Test fixed, dead classes removed

SVN: 23149

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.generic.shared.basic.GridRowModel;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
-
-public final class InternalAbundanceColumnDefinition extends AbstractColumnDefinition<ProteinInfo>
-{
-    private static final Double ZERO = new Double(1e-40);
-
-    private long sampleID;
-
-    private Map<String, String> properties;
-
-    // GWT only
-    public InternalAbundanceColumnDefinition()
-    {
-        super();
-    }
-
-    public InternalAbundanceColumnDefinition(String headerTextOrNull,
-            Map<String, String> propertiesOrNull, int width, boolean isHidden, long sampleID)
-    {
-        super(headerTextOrNull, width, isHidden, true, false);
-        this.properties = propertiesOrNull;
-        this.sampleID = sampleID;
-    }
-
-    public String getIdentifier()
-    {
-        return "abundance-" + Long.toString(sampleID);
-    }
-
-    @Override
-    protected String tryGetValue(ProteinInfo entity)
-    {
-        Double abundance = tryToGetAbundance(entity);
-        return abundance == null ? null : Double.toString(abundance);
-    }
-
-    @Override
-    public Comparable<?> tryGetComparableValue(GridRowModel<ProteinInfo> rowModel)
-    {
-        Double abundance = tryToGetAbundance(rowModel.getOriginalObject());
-        return abundance == null ? ZERO : abundance;
-    }
-
-    @Override
-    public String tryToGetProperty(String key)
-    {
-        return properties == null ? null : properties.get(key);
-    }
-
-    private Double tryToGetAbundance(ProteinInfo entity)
-    {
-        Map<Long, Double> abundances = entity.getAbundances();
-        if (abundances == null)
-        {
-            return null;
-        }
-        return abundances.get(sampleID);
-    }
-
-}
\ No newline at end of file

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/ProteinColDefKind.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 ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.AbstractColumnDefinitionKind;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.IColumnDefinitionKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.GridRowModel;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.Dict;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
-
-/**
- * @author Franz-Josef Elmer
- */
-public enum ProteinColDefKind implements IColumnDefinitionKind<ProteinInfo>
-{
-    ACCESSION_NUMBER(new AbstractColumnDefinitionKind<ProteinInfo>(Dict.ACCESSION_NUMBER)
-        {
-            @Override
-            public String tryGetValue(ProteinInfo entity)
-            {
-                return entity.getAccessionNumber();
-            }
-        }),
-
-    DESCRIPTION(new AbstractColumnDefinitionKind<ProteinInfo>(Dict.PROTEIN_DESCRIPTION)
-        {
-            @Override
-            public String tryGetValue(ProteinInfo entity)
-            {
-                return entity.getDescription();
-            }
-        }),
-
-    COVERAGE(new AbstractColumnDefinitionKind<ProteinInfo>(Dict.COVERAGE, 100, false, true)
-        {
-            @Override
-            public String tryGetValue(ProteinInfo entity)
-            {
-                return Double.toString(entity.getCoverage());
-            }
-            
-            @Override
-            public Comparable<?> getComparableValue(GridRowModel<ProteinInfo> entity)
-            {
-                return entity.getOriginalObject().getCoverage();
-            }
-        }),    ;
-
-    private final AbstractColumnDefinitionKind<ProteinInfo> columnDefinitionKind;
-
-    private ProteinColDefKind(AbstractColumnDefinitionKind<ProteinInfo> columnDefinitionKind)
-    {
-        this.columnDefinitionKind = columnDefinitionKind;
-    }
-
-    public String id()
-    {
-        return name();
-    }
-
-    public AbstractColumnDefinitionKind<ProteinInfo> getDescriptor()
-    {
-        return columnDefinitionKind;
-    }
-
-}

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinOriginalDataProvider.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.server;
-
-import java.util.List;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.client.web.server.AbstractOriginalDataProviderWithoutHeaders;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
-
-/**
- * 
- *
- * @author Franz-Josef Elmer
- */
-class ListProteinOriginalDataProvider extends AbstractOriginalDataProviderWithoutHeaders<ProteinInfo>
-{
-    private final IPhosphoNetXServer server;
-    private final String sessionToken;
-    private final TechId experimentID;
-    private final double falseDiscoveryRate;
-    private final AggregateFunction aggregateFunction;
-    private final String treatmentTypeCode;
-    private final boolean aggregateOnOriginal;
-
-    ListProteinOriginalDataProvider(IPhosphoNetXServer server, String sessionToken,
-            TechId experimentID, double falseDiscoveryRate, AggregateFunction function,
-            String treatmentTypeCode, boolean aggregateOnOriginal)
-    {
-        this.server = server;
-        this.sessionToken = sessionToken;
-        this.experimentID = experimentID;
-        this.falseDiscoveryRate = falseDiscoveryRate;
-        this.aggregateFunction = function;
-        this.treatmentTypeCode = treatmentTypeCode;
-        this.aggregateOnOriginal = aggregateOnOriginal;
-    }
-    
-    @Override
-    public List<ProteinInfo> getFullOriginalData() throws UserFailureException
-    {
-        return server.listProteinsByExperiment(sessionToken, experimentID, falseDiscoveryRate,
-                aggregateFunction, treatmentTypeCode, aggregateOnOriginal);
-    }
-
-}

rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientServiceTest.java

@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.server;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Properties;
 
@@ -190,6 +191,12 @@ public class PhosphoNetXClientServiceTest extends AbstractFileSystemTestCase
     {
         final TechId experimentID1 = new TechId(42L);
         final TechId experimentID2 = new TechId(4711L);
+        final AbundanceColumnDefinition colDef = new AbundanceColumnDefinition();
+        colDef.setSampleCode("S1");
+        Treatment treatment = new Treatment();
+        treatment.setType("type1");
+        treatment.setTypeCode("code");
+        colDef.setTreatments(Arrays.asList(treatment));
         final double fdr1 = 0.125;
         final double fdr2 = 0.25;
         final AggregateFunction f1 = AggregateFunction.MAX;
@@ -205,6 +212,15 @@ public class PhosphoNetXClientServiceTest extends AbstractFileSystemTestCase
         context.checking(new Expectations()
             {
                 {
+                    one(server).getAbundanceColumnDefinitionsForProteinByExperiment(SESSION_TOKEN,
+                            experimentID1, treatment1);
+                    will(returnValue(Arrays.asList(colDef)));
+                    one(server).getAbundanceColumnDefinitionsForProteinByExperiment(SESSION_TOKEN,
+                            experimentID1, treatment2);
+                    will(returnValue(Arrays.asList(colDef)));
+                    one(server).getAbundanceColumnDefinitionsForProteinByExperiment(SESSION_TOKEN,
+                            experimentID2, treatment1);
+                    will(returnValue(Arrays.asList(colDef)));
                     one(server).listProteinsByExperiment(SESSION_TOKEN, experimentID1, fdr1, f1,
                             treatment1, false);
                     will(returnValue(Arrays.asList(p1)));
@@ -239,7 +255,7 @@ public class PhosphoNetXClientServiceTest extends AbstractFileSystemTestCase
         listAndCheckProteins(p4, experimentID1, fdr1, f2, treatment1, false);
         listAndCheckProteins(p5, experimentID1, fdr1, f1, treatment2, false);
         listAndCheckProteins(p6, experimentID1, fdr1, f1, treatment1, true);
-        assertEquals(13, cacheFolder.listFiles().length);
+        assertEquals(19, cacheFolder.listFiles().length);
         
         context.assertIsSatisfied();
     }
@@ -267,6 +283,7 @@ public class PhosphoNetXClientServiceTest extends AbstractFileSystemTestCase
         ProteinInfo protein = new ProteinInfo();
         protein.setId(new TechId(id));
         protein.setDescription("Protein " + id);
+        protein.setAbundances(new HashMap<Long, Double>());
         return protein;
     }