diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractCommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractCommonServer.java
index b13229d1551f3093c5fd895a0aa691ee281e137c..eff5902fbc383bd13a9975ee9426a6e3f5ddb7a1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractCommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractCommonServer.java
@@ -33,6 +33,7 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DisplaySettings;
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.server.IPropertiesBatchManager;
/**
* @author Franz-Josef Elmer
@@ -46,9 +47,10 @@ abstract class AbstractCommonServer<T extends IServer> extends AbstractServer<T>
public AbstractCommonServer(IAuthenticationService authenticationService,
ISessionManager<Session> sessionManager, IDAOFactory daoFactory,
+ IPropertiesBatchManager propertiesBatchManager,
ICommonBusinessObjectFactory businessObjectFactory)
{
- super(sessionManager, daoFactory);
+ super(sessionManager, daoFactory, propertiesBatchManager);
this.authenticationService = authenticationService;
this.businessObjectFactory = businessObjectFactory;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java
index 8f0f85f4b0690e6cea86de045df99684e33cf284..bd6dfa4938e4fabfb0199b3e306f4c6c66a9e79e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java
@@ -52,18 +52,20 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.GridCustomColumnPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityInformationWithPropertiesHolder;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.IAuthSession;
+import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityInformationWithPropertiesHolder;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleSession;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.translator.GridCustomExpressionTranslator.GridCustomColumnTranslator;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
import ch.systemsx.cisd.openbis.generic.shared.util.ServerUtils;
+import ch.systemsx.cisd.openbis.plugin.generic.server.IPropertiesBatchManager;
+import ch.systemsx.cisd.openbis.plugin.generic.server.PropertiesBatchManager;
/**
* An <i>abstract</i> {@link IServer} implementation.
@@ -93,6 +95,8 @@ public abstract class AbstractServer<T> extends AbstractServiceWithLogger<T> imp
@Resource(name = ComponentNames.REMOTE_HOST_VALIDATOR)
private IRemoteHostValidator remoteHostValidator;
+ private IPropertiesBatchManager propertiesBatchManager;
+
protected AbstractServer()
{
operationLog.info(String.format("Creating new '%s' implementation: '%s'.",
@@ -100,23 +104,33 @@ public abstract class AbstractServer<T> extends AbstractServiceWithLogger<T> imp
}
protected AbstractServer(final ISessionManager<Session> sessionManager,
- final IDAOFactory daoFactory)
+ final IDAOFactory daoFactory, IPropertiesBatchManager propertiesBatchManager)
{
this();
this.sessionManager = sessionManager;
this.daoFactory = daoFactory;
+ this.propertiesBatchManager = propertiesBatchManager;
}
// For testing purpose.
protected AbstractServer(final ISessionManager<Session> sessionManager,
- final IDAOFactory daoFactory,
+ final IDAOFactory daoFactory, IPropertiesBatchManager propertiesBatchManager,
final ISampleTypeSlaveServerPlugin sampleTypeSlaveServerPlugin,
final IDataSetTypeSlaveServerPlugin dataSetTypeSlaveServerPlugin)
{
- this(sessionManager, daoFactory);
+ this(sessionManager, daoFactory, propertiesBatchManager);
this.sampleTypeSlaveServerPlugin = sampleTypeSlaveServerPlugin;
this.dataSetTypeSlaveServerPlugin = dataSetTypeSlaveServerPlugin;
}
+
+ protected IPropertiesBatchManager getPropertiesBatchManager()
+ {
+ if (propertiesBatchManager == null)
+ {
+ propertiesBatchManager = new PropertiesBatchManager(daoFactory);
+ }
+ return propertiesBatchManager;
+ }
public final void setSampleTypeSlaveServerPlugin(
ISampleTypeSlaveServerPlugin sampleTypeSlaveServerPlugin)
@@ -432,6 +446,7 @@ public abstract class AbstractServer<T> extends AbstractServiceWithLogger<T> imp
protected void registerSamples(final Session session,
final NewSamplesWithTypes newSamplesWithType, PersonPE registratorOrNull)
{
+ getPropertiesBatchManager().manageProperties(newSamplesWithType);
final SampleType sampleType = newSamplesWithType.getSampleType();
final List<NewSample> newSamples = newSamplesWithType.getNewSamples();
assert sampleType != null : "Unspecified sample type.";
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
index ccbfdf9426eeb578217dafca0674e16d36d5c91a..14618d72957b16b6a25197aae936ea78d86828a3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
@@ -209,6 +209,7 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTermTranslat
import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTranslator;
import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
+import ch.systemsx.cisd.openbis.plugin.generic.server.IPropertiesBatchManager;
public final class CommonServer extends AbstractCommonServer<ICommonServerForInternalUse> implements
ICommonServerForInternalUse
@@ -220,10 +221,20 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
final ICommonBusinessObjectFactory businessObjectFactory,
final LastModificationState lastModificationState)
{
- super(authenticationService, sessionManager, daoFactory, businessObjectFactory);
- this.lastModificationState = lastModificationState;
+ this(authenticationService, sessionManager, daoFactory, null, businessObjectFactory,
+ lastModificationState);
}
+ CommonServer(final IAuthenticationService authenticationService,
+ final ISessionManager<Session> sessionManager, final IDAOFactory daoFactory,
+ IPropertiesBatchManager propertiesBatchManager,
+ final ICommonBusinessObjectFactory businessObjectFactory,
+ final LastModificationState lastModificationState)
+ {
+ super(authenticationService, sessionManager, daoFactory, propertiesBatchManager, businessObjectFactory);
+ this.lastModificationState = lastModificationState;
+ }
+
ICommonBusinessObjectFactory getBusinessObjectFactory()
{
return businessObjectFactory;
@@ -1691,7 +1702,21 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
{
if (etpt.isDynamic() == false)
{
- columns.add(etpt.getPropertyType().getCode());
+ String code = etpt.getPropertyType().getCode();
+ if (etpt.isManaged())
+ {
+ String script = etpt.getScript().getScript();
+ ManagedPropertyEvaluator evaluator = new ManagedPropertyEvaluator(script);
+ List<String> batchColumnNames = evaluator.getBatchColumnNames();
+ Collections.sort(batchColumnNames);
+ for (String name : batchColumnNames)
+ {
+ columns.add(code + ':' + name);
+ }
+ } else
+ {
+ columns.add(code);
+ }
}
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
index a5b912956262a6530d7b88214e6140e81173eca8..fbb836599f492501a3f87d6dfedaf223044d58f9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
@@ -117,6 +117,7 @@ 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.translator.VocabularyTermTranslator;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
+import ch.systemsx.cisd.openbis.plugin.generic.server.IPropertiesBatchManager;
/**
* @author Franz-Josef Elmer
@@ -131,11 +132,19 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
ISessionManager<Session> sessionManager, IDAOFactory daoFactory,
ICommonBusinessObjectFactory boFactory, IDataStoreServiceFactory dssFactory)
{
- super(authenticationService, sessionManager, daoFactory, boFactory);
+ this(authenticationService, sessionManager, daoFactory, null, boFactory, dssFactory);
+ }
+
+ ETLService(IAuthenticationService authenticationService,
+ ISessionManager<Session> sessionManager, IDAOFactory daoFactory,
+ IPropertiesBatchManager propertiesBatchManager,
+ ICommonBusinessObjectFactory boFactory, IDataStoreServiceFactory dssFactory)
+ {
+ super(authenticationService, sessionManager, daoFactory, propertiesBatchManager, boFactory);
this.daoFactory = daoFactory;
this.dssFactory = dssFactory;
}
-
+
public IETLService createLogger(IInvocationLoggerContext context)
{
return new ETLServiceLogger(getSessionManager(), context);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServer.java
index b1cd9b867fa5fad6822eeb6d944989157f50d057..1d0cfd79de254ce6ebdfabe820dcfc3e68e9df5e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServer.java
@@ -36,6 +36,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingDataSetCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.plugin.generic.server.IPropertiesBatchManager;
public final class TrackingServer extends AbstractServer<ITrackingServer> implements
ITrackingServer
@@ -43,12 +44,20 @@ public final class TrackingServer extends AbstractServer<ITrackingServer> implem
private final ICommonBusinessObjectFactory businessObjectFactory;
public TrackingServer(final ISessionManager<Session> sessionManager,
- final IDAOFactory daoFactory, final ICommonBusinessObjectFactory businessObjectFactory)
+ final IDAOFactory daoFactory,
+ final ICommonBusinessObjectFactory businessObjectFactory)
{
- super(sessionManager, daoFactory);
- this.businessObjectFactory = businessObjectFactory;
+ this(sessionManager, daoFactory, null, businessObjectFactory);
}
+ TrackingServer(final ISessionManager<Session> sessionManager,
+ final IDAOFactory daoFactory, IPropertiesBatchManager propertiesBatchManager,
+ final ICommonBusinessObjectFactory businessObjectFactory)
+ {
+ super(sessionManager, daoFactory, propertiesBatchManager);
+ this.businessObjectFactory = businessObjectFactory;
+ }
+
ICommonBusinessObjectFactory getBusinessObjectFactory()
{
return businessObjectFactory;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
index 494b758616d186566f06984ad017eb570a5df268..62c387ad3580da164a97dcaa2372d809dae70337 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
@@ -64,6 +64,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
+import ch.systemsx.cisd.openbis.plugin.generic.server.IPropertiesBatchManager;
/**
* @author Franz-Josef Elmer
@@ -81,9 +82,9 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
}
GeneralInformationService(ISessionManager<Session> sessionManager, IDAOFactory daoFactory,
- ICommonServer commonServer)
+ IPropertiesBatchManager propertiesBatchManager, ICommonServer commonServer)
{
- super(sessionManager, daoFactory);
+ super(sessionManager, daoFactory, propertiesBatchManager);
this.commonServer = commonServer;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/BasicConstant.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/BasicConstant.java
index cbc8e53621827c4171b2effcde86f527b0a82b71..0e4e9e01029eec661f3d6919a47b22b4c6890f21 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/BasicConstant.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/BasicConstant.java
@@ -41,7 +41,7 @@ public class BasicConstant
private static final char UNI_REPLACEMENT_CHAR = 0xFFFD;
/** Prefix of property value that contains error message. */
- public static final String ERROR_PROPERTY_PREFIX = "" + UNI_REPLACEMENT_CHAR;
+ public static final String ERROR_PROPERTY_PREFIX = Character.toString(UNI_REPLACEMENT_CHAR);
/** Value of dynamic property before it is evaluated. */
public static final String DYNAMIC_PROPERTY_PLACEHOLDER_VALUE = ERROR_PROPERTY_PREFIX
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IPropertiesBean.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IPropertiesBean.java
new file mode 100644
index 0000000000000000000000000000000000000000..8dfb9110404b71c603d06cd950929622f244f039
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/IPropertiesBean.java
@@ -0,0 +1,30 @@
+/*
+ * 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.shared.basic.dto;
+
+
+/**
+ * Interface implemented by beans with properties attribute.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IPropertiesBean
+{
+ public IEntityProperty[] getProperties();
+
+ public void setProperties(IEntityProperty[] properties);
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java
index 9168598c8028fc33e8281d8d33cf1ae508e5cd33..ee95ab2649c273873522e7fbc40761863d0ca9b3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java
@@ -25,7 +25,7 @@ import ch.systemsx.cisd.common.annotation.BeanProperty;
*
* @author Christian Ribeaud
*/
-public class NewSample extends Identifier<NewSample> implements Comparable<NewSample>
+public class NewSample extends Identifier<NewSample> implements Comparable<NewSample>, IPropertiesBean
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/ValidationException.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/ValidationException.java
new file mode 100644
index 0000000000000000000000000000000000000000..6ecd9701cc6fa431dbd8e3e96d0c223eb3418e74
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/api/ValidationException.java
@@ -0,0 +1,40 @@
+/*
+ * 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.shared.basic.dto.api;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+/**
+ * Exception thrown by jython scripts in case of invalid input.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ValidationException extends UserFailureException
+{
+ private static final long serialVersionUID = 1L;
+
+ public ValidationException(String message)
+ {
+ super(message);
+ }
+
+ public ValidationException(String message, Throwable cause)
+ {
+ super(message, cause);
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/ManagedPropertyEvaluator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/ManagedPropertyEvaluator.java
index 300a7b9ba6dd456e736d4da8f5a77b88af241b39..a0c60f175cbbf899985d20283eb60ba90e2a7267 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/ManagedPropertyEvaluator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/ManagedPropertyEvaluator.java
@@ -16,42 +16,57 @@
package ch.systemsx.cisd.openbis.generic.shared.managed_property;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
import org.apache.log4j.Logger;
import ch.systemsx.cisd.common.evaluator.Evaluator;
+import ch.systemsx.cisd.common.evaluator.EvaluatorException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ManagedProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.IManagedProperty;
-import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.ISimpleTableModelBuilderAdaptor;
+import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.ScriptUtilityFactory;
/**
* Class for evaluating scripts that control managed properties.
*
* @author Chandrasekhar Ramakrishnan
*/
-// TODO 2011-01-14, Piotr Buczek: it should be possible to reuse evaluator by set of properties
public class ManagedPropertyEvaluator
{
private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
ManagedPropertyEvaluator.class);
- private final String scriptExpression;
-
/**
* The name of the script that expects the property to be there and updates ui configuration.
*/
- private static final String CONFIGURE_UI_EXPRESSION = "configureUI()";
+ private static final String CONFIGURE_UI_EXPRESSION = "configureUI";
/**
* The name of the script that expects the property to be there and updates the value.
*/
- private static final String UPDATE_VALUE_EXPRESSION = "updateValue()";
+ private static final String UPDATE_VALUE_EXPRESSION = "updateValue";
+ /**
+ * The name of the function that returns an array of column names.
+ */
+ private static final String BATCH_COLUMN_NAMES_FUNCTION = "batchColumnNames";
+
+ /**
+ * The name of the function that expects a map of bindings.
+ */
+ private static final String UPDATE_FROM_BATCH_INPUT_FUNCTION = "updateFromBatchInput";
+
private static final String PROPERTY_VARIABLE_NAME = "property";
+
+ private final Evaluator evaluator;
public ManagedPropertyEvaluator(String scriptExpression)
{
- this.scriptExpression = scriptExpression;
+ evaluator = new Evaluator("", ScriptUtilityFactory.class, scriptExpression);
}
public void evalConfigureProperty(IManagedProperty managedProperty)
@@ -62,10 +77,8 @@ public class ManagedPropertyEvaluator
managedProperty));
}
- Evaluator evaluator =
- new Evaluator(CONFIGURE_UI_EXPRESSION, ScriptUtilityFactory.class, scriptExpression);
evaluator.set(PROPERTY_VARIABLE_NAME, managedProperty);
- evaluator.eval();
+ evaluator.evalFunction(CONFIGURE_UI_EXPRESSION);
}
public void evaluateUpdateProperty(IManagedProperty managedProperty)
@@ -76,25 +89,34 @@ public class ManagedPropertyEvaluator
managedProperty));
}
- Evaluator evaluator =
- new Evaluator(UPDATE_VALUE_EXPRESSION, ScriptUtilityFactory.class, scriptExpression);
evaluator.set(PROPERTY_VARIABLE_NAME, managedProperty);
- evaluator.eval();
+ evaluator.evalFunction(UPDATE_VALUE_EXPRESSION);
}
-
- //
- // utlilities
- //
-
- /**
- * This utility class should shouldn't expose anything outside of Managed Property API. No
- * method should return or take as an argument anything outside of the API.
- */
- public static class ScriptUtilityFactory
+
+ public List<String> getBatchColumnNames()
{
- public static ISimpleTableModelBuilderAdaptor createTableBuilder()
+ Object result = evaluator.evalFunction(BATCH_COLUMN_NAMES_FUNCTION);
+ if (result instanceof List == false)
+ {
+ throw new EvaluatorException("Function '" + BATCH_COLUMN_NAMES_FUNCTION
+ + "' doesn't return a List but an object of type '"
+ + result.getClass().getName() + "': " + result);
+ }
+ List<?> list = (List<?>) result;
+ ArrayList<String> columnNames = new ArrayList<String>();
+ for (Object element : list)
{
- return SimpleTableModelBuilderAdaptor.create();
+ columnNames.add(element.toString());
}
+ return columnNames;
}
+
+ public String updateFromBatchInput(Map<String, String> bindings)
+ {
+ ManagedProperty property = new ManagedProperty();
+ evaluator.set(PROPERTY_VARIABLE_NAME, property);
+ evaluator.evalFunction(UPDATE_FROM_BATCH_INPUT_FUNCTION, bindings);
+ return property.getValue();
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/ScriptUtilityFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/ScriptUtilityFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..90a7f94ca8d218d2578f52b0a2df91122356f5f7
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/ScriptUtilityFactory.java
@@ -0,0 +1,30 @@
+package ch.systemsx.cisd.openbis.generic.shared.managed_property.api;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.ValidationException;
+import ch.systemsx.cisd.openbis.generic.shared.managed_property.SimpleTableModelBuilderAdaptor;
+
+/**
+ * This utility class with function to be used by jython scripts for managed properties.
+ * <p>
+ * All methods of this class are part of the Managed Properties API.
+ */
+public class ScriptUtilityFactory
+{
+ /**
+ * Creates a table builder.
+ */
+ public static ISimpleTableModelBuilderAdaptor createTableBuilder()
+ {
+ return SimpleTableModelBuilderAdaptor.create();
+ }
+
+ /**
+ * Creates a {@link ValidationException} with specified message.
+ */
+ // Violates Java naming conventions for method because it should look like a constructor
+ // for invocations in jython.
+ public static ValidationException ValidationException(String message)
+ {
+ return new ValidationException(message);
+ }
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/server/DemoServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/server/DemoServer.java
index f1b69d6e9a54fbc6fd3d2893ebb2b3d954c2fd89..c8412ff0fea785b6c03d961a9140f640ace9dc04 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/server/DemoServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/demo/server/DemoServer.java
@@ -42,6 +42,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
import ch.systemsx.cisd.openbis.plugin.demo.shared.IDemoServer;
import ch.systemsx.cisd.openbis.plugin.demo.shared.ResourceNames;
+import ch.systemsx.cisd.openbis.plugin.generic.server.IPropertiesBatchManager;
/**
* The concrete {@link IDemoServer} implementation.
@@ -60,11 +61,13 @@ public final class DemoServer extends AbstractServer<IDemoServer> implements IDe
@Private
DemoServer(final ISessionManager<Session> sessionManager, final IDAOFactory daoFactory,
+ IPropertiesBatchManager propertiesBatchManager,
final IDemoBusinessObjectFactory businessObjectFactory,
final ISampleTypeSlaveServerPlugin sampleTypeSlaveServerPlugin,
final IDataSetTypeSlaveServerPlugin dataSetTypeSlaveServerPlugin)
{
- super(sessionManager, daoFactory, sampleTypeSlaveServerPlugin, dataSetTypeSlaveServerPlugin);
+ super(sessionManager, daoFactory, propertiesBatchManager, sampleTypeSlaveServerPlugin,
+ dataSetTypeSlaveServerPlugin);
this.businessObjectFactory = businessObjectFactory;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
index 084ced56627a528b59730bd1d8f3099beb2d8c09..def1780070aa0b54cfd2ac013946b0795d08e6c8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
@@ -141,11 +141,13 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
@Private
GenericServer(final ISessionManager<Session> sessionManager, final IDAOFactory daoFactory,
+ IPropertiesBatchManager propertiesBatchManager,
final IGenericBusinessObjectFactory businessObjectFactory,
final ISampleTypeSlaveServerPlugin sampleTypeSlaveServerPlugin,
final IDataSetTypeSlaveServerPlugin dataSetTypeSlaveServerPlugin)
{
- super(sessionManager, daoFactory, sampleTypeSlaveServerPlugin, dataSetTypeSlaveServerPlugin);
+ super(sessionManager, daoFactory, propertiesBatchManager, sampleTypeSlaveServerPlugin,
+ dataSetTypeSlaveServerPlugin);
this.businessObjectFactory = businessObjectFactory;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/IPropertiesBatchManager.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/IPropertiesBatchManager.java
new file mode 100644
index 0000000000000000000000000000000000000000..0bb13c1c0f084f9fc48bdf11f7def27b15a08447
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/IPropertiesBatchManager.java
@@ -0,0 +1,29 @@
+/*
+ * 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.generic.server;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
+
+/**
+ * Interface of classes which manage managed properties in batch updates.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IPropertiesBatchManager
+{
+ public void manageProperties(NewSamplesWithTypes newSamplesWithTypes);
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/PropertiesBatchManager.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/PropertiesBatchManager.java
new file mode 100644
index 0000000000000000000000000000000000000000..8d9750f10f669c0df704f50af0e8ea496ff40dbb
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/PropertiesBatchManager.java
@@ -0,0 +1,162 @@
+/*
+ * 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.generic.server;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+
+import ch.systemsx.cisd.common.evaluator.EvaluatorException;
+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.BasicConstant;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IPropertiesBean;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.ValidationException;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePropertyTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ScriptPE;
+import ch.systemsx.cisd.openbis.generic.shared.managed_property.ManagedPropertyEvaluator;
+
+/**
+ * Handles Managed Properties of batch uploads/updates.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class PropertiesBatchManager implements IPropertiesBatchManager
+{
+ final IDAOFactory daoFactory;
+
+ public PropertiesBatchManager(IDAOFactory daoFactory)
+ {
+ this.daoFactory = daoFactory;
+ }
+
+ public void manageProperties(NewSamplesWithTypes newSamplesWithTypes)
+ {
+ List<NewSample> newSamples = newSamplesWithTypes.getNewSamples();
+ ISampleTypeDAO sampleTypeDAO = daoFactory.getSampleTypeDAO();
+ String code = newSamplesWithTypes.getSampleType().getCode();
+ SampleTypePE sampleType = sampleTypeDAO.tryFindSampleTypeByCode(code);
+ Set<? extends EntityTypePropertyTypePE> sampleTypePropertyTypes =
+ sampleType.getSampleTypePropertyTypes();
+
+ managePropertiesBeans(newSamples, sampleTypePropertyTypes);
+ }
+
+ private void managePropertiesBeans(List<? extends IPropertiesBean> propertiesBeans,
+ Set<? extends EntityTypePropertyTypePE> entityTypePropertyTypes)
+ {
+ Map<String, ManagedPropertyEvaluator> evaluators =
+ createEvaluators(entityTypePropertyTypes);
+ for (int i = 0; i < propertiesBeans.size(); i++)
+ {
+ IPropertiesBean propertiesBean = propertiesBeans.get(i);
+ IEntityProperty[] properties = propertiesBean.getProperties();
+ List<IEntityProperty> newProperties = new ArrayList<IEntityProperty>();
+ Map<String, Map<String, String>> subColumnBindings =
+ createColumnBindingsMap(properties);
+ for (Entry<String, Map<String, String>> entry : subColumnBindings.entrySet())
+ {
+ String code = entry.getKey();
+ Map<String, String> bindings = entry.getValue();
+ ManagedPropertyEvaluator evaluator = evaluators.get(code);
+ EntityProperty entityProperty = new EntityProperty();
+ PropertyType propertyType = new PropertyType();
+ propertyType.setCode(code);
+ propertyType.setDataType(new DataType(DataTypeCode.VARCHAR));
+ entityProperty.setPropertyType(propertyType);
+ if (evaluator == null)
+ {
+ entityProperty.setValue(bindings.get(""));
+ } else
+ {
+ try
+ {
+ String result = evaluator.updateFromBatchInput(bindings);
+ entityProperty.setValue(result);
+ } catch (EvaluatorException ex)
+ {
+ Throwable cause = ex.getCause();
+ if (cause instanceof ValidationException)
+ {
+ throw new ValidationException("Error in row " + (i + 1) + ": "
+ + cause.getMessage());
+ }
+ entityProperty.setValue(BasicConstant.ERROR_PROPERTY_PREFIX
+ + ex.getMessage());
+ }
+ }
+ newProperties.add(entityProperty);
+ }
+ propertiesBean.setProperties(newProperties.toArray(new IEntityProperty[newProperties
+ .size()]));
+ }
+ }
+
+ private Map<String, Map<String, String>> createColumnBindingsMap(IEntityProperty[] properties)
+ {
+ Map<String, Map<String, String>> subColumnBindings =
+ new HashMap<String, Map<String, String>>();
+ for (IEntityProperty property : properties)
+ {
+ String code = property.getPropertyType().getCode().toUpperCase();
+ int indexOfColon = code.indexOf(':');
+ String propertyCode = code;
+ String subColumn = "";
+ if (indexOfColon >= 0)
+ {
+ propertyCode = code.substring(0, indexOfColon);
+ subColumn = code.substring(indexOfColon + 1);
+ }
+ Map<String, String> bindings = subColumnBindings.get(propertyCode);
+ if (bindings == null)
+ {
+ bindings = new HashMap<String, String>();
+ subColumnBindings.put(propertyCode, bindings);
+ }
+ bindings.put(subColumn, property.getValue());
+ }
+ return subColumnBindings;
+ }
+
+ private Map<String, ManagedPropertyEvaluator> createEvaluators(
+ Set<? extends EntityTypePropertyTypePE> entityTypePropertyTypes)
+ {
+ Map<String, ManagedPropertyEvaluator> evaluators =
+ new HashMap<String, ManagedPropertyEvaluator>();
+ for (EntityTypePropertyTypePE entityTypePropertyType : entityTypePropertyTypes)
+ {
+ if (entityTypePropertyType.isManaged())
+ {
+ String propertyTypeCode = entityTypePropertyType.getPropertyType().getCode();
+ ScriptPE script = entityTypePropertyType.getScript();
+ evaluators.put(propertyTypeCode, new ManagedPropertyEvaluator(script.getScript()));
+ }
+ }
+ return evaluators;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/QueryServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/QueryServer.java
index 9746b81e8e25229f577be5c3b21d4ef532d5bdbb..9ab7ab75cb70f9871fea5fd0bcac1d8ca8762da3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/QueryServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/server/QueryServer.java
@@ -44,6 +44,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.QueryType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.QueryPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.plugin.generic.server.IPropertiesBatchManager;
import ch.systemsx.cisd.openbis.plugin.query.shared.DatabaseDefinition;
import ch.systemsx.cisd.openbis.plugin.query.shared.IQueryDatabaseDefinitionProvider;
import ch.systemsx.cisd.openbis.plugin.query.shared.IQueryServer;
@@ -79,11 +80,13 @@ public class QueryServer extends AbstractServer<IQueryServer> implements IQueryS
@Private
QueryServer(final ISessionManager<Session> sessionManager, final IDAOFactory daoFactory,
+ IPropertiesBatchManager propertiesBatchManager,
final ISampleTypeSlaveServerPlugin sampleTypeSlaveServerPlugin,
final IDataSetTypeSlaveServerPlugin dataSetTypeSlaveServerPlugin,
IQueryDatabaseDefinitionProvider dbDefinitionProvider)
{
- super(sessionManager, daoFactory, sampleTypeSlaveServerPlugin, dataSetTypeSlaveServerPlugin);
+ super(sessionManager, daoFactory, propertiesBatchManager, sampleTypeSlaveServerPlugin,
+ dataSetTypeSlaveServerPlugin);
this.dbDefinitionProvider = dbDefinitionProvider;
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
index 26a4a4bfe4e015404512d95cda586ab781f05604..a66aed46d1488f3d6c0e4a84ddfe722236372ee9 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
@@ -114,7 +114,8 @@ public final class CommonServerTest extends AbstractServerTestCase
{
CommonServer server =
new CommonServer(authenticationService, sessionManager, daoFactory,
- commonBusinessObjectFactory, new LastModificationState());
+ propertiesBatchManager, commonBusinessObjectFactory,
+ new LastModificationState());
server.setSampleTypeSlaveServerPlugin(sampleTypeSlaveServerPlugin);
server.setDataSetTypeSlaveServerPlugin(dataSetTypeSlaveServerPlugin);
server.setBaseIndexURL(SESSION_TOKEN, BASE_INDEX_URL);
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java
index 719799a8264644079325bc993ae0ec9468d3b87b..c37197ed752b775912f155dcf51340de59c10945 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java
@@ -899,8 +899,8 @@ public class ETLServiceTest extends AbstractServerTestCase
private IETLLIMSService createService()
{
- return new ETLService(authenticationService, sessionManager, daoFactory, boFactory,
- dssfactory);
+ return new ETLService(authenticationService, sessionManager, daoFactory,
+ propertiesBatchManager, boFactory, dssfactory);
}
private DataStoreServerInfo createDSSInfo()
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceTest.java
index d3cac9d9e0b6874a405a49022329c3c9585866fe..8af35e94c7bf6fe41ffa94b89f948fe7ad0778a0 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceTest.java
@@ -76,7 +76,9 @@ public class GeneralInformationServiceTest extends AbstractServerTestCase
{
super.setUp();
commonServer = context.mock(ICommonServer.class);
- service = new GeneralInformationService(sessionManager, daoFactory, commonServer);
+ service =
+ new GeneralInformationService(sessionManager, daoFactory, propertiesBatchManager,
+ commonServer);
}
@Test
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
index f9d9330a22cc01fddf03ea242cb2eadc6a34ae5a..368e80c69d8a11876f9c6cfa60a3039cb380cb23 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
@@ -58,7 +58,6 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IFileFormatTypeDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISpaceDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IPersonDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProjectDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IPropertyTypeDAO;
@@ -66,6 +65,7 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IQueryDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IRoleAssignmentDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleTypeDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISpaceDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IVocabularyDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.IPermIdDAO;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DisplaySettings;
@@ -73,10 +73,11 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
+import ch.systemsx.cisd.openbis.plugin.generic.server.IPropertiesBatchManager;
/**
* An <i>abstract</i> test infrastructure for {@link IServer} implementations.
@@ -175,6 +176,8 @@ public abstract class AbstractServerTestCase extends AssertJUnit
protected IDynamicPropertyEvaluationScheduler evaluator;
+ protected IPropertiesBatchManager propertiesBatchManager;
+
@BeforeMethod
@SuppressWarnings("unchecked")
public void setUp()
@@ -184,6 +187,7 @@ public abstract class AbstractServerTestCase extends AssertJUnit
context = new Mockery();
authenticationService = context.mock(IAuthenticationService.class);
sessionManager = context.mock(ISessionManager.class);
+ propertiesBatchManager = context.mock(IPropertiesBatchManager.class);
// DAO
daoFactory = context.mock(IDAOFactory.class);
databaseInstanceDAO = context.mock(IDatabaseInstanceDAO.class);
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/demo/server/DemoServerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/demo/server/DemoServerTest.java
index 251703464e207502573b0f5073df07663de3d7cc..58f5355984408da91e869b6da05ea74b269d623d 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/demo/server/DemoServerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/demo/server/DemoServerTest.java
@@ -23,6 +23,7 @@ import ch.systemsx.cisd.openbis.generic.server.plugin.IDataSetTypeSlaveServerPlu
import ch.systemsx.cisd.openbis.generic.server.plugin.ISampleTypeSlaveServerPlugin;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
import ch.systemsx.cisd.openbis.plugin.demo.shared.IDemoServer;
+import ch.systemsx.cisd.openbis.plugin.generic.server.IPropertiesBatchManager;
/**
* Test cases for corresponding {@link DemoServer} class.
@@ -38,11 +39,14 @@ public final class DemoServerTest extends AbstractServerTestCase
private IDataSetTypeSlaveServerPlugin dataSetTypeSlaveServerPlugin;
+ private IPropertiesBatchManager propertiesBatchManager;
+
@SuppressWarnings("unused")
private final IDemoServer createServer()
{
- return new DemoServer(sessionManager, daoFactory, demoBusinessObjectFactory,
- sampleTypeSlaveServerPlugin, dataSetTypeSlaveServerPlugin);
+ return new DemoServer(sessionManager, daoFactory, propertiesBatchManager,
+ demoBusinessObjectFactory, sampleTypeSlaveServerPlugin,
+ dataSetTypeSlaveServerPlugin);
}
//
@@ -57,5 +61,7 @@ public final class DemoServerTest extends AbstractServerTestCase
sampleTypeSlaveServerPlugin = context.mock(ISampleTypeSlaveServerPlugin.class);
demoBusinessObjectFactory = context.mock(IDemoBusinessObjectFactory.class);
dataSetTypeSlaveServerPlugin = context.mock(IDataSetTypeSlaveServerPlugin.class);
+ propertiesBatchManager = context.mock(IPropertiesBatchManager.class);
+
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java
index 356a37d1dc94882c6292f87e819f9cc2f2d1bfcf..522eabd5cc2fb1bdb50e66402d954ebef02d893b 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java
@@ -110,8 +110,9 @@ public final class GenericServerTest extends AbstractServerTestCase
private final IGenericServer createServer()
{
GenericServer genericServer =
- new GenericServer(sessionManager, daoFactory, genericBusinessObjectFactory,
- sampleTypeSlaveServerPlugin, dataSetTypeSlaveServerPlugin);
+ new GenericServer(sessionManager, daoFactory, propertiesBatchManager,
+ genericBusinessObjectFactory, sampleTypeSlaveServerPlugin,
+ dataSetTypeSlaveServerPlugin);
genericServer.commonServer = commonServer;
return genericServer;
}
@@ -248,7 +249,15 @@ public final class GenericServerTest extends AbstractServerTestCase
newSamples.add(createNewSample("same"));
newSamples.add(createNewSample("same"));
List<NewSamplesWithTypes> samplesWithTypes = new ArrayList<NewSamplesWithTypes>();
- samplesWithTypes.add(new NewSamplesWithTypes(new SampleType(), newSamples));
+ final NewSamplesWithTypes newSamplesWithType = new NewSamplesWithTypes(new SampleType(), newSamples);
+ samplesWithTypes.add(newSamplesWithType);
+ context.checking(new Expectations()
+ {
+ {
+ one(propertiesBatchManager).manageProperties(newSamplesWithType);
+ }
+ });
+
try
{
server.registerSamples(SESSION_TOKEN, samplesWithTypes);
@@ -271,7 +280,8 @@ public final class GenericServerTest extends AbstractServerTestCase
newSamples.add(createNewSample("one"));
newSamples.add(createNewSample("two"));
List<NewSamplesWithTypes> samplesWithTypes = new ArrayList<NewSamplesWithTypes>();
- samplesWithTypes.add(new NewSamplesWithTypes(sampleType, newSamples));
+ final NewSamplesWithTypes newSamplesWithType = new NewSamplesWithTypes(sampleType, newSamples);
+ samplesWithTypes.add(newSamplesWithType);
context.checking(new Expectations()
{
{
@@ -279,6 +289,8 @@ public final class GenericServerTest extends AbstractServerTestCase
will(returnValue(sampleTypePE));
one(sampleTypeSlaveServerPlugin).registerSamples(SESSION, newSamples, null);
+
+ one(propertiesBatchManager).manageProperties(newSamplesWithType);
}
});
createServer().registerOrUpdateSamples(SESSION_TOKEN, samplesWithTypes);
@@ -296,7 +308,9 @@ public final class GenericServerTest extends AbstractServerTestCase
newSamples.add(createNewSample("one"));
newSamples.add(createNewSample("two"));
List<NewSamplesWithTypes> samplesWithTypes = new ArrayList<NewSamplesWithTypes>();
- samplesWithTypes.add(new NewSamplesWithTypes(sampleType, newSamples));
+ final NewSamplesWithTypes newSamplesWithType =
+ new NewSamplesWithTypes(sampleType, newSamples);
+ samplesWithTypes.add(newSamplesWithType);
context.checking(new Expectations()
{
{
@@ -304,6 +318,8 @@ public final class GenericServerTest extends AbstractServerTestCase
will(returnValue(sampleTypePE));
one(sampleTypeSlaveServerPlugin).registerSamples(SESSION, newSamples, null);
+
+ one(propertiesBatchManager).manageProperties(newSamplesWithType);
}
});
createServer().registerSamples(SESSION_TOKEN, samplesWithTypes);
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/query/server/QueryServerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/query/server/QueryServerTest.java
index 1eba9fd9dbbc6142f43c8f18daba466414727190..782d7066c7f859de3b20ae045b950009d9f29d58 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/query/server/QueryServerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/query/server/QueryServerTest.java
@@ -62,8 +62,8 @@ public final class QueryServerTest extends AbstractServerTestCase
private final IQueryServer createServer()
{
- return new QueryServer(sessionManager, daoFactory, sampleTypeSlaveServerPlugin,
- dataSetTypeSlaveServerPlugin, dbDefinitionProvider);
+ return new QueryServer(sessionManager, daoFactory, propertiesBatchManager,
+ sampleTypeSlaveServerPlugin, dataSetTypeSlaveServerPlugin, dbDefinitionProvider);
}
//
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
index 8caa9faee0aaa00b39d5256e805c43bfdb608ce5..ebfcb25bec61cc023c83bc84ce9f8d5a99f47927 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
@@ -39,6 +39,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyPE;
import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTranslator;
+import ch.systemsx.cisd.openbis.plugin.generic.server.IPropertiesBatchManager;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.AccessionNumberBuilder;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IAbundanceColumnDefinitionTable;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IBusinessObjectFactory;
@@ -83,11 +84,13 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
@Private
PhosphoNetXServer(ISessionManager<Session> sessionManager, IDAOFactory daoFactory,
+ IPropertiesBatchManager propertiesBatchManager,
IPhosphoNetXDAOFactory specificDAOFactory, IBusinessObjectFactory specificBOFactory,
ISampleTypeSlaveServerPlugin sampleTypeSlaveServerPlugin,
IDataSetTypeSlaveServerPlugin dataSetTypeSlaveServerPlugin)
{
- super(sessionManager, daoFactory, sampleTypeSlaveServerPlugin, dataSetTypeSlaveServerPlugin);
+ super(sessionManager, daoFactory, propertiesBatchManager, sampleTypeSlaveServerPlugin,
+ dataSetTypeSlaveServerPlugin);
this.specificDAOFactory = specificDAOFactory;
this.specificBOFactory = specificBOFactory;
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java
index ba4b3efca6417b3e337360f41887983a1d9c8130..5673cf414a7bb47b4996d2480931c0078767a7fc 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java
@@ -52,6 +52,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
+import ch.systemsx.cisd.openbis.plugin.generic.server.IPropertiesBatchManager;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.ExperimentLoader;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IBusinessObjectFactory;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.ISampleLoader;
@@ -94,7 +95,14 @@ public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDat
public ProteomicsDataServiceInternal(ISessionManager<Session> sessionManager, IDAOFactory daoFactory,
ICommonBusinessObjectFactory businessObjectFactory, IBusinessObjectFactory boFactory)
{
- super(sessionManager, daoFactory);
+ this(sessionManager, daoFactory, null, businessObjectFactory, boFactory);
+ }
+
+ ProteomicsDataServiceInternal(ISessionManager<Session> sessionManager, IDAOFactory daoFactory,
+ IPropertiesBatchManager propertiesBatchManager,
+ ICommonBusinessObjectFactory businessObjectFactory, IBusinessObjectFactory boFactory)
+ {
+ super(sessionManager, daoFactory, propertiesBatchManager);
sessionManagerFromConstructor = sessionManager;
this.commonBoFactory = businessObjectFactory;
this.boFactory = boFactory;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java
index b69fbe54a8c02410bb05fb347353d11ec5eca508..24707207de229d0a9fac3480333169a945310e8b 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java
@@ -48,6 +48,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
import ch.systemsx.cisd.openbis.generic.shared.util.DataTypeUtils;
+import ch.systemsx.cisd.openbis.plugin.generic.server.IPropertiesBatchManager;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IProteomicsDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IProteomicsDataService;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.DataSet;
@@ -75,9 +76,10 @@ public class ProteomicsDataService extends AbstractServer<IProteomicsDataService
}
public ProteomicsDataService(final ISessionManager<Session> sessionManager,
- final IDAOFactory daoFactory, IProteomicsDataServiceInternal service)
+ final IDAOFactory daoFactory, IPropertiesBatchManager propertiesBatchManager,
+ IProteomicsDataServiceInternal service)
{
- super(sessionManager, daoFactory);
+ super(sessionManager, daoFactory, propertiesBatchManager);
this.service = service;
}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerTest.java
index 32ea695b4701ccd59d81d3d55179dc0ab7276459..b1f8fdd9ec3fce46c88c7a96f27be125bc1b5045 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerTest.java
@@ -69,8 +69,9 @@ public class PhosphoNetXServerTest extends AbstractServerTestCase
abundanceColumnDefinitionTable = context.mock(IAbundanceColumnDefinitionTable.class);
sampleProvider = context.mock(ISampleProvider.class);
server =
- new PhosphoNetXServer(sessionManager, daoFactory, phosphoNetXDAOFactory, boFactory,
- sampleTypeSlaveServerPlugin, dataSetTypeSlaveServerPlugin);
+ new PhosphoNetXServer(sessionManager, daoFactory, propertiesBatchManager,
+ phosphoNetXDAOFactory, boFactory, sampleTypeSlaveServerPlugin,
+ dataSetTypeSlaveServerPlugin);
context.checking(new Expectations()
{
{
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java
index 746a449c2cc7b76f4b972bc34f1a4ecd91254b1d..b8f168f569e8b7a3f8dd24697cce3280495affc8 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java
@@ -94,7 +94,9 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
commonBoFactory = context.mock(ICommonBusinessObjectFactory.class);
boFactory = context.mock(IBusinessObjectFactory.class);
sampleLoader = context.mock(ISampleLoader.class);
- service = new ProteomicsDataServiceInternal(sessionManager, daoFactory, commonBoFactory, boFactory);
+ service =
+ new ProteomicsDataServiceInternal(sessionManager, daoFactory,
+ propertiesBatchManager, commonBoFactory, boFactory);
experimentType = new ExperimentTypePE();
experimentType.setCode(EXPERIMENT_TYPE);
experimentType.setDatabaseInstance(CommonTestUtils.createHomeDatabaseInstance());
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceTest.java
index 8400078039096c118ecb39c71168e11c91b20a58..fd3133c5def4172f4a04e4ec33d014f4fe3e22bf 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceTest.java
@@ -80,7 +80,9 @@ public class ProteomicsDataServiceTest extends AbstractServerTestCase
{
super.setUp();
internalService = context.mock(IProteomicsDataServiceInternal.class);
- service = new ProteomicsDataService(sessionManager, daoFactory, internalService);
+ service =
+ new ProteomicsDataService(sessionManager, daoFactory, propertiesBatchManager,
+ internalService);
session2 = new SessionContextDTO();
session2.setSessionToken(SESSION_TOKEN + "2");
}
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 00fb39aa2220a66ec76fb3dd1b36780691e801b4..94d68c2e9e290e8e6e0cf7723493edd60c3eeca5 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
@@ -62,6 +62,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyPE;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTranslator;
+import ch.systemsx.cisd.openbis.plugin.generic.server.IPropertiesBatchManager;
import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQuery;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.PlateContentLoader;
@@ -124,11 +125,13 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
@Private
ScreeningServer(final ISessionManager<Session> sessionManager, final IDAOFactory daoFactory,
+ IPropertiesBatchManager propertiesBatchManager,
final IScreeningBusinessObjectFactory businessObjectFactory,
final ISampleTypeSlaveServerPlugin sampleTypeSlaveServerPlugin,
final IDataSetTypeSlaveServerPlugin dataSetTypeSlaveServerPlugin)
{
- super(sessionManager, daoFactory, sampleTypeSlaveServerPlugin, dataSetTypeSlaveServerPlugin);
+ super(sessionManager, daoFactory, propertiesBatchManager, sampleTypeSlaveServerPlugin,
+ dataSetTypeSlaveServerPlugin);
this.businessObjectFactory = businessObjectFactory;
}