diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
index 492e7f68bccb7ff10212d8d3067a559b5b0b267c..4990d245edbeaa1be13199b4ee2a68fac1a63df0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
@@ -55,7 +55,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyPE;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTranslator;
import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQuery;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.GenePlateLocationsLoader;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.PlateMaterialLocationsLoader;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.PlateContentLoader;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.ScreeningApiImpl;
import ch.systemsx.cisd.openbis.plugin.screening.shared.IScreeningServer;
@@ -155,7 +155,7 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
PlateMaterialsSearchCriteria materialCriteria)
{
Session session = getSession(sessionToken);
- return GenePlateLocationsLoader.load(session, businessObjectFactory, getDAOFactory(),
+ return PlateMaterialLocationsLoader.load(session, businessObjectFactory, getDAOFactory(),
materialCriteria, true);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/GenePlateLocationsLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateMaterialLocationsLoader.java
similarity index 93%
rename from screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/GenePlateLocationsLoader.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateMaterialLocationsLoader.java
index 6030713c3938da2c8fcb48958038731f3884a215..005266255e087337b450a35b88304d6dc33413a4 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/GenePlateLocationsLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateMaterialLocationsLoader.java
@@ -70,33 +70,40 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterials
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria.SingleExperimentSearchCriteria;
/**
+ * Loades selected wells content: metadata and (if available) image dataset and feature vectors.
+ *
* @author Tomasz Pylak
*/
@Friend(toClasses = IScreeningQuery.class)
-public class GenePlateLocationsLoader
+public class PlateMaterialLocationsLoader
{
+ /**
+ * Finds wells containing the specified material and belonging to the specified experiment.
+ * Loads wells content: metadata and (if available) image dataset and feature vectors.
+ */
public static List<WellContent> load(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
TechId geneMaterialId, String experimentPermId, boolean enrichWithImages)
{
- return new GenePlateLocationsLoader(session, businessObjectFactory, daoFactory)
+ return new PlateMaterialLocationsLoader(session, businessObjectFactory, daoFactory)
.getPlateLocations(geneMaterialId, experimentPermId, enrichWithImages);
}
public static List<WellContent> load(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
- TechId geneMaterialId)
+ PlateMaterialsSearchCriteria materialCriteria, boolean enrichWithImages)
{
- return new GenePlateLocationsLoader(session, businessObjectFactory, daoFactory)
- .getPlateLocations(geneMaterialId);
+ return new PlateMaterialLocationsLoader(session, businessObjectFactory, daoFactory)
+ .getPlateLocations(materialCriteria, enrichWithImages);
}
- public static List<WellContent> load(Session session,
+ /** loads wells metadata, but no information about image or image analysis datasets */
+ public static List<WellContent> loadOnlyMetadata(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
- PlateMaterialsSearchCriteria materialCriteria, boolean enrichWithImages)
+ TechId geneMaterialId)
{
- return new GenePlateLocationsLoader(session, businessObjectFactory, daoFactory)
- .getPlateLocations(materialCriteria, enrichWithImages);
+ return new PlateMaterialLocationsLoader(session, businessObjectFactory, daoFactory)
+ .getPlateLocations(geneMaterialId);
}
private final Session session;
@@ -105,7 +112,7 @@ public class GenePlateLocationsLoader
private final IDAOFactory daoFactory;
- private GenePlateLocationsLoader(Session session,
+ private PlateMaterialLocationsLoader(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory)
{
this.session = session;
@@ -119,7 +126,7 @@ public class GenePlateLocationsLoader
List<WellContent> locations = loadLocations(materialCriteria);
if (enrichWithImages)
{
- return enrichWithImages(locations);
+ return enrichWithDatasets(locations);
} else
{
return locations;
@@ -132,7 +139,7 @@ public class GenePlateLocationsLoader
List<WellContent> locations = loadLocations(geneMaterialId, experimentPermId);
if (enrichWithImages)
{
- return enrichWithImages(locations);
+ return enrichWithDatasets(locations);
} else
{
return locations;
@@ -144,7 +151,7 @@ public class GenePlateLocationsLoader
return loadLocations(geneMaterialId);
}
- private List<WellContent> enrichWithImages(List<WellContent> locations)
+ private List<WellContent> enrichWithDatasets(List<WellContent> locations)
{
List<ExternalData> imageDatasets = loadImageDatasets(locations);
Map<Long/* plate id */, List<ExternalData>> plateToDatasetMap =
@@ -274,13 +281,13 @@ public class GenePlateLocationsLoader
if (expId == null)
{
locations =
- dao.getPlateLocationsForMaterialCodes(ids, codesCriteria
- .getMaterialTypeCodes());
+ dao.getPlateLocationsForMaterialCodes(ids,
+ codesCriteria.getMaterialTypeCodes());
} else
{
locations =
- dao.getPlateLocationsForMaterialCodes(ids, codesCriteria
- .getMaterialTypeCodes(), expId);
+ dao.getPlateLocationsForMaterialCodes(ids,
+ codesCriteria.getMaterialTypeCodes(), expId);
}
} else if (materialSearchCriteria.tryGetMaterialId() != null)
@@ -331,9 +338,10 @@ public class GenePlateLocationsLoader
}
criteria.setCriteria(listOfCriteria);
criteria.setConnection(SearchCriteriaConnection.MATCH_ANY);
- return ArrayUtils.toPrimitive(daoFactory.getHibernateSearchDAO().searchForEntityIds(
- criteria,
- ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind.MATERIAL)
+ return ArrayUtils.toPrimitive(daoFactory
+ .getHibernateSearchDAO()
+ .searchForEntityIds(criteria,
+ ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind.MATERIAL)
.toArray(new Long[0]));
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
index efe887c4a285e70c2a379de904ec0e0aaa152e6a..2d7102f23a45c158a52d8a72a9e39f6796f6a976 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
@@ -254,7 +254,7 @@ public class ScreeningApiImpl
final ExperimentIdentifier fullExperimentIdentifier =
getExperimentIdentifierFromDB(experimentIdentifier);
wellContent =
- GenePlateLocationsLoader.load(session, businessObjectFactory, daoFactory,
+ PlateMaterialLocationsLoader.load(session, businessObjectFactory, daoFactory,
new TechId(materialOrNull.getId()), fullExperimentIdentifier.getPermId(),
false);
if (findDatasets)
@@ -294,7 +294,7 @@ public class ScreeningApiImpl
materialIdentifier.getAugmentedCode());
}
final List<WellContent> wellContent =
- GenePlateLocationsLoader.load(session, businessObjectFactory, daoFactory,
+ PlateMaterialLocationsLoader.loadOnlyMetadata(session, businessObjectFactory, daoFactory,
new TechId(materialOrNull.getId()));
if (findDatasets)