From 8f08c28e669671c1421b124e0369bf6984f9daed Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Tue, 13 Sep 2011 11:56:25 +0000
Subject: [PATCH] [LMS-2500] allow to access all well properties via the public
screening API
SVN: 22911
---
.../generic/shared/util/EntityHelper.java | 15 +++
.../api/v1/ScreeningOpenbisServiceFacade.java | 7 ++
.../screening/server/ScreeningServer.java | 9 +-
.../server/ScreeningServerLogger.java | 9 ++
.../server/logic/PlateContentLoader.java | 25 ++++
.../server/logic/ScreeningApiImpl.java | 105 ++++++++++++++++-
.../shared/api/v1/IScreeningApiServer.java | 16 +++
.../screening/shared/api/v1/dto/Material.java | 50 ++++++++
.../shared/api/v1/dto/PlateWithWells.java | 90 +++++++++++++++
.../screening/shared/api/v1/dto/Well.java | 109 ++++++++++++++++++
10 files changed, 432 insertions(+), 3 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/Material.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/PlateWithWells.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/Well.java
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java
index 5ed0db8bc64..c534b618bc4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.generic.shared.util;
import java.util.ArrayList;
import java.util.Collections;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
@@ -199,6 +200,20 @@ public class EntityHelper
return property;
}
+ public static Map<String, String> convertToStringMap(List<IEntityProperty> properties)
+ {
+ Map<String, String> map = new HashMap<String, String>();
+ if (properties != null)
+ {
+ for (IEntityProperty prop : properties)
+ {
+ map.put(prop.getPropertyType().getCode(), prop.tryGetAsString());
+ }
+ }
+
+ return map;
+ }
+
private static IEntityProperty createNewProperty(String propertyCode)
{
IEntityProperty property = new EntityProperty();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
index 490ed0fcef0..6538d7a8f88 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
@@ -71,6 +71,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifi
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWithWells;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
@@ -276,6 +277,12 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
return openbisScreeningServer.listPlates(sessionToken);
}
+ public List<PlateWithWells> getPlates(List<? extends PlateIdentifier> plateIdentifiers)
+ {
+ checkASMinimalMinorVersion("getPlates", List.class);
+ return openbisScreeningServer.getPlates(sessionToken, plateIdentifiers);
+ }
+
/**
* Return the list of all plates for the given <var>experiment</var>.
*/
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 24596df1974..0c77afe61dd 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
@@ -86,6 +86,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWithWells;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.AnalysisProcedures;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
@@ -124,7 +125,7 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
/**
* The minor version of this service.
*/
- public static final int MINOR_VERSION = 7;
+ public static final int MINOR_VERSION = 8;
@Resource(name = ResourceNames.SCREENING_BUSINESS_OBJECT_FACTORY)
private IScreeningBusinessObjectFactory businessObjectFactory;
@@ -516,4 +517,10 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
return MINOR_VERSION;
}
+ public List<PlateWithWells> getPlates(String sessionToken,
+ List<? extends PlateIdentifier> plateIdentifiers) throws IllegalArgumentException
+ {
+ return createScreeningApiImpl(sessionToken).getPlates(plateIdentifiers);
+ }
+
}
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 fccb762e2f4..489ef8d08fc 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
@@ -49,6 +49,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWithWells;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.AnalysisProcedures;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
@@ -388,4 +389,12 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
experimentSearchCriteria);
return null;
}
+
+ public List<PlateWithWells> getPlates(
+ String sessionToken, List<? extends PlateIdentifier> plates)
+ throws IllegalArgumentException
+ {
+ logAccess(sessionToken, "getPlates", "plates(%s)", plates);
+ return null;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
index 96c3067381e..e0794eeb092 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
@@ -115,6 +115,13 @@ public class PlateContentLoader
.getImageDatasetInfosForSample(sampleId, wellLocationOrNull);
}
+ public static List<PlateMetadata> loadPlateMetadatas(Session session,
+ IScreeningBusinessObjectFactory businessObjectFactory, List<TechId> plateIds)
+ {
+ return new PlateContentLoader(session, businessObjectFactory).getPlateMetadatas(plateIds);
+
+ }
+
private final Session session;
private final IScreeningBusinessObjectFactory businessObjectFactory;
@@ -423,4 +430,22 @@ public class PlateContentLoader
List<DatasetReference> unknownDatasetReferences = extractUnknownDatasets(datasets);
return new ImageSampleContent(logicalImages, unknownDatasetReferences);
}
+
+ private List<PlateMetadata> getPlateMetadatas(List<TechId> plateIds)
+ {
+ ArrayList<PlateMetadata> result = new ArrayList<PlateMetadata>();
+ for (TechId plateId : plateIds)
+ {
+ Sample plate = loadPlate(plateId);
+ List<WellMetadata> wells = loadWells(plateId);
+ Geometry plateGeometry = PlateDimensionParser.getPlateGeometry(plate.getProperties());
+ int rows = plateGeometry.getNumberOfRows();
+ int cols = plateGeometry.getNumberOfColumns();
+ PlateMetadata plateMetadata = new PlateMetadata(plate, wells, rows, cols);
+ result.add(plateMetadata);
+ }
+
+ return result;
+ }
+
}
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 97a4f30db6a..1421dd59c7c 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
@@ -43,6 +43,7 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleTypeDAO;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
@@ -63,6 +64,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleOwnerIdentif
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTypeTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
import ch.systemsx.cisd.openbis.generic.shared.util.SpaceCodeHelper;
import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQuery;
@@ -74,17 +76,22 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Material;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialTypeIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWithWells;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Well;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMetadata;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
/**
* Contains implementations of the screening public API calls.
@@ -524,8 +531,6 @@ public class ScreeningApiImpl
ScreeningUtils.tryCreateLocationFromMatrixCoordinate(sample.getSubCode());
if (location == null)
{
- new IllegalArgumentException(String.format(
- "Failed to retrieve location of sample '%s'.", sample.getCode()));
return null;
}
WellPosition position = new WellPosition(location.getRow(), location.getColumn());
@@ -863,4 +868,100 @@ public class ScreeningApiImpl
return plateWellReferences;
}
+ public List<PlateWithWells> getPlates(List<? extends PlateIdentifier> plateIdentifiers)
+ {
+ List<TechId> techIds = new ArrayList<TechId>();
+ for (PlateIdentifier identifier : plateIdentifiers)
+ {
+ TechId techId = getSampleTechId(identifier);
+ if (techId != null)
+ {
+ techIds.add(techId);
+ }
+ }
+
+ List<PlateMetadata> plateMetadatas =
+ PlateContentLoader.loadPlateMetadatas(session, businessObjectFactory, techIds);
+
+ List<PlateWithWells> result = new ArrayList<PlateWithWells>();
+ Map<Long, Material> materialsCache = new HashMap<Long, Material>();
+ for (PlateMetadata plateMetaData : plateMetadatas)
+ {
+ result.add(asPlateWithWells(plateMetaData, materialsCache));
+ }
+ return result;
+ }
+
+ private PlateWithWells asPlateWithWells(PlateMetadata plateMetadata,
+ Map<Long, Material> materialsCache)
+ {
+ Sample plate = plateMetadata.getPlate();
+ String spaceCodeOrNull = plate.getSpace() == null ? null : plate.getSpace().getCode();
+ PlateIdentifier plateIdentifier =
+ new PlateIdentifier(plate.getCode(), spaceCodeOrNull, plate.getPermId());
+ List<Well> wells = new ArrayList<Well>();
+ if (plateMetadata.getWells() != null)
+ {
+ for (WellMetadata wellMetadata : plateMetadata.getWells())
+ {
+ Well well = asWell(plateIdentifier, wellMetadata, materialsCache);
+ wells.add(well);
+ }
+ }
+ Geometry geometry =
+ Geometry.createFromRowColDimensions(plateMetadata.getRowsNum(),
+ plateMetadata.getColsNum());
+ Map<String, String> properties = EntityHelper.convertToStringMap(plate.getProperties());
+
+ return new PlateWithWells(plateIdentifier, geometry, properties, wells);
+ }
+
+ private Well asWell(PlateIdentifier plateIdentifier, WellMetadata wellMetadata,
+ Map<Long, Material> materialsCache)
+ {
+ Sample well = wellMetadata.getWellSample();
+ WellLocation location = wellMetadata.tryGetLocation();
+ WellPosition wellPosition = new WellPosition(location.getRow(), location.getColumn());
+ Map<String, String> properties = EntityHelper.convertToStringMap(well.getProperties());
+ Map<String, Material> materialProperties =
+ convertMaterialProperties(well.getProperties(), materialsCache);
+ return new Well(plateIdentifier, well.getCode(), well.getPermId(), wellPosition,
+ properties, materialProperties);
+ }
+
+ private Map<String, Material> convertMaterialProperties(List<IEntityProperty> properties,
+ Map<Long, Material> materialsCache)
+ {
+ HashMap<String, Material> result = new HashMap<String, Material>();
+ if (properties != null)
+ {
+ for (IEntityProperty property : properties)
+ {
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material material =
+ property.getMaterial();
+ if (material != null)
+ {
+ Material apiMaterial = materialsCache.get(material.getId());
+ if (apiMaterial == null)
+ {
+ apiMaterial = asApiMaterial(material);
+ materialsCache.put(material.getId(), apiMaterial);
+ }
+ String propCode = property.getPropertyType().getCode();
+ result.put(propCode, apiMaterial);
+ }
+ }
+ }
+ return result;
+ }
+
+ private Material asApiMaterial(
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material materialDto)
+ {
+ MaterialTypeIdentifier typeIdentifier = new MaterialTypeIdentifier(materialDto.getMaterialType().getCode());
+ Map<String, String> properties =
+ EntityHelper.convertToStringMap(materialDto.getProperties());
+ return new Material(typeIdentifier, materialDto.getCode(), properties);
+ }
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java
index 38f3ef90065..2b67aba777f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java
@@ -45,6 +45,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWithWells;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier;
/**
@@ -94,6 +95,7 @@ public interface IScreeningApiServer extends IRpcService
@ReturnValueFilter(validatorClass = ScreeningPlateValidator.class)
List<Plate> listPlates(String sessionToken) throws IllegalArgumentException;
+
/**
* Return the list of all plates assigned to the given experiment.
*
@@ -107,6 +109,20 @@ public interface IScreeningApiServer extends IRpcService
@AuthorizationGuard(guardClass = ExperimentIdentifierPredicate.class) ExperimentIdentifier experiment)
throws IllegalArgumentException;
+ /**
+ * Fetches the contents of a given list of plates. The result will contain well and material
+ * properties.
+ *
+ * @since 1.8
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
+ @MinimalMinorVersion(8)
+ List<PlateWithWells> getPlates(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = ScreeningPlateListReadOnlyPredicate.class) List<? extends PlateIdentifier> plates)
+ throws IllegalArgumentException;
+
/**
* Return the list of all visible experiments, along with their hierarchical context (space,
* project).
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/Material.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/Material.java
new file mode 100644
index 00000000000..6b03179f7f0
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/Material.java
@@ -0,0 +1,50 @@
+/*
+ * 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.shared.api.v1.dto;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Material with properties.
+ *
+ * @since 1.8
+ * @author Kaloyan Enimanev
+ */
+public class Material extends MaterialIdentifier
+{
+ private static final long serialVersionUID = 1L;
+
+ private final Map<String, String> properties;
+
+ public Material(MaterialTypeIdentifier materialTypeIdentifier, String materialCode,
+ Map<String, String> properties)
+ {
+ super(materialTypeIdentifier, materialCode);
+ this.properties = new HashMap<String, String>(properties);
+ }
+
+ /**
+ * @return the material properties
+ */
+ public Map<String, String> getProperties()
+ {
+ return Collections.unmodifiableMap(properties);
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/PlateWithWells.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/PlateWithWells.java
new file mode 100644
index 00000000000..265a1ac521f
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/PlateWithWells.java
@@ -0,0 +1,90 @@
+/*
+ * 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.shared.api.v1.dto;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Holds the complete metadata of a plate and its wells.
+ *
+ * @since 1.8
+ * @author Kaloyan Enimanev
+ */
+public class PlateWithWells extends PlateIdentifier
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private final Geometry plateGeometry;
+
+ private final Map<String, String> properties;
+
+ private final List<Well> wells;
+
+ public PlateWithWells(PlateIdentifier identifier, Geometry plateGeometry, Map<String, String> properties,
+ List<Well> unsortedWells)
+ {
+ super(identifier.getPlateCode(), identifier.tryGetSpaceCode(), identifier.getPermId());
+ this.plateGeometry = plateGeometry;
+ this.properties = new HashMap<String, String>(properties);
+ this.wells = sortWells(unsortedWells);
+ }
+
+ public Geometry getPlateGeometry()
+ {
+ return plateGeometry;
+ }
+
+ public Map<String, String> getProperties()
+ {
+ return properties;
+ }
+
+ public List<Well> getWells()
+ {
+ return Collections.unmodifiableList(wells);
+ }
+
+ public Well getWell(int row, int col)
+ {
+ int idx = getWellIndexForRowAndCol(row, col);
+ return wells.get(idx);
+ }
+
+ private int getWellIndexForRowAndCol(int row, int col)
+ {
+ return (row - 1) * plateGeometry.getNumberOfColumns() + (col - 1);
+ }
+
+ private List<Well> sortWells(List<Well> unsortedWells)
+ {
+ Well[] wellsArray =
+ new Well[plateGeometry.getNumberOfRows() * plateGeometry.getNumberOfColumns()];
+ for (Well well : unsortedWells)
+ {
+ int row = well.getWellPosition().getWellRow();
+ int col = well.getWellPosition().getWellColumn();
+ wellsArray[getWellIndexForRowAndCol(row, col)] = well;
+ }
+ return Arrays.asList(wellsArray);
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/Well.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/Well.java
new file mode 100644
index 00000000000..2e3a43fc0b0
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/Well.java
@@ -0,0 +1,109 @@
+/*
+ * 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.shared.api.v1.dto;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * {@link Well} holds a complete set of metadata for an openBIS well. Material properties of wells
+ * are given a special treatment - API users can retrieve {@link Material} property values via the method {@link #getMaterialProperties()}. All other property values are available via {@link #getProperties()}.
+ * @since 1.8
+ * @author Kaloyan Enimanev
+ */
+public class Well extends WellIdentifier
+{
+ private static final long serialVersionUID = 1L;
+
+ private final String code;
+
+ private final Map<String, String> properties;
+
+ private final Map<String, Material> materialProperties;
+
+ public Well(PlateIdentifier plateIdentifier, String code, String permId,
+ WellPosition wellPosition, Map<String, String> properties,
+ Map<String, Material> materialProperties)
+ {
+ super(plateIdentifier, wellPosition, permId);
+ this.code = code;
+ this.properties = new HashMap<String, String>(properties);
+ this.materialProperties = new HashMap<String, Material>(materialProperties);
+ }
+
+ public String getCode()
+ {
+ return code;
+ }
+
+ public Map<String, String> getProperties()
+ {
+ return Collections.unmodifiableMap(properties);
+ }
+
+ public Map<String, Material> getMaterialProperties()
+ {
+ return Collections.unmodifiableMap(materialProperties);
+ }
+
+ @Override
+ public int hashCode()
+ {
+ final int prime = 31;
+ int result = super.hashCode();
+ result = prime * result + ((code == null) ? 0 : code.hashCode());
+ return result;
+ }
+
+ @Override
+ public String toString()
+ {
+ return getPermId() + " " + getCode() + " " + getWellPosition() + ", plate: "
+ + getPlateIdentifier();
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ {
+ return true;
+ }
+ if (!super.equals(obj))
+ {
+ return false;
+ }
+ if (!(obj instanceof Well))
+ {
+ return false;
+ }
+ Well other = (Well) obj;
+ if (code == null)
+ {
+ if (other.code != null)
+ {
+ return false;
+ }
+ } else if (false == code.equals(other.code))
+ {
+ return false;
+ }
+ return true;
+ }
+
+}
--
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