diff --git a/openbis/.classpath b/openbis/.classpath
index 704866c1ac9eba2501106eecde9a8b8715d70b76..0255cd3acbeb0a58e5100f4462992c9cd844e7f0 100644
--- a/openbis/.classpath
+++ b/openbis/.classpath
@@ -81,5 +81,6 @@
<classpathentry kind="lib" path="/libraries/poi/poi.jar"/>
<classpathentry kind="lib" path="/libraries/jetty7/lib/server/jetty-deploy.jar"/>
<classpathentry kind="lib" path="/libraries/jetty7/lib/server/jetty-webapp.jar"/>
+ <classpathentry kind="lib" path="/libraries/lucene-queries/lucene-queries.jar"/>
<classpathentry kind="output" path="targets/www/WEB-INF/classes"/>
</classpath>
diff --git a/openbis/build/build.xml b/openbis/build/build.xml
index aa416782eecefb611b46a8922f98e8bed21056d3..71b0f6c22cb72cd8eeddf7a08d509b677c5d8786 100644
--- a/openbis/build/build.xml
+++ b/openbis/build/build.xml
@@ -528,7 +528,10 @@
<fileset dir="${lib}/lucene-memory">
<include name="lucene-memory.jar" />
</fileset>
- <fileset dir="${lib}/cisd-args4j">
+ <fileset dir="${lib}/lucene-queries">
+ <include name="lucene-queries.jar" />
+ </fileset>
+ <fileset dir="${lib}/cisd-args4j">
<include name="cisd-args4j.jar" />
</fileset>
<fileset dir="${lib}/jython">
@@ -844,7 +847,10 @@
<lib dir="${lib}/lucene-memory">
<include name="lucene-memory.jar" />
</lib>
- <lib dir="${lib}/cisd-args4j">
+ <lib dir="${lib}/lucene-queries">
+ <include name="lucene-queries.jar" />
+ </lib>
+ <lib dir="${lib}/cisd-args4j">
<include name="cisd-args4j.jar" />
</lib>
<lib dir="${lib}/jython">
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 42fa141801690c5e6025ca22e66e56678e389ff4..e5f348f411f462123ab37c65da669aecbc6f144e 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
@@ -3190,7 +3190,9 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
DynamicPropertyCalculator.create(info.getScript());
IDynamicPropertyEvaluator evaluator =
new DynamicPropertyEvaluator(getDAOFactory(), null);
- IEntityAdaptor adaptor = EntityAdaptorFactory.create(entity, evaluator);
+ IEntityAdaptor adaptor =
+ EntityAdaptorFactory.create(entity, evaluator, getDAOFactory()
+ .getSessionFactory().getCurrentSession());
calculator.setEntity(adaptor);
return calculator.evalAsString();
} catch (Throwable e)
@@ -3228,7 +3230,9 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
});
IDynamicPropertyEvaluator evaluator =
new DynamicPropertyEvaluator(getDAOFactory(), null);
- IEntityAdaptor adaptor = EntityAdaptorFactory.create(entity, evaluator);
+ IEntityAdaptor adaptor =
+ EntityAdaptorFactory.create(entity, evaluator, getDAOFactory()
+ .getSessionFactory().getCurrentSession());
calculator.setEntity(adaptor);
calculator.setIsNewEntity(info.isNew());
String result = calculator.evalAsString();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityValidationInterceptor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityValidationInterceptor.java
index 413004a24b5857f887421fee2d01b26aaaed191a..98e725942c90394053e7c6fdc404c1ee91e38b4d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityValidationInterceptor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityValidationInterceptor.java
@@ -27,9 +27,9 @@ import org.hibernate.Interceptor;
import org.hibernate.Transaction;
import org.hibernate.type.Type;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.common.conversation.context.ServiceConversationsThreadContext;
import ch.systemsx.cisd.openbis.common.conversation.progress.IServiceConversationProgressListener;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.DynamicPropertyEvaluator;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.IDynamicPropertyEvaluator;
@@ -253,7 +253,9 @@ public class EntityValidationInterceptor extends EmptyInterceptor implements
EntityValidationCalculator calculator =
EntityValidationCalculator.create(script.getScript(), this);
IDynamicPropertyEvaluator evaluator = new DynamicPropertyEvaluator(daoFactory, null);
- IEntityAdaptor adaptor = EntityAdaptorFactory.create(entity, evaluator);
+ IEntityAdaptor adaptor =
+ EntityAdaptorFactory.create(entity, evaluator, daoFactory.getSessionFactory()
+ .getCurrentSession());
calculator.setEntity(adaptor);
calculator.setIsNewEntity(isNewEntity);
return calculator.evalAsString();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/DefaultBatchDynamicPropertyEvaluator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/DefaultBatchDynamicPropertyEvaluator.java
index 3004dd5f587f66e0b55f47e9bc6960ae1d4ddd2b..b415001a1df42a6fe4da3e27c248a7240e0b4860 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/DefaultBatchDynamicPropertyEvaluator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/DefaultBatchDynamicPropertyEvaluator.java
@@ -213,7 +213,7 @@ final class DefaultBatchDynamicPropertyEvaluator implements IBatchDynamicPropert
{
for (T entity : entities)
{
- evaluator.evaluateProperties(entity);
+ evaluator.evaluateProperties(entity, session);
}
session.flush();
session.clear();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/DynamicPropertyEvaluator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/DynamicPropertyEvaluator.java
index 8917897b6e8868266d24da2ec27304883b4081e0..eeeb998892acb260452e93e5a9b39264c6a750b6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/DynamicPropertyEvaluator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/DynamicPropertyEvaluator.java
@@ -24,6 +24,7 @@ import java.util.Map;
import java.util.Set;
import org.apache.log4j.Logger;
+import org.hibernate.Session;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
@@ -92,14 +93,16 @@ public class DynamicPropertyEvaluator implements IDynamicPropertyEvaluator
}
@Override
- public <T extends IEntityInformationWithPropertiesHolder> void evaluateProperties(T entity)
+ public <T extends IEntityInformationWithPropertiesHolder> void evaluateProperties(T entity,
+ Session session)
{
if (operationLog.isDebugEnabled())
{
operationLog.debug(String.format("Evaluating dynamic properties of entity '%s'.",
entity));
}
- final IEntityAdaptor entityAdaptor = EntityAdaptorFactory.create(entity, this);
+ final IEntityAdaptor entityAdaptor =
+ EntityAdaptorFactory.create(entity, this, session);
Set<EntityPropertyPE> propertiesToRemove = new HashSet<EntityPropertyPE>();
for (EntityPropertyPE property : entity.getProperties())
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/IDynamicPropertyEvaluator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/IDynamicPropertyEvaluator.java
index 8496c56e67f692fbcc028642e32c3b07ff620617..a86739cf558003f913a9706676d218a2550952f4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/IDynamicPropertyEvaluator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/IDynamicPropertyEvaluator.java
@@ -18,6 +18,8 @@ package ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property;
import java.util.List;
+import org.hibernate.Session;
+
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.calculator.api.IEntityAdaptor;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityInformationWithPropertiesHolder;
@@ -34,7 +36,8 @@ public interface IDynamicPropertyEvaluator
* Evaluates all dynamic properties of specified entity. Replaces placeholders with evaluated
* values.
*/
- public <T extends IEntityInformationWithPropertiesHolder> void evaluateProperties(T entity);
+ public <T extends IEntityInformationWithPropertiesHolder> void evaluateProperties(T entity,
+ Session session);
/**
* Evaluates value of specified dynamic property on specified entity.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/AbstractEntityAdaptor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/AbstractEntityAdaptor.java
index ce02a66c0b05c0cadeffad758d7686d1b16acdce..c4ef867c9bb8dc00ed0cb5cc00de59594c4a79fb 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/AbstractEntityAdaptor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/AbstractEntityAdaptor.java
@@ -20,6 +20,19 @@ import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
+import org.apache.lucene.index.Term;
+import org.apache.lucene.search.BooleanClause;
+import org.apache.lucene.search.BooleanQuery;
+import org.apache.lucene.search.Query;
+import org.apache.lucene.search.regex.RegexQuery;
+import org.hibernate.ScrollMode;
+import org.hibernate.ScrollableResults;
+import org.hibernate.Session;
+import org.hibernate.search.FullTextQuery;
+import org.hibernate.search.FullTextSession;
+import org.hibernate.search.Search;
+
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.search.LuceneQueryBuilder;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.IDynamicPropertyEvaluator;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.calculator.api.IEntityAdaptor;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.calculator.api.IEntityPropertyAdaptor;
@@ -29,6 +42,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityPropertiesHolder;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.hibernate.SearchFieldConstants;
/**
* Abstract {@link IEntityAdaptor} implementation.
@@ -44,6 +58,9 @@ public class AbstractEntityAdaptor implements IEntityAdaptor
protected final IDynamicPropertyEvaluator evaluator;
+ protected static String ENTITY_TYPE_CODE_FIELD = SearchFieldConstants.PREFIX_ENTITY_TYPE
+ + SearchFieldConstants.CODE;
+
public AbstractEntityAdaptor(String code)
{
this(code, null);
@@ -135,4 +152,32 @@ public class AbstractEntityAdaptor implements IEntityAdaptor
return propertiesByCode.values();
}
+ protected Query regexpConstraint(String field, String value)
+ {
+ return new RegexQuery(new Term(field, value.toLowerCase()));
+ }
+
+ protected Query constraint(String field, String value)
+ {
+ return LuceneQueryBuilder.parseQuery(field, value, LuceneQueryBuilder
+ .createSearchAnalyzer());
+ }
+
+ protected Query and(Query... queries)
+ {
+ BooleanQuery query = new BooleanQuery();
+ for (Query subquery : queries)
+ {
+ query.add(subquery, BooleanClause.Occur.MUST);
+ }
+ return query;
+ }
+
+ protected ScrollableResults execute(Query query, Class<?> resultClass, Session session)
+ {
+ FullTextSession fullTextSession = Search.getFullTextSession(session);
+ FullTextQuery ftQuery = fullTextSession.createFullTextQuery(query, resultClass);
+ ftQuery.setFetchSize(10);
+ return ftQuery.scroll(ScrollMode.FORWARD_ONLY);
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/EntityAdaptorFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/EntityAdaptorFactory.java
index aab59e2b4c0477d7bed363fb4aa231e35d89c92a..d09040484d3b46880ea36a953416771af950d2e7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/EntityAdaptorFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/EntityAdaptorFactory.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.calculator;
+import org.hibernate.Session;
+
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.IDynamicPropertyEvaluator;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.calculator.api.IDataAdaptor;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.calculator.api.IEntityAdaptor;
@@ -35,19 +37,23 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
*/
public class EntityAdaptorFactory
{
- /** Returns an adaptor for specified entity based on its kind. */
+ /**
+ * Returns an adaptor for specified entity based on its kind.
+ *
+ * @param session
+ */
public static IEntityAdaptor create(IEntityInformationWithPropertiesHolder entity,
- IDynamicPropertyEvaluator evaluator)
+ IDynamicPropertyEvaluator evaluator, Session session)
{
switch (entity.getEntityKind())
{
case SAMPLE:
- return new SampleAdaptor((SamplePE) entity, evaluator);
+ return new SampleAdaptor((SamplePE) entity, evaluator, session);
case EXPERIMENT:
- return new ExperimentAdaptor((ExperimentPE) entity, evaluator);
+ return new ExperimentAdaptor((ExperimentPE) entity, evaluator, session);
case DATA_SET:
- return new ExternalDataAdaptor((DataPE) entity, evaluator);
+ return new ExternalDataAdaptor((DataPE) entity, evaluator, session);
case MATERIAL:
return new MaterialAdaptor((MaterialPE) entity, evaluator);
default:
@@ -55,19 +61,22 @@ public class EntityAdaptorFactory
}
}
- public static IExperimentAdaptor create(ExperimentPE entity, IDynamicPropertyEvaluator evaluator)
+ public static IExperimentAdaptor create(ExperimentPE entity,
+ IDynamicPropertyEvaluator evaluator, Session session)
{
- return new ExperimentAdaptor(entity, evaluator);
+ return new ExperimentAdaptor(entity, evaluator, session);
}
- public static ISampleAdaptor create(SamplePE entity, IDynamicPropertyEvaluator evaluator)
+ public static ISampleAdaptor create(SamplePE entity, IDynamicPropertyEvaluator evaluator,
+ Session session)
{
- return new SampleAdaptor(entity, evaluator);
+ return new SampleAdaptor(entity, evaluator, session);
}
- public static IDataAdaptor create(DataPE entity, IDynamicPropertyEvaluator evaluator)
+ public static IDataAdaptor create(DataPE entity, IDynamicPropertyEvaluator evaluator,
+ Session session)
{
- return new ExternalDataAdaptor(entity, evaluator);
+ return new ExternalDataAdaptor(entity, evaluator, session);
}
public static IMaterialAdaptor create(MaterialPE entity, IDynamicPropertyEvaluator evaluator)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/EntityAdaptorIterator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/EntityAdaptorIterator.java
new file mode 100644
index 0000000000000000000000000000000000000000..da660755ec5c197d8ec509cd82f6a0616d943cfa
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/EntityAdaptorIterator.java
@@ -0,0 +1,61 @@
+/*
+ * Copyright 2012 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.server.dataaccess.dynamic_property.calculator;
+
+import org.hibernate.ScrollableResults;
+import org.hibernate.Session;
+
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.IDynamicPropertyEvaluator;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+
+/**
+ * @author anttil
+ */
+public class EntityAdaptorIterator<T> extends ScrollableResultsIterator<T>
+{
+
+ private final IDynamicPropertyEvaluator evaluator;
+
+ private final Session session;
+
+ public EntityAdaptorIterator(ScrollableResults scroll, IDynamicPropertyEvaluator evaluator,
+ Session session)
+ {
+ super(scroll);
+ this.evaluator = evaluator;
+ this.session = session;
+
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public T parseValue(Object[] result)
+ {
+ Object o = result[0];
+ if (o instanceof SamplePE)
+ {
+ return (T) EntityAdaptorFactory.create((SamplePE) o, evaluator, session);
+ } else if (o instanceof DataPE)
+ {
+ return (T) EntityAdaptorFactory.create((DataPE) o, evaluator, session);
+ } else
+ {
+ throw new IllegalStateException("Unknown result type: " + o);
+ }
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/ExperimentAdaptor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/ExperimentAdaptor.java
index 915b42996f109b4575c6d33cdbb178f77f474bc5..7da2d2852505009edb7b3cdf3d0d77759fc4d094 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/ExperimentAdaptor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/ExperimentAdaptor.java
@@ -16,8 +16,9 @@
package ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.calculator;
-import java.util.ArrayList;
-import java.util.List;
+import org.apache.lucene.search.Query;
+import org.hibernate.ScrollableResults;
+import org.hibernate.Session;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.IDynamicPropertyEvaluator;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.calculator.api.IDataAdaptor;
@@ -27,6 +28,7 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.calcu
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.hibernate.SearchFieldConstants;
/**
* {@link IEntityAdaptor} implementation for {@link ExperimentPE}.
@@ -38,9 +40,13 @@ public class ExperimentAdaptor extends AbstractEntityAdaptor implements IExperim
{
private final ExperimentPE experimentPE;
- public ExperimentAdaptor(ExperimentPE experimentPE, IDynamicPropertyEvaluator evaluator)
+ private final Session session;
+
+ public ExperimentAdaptor(ExperimentPE experimentPE, IDynamicPropertyEvaluator evaluator,
+ Session session)
{
super(experimentPE.getCode(), evaluator);
+ this.session = session;
initProperties(experimentPE);
this.experimentPE = experimentPE;
}
@@ -57,25 +63,40 @@ public class ExperimentAdaptor extends AbstractEntityAdaptor implements IExperim
}
@Override
- public List<ISampleAdaptor> samples()
+ public Iterable<ISampleAdaptor> samples()
+ {
+ return samplesOfType(".*");
+ }
+
+ @Override
+ public Iterable<ISampleAdaptor> samplesOfType(String typeRegexp)
{
- List<ISampleAdaptor> list = new ArrayList<ISampleAdaptor>();
- for (SamplePE sample : experimentPE.getSamples())
- {
- list.add(EntityAdaptorFactory.create(sample, evaluator));
- }
- return list;
+ Query typeConstraint =
+ regexpConstraint(ENTITY_TYPE_CODE_FIELD, typeRegexp.toLowerCase());
+ Query experimentCodeConstraint =
+ constraint(SearchFieldConstants.EXPERIMENT_ID, Long.toString(experimentPE.getId()));
+ Query query = and(typeConstraint, experimentCodeConstraint);
+
+ ScrollableResults results = execute(query, SamplePE.class, session);
+ return new EntityAdaptorIterator<ISampleAdaptor>(results, evaluator, session);
}
@Override
- public List<IDataAdaptor> dataSets()
+ public Iterable<IDataAdaptor> dataSets()
{
- List<IDataAdaptor> list = new ArrayList<IDataAdaptor>();
- for (DataPE dataset : experimentPE.getDataSets())
- {
- list.add(EntityAdaptorFactory.create(dataset, evaluator));
- }
- return list;
+ return dataSetsOfType(".*");
}
+ @Override
+ public Iterable<IDataAdaptor> dataSetsOfType(String typeRegexp)
+ {
+ Query typeConstraint =
+ regexpConstraint(ENTITY_TYPE_CODE_FIELD, typeRegexp.toLowerCase());
+ Query experimentCodeConstraint =
+ constraint(SearchFieldConstants.EXPERIMENT_ID, Long.toString(experimentPE.getId()));
+ Query query = and(typeConstraint, experimentCodeConstraint);
+
+ ScrollableResults results = execute(query, DataPE.class, session);
+ return new EntityAdaptorIterator<IDataAdaptor>(results, evaluator, session);
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/ExternalDataAdaptor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/ExternalDataAdaptor.java
index 693bde2062ce6438d51be41f8a6a846cb6f5f3ea..c63475b6db0cc788c38704f6c2479bba57c96cd9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/ExternalDataAdaptor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/ExternalDataAdaptor.java
@@ -19,6 +19,8 @@ package ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.calc
import java.util.ArrayList;
import java.util.List;
+import org.hibernate.Session;
+
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.IDynamicPropertyEvaluator;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.calculator.api.IDataAdaptor;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.calculator.api.IEntityAdaptor;
@@ -37,9 +39,13 @@ public class ExternalDataAdaptor extends AbstractEntityAdaptor implements IDataA
{
private final DataPE externalDataPE;
- public ExternalDataAdaptor(DataPE externalDataPE, IDynamicPropertyEvaluator evaluator)
+ private final Session session;
+
+ public ExternalDataAdaptor(DataPE externalDataPE, IDynamicPropertyEvaluator evaluator,
+ Session session)
{
super(externalDataPE.getCode(), evaluator);
+ this.session = session;
initProperties(externalDataPE);
this.externalDataPE = externalDataPE;
}
@@ -58,7 +64,7 @@ public class ExternalDataAdaptor extends AbstractEntityAdaptor implements IDataA
@Override
public IExperimentAdaptor experiment()
{
- return EntityAdaptorFactory.create(externalDataPE.getExperiment(), evaluator);
+ return EntityAdaptorFactory.create(externalDataPE.getExperiment(), evaluator, session);
}
@Override
@@ -68,7 +74,7 @@ public class ExternalDataAdaptor extends AbstractEntityAdaptor implements IDataA
for (DataSetRelationshipPE relationship : externalDataPE.getParentRelationships())
{
DataPE parent = relationship.getParentDataSet();
- list.add(EntityAdaptorFactory.create(parent, evaluator));
+ list.add(EntityAdaptorFactory.create(parent, evaluator, session));
}
return list;
}
@@ -80,7 +86,7 @@ public class ExternalDataAdaptor extends AbstractEntityAdaptor implements IDataA
for (DataSetRelationshipPE relationship : externalDataPE.getChildRelationships())
{
DataPE child = relationship.getChildDataSet();
- list.add(EntityAdaptorFactory.create(child, evaluator));
+ list.add(EntityAdaptorFactory.create(child, evaluator, session));
}
return list;
}
@@ -91,7 +97,7 @@ public class ExternalDataAdaptor extends AbstractEntityAdaptor implements IDataA
List<IDataAdaptor> list = new ArrayList<IDataAdaptor>();
for (DataPE contained : externalDataPE.getContainedDataSets())
{
- list.add(EntityAdaptorFactory.create(contained, evaluator));
+ list.add(EntityAdaptorFactory.create(contained, evaluator, session));
}
return list;
}
@@ -102,7 +108,7 @@ public class ExternalDataAdaptor extends AbstractEntityAdaptor implements IDataA
DataPE container = externalDataPE.getContainer();
if (container != null)
{
- return EntityAdaptorFactory.create(container, evaluator);
+ return EntityAdaptorFactory.create(container, evaluator, session);
} else
{
return null;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/SampleAdaptor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/SampleAdaptor.java
index d2895cb73385a4622f0187bff757c989d47c30eb..2487d63405a37c42fb020993a2e9aedfeed6fa7e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/SampleAdaptor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/SampleAdaptor.java
@@ -19,6 +19,8 @@ package ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.calc
import java.util.ArrayList;
import java.util.List;
+import org.hibernate.Session;
+
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.IDynamicPropertyEvaluator;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.calculator.api.IEntityAdaptor;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.calculator.api.IExperimentAdaptor;
@@ -36,9 +38,12 @@ public class SampleAdaptor extends AbstractEntityAdaptor implements ISampleAdapt
{
private final SamplePE samplePE;
- public SampleAdaptor(SamplePE samplePE, IDynamicPropertyEvaluator evaluator)
+ private final Session session;
+
+ public SampleAdaptor(SamplePE samplePE, IDynamicPropertyEvaluator evaluator, Session session)
{
super(samplePE.getCode(), evaluator);
+ this.session = session;
initProperties(samplePE);
this.samplePE = samplePE;
}
@@ -57,7 +62,7 @@ public class SampleAdaptor extends AbstractEntityAdaptor implements ISampleAdapt
@Override
public IExperimentAdaptor experiment()
{
- return EntityAdaptorFactory.create(samplePE.getExperiment(), evaluator);
+ return EntityAdaptorFactory.create(samplePE.getExperiment(), evaluator, session);
}
@Override
@@ -66,7 +71,7 @@ public class SampleAdaptor extends AbstractEntityAdaptor implements ISampleAdapt
List<ISampleAdaptor> list = new ArrayList<ISampleAdaptor>();
for (SamplePE parent : samplePE.getParents())
{
- list.add(EntityAdaptorFactory.create(parent, evaluator));
+ list.add(EntityAdaptorFactory.create(parent, evaluator, session));
}
return list;
}
@@ -78,7 +83,7 @@ public class SampleAdaptor extends AbstractEntityAdaptor implements ISampleAdapt
for (SampleRelationshipPE relationship : samplePE.getChildRelationships())
{
SamplePE child = relationship.getChildSample();
- list.add(EntityAdaptorFactory.create(child, evaluator));
+ list.add(EntityAdaptorFactory.create(child, evaluator, session));
}
return list;
}
@@ -89,7 +94,7 @@ public class SampleAdaptor extends AbstractEntityAdaptor implements ISampleAdapt
List<ISampleAdaptor> list = new ArrayList<ISampleAdaptor>();
for (SamplePE contained : samplePE.getContained())
{
- list.add(EntityAdaptorFactory.create(contained, evaluator));
+ list.add(EntityAdaptorFactory.create(contained, evaluator, session));
}
return list;
}
@@ -100,7 +105,7 @@ public class SampleAdaptor extends AbstractEntityAdaptor implements ISampleAdapt
SamplePE container = samplePE.getContainer();
if (container != null)
{
- return EntityAdaptorFactory.create(container, evaluator);
+ return EntityAdaptorFactory.create(container, evaluator, session);
} else
{
return null;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/ScrollableResultsIterator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/ScrollableResultsIterator.java
new file mode 100644
index 0000000000000000000000000000000000000000..bdd9c4fe5ebd7c57fc180cea88aca2fccaf77033
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/ScrollableResultsIterator.java
@@ -0,0 +1,88 @@
+/*
+ * Copyright 2012 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.server.dataaccess.dynamic_property.calculator;
+
+import java.util.Iterator;
+
+import org.hibernate.ScrollableResults;
+
+/**
+ * @author anttil
+ */
+public abstract class ScrollableResultsIterator<T> implements Iterable<T>
+{
+
+ private final ScrollableResults scroll;
+
+ public ScrollableResultsIterator(ScrollableResults scroll)
+ {
+ this.scroll = scroll;
+ }
+
+ public abstract T parseValue(Object[] result);
+
+ @Override
+ public Iterator<T> iterator()
+ {
+ return new Iterator<T>()
+ {
+ Object[] current = null;
+
+ @Override
+ public boolean hasNext()
+ {
+ if (current != null)
+ {
+ return true;
+ }
+
+ if (scroll.next())
+ {
+ current = scroll.get();
+ return true;
+ } else
+ {
+ return false;
+ }
+
+ }
+
+ @Override
+ public T next()
+ {
+ if (current == null)
+ {
+ if (scroll.next() == false)
+ {
+ return null;
+ }
+ current = scroll.get();
+ }
+
+ Object[] o = current;
+ current = null;
+ return parseValue(o);
+ }
+
+ @Override
+ public void remove()
+ {
+ throw new UnsupportedOperationException();
+ }
+ };
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/api/IExperimentAdaptor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/api/IExperimentAdaptor.java
index 5650d2a3adc99a86033df49075aae2296c14da32..fe857c5363dd06b4a095bbb038cf9538639f13b4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/api/IExperimentAdaptor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/calculator/api/IExperimentAdaptor.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.server.dataaccess.dynamic_property.calculator.api;
-import java.util.List;
/**
* @author Jakub Straszewski
@@ -24,8 +23,12 @@ import java.util.List;
public interface IExperimentAdaptor
{
/** Return the samples belonging to this experiment */
- List<ISampleAdaptor> samples();
+ Iterable<ISampleAdaptor> samples();
+
+ Iterable<ISampleAdaptor> samplesOfType(String typeCodeRegexp);
/** Return the datasets belonging to this experiment */
- List<IDataAdaptor> dataSets();
+ Iterable<IDataAdaptor> dataSets();
+
+ Iterable<IDataAdaptor> dataSetsOfType(String typeCodeRegexp);
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/DynamicPropertyEvaluatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/DynamicPropertyEvaluatorTest.java
index 0cde9d758ecef590ff006cf5ce648a808dda2848..3be836117145f0f3828ff17a6a3ad9dad99741fb 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/DynamicPropertyEvaluatorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/dynamic_property/DynamicPropertyEvaluatorTest.java
@@ -140,7 +140,7 @@ public class DynamicPropertyEvaluatorTest extends AbstractBOTest
// create sample with all properties created above and evaluate dynamic properties
final SamplePE sample = createSample("s1", properties);
- evaluator.evaluateProperties(sample);
+ evaluator.evaluateProperties(sample, null);
// check if evaluated values are correct
final String expectedDp1Value = String.format("%s %s", p1.getValue(), p2.getValue());
@@ -200,7 +200,7 @@ public class DynamicPropertyEvaluatorTest extends AbstractBOTest
// create sample with all properties created above and evaluate dynamic properties
final SamplePE sample = createSample("s1", properties);
- evaluator.evaluateProperties(sample);
+ evaluator.evaluateProperties(sample, null);
// check if evaluated values are correct
assertEquals(term2.getCode(), dpVarchar.getValue());
@@ -298,7 +298,7 @@ public class DynamicPropertyEvaluatorTest extends AbstractBOTest
// create sample with all properties created above and evaluate dynamic properties
final SamplePE sample = createSample("s1", properties);
- evaluator.evaluateProperties(sample);
+ evaluator.evaluateProperties(sample, null);
// check if evaluated values are correct
final String materialIdentifier =
@@ -350,7 +350,7 @@ public class DynamicPropertyEvaluatorTest extends AbstractBOTest
properties.add(dp2);
properties.add(dp3);
SamplePE sample = createSample("s1", properties);
- evaluator.evaluateProperties(sample);
+ evaluator.evaluateProperties(sample, null);
// all values should be equal to value of p1
assertEquals(p1.getValue(), dp1.getValue());
assertEquals(p1.getValue(), dp2.getValue());
@@ -363,7 +363,7 @@ public class DynamicPropertyEvaluatorTest extends AbstractBOTest
properties.add(p1);
properties.add(dp1);
sample = createSample("s1", properties);
- evaluator.evaluateProperties(sample);
+ evaluator.evaluateProperties(sample, null);
// cyclic dependency should be found
assertEquals(expectedCyclicDependencyErrorMessage(dp1, dp1), dp1.getValue());
@@ -375,7 +375,7 @@ public class DynamicPropertyEvaluatorTest extends AbstractBOTest
properties.add(dp1);
properties.add(dp2);
sample = createSample("s1", properties);
- evaluator.evaluateProperties(sample);
+ evaluator.evaluateProperties(sample, null);
// cyclic dependency should be found
assertEquals(expectedCyclicDependencyErrorMessage(dp2, dp1, dp2), dp1.getValue());
assertEquals(expectedCyclicDependencyErrorMessage(dp2, dp1, dp2), dp2.getValue());
@@ -390,7 +390,7 @@ public class DynamicPropertyEvaluatorTest extends AbstractBOTest
properties.add(dp2);
properties.add(dp3);
sample = createSample("s1", properties);
- evaluator.evaluateProperties(sample);
+ evaluator.evaluateProperties(sample, null);
// cyclic dependency should be found
assertEquals(expectedCyclicDependencyErrorMessage(dp2, dp3, dp1, dp2), dp1.getValue());
assertEquals(expectedCyclicDependencyErrorMessage(dp2, dp3, dp1, dp2), dp2.getValue());