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 ca845babddb501a35d2979cc3fec0f6067b535a9..a4ea41631590d1763ac2e17e6bae00221ad06876 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
@@ -19,10 +19,12 @@ 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.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.exception.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
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;
@@ -83,5 +85,12 @@ public interface IPhosphoNetXClientService extends IClientService
TableExportCriteria<SampleWithPropertiesAndAbundance> exportCriteria)
throws UserFailureException;
+ public ResultSet<Sample> listRawDataSamples(IResultSetConfig<String, Sample> criteria)
+ throws UserFailureException;
+
+ public String prepareExportRawDataSamples(TableExportCriteria<Sample> exportCriteria)
+ throws UserFailureException;
+ public void copyRawData(long[] rawDataSampleIDs) throws UserFailureException;
+
}
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 a3c740ee2bd63bcd54a3ad24b7eb68802784172c..256196ea6d8fdb92a57d1a935d7bc047d6ae9d68 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
@@ -21,9 +21,11 @@ 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.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.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
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;
@@ -99,4 +101,15 @@ public interface IPhosphoNetXClientServiceAsync extends IClientServiceAsync
public void prepareExportSamplesWithAbundance(
TableExportCriteria<SampleWithPropertiesAndAbundance> exportCriteria,
AsyncCallback<String> callback);
+
+ /** @see IPhosphoNetXClientService#listRawDataSamples(IResultSetConfig) */
+ public void listRawDataSamples(IResultSetConfig<String, Sample> criteria,
+ AsyncCallback<ResultSet<Sample>> callback);
+
+ /** @see IPhosphoNetXClientService#prepareExportRawDataSamples(TableExportCriteria) */
+ public void prepareExportRawDataSamples(TableExportCriteria<Sample> exportCriteria,
+ AsyncCallback<String> callback);
+
+ /** @see IPhosphoNetXClientService#copyRawData(long[]) */
+ public void copyRawData(long[] rawDataSampleIDs, AsyncCallback<Void> callback);
}
\ No newline at end of file
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 0e2904ddc8fdd729a41a95232b1a42fba56a0c83..8ce60800da90df12737a0eae71d0a0979475de15 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
@@ -78,5 +78,14 @@ public class Dict
// SampleAbundance Browser
public static final String ABUNDANCE = "abundance";
+
+ // RawDataSample Browser
+
+ public static final String BIOLOGICAL_SAMPLE_IDENTIFIER = "biological_sample_identifier";
+ public static final String MS_INJECTION_SAMPLE_CODE = "ms_injection_sample_code";
+
+ public static final String COPY_DATA_SETS_BUTTON_LABEL = "copy_data_sets_button_label";
+ public static final String COPY_DATA_SETS_TITLE = "copy_data_sets_title";
+ public static final String COPY_DATA_SETS_MESSAGE = "copy_data_sets_message";
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXDisplayTypeIDGenerator.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXDisplayTypeIDGenerator.java
index 72097342eadac84137e23f934fa6814d793f471d..d39c574f91f5135f117e7f6ad4a70102be1cfec5 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXDisplayTypeIDGenerator.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXDisplayTypeIDGenerator.java
@@ -29,7 +29,10 @@ public enum PhosphoNetXDisplayTypeIDGenerator implements IDisplayTypeIDGenerator
PROTEIN_SUMMARY_BROWSER_GRID("protein-summary-browser-grid"),
- DATA_SET_PROTEIN_BROWSER_GRID("data-set-protein-browser-grid"), ;
+ DATA_SET_PROTEIN_BROWSER_GRID("data-set-protein-browser-grid"),
+
+ RAW_DATA_SAMPLE_BROWSER_GRID("raw-data-sample-browser-grid"),
+ ;
private final String genericNameOrPrefix;
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 983a633cb7f45fb9172c18cb6e8c0bcc67077ef6..8c32c533cfe5e17ddda8d1c40e6f4e83fec36a16 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
@@ -49,6 +49,15 @@ public class QueryMenu extends TopMenuItem
{
return ProteinByExperimentBrowserGrid.create(viewContext);
}
+ },
+ ALL_RAW_DATA_SAMPLES()
+ {
+ @Override
+ IDisposableComponent createComponent(
+ IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
+ {
+ return RawDataSampleGrid.create(viewContext);
+ }
}
;
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
new file mode 100644
index 0000000000000000000000000000000000000000..0dac34d682d302cdb81e42c8584f030328696354
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RawDataSampleGrid.java
@@ -0,0 +1,196 @@
+/*
+ * 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.client.web.client.application;
+
+import static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.createOrDelete;
+import static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.edit;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.Dict.COPY_DATA_SETS_BUTTON_LABEL;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.Dict.COPY_DATA_SETS_MESSAGE;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.Dict.COPY_DATA_SETS_TITLE;
+
+import java.util.List;
+
+import com.extjs.gxt.ui.client.widget.Dialog;
+import com.extjs.gxt.ui.client.widget.button.Button;
+import com.extjs.gxt.ui.client.widget.grid.GridCellRenderer;
+
+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.VoidAsyncCallback;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.BaseEntityModel;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.IColumnDefinitionKind;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.AbstractSimpleBrowserGrid;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.ColumnDefsAndConfigs;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IBrowserGridActionInvoker;
+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.IDisposableComponent;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.AbstractDataConfirmationDialog;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
+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.shared.basic.IColumnDefinition;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.ObjectKind;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.columns.RawDataSampleColDefKind;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+class RawDataSampleGrid extends AbstractSimpleBrowserGrid<Sample>
+{
+ private static final class CopyConfirmationDialog extends
+ AbstractDataConfirmationDialog<List<Sample>>
+ {
+ private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
+ private final List<Sample> samples;
+
+ private CopyConfirmationDialog(IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext,
+ List<Sample> samples, String title)
+ {
+ super(specificViewContext, samples, title);
+ this.specificViewContext = specificViewContext;
+ this.samples = samples;
+ }
+
+ @Override
+ protected String createMessage()
+ {
+ String list = "[";
+ String delim = "";
+ for (Sample sample : samples)
+ {
+ list += delim + sample.getCode();
+ delim = ", ";
+ }
+ list += "]";
+ return specificViewContext.getMessage(COPY_DATA_SETS_MESSAGE, list);
+ }
+
+ @Override
+ protected void executeConfirmedAction()
+ {
+ long[] rawDataSampleIDs = new long[samples.size()];
+ for (int i = 0; i < samples.size(); i++)
+ {
+ rawDataSampleIDs[i] = samples.get(i).getId();
+ }
+ specificViewContext.getService().copyRawData(rawDataSampleIDs,
+ new VoidAsyncCallback<Void>(specificViewContext));
+ }
+
+ @Override
+ protected void extendForm()
+ {
+ }
+ }
+
+ public static final String BROWSER_ID =
+ GenericConstants.ID_PREFIX + "raw-data-sample-browser";
+
+ public static final String GRID_ID = BROWSER_ID + "-grid";
+
+ public static IDisposableComponent create(
+ final IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
+ {
+ RawDataSampleGrid grid = new RawDataSampleGrid(viewContext);
+ return grid.asDisposableWithoutToolbar();
+ }
+
+ private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
+
+ RawDataSampleGrid(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
+ {
+ super(viewContext.getCommonViewContext(), BROWSER_ID, GRID_ID, true,
+ PhosphoNetXDisplayTypeIDGenerator.RAW_DATA_SAMPLE_BROWSER_GRID);
+ specificViewContext = viewContext;
+ allowMultipleSelection();
+ registerLinkClickListenerFor(RawDataSampleColDefKind.CODE.id(), new ICellListener<Sample>()
+ {
+ public void handle(Sample rowItem)
+ {
+ showEntityViewer(rowItem, false);
+ }
+ });
+ addEntityOperationsLabel();
+ Button uploadButton =
+ new Button(viewContext.getMessage(COPY_DATA_SETS_BUTTON_LABEL),
+ new AbstractCreateDialogListener()
+ {
+ @Override
+ protected Dialog createDialog(List<Sample> samples,
+ IBrowserGridActionInvoker invoker)
+ {
+ return new CopyConfirmationDialog(specificViewContext, samples,
+ specificViewContext.getMessage(COPY_DATA_SETS_TITLE));
+ }
+ });
+ addButton(uploadButton);
+ }
+
+ @Override
+ protected IColumnDefinitionKind<Sample>[] getStaticColumnsDefinition()
+ {
+ return RawDataSampleColDefKind.values();
+ }
+
+ @Override
+ protected ColumnDefsAndConfigs<Sample> createColumnsDefinition()
+ {
+ ColumnDefsAndConfigs<Sample> schema = super.createColumnsDefinition();
+ GridCellRenderer<BaseEntityModel<?>> linkCellRenderer = createInternalLinkCellRenderer();
+ schema.setGridCellRendererFor(RawDataSampleColDefKind.CODE.id(), linkCellRenderer);
+ return schema;
+ }
+
+ @Override
+ protected List<IColumnDefinition<Sample>> getInitialFilters()
+ {
+ return asColumnFilters(new RawDataSampleColDefKind[] {RawDataSampleColDefKind.CODE});
+ }
+
+ @Override
+ protected void listEntities(DefaultResultSetConfig<String, Sample> resultSetConfig,
+ AbstractAsyncCallback<ResultSet<Sample>> callback)
+ {
+ specificViewContext.getService().listRawDataSamples(resultSetConfig, callback);
+ }
+
+ @Override
+ protected void prepareExportEntities(TableExportCriteria<Sample> exportCriteria,
+ AbstractAsyncCallback<String> callback)
+ {
+ specificViewContext.getService().prepareExportRawDataSamples(exportCriteria, callback);
+ }
+
+ public DatabaseModificationKind[] getRelevantModifications()
+ {
+ return new DatabaseModificationKind[]
+ { createOrDelete(ObjectKind.SAMPLE_TYPE), edit(ObjectKind.SAMPLE_TYPE),
+ createOrDelete(ObjectKind.GROUP),
+ createOrDelete(ObjectKind.PROPERTY_TYPE_ASSIGNMENT),
+ edit(ObjectKind.PROPERTY_TYPE_ASSIGNMENT) };
+ }
+
+ @Override
+ protected void showEntityViewer(Sample entity, boolean editMode)
+ {
+ showEntityInformationHolderViewer(entity, editMode);
+ }
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/SampleAbundanceBrowserGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/SampleAbundanceBrowserGrid.java
index e87a5f2a789215c0ab6700d76c9650c6a04703e1..517b6fd8033c45396e3d790a7404ac745ede8a8f 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/SampleAbundanceBrowserGrid.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/SampleAbundanceBrowserGrid.java
@@ -28,12 +28,8 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAs
import ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict;
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.DispatcherHelper;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DisplayTypeIDGenerator;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.ITabItemFactory;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.BaseEntityModel;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.plugin.IClientPlugin;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.plugin.IClientPluginFactory;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.renderer.LinkRenderer;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.renderer.RealNumberRenderer;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.IColumnDefinitionKind;
@@ -50,13 +46,11 @@ 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.shared.basic.GridRowModel;
import ch.systemsx.cisd.openbis.generic.shared.basic.IColumnDefinition;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IIdentifiable;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.ObjectKind;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.columns.SampleAbundanceColDefKind;
@@ -293,21 +287,7 @@ public class SampleAbundanceBrowserGrid
@Override
protected void showEntityViewer(SampleWithPropertiesAndAbundance sample, boolean editMode)
{
- final EntityKind entityKind = EntityKind.SAMPLE;
- final ITabItemFactory tabView;
- final IClientPluginFactory clientPluginFactory =
- viewContext.getClientPluginFactoryProvider().getClientPluginFactory(entityKind,
- sample.getSampleType());
- final IClientPlugin<SampleType, IIdentifiable> createClientPlugin =
- clientPluginFactory.createClientPlugin(entityKind);
- if (editMode)
- {
- tabView = createClientPlugin.createEntityEditor(sample);
- } else
- {
- tabView = createClientPlugin.createEntityViewer(sample);
- }
- DispatcherHelper.dispatchNaviEvent(tabView);
+ showEntityInformationHolderViewer(sample, editMode);
}
@Override
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/RawDataSampleColDefKind.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/RawDataSampleColDefKind.java
new file mode 100644
index 0000000000000000000000000000000000000000..809c602e0bd2d3133d05497c8583c793a39b82b3
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/RawDataSampleColDefKind.java
@@ -0,0 +1,77 @@
+/*
+ * Copyright 2008 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 static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.Dict.MS_INJECTION_SAMPLE_CODE;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.Dict.BIOLOGICAL_SAMPLE_IDENTIFIER;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict;
+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.dto.Sample;
+
+public enum RawDataSampleColDefKind implements IColumnDefinitionKind<Sample>
+{
+ CODE(new AbstractColumnDefinitionKind<Sample>(MS_INJECTION_SAMPLE_CODE)
+ {
+ @Override
+ public String tryGetValue(Sample entity)
+ {
+ return entity.getCode();
+ }
+ }),
+
+ REGISTRATION_DATE(new AbstractColumnDefinitionKind<Sample>(Dict.REGISTRATION_DATE,
+ AbstractColumnDefinitionKind.DATE_COLUMN_WIDTH)
+ {
+ @Override
+ public String tryGetValue(Sample entity)
+ {
+ return renderRegistrationDate(entity);
+ }
+ }),
+
+ SAMPLE_IDENTIFIER(new AbstractColumnDefinitionKind<Sample>(BIOLOGICAL_SAMPLE_IDENTIFIER, 150,
+ false)
+ {
+ @Override
+ public String tryGetValue(Sample entity)
+ {
+ return entity.getGeneratedFrom().getIdentifier();
+ }
+ }),
+
+ ;
+
+ private final AbstractColumnDefinitionKind<Sample> columnDefinitionKind;
+
+ private RawDataSampleColDefKind(AbstractColumnDefinitionKind<Sample> columnDefinitionKind)
+ {
+ this.columnDefinitionKind = columnDefinitionKind;
+ }
+
+ public String id()
+ {
+ return name();
+ }
+
+ public AbstractColumnDefinitionKind<Sample> getDescriptor()
+ {
+ return columnDefinitionKind;
+ }
+
+}
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 6a2876facb3f11b110f31db69426bd40d1d34ebe..cf433b72061d02944c87cba1aac8bf3e701ae155 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
@@ -35,6 +35,16 @@ var phosphonetx = {
// SampleAbudndance Browser
abundance: "Abundance",
+ // RawDataSample Browser
+
+ ALL_RAW_DATA_SAMPLES_menu_item: "All MS INJECTION Samples",
+ ALL_RAW_DATA_SAMPLES_tab_label: "MS INJECTION Samples and Related Biological Samples",
+ ms_injection_sample_code: "MS INJECTION Sample",
+ biological_sample_identifier: "Biological Sample",
+ copy_data_sets_button_label: "Copy Data Sets",
+ copy_data_sets_title: "Copy Data Sets Confirmation",
+ copy_data_sets_message: "Do you want to make the data sets of the samples {0} available for processing?",
+
// LAST LINE: KEEP IT AT THE END
lastline: "" // we need a line without a comma
};
\ No newline at end of file
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 c09d71483689611e82233f3296718e570b63ce82..0782a2ac3cd0683ec26bb5817ac788019f38ad23 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
@@ -24,12 +24,14 @@ 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.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.server.AbstractClientService;
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.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientService;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentAndReferenceCriteria;
@@ -38,6 +40,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListPro
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinSummaryByExperimentCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListSampleAbundanceByProteinCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ResourceNames;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceColumnDefinition;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
@@ -57,6 +60,9 @@ public class PhosphoNetXClientService extends AbstractClientService implements
{
@Resource(name = ResourceNames.PHOSPHONETX_PLUGIN_SERVER)
private IPhosphoNetXServer server;
+
+ @Resource(name = ResourceNames.PHOSPHONETX_RAW_DATA_SERVICE_WEB)
+ private IRawDataServiceInternal rawDataService;
public PhosphoNetXClientService()
{
@@ -179,4 +185,24 @@ public class PhosphoNetXClientService extends AbstractClientService implements
return prepareExportEntities(exportCriteria);
}
+ public ResultSet<Sample> listRawDataSamples(IResultSetConfig<String, Sample> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ final String sessionToken = getSessionToken();
+ return listEntities(criteria, new RawDataSampleProvider(rawDataService, sessionToken));
+ }
+
+ public String prepareExportRawDataSamples(TableExportCriteria<Sample> exportCriteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return prepareExportEntities(exportCriteria);
+ }
+
+ public void copyRawData(long[] rawDataSampleIDs)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ rawDataService.copyRawData(getSessionToken(), rawDataSampleIDs);
+ }
+
+
}
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
new file mode 100644
index 0000000000000000000000000000000000000000..11cabcd2c10cdccc99c31ae91efebd9775549a64
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProvider.java
@@ -0,0 +1,48 @@
+/*
+ * 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.client.web.server;
+
+import java.util.List;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.IOriginalDataProvider;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class RawDataSampleProvider implements IOriginalDataProvider<Sample>
+{
+ private final IRawDataServiceInternal service;
+ private final String sessionToken;
+
+ RawDataSampleProvider(IRawDataServiceInternal service, String sessionToken)
+ {
+ this.service = service;
+ this.sessionToken = sessionToken;
+ }
+
+ public List<Sample> getOriginalData() throws UserFailureException
+ {
+ List<Sample> samples = service.listRawDataSamples(sessionToken);
+ return samples;
+ }
+
+}
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 22d6db2af853a8e9e01bf4c101ea787d44cedf91..a0c44142b195e0f13b1728e6ff0118579a8f09c5 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
@@ -33,6 +33,8 @@ public class ResourceNames
public final static String PHOSPHONETX_RAW_DATA_SERVICE = "phosphonetx-raw-data-service";
+ public final static String PHOSPHONETX_RAW_DATA_SERVICE_WEB = "phosphonetx-raw-data-service-web";
+
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/phosphonetx-applicationContext.xml b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
index 49fe1a591d1ed9507d5d83d34a29244040d303ab..98883e8bd1f54ae2e7fb5d3145091b56f50ee49a 100644
--- a/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
+++ b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
@@ -86,6 +86,13 @@
<constructor-arg ref="dao-factory"/>
<constructor-arg ref="common-business-object-factory" />
</bean>
+
+ <bean id="phosphonetx-raw-data-service-web"
+ class="ch.systemsx.cisd.openbis.plugin.phosphonetx.server.RawDataServiceInternal">
+ <constructor-arg ref="session-manager" />
+ <constructor-arg ref="dao-factory"/>
+ <constructor-arg ref="common-business-object-factory" />
+ </bean>
</beans>
\ No newline at end of file