diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
index 1195eca66e64d612bf06569e916d7bc6cfc21f15..52968f6e8a673a32072b27af31d97d8dc93554f1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
@@ -39,6 +39,7 @@ 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.WellIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
/**
@@ -105,6 +106,11 @@ public interface IScreeningOpenbisServiceFacade
public List<PlateWellReferenceWithDatasets> listPlateWells(
MaterialIdentifier materialIdentifier, boolean findDatasets);
+ /**
+ * For the given <var>plateIdentifier</var> find all wells that are connected to it.
+ */
+ public List<WellIdentifier> listPlateWells(PlateIdentifier plateIdentifier);
+
/**
* Converts the given list of {@link PlateWellReferenceWithDatasets} into a list of
* {@link FeatureVectorDatasetWellReference}.
@@ -251,7 +257,7 @@ public interface IScreeningOpenbisServiceFacade
public void loadImages(List<PlateImageReference> imageReferences,
IImageOutputStreamProvider outputStreamProvider, boolean convertToPNG)
throws IOException;
-
+
/**
* Loads original images or thumbnails for a specified data set, a list of well positions (empty
* list means all wells), a channel, and an optional thumb nail size. Images of all tiles are
@@ -264,30 +270,29 @@ public interface IScreeningOpenbisServiceFacade
public List<byte[]> loadImages(IDatasetIdentifier dataSetIdentifier,
List<WellPosition> wellPositions, String channel, ImageSize thumbnailSizeOrNull)
throws IOException;
-
+
/**
- * Loads PNG-encoded images for specified data set, list of well positions (empty
- * list means all wells), channel, and optional thumb nail size. Images of all tiles are
- * delivered. If thumb nail size isn't specified the original image is delivered otherwise a
- * thumb nail image with same aspect ratio as the original image but which fits into specified
- * size will be delivered.
+ * Loads PNG-encoded images for specified data set, list of well positions (empty list means all
+ * wells), channel, and optional thumb nail size. Images of all tiles are delivered. If thumb
+ * nail size isn't specified the original image is delivered otherwise a thumb nail image with
+ * same aspect ratio as the original image but which fits into specified size will be delivered.
*
* @param plateImageHandler Handles delivered images.
*/
public void loadImages(IDatasetIdentifier datasetIdentifier, List<WellPosition> wellPositions,
String channel, ImageSize thumbnailSizeOrNull, IPlateImageHandler plateImageHandler)
throws IOException;
-
+
/**
- * Saves the specified transformer factory for the specified channel and the experiment to
- * which the specified data sets belong.
+ * Saves the specified transformer factory for the specified channel and the experiment to which
+ * the specified data sets belong.
*/
- public void saveImageTransformerFactory(List<IDatasetIdentifier> dataSetIdentifiers, String channel,
- IImageTransformerFactory transformerFactoryOrNull);
+ public void saveImageTransformerFactory(List<IDatasetIdentifier> dataSetIdentifiers,
+ String channel, IImageTransformerFactory transformerFactoryOrNull);
/**
- * Returns the transformer factory for the specified channel and the experiment to which
- * the specified data sets belong.
+ * Returns the transformer factory for the specified channel and the experiment to which the
+ * specified data sets belong.
*
* @return <code>null</code> if such a factory has been defined yet.
*/
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 943dc7e6ec052f38e1c8af33ac963f8648768afa..73a1476e4a814fa2efa6a23f6b4f4daae92c2eda 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
@@ -11,8 +11,8 @@ import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
-import java.util.Set;
import java.util.Map.Entry;
+import java.util.Set;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
import ch.systemsx.cisd.common.api.MinimalMinorVersion;
@@ -38,6 +38,7 @@ 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.WellIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
/**
@@ -237,6 +238,18 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
.listPlateWells(sessionToken, materialIdentifier, findDatasets);
}
+ /**
+ * For the given <var>plateIdentifier</var> find all wells that are connected to it.
+ */
+ public List<WellIdentifier> listPlateWells(PlateIdentifier plateIdentifier)
+ {
+ checkASMinimalMinorVersion("listPlateWells", PlateIdentifier.class);
+ return openbisScreeningServer.listPlateWells(sessionToken, plateIdentifier);
+ }
+
+ // IDataSetDss getDataSet(WellIdentifier well)
+ // IDataSetDss putDataSet(WellIdentifier well, File dataSetFile)
+
/**
* Converts a given list of dataset codes to dataset identifiers which can be used in other API
* calls.
@@ -499,8 +512,8 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
{
// Only available since v1.3
stream =
- dssService.getService().loadImages(sessionToken,
- references, convertToPNG);
+ dssService.getService().loadImages(sessionToken,
+ references, convertToPNG);
} else
{
checkDSSMinimalMinorVersion(dssService, "loadImages",
@@ -540,7 +553,7 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
throw ex.getIoException();
}
}
-
+
public List<byte[]> loadImages(IDatasetIdentifier dataSetIdentifier,
List<WellPosition> wellPositions, String channel, ImageSize thumbnailSizeOrNull)
throws IOException
@@ -595,16 +608,18 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
} while (size >= 0);
}
- public void saveImageTransformerFactory(List<IDatasetIdentifier> dataSetIdentifiers, String channel,
- IImageTransformerFactory transformerFactoryOrNull)
+ public void saveImageTransformerFactory(List<IDatasetIdentifier> dataSetIdentifiers,
+ String channel, IImageTransformerFactory transformerFactoryOrNull)
{
Map<String, List<IDatasetIdentifier>> map = getReferencesPerDss(dataSetIdentifiers);
Set<Entry<String, List<IDatasetIdentifier>>> entrySet = map.entrySet();
for (Entry<String, List<IDatasetIdentifier>> entry : entrySet)
{
String serverUrl = entry.getKey();
- IDssServiceRpcScreening service = dssServiceCache.createDssService(serverUrl).getService();
- service.saveImageTransformerFactory(sessionToken, entry.getValue(), channel, transformerFactoryOrNull);
+ IDssServiceRpcScreening service =
+ dssServiceCache.createDssService(serverUrl).getService();
+ service.saveImageTransformerFactory(sessionToken, entry.getValue(), channel,
+ transformerFactoryOrNull);
}
}
@@ -615,10 +630,12 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
Set<Entry<String, List<IDatasetIdentifier>>> entrySet = map.entrySet();
if (entrySet.size() != 1)
{
- throw new IllegalArgumentException("Only one data store expected instead of " + map.keySet());
+ throw new IllegalArgumentException("Only one data store expected instead of "
+ + map.keySet());
}
Entry<String, List<IDatasetIdentifier>> entry = entrySet.iterator().next();
- IDssServiceRpcScreening service = dssServiceCache.createDssService(entry.getKey()).getService();
+ IDssServiceRpcScreening service =
+ dssServiceCache.createDssService(entry.getKey()).getService();
return service.getImageTransformerFactoryOrNull(sessionToken, dataSetIdentifiers, channel);
}
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 23532bf6e237e4d19b2fb97589a43420234bd899..1018a666056c32f4e5d935d4a4ae73b843068cb9 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
@@ -71,6 +71,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMate
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageSampleContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LogicalImageInfo;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
@@ -89,7 +90,7 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
/**
* The minor version of this service.
*/
- public static final int MINOR_VERSION = 2;
+ public static final int MINOR_VERSION = 3;
@Resource(name = ResourceNames.SCREENING_BUSINESS_OBJECT_FACTORY)
private IScreeningBusinessObjectFactory businessObjectFactory;
@@ -217,6 +218,11 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
.listPlateWells(materialIdentifier, findDatasets);
}
+ public List<WellIdentifier> listPlateWells(String sessionToken, PlateIdentifier plateIdentifier)
+ {
+ return null; // TODO
+ }
+
public List<Plate> listPlates(String sessionToken)
{
return createScreeningApiImpl(sessionToken).listPlates();
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 a35c0f747f43b436b43d6fe3e3941ec88bd697b7..4c007300c46beadef57be47fbd39483c3db67088 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
@@ -44,6 +44,7 @@ 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.WellIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageSampleContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LogicalImageInfo;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
@@ -183,6 +184,12 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
return null;
}
+ public List<WellIdentifier> listPlateWells(String sessionToken, PlateIdentifier plateIdentifier)
+ {
+ logAccess(sessionToken, "listPlateWells", "plate: %s", plateIdentifier);
+ return null;
+ }
+
public List<Plate> listPlates(String sessionToken)
{
logAccess(sessionToken, "listPlates");
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/authorization/PlateIdentifierPredicate.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/authorization/PlateIdentifierPredicate.java
new file mode 100644
index 0000000000000000000000000000000000000000..b5cdbb55097c49ee5ec58279610681c09edee1ef
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/authorization/PlateIdentifierPredicate.java
@@ -0,0 +1,56 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.shared.api.authorization;
+
+import java.util.List;
+
+import ch.systemsx.cisd.common.exceptions.Status;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.RoleWithIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractSpacePredicate;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
+
+/**
+ * A predicate for {@link PlateIdentifier}.
+ *
+ * @author Piotr Buczek
+ */
+public class PlateIdentifierPredicate extends AbstractSpacePredicate<PlateIdentifier>
+{
+
+ @Override
+ public String getCandidateDescription()
+ {
+ return "experiment";
+ }
+
+ @Override
+ protected Status doEvaluation(PersonPE person, List<RoleWithIdentifier> allowedRoles,
+ PlateIdentifier value)
+ {
+ // TODO 2010-12-13, Piotr Buczek: implement dealing with shared plates and permIds
+ if (value.getPermId() != null)
+ {
+ return null;
+ }
+
+ final String spaceCode = value.tryGetSpaceCode();
+ return evaluate(person, allowedRoles, authorizationDataProvider.getHomeDatabaseInstance(),
+ spaceCode);
+ }
+
+}
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 00286fc3ed211a4c5109909ddd4e694ec2b4ae0a..b011981e8d72ce822b2817a62db2ea138126df80 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
@@ -28,6 +28,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAll
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCodeCollectionPredicate;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.authorization.ExperimentIdentifierPredicate;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.authorization.PlateIdentifierPredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.authorization.PlateWellReferenceWithDatasetsValidator;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.authorization.ScreeningExperimentValidator;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.authorization.ScreeningPlateListReadOnlyPredicate;
@@ -42,6 +43,7 @@ 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.WellIdentifier;
/**
* This interface is a part of the official public screening API. It is forbidden to change it in a
@@ -69,7 +71,7 @@ public interface IScreeningApiServer extends IRpcService
/**
* Authenticates the user with a given password.
*
- *@return sessionToken if authentication succeeded, <code>null</code> otherwise.
+ * @return sessionToken if authentication succeeded, <code>null</code> otherwise.
*/
@Transactional
// this is not a readOnly transaction - it can create new users
@@ -162,6 +164,18 @@ public interface IScreeningApiServer extends IRpcService
List<PlateWellReferenceWithDatasets> listPlateWells(String sessionToken,
MaterialIdentifier materialIdentifier, boolean findDatasets);
+ /**
+ * For the given <var>plateIdentifier</var> find all wells that are connected to it.
+ *
+ * @since 1.3
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
+ @MinimalMinorVersion(3)
+ public List<WellIdentifier> listPlateWells(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = PlateIdentifierPredicate.class) PlateIdentifier plateIdentifier);
+
/**
* For a given list of <var>plates</var>, return the mapping of plate wells to materials
* contained in each well.