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 253cf47e82d13e0138a2f328b8b93e4cfceee143..4e55fc527f67ee85a900bb8044edfe8d693cfd40 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 +19,13 @@ 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.ResultSetWithEntityTypes;
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.GenericTableRow;
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;
@@ -86,10 +86,10 @@ public interface IPhosphoNetXClientService extends IClientService
TableExportCriteria<SampleWithPropertiesAndAbundance> exportCriteria)
throws UserFailureException;
- public ResultSetWithEntityTypes<Sample> listRawDataSamples(IResultSetConfig<String, Sample> criteria)
+ public GenericTableResultSet listRawDataSamples(IResultSetConfig<String, GenericTableRow> criteria)
throws UserFailureException;
-
- public String prepareExportRawDataSamples(TableExportCriteria<Sample> exportCriteria)
+
+ public String prepareExportRawDataSamples(TableExportCriteria<GenericTableRow> 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 d2ed071900908be4b02b0ca866fc04b0e23f12ee..6d522eb5d2d2fd679a04bcd9553b3af32f4fe404 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 +21,12 @@ 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.ResultSetWithEntityTypes;
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.GenericTableRow;
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 +104,11 @@ public interface IPhosphoNetXClientServiceAsync extends IClientServiceAsync
AsyncCallback<String> callback);
/** @see IPhosphoNetXClientService#listRawDataSamples(IResultSetConfig) */
- public void listRawDataSamples(IResultSetConfig<String, Sample> criteria,
- AsyncCallback<ResultSetWithEntityTypes<Sample>> callback);
+ public void listRawDataSamples(IResultSetConfig<String, GenericTableRow> criteria,
+ AsyncCallback<GenericTableResultSet> callback);
/** @see IPhosphoNetXClientService#prepareExportRawDataSamples(TableExportCriteria) */
- public void prepareExportRawDataSamples(TableExportCriteria<Sample> exportCriteria,
+ public void prepareExportRawDataSamples(TableExportCriteria<GenericTableRow> exportCriteria,
AsyncCallback<String> callback);
/** @see IPhosphoNetXClientService#copyRawData(long[]) */
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 23292509eda0192e4a124febb89ab37313ae65f0..491b89c32a72cc7fb24815fe0e6bb0268f9bba51 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
@@ -16,101 +16,26 @@
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.ArrayList;
-import java.util.List;
-import java.util.Set;
-
-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 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.VoidAsyncCallback;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.BaseEntityModel;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.EntityGridModelFactory;
-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.GenericTableBrowserGrid;
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.ResultSetWithEntityTypes;
+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.TableExportCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IColumnDefinition;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicEntityType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityTypePropertyType;
-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.DatabaseModificationKind.ObjectKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericTableRow;
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>
+class RawDataSampleGrid extends GenericTableBrowserGrid
{
- 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 BROWSER_ID = GenericConstants.ID_PREFIX + "raw_data_sample_browser";
public static final String GRID_ID = BROWSER_ID + "-grid";
@@ -123,103 +48,24 @@ class RawDataSampleGrid extends AbstractSimpleBrowserGrid<Sample>
private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
- private Set<BasicEntityType> shownEntityTypesOrNull;
-
RawDataSampleGrid(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
{
- super(viewContext.getCommonViewContext(), BROWSER_ID, GRID_ID, true,
+ super(viewContext.getCommonViewContext(), BROWSER_ID, GRID_ID, true, 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()
- {
- IColumnDefinitionKind<Sample>[] columnsDefinition = getStaticColumnsDefinition();
- EntityGridModelFactory<Sample> factory = new EntityGridModelFactory<Sample>(columnsDefinition);
- ArrayList<PropertyType> propertyTypes = new ArrayList<PropertyType>();
- if (shownEntityTypesOrNull != null)
- {
- for (BasicEntityType type : shownEntityTypesOrNull)
- {
- if (type instanceof EntityType)
- {
- EntityType entityType = (EntityType) type;
- List<? extends EntityTypePropertyType<?>> etpts = entityType.getAssignedPropertyTypes();
- for (EntityTypePropertyType<?> entityTypePropertyType : etpts)
- {
- propertyTypes.add(entityTypePropertyType.getPropertyType());
- }
- }
- }
- }
- System.out.println(shownEntityTypesOrNull + " " + propertyTypes);
- ColumnDefsAndConfigs<Sample> schema = factory.createColumnsSchema(viewContext, propertyTypes);
- 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,
- final AbstractAsyncCallback<ResultSet<Sample>> callback)
+ protected void listTableRows(IResultSetConfig<String, GenericTableRow> resultSetConfig,
+ AsyncCallback<GenericTableResultSet> callback)
{
- AbstractAsyncCallback<ResultSetWithEntityTypes<Sample>> extendedCallback =
- new AbstractAsyncCallback<ResultSetWithEntityTypes<Sample>>(viewContext)
- {
- @Override
- protected void process(ResultSetWithEntityTypes<Sample> result)
- {
- shownEntityTypesOrNull = result.getAvailableEntityTypes();
- callback.onSuccess(result.getResultSet());
-// refreshColumnsSettingsIfNecessary();
- }
-
- @Override
- public void finishOnFailure(Throwable caught)
- {
- callback.finishOnFailure(caught);
- }
- };
- specificViewContext.getService().listRawDataSamples(resultSetConfig, extendedCallback);
+ specificViewContext.getService().listRawDataSamples(resultSetConfig, callback);
}
@Override
- protected void prepareExportEntities(TableExportCriteria<Sample> exportCriteria,
+ protected void prepareExportEntities(TableExportCriteria<GenericTableRow> exportCriteria,
AbstractAsyncCallback<String> callback)
{
specificViewContext.getService().prepareExportRawDataSamples(exportCriteria, callback);
@@ -227,16 +73,7 @@ class RawDataSampleGrid extends AbstractSimpleBrowserGrid<Sample>
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);
+ return new DatabaseModificationKind[] {};
}
+
}
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 9c8e3e50ea26a954327903346bcbbdd1ecda1554..ac8ee59a99fc58910da39925f3ebdc1dd2f9ad97 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
@@ -40,8 +40,9 @@ var phosphonetx = {
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",
+ openbis_raw_data_sample_browser_CODE: "MS INJECTION Sample",
+ openbis_raw_data_sample_browser_REGISTRATION_DATE: "Regustration Date",
+ openbis_raw_data_sample_browser_PARENT: "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?",
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 75e3d1843aede398fd7601580ff79f7efae3d73d..a78874bc47f07f5d537ab00f9df64a79ba66ad7c 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
@@ -24,15 +24,15 @@ 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.ResultSetWithEntityTypes;
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.GenericTableRow;
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;
@@ -186,19 +186,21 @@ public class PhosphoNetXClientService extends AbstractClientService implements
return prepareExportEntities(exportCriteria);
}
- public ResultSetWithEntityTypes<Sample> listRawDataSamples(IResultSetConfig<String, Sample> criteria)
+ public GenericTableResultSet listRawDataSamples(IResultSetConfig<String, GenericTableRow> criteria)
throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
{
final String sessionToken = getSessionToken();
- return listEntitiesWithTypes(criteria, new RawDataSampleProvider(rawDataService, sessionToken));
+ RawDataSampleProvider rawDataSampleProvider = new RawDataSampleProvider(rawDataService, sessionToken);
+ ResultSet<GenericTableRow> resultSet = listEntities(criteria, rawDataSampleProvider);
+ return new GenericTableResultSet(resultSet, rawDataSampleProvider.getHeaders());
}
- public String prepareExportRawDataSamples(TableExportCriteria<Sample> exportCriteria)
+ public String prepareExportRawDataSamples(TableExportCriteria<GenericTableRow> 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
{
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 11cabcd2c10cdccc99c31ae91efebd9775549a64..bafc24a09dd65b77e0ba5048b73961a8a629ae6c 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
@@ -16,11 +16,28 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.server;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Date;
+import java.util.HashSet;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.IOriginalDataProvider;
+import ch.systemsx.cisd.openbis.generic.client.web.server.util.DataTypeUtils;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DateTableCell;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericTableColumnHeader;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericTableRow;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IntegerTableCell;
+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.StringTableCell;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
/**
@@ -28,8 +45,138 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInterna
*
* @author Franz-Josef Elmer
*/
-class RawDataSampleProvider implements IOriginalDataProvider<Sample>
+class RawDataSampleProvider implements IOriginalDataProvider<GenericTableRow>
{
+ private static final class Column
+ {
+ private final List<ISerializableComparable> values = new ArrayList<ISerializableComparable>();
+ private final GenericTableColumnHeader header;
+
+ Column(GenericTableColumnHeader header)
+ {
+ this.header = header;
+ }
+
+ GenericTableColumnHeader getHeader()
+ {
+ return header;
+ }
+
+ List<ISerializableComparable> getValues()
+ {
+ return values;
+ }
+
+ void add(int index, ISerializableComparable value)
+ {
+ while (values.size() < index)
+ {
+ values.add(null);
+ }
+ values.add(value);
+ }
+
+ void addNumber(int index, Long number)
+ {
+ add(index, new IntegerTableCell(number));
+ }
+
+ void addString(int index, String string)
+ {
+ add(index, new StringTableCell(string));
+ }
+
+ void addDate(int index, Date date)
+ {
+ add(index, new DateTableCell(date));
+ }
+
+ void addPrefixToColumnHeaderCodes(String prefix)
+ {
+ header.setCode(prefix + header.getCode());
+ }
+
+ void setIndex(int index)
+ {
+ header.setIndex(index);
+ }
+ }
+
+ private static final class PropertyColumns
+ {
+ private final Map<String, Column> columns = new TreeMap<String, Column>();
+
+ void add(int index, IEntityProperty property)
+ {
+ PropertyType propertyType = property.getPropertyType();
+ DataTypeCode dataType = propertyType.getDataType().getCode();
+ String key = propertyType.getCode();
+ Column column = columns.get(key);
+ if (column == null)
+ {
+ GenericTableColumnHeader header = new GenericTableColumnHeader();
+ header.setCode(key);
+ header.setIndex(columns.size());
+ header.setTitle(propertyType.getLabel());
+ header.setType(dataType);
+ column = new Column(header);
+ columns.put(key, column);
+ }
+ column.add(index, DataTypeUtils.convertTo(dataType, property.getValue()));
+ }
+
+ Set<String> getColumnCodes()
+ {
+ return columns.keySet();
+ }
+
+ void addPrefixToColumnHeaderCodes(String prefix)
+ {
+ for (Map.Entry<String, Column> entry : columns.entrySet())
+ {
+ entry.getValue().addPrefixToColumnHeaderCodes(prefix);
+ }
+ }
+
+ int reindexColumns(int startIndex)
+ {
+ int index = startIndex;
+ for (Map.Entry<String, Column> entry : columns.entrySet())
+ {
+ entry.getValue().setIndex(index++);
+ }
+ return index;
+ }
+
+ Collection<? extends Column> getColumns()
+ {
+ return columns.values();
+ }
+ }
+
+ private static final class ColumnsWithIDColumn
+ {
+ private final List<Column> columns;
+ private final Column idColumn;
+
+ public ColumnsWithIDColumn(List<Column> columns, Column idColumn)
+ {
+ this.columns = columns;
+ this.idColumn = idColumn;
+ }
+
+ public List<Column> getColumns()
+ {
+ return columns;
+ }
+
+ public Column getIdColumn()
+ {
+ return idColumn;
+ }
+
+ }
+
private final IRawDataServiceInternal service;
private final String sessionToken;
@@ -39,10 +186,80 @@ class RawDataSampleProvider implements IOriginalDataProvider<Sample>
this.sessionToken = sessionToken;
}
- public List<Sample> getOriginalData() throws UserFailureException
+ public List<GenericTableRow> getOriginalData() throws UserFailureException
+ {
+ ColumnsWithIDColumn columnsWithIDColumn = getColumns();
+ List<Column> columns = columnsWithIDColumn.getColumns();
+ int numberOfRows = columns.get(0).getValues().size();
+ List<GenericTableRow> result = new ArrayList<GenericTableRow>(numberOfRows);
+ for(int i = 0; i < numberOfRows; i++)
+ {
+ ISerializableComparable[] row = new ISerializableComparable[columns.size()];
+ for (int j = 0; j < row.length; j++)
+ {
+ Column column = columns.get(j);
+ List<ISerializableComparable> values = column.getValues();
+ row[j] = i < values.size() ? values.get(i) : null;
+ }
+ result.add(new GenericTableRow(row));
+ }
+ return result;
+ }
+
+ public List<GenericTableColumnHeader> getHeaders()
+ {
+ List<Column> columns = getColumns().getColumns();
+ List<GenericTableColumnHeader> headers = new ArrayList<GenericTableColumnHeader>(columns.size());
+ for (Column column : columns)
+ {
+ headers.add(column.getHeader());
+ }
+ return headers;
+ }
+
+ private ColumnsWithIDColumn getColumns()
{
List<Sample> samples = service.listRawDataSamples(sessionToken);
- return samples;
+ Column idColumn = new Column(GenericTableColumnHeader.untitledStringHeader(0, "ID"));
+ Column codeColumn = new Column(GenericTableColumnHeader.untitledStringHeader(0, "CODE"));
+ Column dateColumn = new Column(GenericTableColumnHeader.untitledStringHeader(1, "REGISTRATION_DATE"));
+ Column parentColumn = new Column(GenericTableColumnHeader.untitledStringHeader(2, "PARENT"));
+ List<Column> columns = new ArrayList<Column>();
+ columns.add(codeColumn);
+ columns.add(dateColumn);
+ columns.add(parentColumn);
+ 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);
+ idColumn.addNumber(i, sample.getId());
+ codeColumn.addString(i, sample.getCode());
+ dateColumn.addDate(i, sample.getRegistrationDate());
+ parentColumn.addString(i, sample.getGeneratedFrom().getIdentifier());
+ 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 new ColumnsWithIDColumn(columns, idColumn);
+ }
+
+ private void addPropertyTypes(PropertyColumns columns, int index, Sample sample)
+ {
+ for (IEntityProperty property : sample.getProperties())
+ {
+ columns.add(index, property);
+ }
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
index 9480b1c67f0b53b01e35bd609665383efd16a5ed..3f9cca5ce6ae1bb18be42b280430b49b842edf49 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
@@ -135,7 +135,9 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
criteria.setSampleType(SampleTypeTranslator.translate(sampleTypePE, null));
criteria.setIncludeGroup(true);
criteria.setGroupCode(GROUP_CODE);
- return sampleLister.list(new ListOrSearchSampleCriteria(criteria));
+ ListOrSearchSampleCriteria criteria2 = new ListOrSearchSampleCriteria(criteria);
+ criteria2.setEnrichDependentSamplesWithProperties(true);
+ return sampleLister.list(criteria2);
}
private String findDataStoreServer()