From f24d947eb2a80fae6debab6f39068318111b7824 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Tue, 29 Mar 2011 09:07:07 +0000
Subject: [PATCH] LMS-2139 HCSPubPortal: finding a gene - disambiguation page
SVN: 20523
---
.../client/application/ui/TypedTableGrid.java | 13 +-
.../ui/grid/AbstractBrowserGrid.java | 26 +-
.../ui/vocabulary/VocabularyTermGrid.java | 4 +-
.../web/client/dto/MaterialGridColumnIDs.java | 35 +++
.../resultset/AbstractTableModelProvider.java | 11 +-
.../resultset/MatchingEntitiesProvider.java | 24 +-
.../server/resultset/MaterialProvider.java | 78 +++++
.../ProteinSequenceProviderTest.java | 2 +-
.../resultset/ProteinSummaryProviderTest.java | 2 +-
.../web/client/IScreeningClientService.java | 15 +-
.../client/IScreeningClientServiceAsync.java | 19 +-
.../application/ClientPluginFactory.java | 25 +-
.../client/web/client/application/Dict.java | 16 ++
.../ScreeningDisplayTypeIDGenerator.java | 5 +-
.../client/application/ScreeningModule.java | 67 +++--
.../detailviewers/ImagingMaterialViewer.java | 2 +-
.../MaterialDetailsComponent.java | 111 --------
.../MaterialDisambiguationGrid.java | 266 ++++++++++++++++++
.../detailviewers/PlateMetadataBrowser.java | 4 +-
...sSection.java => WellSearchComponent.java} | 58 ++--
.../detailviewers/WellSearchGrid.java | 63 +++--
...on.java => WellSearchMaterialSection.java} | 7 +-
.../GlobalWellSearchLocatorResolver.java | 13 +-
.../locator/WellSearchLocatorResolver.java | 9 +-
.../specific/ScreeningLinkExtractor.java | 54 +++-
.../client/web/public/screening-dictionary.js | 186 ++++++------
.../web/server/PlateMetadataProvider.java | 4 +-
.../web/server/ScreeningClientService.java | 20 +-
.../web/server/WellContentProvider.java | 94 ++-----
.../screening/server/ScreeningServer.java | 7 +
.../server/ScreeningServerLogger.java | 9 +-
.../server/logic/WellContentLoader.java | 38 ++-
.../screening/shared/IScreeningServer.java | 11 +
.../PlateMetadataGridColumnIDs.java} | 9 +-
.../{ => grids}/WellSearchGridColumnIds.java | 2 +-
.../web/server/PlateMetadataProviderTest.java | 6 +-
.../server/logic/WellContentLoaderTest.java | 3 +-
37 files changed, 878 insertions(+), 440 deletions(-)
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/dto/MaterialGridColumnIDs.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/MaterialProvider.java
delete mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialDetailsComponent.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialDisambiguationGrid.java
rename screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/{ExperimentPlateLocationsSection.java => WellSearchComponent.java} (76%)
rename screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/{PlateLocationsMaterialSection.java => WellSearchMaterialSection.java} (91%)
rename screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/{PlateMetadataGridIDs.java => grids/PlateMetadataGridColumnIDs.java} (85%)
rename screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/{ => grids}/WellSearchGridColumnIds.java (99%)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/TypedTableGrid.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/TypedTableGrid.java
index effed877c22..fcb4c744595 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/TypedTableGrid.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/TypedTableGrid.java
@@ -132,7 +132,7 @@ public abstract class TypedTableGrid<T extends ISerializable>
EntityTableCell entityTableCell = (EntityTableCell) value;
if (entityTableCell.isMissing())
{
- return null;
+ return null;
}
String permId = entityTableCell.getPermId();
if (entityTableCell.getEntityKind() == EntityKind.MATERIAL)
@@ -461,4 +461,15 @@ public abstract class TypedTableGrid<T extends ISerializable>
{
refreshGridSilently();
}
+
+ protected List<T> getContainedGridElements()
+ {
+ List<TableModelRowWithObject<T>> wrappedElements = super.getGridElements();
+ List<T> elements = new ArrayList<T>();
+ for (TableModelRowWithObject<T> wrappedElement : wrappedElements)
+ {
+ elements.add(wrappedElement.getObjectOrNull());
+ }
+ return elements;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/AbstractBrowserGrid.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/AbstractBrowserGrid.java
index 2db04b7e09e..0fd0f1ff1a5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/AbstractBrowserGrid.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/AbstractBrowserGrid.java
@@ -435,9 +435,15 @@ public abstract class AbstractBrowserGrid<T/* Entity */, M extends BaseEntityMod
grid.getSelectionModel().setSelectionMode(SelectionMode.MULTI);
}
- protected final List<M> getGridModels()
+ protected List<T> getGridElements()
{
- return grid.getStore().getModels();
+ List<M> models = grid.getStore().getModels();
+ List<T> elements = new ArrayList<T>();
+ for (M model : models)
+ {
+ elements.add(model.getBaseObject());
+ }
+ return elements;
}
private IDelegatedAction createApplyFiltersDelagator()
@@ -490,15 +496,23 @@ public abstract class AbstractBrowserGrid<T/* Entity */, M extends BaseEntityMod
final LayoutContainer subContainer = new LayoutContainer();
subContainer.setLayout(new RowLayout(Orientation.HORIZONTAL));
subContainer.add(tree, new RowData(300, 1));
+ setHeader(headerOrNull);
+ subContainer.add(this, new RowData(1, 1));
+ container.add(subContainer, new RowData(1, 1));
+
+ return asDisposableEntityChooser(container, toolbar);
+ }
+
+ protected final void setHeader(String headerOrNull)
+ {
if (headerOrNull != null)
{
this.contentPanel.setHeaderVisible(true);
this.contentPanel.setHeading(headerOrNull);
+ } else
+ {
+ this.contentPanel.setHeaderVisible(false);
}
- subContainer.add(this, new RowData(1, 1));
- container.add(subContainer, new RowData(1, 1));
-
- return asDisposableEntityChooser(container, toolbar);
}
private DisposableEntityChooser<T> asDisposableEntityChooser(final Component mainComponent,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/vocabulary/VocabularyTermGrid.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/vocabulary/VocabularyTermGrid.java
index c06f347ea69..a24f82ddec3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/vocabulary/VocabularyTermGrid.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/vocabulary/VocabularyTermGrid.java
@@ -660,9 +660,9 @@ public class VocabularyTermGrid extends TypedTableGrid<VocabularyTermWithStats>
private List<VocabularyTerm> getTerms()
{
List<VocabularyTerm> terms = new ArrayList<VocabularyTerm>();
- for (BaseEntityModel<TableModelRowWithObject<VocabularyTermWithStats>> model : getGridModels())
+ for (VocabularyTermWithStats v : getContainedGridElements())
{
- terms.add(model.getBaseObject().getObjectOrNull().getTerm());
+ terms.add(v.getTerm());
}
return terms;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/dto/MaterialGridColumnIDs.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/dto/MaterialGridColumnIDs.java
new file mode 100644
index 00000000000..312596721ff
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/dto/MaterialGridColumnIDs.java
@@ -0,0 +1,35 @@
+/*
+ * Copyright 2011 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.generic.client.web.client.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+
+/**
+ * Columns of a grid which shows {@link Material} rows.
+ *
+ * @author Tomasz Pylak
+ */
+public class MaterialGridColumnIDs
+{
+ public static final String CODE = "CODE";
+
+ public static final String REGISTRATOR = "REGISTRATOR";
+
+ public static final String REGISTRATION_DATE = "REGISTRATION_DATE";
+
+ public static final String MATERIAL_TYPE = "MATERIAL_TYPE";
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/AbstractTableModelProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/AbstractTableModelProvider.java
index b6007c3616b..4ef63c7d91b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/AbstractTableModelProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/AbstractTableModelProvider.java
@@ -33,9 +33,14 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
public abstract class AbstractTableModelProvider<T extends ISerializable> implements
ITableModelProvider<T>
{
+
+ /**
+ * Creates the table model with the specified maximum number of rows. If
+ * {@link Integer#MAX_VALUE} is specified the complete table will be created.
+ */
public TypedTableModel<T> getTableModel(int maxSize)
{
- TypedTableModel<T> tableModel = createTableModel(maxSize);
+ TypedTableModel<T> tableModel = createTableModel(Integer.MAX_VALUE);
List<TableModelColumnHeader> headers = tableModel.getHeader();
List<TableModelRowWithObject<T>> rows = tableModel.getRows();
List<TableModelRowWithObject<T>> limitedRows = new ArrayList<TableModelRowWithObject<T>>();
@@ -51,8 +56,8 @@ public abstract class AbstractTableModelProvider<T extends ISerializable> implem
}
/**
- * Creates the table model with the specified maximum number of rows. If
- * {@link Integer#MAX_VALUE} is specified the complete table will be created.
+ * Creates the complete table model.
+ * @param maxSize TODO
*/
protected abstract TypedTableModel<T> createTableModel(int maxSize);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/MatchingEntitiesProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/MatchingEntitiesProvider.java
index 32e1cdc4cc1..e3edc4415da 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/MatchingEntitiesProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/MatchingEntitiesProvider.java
@@ -32,32 +32,38 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SearchableEntity;
import ch.systemsx.cisd.openbis.generic.shared.util.TypedTableModelBuilder;
/**
- *
- *
* @author Franz-Josef Elmer
*/
-public class MatchingEntitiesProvider extends AbstractCommonTableModelProvider<MatchingEntity>
+public class MatchingEntitiesProvider implements ITableModelProvider<MatchingEntity>
{
+ private final ICommonServer commonServer;
+
+ private final String sessionToken;
+
private final SearchableEntity[] matchingEntities;
+
private final String queryText;
+
private final boolean useWildcardSearchMode;
public MatchingEntitiesProvider(ICommonServer commonServer, String sessionToken,
SearchableEntity[] matchingEntities, String queryText, boolean useWildcardSearchMode)
{
- super(commonServer, sessionToken);
+ this.commonServer = commonServer;
+ this.sessionToken = sessionToken;
+
this.matchingEntities = matchingEntities;
this.queryText = queryText;
this.useWildcardSearchMode = useWildcardSearchMode;
}
- @Override
- protected TypedTableModel<MatchingEntity> createTableModel(int maxSize)
+ public TypedTableModel<MatchingEntity> getTableModel(int maxSize)
{
List<MatchingEntity> entities =
- commonServer.listMatchingEntities(sessionToken, matchingEntities, queryText,
- useWildcardSearchMode, maxSize);
- TypedTableModelBuilder<MatchingEntity> builder = new TypedTableModelBuilder<MatchingEntity>();
+ commonServer.listMatchingEntities(sessionToken, matchingEntities, queryText,
+ useWildcardSearchMode, maxSize);
+ TypedTableModelBuilder<MatchingEntity> builder =
+ new TypedTableModelBuilder<MatchingEntity>();
builder.addColumn(ENTITY_KIND);
builder.addColumn(ENTITY_TYPE);
builder.addColumn(IDENTIFIER).withDefaultWidth(140);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/MaterialProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/MaterialProvider.java
new file mode 100644
index 00000000000..8764597a1eb
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/resultset/MaterialProvider.java
@@ -0,0 +1,78 @@
+/*
+ * Copyright 2011 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.generic.client.web.server.resultset;
+
+import static ch.systemsx.cisd.openbis.generic.client.web.client.dto.MaterialGridColumnIDs.CODE;
+import static ch.systemsx.cisd.openbis.generic.client.web.client.dto.MaterialGridColumnIDs.MATERIAL_TYPE;
+import static ch.systemsx.cisd.openbis.generic.client.web.client.dto.MaterialGridColumnIDs.REGISTRATION_DATE;
+import static ch.systemsx.cisd.openbis.generic.client.web.client.dto.MaterialGridColumnIDs.REGISTRATOR;
+
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
+import ch.systemsx.cisd.openbis.generic.shared.util.TypedTableModelBuilder;
+
+/**
+ * Table model provider of {@link Material} instances.
+ *
+ * @author Tomasz Pylak
+ */
+public class MaterialProvider extends AbstractTableModelProvider<Material>
+{
+ private static final String PROPERTIES_GROUP = "property-";
+
+ private final List<Material> materials;
+
+ public MaterialProvider(List<Material> materials)
+ {
+ this.materials = materials;
+ }
+
+ @Override
+ protected TypedTableModel<Material> createTableModel(int maxSize)
+ {
+
+ TypedTableModelBuilder<Material> builder = new TypedTableModelBuilder<Material>();
+ addStandardColumns(builder);
+
+ for (Material material : materials)
+ {
+ addRow(builder, material);
+ }
+ return builder.getModel();
+ }
+
+ private void addStandardColumns(TypedTableModelBuilder<Material> builder)
+ {
+ builder.addColumn(CODE);
+ builder.addColumn(MATERIAL_TYPE);
+ builder.addColumn(REGISTRATION_DATE).withDefaultWidth(300).hideByDefault();
+ builder.addColumn(REGISTRATOR).withDefaultWidth(200).hideByDefault();
+ }
+
+ private void addRow(TypedTableModelBuilder<Material> builder, Material material)
+ {
+ builder.addRow(material);
+ builder.column(CODE).addString(material.getCode());
+ builder.column(MATERIAL_TYPE).addString(material.getEntityType().getCode());
+ builder.column(REGISTRATION_DATE).addDate(material.getRegistrationDate());
+ builder.column(REGISTRATOR).addPerson(material.getRegistrator());
+
+ builder.columnGroup(PROPERTIES_GROUP).addProperties(material.getProperties());
+ }
+}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ProteinSequenceProviderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ProteinSequenceProviderTest.java
index 04459e7915b..85c89b76957 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ProteinSequenceProviderTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ProteinSequenceProviderTest.java
@@ -52,7 +52,7 @@ public class ProteinSequenceProviderTest extends AbstractProviderTest
ProteinSequenceProvider provider =
new ProteinSequenceProvider(phosphonetxServer, SESSION_TOKEN, new TechId(42));
- TypedTableModel<ProteinSequence> model = provider.createTableModel(10);
+ TypedTableModel<ProteinSequence> model = provider.createTableModel(Integer.MAX_VALUE);
assertEquals("[SEQUENCE_SHORT_NAME, DATABASE_NAME_AND_VERSION, SEQUENCE]", getHeaderIDs(model).toString());
assertEquals("[VARCHAR, VARCHAR, VARCHAR]", getHeaderDataTypes(model).toString());
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ProteinSummaryProviderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ProteinSummaryProviderTest.java
index 7ea01c1ed43..e98a8c3b3ea 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ProteinSummaryProviderTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ProteinSummaryProviderTest.java
@@ -51,7 +51,7 @@ public class ProteinSummaryProviderTest extends AbstractProviderTest
ProteinSummaryProvider provider =
new ProteinSummaryProvider(phosphonetxServer, SESSION_TOKEN, new TechId(12));
- TypedTableModel<ProteinSummary> model = provider.createTableModel(10);
+ TypedTableModel<ProteinSummary> model = provider.createTableModel(Integer.MAX_VALUE);
assertEquals("[FDR, PROTEIN_COUNT, PEPTIDE_COUNT]", getHeaderIDs(model).toString());
assertEquals("[REAL, INTEGER, INTEGER]", getHeaderDataTypes(model).toString());
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java
index 6266ed1ab60..18ac635f19f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java
@@ -100,10 +100,23 @@ public interface IScreeningClientService extends IClientService
IResultSetConfig<String, TableModelRowWithObject<WellContent>> gridCriteria,
WellSearchCriteria materialCriteria) throws UserFailureException;
- public String prepareExportPlateLocations(
+ public String prepareExportPlateWells(
TableExportCriteria<TableModelRowWithObject<WellContent>> criteria)
throws UserFailureException;
+ /**
+ * @return materials with codes or properties matching to the query. If the experiment is
+ * specified, only materials inside well locations connected through the plate to this
+ * specified experiment(s) will be returned.
+ */
+ public TypedTableResultSet<Material> listMaterials(
+ IResultSetConfig<String, TableModelRowWithObject<Material>> gridCriteria,
+ WellSearchCriteria materialCriteria) throws UserFailureException;
+
+ public String prepareExportMaterials(
+ TableExportCriteria<TableModelRowWithObject<Material>> criteria)
+ throws UserFailureException;
+
/**
* Returns {@link TypedTableResultSet} containing plate metadata.
*/
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java
index 356f115eb3a..0d7ce9d61d0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java
@@ -84,12 +84,27 @@ public interface IScreeningClientServiceAsync extends IClientServiceAsync
AsyncCallback<TypedTableResultSet<WellContent>> callback);
/**
- * @see IScreeningClientService#prepareExportPlateLocations(TableExportCriteria)
+ * @see IScreeningClientService#prepareExportPlateWells(TableExportCriteria)
*/
- public void prepareExportPlateLocations(
+ public void prepareExportPlateWells(
TableExportCriteria<TableModelRowWithObject<WellContent>> criteria,
AsyncCallback<String> callback);
+ /**
+ * @see IScreeningClientService#listMaterials(IResultSetConfig, WellSearchCriteria)
+ */
+ public void listMaterials(
+ IResultSetConfig<String, TableModelRowWithObject<Material>> gridCriteria,
+ WellSearchCriteria materialCriteria,
+ AsyncCallback<TypedTableResultSet<Material>> callback);
+
+ /**
+ * @see IScreeningClientService#prepareExportMaterials(TableExportCriteria)
+ */
+ public void prepareExportMaterials(
+ TableExportCriteria<TableModelRowWithObject<Material>> criteria,
+ AsyncCallback<String> callback);
+
/**
* @see IScreeningClientService#listPlateMetadata(IResultSetConfig, TechId)
*/
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ClientPluginFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ClientPluginFactory.java
index 755242ec77e..907a7c6dfd2 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ClientPluginFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ClientPluginFactory.java
@@ -40,14 +40,12 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.plugin.ICl
import ch.systemsx.cisd.openbis.generic.client.web.client.application.plugin.IModule;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractViewer;
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.IDisposableComponent;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMessageProvider;
import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.basic.ICodeHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
import ch.systemsx.cisd.openbis.generic.shared.basic.IIdAndCodeHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.ViewMode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicEntityType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
@@ -56,11 +54,10 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.sample.GenericSampleViewer;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ImageSampleViewer;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.MaterialDetailsComponent;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ImagingMaterialViewer;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.MicroscopyDatasetViewer;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.PlateDatasetViewer;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.PlateSampleViewer;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ImagingMaterialViewer;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.sample.LibrarySampleBatchRegistrationForm;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.ExperimentSearchCriteria;
@@ -177,6 +174,9 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Scree
/**
* opens material viewer showing wells in which the material is contained, with a selected
* experiment
+ *
+ * @param experimentCriteriaOrNull note that null does NOT mean searching in all experiments,
+ * but that single experiment should be specified by the user.
*/
public static final void openImagingMaterialViewer(
final IEntityInformationHolderWithPermId material,
@@ -200,19 +200,10 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Scree
public ITabItem create()
{
TechId materialTechId = TechId.create(material);
- if (viewContext.getModel().getViewMode() == ViewMode.EMBEDDED)
- {
- IDisposableComponent viewer =
- MaterialDetailsComponent.create(viewContext, materialTechId,
- experimentCriteriaOrNull);
- return DefaultTabItem.create(getTabTitle(), viewer, viewContext);
- } else
- {
- final DatabaseModificationAwareComponent viewer =
- ImagingMaterialViewer.create(viewContext, materialTechId,
- experimentCriteriaOrNull);
- return createViewerTab(viewer, getTabTitle(), viewContext);
- }
+ final DatabaseModificationAwareComponent viewer =
+ ImagingMaterialViewer.create(viewContext, materialTechId,
+ experimentCriteriaOrNull);
+ return createViewerTab(viewer, getTabTitle(), viewContext);
}
@Override
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/Dict.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/Dict.java
index 53a427bf319..d84a32fb764 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/Dict.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/Dict.java
@@ -81,6 +81,22 @@ public final class Dict extends ch.systemsx.cisd.openbis.generic.client.web.clie
public static final String WELLS_SEARCH_MENU_ITEM = "WELLS_SEARCH";
+ public static final String WELLS_SEARCH_SHOW_COMBINED_RESULTS =
+ "WELLS_SEARCH_SHOW_COMBINED_RESULTS";
+
+ public static final String WELL_SEARCH_NO_RESULTS_IN_ANY_EXP_FOUND =
+ "WELL_SEARCH_NO_RESULTS_IN_ANY_EXP_FOUND";
+
+ public static final String WELL_SEARCH_NO_RESULTS_IN_SELECTED_EXP_FOUND =
+ "WELL_SEARCH_NO_RESULTS_IN_SELECTED_EXP_FOUND";
+
+ public static final String WELL_SEARCH_PERFORM_IN_ALL_EXP = "WELL_SEARCH_PERFORM_IN_ALL_EXP";
+
+ public static final String MATERIAL_DISAMBIGUATION_TITLE = "MATERIAL_DISAMBIGUATION_TITLE";
+
+ public static final String MATERIAL_DISAMBIGUATION_GRID_EXPLANATION =
+ "MATERIAL_DISAMBIGUATION_GRID_EXPLANATION";
+
private Dict()
{
// Can not be instantiated.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningDisplayTypeIDGenerator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningDisplayTypeIDGenerator.java
index 50c17bea5b3..13af2c5c42c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningDisplayTypeIDGenerator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningDisplayTypeIDGenerator.java
@@ -25,8 +25,11 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.
*/
public enum ScreeningDisplayTypeIDGenerator implements IDisplayTypeIDGenerator
{
+ PLATE_METADATA_GRID("plate-metadata-grid"),
- PLATE_METADATA_GRID("plate-metadata-grid"), EXPERIMENT_CHANNEL("experiment-channel"), ;
+ EXPERIMENT_CHANNEL("experiment-channel"),
+
+ MATERIAL_DISAMBIGUATION_GRID("material-disambiguation-grid");
private final String genericNameOrPrefix;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningModule.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningModule.java
index 4a31efa682e..ca5faba7da4 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningModule.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningModule.java
@@ -28,14 +28,15 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericCon
import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.TabContent;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DatabaseModificationAwareComponent;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.menu.ActionMenu;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.menu.ITabActionMenuItemDefinition;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.menu.TabActionMenuItemFactory;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.plugin.IModule;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ExperimentPlateLocationsSection;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ExperimentWellMaterialsSection;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.WellSearchComponent;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator.GlobalWellSearchLocatorResolver;
/**
@@ -57,34 +58,40 @@ public class ScreeningModule implements IModule
public List<? extends MenuItem> getMenuItems()
{
- return Collections.singletonList(TabActionMenuItemFactory.createActionMenu(viewContext, ID,
- new ITabActionMenuItemDefinition<IScreeningClientServiceAsync>()
- {
-
- public String getName()
- {
- return Dict.WELLS_SEARCH_MENU_ITEM;
- }
-
- public String getHelpPageTitle()
- {
- return "Global Well Search";
- }
-
- public DatabaseModificationAwareComponent createComponent(
- IViewContext<IScreeningClientServiceAsync> context)
- {
- TabContent wellSearchTab =
- new ExperimentPlateLocationsSection(viewContext, null, null);
- return DatabaseModificationAwareComponent.wrapUnaware(wellSearchTab);
- }
-
- public String tryGetLink()
- {
- return GlobalWellSearchLocatorResolver.createQueryBrowserLink();
- }
-
- }));
+ ActionMenu globalWellSearch =
+ TabActionMenuItemFactory
+ .createActionMenu(viewContext, ID, createGlobalWellSearch());
+ return Collections.singletonList(globalWellSearch);
+ }
+
+ private ITabActionMenuItemDefinition<IScreeningClientServiceAsync> createGlobalWellSearch()
+ {
+ return new ITabActionMenuItemDefinition<IScreeningClientServiceAsync>()
+ {
+ public String getName()
+ {
+ return Dict.WELLS_SEARCH_MENU_ITEM;
+ }
+
+ public String getHelpPageTitle()
+ {
+ return "Global Well Search";
+ }
+
+ public DatabaseModificationAwareComponent createComponent(
+ IViewContext<IScreeningClientServiceAsync> context)
+ {
+ TabContent wellSearchTab =
+ new WellSearchComponent(viewContext, null, true, true);
+ return DatabaseModificationAwareComponent.wrapUnaware(wellSearchTab);
+ }
+
+ public String tryGetLink()
+ {
+ return GlobalWellSearchLocatorResolver.createQueryBrowserLink();
+ }
+
+ };
}
public String getName()
@@ -103,7 +110,7 @@ public class ScreeningModule implements IModule
ArrayList<TabContent> sections = new ArrayList<TabContent>();
if (entity.getEntityKind() == EntityKind.EXPERIMENT)
{
- sections.add(new ExperimentPlateLocationsSection(viewContext, entity));
+ sections.add(new WellSearchComponent(viewContext, entity));
sections.add(new ExperimentWellMaterialsSection(viewContext, entity));
}
return sections;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImagingMaterialViewer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImagingMaterialViewer.java
index a8bdb63df19..f351f2a7cb0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImagingMaterialViewer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImagingMaterialViewer.java
@@ -78,7 +78,7 @@ public class ImagingMaterialViewer extends GenericMaterialViewer
{
List<TabContent> sections = new ArrayList<TabContent>();
- sections.add(new PlateLocationsMaterialSection(screeningViewContext, materialId,
+ sections.add(new WellSearchMaterialSection(screeningViewContext, materialId,
experimentCriteriaOrNull));
return sections;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialDetailsComponent.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialDetailsComponent.java
deleted file mode 100644
index f7da90df827..00000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialDetailsComponent.java
+++ /dev/null
@@ -1,111 +0,0 @@
-/*
- * Copyright 2011 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.screening.client.web.client.application.detailviewers;
-
-import java.util.Set;
-
-import com.extjs.gxt.ui.client.widget.Component;
-import com.extjs.gxt.ui.client.widget.ContentPanel;
-import com.extjs.gxt.ui.client.widget.layout.RowLayout;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.ExperimentSearchCriteria;
-
-/**
- * Shows details about one material (across all plates in one or all experiments). <br>
- * Can be used as a tab in {@link ImagingMaterialViewer} or independently.
- *
- * @author Tomasz Pylak
- */
-// TODO 2011-03-23, Tomasz Pylak: this class will replace the Plate Locations tab on the material
-// detail view in future.
-// For now it is a prototype accessible only in embedded mode.
-public class MaterialDetailsComponent extends ContentPanel
-{
- private final IViewContext<IScreeningClientServiceAsync> screeningViewContext;
-
- private final ExperimentSearchCriteria experimentCriteriaOrNull;
-
- private final TechId materialId;
-
- public MaterialDetailsComponent(IViewContext<IScreeningClientServiceAsync> viewContext,
- TechId materialId, ExperimentSearchCriteria experimentCriteriaOrNull)
- {
- this.screeningViewContext = viewContext;
- this.materialId = materialId;
- this.experimentCriteriaOrNull = experimentCriteriaOrNull;
- }
-
- private IDisposableComponent createWellSearchGrid()
- {
- return WellSearchGrid.create(screeningViewContext, experimentCriteriaOrNull, materialId);
- }
-
- public static IDisposableComponent create(
- IViewContext<IScreeningClientServiceAsync> viewContext, TechId materialId,
- ExperimentSearchCriteria experimentCriteriaOrNull)
- {
- MaterialDetailsComponent materialDetailsComponent =
- new MaterialDetailsComponent(viewContext, materialId, experimentCriteriaOrNull);
- ContentPanel view = new ContentPanel();
- view.setLayout(new RowLayout());
- view.setHeading("Gene ID: " + materialId);
- IDisposableComponent wellSearchGrid = materialDetailsComponent.createWellSearchGrid();
- view.add(wellSearchGrid.getComponent());
- return new DisposableComponentWrapper(view, wellSearchGrid);
- }
-
- private static class DisposableComponentWrapper implements IDisposableComponent
- {
- private final Component component;
-
- private final IDisposableComponent delegator;
-
- public DisposableComponentWrapper(Component component, IDisposableComponent delegator)
- {
- this.component = component;
- this.delegator = delegator;
- }
-
- public Component getComponent()
- {
- return component;
- }
-
- // --- delegate
-
- public void update(Set<DatabaseModificationKind> observedModifications)
- {
- delegator.update(observedModifications);
- }
-
- public DatabaseModificationKind[] getRelevantModifications()
- {
- return delegator.getRelevantModifications();
- }
-
- public void dispose()
- {
- delegator.dispose();
- }
-
- }
-}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialDisambiguationGrid.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialDisambiguationGrid.java
new file mode 100644
index 00000000000..379bcb43e69
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialDisambiguationGrid.java
@@ -0,0 +1,266 @@
+/*
+ * Copyright 2011 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.screening.client.web.client.application.detailviewers;
+
+import java.util.Arrays;
+import java.util.Date;
+import java.util.List;
+
+import com.extjs.gxt.ui.client.widget.Component;
+import com.extjs.gxt.ui.client.widget.Text;
+import com.google.gwt.i18n.client.DateTimeFormat;
+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.AbstractTabItemFactory;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DefaultTabItem;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DispatcherHelper;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.ITabItem;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.help.HelpPageIdentifier;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.TypedTableGrid;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.ICellListenerAndLinkGenerator;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.IDataRefreshCallback;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.MaterialGridColumnIDs;
+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.dto.ISerializableComparable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ClientPluginFactory;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningDisplayTypeIDGenerator;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ui.columns.specific.ScreeningLinkExtractor;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.SingleExperimentSearchCriteria;
+
+/**
+ * Displays a list of well content materials matching the search criteria and allows to go to their
+ * details.
+ *
+ * @author Tomasz Pylak
+ */
+public class MaterialDisambiguationGrid extends TypedTableGrid<Material>
+{
+ private static final String BROWSER_ID = GenericConstants.ID_PREFIX
+ + "material-disambiguation-grid";
+
+ public static void openTab(final IViewContext<IScreeningClientServiceAsync> viewContext,
+ final WellSearchCriteria searchCriteria)
+ {
+ boolean refreshAutomatically = false;
+ final MaterialDisambiguationGrid grid =
+ new MaterialDisambiguationGrid(viewContext, searchCriteria, refreshAutomatically);
+ final AbstractTabItemFactory disambiguationTabFactory =
+ createDisambiguationTab(viewContext, searchCriteria, grid);
+ grid.refresh(new IDataRefreshCallback()
+ {
+ public void postRefresh(boolean wasSuccessful)
+ {
+ if (grid.getRowNumber() == 0)
+ {
+ AbstractTabItemFactory tabFactory =
+ createNoResultsTab(viewContext, searchCriteria);
+ DispatcherHelper.dispatchNaviEvent(tabFactory);
+ } else if (grid.getRowNumber() == 1)
+ {
+ List<Material> materials = grid.getContainedGridElements();
+ Material material = materials.get(0);
+ grid.openImagingMaterialViewer(material);
+ } else
+ {
+ DispatcherHelper.dispatchNaviEvent(disambiguationTabFactory);
+ }
+ }
+ }, false);
+ }
+
+ private static AbstractTabItemFactory createNoResultsTab(
+ IViewContext<IScreeningClientServiceAsync> viewContext,
+ WellSearchCriteria searchCriteria)
+ {
+ boolean searchAllExperiments =
+ searchCriteria.getExperimentCriteria().tryGetExperiment() == null;
+ String msgDictKey =
+ searchAllExperiments ? Dict.WELL_SEARCH_NO_RESULTS_IN_ANY_EXP_FOUND
+ : Dict.WELL_SEARCH_NO_RESULTS_IN_SELECTED_EXP_FOUND;
+ Component component = new Text(viewContext.getMessage(msgDictKey));
+ return createSimpleTab(viewContext, component, Dict.MATERIAL_DISAMBIGUATION_TITLE,
+ "well-search-no-results");
+ }
+
+ private static AbstractTabItemFactory createSimpleTab(final IViewContext<?> viewContext,
+ final Component component, final String titleDictKey, final String idSuffix)
+ {
+ return new AbstractTabItemFactory()
+ {
+ @Override
+ public ITabItem create()
+ {
+ return DefaultTabItem.createUnaware(getTabTitle(), component, false,
+ viewContext);
+ }
+
+ @Override
+ public String getId()
+ {
+ return GenericConstants.ID_PREFIX + idSuffix;
+ }
+
+ @Override
+ public HelpPageIdentifier getHelpPageIdentifier()
+ {
+ return null;
+ }
+
+ @Override
+ public String getTabTitle()
+ {
+ return viewContext.getMessage(titleDictKey);
+ }
+
+ @Override
+ public String tryGetLink()
+ {
+ return null;
+ }
+ };
+ }
+
+ private static AbstractTabItemFactory createDisambiguationTab(
+ final IViewContext<IScreeningClientServiceAsync> viewContext,
+ final WellSearchCriteria searchCriteria, final MaterialDisambiguationGrid grid)
+ {
+ return new AbstractTabItemFactory()
+ {
+ @Override
+ public ITabItem create()
+ {
+ return DefaultTabItem.create(getTabTitle(), grid.asDisposableWithoutToolbar(),
+ viewContext);
+ }
+
+ @Override
+ public String getId()
+ {
+ final String reportDate =
+ DateTimeFormat.getMediumTimeFormat().format(new Date());
+ return GenericConstants.ID_PREFIX + "-MaterialDisambiguationGrid-" + reportDate;
+ }
+
+ @Override
+ public HelpPageIdentifier getHelpPageIdentifier()
+ {
+ return HelpPageIdentifier.createSpecific("Material Disambiguation");
+ }
+
+ @Override
+ public String getTabTitle()
+ {
+ return viewContext.getMessage(Dict.MATERIAL_DISAMBIGUATION_TITLE);
+ }
+
+ @Override
+ public String tryGetLink()
+ {
+ return ScreeningLinkExtractor.createWellsSearchLink(searchCriteria, false);
+ }
+
+ };
+ }
+
+ // ----------------
+
+ private final WellSearchCriteria searchCriteria;
+
+ private final IViewContext<IScreeningClientServiceAsync> screeningViewContext;
+
+ private MaterialDisambiguationGrid(IViewContext<IScreeningClientServiceAsync> viewContext,
+ WellSearchCriteria searchCriteria, boolean refreshAutomatically)
+ {
+ super(viewContext.getCommonViewContext(), BROWSER_ID, refreshAutomatically,
+ ScreeningDisplayTypeIDGenerator.MATERIAL_DISAMBIGUATION_GRID);
+ this.screeningViewContext = viewContext;
+ this.searchCriteria = searchCriteria;
+
+ setHeader(viewContext.getMessage(Dict.MATERIAL_DISAMBIGUATION_GRID_EXPLANATION));
+ linkToMaterialDetails();
+ }
+
+ private void linkToMaterialDetails()
+ {
+ registerListenerAndLinkGenerator(MaterialGridColumnIDs.CODE,
+ new ICellListenerAndLinkGenerator<Material>()
+ {
+ public String tryGetLink(Material material, ISerializableComparable value)
+ {
+ SingleExperimentSearchCriteria experiment =
+ searchCriteria.getExperimentCriteria().tryGetExperiment();
+ String experimentIdentifier =
+ (experiment != null ? experiment.getExperimentIdentifier()
+ : null);
+ return ScreeningLinkExtractor.tryExtractMaterialWithExperiment(
+ material, experimentIdentifier);
+ }
+
+ public void handle(TableModelRowWithObject<Material> row,
+ boolean specialKeyPressed)
+ {
+ openImagingMaterialViewer(row.getObjectOrNull());
+ }
+ });
+ }
+
+ private void openImagingMaterialViewer(Material material)
+ {
+ ClientPluginFactory.openImagingMaterialViewer(material,
+ searchCriteria.getExperimentCriteria(), screeningViewContext);
+ }
+
+ @Override
+ protected void listTableRows(
+ DefaultResultSetConfig<String, TableModelRowWithObject<Material>> resultSetConfig,
+ AsyncCallback<TypedTableResultSet<Material>> callback)
+ {
+ screeningViewContext.getService().listMaterials(resultSetConfig, searchCriteria, callback);
+
+ }
+
+ @Override
+ protected void prepareExportEntities(
+ TableExportCriteria<TableModelRowWithObject<Material>> exportCriteria,
+ AbstractAsyncCallback<String> callback)
+ {
+ screeningViewContext.getService().prepareExportMaterials(exportCriteria, callback);
+ }
+
+ @Override
+ protected String translateColumnIdToDictionaryKey(String columnID)
+ {
+ return columnID.toLowerCase();
+ }
+
+ @Override
+ protected List<String> getColumnIdsOfFilters()
+ {
+ return Arrays.asList(MaterialGridColumnIDs.CODE);
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateMetadataBrowser.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateMetadataBrowser.java
index 347e2cab3e1..3c55b109364 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateMetadataBrowser.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateMetadataBrowser.java
@@ -43,8 +43,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningDisplayTypeIDGenerator;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ui.columns.specific.ScreeningLinkExtractor;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMetadataGridIDs;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.PlateMetadataGridColumnIDs;
/**
* Allows to create a table containing metadata of selected plate.
@@ -145,7 +145,7 @@ public class PlateMetadataBrowser extends TypedTableGrid<WellMetadata>
private void linkWellSample()
{
- registerListenerAndLinkGenerator(PlateMetadataGridIDs.CODE,
+ registerListenerAndLinkGenerator(PlateMetadataGridColumnIDs.CODE,
new ICellListenerAndLinkGenerator<WellMetadata>()
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentPlateLocationsSection.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchComponent.java
similarity index 76%
rename from screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentPlateLocationsSection.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchComponent.java
index 395f1cd9691..6b0442ecc6d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentPlateLocationsSection.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchComponent.java
@@ -5,6 +5,7 @@ import java.util.List;
import com.extjs.gxt.ui.client.Style.Scroll;
import com.extjs.gxt.ui.client.widget.LayoutContainer;
import com.extjs.gxt.ui.client.widget.button.Button;
+import com.extjs.gxt.ui.client.widget.form.CheckBoxGroup;
import com.extjs.gxt.ui.client.widget.layout.MarginData;
import com.extjs.gxt.ui.client.widget.layout.RowLayout;
import com.google.gwt.user.client.ui.Widget;
@@ -18,6 +19,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.renderer.L
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.CheckBoxField;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.MultilineItemsField;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IDelegatedAction;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMessageProvider;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
@@ -30,11 +32,12 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCrit
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.MaterialSearchCriteria;
/**
- * Experiment section panel which allows to find wells were selected genes have been inhibited.
+ * Allows to find wells were selected materials are contained. Used in experiment section panel or
+ * as a standalone module.
*
* @author Tomasz Pylak
*/
-public class ExperimentPlateLocationsSection extends TabContent
+public class WellSearchComponent extends TabContent
{
public static final String ID_SUFFIX = "ExperimentPlateLocationsSection";
@@ -42,12 +45,15 @@ public class ExperimentPlateLocationsSection extends TabContent
private final IViewContext<IScreeningClientServiceAsync> screeningViewContext;
+ // null means that we search in all experiments
private final IEntityInformationHolderWithIdentifier experimentOrNull;
private final MultilineItemsField materialListField;
private final CheckBoxField exactMatchOnly;
+ private final CheckBoxField showCombinedResults;
+
private List<MaterialType> materialTypesOrNull;
public static String getTabTitle(IViewContext<IScreeningClientServiceAsync> viewContext)
@@ -55,9 +61,8 @@ public class ExperimentPlateLocationsSection extends TabContent
return viewContext.getMessage(Dict.EXPERIMENT_PLATE_MATERIAL_REVIEWER_SECTION);
}
- public ExperimentPlateLocationsSection(
- IViewContext<IScreeningClientServiceAsync> screeningViewContext, String materialListOrNull,
- Boolean isExactMatchOrNull)
+ public WellSearchComponent(IViewContext<IScreeningClientServiceAsync> screeningViewContext,
+ String materialListOrNull, Boolean isExactMatchOrNull, Boolean showCombinedResultsOrNull)
{
this(screeningViewContext, null);
@@ -69,23 +74,27 @@ public class ExperimentPlateLocationsSection extends TabContent
{
exactMatchOnly.setValue(isExactMatchOrNull);
}
+ if (showCombinedResultsOrNull != null)
+ {
+ showCombinedResults.setValue(showCombinedResultsOrNull);
+ }
setContentVisible(true);
}
- public ExperimentPlateLocationsSection(
- IViewContext<IScreeningClientServiceAsync> screeningViewContext,
+ public WellSearchComponent(IViewContext<IScreeningClientServiceAsync> screeningViewContext,
IEntityInformationHolderWithIdentifier experimentOrNull)
{
- super(getTabTitle(screeningViewContext),
- screeningViewContext, experimentOrNull);
+ super(getTabTitle(screeningViewContext), screeningViewContext, experimentOrNull);
this.screeningViewContext = screeningViewContext;
this.experimentOrNull = experimentOrNull;
this.materialListField = createMaterialListArea();
- this.exactMatchOnly =
- new CheckBoxField(screeningViewContext.getMessage(Dict.EXACT_MATCH_ONLY), false);
- exactMatchOnly.setBoxLabel(screeningViewContext.getMessage(Dict.EXACT_MATCH_ONLY));
- exactMatchOnly.setValue(true);
+ this.exactMatchOnly = createCheckBox(Dict.EXACT_MATCH_ONLY, true, screeningViewContext);
+ this.showCombinedResults =
+ createCheckBox(Dict.WELLS_SEARCH_SHOW_COMBINED_RESULTS,
+ ScreeningLinkExtractor.WELL_SEARCH_SHOW_COMBINED_RESULTS_DEFAULT,
+ screeningViewContext);
+
setIds(DisplayTypeIDGenerator.EXPERIMENT_PLATE_LOCATIONS_SECTION);
screeningViewContext.getCommonService().listMaterialTypes(
new AbstractAsyncCallback<List<MaterialType>>(screeningViewContext)
@@ -98,6 +107,16 @@ public class ExperimentPlateLocationsSection extends TabContent
});
}
+ private static CheckBoxField createCheckBox(String labelDictKey, Boolean value,
+ IMessageProvider messageProvider)
+ {
+ String label = messageProvider.getMessage(labelDictKey);
+ CheckBoxField checkbox = new CheckBoxField(label, false);
+ checkbox.setBoxLabel(label);
+ checkbox.setValue(value);
+ return checkbox;
+ }
+
private MultilineItemsField createMaterialListArea()
{
MultilineItemsField area = new MultilineItemsField("", true, 10);
@@ -114,7 +133,11 @@ public class ExperimentPlateLocationsSection extends TabContent
{
LayoutContainer container = new LayoutContainer(new RowLayout());
- container.add(exactMatchOnly);
+ CheckBoxGroup checkBoxGroup = new CheckBoxGroup();
+ checkBoxGroup.add(exactMatchOnly);
+ checkBoxGroup.add(showCombinedResults);
+ container.add(checkBoxGroup);
+
container.add(materialListField);
container.add(createSearchLink());
@@ -143,9 +166,10 @@ public class ExperimentPlateLocationsSection extends TabContent
{
return null;
}
- String experimentPermId = (experimentOrNull != null) ? experimentOrNull.getPermId() : null;
+ String experimentPermId =
+ (experimentOrNull != null) ? experimentOrNull.getPermId() : null;
return ScreeningLinkExtractor.createWellsSearchLink(experimentPermId,
- materialCriteria);
+ materialCriteria, showCombinedResults.getValue());
}
};
return LinkRenderer.createButtonLink(searchButton, normalModeAction, urlProvider);
@@ -160,7 +184,7 @@ public class ExperimentPlateLocationsSection extends TabContent
}
ExperimentSearchCriteria experimentCriteria = getExperimentSearchCriteria();
WellSearchGrid.openTab(screeningViewContext, experimentCriteria,
- MaterialSearchCriteria.create(materialCriteria));
+ MaterialSearchCriteria.create(materialCriteria), showCombinedResults.getValue());
}
private ExperimentSearchCriteria getExperimentSearchCriteria()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchGrid.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchGrid.java
index 49f3de12485..5885ad350d2 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchGrid.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchGrid.java
@@ -16,8 +16,8 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
-import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchGridColumnIds.WELL;
-import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchGridColumnIds.WELL_CONTENT_MATERIAL;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.WellSearchGridColumnIds.WELL;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.WellSearchGridColumnIds.WELL_CONTENT_MATERIAL;
import java.util.Arrays;
import java.util.Date;
@@ -88,7 +88,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCrit
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.ExperimentSearchCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.MaterialSearchCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.SingleExperimentSearchCriteria;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchGridColumnIds;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.WellSearchGridColumnIds;
/**
* @author Franz-Josef Elmer
@@ -113,7 +113,8 @@ public class WellSearchGrid extends TypedTableGrid<WellContent>
// by experiment perm id
public static void openTab(
final IViewContext<IScreeningClientServiceAsync> screeningViewContext,
- final String experimentPermId, final MaterialSearchCriteria materialSearchCriteria)
+ final String experimentPermId, final MaterialSearchCriteria materialSearchCriteria,
+ final boolean showCombinedResults)
{
screeningViewContext.getCommonService().getEntityInformationHolder(EntityKind.EXPERIMENT,
experimentPermId,
@@ -125,7 +126,7 @@ public class WellSearchGrid extends TypedTableGrid<WellContent>
{
TechId experimentId = new TechId(experimentIdentifier.getId());
WellSearchGrid.openTab(screeningViewContext, experimentId,
- materialSearchCriteria);
+ materialSearchCriteria, showCombinedResults);
}
});
}
@@ -133,7 +134,8 @@ public class WellSearchGrid extends TypedTableGrid<WellContent>
// by experiment tech id
private static void openTab(
final IViewContext<IScreeningClientServiceAsync> screeningViewContext,
- TechId experimentId, final MaterialSearchCriteria materialSearchCriteria)
+ TechId experimentId, final MaterialSearchCriteria materialSearchCriteria,
+ final boolean showCombinedResults)
{
screeningViewContext.getCommonService().getExperimentInfo(experimentId,
new AbstractAsyncCallback<Experiment>(screeningViewContext)
@@ -145,24 +147,40 @@ public class WellSearchGrid extends TypedTableGrid<WellContent>
ExperimentSearchCriteria.createExperiment(experiment.getId(),
experiment.getPermId(), experiment.getIdentifier());
WellSearchGrid.openTab(screeningViewContext, experimentCriteria,
- materialSearchCriteria);
+ materialSearchCriteria, showCombinedResults);
}
});
}
public static void openTab(final IViewContext<IScreeningClientServiceAsync> viewContext,
final ExperimentSearchCriteria experimentCriteria,
- final MaterialSearchCriteria materialCriteria)
+ final MaterialSearchCriteria materialCriteria, final boolean showCombinedResults)
{
- final AbstractTabItemFactory tabFactory = new AbstractTabItemFactory()
+ WellSearchCriteria searchCriteria =
+ new WellSearchCriteria(experimentCriteria, materialCriteria);
+ if (showCombinedResults)
+ {
+ openWellSearchTab(viewContext, searchCriteria);
+ } else
+ {
+ MaterialDisambiguationGrid.openTab(viewContext, searchCriteria);
+ }
+ }
+
+ private static void openWellSearchTab(
+ final IViewContext<IScreeningClientServiceAsync> viewContext,
+ final WellSearchCriteria searchCriteria)
+ {
+ DispatcherHelper.dispatchNaviEvent(new AbstractTabItemFactory()
{
@Override
public ITabItem create()
{
- IDisposableComponent reviewer =
- WellSearchGrid
- .create(viewContext, experimentCriteria, materialCriteria);
- return DefaultTabItem.create(getTabTitle(), reviewer, viewContext);
+ IDisposableComponent grid =
+ WellSearchGrid.create(viewContext,
+ searchCriteria.getExperimentCriteria(),
+ searchCriteria.getMaterialSearchCriteria());
+ return DefaultTabItem.create(getTabTitle(), grid, viewContext);
}
@Override
@@ -188,15 +206,9 @@ public class WellSearchGrid extends TypedTableGrid<WellContent>
@Override
public String tryGetLink()
{
- SingleExperimentSearchCriteria experimentCriteriaOrNull =
- experimentCriteria.tryGetExperiment();
- return ScreeningLinkExtractor.createWellsSearchLink(
- (experimentCriteriaOrNull != null ? experimentCriteriaOrNull
- .getExperimentPermId() : null), materialCriteria
- .tryGetMaterialCodesOrProperties());
+ return ScreeningLinkExtractor.createWellsSearchLink(searchCriteria, true);
}
- };
- DispatcherHelper.dispatchNaviEvent(tabFactory);
+ });
}
public static IDisposableComponent create(
@@ -220,17 +232,17 @@ public class WellSearchGrid extends TypedTableGrid<WellContent>
public void update(Set<DatabaseModificationKind> observedModifications)
{
}
-
+
public DatabaseModificationKind[] getRelevantModifications()
{
return null;
}
-
+
public Component getComponent()
{
return toolbar;
}
-
+
public void dispose()
{
}
@@ -488,6 +500,7 @@ public class WellSearchGrid extends TypedTableGrid<WellContent>
chooserField.setEditable(false);
if (experimentCriteriaOrNull != null && experimentCriteriaOrNull.tryGetExperiment() != null)
{
+ // we search in a single experiment
updateSingleExperimentChooser(chooserField, experimentCriteriaOrNull.tryGetExperiment());
} else
{
@@ -661,7 +674,7 @@ public class WellSearchGrid extends TypedTableGrid<WellContent>
TableExportCriteria<TableModelRowWithObject<WellContent>> exportCriteria,
AbstractAsyncCallback<String> callback)
{
- viewContext.getService().prepareExportPlateLocations(exportCriteria, callback);
+ viewContext.getService().prepareExportPlateWells(exportCriteria, callback);
}
@Override
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateLocationsMaterialSection.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchMaterialSection.java
similarity index 91%
rename from screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateLocationsMaterialSection.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchMaterialSection.java
index b151fb286dd..83dd8986682 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateLocationsMaterialSection.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchMaterialSection.java
@@ -15,12 +15,12 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCrit
* @author Tomasz Pylak
* @author Izabela Adamczyk
*/
-class PlateLocationsMaterialSection extends TabContent
+class WellSearchMaterialSection extends TabContent
{
private final IDisposableComponent reviewer;
- public PlateLocationsMaterialSection(
+ public WellSearchMaterialSection(
IViewContext<IScreeningClientServiceAsync> screeningViewContext,
final TechId materialId, ExperimentSearchCriteria experimentCriteriaOrNull)
{
@@ -30,8 +30,7 @@ class PlateLocationsMaterialSection extends TabContent
screeningViewContext, materialId);
setHeaderVisible(false);
this.reviewer =
- WellSearchGrid.create(screeningViewContext, experimentCriteriaOrNull,
- materialId);
+ WellSearchGrid.create(screeningViewContext, experimentCriteriaOrNull, materialId);
setIds(DisplayTypeIDGenerator.PLATE_LOCATIONS_MATERIAL_SECTION);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/GlobalWellSearchLocatorResolver.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/GlobalWellSearchLocatorResolver.java
index f8808be0af1..9d8c7d0042e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/GlobalWellSearchLocatorResolver.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/GlobalWellSearchLocatorResolver.java
@@ -13,7 +13,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureE
import ch.systemsx.cisd.openbis.generic.shared.basic.URLMethodWithParameters;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningModule;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ExperimentPlateLocationsSection;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.WellSearchComponent;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ui.columns.specific.ScreeningLinkExtractor;
/**
@@ -51,9 +51,14 @@ public class GlobalWellSearchLocatorResolver extends AbstractViewLocatorResolver
Boolean exactMatchOnly =
getOptionalBooleanParameter(locator,
ScreeningLinkExtractor.WELL_SEARCH_IS_EXACT_PARAMETER_KEY);
+ boolean showCombinedResults =
+ getOptionalBooleanParameter(
+ locator,
+ ScreeningLinkExtractor.WELL_SEARCH_SHOW_COMBINED_RESULTS_PARAMETER_KEY,
+ ScreeningLinkExtractor.WELL_SEARCH_SHOW_COMBINED_RESULTS_DEFAULT);
TabContent wellSearchTab =
- new ExperimentPlateLocationsSection(viewContext, materialsList,
- exactMatchOnly);
+ new WellSearchComponent(viewContext, materialsList, exactMatchOnly,
+ showCombinedResults);
return DefaultTabItem.createUnaware(wellSearchTab, false, viewContext);
}
@@ -66,7 +71,7 @@ public class GlobalWellSearchLocatorResolver extends AbstractViewLocatorResolver
@Override
public String getTabTitle()
{
- return ExperimentPlateLocationsSection.getTabTitle(viewContext);
+ return WellSearchComponent.getTabTitle(viewContext);
}
@Override
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/WellSearchLocatorResolver.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/WellSearchLocatorResolver.java
index 9b3f64de6dd..41cf0639aeb 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/WellSearchLocatorResolver.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/WellSearchLocatorResolver.java
@@ -43,6 +43,10 @@ public class WellSearchLocatorResolver extends AbstractViewLocatorResolver
boolean exactMatchOnly =
getMandatoryBooleanParameter(locator,
ScreeningLinkExtractor.WELL_SEARCH_IS_EXACT_PARAMETER_KEY);
+ boolean showCombinedResults =
+ getOptionalBooleanParameter(locator,
+ ScreeningLinkExtractor.WELL_SEARCH_SHOW_COMBINED_RESULTS_PARAMETER_KEY,
+ ScreeningLinkExtractor.WELL_SEARCH_SHOW_COMBINED_RESULTS_DEFAULT);
MaterialSearchCodesCriteria materialCodesCriteria =
new MaterialSearchCodesCriteria(decodeList(materialCodesOrProperties),
@@ -53,10 +57,11 @@ public class WellSearchLocatorResolver extends AbstractViewLocatorResolver
if (StringUtils.isBlank(experimentPermId))
{
WellSearchGrid.openTab(viewContext, ExperimentSearchCriteria.createAllExperiments(),
- materialSearchCriteria);
+ materialSearchCriteria, showCombinedResults);
} else
{
- WellSearchGrid.openTab(viewContext, experimentPermId, materialSearchCriteria);
+ WellSearchGrid.openTab(viewContext, experimentPermId, materialSearchCriteria,
+ showCombinedResults);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ui/columns/specific/ScreeningLinkExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ui/columns/specific/ScreeningLinkExtractor.java
index ff7d8d9e9d1..b9fc056943b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ui/columns/specific/ScreeningLinkExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ui/columns/specific/ScreeningLinkExtractor.java
@@ -24,7 +24,9 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.PermlinkUtilities;
import ch.systemsx.cisd.openbis.generic.shared.basic.URLMethodWithParameters;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.MaterialSearchCodesCriteria;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.SingleExperimentSearchCriteria;
/**
* Defines the ways simple view mode links for screening specific views are created.
@@ -49,6 +51,12 @@ public class ScreeningLinkExtractor extends LinkExtractor
public final static String WELL_SEARCH_MATERIAL_ITEMS_PARAMETER_KEY = "items";
+ /** should we show disambiguation pge if more than one material matchs the query? */
+ public final static String WELL_SEARCH_SHOW_COMBINED_RESULTS_PARAMETER_KEY =
+ "showCombinedResults";
+
+ public final static boolean WELL_SEARCH_SHOW_COMBINED_RESULTS_DEFAULT = true;
+
public static final String createPlateMetadataBrowserLink(String platePermId)
{
URLMethodWithParameters url = new URLMethodWithParameters("");
@@ -57,15 +65,27 @@ public class ScreeningLinkExtractor extends LinkExtractor
return tryPrint(url);
}
- // action=WELL_SEARCH&experimentPermId=8127361723172863&isExactSearch=true&types=typeCode1,typeCode2&items=code1,property2"
- public static String createWellsSearchLink(final String experimentPermId,
- final MaterialSearchCodesCriteria materialCodesCriteria)
+ // action=WELL_SEARCH&experimentPermId=8127361723172863&isExactSearch=true&types=typeCode1,typeCode2&items=code1,property2&showCombinedResults=false"
+ public static String createWellsSearchLink(WellSearchCriteria searchCriteria,
+ boolean showCombinedResults)
+ {
+ SingleExperimentSearchCriteria expOrNull =
+ searchCriteria.getExperimentCriteria().tryGetExperiment();
+ String experimentPermIdOrNull =
+ (expOrNull == null ? null : expOrNull.getExperimentPermId());
+ MaterialSearchCodesCriteria codesOrProperties =
+ searchCriteria.getMaterialSearchCriteria().tryGetMaterialCodesOrProperties();
+ return createWellsSearchLink(experimentPermIdOrNull, codesOrProperties, showCombinedResults);
+ }
+
+ public static String createWellsSearchLink(final String experimentPermIdOrNull,
+ final MaterialSearchCodesCriteria materialCodesCriteria, boolean showCombinedResults)
{
URLMethodWithParameters url = new URLMethodWithParameters("");
url.addParameter(BasicConstant.LOCATOR_ACTION_PARAMETER, WELL_SEARCH_ACTION);
- if (false == StringUtils.isBlank(experimentPermId))
+ if (false == StringUtils.isBlank(experimentPermIdOrNull))
{
- url.addParameter(EXPERIMENT_PERM_ID_PARAMETER_KEY, experimentPermId);
+ url.addParameter(EXPERIMENT_PERM_ID_PARAMETER_KEY, experimentPermIdOrNull);
}
url.addParameter(WELL_SEARCH_IS_EXACT_PARAMETER_KEY,
materialCodesCriteria.isExactMatchOnly());
@@ -73,31 +93,37 @@ public class ScreeningLinkExtractor extends LinkExtractor
URLListEncoder.encodeItemList(materialCodesCriteria.getMaterialTypeCodes()));
url.addParameterWithoutEncoding(WELL_SEARCH_MATERIAL_ITEMS_PARAMETER_KEY,
URLListEncoder.encodeItemList(materialCodesCriteria.getMaterialCodesOrProperties()));
+ url.addParameterWithoutEncoding(WELL_SEARCH_SHOW_COMBINED_RESULTS_PARAMETER_KEY,
+ showCombinedResults);
+
return tryPrint(url);
}
public static final String tryExtractMaterialWithExperiment(IEntityInformationHolder material,
- String experimentIdentifier)
+ String experimentIdentifierorNull)
{
URLMethodWithParameters url =
tryCreateMaterialWithExperimentLink(material.getCode(), material.getEntityType()
- .getCode(), experimentIdentifier);
+ .getCode(), experimentIdentifierorNull);
return tryPrint(url);
}
private static final URLMethodWithParameters tryCreateMaterialWithExperimentLink(
- String materialCode, String materialTypeCode, String experimentIdentifier)
+ String materialCode, String materialTypeCode, String experimentIdentifierOrNull)
{
- if (materialCode == null || materialTypeCode == null || experimentIdentifier == null)
+ if (materialCode == null || materialTypeCode == null)
{
return null;
}
URLMethodWithParameters url = tryCreateMaterialLink(materialCode, materialTypeCode);
- // We know that experiment identifier cannot contain characters that should be encoded
- // apart from '/'. Encoding '/' makes the URL less readable and on the other hand
- // leaving it as it is doesn't cause us any problems.
- url.addParameterWithoutEncoding(EXPERIMENT_PARAMETER_KEY,
- StringEscapeUtils.unescapeHtml(experimentIdentifier));
+ if (experimentIdentifierOrNull != null)
+ {
+ // We know that experiment identifier cannot contain characters that should be encoded
+ // apart from '/'. Encoding '/' makes the URL less readable and on the other hand
+ // leaving it as it is doesn't cause us any problems.
+ url.addParameterWithoutEncoding(EXPERIMENT_PARAMETER_KEY,
+ StringEscapeUtils.unescapeHtml(experimentIdentifierOrNull));
+ }
return url;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/screening-dictionary.js b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/screening-dictionary.js
index bd351a49dba..70815e48031 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/screening-dictionary.js
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/screening-dictionary.js
@@ -1,93 +1,101 @@
// screening dictionary
var screening = {
-
- // If a dictionary contains 'is_default_dictionary' key and the value is 'true',
- // that dictionary will be treated as a 'default' one. This means that values
- // from that dictionary will override entries with the same keys defined in other dictionaries.
- // There should be at most one default dictionary, otherwise the behavior is undefined.
- is_default_dictionary: "true",
-
-
- GENE_LIBRARY_URL: "http://www.genecards.org/cgi-bin/carddisp.pl?gene={0}",
- GENE_LIBRARY_SEARCH_URL: "http://www.genecards.org//index.php?path=/Search/keyword/{0}",
-
- //
- // General
- //
- PLATE: "Plate",
- WELL_ROW: "Well Row",
- WELL_COLUMN: "Well Column",
- WELL: "Well",
- WELL_IMAGES: "Well Images",
- PREVIEW: "Preview",
- PLATE_VIEWER_TITLE: "Plate {0}",
-
- //
- // Menu items
- //
- WELLS_SEARCH_menu_item: "Wells Search",
- WELLS_SEARCH_tab_label: "Wells Search",
- //
- // Experiment Viewer
- //
- experiment_samples_selction_title: "Plates",
- no_samples_found: "There are no plates in this experiment",
-
- //
- // Sample Viewer
- //
-
- sample_properties_panel_sample_identifier: "ID",
- sample: "Sample",
- sample_type: "Sample Type",
- generated_samples: "Children Samples",
- openbis_plate_metadata_browser_CODE: "Code",
- openbis_plate_metadata_browser_TYPE: "Type",
- openbis_plate_metadata_browser_THUMBNAIL: "Thumbnail",
-
-
- sample_properties_heading: "Properties",
- part_of_heading: "Components",
- derived_samples_heading: "Derived Samples",
- parent_samples_heading: "Parent Samples",
- derived_sample: "Derived Sample",
- external_data_heading: "Data Sets",
- show_only_directly_connected: "directly connected",
-
- //
- // Sample import
- //
- import_scheduled: "Import has started successfully. Notification will be sent to '{0}' upon completion.",
- register: "Register",
- separator: "Separator",
-
- //
- // Gene Viewer
- //
- plate_locations: "Plate Locations",
-
- //
- // Plate Material Reviewer
- //
- SCREENING_MODULE_TITLE: "Screening",
-
- WELL_CONTENT_MATERIAL: "Content",
- WELL_CONTENT_MATERIAL_TYPE: "Content Type",
- WELL_CONTENT_PROPERTIES: "Content Properties",
- WELL_CONTENT_FEATURE_VECTORS: "Feature Vector",
- IMAGE_ANALYSIS_DATA_SET: "Image Analysis Dataset",
- IMAGE_DATA_SET: "Image Dataset",
-
- PLATE_MATERIAL_REVIEWER_TITLE: "Wells Search Results",
- PLATE_MATERIAL_REVIEWER_SPECIFY_METERIAL_ITEMS: "E.g. gene symbols, gene ids, gene descriptions, control names or compound names. Separate items with commas (\",\") or specify one item per line.",
-
- EXPERIMENT_PLATE_MATERIAL_REVIEWER_SECTION: "Wells Search",
- EXPERIMENT_PLATE_MATERIAL_BROWSER_SECTION: "Library Index",
- EXACT_MATCH_ONLY: "Exact Matches Only",
-
- image_viewer_button: "Adjust Colors",
-
- // LAST LINE: KEEP IT AT THE END
- lastline: "" // we need a line without a comma
+// If a dictionary contains 'is_default_dictionary' key and the value is 'true',
+// that dictionary will be treated as a 'default' one. This means that values
+// from that dictionary will override entries with the same keys defined in other dictionaries.
+// There should be at most one default dictionary, otherwise the behavior is undefined.
+is_default_dictionary: "true",
+
+
+GENE_LIBRARY_URL: "http://www.genecards.org/cgi-bin/carddisp.pl?gene={0}",
+GENE_LIBRARY_SEARCH_URL: "http://www.genecards.org//index.php?path=/Search/keyword/{0}",
+
+//
+// General
+//
+PLATE: "Plate",
+WELL_ROW: "Well Row",
+WELL_COLUMN: "Well Column",
+WELL: "Well",
+WELL_IMAGES: "Well Images",
+PREVIEW: "Preview",
+PLATE_VIEWER_TITLE: "Plate {0}",
+
+//
+// Menu items
+//
+WELLS_SEARCH_menu_item: "Wells Search",
+WELLS_SEARCH_tab_label: "Wells Search",
+
+//
+// Experiment Viewer
+//
+experiment_samples_selction_title: "Plates",
+no_samples_found: "There are no plates in this assay",
+
+//
+// Sample Viewer
+//
+
+sample_properties_panel_sample_identifier: "ID",
+sample: "Sample",
+sample_type: "Sample Type",
+generated_samples: "Children Samples",
+openbis_plate_metadata_browser_CODE: "Code",
+openbis_plate_metadata_browser_TYPE: "Type",
+openbis_plate_metadata_browser_THUMBNAIL: "Thumbnail",
+
+
+sample_properties_heading: "Properties",
+part_of_heading: "Components",
+derived_samples_heading: "Derived Samples",
+parent_samples_heading: "Parent Samples",
+derived_sample: "Derived Sample",
+external_data_heading: "Data Sets",
+show_only_directly_connected: "directly connected",
+
+//
+// Sample import
+//
+import_scheduled: "Import has started successfully. Notification will be sent to '{0}' upon completion.",
+register: "Register",
+separator: "Separator",
+
+//
+// Gene Viewer
+//
+plate_locations: "Plate Locations",
+
+//
+// Plate Material Reviewer
+//
+SCREENING_MODULE_TITLE: "Screening",
+
+WELL_CONTENT_MATERIAL: "Content",
+WELL_CONTENT_MATERIAL_TYPE: "Content Type",
+WELL_CONTENT_PROPERTIES: "Content Properties",
+WELL_CONTENT_FEATURE_VECTORS: "Feature Vector",
+IMAGE_ANALYSIS_DATA_SET: "Image Analysis Dataset",
+IMAGE_DATA_SET: "Image Dataset",
+
+PLATE_MATERIAL_REVIEWER_TITLE: "Wells Search Results",
+PLATE_MATERIAL_REVIEWER_SPECIFY_METERIAL_ITEMS: "E.g. gene symbols, gene ids, gene descriptions, control names or compound names. Separate items with commas (\",\") or specify one item per line.",
+
+EXPERIMENT_PLATE_MATERIAL_REVIEWER_SECTION: "Wells Search",
+EXPERIMENT_PLATE_MATERIAL_BROWSER_SECTION: "Library Index",
+
+EXACT_MATCH_ONLY: "Exact Matches Only",
+WELLS_SEARCH_SHOW_COMBINED_RESULTS: "Show all matching results combined",
+WELL_SEARCH_NO_RESULTS_IN_ANY_EXP_FOUND: "All assays have been searched and no results match the query. Please check the spelling.",
+WELL_SEARCH_NO_RESULTS_IN_SELECTED_EXP_FOUND: "No results match the query in the selected assay.",
+WELL_SEARCH_PERFORM_IN_ALL_EXP: "Search in all assays",
+
+MATERIAL_DISAMBIGUATION_TITLE: "Material Disambiguation",
+MATERIAL_DISAMBIGUATION_GRID_EXPLANATION: "More than one result has been found. Click on it to see the details.",
+
+image_viewer_button: "Adjust Colors",
+
+// LAST LINE: KEEP IT AT THE END
+lastline: "" // we need a line without a comma
};
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/PlateMetadataProvider.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/PlateMetadataProvider.java
index a92c2f44831..b867e8f8a11 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/PlateMetadataProvider.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/PlateMetadataProvider.java
@@ -16,8 +16,8 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.server;
-import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMetadataGridIDs.CODE;
-import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMetadataGridIDs.TYPE;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.PlateMetadataGridColumnIDs.CODE;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.PlateMetadataGridColumnIDs.TYPE;
import java.util.List;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java
index 35fd3fca120..ab11777570f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java
@@ -37,6 +37,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.server.AbstractOriginalDataPr
import ch.systemsx.cisd.openbis.generic.client.web.server.UploadedFilesBean;
import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.DataProviderAdapter;
import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.ITableModelProvider;
+import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.MaterialProvider;
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;
@@ -192,12 +193,29 @@ public final class ScreeningClientService extends AbstractClientService implemen
return new TypedTableResultSet<WellContent>(resultSet);
}
- public String prepareExportPlateLocations(
+ public String prepareExportPlateWells(
TableExportCriteria<TableModelRowWithObject<WellContent>> criteria)
{
return prepareExportEntities(criteria);
}
+ public TypedTableResultSet<Material> listMaterials(
+ IResultSetConfig<String, TableModelRowWithObject<Material>> gridCriteria,
+ WellSearchCriteria materialCriteria)
+ {
+ List<Material> materials = server.listMaterials(getSessionToken(), materialCriteria);
+ final ITableModelProvider<Material> provider = new MaterialProvider(materials);
+ ResultSet<TableModelRowWithObject<Material>> resultSet =
+ listEntities(gridCriteria, new DataProviderAdapter<Material>(provider));
+ return new TypedTableResultSet<Material>(resultSet);
+ }
+
+ public String prepareExportMaterials(
+ TableExportCriteria<TableModelRowWithObject<Material>> criteria)
+ {
+ return prepareExportEntities(criteria);
+ }
+
public TypedTableResultSet<WellMetadata> listPlateMetadata(
IResultSetConfig<String, TableModelRowWithObject<WellMetadata>> criteria,
TechId sampleId)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/WellContentProvider.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/WellContentProvider.java
index cfe14c6ed71..5a9bd70879c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/WellContentProvider.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/WellContentProvider.java
@@ -16,27 +16,23 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.server;
-import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchGridColumnIds.EXPERIMENT;
-import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchGridColumnIds.FILE_FORMAT_TYPE;
-import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchGridColumnIds.IMAGE_ANALYSIS_DATA_SET;
-import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchGridColumnIds.IMAGE_DATA_SET;
-import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchGridColumnIds.PLATE;
-import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchGridColumnIds.WELL;
-import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchGridColumnIds.WELL_COLUMN;
-import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchGridColumnIds.WELL_CONTENT_MATERIAL;
-import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchGridColumnIds.WELL_CONTENT_MATERIAL_TYPE;
-import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchGridColumnIds.WELL_IMAGES;
-import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchGridColumnIds.WELL_ROW;
-
-import java.util.HashSet;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.WellSearchGridColumnIds.EXPERIMENT;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.WellSearchGridColumnIds.FILE_FORMAT_TYPE;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.WellSearchGridColumnIds.IMAGE_ANALYSIS_DATA_SET;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.WellSearchGridColumnIds.IMAGE_DATA_SET;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.WellSearchGridColumnIds.PLATE;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.WellSearchGridColumnIds.WELL;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.WellSearchGridColumnIds.WELL_COLUMN;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.WellSearchGridColumnIds.WELL_CONTENT_MATERIAL;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.WellSearchGridColumnIds.WELL_CONTENT_MATERIAL_TYPE;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.WellSearchGridColumnIds.WELL_IMAGES;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.WellSearchGridColumnIds.WELL_ROW;
+
import java.util.List;
-import java.util.Set;
import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.AbstractTableModelProvider;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
import ch.systemsx.cisd.openbis.generic.shared.util.IColumn;
import ch.systemsx.cisd.openbis.generic.shared.util.TypedTableModelBuilder;
@@ -54,6 +50,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCrit
*/
public class WellContentProvider extends AbstractTableModelProvider<WellContent>
{
+ static final String WELL_PROPERTY_ID_PREFIX = "WELL_PROPERTY-";
+
static final String WELL_CONTENT_PROPERTY_ID_PREFIX = "WELL_CONTENT_PROPERTY-";
static final String WELL_CONTENT_FEATURE_VECTOR_PREFIX = "WELL_CONTENT_FEATURE_VECTOR-";
@@ -78,8 +76,6 @@ public class WellContentProvider extends AbstractTableModelProvider<WellContent>
TypedTableModelBuilder<WellContent> builder = new TypedTableModelBuilder<WellContent>();
addStandardWellColumns(builder);
List<WellContent> wells = server.listPlateWells(sessionToken, materialCriteria);
- addWellPropertiesColumns(builder, wells);
-
for (WellContent well : wells)
{
addRow(builder, well);
@@ -102,25 +98,6 @@ public class WellContentProvider extends AbstractTableModelProvider<WellContent>
builder.addColumn(WELL_IMAGES).withDefaultWidth(500);
}
- private void addWellPropertiesColumns(TypedTableModelBuilder<WellContent> builder,
- List<WellContent> wells)
- {
- Set<String> columnNames = new HashSet<String>();
- for (WellContent well : wells)
- {
- for (IEntityProperty property : well.getWellProperties())
- {
- String columnName = property.getPropertyType().getCode();
- columnNames.add(columnName);
- }
- }
-
- for (String columnName : columnNames)
- {
- builder.addColumn(columnName).withTitle(columnName);
- }
- }
-
private void addRow(TypedTableModelBuilder<WellContent> builder, WellContent well)
{
builder.addRow(well);
@@ -152,7 +129,10 @@ public class WellContentProvider extends AbstractTableModelProvider<WellContent>
imageDataset == null ? null : imageDataset.getDatasetReference().getFileTypeCode());
builder.column(WELL_IMAGES).addString(well.tryGetImageDataset() == null ? "" : "[images]");
- addWellProperties(builder, well);
+ if (well.getWellProperties() != null)
+ {
+ builder.columnGroup(WELL_PROPERTY_ID_PREFIX).addProperties(well.getWellProperties());
+ }
}
private void addFeatureColumns(TypedTableModelBuilder<WellContent> builder,
@@ -176,42 +156,4 @@ public class WellContentProvider extends AbstractTableModelProvider<WellContent>
}
}
}
-
- private void addWellProperties(TypedTableModelBuilder<WellContent> builder, WellContent well)
- {
- for (IEntityProperty property : well.getWellProperties())
- {
- PropertyType propertyType = property.getPropertyType();
- String columnCode = propertyType.getCode();
- String columnLabel = propertyType.getLabel();
-
- IColumn column = builder.column(columnCode).withTitle(columnLabel);
- DataTypeCode dataTypeCode = propertyType.getDataType().getCode();
- String value = property.tryGetAsString();
- if (dataTypeCode == DataTypeCode.INTEGER)
- {
- try
- {
- column.addInteger(Long.parseLong(value));
- } catch (NumberFormatException ex)
- {
- column.addString(value);
- }
- } else if (dataTypeCode == DataTypeCode.REAL)
- {
- try
- {
- column.addDouble(Double.parseDouble(value));
- } catch (NumberFormatException ex)
- {
- column.addString(value);
- }
- } else
- {
- column.addString(value);
- }
-
- }
- }
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
index ae96cb19570..ba3c28560d0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
@@ -195,6 +195,13 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
materialCriteria);
}
+ public List<Material> listMaterials(String sessionToken, WellSearchCriteria materialCriteria)
+ {
+ Session session = getSession(sessionToken);
+ return WellContentLoader.loadMaterials(session, businessObjectFactory, getDAOFactory(),
+ materialCriteria);
+ }
+
public FeatureVectorValues getWellFeatureVectorValues(String sessionToken, String datasetCode,
String datastoreCode, WellLocation wellLocation)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
index ee158d6f778..d9e5f93177c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
@@ -112,7 +112,13 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
public List<WellContent> listPlateWells(String sessionToken, WellSearchCriteria materialCriteria)
{
- logAccess(sessionToken, "getPlateLocations", "criteria(%s)", materialCriteria);
+ logAccess(sessionToken, "listPlateWells", "criteria(%s)", materialCriteria);
+ return null;
+ }
+
+ public List<Material> listMaterials(String sessionToken, WellSearchCriteria materialCriteria)
+ {
+ logAccess(sessionToken, "listMaterials", "criteria(%s)", materialCriteria);
return null;
}
@@ -315,5 +321,4 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
"userEmail(%s), newGenesOrNull(%s), newOligosOrNull(%s), newSamplesWithType(%s)",
userEmail, newGenesOrNull, newOligosOrNull, newSamplesWithType);
}
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java
index c2c9485bfbb..7b982c6e84a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java
@@ -134,6 +134,32 @@ public class WellContentLoader
.getFeatureVectorValues(datasetCode, datastoreCode, wellLocation);
}
+ /**
+ * @return list of unique materials with codes or properties matching to the query. If the
+ * experiment is specified, only materials inside well locations connected through the
+ * plate to this specified experiment(s) will be returned.
+ */
+ public static List<Material> loadMaterials(Session session,
+ IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
+ WellSearchCriteria materialCriteria)
+ {
+ List<WellContent> locations =
+ new WellContentLoader(session, businessObjectFactory, daoFactory)
+ .loadLocations(materialCriteria);
+ Set<Material> materials = extractMaterials(locations);
+ return new ArrayList<Material>(materials);
+ }
+
+ private static Set<Material> extractMaterials(List<WellContent> locations)
+ {
+ Set<Material> materials = new HashSet<Material>();
+ for (WellContent location : locations)
+ {
+ materials.add(location.getMaterialContent());
+ }
+ return materials;
+ }
+
private final Session session;
private final IScreeningBusinessObjectFactory businessObjectFactory;
@@ -162,8 +188,9 @@ public class WellContentLoader
List<FeatureVectorValues> features = featureVectors.getFeatures();
if (features.size() == 0)
{
- // TODO throw exception?
- // shouldn't happen
+ // Because of the way we are storing the features it can happen only if dataset contains
+ // no features (NaN are stored in the plate matrix for the wells which have no value
+ // specified).
return null;
} else
{
@@ -610,16 +637,16 @@ public class WellContentLoader
materialSearchCriteria.tryGetMaterialCodesOrProperties();
Long expId = tryGetExperimentId(experiment);
- long[] ids = findMaterialIds(codesCriteria);
+ long[] materialIds = findMaterialIds(codesCriteria);
if (expId == null)
{
locations =
- dao.getPlateLocationsForMaterialCodes(ids,
+ dao.getPlateLocationsForMaterialCodes(materialIds,
codesCriteria.getMaterialTypeCodes());
} else
{
locations =
- dao.getPlateLocationsForMaterialCodes(ids,
+ dao.getPlateLocationsForMaterialCodes(materialIds,
codesCriteria.getMaterialTypeCodes(), expId);
}
@@ -804,5 +831,4 @@ public class WellContentLoader
}
return experiment.getId();
}
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
index 6c69751fda0..d4a9f4c2ef0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
@@ -111,6 +111,17 @@ public interface IScreeningServer extends IServer
String sessionToken,
@AuthorizationGuard(guardClass = WellSearchCriteriaPredicate.class) WellSearchCriteria materialCriteria);
+ /**
+ * @return materials with codes or properties matching to the query. If the experiment is
+ * specified, only materials inside well locations connected through the plate to this
+ * specified experiment(s) will be returned.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
+ public List<Material> listMaterials(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = WellSearchCriteriaPredicate.class) WellSearchCriteria materialCriteria);
+
/**
* Loads all materials of specified type connected with the specified experiment.
*
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateMetadataGridIDs.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/grids/PlateMetadataGridColumnIDs.java
similarity index 85%
rename from screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateMetadataGridIDs.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/grids/PlateMetadataGridColumnIDs.java
index 87119b5ba9c..16209efb7ea 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateMetadataGridIDs.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/grids/PlateMetadataGridColumnIDs.java
@@ -14,15 +14,16 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.PlateMetadataBrowser;
/**
* Defines IDs of {@link PlateMetadataBrowser}.
*/
-public class PlateMetadataGridIDs
+public class PlateMetadataGridColumnIDs
{
- public static final String CODE = "CODE";
- public static final String TYPE = "TYPE";
+ public static final String CODE = "CODE";
+
+ public static final String TYPE = "TYPE";
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellSearchGridColumnIds.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/grids/WellSearchGridColumnIds.java
similarity index 99%
rename from screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellSearchGridColumnIds.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/grids/WellSearchGridColumnIds.java
index 03e27d0aba7..e0951691c61 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellSearchGridColumnIds.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/grids/WellSearchGridColumnIds.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids;
/**
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/PlateMetadataProviderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/PlateMetadataProviderTest.java
index ebce0f8b652..10cb83fbe3b 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/PlateMetadataProviderTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/PlateMetadataProviderTest.java
@@ -39,8 +39,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.IScreeningServer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.ObjectCreationUtilForTests;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMetadata;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMetadataGridIDs;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.PlateMetadataGridColumnIDs;
/**
* @author Franz-Josef Elmer
@@ -89,11 +89,11 @@ public class PlateMetadataProviderTest extends AbstractServerTestCase
List<TableModelColumnHeader> headers = tableModel.getHeader();
assertEquals(null, headers.get(0).getTitle());
- assertEquals(PlateMetadataGridIDs.CODE, headers.get(0).getId());
+ assertEquals(PlateMetadataGridColumnIDs.CODE, headers.get(0).getId());
assertEquals(0, headers.get(0).getIndex());
assertEquals(DataTypeCode.VARCHAR, headers.get(0).getDataType());
assertEquals(null, headers.get(1).getTitle());
- assertEquals(PlateMetadataGridIDs.TYPE, headers.get(1).getId());
+ assertEquals(PlateMetadataGridColumnIDs.TYPE, headers.get(1).getId());
assertEquals(1, headers.get(1).getIndex());
assertEquals(DataTypeCode.VARCHAR, headers.get(1).getDataType());
assertEquals("answer", headers.get(2).getTitle());
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoaderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoaderTest.java
index bfbf8e230fe..0e6f655fbba 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoaderTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoaderTest.java
@@ -69,8 +69,7 @@ public class WellContentLoaderTest extends AbstractScreeningDAOTest
Session session = createSession(getSystemPerson());
List<WellContent> wellContents =
- WellContentLoader.load(session, businessObjectFactory,
- daoFactory, searchCriteria);
+ WellContentLoader.load(session, businessObjectFactory, daoFactory, searchCriteria);
// the test database contains two matching wells
assertEquals(2, wellContents.size());
--
GitLab