,7 @@ class ProteinByExperimentBrowserGrid extends AbstractSimpleBrowserGrid<ProteinIn
}
}
final long sampleID = definition.getSampleID();
- columns.add(new AbstractColumnDefinition<ProteinInfo>(header, 100, false)
- {
- @Override
- protected String tryGetValue(ProteinInfo entity)
- {
- Map<Long, Double> abundances = entity.getAbundances();
- if (abundances == null)
- {
- return null;
- }
- Double abundance = abundances.get(sampleID);
- if (abundance == null)
- {
- return null;
- }
- return Double.toString(abundance);
- }
-
- public String getIdentifier()
- {
- return "abundance-" + Long.toString(sampleID);
- }
- });
+ columns.add(new InternalAbundanceColumnDefinition(header, 100, false, sampleID));
}
definitions.addColumns(columns);
definitions.setGridCellRendererFor(ProteinColDefKind.UNIPROT_ID.id(), LinkRenderer
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/InternalAbundanceColumnDefinition.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/InternalAbundanceColumnDefinition.java
new file mode 100644
index 0000000000000000000000000000000000000000..05125c7e25fb6db55f5fa917b583224ecb1529cf
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/InternalAbundanceColumnDefinition.java
@@ -0,0 +1,62 @@
+/*
+ * 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.client.web.client.application.columns;
+
+import java.util.Map;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.AbstractColumnDefinition;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinInfo;
+
+public final class InternalAbundanceColumnDefinition extends
+ AbstractColumnDefinition<ProteinInfo>
+{
+ private long sampleID;
+
+ // GWT only
+ public InternalAbundanceColumnDefinition()
+ {
+ super();
+ }
+
+ public InternalAbundanceColumnDefinition(String headerTextOrNull, int width,
+ boolean isHidden, long sampleID)
+ {
+ super(headerTextOrNull, width, isHidden);
+ this.sampleID = sampleID;
+ }
+
+ @Override
+ protected String tryGetValue(ProteinInfo entity)
+ {
+ Map<Long, Double> abundances = entity.getAbundances();
+ if (abundances == null)
+ {
+ return null;
+ }
+ Double abundance = abundances.get(sampleID);
+ if (abundance == null)
+ {
+ return null;
+ }
+ return Double.toString(abundance);
+ }
+
+ public String getIdentifier()
+ {
+ return "abundance-" + Long.toString(sampleID);
+ }
+}
\ No newline at end of file
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 70f11f2cc16a6d67589214c9587aade4f39e1f46..e70e1b1ade338b73941e0e7bde6713de7b93495b 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
@@ -40,7 +40,7 @@ public interface IProteinQueryDAO extends BaseQuery
public DataSet<ProbabilityFDRMapping> getProbabilityFDRMapping(long dataSetID);
@Select("select pr.id, pr.uniprot_id, pr.description, d.id as data_set_id, p.probability, "
- + " a.value, samples.id as sample_id "
+ + " a.value as abundance, samples.id as sample_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 "
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 380c6e921f436e3d6d9cfa5ebc8c362857d4fd0b..030e8b8e0a304b5f99d978b81e1fad1f737c0952 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
@@ -31,8 +31,8 @@ public class ProteinReferenceWithProbability extends ProteinReference
@ResultColumn("probability")
private double probability;
- @ResultColumn("value")
- private double abundance;
+ @ResultColumn("abundance")
+ private Double abundance;
@ResultColumn("sample_id")
private Long sampleID;
@@ -57,12 +57,12 @@ public class ProteinReferenceWithProbability extends ProteinReference
this.probability = probability;
}
- public final double getAbundance()
+ public final Double getAbundance()
{
return abundance;
}
- public final void setAbundance(double abundance)
+ public final void setAbundance(Double abundance)
{
this.abundance = abundance;
}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
index c53c2590e385de840d132377e677414c6009b97b..fabb112611bd40e7b1616aa7d787a07256e2ec88 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
@@ -338,7 +338,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
} catch (UserFailureException ex)
{
AssertionUtil.assertContains("Protein '" + PROTEIN_NAME1
- + "' has an abundance value for an unidentified samples: "
+ + "' has an abundance value for an unidentified sample: "
+ upperCaseParameterName, ex.getMessage());
}