From a326ef13594f716eca4cbab9b61351fa8d059e43 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 18 Nov 2014 09:07:30 +0000
Subject: [PATCH] SSDM-1080: Extract search domain functionality from
DataSetTable into new BO class SearchDomainSearcher.
SVN: 32856
---
.../server/CommonBusinessObjectFactory.java | 9 +
.../openbis/generic/server/CommonServer.java | 10 +-
.../business/bo/AbstractBusinessObject.java | 16 +
.../server/business/bo/DataSetTable.java | 225 +----------
.../bo/ICommonBusinessObjectFactory.java | 2 +
.../server/business/bo/IDataSetTable.java | 13 -
.../business/bo/ISearchDomainSearcher.java | 44 +++
.../business/bo/SearchDomainSearcher.java | 264 +++++++++++++
.../server/business/bo/DataSetTableTest.java | 101 -----
.../business/bo/SearchDomainSearcherTest.java | 374 ++++++++++++++++++
10 files changed, 718 insertions(+), 340 deletions(-)
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISearchDomainSearcher.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcher.java
create mode 100644 openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcherTest.java
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonBusinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonBusinessObjectFactory.java
index 408ba01ecaf..66ea1127e91 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonBusinessObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonBusinessObjectFactory.java
@@ -60,6 +60,7 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.IRoleAssignmentTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IScriptBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.ISearchDomainSearcher;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISpaceBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ITrashBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IVocabularyBO;
@@ -74,6 +75,7 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.RoleAssignmentTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.SampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.SampleTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ScriptBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.SearchDomainSearcher;
import ch.systemsx.cisd.openbis.generic.server.business.bo.SpaceBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.TrashBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.VocabularyBO;
@@ -202,6 +204,13 @@ public final class CommonBusinessObjectFactory extends AbstractBusinessObjectFac
getManagedPropertyEvaluatorFactory(), getMultiplexer());
}
+ @Override
+ public ISearchDomainSearcher createSearchDomainSearcher(Session session)
+ {
+ return new SearchDomainSearcher(getDaoFactory(), session, getManagedPropertyEvaluatorFactory(),
+ getDSSFactory());
+ }
+
@Override
public IDeletedDataSetTable createDeletedDataSetTable(Session session)
{
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 32a64769c13..38d278e49f5 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
@@ -115,6 +115,7 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.IRoleAssignmentTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IScriptBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.ISearchDomainSearcher;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISpaceBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ITrashBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IVocabularyBO;
@@ -1621,9 +1622,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
{
Session session = getSession(sessionToken);
- IDataSetTable dataSetTable = businessObjectFactory.createDataSetTable(session);
- return dataSetTable.searchForDataSetsWithSequences(preferredSearchDomainOrNull, searchString,
- optionalParametersOrNull);
+ ISearchDomainSearcher searcher = businessObjectFactory.createSearchDomainSearcher(session);
+ return searcher.searchForEntitiesWithSequences(preferredSearchDomainOrNull, searchString, optionalParametersOrNull);
}
@Override
@@ -1632,8 +1632,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
{
Session session = getSession(sessionToken);
- IDataSetTable dataSetTable = businessObjectFactory.createDataSetTable(session);
- return dataSetTable.listAvailableSearchDomains();
+ ISearchDomainSearcher searcher = businessObjectFactory.createSearchDomainSearcher(session);
+ return searcher.listAvailableSearchDomains();
}
@Override
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBusinessObject.java
index 40328ce3664..d4b768b5e05 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBusinessObject.java
@@ -25,10 +25,12 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
+import org.apache.commons.lang.StringUtils;
import org.hibernate.SessionFactory;
import org.springframework.dao.DataAccessException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.server.business.IDataStoreServiceFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.EntityPropertiesConverter;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAttachmentDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationGroupDAO;
@@ -71,11 +73,13 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.RelationshipUtils;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.ICodeSequenceDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.IPermIdDAO;
import ch.systemsx.cisd.openbis.generic.server.util.SpaceIdentifierHelper;
+import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Identifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentHolderPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityPropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityPropertiesHolder;
@@ -207,6 +211,18 @@ abstract class AbstractBusinessObject implements IDAOFactory
throw UserFailureException.fromTemplate(ERR_MODIFIED_ENTITY, entityName);
}
+ protected static IDataStoreService tryGetDataStoreService(DataStorePE dataStore,
+ IDataStoreServiceFactory dataStoreServiceFactory)
+ {
+ String remoteURL = dataStore.getRemoteUrl();
+ if (StringUtils.isBlank(remoteURL))
+ {
+ // null if DSS URL has not been specified
+ return null;
+ }
+ return dataStoreServiceFactory.create(remoteURL);
+ }
+
/**
* Returns the perm ID of specified identifier or creates a new one if it is <code>null</code>.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
index ca1b3c7a9be..b07c0e87967 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
@@ -21,7 +21,6 @@ import static ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTranslat
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
-import java.util.EnumMap;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
@@ -39,8 +38,6 @@ import org.springframework.dao.DataIntegrityViolationException;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.collection.CollectionUtils;
-import ch.systemsx.cisd.common.collection.IKeyExtractor;
-import ch.systemsx.cisd.common.collection.TableMap;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
@@ -62,13 +59,7 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.event.DeleteDataSetEventBuilder;
import ch.systemsx.cisd.openbis.generic.shared.Constants;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFileSearchResultLocation;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityPropertySearchResultLocation;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ISearchDomainResultLocation;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomain;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
import ch.systemsx.cisd.openbis.generic.shared.basic.TableModelAppender;
import ch.systemsx.cisd.openbis.generic.shared.basic.TableModelAppender.TableModelWithDifferentColumnCountException;
import ch.systemsx.cisd.openbis.generic.shared.basic.TableModelAppender.TableModelWithDifferentColumnIdsException;
@@ -81,7 +72,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetBatchUpdateDetai
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LinkModel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchDomainSearchResultWithFullEntity;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetBatchUpdatesDTO;
@@ -98,8 +88,6 @@ 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.managed_property.IManagedPropertyEvaluatorFactory;
import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
/**
@@ -116,16 +104,6 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
DataSetTable.class);
- private static final IKeyExtractor<String, IEntityInformationHolderWithPermId> PERM_ID_EXTRACTOR =
- new IKeyExtractor<String, IEntityInformationHolderWithPermId>()
- {
- @Override
- public String getKey(IEntityInformationHolderWithPermId e)
- {
- return e.getPermId();
- }
- };
-
@Private
static final String UPLOAD_COMMENT_TEXT = "Uploaded zip file contains the following data sets:";
@@ -293,190 +271,6 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
this.dataSets = dataSets;
}
- @Override
- public List<SearchDomainSearchResultWithFullEntity> searchForDataSetsWithSequences(String preferredSequenceDatabaseOrNull,
- String sequenceSnippet, Map<String, String> optionalParametersOrNull)
- {
- List<SearchDomainSearchResult> searchResults = askAllDataStoreServers(preferredSequenceDatabaseOrNull,
- sequenceSnippet, optionalParametersOrNull);
- return enrichWithEntities(searchResults);
- }
-
- private List<SearchDomainSearchResultWithFullEntity> enrichWithEntities(List<SearchDomainSearchResult> searchResults)
- {
- Map<EntityLoader, List<String>> map = separate(searchResults);
- Map<EntityLoader, TableMap<String, IEntityInformationHolderWithPermId>> result = loadEntities(map);
- List<SearchDomainSearchResultWithFullEntity> filteredResult = new ArrayList<SearchDomainSearchResultWithFullEntity>();
- for (SearchDomainSearchResult searchResult : searchResults)
- {
- Selector selector = new Selector(searchResult.getResultLocation());
- EntityLoader loader = selector.getLoader();
- IEntityInformationHolderWithPermId entity = result.get(loader).getOrDie(selector.getPermId());
- SearchDomainSearchResultWithFullEntity searchResultWithEntity = new SearchDomainSearchResultWithFullEntity();
- searchResultWithEntity.setSearchResult(searchResult);
- searchResultWithEntity.setEntity(entity);
- filteredResult.add(searchResultWithEntity);
- }
- return filteredResult;
- }
-
- private Map<EntityLoader, List<String>> separate(List<SearchDomainSearchResult> searchResults)
- {
- Map<EntityLoader, List<String>> map = new EnumMap<DataSetTable.EntityLoader, List<String>>(EntityLoader.class);
- for (SearchDomainSearchResult searchResult : searchResults)
- {
- ISearchDomainResultLocation resultLocation = searchResult.getResultLocation();
- Selector selector = new Selector(resultLocation);
- EntityLoader loader = selector.getLoader();
- List<String> list = map.get(loader);
- if (list == null)
- {
- list = new ArrayList<String>();
- map.put(loader, list);
- }
- list.add(selector.getPermId());
- }
- return map;
- }
-
- private Map<EntityLoader, TableMap<String, IEntityInformationHolderWithPermId>> loadEntities(Map<EntityLoader, List<String>> map)
- {
- Map<EntityLoader, TableMap<String, IEntityInformationHolderWithPermId>> result =
- new EnumMap<DataSetTable.EntityLoader, TableMap<String, IEntityInformationHolderWithPermId>>(EntityLoader.class);
- Set<Entry<EntityLoader, List<String>>> entrySet = map.entrySet();
- for (Entry<EntityLoader, List<String>> entry : entrySet)
- {
- EntityLoader loader = entry.getKey();
- List<String> permIds = entry.getValue();
- List<IEntityInformationHolderWithPermId> entities = loader.loadEntities(this, managedPropertyEvaluatorFactory, permIds);
- result.put(loader, new TableMap<String, IEntityInformationHolderWithPermId>(entities, PERM_ID_EXTRACTOR));
- }
- return result;
- }
-
- private static enum EntityLoader
- {
- SAMPLE()
- {
- @Override
- public List<? extends IEntityInformationHolderWithPermId> doLoadEntities(IDAOFactory daoFactory,
- IManagedPropertyEvaluatorFactory evaluatorFactory, List<String> permIds)
- {
- return SampleTranslator.translate(daoFactory.getSampleDAO().listByPermID(permIds),
- "", Collections.<Long, Set<Metaproject>>emptyMap(), evaluatorFactory);
- }
- },
- DATA_SET()
- {
- @Override
- public List<? extends IEntityInformationHolderWithPermId> doLoadEntities(IDAOFactory daoFactory,
- IManagedPropertyEvaluatorFactory evaluatorFactory, List<String> permIds)
- {
- return DataSetTranslator.translate(daoFactory.getDataDAO().listByCode(new HashSet<String>(permIds)),
- "", "", Collections.<Long, Set<Metaproject>>emptyMap(), evaluatorFactory);
- }
- },
- EXPERIMENT()
- {
- @Override
- public List<? extends IEntityInformationHolderWithPermId> doLoadEntities(IDAOFactory daoFactory,
- IManagedPropertyEvaluatorFactory evaluatorFactory, List<String> permIds)
- {
- return ExperimentTranslator.translate(daoFactory.getExperimentDAO().listByPermID(permIds),
- "", Collections.<Long, Set<Metaproject>>emptyMap(), evaluatorFactory);
- }
- },
- MATERIAL()
- {
- @Override
- public List<? extends IEntityInformationHolderWithPermId> doLoadEntities(IDAOFactory daoFactory,
- IManagedPropertyEvaluatorFactory evaluatorFactory, List<String> permIds)
- {
- throw new UnsupportedOperationException();
- }
- };
-
- public List<IEntityInformationHolderWithPermId> loadEntities(IDAOFactory daoFactory,
- IManagedPropertyEvaluatorFactory evaluatorFactory, List<String> permIds)
- {
- List<IEntityInformationHolderWithPermId> result = new ArrayList<IEntityInformationHolderWithPermId>();
- for (IEntityInformationHolderWithPermId entity : doLoadEntities(daoFactory, evaluatorFactory, permIds))
- {
- result.add(entity);
- }
- return result;
- }
-
- public abstract List<? extends IEntityInformationHolderWithPermId> doLoadEntities(IDAOFactory daoFactory,
- IManagedPropertyEvaluatorFactory evaluatorFactory, List<String> permIds);
- }
-
- private static final class Selector
- {
- private EntityLoader loader;
-
- private String permId;
-
- Selector(ISearchDomainResultLocation resultLocation)
- {
- permId = null;
- loader = EntityLoader.DATA_SET;
- if (resultLocation instanceof DataSetFileSearchResultLocation)
- {
- permId = ((DataSetFileSearchResultLocation) resultLocation).getDataSetCode();
- } else if (resultLocation instanceof EntityPropertySearchResultLocation)
- {
- EntityPropertySearchResultLocation location = (EntityPropertySearchResultLocation) resultLocation;
- permId = location.getPermId();
- loader = EntityLoader.valueOf(location.getEntityKind().toString());
- }
- }
-
- EntityLoader getLoader()
- {
- return loader;
- }
-
- String getPermId()
- {
- return permId;
- }
-
- }
-
- @Override
- public List<SearchDomain> listAvailableSearchDomains()
- {
- List<SearchDomain> result = new ArrayList<SearchDomain>();
- List<DataStorePE> stores = getDataStoreDAO().listDataStores();
- for (DataStorePE dataStore : stores)
- {
- IDataStoreService service = tryGetDataStoreService(dataStore);
- if (service != null)
- {
- result.addAll(service.listAvailableSearchDomains(dataStore.getSessionToken()));
- }
- }
- return result;
- }
-
- private List<SearchDomainSearchResult> askAllDataStoreServers(String preferredSequenceDatabaseOrNull,
- String sequenceSnippet, Map<String, String> optionalParametersOrNull)
- {
- List<SearchDomainSearchResult> result = new ArrayList<SearchDomainSearchResult>();
- List<DataStorePE> stores = getDataStoreDAO().listDataStores();
- for (DataStorePE dataStore : stores)
- {
- IDataStoreService service = tryGetDataStoreService(dataStore);
- if (service != null)
- {
- result.addAll(service.searchForDataSetsWithSequences(dataStore.getSessionToken(),
- preferredSequenceDatabaseOrNull, sequenceSnippet, optionalParametersOrNull));
- }
- }
- return result;
- }
-
@Override
public void loadByDataSetCodes(List<String> dataSetCodes, boolean withProperties,
boolean lockForUpdate)
@@ -691,23 +485,12 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
service.uploadDataSetsToCIFEX(sessionToken, cleanDataSets, context);
}
- // null if DSS URL has not been specified
- private IDataStoreService tryGetDataStoreService(DataStorePE dataStore)
- {
- String remoteURL = dataStore.getRemoteUrl();
- if (StringUtils.isBlank(remoteURL))
- {
- return null;
- }
- return dssFactory.create(remoteURL);
- }
-
@Override
public void processDatasets(String datastoreServiceKey, String datastoreCode,
List<String> datasetCodes, Map<String, String> parameterBindings)
{
DataStorePE dataStore = findDataStore(datastoreCode);
- IDataStoreService service = tryGetDataStoreService(dataStore);
+ IDataStoreService service = tryGetDataStoreService(dataStore, dssFactory);
if (service == null)
{
throw createUnknownDataStoreServerException();
@@ -763,7 +546,7 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
DataStorePE dataStore = findDataStore(batch.getId());
String sessionToken = dataStore.getSessionToken();
String userSessionToken = session.getSessionToken();
- IDataStoreService service = tryGetDataStoreService(dataStore);
+ IDataStoreService service = tryGetDataStoreService(dataStore, dssFactory);
parameterBindings.put(Constants.USER_PARAMETER, session.tryGetPerson().getUserId());
service.processDatasets(sessionToken, userSessionToken, datastoreServiceKey, batch.getObjects(),
parameterBindings, tryGetLoggedUserId(), tryGetLoggedUserEmail());
@@ -1147,7 +930,7 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
for (Entry<DataStorePE, List<ExternalDataPE>> entry : datasetsByStore.entrySet())
{
DataStorePE dataStore = entry.getKey();
- IDataStoreService service = tryGetDataStoreService(dataStore);
+ IDataStoreService service = tryGetDataStoreService(dataStore, dssFactory);
if (service == null)
{
throw createUnknownDataStoreServerException();
@@ -1381,7 +1164,7 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
public LinkModel retrieveLinkFromDataSet(String key, String datastoreCode, String dataSetCode)
{
DataStorePE dataStore = findDataStore(datastoreCode);
- IDataStoreService service = tryGetDataStoreService(dataStore);
+ IDataStoreService service = tryGetDataStoreService(dataStore, dssFactory);
if (service == null)
{
throw createUnknownDataStoreServerException();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java
index 487489adc49..5d15adaa6fa 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java
@@ -46,6 +46,8 @@ public interface ICommonBusinessObjectFactory extends IAbstractBussinessObjectFa
public IDataBO createDataBO(Session session);
public IDataSetTable createDataSetTable(final Session session);
+
+ public ISearchDomainSearcher createSearchDomainSearcher(Session session);
public IDeletedDataSetTable createDeletedDataSetTable(final Session session);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IDataSetTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IDataSetTable.java
index 86d56e04b7c..afaeb18469a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IDataSetTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IDataSetTable.java
@@ -19,10 +19,8 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo;
import java.util.List;
import java.util.Map;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomain;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LinkModel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchDomainSearchResultWithFullEntity;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetBatchUpdatesDTO;
@@ -37,17 +35,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
*/
public interface IDataSetTable
{
- /**
- * Searchs for data sets with sequences.
- */
- List<SearchDomainSearchResultWithFullEntity> searchForDataSetsWithSequences(String preferredSequenceDatabaseOrNull,
- String sequenceSnippet, Map<String, String> optionalParametersOrNull);
-
- /**
- * Lists all available sequence databases.
- */
- List<SearchDomain> listAvailableSearchDomains();
-
/**
* Loads data sets specified by their codes. Data set codes will be ignored if no {@link DataPE} could be found. Properties will be loaded too
* depending on <var>withProperties</var> value. Optionally if <var>lockForUpdate</var> is <var>true</var> all updates to loaded data sets from
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISearchDomainSearcher.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISearchDomainSearcher.java
new file mode 100644
index 00000000000..6f075c9aa49
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISearchDomainSearcher.java
@@ -0,0 +1,44 @@
+/*
+ * Copyright 2014 ETH Zuerich, SIS
+ *
+ * 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.business.bo;
+
+import java.util.List;
+import java.util.Map;
+
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomain;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchDomainSearchResultWithFullEntity;
+
+/**
+ * Business object for searching in search domains.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface ISearchDomainSearcher
+{
+ /**
+ * Lists all available sequence databases.
+ */
+ List<SearchDomain> listAvailableSearchDomains();
+
+ /**
+ * Searches for entities with sequences.
+ */
+ List<SearchDomainSearchResultWithFullEntity> searchForEntitiesWithSequences(String preferredSearchDomainOrNull,
+ String sequenceSnippet, Map<String, String> optionalParametersOrNull);
+
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcher.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcher.java
new file mode 100644
index 00000000000..40b520bb424
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcher.java
@@ -0,0 +1,264 @@
+/*
+ * Copyright 2014 ETH Zuerich, SIS
+ *
+ * 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.business.bo;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.EnumMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+
+import ch.systemsx.cisd.common.collection.IKeyExtractor;
+import ch.systemsx.cisd.common.collection.TableMap;
+import ch.systemsx.cisd.openbis.generic.server.business.IDataStoreServiceFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFileSearchResultLocation;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityPropertySearchResultLocation;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ISearchDomainResultLocation;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomain;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
+import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchDomainSearchResultWithFullEntity;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
+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.Session;
+import ch.systemsx.cisd.openbis.generic.shared.managed_property.IManagedPropertyEvaluatorFactory;
+import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class SearchDomainSearcher extends AbstractBusinessObject implements ISearchDomainSearcher
+{
+ private static final Map<Long, Set<Metaproject>> EMPTY_METAPROJECTS = Collections.<Long, Set<Metaproject>>emptyMap();
+
+ private static final IKeyExtractor<String, IEntityInformationHolderWithPermId> PERM_ID_EXTRACTOR =
+ new IKeyExtractor<String, IEntityInformationHolderWithPermId>()
+ {
+ @Override
+ public String getKey(IEntityInformationHolderWithPermId e)
+ {
+ return e.getPermId();
+ }
+ };
+
+ private final IDataStoreServiceFactory dssFactory;
+
+ public SearchDomainSearcher(IDAOFactory daoFactory, Session session,
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory, IDataStoreServiceFactory dssFactory)
+ {
+ super(daoFactory, session, managedPropertyEvaluatorFactory);
+ this.dssFactory = dssFactory;
+ }
+
+ @Override
+ public List<SearchDomain> listAvailableSearchDomains()
+ {
+ List<SearchDomain> result = new ArrayList<SearchDomain>();
+ List<DataStorePE> stores = getDataStoreDAO().listDataStores();
+ for (DataStorePE dataStore : stores)
+ {
+ IDataStoreService service = tryGetDataStoreService(dataStore, dssFactory);
+ if (service != null)
+ {
+ result.addAll(service.listAvailableSearchDomains(dataStore.getSessionToken()));
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public List<SearchDomainSearchResultWithFullEntity> searchForEntitiesWithSequences(String preferredSearchDomainOrNull,
+ String sequenceSnippet, Map<String, String> optionalParametersOrNull)
+ {
+ List<SearchDomainSearchResult> searchResults
+ = askAllDataStoreServers(preferredSearchDomainOrNull, sequenceSnippet, optionalParametersOrNull);
+ return enrichWithEntities(searchResults);
+ }
+
+ private List<SearchDomainSearchResult> askAllDataStoreServers(String preferredSearchDomainOrNull,
+ String sequenceSnippet, Map<String, String> optionalParametersOrNull)
+ {
+ List<SearchDomainSearchResult> result = new ArrayList<SearchDomainSearchResult>();
+ List<DataStorePE> stores = getDataStoreDAO().listDataStores();
+ for (DataStorePE dataStore : stores)
+ {
+ IDataStoreService service = tryGetDataStoreService(dataStore, dssFactory);
+ if (service != null)
+ {
+ result.addAll(service.searchForDataSetsWithSequences(dataStore.getSessionToken(),
+ preferredSearchDomainOrNull, sequenceSnippet, optionalParametersOrNull));
+ }
+ }
+ return result;
+ }
+
+ private List<SearchDomainSearchResultWithFullEntity> enrichWithEntities(List<SearchDomainSearchResult> searchResults)
+ {
+ Map<EntityLoader, List<String>> map = separate(searchResults);
+ Map<EntityLoader, TableMap<String, IEntityInformationHolderWithPermId>> result = loadEntities(map);
+ List<SearchDomainSearchResultWithFullEntity> enrichedResults = new ArrayList<SearchDomainSearchResultWithFullEntity>();
+ for (SearchDomainSearchResult searchResult : searchResults)
+ {
+ Selector selector = new Selector(searchResult.getResultLocation());
+ EntityLoader loader = selector.getLoader();
+ IEntityInformationHolderWithPermId entity = result.get(loader).getOrDie(selector.getPermId());
+ SearchDomainSearchResultWithFullEntity searchResultWithEntity = new SearchDomainSearchResultWithFullEntity();
+ searchResultWithEntity.setSearchResult(searchResult);
+ searchResultWithEntity.setEntity(entity);
+ enrichedResults.add(searchResultWithEntity);
+ }
+ return enrichedResults;
+ }
+
+ private Map<EntityLoader, List<String>> separate(List<SearchDomainSearchResult> searchResults)
+ {
+ Map<EntityLoader, List<String>> map = new EnumMap<EntityLoader, List<String>>(EntityLoader.class);
+ for (SearchDomainSearchResult searchResult : searchResults)
+ {
+ ISearchDomainResultLocation resultLocation = searchResult.getResultLocation();
+ Selector selector = new Selector(resultLocation);
+ EntityLoader loader = selector.getLoader();
+ List<String> list = map.get(loader);
+ if (list == null)
+ {
+ list = new ArrayList<String>();
+ map.put(loader, list);
+ }
+ list.add(selector.getPermId());
+ }
+ return map;
+ }
+
+ private Map<EntityLoader, TableMap<String, IEntityInformationHolderWithPermId>> loadEntities(Map<EntityLoader, List<String>> map)
+ {
+ Map<EntityLoader, TableMap<String, IEntityInformationHolderWithPermId>> result =
+ new EnumMap<EntityLoader, TableMap<String, IEntityInformationHolderWithPermId>>(EntityLoader.class);
+ Set<Entry<EntityLoader, List<String>>> entrySet = map.entrySet();
+ for (Entry<EntityLoader, List<String>> entry : entrySet)
+ {
+ EntityLoader loader = entry.getKey();
+ List<String> permIds = entry.getValue();
+ List<IEntityInformationHolderWithPermId> entities
+ = loader.loadEntities(this, managedPropertyEvaluatorFactory, permIds);
+ result.put(loader, new TableMap<String, IEntityInformationHolderWithPermId>(entities, PERM_ID_EXTRACTOR));
+ }
+ return result;
+ }
+
+ private static enum EntityLoader
+ {
+ SAMPLE()
+ {
+ @Override
+ public List<? extends IEntityInformationHolderWithPermId> doLoadEntities(IDAOFactory daoFactory,
+ IManagedPropertyEvaluatorFactory evaluatorFactory, List<String> permIds)
+ {
+ List<SamplePE> samples = daoFactory.getSampleDAO().listByPermID(permIds);
+ return SampleTranslator.translate(samples, "", EMPTY_METAPROJECTS, evaluatorFactory);
+ }
+ },
+ DATA_SET()
+ {
+ @Override
+ public List<? extends IEntityInformationHolderWithPermId> doLoadEntities(IDAOFactory daoFactory,
+ IManagedPropertyEvaluatorFactory evaluatorFactory, List<String> permIds)
+ {
+ List<DataPE> dataSets = daoFactory.getDataDAO().listByCode(new HashSet<String>(permIds));
+ return DataSetTranslator.translate(dataSets, "", "", EMPTY_METAPROJECTS, evaluatorFactory);
+ }
+ },
+ EXPERIMENT()
+ {
+ @Override
+ public List<? extends IEntityInformationHolderWithPermId> doLoadEntities(IDAOFactory daoFactory,
+ IManagedPropertyEvaluatorFactory evaluatorFactory, List<String> permIds)
+ {
+ List<ExperimentPE> experiments = daoFactory.getExperimentDAO().listByPermID(permIds);
+ return ExperimentTranslator.translate(experiments, "", EMPTY_METAPROJECTS, evaluatorFactory);
+ }
+ },
+ MATERIAL()
+ {
+ @Override
+ public List<? extends IEntityInformationHolderWithPermId> doLoadEntities(IDAOFactory daoFactory,
+ IManagedPropertyEvaluatorFactory evaluatorFactory, List<String> permIds)
+ {
+ throw new UnsupportedOperationException();
+ }
+ };
+
+ public List<IEntityInformationHolderWithPermId> loadEntities(IDAOFactory daoFactory,
+ IManagedPropertyEvaluatorFactory evaluatorFactory, List<String> permIds)
+ {
+ List<IEntityInformationHolderWithPermId> result = new ArrayList<IEntityInformationHolderWithPermId>();
+ for (IEntityInformationHolderWithPermId entity : doLoadEntities(daoFactory, evaluatorFactory, permIds))
+ {
+ result.add(entity);
+ }
+ return result;
+ }
+
+ public abstract List<? extends IEntityInformationHolderWithPermId> doLoadEntities(IDAOFactory daoFactory,
+ IManagedPropertyEvaluatorFactory evaluatorFactory, List<String> permIds);
+ }
+
+ private static final class Selector
+ {
+ private EntityLoader loader;
+
+ private String permId;
+
+ Selector(ISearchDomainResultLocation resultLocation)
+ {
+ permId = null;
+ loader = EntityLoader.DATA_SET;
+ if (resultLocation instanceof DataSetFileSearchResultLocation)
+ {
+ permId = ((DataSetFileSearchResultLocation) resultLocation).getDataSetCode();
+ } else if (resultLocation instanceof EntityPropertySearchResultLocation)
+ {
+ EntityPropertySearchResultLocation location = (EntityPropertySearchResultLocation) resultLocation;
+ permId = location.getPermId();
+ loader = EntityLoader.valueOf(location.getEntityKind().toString());
+ }
+ }
+
+ EntityLoader getLoader()
+ {
+ return loader;
+ }
+
+ String getPermId()
+ {
+ return permId;
+ }
+
+ }
+
+}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTableTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTableTest.java
index b82b8bb38f3..e69c9856d54 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTableTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTableTest.java
@@ -26,9 +26,7 @@ import static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchiving
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
-import java.util.HashSet;
import java.util.List;
-import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
@@ -47,16 +45,12 @@ import ch.systemsx.cisd.openbis.generic.server.business.ManagerTestTool;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.event.DeleteDataSetEventBuilder;
import ch.systemsx.cisd.openbis.generic.shared.CommonTestUtils;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFileSearchResultLocation;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomain;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchDomainSearchResultWithFullEntity;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
@@ -82,12 +76,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
@Friend(toClasses = DataSetTable.class)
public final class DataSetTableTest extends AbstractBOTest
{
- private static final Map<String, String> OPTIONAL_PARAMETERS = Collections.singletonMap("greeting", "hi");
-
- private static final String SEQUENCE_SNIPPET = "GATTACA";
-
- private static final String SEQUENCE_DATABASE = "MY_DB";
-
private IDataStoreServiceFactory dssFactory;
private DataStorePE dss1;
@@ -165,95 +153,6 @@ public final class DataSetTableTest extends AbstractBOTest
});
}
- @Test
- public void testSearchForDataSetsWithSequences()
- {
- DataStorePE store1 = new DataStorePE();
- store1.setRemoteUrl("http://abc1.de");
- DataStorePE store2 = new DataStorePE();
- store2.setRemoteUrl("http://abc2.de");
- store2.setSessionToken("session-2");
- DataStorePE store3 = new DataStorePE();
- prepareListDataStores(store1, store2, store3);
- prepareSearchSequenceDatabase(store1, dataStoreService1, "ds1", "ds2");
- prepareSearchSequenceDatabase(store2, dataStoreService2, "ds3", "ds3");
- final ExternalDataPE ds1 = createDataSet("ds1", store1);
- final ExternalDataPE ds2 = createDataSet("ds2", store1);
- final ExternalDataPE ds3 = createDataSet("ds3", store2);
- context.checking(new Expectations()
- {
- {
- one(dataDAO).listByCode(new HashSet<String>(Arrays.asList("ds1", "ds2", "ds3")));
- will(returnValue(Arrays.asList(new ExternalDataPE[] { ds1, ds2, ds3 })));
- }
- });
-
- List<SearchDomainSearchResultWithFullEntity> results =
- createDataSetTable().searchForDataSetsWithSequences(SEQUENCE_DATABASE, SEQUENCE_SNIPPET, OPTIONAL_PARAMETERS);
-
- assertEquals("Search Domain: test-db, Result location: [Data set: ds1, path: ds1/path, "
- + "identifier: [id-ds1], position: 42]",
- results.get(0).getSearchResult().toString());
- assertEquals(ds1.getCode(), ((AbstractExternalData) results.get(0).getEntity()).getCode());
- assertEquals("/G1/P1/exp1", ((AbstractExternalData) results.get(0).getEntity()).getExperiment().getIdentifier());
- assertEquals("Search Domain: test-db, Result location: [Data set: ds2, path: ds2/path, "
- + "identifier: [id-ds2], position: 42]",
- results.get(1).getSearchResult().toString());
- assertEquals(ds2.getCode(), ((AbstractExternalData) results.get(1).getEntity()).getCode());
- assertEquals("/G1/P1/exp1", ((AbstractExternalData) results.get(1).getEntity()).getExperiment().getIdentifier());
- assertEquals("Search Domain: test-db, Result location: [Data set: ds3, path: ds3/path, "
- + "identifier: [id-ds3], position: 42]",
- results.get(2).getSearchResult().toString());
- assertEquals(ds3.getCode(), ((AbstractExternalData) results.get(2).getEntity()).getCode());
- assertEquals("/G1/P1/exp1", ((AbstractExternalData) results.get(2).getEntity()).getExperiment().getIdentifier());
- assertEquals(ds3.getCode(), ((AbstractExternalData) results.get(3).getEntity()).getCode());
- assertEquals("/G1/P1/exp1", ((AbstractExternalData) results.get(3).getEntity()).getExperiment().getIdentifier());
- assertEquals(4, results.size());
- context.assertIsSatisfied();
- }
-
- private void prepareListDataStores(final DataStorePE... dataStores)
- {
- context.checking(new Expectations()
- {
- {
- one(dataStoreDAO).listDataStores();
- will(returnValue(Arrays.asList(dataStores)));
- }
- });
- }
-
- private void prepareSearchSequenceDatabase(final DataStorePE dataStore, final IDataStoreService service,
- final String... foundDataSets)
- {
- context.checking(new Expectations()
- {
- {
- allowing(dssFactory).create(dataStore.getRemoteUrl());
- will(returnValue(service));
-
- one(service).searchForDataSetsWithSequences(dataStore.getSessionToken(),
- SEQUENCE_DATABASE, SEQUENCE_SNIPPET, OPTIONAL_PARAMETERS);
- List<SearchDomainSearchResult> results = new ArrayList<SearchDomainSearchResult>();
- for (String foundDataSet : foundDataSets)
- {
- SearchDomainSearchResult result = new SearchDomainSearchResult();
- SearchDomain searchDomain = new SearchDomain();
- searchDomain.setName("test-db");
- result.setSearchDomain(searchDomain);
- DataSetFileSearchResultLocation resultLocation = new DataSetFileSearchResultLocation();
- resultLocation.setDataSetCode(foundDataSet);
- resultLocation.setPathInDataSet(foundDataSet + "/path");
- resultLocation.setPosition(42);
- resultLocation.setIdentifier("id-" + foundDataSet);
- result.setResultLocation(resultLocation);
- results.add(result);
- }
- will(returnValue(results));
- }
- });
- }
-
@Test
public final void testLoadBySampleTechIdWithNullSampleId()
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcherTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcherTest.java
new file mode 100644
index 00000000000..905ca0b3e67
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcherTest.java
@@ -0,0 +1,374 @@
+/*
+ * Copyright 2014 ETH Zuerich, SIS
+ *
+ * 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.business.bo;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+
+import org.jmock.Expectations;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.generic.server.business.IDataStoreServiceFactory;
+import ch.systemsx.cisd.openbis.generic.server.business.ManagerTestTool;
+import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFileSearchResultLocation;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityKind;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityPropertySearchResultLocation;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomain;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
+import ch.systemsx.cisd.openbis.generic.shared.basic.IPermIdHolder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchDomainSearchResultWithFullEntity;
+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.ExperimentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.FileFormatTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class SearchDomainSearcherTest extends AbstractBOTest
+{
+ private static final Map<String, String> OPTIONAL_PARAMETERS = Collections.singletonMap("greeting", "hi");
+
+ private static final String SEQUENCE_SNIPPET = "GATTACA";
+
+ private static final String SEQUENCE_DATABASE = "MY_DB";
+
+ private IDataStoreServiceFactory dssFactory;
+
+ private IDataStoreService dataStoreService1;
+
+ private IDataStoreService dataStoreService2;
+
+ private DataStorePE store1;
+
+ private DataStorePE store2;
+
+ private DataStorePE store3;
+
+ @BeforeMethod
+ @Override
+ public void beforeMethod()
+ {
+ super.beforeMethod();
+ dssFactory = context.mock(IDataStoreServiceFactory.class);
+ dataStoreService1 = context.mock(IDataStoreService.class, "dataStoreService1");
+ dataStoreService2 = context.mock(IDataStoreService.class, "dataStoreService2");
+ store1 = new DataStorePE();
+ store1.setRemoteUrl("http://abc1.de");
+ store1.setSessionToken("session-1");
+ store2 = new DataStorePE();
+ store2.setRemoteUrl("http://abc2.de");
+ store2.setSessionToken("session-2");
+ store3 = new DataStorePE();
+ prepareListDataStores(store1, store2, store3);
+ prepareCreateService(dataStoreService1, store1);
+ prepareCreateService(dataStoreService2, store2);
+ }
+
+ @Test
+ public void testListAvailableSearchDomains()
+ {
+ final SearchDomain searchDomain1 = new SearchDomain();
+ final SearchDomain searchDomain2 = new SearchDomain();
+ final SearchDomain searchDomain3 = new SearchDomain();
+ context.checking(new Expectations()
+ {
+ {
+ one(dataStoreService1).listAvailableSearchDomains(store1.getSessionToken());
+ will(returnValue(Arrays.asList(searchDomain1)));
+
+ one(dataStoreService2).listAvailableSearchDomains(store2.getSessionToken());
+ will(returnValue(Arrays.asList(searchDomain2, searchDomain3)));
+ }
+ });
+
+ List<SearchDomain> searchDomains = createSearcher().listAvailableSearchDomains();
+
+ assertSame(searchDomain1, searchDomains.get(0));
+ assertSame(searchDomain2, searchDomains.get(1));
+ assertSame(searchDomain3, searchDomains.get(2));
+ assertEquals(3, searchDomains.size());
+ context.assertIsSatisfied();
+
+ }
+
+ @Test
+ public void testSearchForEntitiesWithSequences()
+ {
+ prepareSearchForEntityPropertiesWithSequences(store1, dataStoreService1, "DATA_SET:DS1:SEQ");
+ prepareSearchForEntityPropertiesWithSequences(store2, dataStoreService2,
+ "SAMPLE:S1:OLIGO", "SAMPLE:S2:OLIGO", "EXPERIMENT:E1:S");
+ ExternalDataPE ds1 = createDataSet("DS1", store1);
+ prepareListDataSetsByCode(ds1);
+ SamplePE s1 = createSample("S1");
+ SamplePE s2 = createSample("S2");
+ prepareListSamplesByPermId(s1, s2);
+ ExperimentPE e1 = createExperiment("E1");
+ prepareListExperimentsByPermId(e1);
+
+ List<SearchDomainSearchResultWithFullEntity> results =
+ createSearcher().searchForEntitiesWithSequences(SEQUENCE_DATABASE, SEQUENCE_SNIPPET, OPTIONAL_PARAMETERS);
+
+ assertEquals("DS1", results.get(0).getEntity().getPermId());
+ assertEquals("Search Domain: test-db, Result location: [Data_set perm id: DS1, property type: SEQ, position: 24]",
+ results.get(0).getSearchResult().toString());
+ assertEquals("S1", results.get(1).getEntity().getPermId());
+ assertEquals("Search Domain: test-db, Result location: [Sample perm id: S1, property type: OLIGO, position: 24]",
+ results.get(1).getSearchResult().toString());
+ assertEquals("S2", results.get(2).getEntity().getPermId());
+ assertEquals("Search Domain: test-db, Result location: [Sample perm id: S2, property type: OLIGO, position: 24]",
+ results.get(2).getSearchResult().toString());
+ assertEquals("E1", results.get(3).getEntity().getPermId());
+ assertEquals("Search Domain: test-db, Result location: [Experiment perm id: E1, property type: S, position: 24]",
+ results.get(3).getSearchResult().toString());
+ assertEquals(4, results.size());
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testSearchForDataSetsWithSequences()
+ {
+ prepareSearchForDataSetsWithSequences(store1, dataStoreService1, "ds1", "ds2");
+ prepareSearchForDataSetsWithSequences(store2, dataStoreService2, "ds3", "ds3");
+ final ExternalDataPE ds1 = createDataSet("ds1", store1);
+ final ExternalDataPE ds2 = createDataSet("ds2", store1);
+ final ExternalDataPE ds3 = createDataSet("ds3", store2);
+ prepareListDataSetsByCode(ds1, ds2, ds3);
+
+ List<SearchDomainSearchResultWithFullEntity> results =
+ createSearcher().searchForEntitiesWithSequences(SEQUENCE_DATABASE, SEQUENCE_SNIPPET, OPTIONAL_PARAMETERS);
+
+ assertEquals("Search Domain: test-db, Result location: [Data set: ds1, path: ds1/path, "
+ + "identifier: [id-ds1], position: 42]",
+ results.get(0).getSearchResult().toString());
+ assertEquals(ds1.getCode(), ((AbstractExternalData) results.get(0).getEntity()).getCode());
+ assertEquals("/G1/P1/exp1", ((AbstractExternalData) results.get(0).getEntity()).getExperiment().getIdentifier());
+ assertEquals("Search Domain: test-db, Result location: [Data set: ds2, path: ds2/path, "
+ + "identifier: [id-ds2], position: 42]",
+ results.get(1).getSearchResult().toString());
+ assertEquals(ds2.getCode(), ((AbstractExternalData) results.get(1).getEntity()).getCode());
+ assertEquals("/G1/P1/exp1", ((AbstractExternalData) results.get(1).getEntity()).getExperiment().getIdentifier());
+ assertEquals("Search Domain: test-db, Result location: [Data set: ds3, path: ds3/path, "
+ + "identifier: [id-ds3], position: 42]",
+ results.get(2).getSearchResult().toString());
+ assertEquals(ds3.getCode(), ((AbstractExternalData) results.get(2).getEntity()).getCode());
+ assertEquals("/G1/P1/exp1", ((AbstractExternalData) results.get(2).getEntity()).getExperiment().getIdentifier());
+ assertEquals(ds3.getCode(), ((AbstractExternalData) results.get(3).getEntity()).getCode());
+ assertEquals("/G1/P1/exp1", ((AbstractExternalData) results.get(3).getEntity()).getExperiment().getIdentifier());
+ assertEquals(4, results.size());
+ context.assertIsSatisfied();
+ }
+
+ private void prepareListDataStores(final DataStorePE... dataStores)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(dataStoreDAO).listDataStores();
+ will(returnValue(Arrays.asList(dataStores)));
+ }
+ });
+ }
+
+ private void prepareCreateService(final IDataStoreService service, final DataStorePE... dataStores)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ for (DataStorePE dataStore : dataStores)
+ {
+ allowing(dssFactory).create(dataStore.getRemoteUrl());
+ will(returnValue(service));
+ }
+ }
+ });
+
+ }
+
+ private void prepareSearchForDataSetsWithSequences(final DataStorePE dataStore, final IDataStoreService service,
+ final String... foundDataSets)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(service).searchForDataSetsWithSequences(dataStore.getSessionToken(),
+ SEQUENCE_DATABASE, SEQUENCE_SNIPPET, OPTIONAL_PARAMETERS);
+ List<SearchDomainSearchResult> results = new ArrayList<SearchDomainSearchResult>();
+ for (String foundDataSet : foundDataSets)
+ {
+ SearchDomainSearchResult result = new SearchDomainSearchResult();
+ SearchDomain searchDomain = new SearchDomain();
+ searchDomain.setName("test-db");
+ result.setSearchDomain(searchDomain);
+ DataSetFileSearchResultLocation resultLocation = new DataSetFileSearchResultLocation();
+ resultLocation.setDataSetCode(foundDataSet);
+ resultLocation.setPathInDataSet(foundDataSet + "/path");
+ resultLocation.setPosition(42);
+ resultLocation.setIdentifier("id-" + foundDataSet);
+ result.setResultLocation(resultLocation);
+ results.add(result);
+ }
+ will(returnValue(results));
+ }
+ });
+ }
+
+ private void prepareSearchForEntityPropertiesWithSequences(final DataStorePE dataStore,
+ final IDataStoreService service, final String... foundLocations)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(service).searchForDataSetsWithSequences(dataStore.getSessionToken(),
+ SEQUENCE_DATABASE, SEQUENCE_SNIPPET, OPTIONAL_PARAMETERS);
+ List<SearchDomainSearchResult> results = new ArrayList<SearchDomainSearchResult>();
+ for (String foundLocation : foundLocations)
+ {
+ SearchDomainSearchResult result = new SearchDomainSearchResult();
+ SearchDomain searchDomain = new SearchDomain();
+ searchDomain.setName("test-db");
+ result.setSearchDomain(searchDomain);
+ EntityPropertySearchResultLocation resultLocation = new EntityPropertySearchResultLocation();
+ String[] splittedLocation = foundLocation.split(":");
+ resultLocation.setEntityKind(EntityKind.valueOf(splittedLocation[0]));
+ resultLocation.setPermId(splittedLocation[1]);
+ resultLocation.setPropertyType(splittedLocation[2]);
+ resultLocation.setPosition(24);
+ result.setResultLocation(resultLocation);
+ results.add(result);
+ }
+ will(returnValue(results));
+ }
+ });
+ }
+
+ private void prepareListDataSetsByCode(final ExternalDataPE... dataSets)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(dataDAO).listByCode(new LinkedHashSet<String>(getPermIds(dataSets)));
+ will(returnValue(Arrays.asList(dataSets)));
+ }
+ });
+ }
+
+ private void prepareListSamplesByPermId(final SamplePE... samples)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(sampleDAO).listByPermID(getPermIds(samples));
+ will(returnValue(Arrays.asList(samples)));
+ }
+ });
+ }
+
+ private void prepareListExperimentsByPermId(final ExperimentPE... experiments)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(experimentDAO).listByPermID(getPermIds(experiments));
+ will(returnValue(Arrays.asList(experiments)));
+ }
+ });
+ }
+
+ private ExternalDataPE createDataSet(String code, DataStorePE dataStore)
+ {
+ ExternalDataPE data = new ExternalDataPE();
+ data.setId((long) code.hashCode());
+ data.setCode(code);
+ data.setDataStore(dataStore);
+ data.setLocation("here/" + code);
+ ExperimentPE experiment = new ExperimentPE();
+ experiment.setCode("exp1");
+ experiment.setExperimentType(new ExperimentTypePE());
+ ProjectPE project = new ProjectPE();
+ project.setCode("p1");
+ SpacePE group = new SpacePE();
+ group.setCode("g1");
+ project.setSpace(group);
+ experiment.setProject(project);
+ data.setExperiment(experiment);
+ DataSetTypePE type = new DataSetTypePE();
+ type.setDataSetKind(DataSetKind.PHYSICAL.name());
+ data.setDataSetType(type);
+ FileFormatTypePE fileFormatType = new FileFormatTypePE();
+ fileFormatType.setCode("fileFormat");
+ data.setFileFormatType(fileFormatType);
+ return data;
+ }
+
+ private SamplePE createSample(String permID)
+ {
+ SamplePE sample = new SamplePE();
+ sample.setPermId(permID);
+ SampleTypePE sampleType = new SampleTypePE();
+ sampleType.setCode("TYPE");
+ sampleType.setListable(true);
+ sampleType.setSubcodeUnique(false);
+ sampleType.setAutoGeneratedCode(false);
+ sampleType.setShowParentMetadata(false);
+ sampleType.setContainerHierarchyDepth(0);
+ sampleType.setGeneratedFromHierarchyDepth(0);
+ sample.setSampleType(sampleType);
+ return sample;
+ }
+
+ private ExperimentPE createExperiment(String permID)
+ {
+ ExperimentPE experiment = new ExperimentPE();
+ experiment.setPermId(permID);
+ experiment.setExperimentType(new ExperimentTypePE());
+ ProjectPE project = new ProjectPE();
+ project.setSpace(new SpacePE());
+ experiment.setProject(project);
+ return experiment;
+ }
+
+ private SearchDomainSearcher createSearcher()
+ {
+ return new SearchDomainSearcher(daoFactory, ManagerTestTool.EXAMPLE_SESSION,
+ managedPropertyEvaluatorFactory, dssFactory);
+ }
+
+ protected List<String> getPermIds(final IPermIdHolder... permIdHolders)
+ {
+ List<String> permIds = new ArrayList<String>();
+ for (IPermIdHolder permIdHolder : permIdHolders)
+ {
+ permIds.add(permIdHolder.getPermId());
+ }
+ return permIds;
+ }
+}
--
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