SE-126, SE-127 bugs fixed

SVN: 12303

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;
     }
 }

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

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/InternalAbundanceColumnDefinition.java

+/*
+ * 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

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 "

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;
     }

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());
         }