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 cac7bb848dff08faec3354d02c386fe0d07b97fa..3dcf65ef7eceefb90f907cf00c2d67c0e163ae40 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
@@ -51,7 +51,6 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IGridCustomFilterOrColumnBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IGroupBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IProjectBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IPropertyTypeBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IPropertyTypeTable;
@@ -60,6 +59,7 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IVocabularyBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IVocabularyTermBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
+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.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
@@ -141,7 +141,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.FileFormatTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.GridCustomFilterPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityInformationHolderDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewRoleAssignment;
@@ -167,7 +166,6 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.DtoConverters;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.GroupTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.MaterialTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.MaterialTypeTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.PersonTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.ProjectTranslator;
@@ -852,11 +850,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServer> impl
public List<Material> listMaterials(String sessionToken, MaterialType materialType)
{
final Session session = getSession(sessionToken);
- final IMaterialTable materialTable = businessObjectFactory.createMaterialTable(session);
- materialTable.load(materialType.getCode());
- final List<MaterialPE> materials = materialTable.getMaterials();
- Collections.sort(materials);
- return MaterialTranslator.translate(materials);
+ final IMaterialLister materialLister = businessObjectFactory.createMaterialLister(session);
+ return materialLister.list(materialType);
}
public void registerSampleType(String sessionToken, SampleType entityType)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IMaterialTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IMaterialTable.java
index 437489966c92f341eb463e8b687780ffb5220204..52753e19928f89ea44b1c172ccf6867e94be2f32 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IMaterialTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IMaterialTable.java
@@ -34,6 +34,7 @@ public interface IMaterialTable
*
* @param materialTypeCodeOrNull the material type code or <code>null</code>.
*/
+ @Deprecated
public void load(String materialTypeCodeOrNull);
/** Returns the loaded {@link MaterialPE}. */
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java
index 0418e32ed690243f66256e9d6e93dfd6bab2c0f6..243a56659a64ac84ef9b43814fe20dbf465c63f1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java
@@ -33,8 +33,6 @@ public interface IDatasetLister
/** @return datasets connected to the experiment with the specified id */
List<ExternalData> listByExperimentTechId(TechId experimentId);
- // TODO 2009-09-10, Piotr Buczek: write tests
-
/**
* @return datasets connected to the sample with the specified id
* @param showOnlyDirectlyConnected whether to return only directly connected datasets, or also
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialLister.java
index 0ec60bdefc3c3680cf303193d7daf12134ad4dca..3fda0e9baedbc9d25201d250729f80fa0375af2e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialLister.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
/**
* A class for fast material listing.
@@ -29,4 +30,9 @@ public interface IMaterialLister
{
/** fetches and sets all properties of specified materials */
void enrichWithProperties(List<Material> materials);
+
+ /**
+ * Returns a sorted list of {@link Material}s of given {@link MaterialType}.
+ */
+ public List<Material> list(MaterialType materialType);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialListingQuery.java
index c07f003cc3a96508b98f894d87f2096178a564b0..759d98ca45abe2519a9afc3e9dc3a9cf91192beb 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialListingQuery.java
@@ -42,6 +42,16 @@ public interface IMaterialListingQuery extends TransactionQuery, IPropertyListin
{
public static final int FETCH_SIZE = 1000;
+ /**
+ * Returns the materials for the given <var>materialTypeId</var>
+ */
+ @Select(sql = "select m.id, m.code, m.dbin_id, m.maty_id, "
+ + " m.registration_timestamp, m.pers_id_registerer "
+ + " from materials m where m.dbin_id=?{1} and m.maty_id=?{2} "
+ + " order by m.code", fetchSize = FETCH_SIZE)
+ public DataIterator<MaterialRecord> getMaterialsForMaterialType(long dbInstanceId,
+ long materialTypeId);
+
//
// Entity Properties
//
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/MaterialLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/MaterialLister.java
index b652b1130b90b263b5176a0aaa4eaa4c580196fb..09af3162c3cdbc9d3f3096fff294a07c7a1ae3fa 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/MaterialLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/MaterialLister.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister;
+import static org.apache.commons.lang.StringEscapeUtils.escapeHtml;
import it.unimi.dsi.fastutil.longs.Long2ObjectMap;
import it.unimi.dsi.fastutil.longs.Long2ObjectOpenHashMap;
@@ -28,20 +29,49 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.common.IEntityPropert
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.IEntityPropertiesHolderResolver;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.entity.SecondaryEntityDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
/**
- * Fast bd operations on material table.
+ * Fast DB operations on material table.
*
* @author Tomasz Pylak
+ * @author Piotr Buczek
*/
@Friend(toClasses =
{ IMaterialListingQuery.class })
public class MaterialLister implements IMaterialLister
{
+
+ //
+ // Input
+ //
+
+ private final long databaseInstanceId;
+
+ private final DatabaseInstance databaseInstance;
+
+ //
+ // Working interfaces
+ //
+
+ private final IMaterialListingQuery query;
+
private final IEntityPropertiesEnricher propertiesEnricher;
+ private SecondaryEntityDAO referencedEntityDAO;
+
+ //
+ // Working data structures
+ //
+
+ private final Long2ObjectMap<Person> persons = new Long2ObjectOpenHashMap<Person>();
+
+ //
+
public static IMaterialLister create(IDAOFactory daoFactory, String baseIndexURL)
{
MaterialListerDAO dao = MaterialListerDAO.create(daoFactory);
@@ -56,13 +86,107 @@ public class MaterialLister implements IMaterialLister
IMaterialListingQuery query = dao.getQuery();
EntityPropertiesEnricher propertiesEnricher =
new EntityPropertiesEnricher(query, dao.getPropertySetQuery());
- return new MaterialLister(propertiesEnricher);
+ return new MaterialLister(dao.getDatabaseInstanceId(), dao.getDatabaseInstance(), query,
+ propertiesEnricher, referencedEntityDAO);
}
// For unit tests
- MaterialLister(IEntityPropertiesEnricher propertiesEnricher)
+ MaterialLister(final long databaseInstanceId, DatabaseInstance databaseInstance,
+ final IMaterialListingQuery query, IEntityPropertiesEnricher propertiesEnricher,
+ SecondaryEntityDAO referencedEntityDAO)
{
+ assert query != null;
+
+ this.databaseInstanceId = databaseInstanceId;
+ this.databaseInstance = databaseInstance;
+ this.query = query;
this.propertiesEnricher = propertiesEnricher;
+ this.referencedEntityDAO = referencedEntityDAO;
+ }
+
+ //
+ // Listing
+ //
+
+ public List<Material> list(MaterialType materialType)
+ {
+ return enrichMaterials(query.getMaterialsForMaterialType(databaseInstanceId, materialType
+ .getId()), materialType);
+ }
+
+ //
+ // Enriching
+ //
+
+ private List<Material> enrichMaterials(Iterable<MaterialRecord> materials,
+ MaterialType materialType)
+ {
+ List<MaterialRecord> materialRecords = asList(materials);
+ final Long2ObjectMap<Material> materialMap = createMaterials(materialRecords, materialType);
+ enrichWithProperties(materialMap);
+ return asList(materialMap);
+ }
+
+ private Long2ObjectMap<Material> createMaterials(Iterable<MaterialRecord> records,
+ MaterialType materialType)
+ {
+ Long2ObjectMap<Material> materials = new Long2ObjectOpenHashMap<Material>();
+ for (MaterialRecord record : records)
+ {
+ materials.put(record.id, createMaterial(record, materialType));
+ }
+ return materials;
+ }
+
+ private Material createMaterial(MaterialRecord record, MaterialType materialType)
+ {
+ Material material = new Material();
+ material.setId(record.id);
+ material.setCode(escapeHtml(record.code));
+
+ assert record.maty_id == materialType.getId();
+ material.setMaterialType(materialType);
+ assert record.dbin_id == databaseInstanceId;
+ material.setDatabaseInstance(databaseInstance);
+
+ material.setRegistrator(getOrCreateRegistrator(record));
+ material.setRegistrationDate(record.registration_timestamp);
+ material.setProperties(new ArrayList<IEntityProperty>());
+
+ return material;
+ }
+
+ private Person getOrCreateRegistrator(MaterialRecord row)
+ {
+ return getOrCreateRegistrator(row.pers_id_registerer);
+ }
+
+ private Person getOrCreateRegistrator(long personId)
+ {
+ Person registrator = persons.get(personId);
+ if (registrator == null)
+ {
+ registrator = referencedEntityDAO.getPerson(personId);
+ persons.put(personId, registrator);
+ }
+ return registrator;
+ }
+
+ private static <T> List<T> asList(Iterable<T> items)
+ {
+ List<T> result = new ArrayList<T>();
+ for (T item : items)
+ {
+ result.add(item);
+ }
+ return result;
+ }
+
+ private static <T> List<T> asList(Long2ObjectMap<T> items)
+ {
+ List<T> result = new ArrayList<T>();
+ org.apache.commons.collections.CollectionUtils.addAll(result, items.values().iterator());
+ return result;
}
private void enrichWithProperties(final Long2ObjectMap<Material> resultMap)
@@ -99,4 +223,5 @@ public class MaterialLister implements IMaterialLister
material.setProperties(new ArrayList<IEntityProperty>());
}
}
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/MaterialRecord.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/MaterialRecord.java
new file mode 100644
index 0000000000000000000000000000000000000000..150838de9b591de4bbf0221fc2563aed5cc541c7
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/MaterialRecord.java
@@ -0,0 +1,28 @@
+package ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister;
+
+import java.util.Date;
+
+import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.common.CodeRecord;
+
+/**
+ * A record object representing one row of the material table.
+ */
+// CREATE TABLE materials (
+// id tech_id NOT NULL,
+// code code NOT NULL,
+// maty_id tech_id NOT NULL,
+// pers_id_registerer tech_id NOT NULL,
+// registration_timestamp time_stamp_dfl NOT NULL DEFAULT now(),
+// dbin_id tech_id NOT NULL);
+@Private
+public class MaterialRecord extends CodeRecord
+{
+ public Long dbin_id;
+
+ public long maty_id;
+
+ public long pers_id_registerer;
+
+ public Date registration_timestamp;
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IMaterialDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IMaterialDAO.java
index 79c33db9d2d1f2b5ebf18b7a0f420f4d3d6593aa..969a472c0f3d65501763531361986179f42d801c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IMaterialDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IMaterialDAO.java
@@ -33,6 +33,7 @@ public interface IMaterialDAO extends IGenericDAO<MaterialPE>
/**
* Lists materials of given type. Fetches also properties and inhibitor.
*/
+ @Deprecated
public List<MaterialPE> listMaterialsWithPropertiesAndInhibitor(MaterialTypePE type);
/** Inserts given {@link MaterialPE}s into the database. */
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/MaterialType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/MaterialType.java
index 67bf774740e0f04fe87a098cae63e6a24dee28fa..8b35fafe8d05242d1fae9f5e0c38f53c7d693a0b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/MaterialType.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/MaterialType.java
@@ -27,8 +27,20 @@ public class MaterialType extends EntityType
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
+ private Long id;
+
private List<MaterialTypePropertyType> materialTypePropertyTypes;
+ public Long getId()
+ {
+ return id;
+ }
+
+ public void setId(Long id)
+ {
+ this.id = id;
+ }
+
@Override
public List<MaterialTypePropertyType> getAssignedPropertyTypes()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/MaterialTypeTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/MaterialTypeTranslator.java
index 239a59c0b4f63a565aaf8c0fe971409592afa1ae..aa28e3b7f77df291b8e64c1366a9a2ccdcbd010f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/MaterialTypeTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/MaterialTypeTranslator.java
@@ -57,6 +57,7 @@ public class MaterialTypeTranslator
return null;
}
final MaterialType result = new MaterialType();
+ result.setId(HibernateUtils.getId(entityTypeOrNull));
result.setCode(StringEscapeUtils.escapeHtml(entityTypeOrNull.getCode()));
result.setDescription(StringEscapeUtils.escapeHtml(entityTypeOrNull.getDescription()));
result.setDatabaseInstance(DatabaseInstanceTranslator.translate(entityTypeOrNull
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
index 74154eaadc436e14d5cfef4c5e9be92c6135aaac..e9f44ecc77b6ad3c6c78085374c2c7423ad59e23 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
@@ -348,7 +348,6 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
new SampleIdentifier(new GroupIdentifier(experimentIdentifierOrNull
.getDatabaseInstanceCode(), experimentIdentifierOrNull
.getGroupCode()), oldSampleIdentifier.getSampleCode());
- // TODO 2009-12-08, Piotr Buczek: does it work well with subcodes?
} else
{
// no experiment - leave sample identifier unchanged