diff --git a/rtd_phosphonetx/.classpath b/rtd_phosphonetx/.classpath
index efc56346735878751c8c2a0b1a7f889b73e3c206..06912ae07f796a366c8742cbc0fb3ce79a44b8eb 100644
--- a/rtd_phosphonetx/.classpath
+++ b/rtd_phosphonetx/.classpath
@@ -26,5 +26,9 @@
<classpathentry kind="lib" path="/libraries/spring/spring.jar" sourcepath="/libraries/spring/src.jar"/>
<classpathentry kind="lib" path="/libraries/spring/webmvc/spring-webmvc.jar" sourcepath="/libraries/spring/webmvc/src.jar"/>
<classpathentry kind="lib" path="/libraries/hibernate-search/jms.jar"/>
+ <classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-core.jar"/>
+ <classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-library.jar"/>
+ <classpathentry kind="lib" path="/libraries/jmock/objenesis/objenesis-1.0.jar"/>
+ <classpathentry kind="lib" path="/libraries/jmock/jmock.jar"/>
<classpathentry kind="output" path="targets/classes"/>
</classpath>
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java
index 219b0bf17c0282aebd41baee70c200d3062b63cf..436cb61e780910740d5a8a120abc6a11fd47e069 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java
@@ -24,8 +24,8 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.applicatio
class Dict
{
public static final String QUERY_MENU_TITLE = "query_menu_title";
- public static final String QUERY_ALL_PROTEINS_BY_EXPERIMENT = "query_all_proteins_by_experiment";
public static final String SELECTED_EXPERIMENT_LABEL = "selected_experiment_label";
public static final String PROTEIN_DESCRIPTION = "protein_description";
+ public static final String FALSE_DISCOVERY_RATE = "false_discovery_rate";
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowerToolBar.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowerToolBar.java
index cb73747241eb4f7dd6074c7cafa5a5a554f3f331..b39eb3b8f235516f87c6b40cbc61fa8e762881ea 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowerToolBar.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowerToolBar.java
@@ -16,10 +16,6 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application;
-import com.extjs.gxt.ui.client.Events;
-import com.extjs.gxt.ui.client.event.BaseEvent;
-import com.extjs.gxt.ui.client.event.Listener;
-import com.extjs.gxt.ui.client.widget.form.TextField;
import com.extjs.gxt.ui.client.widget.toolbar.AdapterToolItem;
import com.extjs.gxt.ui.client.widget.toolbar.LabelToolItem;
import com.extjs.gxt.ui.client.widget.toolbar.ToolBar;
@@ -27,7 +23,9 @@ import com.extjs.gxt.ui.client.widget.toolbar.ToolBar;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.ExperimentChooserField;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.IChosenEntityListener;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.ExperimentChooserField.ExperimentChooserFieldAdaptor;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
@@ -45,20 +43,19 @@ class ProteinByExperimentBrowerToolBar extends ToolBar
+ GenericConstants.LABEL_SEPARATOR));
final ExperimentChooserFieldAdaptor chooser =
ExperimentChooserField.create("", false, null, viewContext.getCommonViewContext());
- TextField<String> textField = chooser.getTextField();
- textField.setReadOnly(true);
- textField.addListener(Events.Valid, new Listener<BaseEvent>()
+ ExperimentChooserField chooserField = chooser.getChooserField();
+ chooserField.setReadOnly(true);
+ chooserField.addChosenEntityListener(new IChosenEntityListener<Experiment>()
{
- public void handleEvent(BaseEvent be)
+ public void entityChosen(Experiment entity)
{
- ExperimentIdentifier identifier = chooser.getValue();
- if (identifier != null)
+ if (entity != null)
{
- browserGrid.update(identifier);
+ browserGrid.update(ExperimentIdentifier.createIdentifier(entity));
}
}
});
- add(new AdapterToolItem(textField));
+ add(new AdapterToolItem(chooserField));
add(new AdapterToolItem(chooser.getChooseButton()));
}
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 c1ae86334df70afd9ceaf707a1d4217e7d725b26..77f2e9b2b42c5ea26585b260f4bbe2cc0d7e782f 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
@@ -66,16 +66,17 @@ class ProteinByExperimentBrowserGrid extends AbstractSimpleBrowserGrid<ProteinIn
private ProteinByExperimentBrowserGrid(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
{
- super(viewContext.getCommonViewContext(), BROWSER_ID, GRID_ID);
+ super(viewContext.getCommonViewContext(), BROWSER_ID, GRID_ID, false);
specificViewContext = viewContext;
setDisplayTypeIDGenerator(PhosphoNetXDisplayTypeIDGenerator.PROTEIN_BY_EXPERIMENT_BROWSER_GRID);
}
void update(ExperimentIdentifier identifier)
{
+ System.out.println("ProteinByExperimentBrowserGrid.update() "+identifier);
criteria = new ListProteinByExperimentCriteria();
criteria.setExperimentID(identifier.getTechID());
- refresh();
+ refresh();
}
@Override
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinColDefKind.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinColDefKind.java
index 2feab25bf751537470fa52d1e23661fbbec7f7b9..bdc81acb123e96873552e4a7950b845d3586a1ba 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinColDefKind.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinColDefKind.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application;
+import com.google.gwt.i18n.client.NumberFormat;
+
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.plugin.phosphonetx.client.web.client.dto.ProteinInfo;
@@ -25,7 +27,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.Protein
*/
public enum ProteinColDefKind implements IColumnDefinitionKind<ProteinInfo>
{
- DESCRIPTION(new AbstractColumnDefinitionKind<ProteinInfo>(Dict.PROTEIN_DESCRIPTION, false)
+ DESCRIPTION(new AbstractColumnDefinitionKind<ProteinInfo>(Dict.PROTEIN_DESCRIPTION)
{
@Override
public String tryGetValue(ProteinInfo entity)
@@ -33,8 +35,22 @@ public enum ProteinColDefKind implements IColumnDefinitionKind<ProteinInfo>
return entity.getDescription();
}
}),
- ;
+ FALSE_DISCOVERY_RATE(new AbstractColumnDefinitionKind<ProteinInfo>(Dict.FALSE_DISCOVERY_RATE)
+ {
+ @Override
+ public String tryGetValue(ProteinInfo entity)
+ {
+ return render(entity.getFalseDiscoveryRate());
+ }
+ }), ;
+ private static final NumberFormat DECIMAL_FORMAT = NumberFormat.getDecimalFormat();
+
+ protected static String render(double value)
+ {
+ return DECIMAL_FORMAT.format(value);
+ }
+
private final AbstractColumnDefinitionKind<ProteinInfo> columnDefinitionKind;
private ProteinColDefKind(AbstractColumnDefinitionKind<ProteinInfo> columnDefinitionKind)
@@ -51,4 +67,5 @@ public enum ProteinColDefKind implements IColumnDefinitionKind<ProteinInfo>
{
return columnDefinitionKind;
}
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/QueryMenu.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/QueryMenu.java
index b97cf019459624d0619e32a222fcfe12d62bd524..9c456fb22cbf2b54bf4148e6c14625ebfdb37fdb 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/QueryMenu.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/QueryMenu.java
@@ -42,7 +42,16 @@ public class QueryMenu extends TopMenuItem
private static enum ActionMenuKind implements IActionMenuItem
{
- ALL_PROTEINS_OF_AN_EXPERIMENT;
+ ALL_PROTEINS_OF_AN_EXPERIMENT()
+ {
+ @Override
+ IDisposableComponent createComponent(
+ IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
+ {
+ return ProteinByExperimentBrowserGrid.create(viewContext);
+ }
+ }
+ ;
public String getMenuId()
{
@@ -51,36 +60,33 @@ public class QueryMenu extends TopMenuItem
public String getMenuText(IMessageProvider messageProvider)
{
- return messageProvider.getMessage(this.name());
- }
- }
-
- private static final class TabItemFactory implements ITabItemFactory
- {
- protected final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
- private final String id;
- private final String tabLabelKey;
- private final IDisposableComponent disposableComponent;
-
- TabItemFactory(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- String tabLabelKey, IDisposableComponent disposableComponent)
- {
- this.viewContext = viewContext;
- this.tabLabelKey = tabLabelKey;
- this.disposableComponent = disposableComponent;
- this.id = ID + tabLabelKey;
+ return messageProvider.getMessage(this.name() + "_menu_item");
}
-
- public String getId()
+
+ String getTabLabelKey()
{
- return id;
+ return this.name() + "_tab_label";
}
- public ITabItem create()
+ ActionMenu createActionMenu(final IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
{
- String menuItemText = viewContext.getMessage(tabLabelKey);
- return DefaultTabItem.create(menuItemText, disposableComponent, viewContext);
+ return new ActionMenu(this, viewContext, new ITabItemFactory()
+ {
+ public String getId()
+ {
+ return ID + getTabLabelKey();
+ }
+
+ public ITabItem create()
+ {
+ String menuItemText = viewContext.getMessage(getTabLabelKey());
+ return DefaultTabItem.create(menuItemText, createComponent(viewContext),
+ viewContext);
+ }
+ });
}
+
+ abstract IDisposableComponent createComponent(IViewContext<IPhosphoNetXClientServiceAsync> viewContext);
}
public QueryMenu(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
@@ -89,14 +95,10 @@ public class QueryMenu extends TopMenuItem
setIconStyle(TopMenu.ICON_STYLE);
Menu menu = new Menu();
- IDisposableComponent disposableComponent =
- ProteinByExperimentBrowserGrid.create(viewContext);
- TabItemFactory factory =
- new TabItemFactory(viewContext, Dict.QUERY_ALL_PROTEINS_BY_EXPERIMENT,
- disposableComponent);
- ActionMenu actionMenu =
- new ActionMenu(ActionMenuKind.ALL_PROTEINS_OF_AN_EXPERIMENT, viewContext, factory);
- menu.add(actionMenu);
+ for (ActionMenuKind actionMenuKind : ActionMenuKind.values())
+ {
+ menu.add(actionMenuKind.createActionMenu(viewContext));
+ }
setMenu(menu);
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ProteinInfo.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ProteinInfo.java
index 909f359260892a853e0f3de2994e77df9bf4c6d0..a73faf2f2ef1558693d508f0ca699c0215d0161f 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ProteinInfo.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ProteinInfo.java
@@ -27,27 +27,41 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
*/
public class ProteinInfo implements IsSerializable
{
- private TechId annotationID;
+ private TechId id;
+
private String description;
+
+ private double falseDiscoveryRate;
- public final String getDescription()
+ public final TechId getId()
{
- return description;
+ return id;
}
- public final void setDescription(String description)
+ public final void setId(TechId id)
{
- this.description = description;
+ this.id = id;
}
- public final TechId getAnnotationID()
+ public final double getFalseDiscoveryRate()
{
- return annotationID;
+ return falseDiscoveryRate;
}
- public final void setAnnotationID(TechId annotationID)
+ public final void setFalseDiscoveryRate(double falseDiscoveryRate)
{
- this.annotationID = annotationID;
+ this.falseDiscoveryRate = falseDiscoveryRate;
}
+ public final String getDescription()
+ {
+ return description;
+ }
+
+ public final void setDescription(String description)
+ {
+ this.description = description;
+ }
+
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js
index a216d3e77b1c781db91486a7b50cabd39a121d3c..c44e230eec8852d8b61a6c5c50a51b637217bc47 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js
@@ -1,10 +1,13 @@
// PhosphoNetX dictionary
var phosphonetx = {
query_menu_title: "Queries",
- ALL_PROTEINS_OF_AN_EXPERIMENT: "All Proteins of an Experiment",
- query_all_proteins_by_experiment: "Proteins of an Experiment",
+ ALL_PROTEINS_OF_AN_EXPERIMENT_menu_item: "All Proteins of an Experiment",
+ ALL_PROTEINS_OF_AN_EXPERIMENT_tab_label: "Proteins of an Experiment",
selected_experiment_label: "Experiment",
+
+ // Protein grid
protein_description: "Protein",
+ false_discovery_rate: "FDR",
// LAST LINE: KEEP IT AT THE END
lastline: "" // we need a line without a comma
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
index 31fb6cc1dd37ef1a7397bf0e0e652eb7e11f1e39..c07c72409a7cf4296c2b456fb7bff7a8ddb19574 100644
--- 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
@@ -24,7 +24,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.IOriginalDat
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedProtein;
/**
*
@@ -46,13 +46,14 @@ class ListProteinOriginalDataProvider implements IOriginalDataProvider<ProteinIn
public List<ProteinInfo> getOriginalData() throws UserFailureException
{
- List<ProteinReference> references = server.listProteinReferencesByExperiment(sessionToken, experimentID);
- List<ProteinInfo> infos = new ArrayList<ProteinInfo>(references.size());
- for (ProteinReference proteinReference : references)
+ List<IdentifiedProtein> proteins = server.listProteinsByExperiment(sessionToken, experimentID);
+ List<ProteinInfo> infos = new ArrayList<ProteinInfo>(proteins.size());
+ for (IdentifiedProtein protein : proteins)
{
ProteinInfo proteinInfo = new ProteinInfo();
- proteinInfo.setAnnotationID(new TechId(proteinReference.getAnnotationID()));
- proteinInfo.setDescription(proteinReference.getDescription());
+ proteinInfo.setId(new TechId(protein.getId()));
+ proteinInfo.setDescription(protein.getDescription());
+ proteinInfo.setFalseDiscoveryRate(protein.getFalseDiscoveryRate());
infos.add(proteinInfo);
}
return infos;
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 df08222c02f2a2a90379a60cfdf288b16714dd63..943c6d170b0fdb5b5a18d5238d4484e93aed37a5 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
@@ -16,13 +16,10 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server;
-import java.util.ArrayList;
import java.util.List;
import javax.annotation.Resource;
-import net.lemnik.eodsql.DataSet;
-
import org.springframework.stereotype.Component;
import ch.rinn.restrictions.Private;
@@ -35,10 +32,12 @@ import ch.systemsx.cisd.openbis.generic.server.plugin.ISampleTypeSlaveServerPlug
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IIdentifiedProteinTable;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IPhosphoNetXDAOFactory;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ResourceNames;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedProtein;
/**
* @author Franz-Josef Elmer
@@ -49,6 +48,9 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
{
@Resource(name = ResourceNames.PHOSPHONETX_DAO_FACTORY)
private IPhosphoNetXDAOFactory specificDAOFactory;
+
+ @Resource(name = ResourceNames.PHOSPHONETX_BO_FACTORY)
+ private IBusinessObjectFactory specificBOFactory;
public PhosphoNetXServer()
{
@@ -58,11 +60,13 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
@Private
PhosphoNetXServer(ISessionManager<Session> sessionManager, IDAOFactory daoFactory,
IPhosphoNetXDAOFactory specificDAOFactory,
+ IBusinessObjectFactory specificBOFactory,
ISampleTypeSlaveServerPlugin sampleTypeSlaveServerPlugin,
IDataSetTypeSlaveServerPlugin dataSetTypeSlaveServerPlugin)
{
super(sessionManager, daoFactory, sampleTypeSlaveServerPlugin, dataSetTypeSlaveServerPlugin);
this.specificDAOFactory = specificDAOFactory;
+ this.specificBOFactory = specificBOFactory;
}
@Override
@@ -76,16 +80,14 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
return new PhosphoNetXServerLogger(getSessionManager(), invocationSuccessful, elapsedTime);
}
- public List<ProteinReference> listProteinReferencesByExperiment(String sessionToken,
+ public List<IdentifiedProtein> listProteinsByExperiment(String sessionToken,
TechId experimentId) throws UserFailureException
{
+ final Session session = getSessionManager().getSession(sessionToken);
+ IIdentifiedProteinTable proteinTable = specificBOFactory.createProteinTable(session);
ExperimentPE experiment = getDAOFactory().getExperimentDAO().getByTechId(experimentId);
- String permId = experiment.getPermId();
- DataSet<ProteinReference> resultSet =
- specificDAOFactory.getProteinQueryDAO().listProteinsByExperiment(permId);
- ArrayList<ProteinReference> refrences = new ArrayList<ProteinReference>();
- refrences.addAll(resultSet);
- return refrences;
+ proteinTable.load(experiment.getPermId());
+ return proteinTable.getIdentifiedProteins();
}
}
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 5baa17ea4144394e25362768381b894580ce6a09..d399812e41c74a048ac969461fbf35efdbb050e8 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
@@ -28,7 +28,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SampleGenerationDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedProtein;
/**
* @author Franz-Josef Elmer
@@ -62,10 +62,10 @@ public class PhosphoNetXServerLogger extends AbstractServerLogger implements IPh
newSample.getSampleType(), newSample.getIdentifier(), attachments.size());
}
- public List<ProteinReference> listProteinReferencesByExperiment(String sessionToken,
+ public List<IdentifiedProtein> listProteinsByExperiment(String sessionToken,
TechId experimentId) throws UserFailureException
{
- logAccess(sessionToken, "list_protein_references_by_experiment", "ID(%s)", experimentId);
+ logAccess(sessionToken, "list_proteins_by_experiment", "ID(%s)", experimentId);
return null;
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbstractBusinessObject.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbstractBusinessObject.java
new file mode 100644
index 0000000000000000000000000000000000000000..2410c8bca14c33a72bcb8abbcb925e14657c7426
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbstractBusinessObject.java
@@ -0,0 +1,58 @@
+/*
+ * 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.server.business;
+
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IPhosphoNetXDAOFactory;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+abstract class AbstractBusinessObject
+{
+ private final IDAOFactory daoFactory;
+ private final IPhosphoNetXDAOFactory specificDAOFactory;
+ private final Session session;
+
+ AbstractBusinessObject(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory, Session session)
+ {
+ this.daoFactory = daoFactory;
+ this.specificDAOFactory = specificDAOFactory;
+ this.session = session;
+ }
+
+ protected final PersonPE getRegistrator()
+ {
+ PersonPE registrator = session.tryGetPerson();
+ assert registrator != null : "Session with unknown person: " + session;
+ return registrator;
+ }
+
+ protected final IDAOFactory getDaoFactory()
+ {
+ return daoFactory;
+ }
+
+ protected final IPhosphoNetXDAOFactory getSpecificDAOFactory()
+ {
+ return specificDAOFactory;
+ }
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..9caaee3c2d94732bc158d4b2382dde0bce56a270
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
@@ -0,0 +1,44 @@
+/*
+ * 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.server.business;
+
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IPhosphoNetXDAOFactory;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class BusinessObjectFactory implements IBusinessObjectFactory
+{
+ private final IDAOFactory daoFactory;
+ private final IPhosphoNetXDAOFactory specificDAOFactory;
+
+ public BusinessObjectFactory(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory)
+ {
+ this.daoFactory = daoFactory;
+ this.specificDAOFactory = specificDAOFactory;
+ }
+
+ public IIdentifiedProteinTable createProteinTable(Session session)
+ {
+ return new IdentifiedProteinTable(daoFactory, specificDAOFactory, session);
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModel.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModel.java
new file mode 100644
index 0000000000000000000000000000000000000000..ba47c2d503bd60fe45300680245e92bf310ea82b
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModel.java
@@ -0,0 +1,130 @@
+/*
+ * 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.server.business;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import net.lemnik.eodsql.DataSet;
+
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IPhosphoNetXDAOFactory;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedProtein;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProbabilityFDRMapping;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class ErrorModel
+{
+ private static final class ProbabilityToFDRCalculator
+ {
+ private static final class MappingEntry implements Comparable<MappingEntry>
+ {
+ private final double probability;
+ private final double fdr;
+
+ MappingEntry(double probability, double fdr)
+ {
+ this.probability = probability;
+ this.fdr = fdr;
+ }
+
+ public int compareTo(MappingEntry that)
+ {
+ return probability < that.probability ? -1 : (probability > that.probability ? 1 : 0);
+ }
+
+ @Override
+ public String toString()
+ {
+ return probability + " = " + fdr;
+ }
+ }
+
+ private final List<MappingEntry> mappingEntries = new ArrayList<MappingEntry>();
+
+ void add(double probability, double falseDiscoveryRate)
+ {
+ mappingEntries.add(new MappingEntry(probability, falseDiscoveryRate));
+ }
+
+ void init()
+ {
+ Collections.sort(mappingEntries);
+ }
+
+ double calculateFDR(double probability)
+ {
+ int index = Collections.binarySearch(mappingEntries, new MappingEntry(probability, 0));
+ if (index >= 0)
+ {
+ return mappingEntries.get(index).fdr;
+ }
+ // calculate by linear interpolation
+ int index1 = -index - 1;
+ int index0 = index1 - 1;
+ assert index0 >= 0;
+ MappingEntry m0 = mappingEntries.get(index0);
+ MappingEntry m1 = mappingEntries.get(index1);
+ double scale = (m1.fdr - m0.fdr) / (m1.probability - m0.probability);
+ return m0.fdr + scale * (probability - m0.probability);
+ }
+ }
+
+ private final Map<Long, ProbabilityToFDRCalculator> calculators =
+ new HashMap<Long, ProbabilityToFDRCalculator>();
+
+ private final IPhosphoNetXDAOFactory specificDAOFactory;
+
+ ErrorModel(IPhosphoNetXDAOFactory specificDAOFactory)
+ {
+ this.specificDAOFactory = specificDAOFactory;
+ }
+
+ void setFalseDiscoveryRateFor(IdentifiedProtein protein)
+ {
+ ProbabilityToFDRCalculator calculator = getCalculator(protein.getDataSetID());
+ protein.setFalseDiscoveryRate(calculator.calculateFDR(protein.getProbability()));
+ }
+
+ private ProbabilityToFDRCalculator getCalculator(long dataSetID)
+ {
+ ProbabilityToFDRCalculator calculator = calculators.get(dataSetID);
+ if (calculator == null)
+ {
+ calculator = new ProbabilityToFDRCalculator();
+ IProteinQueryDAO dao = specificDAOFactory.getProteinQueryDAO();
+ DataSet<ProbabilityFDRMapping> mmappings = dao.getProbabilityFDRMapping(dataSetID);
+ for (ProbabilityFDRMapping probabilityFDRMapping : mmappings)
+ {
+ double probability = probabilityFDRMapping.getProbability();
+ double falseDiscoveryRate = probabilityFDRMapping.getFalseDiscoveryRate();
+ calculator.add(probability, falseDiscoveryRate);
+ }
+ calculator.init();
+ calculators.put(dataSetID, calculator);
+ }
+ return calculator;
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..5555bf0c91f4a3e5a338b4a998ff72e066c2c52d
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java
@@ -0,0 +1,29 @@
+/*
+ * 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.server.business;
+
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IBusinessObjectFactory
+{
+ public IIdentifiedProteinTable createProteinTable(Session session);
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IIdentifiedProteinTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IIdentifiedProteinTable.java
new file mode 100644
index 0000000000000000000000000000000000000000..c9f48e107962c2cc40fe8b74869d5b7848653f50
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IIdentifiedProteinTable.java
@@ -0,0 +1,33 @@
+/*
+ * 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.server.business;
+
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedProtein;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IIdentifiedProteinTable
+{
+ public void load(String experimentPermID);
+
+ public List<IdentifiedProtein> getIdentifiedProteins();
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IdentifiedProteinTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IdentifiedProteinTable.java
new file mode 100644
index 0000000000000000000000000000000000000000..1221ddd1789d9661619bf0cb0651601928520437
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IdentifiedProteinTable.java
@@ -0,0 +1,66 @@
+/*
+ * 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.server.business;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import net.lemnik.eodsql.DataSet;
+
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IPhosphoNetXDAOFactory;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedProtein;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class IdentifiedProteinTable extends AbstractBusinessObject implements IIdentifiedProteinTable
+{
+ private List<IdentifiedProtein> proteins;
+
+ public IdentifiedProteinTable(IDAOFactory daoFactory,
+ IPhosphoNetXDAOFactory specificDAOFactory, Session session)
+ {
+ super(daoFactory, specificDAOFactory, session);
+ }
+
+ public List<IdentifiedProtein> getIdentifiedProteins()
+ {
+ if (proteins == null)
+ {
+ throw new IllegalStateException("No proteins loaded.");
+ }
+ return proteins;
+ }
+
+ public void load(String experimentPermID)
+ {
+ proteins = new ArrayList<IdentifiedProtein>();
+ DataSet<IdentifiedProtein> resultSet =
+ getSpecificDAOFactory().getProteinQueryDAO().listProteinsByExperiment(experimentPermID);
+ ErrorModel errorModel = new ErrorModel(getSpecificDAOFactory());
+ for (IdentifiedProtein protein : resultSet)
+ {
+ errorModel.setFalseDiscoveryRateFor(protein);
+ proteins.add(protein);
+ }
+ }
+
+}
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 5407d2a0cae965e7bb8885c1f4e7098468d1c48a..b9ffe904a1638513270348cd8b672005ab9a07da 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
@@ -20,7 +20,8 @@ import net.lemnik.eodsql.BaseQuery;
import net.lemnik.eodsql.DataSet;
import net.lemnik.eodsql.Select;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProbabilityFDRMapping;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedProtein;
/**
*
@@ -29,9 +30,12 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
*/
public interface IProteinQueryDAO extends BaseQuery
{
- @Select("select a.id, a.protein_description "
- + "from annotations as a left join proteins as p on a.prot_id = p.id "
+ @Select("select * from probability_fdr_mappings where dase_id = ?{1}")
+ public DataSet<ProbabilityFDRMapping> getProbabilityFDRMapping(long dataSetID);
+
+ @Select("select ip.id as id, d.id as data_set_id, p.id as protein_id, p.probability, ip.description "
+ + "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 where e.perm_id = ?{1}")
- public DataSet<ProteinReference> listProteinsByExperiment(String experimentPermID);
+ public DataSet<IdentifiedProtein> listProteinsByExperiment(String experimentPermID);
}
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 acca2830dd8d829825deb09a87397df394c882e9..b271d168e3f25d8bb155103a9019d9a6459ca3db 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
@@ -27,7 +27,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RoleSet;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedProtein;
/**
*
@@ -38,7 +38,7 @@ public interface IPhosphoNetXServer extends IServer
{
@Transactional
@RolesAllowed(RoleSet.OBSERVER)
- public List<ProteinReference> listProteinReferencesByExperiment(String sessionToken,
+ public List<IdentifiedProtein> listProteinsByExperiment(String sessionToken,
@AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class)
TechId experimentId) throws UserFailureException;
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/ResourceNames.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/ResourceNames.java
index e12af898d9c5ec7c2585122ba8ca5e8ec6360a3a..a691b156c81abb4cf0f752648b82ed4727146977 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/ResourceNames.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/ResourceNames.java
@@ -32,5 +32,7 @@ public class ResourceNames
public final static String PHOSPHONETX_PLUGIN_SERVER = "phosphonetx-plugin-server";
public final static String PHOSPHONETX_DAO_FACTORY = "phosphonetx-dao-factory";
+
+ public final static String PHOSPHONETX_BO_FACTORY = "phosphonetx-bo-factory";
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java
new file mode 100644
index 0000000000000000000000000000000000000000..96536a6de418ffa869e39a7d7cccb20f7b16bff9
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java
@@ -0,0 +1,106 @@
+/*
+ * 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.shared.dto;
+
+import net.lemnik.eodsql.ResultColumn;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class IdentifiedProtein
+{
+ @ResultColumn("id")
+ private long id;
+
+ @ResultColumn("data_set_id")
+ private long dataSetID;
+
+ @ResultColumn("protein_id")
+ private long proteinID;
+
+ @ResultColumn("description")
+ private String description;
+
+ @ResultColumn("probability")
+ private double probability;
+
+ private double falseDiscoveryRate;
+
+ public final long getId()
+ {
+ return id;
+ }
+
+ public final void setId(long id)
+ {
+ this.id = id;
+ }
+
+ public final String getDescription()
+ {
+ return description;
+ }
+
+ public final void setDescription(String description)
+ {
+ this.description = description;
+ }
+
+ public final long getDataSetID()
+ {
+ return dataSetID;
+ }
+
+ public final void setDataSetID(long dataSetID)
+ {
+ this.dataSetID = dataSetID;
+ }
+
+ public final long getProteinID()
+ {
+ return proteinID;
+ }
+
+ public final void setProteinID(long proteinID)
+ {
+ this.proteinID = proteinID;
+ }
+
+ public final double getProbability()
+ {
+ return probability;
+ }
+
+ public final void setProbability(double probability)
+ {
+ this.probability = probability;
+ }
+
+ public final double getFalseDiscoveryRate()
+ {
+ return falseDiscoveryRate;
+ }
+
+ public final void setFalseDiscoveryRate(double falseDiscoveryRate)
+ {
+ this.falseDiscoveryRate = falseDiscoveryRate;
+ }
+
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReference.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProbabilityFDRMapping.java
similarity index 59%
rename from rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReference.java
rename to rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProbabilityFDRMapping.java
index 2024769e817fcf0ec062308cd225dd70fd2ea185..8739170f579b9d3b09a8f4dbb33da8da569ce928 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReference.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProbabilityFDRMapping.java
@@ -23,33 +23,31 @@ import net.lemnik.eodsql.ResultColumn;
*
* @author Franz-Josef Elmer
*/
-public class ProteinReference
+public class ProbabilityFDRMapping
{
- @ResultColumn("id")
- private long annotationID;
+ @ResultColumn("probability")
+ private double probability;
- @ResultColumn("protein_description")
- private String description;
+ @ResultColumn("false_discovery_rate")
+ private double falseDiscoveryRate;
- public final String getDescription()
+ public final double getProbability()
{
- return description;
+ return probability;
}
- public final void setDescription(String description)
+ public final void setProbability(double probability)
{
- this.description = description;
+ this.probability = probability;
}
- public final long getAnnotationID()
+ public final double getFalseDiscoveryRate()
{
- return annotationID;
+ return falseDiscoveryRate;
}
- public final void setAnnotationID(long annotationID)
+ public final void setFalseDiscoveryRate(double falseDiscoveryRate)
{
- this.annotationID = annotationID;
+ this.falseDiscoveryRate = falseDiscoveryRate;
}
-
-
}
diff --git a/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
index c68cbeee9d45bd8739f1ea846a5f62ff6a0493e1..3af8c91f3616e68c737e3f4f7dab30daa5513c3e 100644
--- a/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
+++ b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
@@ -33,4 +33,10 @@
class="ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.db.PhosphoNetXDAOFactory">
<constructor-arg ref="phosphonetx-db-configuration-context"/>
</bean>
+
+ <bean id="phosphonetx-bo-factory"
+ class="ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.BusinessObjectFactory">
+ <constructor-arg ref="dao-factory"/>
+ <constructor-arg ref="phosphonetx-dao-factory"/>
+ </bean>
</beans>
\ No newline at end of file
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/MockDataSet.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/MockDataSet.java
new file mode 100644
index 0000000000000000000000000000000000000000..3612944c3a88718c2fa78d573bc56b7d69ad4daf
--- /dev/null
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/MockDataSet.java
@@ -0,0 +1,45 @@
+/*
+ * 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.server;
+
+import java.util.ArrayList;
+
+import net.lemnik.eodsql.DataSet;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class MockDataSet<T> extends ArrayList<T> implements DataSet<T>
+{
+ private static final long serialVersionUID = 1L;
+
+ public void close()
+ {
+ }
+
+ public void disconnect()
+ {
+ }
+
+ public boolean isConnected()
+ {
+ return false;
+ }
+
+}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModelTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModelTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..3aace8dbac0cb58a66364b8fc1677e99442d7ffb
--- /dev/null
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModelTest.java
@@ -0,0 +1,146 @@
+/*
+ * 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.server.business;
+
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.MockDataSet;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IPhosphoNetXDAOFactory;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedProtein;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProbabilityFDRMapping;
+
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ErrorModelTest extends AssertJUnit
+{
+ private static final double TOL = 1e-6;
+ private static final long DATA_SET1_ID = 42;
+ private static final long DATA_SET2_ID = 43;
+
+ private Mockery context;
+ private IPhosphoNetXDAOFactory specificDAOFactory;
+ private IProteinQueryDAO proteinQueryDAO;
+ private ErrorModel errorModel;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ context = new Mockery();
+ specificDAOFactory = context.mock(IPhosphoNetXDAOFactory.class);
+ proteinQueryDAO = context.mock(IProteinQueryDAO.class);
+ errorModel = new ErrorModel(specificDAOFactory);
+ context.checking(new Expectations()
+ {
+ {
+ allowing(specificDAOFactory).getProteinQueryDAO();
+ will(returnValue(proteinQueryDAO));
+
+ atMost(1).of(proteinQueryDAO).getProbabilityFDRMapping(DATA_SET1_ID);
+ MockDataSet<ProbabilityFDRMapping> dataSet1 = new MockDataSet<ProbabilityFDRMapping>();
+ createEntry(dataSet1, 0.4, 0.9);
+ createEntry(dataSet1, 0.5, 0.95);
+ will(returnValue(dataSet1));
+
+ atMost(1).of(proteinQueryDAO).getProbabilityFDRMapping(DATA_SET2_ID);
+ MockDataSet<ProbabilityFDRMapping> dataSet2 = new MockDataSet<ProbabilityFDRMapping>();
+ createEntry(dataSet2, 1, 1);
+ createEntry(dataSet2, 0.4, 0.9);
+ createEntry(dataSet2, 0.1, 0.7);
+ createEntry(dataSet2, 0.0, 0.6);
+ will(returnValue(dataSet2));
+ }
+ });
+ }
+
+ @AfterMethod
+ public void afterMethod()
+ {
+ // To following line of code should also be called at the end of each test method.
+ // Otherwise one do not known which test failed.
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testExact()
+ {
+ IdentifiedProtein protein = create(DATA_SET1_ID, 0.4);
+ errorModel.setFalseDiscoveryRateFor(protein);
+
+ assertEquals(0.9, protein.getFalseDiscoveryRate(), TOL);
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testInterpolation()
+ {
+ IdentifiedProtein protein = create(DATA_SET1_ID, 0.42);
+ errorModel.setFalseDiscoveryRateFor(protein);
+
+ assertEquals(0.91, protein.getFalseDiscoveryRate(), TOL);
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testCachedMapping()
+ {
+ IdentifiedProtein protein = create(DATA_SET1_ID, 0.42);
+ errorModel.setFalseDiscoveryRateFor(protein);
+
+ assertEquals(0.91, protein.getFalseDiscoveryRate(), TOL);
+
+ protein = create(DATA_SET2_ID, 0.25);
+ errorModel.setFalseDiscoveryRateFor(protein);
+
+ assertEquals(0.8, protein.getFalseDiscoveryRate(), TOL);
+
+ protein = create(DATA_SET1_ID, 0.5);
+ errorModel.setFalseDiscoveryRateFor(protein);
+
+ assertEquals(0.95, protein.getFalseDiscoveryRate(), TOL);
+
+ context.assertIsSatisfied();
+ }
+
+ private IdentifiedProtein create(long dataSetID, double probability)
+ {
+ IdentifiedProtein protein = new IdentifiedProtein();
+ protein.setDataSetID(dataSetID);
+ protein.setProbability(probability);
+ return protein;
+ }
+
+ private void createEntry(MockDataSet<ProbabilityFDRMapping> dataSet, double propability,
+ double falseDiscoveryRate)
+ {
+ ProbabilityFDRMapping mapping = new ProbabilityFDRMapping();
+ mapping.setProbability(propability);
+ mapping.setFalseDiscoveryRate(falseDiscoveryRate);
+ dataSet.add(mapping);
+ }
+}