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
deleted file mode 100644
index 98cb74c6a6b9ec5f6102047a2710bb596e502574..0000000000000000000000000000000000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/InternalAbundanceColumnDefinition.java
+++ /dev/null
@@ -1,82 +0,0 @@
-/*
- * 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
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/ProteinColDefKind.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/ProteinColDefKind.java
deleted file mode 100644
index 4e762dfb3dc2f4b98f6ba82e0572eb301f41e737..0000000000000000000000000000000000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/ProteinColDefKind.java
+++ /dev/null
@@ -1,80 +0,0 @@
-/*
- * 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;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinOriginalDataProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinOriginalDataProvider.java
deleted file mode 100644
index 6b6c6bdd7eb3ac359ce4745430d4d7a95f0ea96a..0000000000000000000000000000000000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinOriginalDataProvider.java
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
- * 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);
- }
-
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientServiceTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientServiceTest.java
index 2e4efa310146530271232e592d52e6a9aa0555fe..7f671cb5afbc4d5012160e25bd964abc147df07d 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientServiceTest.java
+++ b/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;
}