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 938f91c4122553dfebfa5040540cea6490fe9a87..6239fa321ad137b99dbe89669358f88a34c1e77f 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
@@ -71,7 +71,6 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.dynamic_property.calc
import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.server.business.search.DataSetSearchManager;
-import ch.systemsx.cisd.openbis.generic.server.business.search.SampleSearchManager;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataStoreDAO;
@@ -266,7 +265,7 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
return businessObjectFactory;
}
- private static UserFailureException createUserFailureException(final DataAccessException ex)
+ static UserFailureException createUserFailureException(final DataAccessException ex)
{
return new UserFailureException(ex.getMostSpecificCause().getMessage(), ex);
}
@@ -492,15 +491,9 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
public List<Sample> searchForSamples(String sessionToken, DetailedSearchCriteria criteria)
{
final Session session = getSession(sessionToken);
- try
- {
- final ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
- final IHibernateSearchDAO searchDAO = getDAOFactory().getHibernateSearchDAO();
- return new SampleSearchManager(searchDAO, sampleLister).searchForSamples(criteria);
- } catch (final DataAccessException ex)
- {
- throw createUserFailureException(ex);
- }
+ SearchHelper searchHelper =
+ new SearchHelper(session, businessObjectFactory, getDAOFactory());
+ return searchHelper.searchForSamples(criteria);
}
public final List<ExternalData> listSampleExternalData(final String sessionToken,
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 3caa53ff5be80301626cb54b82f284eda0e366aa..af1f540cc45529c76fd7e0db0b8c6f8152f7007c 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
@@ -31,6 +31,7 @@ import ch.systemsx.cisd.common.collections.CollectionUtils;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
+import ch.systemsx.cisd.openbis.generic.server.api.v1.SearchCriteriaToDetailedSearchCriteriaTranslator;
import ch.systemsx.cisd.openbis.generic.server.business.IDataStoreServiceFactory;
import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
@@ -54,6 +55,8 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.plugin.IDataSetTypeSlaveServerPlugin;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchableEntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ArchiverDataSetCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSet;
@@ -63,6 +66,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletedDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
@@ -1106,16 +1110,14 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
samplesUpdated, samplesCreated, dataSetsCreated, dataSetsUpdated);
}
- private List<Space> createSpaces(Session session,
- AtomicEntityOperationDetails operationDetails)
+ private List<Space> createSpaces(Session session, AtomicEntityOperationDetails operationDetails)
{
ArrayList<SpacePE> spacePEsCreated = new ArrayList<SpacePE>();
List<NewSpace> newSpaces = operationDetails.getSpaceRegistrations();
for (NewSpace newSpace : newSpaces)
{
SpacePE spacePE =
- registerSpaceInternal(session, newSpace,
- operationDetails.tryUserIdOrNull());
+ registerSpaceInternal(session, newSpace, operationDetails.tryUserIdOrNull());
spacePEsCreated.add(spacePE);
}
return GroupTranslator.translate(spacePEsCreated);
@@ -1161,8 +1163,7 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
for (NewProject newProject : newProjects)
{
ProjectPE projectPE =
- registerProjectInternal(session, newProject,
- operationDetails.tryUserIdOrNull());
+ registerProjectInternal(session, newProject, operationDetails.tryUserIdOrNull());
projectPEsCreated.add(projectPE);
}
return ProjectTranslator.translate(projectPEsCreated);
@@ -1193,8 +1194,7 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
for (NewSample newSample : newSamples)
{
SamplePE samplePE =
- registerSampleInternal(session, newSample,
- operationDetails.tryUserIdOrNull());
+ registerSampleInternal(session, newSample, operationDetails.tryUserIdOrNull());
samplePEsCreated.add(samplePE);
}
return SampleTranslator.translate(samplePEsCreated, session.getBaseIndexURL());
@@ -1354,4 +1354,15 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
return externalDataBO;
}
+ public List<Sample> searchForSamples(String sessionToken, SearchCriteria searchCriteria)
+ {
+ Session session = getSession(sessionToken);
+ DetailedSearchCriteria detailedSearchCriteria =
+ SearchCriteriaToDetailedSearchCriteriaTranslator.convert(
+ SearchableEntityKind.SAMPLE, searchCriteria);
+ SearchHelper searchHelper =
+ new SearchHelper(session, businessObjectFactory, getDAOFactory());
+ return searchHelper.searchForSamples(detailedSearchCriteria);
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
index 31c61ec419a3ce2c1cc14121b31f2d2efbfe2de7..7c503106f226a8312146ad5b556b167e40676691 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
@@ -24,6 +24,7 @@ import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerLogger;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ArchiverDataSetCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus;
@@ -342,8 +343,8 @@ public class ETLServiceLogger extends AbstractServerLogger implements IETLServic
public void updateShareIdAndSize(String sessionToken, String dataSetCode, String shareId,
long size) throws UserFailureException
{
- logTracking(sessionToken, "updateShareIdAndSize", "DATA_SET_CODE(%s) SHARE_ID(%s) SIZE(%s)",
- dataSetCode, shareId, size);
+ logTracking(sessionToken, "updateShareIdAndSize",
+ "DATA_SET_CODE(%s) SHARE_ID(%s) SIZE(%s)", dataSetCode, shareId, size);
}
public void updateDataSetStatuses(String sessionToken, List<String> dataSetCodes,
@@ -475,4 +476,10 @@ public class ETLServiceLogger extends AbstractServerLogger implements IETLServic
return null;
}
+ public List<Sample> searchForSamples(String sessionToken, SearchCriteria searchCriteria)
+ {
+ logAccess(sessionToken, "searchForSamples", "%s", searchCriteria);
+ return null;
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/SearchHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/SearchHelper.java
new file mode 100644
index 0000000000000000000000000000000000000000..8df2ff513f209b97606c55c67b1f1d6db909620a
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/SearchHelper.java
@@ -0,0 +1,66 @@
+/*
+ * 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.server;
+
+import java.util.List;
+
+import org.springframework.dao.DataAccessException;
+
+import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
+import ch.systemsx.cisd.openbis.generic.server.business.search.SampleSearchManager;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IHibernateSearchDAO;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+
+/**
+ * A class with helper methods for implementing search. This is the shared code for that searches
+ * originating from CommonServer and ETLService.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+class SearchHelper
+{
+ private final Session session;
+
+ private final ICommonBusinessObjectFactory businessObjectFactory;
+
+ private final IDAOFactory daoFactory;
+
+ public SearchHelper(Session session, ICommonBusinessObjectFactory businessObjectFactory,
+ IDAOFactory daoFactory)
+ {
+ this.session = session;
+ this.businessObjectFactory = businessObjectFactory;
+ this.daoFactory = daoFactory;
+ }
+
+ public List<Sample> searchForSamples(DetailedSearchCriteria criteria)
+ {
+ try
+ {
+ final ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
+ final IHibernateSearchDAO searchDAO = daoFactory.getHibernateSearchDAO();
+ return new SampleSearchManager(searchDAO, sampleLister).searchForSamples(criteria);
+ } catch (final DataAccessException ex)
+ {
+ throw CommonServer.createUserFailureException(ex);
+ }
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SearchCriteriaToDetailedSearchCriteriaTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SearchCriteriaToDetailedSearchCriteriaTranslator.java
index 133742196d06d0e7f310fde93dde65e2203ee3bb..3c043796aeeb946420303c98b51d3b0a13ac2bc9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SearchCriteriaToDetailedSearchCriteriaTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SearchCriteriaToDetailedSearchCriteriaTranslator.java
@@ -47,7 +47,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchCriteriaConnectio
*
* @author Chandrasekhar Ramakrishnan
*/
-class SearchCriteriaToDetailedSearchCriteriaTranslator
+public class SearchCriteriaToDetailedSearchCriteriaTranslator
{
private final static String INVALID_SEARCH_ATTRIBUTE_TEMPLATE =
"%s is not a valid search attribute for %s";
@@ -288,7 +288,7 @@ class SearchCriteriaToDetailedSearchCriteriaTranslator
((AttributeMatchClause) matchClause).getAttribute();
IAttributeSearchFieldKind searchFieldKind =
attributeTranslator
- .convertMatchClauseAttributeToAttributeSearchFieldKind(attribute);
+ .convertMatchClauseAttributeToAttributeSearchFieldKind(attribute);
searchField = DetailedSearchField.createAttributeField(searchFieldKind);
break;
default:
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
index 07d95e038ab952277e5c5ec7fc496065ed8bd65c..f955a5d60f3ad38506dc0505b87d6c60ad51c6cd 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
@@ -23,6 +23,7 @@ import java.util.List;
import org.springframework.transaction.annotation.Transactional;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.authorization.ISessionProvider;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.AuthorizationGuard;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.ReturnValueFilter;
@@ -111,7 +112,8 @@ public interface IETLLIMSService extends IServer, ISessionProvider
* @param experimentIdentifier an identifier which uniquely identifies the experiment.
*/
@Transactional(readOnly = true)
- @RolesAllowed({RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER})
+ @RolesAllowed(
+ { RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
public Experiment tryToGetExperiment(
String sessionToken,
@AuthorizationGuard(guardClass = ExistingSpaceIdentifierPredicate.class) ExperimentIdentifier experimentIdentifier)
@@ -183,7 +185,8 @@ public interface IETLLIMSService extends IServer, ISessionProvider
* @return a sorted list of {@link ExternalData}.
*/
@Transactional(readOnly = true)
- @RolesAllowed({RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER})
+ @RolesAllowed(
+ { RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
public List<ExternalData> listDataSetsByExperimentID(
final String sessionToken,
@AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class) final TechId experimentID)
@@ -349,7 +352,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.INSTANCE_ADMIN)
public void checkInstanceAdminAuthorization(String sessionToken) throws UserFailureException;
-
+
/**
* Checks that the user of specified session has SPACE_POWER_USER access rights.
*/
@@ -428,8 +431,8 @@ public interface IETLLIMSService extends IServer, ISessionProvider
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
- public List<DataSetShareId> listShareIds(final String sessionToken,
- String dataStore) throws UserFailureException;
+ public List<DataSetShareId> listShareIds(final String sessionToken, String dataStore)
+ throws UserFailureException;
/**
* Lists data sets belonging to chosen data store.
@@ -438,7 +441,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
public List<SimpleDataSetInformationDTO> listDataSets(final String sessionToken,
String dataStore) throws UserFailureException;
-
+
/**
* List data sets deleted after specified date.
*/
@@ -460,7 +463,8 @@ public interface IETLLIMSService extends IServer, ISessionProvider
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
- public List<ExternalData> listDataSets(String sessionToken, String dataStoreCode, TrackingDataSetCriteria criteria);
+ public List<ExternalData> listDataSets(String sessionToken, String dataStoreCode,
+ TrackingDataSetCriteria criteria);
/**
* List all experiments for a given project identifier.
@@ -480,7 +484,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider
{ RoleWithHierarchy.SPACE_OBSERVER })
@ReturnValueFilter(validatorClass = ProjectValidator.class)
public List<Project> listProjects(String sessionToken);
-
+
/**
* Adds specified properties of given data set. Properties defined before will not be updated.
*/
@@ -677,4 +681,15 @@ public interface IETLLIMSService extends IServer, ISessionProvider
public Project tryGetProject(
String sessionToken,
@AuthorizationGuard(guardClass = ExistingSpaceIdentifierPredicate.class) ProjectIdentifier projectIdentifier);
+
+ /**
+ * Search for samples matching the provided criteria.
+ *
+ * @param sessionToken The user authentication token. Must not be <code>null</code>.
+ * @param searchCriteria The criteria for samples.
+ * @return A collection of samples matching the search criteria.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<Sample> searchForSamples(String sessionToken, SearchCriteria searchCriteria);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSet.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSet.java
index 8e0631296b29d41fd910241cb75cc63c5ef55c16..42d4b44ec4ce22bfabc2e5e94d7cbc442a2a1c1b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSet.java
@@ -281,7 +281,26 @@ public final class DataSet implements Serializable
builder.append(getExperimentIdentifier());
builder.append(getSampleIdentifierOrNull());
builder.append(getDataSetTypeCode());
- builder.append(getProperties());
+
+ // Append properties alphabetically for consistency
+ HashMap<String, String> props = getProperties();
+ ArrayList<String> sortedKeys = new ArrayList<String>(props.size());
+ sortedKeys.addAll(props.keySet());
+ Collections.sort(sortedKeys);
+ StringBuilder propString = new StringBuilder();
+ propString.append("{");
+ for (String key : sortedKeys)
+ {
+ propString.append(key);
+ propString.append("=");
+ propString.append(props.get(key));
+ propString.append(", ");
+ }
+ // Get rid of the trailing ,
+ propString.deleteCharAt(propString.length() - 1);
+ propString.deleteCharAt(propString.length() - 1);
+ propString.append("}");
+ builder.append(propString);
if (retrievedConnections.contains(Connections.PARENTS))
{
builder.append(getParentCodes());
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 62e2d313715d917ddaabd33084cca89ede988cf4..3ea32e1518a9226db55cf9883e5ece79e19bf809 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
@@ -39,16 +39,22 @@ import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.business.IDataStoreServiceFactory;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IHibernateSearchDAO;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
import ch.systemsx.cisd.openbis.generic.shared.CommonTestUtils;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
@@ -62,6 +68,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SourceType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetBuilder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataStoreBuilder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.SampleBuilder;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationResult;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
@@ -88,6 +95,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
/**
* @author Franz-Josef Elmer
@@ -117,6 +125,8 @@ public class ETLServiceTest extends AbstractServerTestCase
private IDataStoreService dataStoreService;
+ private IHibernateSearchDAO hibernateSearchDao;
+
@Override
@BeforeMethod
public final void setUp()
@@ -125,6 +135,7 @@ public class ETLServiceTest extends AbstractServerTestCase
boFactory = context.mock(ICommonBusinessObjectFactory.class);
dssfactory = context.mock(IDataStoreServiceFactory.class);
dataStoreService = context.mock(IDataStoreService.class);
+ hibernateSearchDao = context.mock(IHibernateSearchDAO.class);
}
@Test
@@ -1007,6 +1018,48 @@ public class ETLServiceTest extends AbstractServerTestCase
context.assertIsSatisfied();
}
+ @SuppressWarnings("unchecked")
+ @Test
+ public void testSearchForSamples()
+ {
+ prepareGetSession();
+ context.checking(new Expectations()
+ {
+ {
+ one(boFactory).createSampleLister(SESSION);
+ will(returnValue(sampleLister));
+
+ one(daoFactory).getHibernateSearchDAO();
+ will(returnValue(hibernateSearchDao));
+
+ one(hibernateSearchDao).searchForEntityIds(
+ with(aNonNull(DetailedSearchCriteria.class)),
+ with(equal(EntityKind.SAMPLE)), with(aNonNull(List.class)));
+ will(returnValue(Arrays.asList(new Long(1), new Long(2))));
+
+ one(sampleLister).list(with(aNonNull(ListOrSearchSampleCriteria.class)));
+ SampleBuilder sample1 = new SampleBuilder().id(1);
+ SampleBuilder sample2 = new SampleBuilder().id(2);
+ will(returnValue(Arrays.asList(sample1, sample2)));
+
+ }
+ });
+
+ List<Sample> sample =
+ createService().searchForSamples(SESSION_TOKEN, createSearchCriteriaForSample());
+
+ assertEquals(2, sample.size());
+ context.assertIsSatisfied();
+ }
+
+ private SearchCriteria createSearchCriteriaForSample()
+ {
+ SearchCriteria sc = new SearchCriteria();
+ sc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "a code"));
+ sc.addMatchClause(MatchClause.createPropertyMatch("MY_PROPERTY2", "a property value"));
+ return sc;
+ }
+
private void prepareRegisterDataSet(final SampleIdentifier sampleIdentifier,
final ExperimentPE experiment, final SourceType sourceType,
final NewExternalData externalData)
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
index 07d95e038ab952277e5c5ec7fc496065ed8bd65c..f955a5d60f3ad38506dc0505b87d6c60ad51c6cd 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
@@ -23,6 +23,7 @@ import java.util.List;
import org.springframework.transaction.annotation.Transactional;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.authorization.ISessionProvider;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.AuthorizationGuard;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.ReturnValueFilter;
@@ -111,7 +112,8 @@ public interface IETLLIMSService extends IServer, ISessionProvider
* @param experimentIdentifier an identifier which uniquely identifies the experiment.
*/
@Transactional(readOnly = true)
- @RolesAllowed({RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER})
+ @RolesAllowed(
+ { RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
public Experiment tryToGetExperiment(
String sessionToken,
@AuthorizationGuard(guardClass = ExistingSpaceIdentifierPredicate.class) ExperimentIdentifier experimentIdentifier)
@@ -183,7 +185,8 @@ public interface IETLLIMSService extends IServer, ISessionProvider
* @return a sorted list of {@link ExternalData}.
*/
@Transactional(readOnly = true)
- @RolesAllowed({RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER})
+ @RolesAllowed(
+ { RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
public List<ExternalData> listDataSetsByExperimentID(
final String sessionToken,
@AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class) final TechId experimentID)
@@ -349,7 +352,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.INSTANCE_ADMIN)
public void checkInstanceAdminAuthorization(String sessionToken) throws UserFailureException;
-
+
/**
* Checks that the user of specified session has SPACE_POWER_USER access rights.
*/
@@ -428,8 +431,8 @@ public interface IETLLIMSService extends IServer, ISessionProvider
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
- public List<DataSetShareId> listShareIds(final String sessionToken,
- String dataStore) throws UserFailureException;
+ public List<DataSetShareId> listShareIds(final String sessionToken, String dataStore)
+ throws UserFailureException;
/**
* Lists data sets belonging to chosen data store.
@@ -438,7 +441,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
public List<SimpleDataSetInformationDTO> listDataSets(final String sessionToken,
String dataStore) throws UserFailureException;
-
+
/**
* List data sets deleted after specified date.
*/
@@ -460,7 +463,8 @@ public interface IETLLIMSService extends IServer, ISessionProvider
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
- public List<ExternalData> listDataSets(String sessionToken, String dataStoreCode, TrackingDataSetCriteria criteria);
+ public List<ExternalData> listDataSets(String sessionToken, String dataStoreCode,
+ TrackingDataSetCriteria criteria);
/**
* List all experiments for a given project identifier.
@@ -480,7 +484,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider
{ RoleWithHierarchy.SPACE_OBSERVER })
@ReturnValueFilter(validatorClass = ProjectValidator.class)
public List<Project> listProjects(String sessionToken);
-
+
/**
* Adds specified properties of given data set. Properties defined before will not be updated.
*/
@@ -677,4 +681,15 @@ public interface IETLLIMSService extends IServer, ISessionProvider
public Project tryGetProject(
String sessionToken,
@AuthorizationGuard(guardClass = ExistingSpaceIdentifierPredicate.class) ProjectIdentifier projectIdentifier);
+
+ /**
+ * Search for samples matching the provided criteria.
+ *
+ * @param sessionToken The user authentication token. Must not be <code>null</code>.
+ * @param searchCriteria The criteria for samples.
+ * @return A collection of samples matching the search criteria.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<Sample> searchForSamples(String sessionToken, SearchCriteria searchCriteria);
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
index 4d2f07aaf9b1f99566678ac76b3e4a792ebe70b8..50e089de90274b85e6252a507aa7906b5077e43c 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
@@ -470,7 +470,7 @@ public class GeneralInformationServiceTest extends SystemTestCase
assertEquals(4, result.size());
assertEquals(
"[DataSet[20081105092158673-1,/CISD/NEMO/EXP1,/CISD/3VCP1,HCS_IMAGE,{COMMENT=no comment},[]], "
- + "DataSet[20081105092159111-1,/CISD/NEMO/EXP-TEST-1,/CISD/CP-TEST-1,HCS_IMAGE,{ANY_MATERIAL=null, GENDER=null, COMMENT=no comment, BACTERIUM=null},[]], "
+ + "DataSet[20081105092159111-1,/CISD/NEMO/EXP-TEST-1,/CISD/CP-TEST-1,HCS_IMAGE,{ANY_MATERIAL=null, BACTERIUM=null, COMMENT=no comment, GENDER=null},[]], "
+ "DataSet[20081105092159222-2,/CISD/NOE/EXP-TEST-2,/CISD/CP-TEST-2,HCS_IMAGE,{COMMENT=no comment},[]], "
+ "DataSet[20081105092159333-3,/CISD/NEMO/EXP-TEST-2,/CISD/CP-TEST-3,HCS_IMAGE,{COMMENT=no comment},[]]]",
result.toString());