From 52c0089d600d0627036fb77808b6ec92ae923ea4 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 12 Oct 2010 15:35:25 +0000
Subject: [PATCH] LMS-1782 RawDataSampleGrid is now subclass of TypedTableGrid
SVN: 18272
---
.../web/client/IPhosphoNetXClientService.java | 11 +-
.../IPhosphoNetXClientServiceAsync.java | 11 +-
.../application/RawDataProcessingMenu.java | 24 ++--
.../client/application/RawDataSampleGrid.java | 123 ++++++++---------
.../web/server/PhosphoNetXClientService.java | 19 ++-
.../web/server/RawDataSampleProvider.java | 124 +++++-------------
.../basic/dto/RawDataSampleGridIDs.java | 40 ++++++
.../web/server/RawDataSampleProviderTest.java | 64 +++++----
8 files changed, 202 insertions(+), 214 deletions(-)
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/RawDataSampleGridIDs.java
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientService.java
index 1ac8e9d605c..a96a353f59c 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientService.java
@@ -19,13 +19,14 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.client.web.client.IClientService;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GenericTableResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.IResultSetConfig;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentAndReferenceCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
@@ -91,10 +92,10 @@ public interface IPhosphoNetXClientService extends IClientService
TableExportCriteria<SampleWithPropertiesAndAbundance> exportCriteria)
throws UserFailureException;
- public GenericTableResultSet listRawDataSamples(
- IResultSetConfig<String, TableModelRow> criteria) throws UserFailureException;
+ public TypedTableResultSet<Sample> listRawDataSamples(
+ IResultSetConfig<String, TableModelRowWithObject<Sample>> criteria) throws UserFailureException;
- public String prepareExportRawDataSamples(TableExportCriteria<TableModelRow> exportCriteria)
+ public String prepareExportRawDataSamples(TableExportCriteria<TableModelRowWithObject<Sample>> exportCriteria)
throws UserFailureException;
public void processRawData(String dataSetProcessingKey, long[] rawDataSampleIDs,
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientServiceAsync.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientServiceAsync.java
index 6070c64ed03..58fa462c1c2 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientServiceAsync.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientServiceAsync.java
@@ -21,12 +21,13 @@ import java.util.List;
import com.google.gwt.user.client.rpc.AsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.IClientServiceAsync;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GenericTableResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.IResultSetConfig;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentAndReferenceCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
@@ -104,11 +105,11 @@ public interface IPhosphoNetXClientServiceAsync extends IClientServiceAsync
AsyncCallback<String> callback);
/** @see IPhosphoNetXClientService#listRawDataSamples(IResultSetConfig) */
- public void listRawDataSamples(IResultSetConfig<String, TableModelRow> criteria,
- AsyncCallback<GenericTableResultSet> callback);
+ public void listRawDataSamples(IResultSetConfig<String, TableModelRowWithObject<Sample>> criteria,
+ AsyncCallback<TypedTableResultSet<Sample>> callback);
/** @see IPhosphoNetXClientService#prepareExportRawDataSamples(TableExportCriteria) */
- public void prepareExportRawDataSamples(TableExportCriteria<TableModelRow> exportCriteria,
+ public void prepareExportRawDataSamples(TableExportCriteria<TableModelRowWithObject<Sample>> exportCriteria,
AsyncCallback<String> callback);
/** @see IPhosphoNetXClientService#processRawData(String, long[], String) */
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RawDataProcessingMenu.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RawDataProcessingMenu.java
index c5b6a051489..be8e69c95c8 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RawDataProcessingMenu.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RawDataProcessingMenu.java
@@ -37,9 +37,9 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMess
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.TextToolItem;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SerializableComparableIDDecorator;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
/**
@@ -50,11 +50,11 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNet
public class RawDataProcessingMenu extends TextToolItem
{
private static final class CopyConfirmationDialog extends
- AbstractDataConfirmationDialog<List<TableModelRow>>
+ AbstractDataConfirmationDialog<List<TableModelRowWithObject<Sample>>>
{
private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
- private final List<TableModelRow> samples;
+ private final List<TableModelRowWithObject<Sample>> samples;
private final DatastoreServiceDescription datastoreServiceDescription;
@@ -63,7 +63,7 @@ public class RawDataProcessingMenu extends TextToolItem
private CopyConfirmationDialog(
IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext,
DatastoreServiceDescription datastoreServiceDescription,
- List<TableModelRow> samples, String title)
+ List<TableModelRowWithObject<Sample>> samples, String title)
{
super(specificViewContext, samples, title);
this.specificViewContext = specificViewContext;
@@ -93,13 +93,7 @@ public class RawDataProcessingMenu extends TextToolItem
long[] rawDataSampleIDs = new long[samples.size()];
for (int i = 0; i < samples.size(); i++)
{
- TableModelRow row = samples.get(i);
- ISerializableComparable c = row.getValues().get(0);
- if (c instanceof SerializableComparableIDDecorator == false)
- {
- throw new IllegalArgumentException("Missing id: " + c);
- }
- rawDataSampleIDs[i] = ((SerializableComparableIDDecorator) c).getID();
+ rawDataSampleIDs[i] = samples.get(i).getObjectOrNull().getId();
}
specificViewContext.getService().processRawData(datastoreServiceDescription.getKey(),
rawDataSampleIDs, dataSetTypeField.getValue(),
@@ -120,10 +114,10 @@ public class RawDataProcessingMenu extends TextToolItem
}
private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
- private final IDelegatedActionWithResult<List<TableModelRow>> selectedDataProvider;
+ private final IDelegatedActionWithResult<List<TableModelRowWithObject<Sample>>> selectedDataProvider;
public RawDataProcessingMenu(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- IDelegatedActionWithResult<List<TableModelRow>> selectedDataProvider)
+ IDelegatedActionWithResult<List<TableModelRowWithObject<Sample>>> selectedDataProvider)
{
super(viewContext.getMessage(Dict.COPY_DATA_SETS_BUTTON_LABEL));
this.viewContext = viewContext;
@@ -166,7 +160,7 @@ public class RawDataProcessingMenu extends TextToolItem
public void execute()
{
String title = viewContext.getMessage(COPY_DATA_SETS_TITLE);
- List<TableModelRow> selectedSamples = selectedDataProvider.execute();
+ List<TableModelRowWithObject<Sample>> selectedSamples = selectedDataProvider.execute();
new CopyConfirmationDialog(viewContext, datastoreServiceDescription,
selectedSamples, title).show();
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RawDataSampleGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RawDataSampleGrid.java
index aaa17d03e99..bdb907fef27 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RawDataSampleGrid.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RawDataSampleGrid.java
@@ -24,39 +24,35 @@ import java.util.List;
import com.google.gwt.user.client.rpc.AsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
-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.framework.DatabaseModificationAwareComponent;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.TypedTableGrid;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.LinkExtractor;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.DisposableEntityChooser;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.GenericTableBrowserGrid;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.ICellListener;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.ICellListenerAndLinkGenerator;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IDelegatedActionWithResult;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GenericTableResultSet;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.IResultSetConfig;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicEntityType;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
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.generic.shared.basic.dto.EntityKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SerializableComparableIDDecorator;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.RawDataSampleGridIDs;
/**
* @author Franz-Josef Elmer
*/
-class RawDataSampleGrid extends GenericTableBrowserGrid
+class RawDataSampleGrid extends TypedTableGrid<Sample>
{
- public static final String BROWSER_ID = GenericConstants.ID_PREFIX + "raw_data_sample_browser";
-
- public static final String GRID_ID = BROWSER_ID + "-grid";
+ public static final String GRID_ID = RawDataSampleGridIDs.BROWSER_ID + "-grid";
public static DatabaseModificationAwareComponent create(
final IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
{
RawDataSampleGrid grid = new RawDataSampleGrid(viewContext);
- DisposableEntityChooser<TableModelRow> disposable = grid.asDisposableWithoutToolbar();
+ DisposableEntityChooser<TableModelRowWithObject<Sample>> disposable = grid.asDisposableWithoutToolbar();
return new DatabaseModificationAwareComponent(disposable.getComponent(), disposable);
}
@@ -64,45 +60,83 @@ class RawDataSampleGrid extends GenericTableBrowserGrid
RawDataSampleGrid(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
{
- super(viewContext.getCommonViewContext(), BROWSER_ID, GRID_ID, true,
+ super(viewContext.getCommonViewContext(), GRID_ID, true,
PhosphoNetXDisplayTypeIDGenerator.RAW_DATA_SAMPLE_BROWSER_GRID);
specificViewContext = viewContext;
- registerLinkClickListenerFor("CODE", new ICellListener<TableModelRow>()
- {
- public void handle(TableModelRow rowItem, boolean keyPressed)
- {
- showEntityViewer(rowItem, false, keyPressed);
- }
- });
allowMultipleSelection();
addEntityOperationsLabel();
RawDataProcessingMenu button =
new RawDataProcessingMenu(viewContext,
- new IDelegatedActionWithResult<List<TableModelRow>>()
+ new IDelegatedActionWithResult<List<TableModelRowWithObject<Sample>>>()
{
- public List<TableModelRow> execute()
+ public List<TableModelRowWithObject<Sample>> execute()
{
return getSelectedBaseObjects();
}
});
enableButtonOnSelectedItems(button);
addButton(button);
+ linkMSInjectionSample();
+ linkBiologicalSample();
+ }
+
+ private void linkMSInjectionSample()
+ {
+ registerListenerAndLinkGenerator(RawDataSampleGridIDs.CODE,
+ new ICellListenerAndLinkGenerator<Sample>()
+ {
+
+ public void handle(TableModelRowWithObject<Sample> rowItem,
+ boolean specialKeyPressed)
+ {
+ showEntityInformationHolderViewer(rowItem.getObjectOrNull(), false,
+ specialKeyPressed);
+ }
+
+ public String tryGetLink(Sample entity)
+ {
+ return LinkExtractor.tryExtract(entity);
+ }
+ });
+ }
+
+ private void linkBiologicalSample()
+ {
+ registerListenerAndLinkGenerator(RawDataSampleGridIDs.PARENT,
+ new ICellListenerAndLinkGenerator<Sample>()
+ {
+
+ public void handle(TableModelRowWithObject<Sample> rowItem,
+ boolean specialKeyPressed)
+ {
+ showEntityInformationHolderViewer(rowItem.getObjectOrNull()
+ .getGeneratedFrom(), false, specialKeyPressed);
+ }
+
+ public String tryGetLink(Sample entity)
+ {
+ return LinkExtractor.tryExtract(entity.getGeneratedFrom());
+ }
+ });
}
@Override
- protected void listTableRows(IResultSetConfig<String, TableModelRow> resultSetConfig,
- AsyncCallback<GenericTableResultSet> callback)
+ protected void listTableRows(
+ DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> resultSetConfig,
+ AsyncCallback<TypedTableResultSet<Sample>> callback)
{
specificViewContext.getService().listRawDataSamples(resultSetConfig, callback);
}
@Override
- protected void prepareExportEntities(TableExportCriteria<TableModelRow> exportCriteria,
+ protected void prepareExportEntities(
+ TableExportCriteria<TableModelRowWithObject<Sample>> exportCriteria,
AbstractAsyncCallback<String> callback)
{
specificViewContext.getService().prepareExportRawDataSamples(exportCriteria, callback);
}
+ @Override
public DatabaseModificationKind[] getRelevantModifications()
{
return new DatabaseModificationKind[]
@@ -112,37 +146,4 @@ class RawDataSampleGrid extends GenericTableBrowserGrid
edit(ObjectKind.PROPERTY_TYPE_ASSIGNMENT) };
}
- @Override
- protected void showEntityViewer(final TableModelRow entity, boolean editMode, boolean active)
- {
- showEntityInformationHolderViewer(new IEntityInformationHolderWithPermId()
- {
-
- public String getCode()
- {
- return entity.getValues().get(0).toString();
- }
-
- public Long getId()
- {
- return ((SerializableComparableIDDecorator) entity.getValues().get(0)).getID();
- }
-
- public BasicEntityType getEntityType()
- {
- return new BasicEntityType("MS_INJECTION");
- }
-
- public EntityKind getEntityKind()
- {
- return EntityKind.SAMPLE;
- }
-
- public String getPermId()
- {
- return null;
- }
-
- }, editMode, active);
- }
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
index 3ff68d5ee71..7617666ad7e 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
@@ -25,15 +25,17 @@ import org.springframework.stereotype.Component;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.servlet.IRequestContextProvider;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GenericTableResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.IResultSetConfig;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.server.AbstractClientService;
+import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.DataProviderAdapter;
import ch.systemsx.cisd.openbis.generic.client.web.server.translator.UserFailureExceptionTranslator;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.BuildAndEnvironmentInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientService;
@@ -210,17 +212,20 @@ public class PhosphoNetXClientService extends AbstractClientService implements
return prepareExportEntities(exportCriteria);
}
- public GenericTableResultSet listRawDataSamples(
- IResultSetConfig<String, TableModelRow> criteria)
+ public TypedTableResultSet<Sample> listRawDataSamples(
+ IResultSetConfig<String, TableModelRowWithObject<Sample>> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
{
final String sessionToken = getSessionToken();
RawDataSampleProvider rawDataSampleProvider =
new RawDataSampleProvider(proteomicsDataService, sessionToken);
- ResultSet<TableModelRow> resultSet = listEntities(criteria, rawDataSampleProvider);
- return new GenericTableResultSet(resultSet, rawDataSampleProvider.getGenericHeaders());
+ DataProviderAdapter<Sample> dataProvider =
+ new DataProviderAdapter<Sample>(rawDataSampleProvider);
+ ResultSet<TableModelRowWithObject<Sample>> resultSet = listEntities(criteria, dataProvider);
+ return new TypedTableResultSet<Sample>(resultSet);
}
- public String prepareExportRawDataSamples(TableExportCriteria<TableModelRow> exportCriteria)
+ public String prepareExportRawDataSamples(TableExportCriteria<TableModelRowWithObject<Sample>> exportCriteria)
{
return prepareExportEntities(exportCriteria);
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProvider.java
index fa2a5b588ed..2bb47a0b14e 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProvider.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProvider.java
@@ -16,120 +16,68 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.server;
-import java.util.ArrayList;
-import java.util.HashSet;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.RawDataSampleGridIDs.CODE;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.RawDataSampleGridIDs.EXPERIMENT;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.RawDataSampleGridIDs.PARENT;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.RawDataSampleGridIDs.REGISTRATION_DATE;
+
import java.util.List;
-import ch.rinn.restrictions.Private;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.client.web.server.AbstractOriginalDataProviderWithoutHeaders;
-import ch.systemsx.cisd.openbis.generic.client.web.server.GenericColumnsHelper;
-import ch.systemsx.cisd.openbis.generic.client.web.server.GenericColumnsHelper.Column;
-import ch.systemsx.cisd.openbis.generic.client.web.server.GenericColumnsHelper.PropertyColumns;
+import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.ITableModelProvider;
+import ch.systemsx.cisd.openbis.generic.server.util.TypedTableModelBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelColumnHeader;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IProteomicsDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
/**
* @author Franz-Josef Elmer
*/
-class RawDataSampleProvider extends AbstractOriginalDataProviderWithoutHeaders<TableModelRow>
+class RawDataSampleProvider implements ITableModelProvider<Sample>
{
-
- @Private
- static final String EXPERIMENT = "EXPERIMENT";
-
- @Private
- static final String PARENT = "PARENT";
-
- @Private
- static final String REGISTRATION_DATE = "REGISTRATION_DATE";
-
- @Private
- static final String CODE = "CODE";
-
private final IProteomicsDataServiceInternal service;
private final String sessionToken;
+ private TypedTableModel<Sample> model;
+
RawDataSampleProvider(IProteomicsDataServiceInternal service, String sessionToken)
{
this.service = service;
this.sessionToken = sessionToken;
}
- public List<TableModelRow> getOriginalData() throws UserFailureException
+ public TypedTableModel<Sample> getTableModel()
{
- return GenericColumnsHelper.createTableRows(getColumns());
- }
-
- public List<TableModelColumnHeader> getGenericHeaders()
- {
- List<Column> columns = getColumns();
- List<TableModelColumnHeader> headers =
- new ArrayList<TableModelColumnHeader>(columns.size());
- for (Column column : columns)
+ if (model == null)
{
- headers.add(column.getHeader());
- }
- return headers;
- }
-
- private List<Column> getColumns()
- {
- List<MsInjectionSample> samples = service.listRawDataSamples(sessionToken);
- Column codeColumn =
- new Column(TableModelColumnHeader.untitledLinkableStringHeader(0, CODE));
- Column dateColumn =
- new Column(TableModelColumnHeader.untitledStringHeader(1, REGISTRATION_DATE));
- Column parentColumn = new Column(TableModelColumnHeader.untitledStringHeader(2, PARENT));
- Column experimentColumn = new Column(TableModelColumnHeader.untitledStringHeader(3, EXPERIMENT));
- List<Column> columns = new ArrayList<Column>();
- columns.add(codeColumn);
- columns.add(dateColumn);
- columns.add(parentColumn);
- columns.add(experimentColumn);
- int fixedColumns = columns.size();
- PropertyColumns samplePropertyColumns = new PropertyColumns();
- PropertyColumns parentPropertyColumns = new PropertyColumns();
- for (int i = 0; i < samples.size(); i++)
- {
- Sample sample = samples.get(i).getSample();
- codeColumn.addStringWithID(i, sample.getCode(), sample.getId());
- dateColumn.addDate(i, sample.getRegistrationDate());
- Sample parent = sample.getGeneratedFrom();
- parentColumn.addStringWithID(i, parent.getIdentifier(), parent.getId());
- Experiment experiment = parent.getExperiment();
- if (experiment != null)
+ List<MsInjectionSample> samples = service.listRawDataSamples(sessionToken);
+ TypedTableModelBuilder<Sample> builder = new TypedTableModelBuilder<Sample>();
+ builder.addColumn(CODE).withDataType(DataTypeCode.VARCHAR);
+ builder.addColumn(REGISTRATION_DATE).withDataType(DataTypeCode.TIMESTAMP).withDefaultWidth(190);
+ builder.addColumn(PARENT).withDataType(DataTypeCode.VARCHAR);
+ builder.addColumn(EXPERIMENT).withDataType(DataTypeCode.VARCHAR);
+ for (MsInjectionSample msInjectionSample : samples)
{
- experimentColumn.addStringWithID(i, experiment.getIdentifier(), experiment.getId());
+ Sample sample = msInjectionSample.getSample();
+ builder.addRow(sample);
+ builder.column(CODE).addString(sample.getCode());
+ builder.column(REGISTRATION_DATE).addDate(sample.getRegistrationDate());
+ Sample parent = sample.getGeneratedFrom();
+ builder.column(PARENT).addString(parent.getIdentifier());
+ Experiment experiment = parent.getExperiment();
+ if (experiment != null)
+ {
+ builder.column(EXPERIMENT).addString(experiment.getIdentifier());
+ }
+ builder.columnGroup("MS").addProperties("", sample.getProperties());
+ builder.columnGroup("BIO_").addProperties(parent.getProperties());
}
- addPropertyTypes(samplePropertyColumns, i, sample);
- addPropertyTypes(parentPropertyColumns, i, sample.getGeneratedFrom());
- }
- int nextIndex = samplePropertyColumns.reindexColumns(fixedColumns);
- parentPropertyColumns.reindexColumns(nextIndex);
- HashSet<String> commonColumns = new HashSet<String>(samplePropertyColumns.getColumnCodes());
- commonColumns.retainAll(parentPropertyColumns.getColumnCodes());
- if (commonColumns.isEmpty() == false)
- {
- parentPropertyColumns.addPrefixToColumnHeaderCodes("BIO_");
- }
- columns.addAll(samplePropertyColumns.getColumns());
- columns.addAll(parentPropertyColumns.getColumns());
- return columns;
- }
-
- private void addPropertyTypes(PropertyColumns columns, int index, Sample sample)
- {
- for (IEntityProperty property : sample.getProperties())
- {
- columns.add(index, property);
+ model = builder.getModel();
}
+ return model;
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/RawDataSampleGridIDs.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/RawDataSampleGridIDs.java
new file mode 100644
index 00000000000..448c219661a
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/RawDataSampleGridIDs.java
@@ -0,0 +1,40 @@
+/*
+ * Copyright 2010 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.basic.dto;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
+
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class RawDataSampleGridIDs
+{
+ public static final String BROWSER_ID = GenericConstants.ID_PREFIX + "raw_data_sample_browser";
+
+ public static final String EXPERIMENT = BROWSER_ID + "_" + "EXPERIMENT";
+
+ public static final String PARENT = BROWSER_ID + "_" + "PARENT";
+
+ public static final String REGISTRATION_DATE = BROWSER_ID + "_" + "REGISTRATION_DATE";
+
+ public static final String CODE = BROWSER_ID + "_" + "CODE";
+
+
+}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProviderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProviderTest.java
index aca3bb7dec8..61c92451561 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProviderTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProviderTest.java
@@ -16,9 +16,9 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.server;
-import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.server.RawDataSampleProvider.CODE;
-import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.server.RawDataSampleProvider.PARENT;
-import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.server.RawDataSampleProvider.REGISTRATION_DATE;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.RawDataSampleGridIDs.CODE;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.RawDataSampleGridIDs.PARENT;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.RawDataSampleGridIDs.REGISTRATION_DATE;
import java.util.ArrayList;
import java.util.Date;
@@ -39,6 +39,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelColumnHeader;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IProteomicsDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
@@ -67,9 +69,10 @@ public class RawDataSampleProviderTest extends AbstractServerTestCase
{
prepareListRawDataSamples();
- List<TableModelColumnHeader> headers = provider.getGenericHeaders();
+ List<TableModelColumnHeader> headers = provider.getTableModel().getHeader();
- assertColumns(headers);
+ assertFixedColumns(headers);
+ assertEquals(4, headers.size());
context.assertIsSatisfied();
}
@@ -81,9 +84,15 @@ public class RawDataSampleProviderTest extends AbstractServerTestCase
Sample ms3 = sample("MS3", sample("DE", "gamma", "alpha"), "two");
prepareListRawDataSamples(ms1, ms2, ms3);
- List<TableModelColumnHeader> headers = provider.getGenericHeaders();
+ List<TableModelColumnHeader> headers = provider.getTableModel().getHeader();
- assertColumns(headers, "one", "two", "alpha", "beta", "gamma");
+ assertFixedColumns(headers);
+ assertPropertyHeader("one", "ONE", 4, headers);
+ assertPropertyHeader("two", "TWO", 5, headers);
+ assertPropertyHeader("alpha", "BIO_ALPHA", 6, headers);
+ assertPropertyHeader("beta", "BIO_BETA", 7, headers);
+ assertPropertyHeader("gamma", "BIO_GAMMA", 8, headers);
+ assertEquals(9, headers.size());
context.assertIsSatisfied();
}
@@ -92,7 +101,7 @@ public class RawDataSampleProviderTest extends AbstractServerTestCase
{
prepareListRawDataSamples();
- List<TableModelRow> data = provider.getOriginalData();
+ List<TableModelRowWithObject<Sample>> data = provider.getTableModel().getRows();
assertEquals(0, data.size());
context.assertIsSatisfied();
@@ -110,12 +119,14 @@ public class RawDataSampleProviderTest extends AbstractServerTestCase
Sample ms3 = sample("MS3", parent, "2");
prepareListRawDataSamples(ms1, ms2, ms3);
- List<TableModelRow> data = provider.getOriginalData();
+ TypedTableModel<Sample> tableModel = provider.getTableModel();
+ List<TableModelRowWithObject<Sample>> data = tableModel.getRows();
assertEquals(3, data.size());
- assertRow("MS1, Mon Mar 30 17:18:20 CET 1970, /G/ABC, null, null, 3.0, 6, 4, null", data.get(0));
- assertRow("MS2, Mon Mar 30 17:20:00 CET 1970, /G/DE, null, null, 3.0, null, 5, 5", data.get(1));
- assertRow("MS3, Mon Mar 30 17:21:40 CET 1970, /G/FG, /G/P/E1, 1, null, 5, null, 6", data.get(2));
+ assertEquals("[null, null, null, null, 2, one, alpha, beta, gamma]", tableModel.getHeader().toString());
+ assertRow("MS1, Mon Mar 30 17:18:20 CET 1970, /G/ABC, , , 3.0, 6, 4, ", data.get(0));
+ assertRow("MS2, Mon Mar 30 17:20:00 CET 1970, /G/DE, , , 3.0, , 5, 5", data.get(1));
+ assertRow("MS3, Mon Mar 30 17:21:40 CET 1970, /G/FG, /G/P/E1, 1, , 5, , 6", data.get(2));
context.assertIsSatisfied();
}
@@ -134,45 +145,32 @@ public class RawDataSampleProviderTest extends AbstractServerTestCase
assertEquals(expectedRow, builder.toString());
}
- private void assertColumns(List<TableModelColumnHeader> headers,
- String... expectedTitles)
- {
- assertFixedColumns(headers);
- for (int i = 0; i < expectedTitles.length; i++)
- {
- assertPropertyHeader(expectedTitles[i], i + 4, headers);
- }
- assertEquals(expectedTitles.length + 4, headers.size());
- }
-
private void assertFixedColumns(List<TableModelColumnHeader> headers)
{
- assertUntitledHeader(CODE, 0, true, DataTypeCode.VARCHAR, headers.get(0));
- assertUntitledHeader(REGISTRATION_DATE, 1, false, DataTypeCode.VARCHAR, headers.get(1));
- assertUntitledHeader(PARENT, 2, false, DataTypeCode.VARCHAR, headers.get(2));
+ assertUntitledHeader(CODE, 0, DataTypeCode.VARCHAR, headers.get(0));
+ assertUntitledHeader(REGISTRATION_DATE, 1, DataTypeCode.TIMESTAMP, headers.get(1));
+ assertUntitledHeader(PARENT, 2, DataTypeCode.VARCHAR, headers.get(2));
}
private void assertUntitledHeader(String expectedCode, int expectedIndex,
- boolean expectedlinkableFlag, DataTypeCode expectedType, TableModelColumnHeader header)
+ DataTypeCode expectedType, TableModelColumnHeader header)
{
- assertHeader(null, expectedCode, expectedIndex, expectedlinkableFlag, expectedType,
- header);
+ assertHeader(null, expectedCode, expectedIndex, expectedType, header);
}
- private void assertPropertyHeader(String expectedLabel, int index, List<TableModelColumnHeader> headers)
+ private void assertPropertyHeader(String expectedLabel, String expectedCode, int index, List<TableModelColumnHeader> headers)
{
DataTypeCode type = DataTypeCode.values()[expectedLabel.length()];
TableModelColumnHeader header = headers.get(index);
- assertHeader(expectedLabel, expectedLabel.toUpperCase(), index, false, type, header);
+ assertHeader(expectedLabel, expectedCode, index, type, header);
}
private void assertHeader(String expectedTitle, String expectedCode, int expectedIndex,
- boolean expectedlinkableFlag, DataTypeCode expectedType, TableModelColumnHeader header)
+ DataTypeCode expectedType, TableModelColumnHeader header)
{
assertEquals(expectedTitle, header.getTitle());
assertEquals(expectedCode, header.getId());
assertEquals(expectedIndex, header.getIndex());
- assertEquals(expectedlinkableFlag, header.isLinkable());
assertEquals(expectedType, header.getDataType());
}
--
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