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 b91694f61143c0d50aaa8f96842957a727ab1e5a..7ec4de82a1fe38ff8e92cf09e78dbf68b57c4d8b 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
@@ -17,7 +17,6 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
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;
@@ -70,10 +69,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKin
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
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.DisplayTypeIDGenerator;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningDisplayTypeIDGenerator;
@@ -81,7 +78,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.d
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.DatasetImagesReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria;
@@ -272,7 +268,6 @@ public class WellSearchGrid extends TypedTableGrid<WellContent>
final IDefaultChannelState defaultChannelState =
createDefaultChannelState(viewContext, experimentCriteriaOrNull);
channelChooser = new ChannelChooserPanel(defaultChannelState);
- linkWellContent();
linkExperiment();
linkPlate();
linkWell();
@@ -301,38 +296,6 @@ public class WellSearchGrid extends TypedTableGrid<WellContent>
return new DefaultChannelState(viewContext, displayTypeId);
}
- private void linkWellContent()
- {
- registerListenerAndLinkGenerator(WELL_CONTENT_MATERIAL,
- new ICellListenerAndLinkGenerator<WellContent>()
- {
- public String tryGetLink(WellContent entity, ISerializableComparable value)
- {
- Material material = entity.getMaterialContent();
- String experimentIdentifier =
- entity.getExperiment().getExperimentIdentifier();
- return ScreeningLinkExtractor.tryCreateMaterialDetailsLink(material,
- experimentIdentifier);
- }
-
- public void handle(TableModelRowWithObject<WellContent> wellContent,
- boolean specialKeyPressed)
- {
- Material contentMaterial =
- wellContent.getObjectOrNull().getMaterialContent();
- ExperimentReference experiment =
- wellContent.getObjectOrNull().getExperiment();
- ExperimentSearchCriteria experimentCriteria =
- ExperimentSearchCriteria.createExperiment(experiment.getId(),
- experiment.getPermId(),
- experiment.getExperimentIdentifier());
-
- ClientPluginFactory.openImagingMaterialViewer(contentMaterial,
- experimentCriteria, viewContext);
- }
- });
- }
-
private void linkExperiment()
{
registerListenerAndLinkGenerator(WellSearchGridColumnIds.EXPERIMENT,
@@ -680,7 +643,7 @@ public class WellSearchGrid extends TypedTableGrid<WellContent>
@Override
protected List<String> getColumnIdsOfFilters()
{
- return Arrays.asList(WELL_CONTENT_MATERIAL, WELL);
+ return Arrays.asList(WELL);
}
}
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 887084b72ec60b5f1b176657f6bf8ccdae25ddf5..44808cda3d1c2997c5a5cadf6d2972051b6de0c5 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
@@ -23,8 +23,6 @@ import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.W
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;
@@ -32,6 +30,7 @@ import java.util.List;
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.TypedTableModel;
import ch.systemsx.cisd.openbis.generic.shared.util.IColumn;
@@ -52,6 +51,8 @@ public class WellContentProvider extends AbstractTableModelProvider<WellContent>
{
static final String WELL_PROPERTY_ID_PREFIX = "WELL_PROPERTY-";
+ static final String MATERIAL_PROPERTY_ID_PREFIX = "MATERIAL-PROPERTY-";
+
static final String WELL_CONTENT_PROPERTY_ID_PREFIX = "WELL_CONTENT_PROPERTY-";
static final String WELL_CONTENT_FEATURE_VECTOR_PREFIX = "WELL_CONTENT_FEATURE_VECTOR-";
@@ -85,8 +86,6 @@ public class WellContentProvider extends AbstractTableModelProvider<WellContent>
private void addStandardWellColumns(TypedTableModelBuilder<WellContent> builder)
{
- builder.addColumn(WELL_CONTENT_MATERIAL);
- builder.addColumn(WELL_CONTENT_MATERIAL_TYPE);
builder.addColumn(EXPERIMENT);
builder.addColumn(PLATE);
builder.addColumn(WELL);
@@ -101,12 +100,6 @@ public class WellContentProvider extends AbstractTableModelProvider<WellContent>
private void addRow(TypedTableModelBuilder<WellContent> builder, WellContent well)
{
builder.addRow(well);
- Material material = well.getMaterialContent();
- String value = material.getCode();
- builder.column(WELL_CONTENT_MATERIAL).addString(value);
- builder.column(WELL_CONTENT_MATERIAL_TYPE).addString(material.getEntityType().getCode());
- builder.columnGroup(WELL_CONTENT_PROPERTY_ID_PREFIX)
- .addProperties(material.getProperties());
NamedFeatureVector featureVector = well.tryGetFeatureVectorValues();
if (featureVector != null)
{
@@ -129,12 +122,45 @@ public class WellContentProvider extends AbstractTableModelProvider<WellContent>
imageDataset == null ? null : imageDataset.getDatasetReference().getFileTypeCode());
builder.column(WELL_IMAGES).addString(well.tryGetImageDataset() == null ? "" : "[images]");
- if (well.getWellProperties().isEmpty() == false)
+ List<IEntityProperty> wellProperties = well.getWellProperties();
+ builder.columnGroup(WELL_PROPERTY_ID_PREFIX).addProperties(wellProperties);
+ addMaterialProperties(builder, wellProperties);
+ }
+
+ private void addMaterialProperties(TypedTableModelBuilder<WellContent> builder,
+ List<IEntityProperty> wellProperties)
+ {
+ for (IEntityProperty property : wellProperties)
+ {
+ DataTypeCode propertyDataTypeCode = property.getPropertyType().getDataType().getCode();
+ if (propertyDataTypeCode == DataTypeCode.MATERIAL)
+ {
+ addMaterialProperties(builder, property);
+ }
+ }
+ }
+
+ private void addMaterialProperties(TypedTableModelBuilder<WellContent> builder,
+ IEntityProperty materialProperty)
+ {
+ Material materialOrNull = materialProperty.getMaterial();
+ if (materialOrNull != null)
{
- builder.columnGroup(WELL_PROPERTY_ID_PREFIX).addProperties(well.getWellProperties());
+ List<IEntityProperty> materialProperties = materialOrNull.getProperties();
+ if (materialProperties != null)
+ {
+ String materialPropsGroupId = getMaterialPropsGroupId(materialProperty);
+ builder.columnGroup(materialPropsGroupId)
+ .addProperties(materialOrNull.getProperties());
+ }
}
}
+ private String getMaterialPropsGroupId(IEntityProperty property)
+ {
+ return MATERIAL_PROPERTY_ID_PREFIX + property.getPropertyType().getSimpleCode() + "-";
+ }
+
private void addFeatureColumns(TypedTableModelBuilder<WellContent> builder,
NamedFeatureVector featureVector)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningQuery.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningQuery.java
index 6cbb8fd87939ad803f07a8c32c75812821de8e2a..f840a825259a1bdfe37f870c255d8f625e090a1a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningQuery.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningQuery.java
@@ -32,7 +32,7 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.StringArrayMapper;
* @author Tomasz Pylak
*/
@Private
-@Friend(toClasses = WellContent.class)
+@Friend(toClasses = WellContentQueryResult.class)
public interface IScreeningQuery extends BaseQuery
{
@@ -73,7 +73,7 @@ public interface IScreeningQuery extends BaseQuery
* Each well will have a material property (e.g. gene) with the specified id.
*/
@Select(sql = WELLS_FOR_MATERIAL_ID_SELECT + " where well_material.id = ?{1} and exp.id = ?{2}")
- public DataIterator<WellContent> getPlateLocationsForMaterialId(long materialId,
+ public DataIterator<WellContentQueryResult> getPlateLocationsForMaterialId(long materialId,
long experimentId);
/**
@@ -81,7 +81,7 @@ public interface IScreeningQuery extends BaseQuery
* id.
*/
@Select(sql = WELLS_FOR_MATERIAL_ID_SELECT + " where well_material.id = ?{1}")
- public DataIterator<WellContent> getPlateLocationsForMaterialId(long materialId);
+ public DataIterator<WellContentQueryResult> getPlateLocationsForMaterialId(long materialId);
/**
* @return well locations which belong to a parent plate connected to a specified experiment.
@@ -91,7 +91,7 @@ public interface IScreeningQuery extends BaseQuery
@Select(sql = WELLS_FOR_MATERIAL_ID_SELECT + " where well_material.id = any(?{1}) and "
+ "well_material_type.code = any(?{2}) and exp.id = ?{3}", parameterBindings =
{ LongArrayMapper.class, StringArrayMapper.class, TypeMapper.class /* default mapper */}, fetchSize = FETCH_SIZE)
- public DataIterator<WellContent> getPlateLocationsForMaterialCodes(long[] materialIds,
+ public DataIterator<WellContentQueryResult> getPlateLocationsForMaterialCodes(long[] materialIds,
String[] materialTypeCodes, long experimentId);
/**
@@ -102,7 +102,7 @@ public interface IScreeningQuery extends BaseQuery
@Select(sql = WELLS_FOR_MATERIAL_ID_SELECT + " where well_material.id = any(?{1}) and "
+ "well_material_type.code = any(?{2})", parameterBindings =
{ LongArrayMapper.class, StringArrayMapper.class }, fetchSize = FETCH_SIZE)
- public DataIterator<WellContent> getPlateLocationsForMaterialCodes(long[] materialIds,
+ public DataIterator<WellContentQueryResult> getPlateLocationsForMaterialCodes(long[] materialIds,
String[] materialTypeCodes);
/**
@@ -120,7 +120,7 @@ public interface IScreeningQuery extends BaseQuery
+ " join materials well_material on well_props.mate_prop_id = well_material.id"
+ " join material_types well_material_type on well_material.maty_id = well_material_type.id"
+ " where well_material_type.code=?{2} and pl.perm_id=?{1}")
- public DataIterator<WellContent> getPlateMappingForMaterialType(String platePermId,
+ public DataIterator<WellContentQueryResult> getPlateMappingForMaterialType(String platePermId,
String materialTypeCode);
/**
@@ -139,7 +139,7 @@ public interface IScreeningQuery extends BaseQuery
+ " join materials well_material on well_props.mate_prop_id = well_material.id"
+ " join material_types well_material_type on well_material.maty_id = well_material_type.id"
+ " where pl.perm_id=?{1} order by material_content_type_code")
- public DataIterator<WellContent> getPlateMapping(String platePermId);
+ public DataIterator<WellContentQueryResult> getPlateMapping(String platePermId);
/**
* @return the material to well plate mapping for the given <var>spaceCode</var> and
@@ -157,7 +157,7 @@ public interface IScreeningQuery extends BaseQuery
+ " join materials well_material on well_props.mate_prop_id = well_material.id"
+ " join material_types well_material_type on well_material.maty_id = well_material_type.id"
+ " where well_material_type.code = ?{3} and pl.code = ?{2} and sp.code = ?{1}")
- public DataIterator<WellContent> getPlateMappingForMaterialType(String spaceCode,
+ public DataIterator<WellContentQueryResult> getPlateMappingForMaterialType(String spaceCode,
String plateCode, String materialTypeCode);
/**
@@ -177,7 +177,7 @@ public interface IScreeningQuery extends BaseQuery
+ " join materials well_material on well_props.mate_prop_id = well_material.id"
+ " join material_types well_material_type on well_material.maty_id = well_material_type.id"
+ " where sp.code = ?{1} and pl.code = ?{2} order by material_content_type_code")
- public DataIterator<WellContent> getPlateMapping(String spaceCode, String plateCode);
+ public DataIterator<WellContentQueryResult> getPlateMapping(String spaceCode, String plateCode);
/**
* Returns the plate geometry string for the plate with given <var>platePermId</var>, or
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/WellContent.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/WellContentQueryResult.java
similarity index 97%
rename from screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/WellContent.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/WellContentQueryResult.java
index 29abf1eecfcef65427f15256dee29361fa769e85..17f82ddad7ccd3484d5c606f81124947f463b9a8 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/WellContent.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/WellContentQueryResult.java
@@ -22,7 +22,7 @@ import ch.rinn.restrictions.Private;
* @author Tomasz Pylak
*/
@Private
-public class WellContent
+public class WellContentQueryResult
{
// well pointer
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
index 931634aa7cd439b53c8c55f366c95bde93d7577e..95d9e637caa7dcc2a3b28bff2677ebc52373b967 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
@@ -92,7 +92,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
* @author Tomasz Pylak
*/
@Friend(toClasses =
- { ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContent.class,
+ { ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContentQueryResult.class,
PlateGeometryContainer.class })
public class ScreeningApiImpl
{
@@ -529,7 +529,7 @@ public class ScreeningApiImpl
PlateIdentifier plateIdentifier,
MaterialTypeIdentifier materialTypeIdentifierOrNull,
PlateGeometryContainer plateGeometryContainer,
- DataIterator<ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContent> wellContentList)
+ DataIterator<ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContentQueryResult> wellContentList)
{
final Geometry plateGeometry =
Geometry.createFromPlateGeometryString(plateGeometryContainer.plate_geometry);
@@ -540,7 +540,7 @@ public class ScreeningApiImpl
new PlateWellMaterialMapping(finalPlateIdentifier, plateGeometry, 1);
if (materialTypeIdentifierOrNull != null)
{
- for (ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContent wellContent : wellContentList)
+ for (ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContentQueryResult wellContent : wellContentList)
{
final WellLocation location =
ScreeningUtils.tryCreateLocationFromMatrixCoordinate(wellContent.well_code);
@@ -552,7 +552,7 @@ public class ScreeningApiImpl
{
final Map<String, MaterialTypeIdentifier> map =
new HashMap<String, MaterialTypeIdentifier>();
- for (ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContent wellContent : wellContentList)
+ for (ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContentQueryResult wellContent : wellContentList)
{
MaterialTypeIdentifier typeId = map.get(wellContent.material_content_type_code);
if (typeId == null)
@@ -597,7 +597,7 @@ public class ScreeningApiImpl
return plateGeometryContainer;
}
- private DataIterator<ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContent> getPlateMapping(
+ private DataIterator<ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContentQueryResult> getPlateMapping(
IScreeningQuery query, PlateIdentifier plate,
MaterialTypeIdentifier materialTypeIdentifierOrNull)
{
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 3c09d44d421baf1e72c26a5c84aa0a082e7b7652..1a1c483c3703ee34731afe2c277628d1131a9cb1 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
@@ -54,7 +54,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialAttributeSearchFieldKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchCriteriaConnection;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
@@ -63,6 +62,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQuery;
+import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContentQueryResult;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetImagesReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
@@ -82,7 +82,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoa
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSFeatureVectorLoader;
/**
- * Loades selected wells content: metadata and (if available) image dataset and feature vectors.
+ * Loades selected wells content: metadata and (if available) image dataset.
*
* @author Tomasz Pylak
*/
@@ -103,8 +103,7 @@ public class WellContentLoader
WellContentLoader loader =
new WellContentLoader(session, businessObjectFactory, daoFactory);
- List<WellContent> contents = loader.loadLocations(geneMaterialId, experimentPermId);
- return loader.enrichWithWellProperties(contents);
+ return loader.loadLocations(geneMaterialId, experimentPermId);
}
/** loads wells metadata, but no information about image or image analysis datasets */
@@ -113,8 +112,7 @@ public class WellContentLoader
TechId geneMaterialId)
{
final WellContentLoader loader = new WellContentLoader(session, businessObjectFactory, daoFactory);
- List<WellContent> contents = loader.loadLocations(geneMaterialId);
- return loader.enrichWithWellProperties(contents);
+ return loader.loadLocations(geneMaterialId);
}
/**
@@ -130,9 +128,7 @@ public class WellContentLoader
new WellContentLoader(session, businessObjectFactory, daoFactory);
List<WellContent> locations = loader.loadLocations(materialCriteria);
- List<WellContent> uniqueLocations = loader.filterWellDuplicates(locations);
- List<WellContent> withProperties = loader.enrichWithWellProperties(uniqueLocations);
- List<WellContent> withPropsAndDataSets = loader.enrichWithDatasets(withProperties);
+ List<WellContent> withPropsAndDataSets = loader.enrichWithDatasets(locations);
return loader.enrichWithFeatureVectors(withPropsAndDataSets);
}
@@ -152,16 +148,6 @@ public class WellContentLoader
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;
@@ -176,24 +162,6 @@ public class WellContentLoader
this.daoFactory = daoFactory;
}
- private List<WellContent> filterWellDuplicates(List<WellContent> wellContents)
- {
- Set<String> seenPermIds = new HashSet<String>();
- ArrayList<WellContent> filtered = new ArrayList<WellContent>();
-
- for (WellContent content : wellContents)
- {
- String wellPermId = content.getWell().getPermId();
- if (false == seenPermIds.contains(wellPermId))
- {
- seenPermIds.add(wellPermId);
- filtered.add(content);
- }
- }
-
- return filtered;
- }
-
private List<WellContent> enrichWithWellProperties(List<WellContent> locations)
{
Map<Long /* id */, WellContent> wellContents = new HashMap<Long/* id */, WellContent>();
@@ -614,7 +582,7 @@ public class WellContentLoader
private List<WellContent> loadLocations(WellSearchCriteria materialCriteria)
{
- DataIterator<ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContent> locations;
+ DataIterator<WellContentQueryResult> locations;
MaterialSearchCriteria materialSearchCriteria =
materialCriteria.getMaterialSearchCriteria();
ExperimentSearchCriteria experiment = materialCriteria.getExperimentCriteria();
@@ -724,7 +692,7 @@ public class WellContentLoader
{
final long experimentId = loadExperimentIdByPermId(experimentPermId);
- DataIterator<ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContent> locations =
+ DataIterator<WellContentQueryResult> locations =
createDAO(daoFactory).getPlateLocationsForMaterialId(geneMaterialId.getId(),
experimentId);
@@ -733,71 +701,102 @@ public class WellContentLoader
private List<WellContent> loadLocations(TechId geneMaterialId)
{
- DataIterator<ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContent> locations =
+ DataIterator<WellContentQueryResult> locations =
createDAO(daoFactory).getPlateLocationsForMaterialId(geneMaterialId.getId());
return convert(locations);
}
- private List<WellContent> convert(
- DataIterator<ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContent> locations)
+ private List<WellContent> convert(DataIterator<WellContentQueryResult> queryResults)
{
- List<WellContent> wellLocations = new ArrayList<WellContent>();
+ List<WellContentQueryResult> uniqueResults = removeDuplicateWells(queryResults);
- for (ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContent location : locations)
+ ArrayList<WellContent> wellContents = new ArrayList<WellContent>();
+ for (WellContentQueryResult uniqueWell : uniqueResults)
{
- wellLocations.add(convert(location));
+ wellContents.add(convert(uniqueWell));
}
- sortByMaterialName(wellLocations);
+ sortByWellCode(wellContents);
+ List<WellContent> withProperties = enrichWithWellProperties(wellContents);
IMaterialLister materialLister = businessObjectFactory.createMaterialLister(session);
- List<Material> containedMaterials = getMaterials(wellLocations);
+ List<Material> containedMaterials = getMaterialsWithDuplicates(withProperties);
materialLister.enrichWithProperties(containedMaterials);
- return wellLocations;
+ return wellContents;
+ }
+
+ private static Set<Material> extractMaterials(List<WellContent> locations)
+ {
+ Set<Material> materials = new HashSet<Material>();
+ for (WellContent location : locations)
+ {
+ materials.addAll(location.getMaterialContents());
+ }
+ return materials;
}
- private static List<Material> getMaterials(List<WellContent> wellLocations)
+ /**
+ * Return *all* material objects contained in the wells as list. The list can contained
+ * different objects representing the same entity in the database, but we need the duplication
+ * to be able to populate an object graph with wells correctly.
+ */
+ private static List<Material> getMaterialsWithDuplicates(List<WellContent> wellLocations)
{
List<Material> materials = new ArrayList<Material>();
for (WellContent wc : wellLocations)
{
- materials.add(wc.getMaterialContent());
+ materials.addAll(wc.getMaterialContents());
}
return materials;
}
- private static void sortByMaterialName(List<? extends WellContent> wellLocations)
+ // TODO KE: talk with Tomek : sorting by material code will appear artificial
+ // Material m1 = o1.getMaterialContents();
+ // Material m2 = o2.getMaterialContents();
+ private static void sortByWellCode(List<? extends WellContent> wellLocations)
{
Collections.sort(wellLocations, new Comparator<WellContent>()
{
public int compare(WellContent o1, WellContent o2)
{
- Material m1 = o1.getMaterialContent();
- Material m2 = o2.getMaterialContent();
- return m1.getCode().compareTo(m2.getCode());
+ String o1Code = o1.getWell().getCode();
+ String o2Code = o2.getWell().getCode();
+ return o1Code.compareTo(o2Code);
}
});
}
- private static WellContent convert(
- ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContent loc)
+ private List<WellContentQueryResult> removeDuplicateWells(
+ DataIterator<WellContentQueryResult> queryResults)
{
- WellLocation location = ScreeningUtils.tryCreateLocationFromMatrixCoordinate(loc.well_code);
- EntityReference well =
- new EntityReference(loc.well_id, loc.well_code, loc.well_type_code,
- EntityKind.SAMPLE, loc.well_perm_id);
+ Set<String> seenWellPermIds = new HashSet<String>();
+ List<WellContentQueryResult> result = new ArrayList<WellContentQueryResult>();
+
+ for (WellContentQueryResult queryResult : queryResults)
+ {
+ String permId = queryResult.well_perm_id;
+ if (false == seenWellPermIds.contains(permId))
+ {
+ seenWellPermIds.add(permId);
+ result.add(queryResult);
+ }
+ }
+ return result;
+ }
+
+ private static WellContent convert(WellContentQueryResult well)
+ {
+ WellLocation location =
+ ScreeningUtils.tryCreateLocationFromMatrixCoordinate(well.well_code);
+ EntityReference wellReference =
+ new EntityReference(well.well_id, well.well_code,
+ well.well_type_code, EntityKind.SAMPLE, well.well_perm_id);
EntityReference plate =
- new EntityReference(loc.plate_id, loc.plate_code, loc.plate_type_code,
- EntityKind.SAMPLE, loc.plate_perm_id);
- Material materialContent = new Material();
- materialContent.setCode(loc.material_content_code);
- materialContent.setId(loc.material_content_id);
- MaterialType type = new MaterialType();
- type.setCode(loc.material_content_type_code);
- materialContent.setMaterialType(type);
- return new WellContent(location, well, plate, convertExperiment(loc), materialContent);
- }
-
- private static ExperimentReference convertExperiment(
- ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContent loc)
+ new EntityReference(well.plate_id, well.plate_code,
+ well.plate_type_code, EntityKind.SAMPLE, well.plate_perm_id);
+
+ return new WellContent(location, wellReference, plate, convertExperiment(well));
+ }
+
+ private static ExperimentReference convertExperiment(WellContentQueryResult loc)
{
return new ExperimentReference(loc.exp_id, loc.exp_perm_id, loc.exp_code,
loc.exp_type_code, loc.proj_code, loc.space_code);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellContent.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellContent.java
index 17ab75566346976fa6f96ba589a2eb66799a776d..c9fef632223b01f9c0f3dd1117886d82a6ee46f2 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellContent.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellContent.java
@@ -21,6 +21,7 @@ import java.util.Collections;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityReference;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
@@ -42,15 +43,16 @@ public class WellContent implements ISerializable
private EntityReference well;
+ /**
+ * well properties also contain the referenced materials (if any) enriched with material
+ * properties.
+ */
private List<IEntityProperty> wellProperties = new ArrayList<IEntityProperty>(0);
private EntityReference plate;
private ExperimentReference experiment;
- // Material which was being searched for inside a well. Enriched with properties.
- private Material materialContent;
-
// ------------ Dataset Data -------------
// dataset which contains images for this well, null if no images have been acquired
@@ -69,13 +71,13 @@ public class WellContent implements ISerializable
}
public WellContent(WellLocation locationOrNull, EntityReference well, EntityReference plate,
- ExperimentReference experiment, Material materialContent)
+ ExperimentReference experiment)
{
- this(locationOrNull, well, plate, experiment, materialContent, null, null, null, null);
+ this(locationOrNull, well, plate, experiment, null, null, null, null);
}
private WellContent(WellLocation locationOrNull, EntityReference well, EntityReference plate,
- ExperimentReference experiment, Material materialContent,
+ ExperimentReference experiment,
List<IEntityProperty> wellProperties, DatasetImagesReference imagesDatasetOrNull,
DatasetReference featureVectorDatasetOrNull, NamedFeatureVector featureVectorOrNull)
{
@@ -83,7 +85,6 @@ public class WellContent implements ISerializable
this.well = well;
this.plate = plate;
this.experiment = experiment;
- this.materialContent = materialContent;
this.imagesDatasetOrNull = imagesDatasetOrNull;
this.featureVectorDatasetOrNull = featureVectorDatasetOrNull;
this.featureVectorOrNull = featureVectorOrNull;
@@ -105,9 +106,22 @@ public class WellContent implements ISerializable
return plate;
}
- public Material getMaterialContent()
+ public List<Material> getMaterialContents()
{
- return materialContent;
+ ArrayList<Material> materials = new ArrayList<Material>();
+ for (IEntityProperty property : wellProperties)
+ {
+ DataTypeCode propertyDataTypeCode = property.getPropertyType().getDataType().getCode();
+ if (propertyDataTypeCode == DataTypeCode.MATERIAL)
+ {
+ Material materialOrNull = property.getMaterial();
+ if (materialOrNull != null)
+ {
+ materials.add(materialOrNull);
+ }
+ }
+ }
+ return materials;
}
public DatasetImagesReference tryGetImageDataset()
@@ -134,14 +148,14 @@ public class WellContent implements ISerializable
DatasetReference newFeatureVectorDatasetOrNull)
{
return new WellContent(this.locationOrNull, this.well, this.plate, this.experiment,
- this.materialContent, this.wellProperties, newImagesDatasetOrNull,
+ this.wellProperties, newImagesDatasetOrNull,
newFeatureVectorDatasetOrNull, this.featureVectorOrNull);
}
public WellContent cloneWithFeatureVector(NamedFeatureVector newFeatureVectorOrNull)
{
return new WellContent(this.locationOrNull, this.well, this.plate, this.experiment,
- this.materialContent, this.wellProperties, this.imagesDatasetOrNull,
+ this.wellProperties, this.imagesDatasetOrNull,
this.featureVectorDatasetOrNull, newFeatureVectorOrNull);
}
@@ -149,7 +163,7 @@ public class WellContent implements ISerializable
public String toString()
{
return "location = " + locationOrNull + ", experiment = " + experiment + ", plate = "
- + plate + ", well = " + well + ", content = " + materialContent;
+ + plate + ", well = " + well;
}
public List<IEntityProperty> getWellProperties()
@@ -167,4 +181,5 @@ public class WellContent implements ISerializable
{
this.wellProperties = properties;
}
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/grids/WellSearchGridColumnIds.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/grids/WellSearchGridColumnIds.java
index e0951691c61d2868edec3c42db771ba1d0e158c5..ef9a42e1da913d481b7b07735ec0e4ed5cbdec00 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/grids/WellSearchGridColumnIds.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/grids/WellSearchGridColumnIds.java
@@ -24,8 +24,6 @@ package ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids;
*/
public class WellSearchGridColumnIds
{
- public static final String WELL_CONTENT_MATERIAL = "WELL_CONTENT_MATERIAL";
- public static final String WELL_CONTENT_MATERIAL_TYPE = "WELL_CONTENT_MATERIAL_TYPE";
public static final String EXPERIMENT = "experiment";
public static final String PLATE = "PLATE";
public static final String WELL = "WELL";
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ScreeningDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ScreeningDAOTest.java
index 73e14d38b22b233e0191d5941e3769bc407e37d7..b03d89a8166405961e065c25fa5a80d40a2b6a13 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ScreeningDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ScreeningDAOTest.java
@@ -65,7 +65,7 @@ public class ScreeningDAOTest extends AbstractScreeningDAOTest
public void testGetPlateLocationsForOneMaterial()
{
// it just tests if the sql runs
- List<WellContent> locations =
+ List<WellContentQueryResult> locations =
EntityListingTestUtils.asList(query.getPlateLocationsForMaterialId(1, 1));
AssertJUnit.assertEquals(0, locations.size());
}
@@ -74,7 +74,7 @@ public class ScreeningDAOTest extends AbstractScreeningDAOTest
public void testGetPlateLocationsForOneMaterialAllExperiments()
{
// it just tests if the sql runs
- List<WellContent> locations =
+ List<WellContentQueryResult> locations =
EntityListingTestUtils.asList(query.getPlateLocationsForMaterialId(1));
AssertJUnit.assertEquals(0, locations.size());
}
@@ -83,7 +83,7 @@ public class ScreeningDAOTest extends AbstractScreeningDAOTest
public void testGetPlateMappingAllTypes()
{
// it just tests if the sql runs
- List<WellContent> locations = EntityListingTestUtils.asList(query.getPlateMapping("xxx"));
+ List<WellContentQueryResult> locations = EntityListingTestUtils.asList(query.getPlateMapping("xxx"));
AssertJUnit.assertEquals(0, locations.size());
}
@@ -91,7 +91,7 @@ public class ScreeningDAOTest extends AbstractScreeningDAOTest
public void testGetPlateMappingAllTypesAugmentedCode()
{
// it just tests if the sql runs
- List<WellContent> locations =
+ List<WellContentQueryResult> locations =
EntityListingTestUtils.asList(query.getPlateMapping("xxx", "yyy"));
AssertJUnit.assertEquals(0, locations.size());
}
@@ -117,7 +117,7 @@ public class ScreeningDAOTest extends AbstractScreeningDAOTest
public void testGetPlateMappingGeneType()
{
// it just tests if the sql runs
- List<WellContent> locations =
+ List<WellContentQueryResult> locations =
EntityListingTestUtils.asList(query.getPlateMappingForMaterialType("xxx", "Gene"));
AssertJUnit.assertEquals(0, locations.size());
}
@@ -126,7 +126,7 @@ public class ScreeningDAOTest extends AbstractScreeningDAOTest
public void testGetPlateMappingGeneTypeAugmentedCode()
{
// it just tests if the sql runs
- List<WellContent> locations =
+ List<WellContentQueryResult> locations =
EntityListingTestUtils.asList(query.getPlateMappingForMaterialType("xxx", "yyy",
"Gene"));
AssertJUnit.assertEquals(0, locations.size());
@@ -143,7 +143,7 @@ public class ScreeningDAOTest extends AbstractScreeningDAOTest
{ 1, 2 };
// one experiment
- List<WellContent> locations =
+ List<WellContentQueryResult> locations =
EntityListingTestUtils.asList(query.getPlateLocationsForMaterialCodes(ids,
materialTypeCodes, 1));
AssertJUnit.assertEquals(0, locations.size());
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 476971ddc86273091d4a044686a804353cea72c4..5afa9de28219954b76d5dcb05a86bd11a29e126c 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
@@ -28,7 +28,6 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.authentication.Principal;
import ch.systemsx.cisd.bds.StringUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
@@ -106,12 +105,14 @@ public class WellContentLoaderTest extends AbstractScreeningDAOTest
assertTrue("At least one property per well is expected", props.size() > 0);
for (IEntityProperty prop : props)
{
- MaterialEntityProperty wellProp = (MaterialEntityProperty) prop;
- assertNotNull(wellProp.getPropertyType().getCode());
- assertNotNull(wellProp.getMaterial());
+ assertNotNull(prop.getPropertyType().getCode());
+ assertNotNull(prop.getMaterial());
+ assertTrue("Material properties should be populated", prop.getMaterial()
+ .getProperties().size() > 0);
// assert the string representation actually has contents
- String stringValue = wellProp.tryGetAsString();
+ String stringValue = prop.tryGetAsString();
assertEquals(false, StringUtils.isBlank(stringValue));
+
}
}