From be9fe9c233225270b60749c5ab1e5841f2a1ac8b Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Fri, 24 Jun 2011 12:59:02 +0000
Subject: [PATCH] [LMS-2347] Jython Dropbox API extension: add the possibility
to create/fetch materials within transactions
SVN: 21840
---
.../DefaultEntityOperationService.java | 7 +-
.../v1/IDataSetRegistrationTransaction.java | 15 +
.../registrator/api/v1/IMaterial.java | 30 ++
.../api/v1/IMaterialImmutable.java | 46 +++
.../api/v1/impl/AbstractTransactionState.java | 36 ++-
.../api/v1/impl/ConversionUtils.java | 10 +
.../impl/DataSetRegistrationTransaction.java | 16 +
.../registrator/api/v1/impl/Material.java | 60 ++++
.../api/v1/impl/MaterialImmutable.java | 83 ++++++
.../server/EncapsulatedOpenBISService.java | 7 +
.../shared/IEncapsulatedOpenBISService.java | 8 +
.../dto/AtomicEntityOperationDetails.java | 12 +
.../EncapsulatedOpenBISServiceTest.java | 4 +
.../openbis/generic/server/ETLService.java | 45 ++-
.../generic/server/ETLServiceLogger.java | 8 +
.../generic/server/MaterialHelper.java | 273 ++++++++++++++++++
.../bo/IAbstractBussinessObjectFactory.java | 35 +++
.../bo/ICommonBusinessObjectFactory.java | 9 +-
.../generic/shared/IETLLIMSService.java | 31 +-
.../dto/AtomicEntityOperationDetails.java | 14 +
.../dto/AtomicEntityOperationResult.java | 15 +-
.../server/GenericBusinessObjectFactory.java | 8 +
.../plugin/generic/server/GenericServer.java | 211 +-------------
.../server/IGenericBusinessObjectFactory.java | 15 +-
.../generic/server/ETLServiceTest.java | 43 ++-
.../shared/IETLLIMSService.java.expected | 31 +-
.../dto/AtomicEntityOperationDetailsTest.java | 15 +-
.../generic/server/GenericServerTest.java | 8 +-
28 files changed, 845 insertions(+), 250 deletions(-)
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IMaterial.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IMaterialImmutable.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Material.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/MaterialImmutable.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/MaterialHelper.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IAbstractBussinessObjectFactory.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityOperationService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityOperationService.java
index 9188f312dd5..4a0d533f91d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityOperationService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityOperationService.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.etlserver.registrator;
import java.util.ArrayList;
import java.util.List;
+import java.util.Map;
import ch.systemsx.cisd.etlserver.ITopLevelDataSetRegistratorDelegate;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
@@ -25,6 +26,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDeta
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetRegistrationInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
@@ -78,6 +80,7 @@ public class DefaultEntityOperationService<T extends DataSetInformation> impleme
List<NewExperiment> experimentRegistrations = details.getExperimentRegistrations();
List<SampleUpdatesDTO> sampleUpdates = details.getSampleUpdates();
List<NewSample> sampleRegistrations = details.getSampleRegistrations();
+ Map<String, List<NewMaterial>> materialRegistrations = details.getMaterialRegistrations();
List<DataSetUpdatesDTO> dataSetUpdates = details.getDataSetUpdates();
List<NewExternalData> dataSetRegistrations = new ArrayList<NewExternalData>();
@@ -89,8 +92,8 @@ public class DefaultEntityOperationService<T extends DataSetInformation> impleme
return new ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails(
details.tryUserIdOrNull(), spaceRegistrations, projectRegistrations,
- experimentRegistrations, sampleUpdates, sampleRegistrations, dataSetRegistrations,
- dataSetUpdates);
+ experimentRegistrations, sampleUpdates, sampleRegistrations, materialRegistrations,
+ dataSetRegistrations, dataSetUpdates);
}
}
\ No newline at end of file
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java
index 2ed6b074ed7..47118f62789 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java
@@ -129,6 +129,21 @@ public interface IDataSetRegistrationTransaction
*/
ISpaceImmutable getSpace(String spaceCode);
+ /**
+ * Get a material from the openBIS AS. Returns null if the space does not exist.
+ *
+ * @return A material or null
+ */
+ IMaterialImmutable getMaterial(String materialCode, String materialType);
+
+ /**
+ * Create a new space to register with the openBIS AS.
+ *
+ * @param materialCode the code of the material
+ * @param materialType the type of the material
+ */
+ IMaterial createNewMaterial(String materialCode, String materialType);
+
// File operations -- The source and destination paths are local to the incoming data set folder
// or incoming directory if the data set is just one file
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IMaterial.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IMaterial.java
new file mode 100644
index 00000000000..cd3a29f038f
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IMaterial.java
@@ -0,0 +1,30 @@
+/*
+ * 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.etlserver.registrator.api.v1;
+
+
+/**
+ * @author Kaloyan Enimanev
+ */
+public interface IMaterial extends IMaterialImmutable
+{
+ /**
+ * Set the value for a property.
+ */
+ void setPropertyValue(String propertyCode, String propertyValue);
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IMaterialImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IMaterialImmutable.java
new file mode 100644
index 00000000000..bf45c55ab90
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IMaterialImmutable.java
@@ -0,0 +1,46 @@
+/*
+ * 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.etlserver.registrator.api.v1;
+
+/**
+ * @author Kaloyan Enimanev
+ */
+public interface IMaterialImmutable
+{
+
+ /**
+ * Return the code for this material.
+ */
+ String getCode();
+
+ /**
+ * Return the type for this material. May be null.
+ */
+ String getMaterialType();
+
+ /**
+ * Return true if the material exists in the database.
+ */
+ boolean isExistingMaterial();
+
+ /**
+ * Return the value of a property specified by a code. May return null of no such property with
+ * code <code>propertyCode</code> is found.
+ */
+ String getPropertyValue(String propertyCode);
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
index d2fdff50800..6e2900d9459 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
@@ -18,7 +18,9 @@ package ch.systemsx.cisd.etlserver.registrator.api.v1.impl;
import java.io.File;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import ch.systemsx.cisd.common.exceptions.NotImplementedException;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
@@ -32,6 +34,7 @@ import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetImmutable;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetUpdatable;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperiment;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperimentImmutable;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IMaterial;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IProject;
import ch.systemsx.cisd.etlserver.registrator.api.v1.ISample;
import ch.systemsx.cisd.etlserver.registrator.api.v1.ISampleImmutable;
@@ -42,6 +45,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetRegistrationInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
@@ -112,6 +116,8 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
private final List<Sample> samplesToBeUpdated = new ArrayList<Sample>();
+ private final List<Material> materialsToBeRegistered = new ArrayList<Material>();
+
private String userIdOrNull = null;
public LiveTransactionState(DataSetRegistrationTransaction<T> parent,
@@ -301,6 +307,13 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
return project;
}
+ public IMaterial createNewMaterial(String materialCode, String materialType)
+ {
+ Material material = new Material(materialCode, materialType);
+ materialsToBeRegistered.add(material);
+ return material;
+ }
+
public String moveFile(String src, IDataSet dst)
{
File srcFile = new File(src);
@@ -436,6 +449,7 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
List<NewExperiment> experimentRegistrations = convertExperimentsToBeRegistered();
List<SampleUpdatesDTO> sampleUpdates = convertSamplesToBeUpdated();
List<NewSample> sampleRegistrations = convertSamplesToBeRegistered();
+ Map<String, List<NewMaterial>> materialRegistrations = convertMaterialsToBeRegistered();
List<DataSetUpdatesDTO> dataSetUpdates = convertDataSetsToBeUpdated();
// experiment updates not yet supported
@@ -444,8 +458,8 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
AtomicEntityOperationDetails<T> registrationDetails =
new AtomicEntityOperationDetails<T>(getUserId(), spaceRegistrations,
projectRegistrations, experimentUpdates, experimentRegistrations,
- sampleUpdates, sampleRegistrations, dataSetRegistrations,
- dataSetUpdates);
+ sampleUpdates, sampleRegistrations, materialRegistrations,
+ dataSetRegistrations, dataSetUpdates);
return registrationDetails;
}
@@ -509,6 +523,24 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
return result;
}
+ private Map<String, List<NewMaterial>> convertMaterialsToBeRegistered()
+ {
+ Map<String, List<NewMaterial>> result = new HashMap<String, List<NewMaterial>>();
+ for (Material material : materialsToBeRegistered)
+ {
+ NewMaterial converted = ConversionUtils.convertToNewMaterial(material);
+ String materialType = material.getMaterialType();
+ List<NewMaterial> materialsOfSameType = result.get(materialType);
+ if (materialsOfSameType == null)
+ {
+ materialsOfSameType = new ArrayList<NewMaterial>();
+ result.put(materialType, materialsOfSameType);
+ }
+ materialsOfSameType.add(converted);
+ }
+ return result;
+ }
+
@Override
public boolean isCommitted()
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ConversionUtils.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ConversionUtils.java
index cc32cb2e3b7..0291f915869 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ConversionUtils.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ConversionUtils.java
@@ -29,6 +29,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
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.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
@@ -222,4 +223,13 @@ public class ConversionUtils
return dataSetUpdate;
}
+ public static NewMaterial convertToNewMaterial(Material material)
+ {
+ NewMaterial newMaterial = new NewMaterial(material.getCode());
+ IEntityProperty[] properties =
+ material.getMaterial().getProperties().toArray(new IEntityProperty[0]);
+ newMaterial.setProperties(properties);
+ return newMaterial;
+ }
+
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
index 1a848328041..07adfb05f05 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
@@ -39,6 +39,8 @@ import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetRegistrationTransac
import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetUpdatable;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperiment;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperimentImmutable;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IMaterial;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IMaterialImmutable;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IProject;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IProjectImmutable;
import ch.systemsx.cisd.etlserver.registrator.api.v1.ISample;
@@ -53,6 +55,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetRegistrationInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
@@ -277,6 +280,19 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
return (null == spaceOrNull) ? null : new SpaceImmutable(spaceOrNull);
}
+ public IMaterialImmutable getMaterial(String materialCode, String materialType)
+ {
+ MaterialIdentifier materialIdentifier = new MaterialIdentifier(materialCode, materialType);
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material materialOrNull =
+ openBisService.tryGetMaterial(materialIdentifier);
+ return (null == materialOrNull) ? null : new MaterialImmutable(materialOrNull);
+ }
+
+ public IMaterial createNewMaterial(String materialCode, String materialType)
+ {
+ return getStateAsLiveState().createNewMaterial(materialCode, materialType);
+ }
+
public String moveFile(String src, IDataSet dst)
{
return getStateAsLiveState().moveFile(src, dst);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Material.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Material.java
new file mode 100644
index 00000000000..8d583bf15ac
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Material.java
@@ -0,0 +1,60 @@
+/*
+ * 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.etlserver.registrator.api.v1.impl;
+
+import java.util.ArrayList;
+
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IMaterial;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
+import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
+
+/**
+ * @author Kaloyan Enimanev
+ */
+public class Material extends MaterialImmutable implements IMaterial
+{
+
+ private static ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material buildMaterialWithCodeAndType(
+ String code, String type)
+ {
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material material =
+ new ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material();
+ material.setCode(code);
+ MaterialType materialType = new MaterialType();
+ materialType.setCode(type);
+ material.setMaterialType(materialType);
+ material.setProperties(new ArrayList<IEntityProperty>());
+
+ return material;
+ }
+
+ public Material(ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material material)
+ {
+ super(material);
+ }
+
+ public Material(String code, String type)
+ {
+ super(buildMaterialWithCodeAndType(code, type), false);
+ }
+
+ public void setPropertyValue(String propertyCode, String propertyValue)
+ {
+ EntityHelper.createOrUpdateProperty(getMaterial(), propertyCode, propertyValue);
+ }
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/MaterialImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/MaterialImmutable.java
new file mode 100644
index 00000000000..f88f0657f97
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/MaterialImmutable.java
@@ -0,0 +1,83 @@
+/*
+ * 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.etlserver.registrator.api.v1.impl;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IMaterialImmutable;
+import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
+
+/**
+ * @author Kaloyan Enimanev
+ */
+public class MaterialImmutable implements IMaterialImmutable
+{
+ private final ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material material;
+
+ private final boolean existingMaterial;
+
+ public MaterialImmutable(ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material material)
+ {
+ this(material, true);
+ }
+
+ public MaterialImmutable(ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material material,
+ boolean existingMaterial)
+ {
+ this.material = material;
+ this.existingMaterial = existingMaterial;
+ }
+
+ public String getCode()
+ {
+ return material.getCode();
+ }
+
+ public String getMaterialType()
+ {
+ if (material.getMaterialType() != null)
+ {
+ return material.getMaterialType().getCode();
+ }
+ return null;
+ }
+
+ public boolean isExistingMaterial()
+ {
+ return existingMaterial;
+ }
+
+ public ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material getMaterial()
+ {
+ return material;
+ }
+
+ /**
+ * Throw an exception if the sample does not exist
+ */
+ protected void checkExists()
+ {
+ if (false == isExistingMaterial())
+ {
+ throw new UserFailureException("Material does not exist.");
+ }
+ }
+
+ public String getPropertyValue(String propertyCode)
+ {
+ return EntityHelper.tryFindPropertyValue(material, propertyCode);
+ }
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
index 9ae22fd6dd4..12b0f51c762 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
@@ -47,6 +47,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
@@ -558,4 +560,9 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return service.listExperiments(session.getToken(), projectIdentifier);
}
+ public Material tryGetMaterial(MaterialIdentifier materialIdentifier)
+ {
+ return service.tryGetMaterial(session.getToken(), materialIdentifier);
+ }
+
}
\ No newline at end of file
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
index 2867468414a..9140450f3a6 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
@@ -34,6 +34,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
@@ -153,6 +155,12 @@ public interface IEncapsulatedOpenBISService
public SampleIdentifier tryToGetSampleIdentifier(String samplePermID)
throws UserFailureException;
+ /**
+ * For given {@link MaterialIdentifier} returns the corresponding {@link Material}.
+ */
+ @ManagedAuthentication
+ public Material tryGetMaterial(MaterialIdentifier materialIdentifier);
+
/**
* Lists vocabulary terms.
*/
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/AtomicEntityOperationDetails.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/AtomicEntityOperationDetails.java
index 218a7ae9dc7..78b7cea0d1a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/AtomicEntityOperationDetails.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/AtomicEntityOperationDetails.java
@@ -18,9 +18,12 @@ package ch.systemsx.cisd.openbis.dss.generic.shared.dto;
import java.io.Serializable;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
@@ -53,6 +56,8 @@ public class AtomicEntityOperationDetails<T extends DataSetInformation> implemen
private final List<NewSample> sampleRegistrations;
+ private final Map<String /* material type */, List<NewMaterial>> materialRegistrations;
+
private final List<DataSetRegistrationInformation<T>> dataSetRegistrations;
private final List<DataSetUpdatesDTO> dataSetUpdates;
@@ -62,6 +67,7 @@ public class AtomicEntityOperationDetails<T extends DataSetInformation> implemen
List<ExperimentUpdatesDTO> experimentUpdates,
List<NewExperiment> experimentRegistrations, List<SampleUpdatesDTO> sampleUpdates,
List<NewSample> sampleRegistrations,
+ Map<String, List<NewMaterial>> materialRegistrations,
List<DataSetRegistrationInformation<T>> dataSetRegistrations,
List<DataSetUpdatesDTO> dataSetUpdates)
{
@@ -72,6 +78,7 @@ public class AtomicEntityOperationDetails<T extends DataSetInformation> implemen
this.experimentRegistrations = new ArrayList<NewExperiment>(experimentRegistrations);
this.sampleUpdates = new ArrayList<SampleUpdatesDTO>(sampleUpdates);
this.sampleRegistrations = new ArrayList<NewSample>(sampleRegistrations);
+ this.materialRegistrations = new HashMap<String, List<NewMaterial>>(materialRegistrations);
this.dataSetRegistrations =
new ArrayList<DataSetRegistrationInformation<T>>(dataSetRegistrations);
this.dataSetUpdates = new ArrayList<DataSetUpdatesDTO>(dataSetUpdates);
@@ -122,4 +129,9 @@ public class AtomicEntityOperationDetails<T extends DataSetInformation> implemen
return projectRegistrations;
}
+ public Map<String, List<NewMaterial>> getMaterialRegistrations()
+ {
+ return materialRegistrations;
+ }
+
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISServiceTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISServiceTest.java
index 6d86c4aaccf..e6dd35f7bcb 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISServiceTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISServiceTest.java
@@ -17,7 +17,9 @@
package ch.systemsx.cisd.openbis.dss.generic.server;
import java.util.Arrays;
+import java.util.Collections;
import java.util.Date;
+import java.util.List;
import org.jmock.Expectations;
import org.jmock.Mockery;
@@ -33,6 +35,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
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.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
@@ -161,6 +164,7 @@ public class EncapsulatedOpenBISServiceTest
new AtomicEntityOperationDetails(null, Arrays.<NewSpace> asList(),
Arrays.<NewProject> asList(), Arrays.<NewExperiment> asList(),
Arrays.<SampleUpdatesDTO> asList(), Arrays.<NewSample> asList(),
+ Collections.<String, List<NewMaterial>> emptyMap(),
Arrays.asList(data), Arrays.<DataSetUpdatesDTO> asList());
context.checking(new Expectations()
{
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 9770d87d735..b8a7dd7ae12 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
@@ -23,6 +23,8 @@ import java.util.Date;
import java.util.HashMap;
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.authentication.IAuthenticationService;
@@ -39,6 +41,7 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentTable;
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.IProjectBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IRoleAssignmentTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
@@ -76,7 +79,10 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Grantee;
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.ListSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
@@ -143,6 +149,7 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator.LoadableFields;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTypeTranslator;
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.PersonTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.ProjectTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
@@ -1070,7 +1077,6 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
// space does not exist
return null;
}
-
}
public Project tryGetProject(String sessionToken, ProjectIdentifier projectIdentifier)
@@ -1089,6 +1095,21 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
}
}
+ public Material tryGetMaterial(String sessionToken, MaterialIdentifier materialIdentifier)
+ {
+ final Session session = getSession(sessionToken);
+ final IMaterialBO bo = businessObjectFactory.createMaterialBO(session);
+ try
+ {
+ bo.loadByMaterialIdentifier(materialIdentifier);
+ return MaterialTranslator.translate(bo.getMaterial());
+ } catch (UserFailureException ufe)
+ {
+ // material does not exist
+ return null;
+ }
+ }
+
public AtomicEntityOperationResult performEntityOperations(String sessionToken,
AtomicEntityOperationDetails operationDetails)
{
@@ -1096,6 +1117,8 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
List<Space> spacesCreated = createSpaces(session, operationDetails);
+ List<Material> materialsCreated = createMaterials(session, operationDetails);
+
List<Project> projectsCreated = createProjects(session, operationDetails);
List<Experiment> experimentsCreated = createExperiments(session, operationDetails);
@@ -1109,7 +1132,7 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
List<ExternalData> dataSetsUpdated = updateDataSets(session, operationDetails);
return new AtomicEntityOperationResult(spacesCreated, projectsCreated, experimentsCreated,
- samplesUpdated, samplesCreated, dataSetsCreated, dataSetsUpdated);
+ samplesUpdated, samplesCreated, materialsCreated, dataSetsCreated, dataSetsUpdated);
}
private List<Space> createSpaces(Session session, AtomicEntityOperationDetails operationDetails)
@@ -1125,6 +1148,24 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
return GroupTranslator.translate(spacePEsCreated);
}
+ private List<Material> createMaterials(Session session,
+ AtomicEntityOperationDetails operationDetails)
+ {
+ MaterialHelper materialHelper =
+ new MaterialHelper(session, businessObjectFactory, getDAOFactory(),
+ getPropertiesBatchManager());
+ Map<String, List<NewMaterial>> materialRegs = operationDetails.getMaterialRegistrations();
+ List<Material> registeredMaterials = new ArrayList<Material>();
+ for (Entry<String, List<NewMaterial>> newMaterialsEntry : materialRegs.entrySet())
+ {
+ String materialType = newMaterialsEntry.getKey();
+ List<NewMaterial> newMaterials = newMaterialsEntry.getValue();
+ List<Material> materials = materialHelper.registerMaterials(materialType, newMaterials);
+ registeredMaterials.addAll(materials);
+ }
+ return registeredMaterials;
+ }
+
private SpacePE registerSpaceInternal(Session session, NewSpace newSpace,
String registratorUserIdOrNull)
{
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 cb7bac3b082..83c305668bd 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
@@ -36,6 +36,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
@@ -487,4 +489,10 @@ public class ETLServiceLogger extends AbstractServerLogger implements IETLServic
logAccess(sessionToken, "searchForDataSets", "%s", searchCriteria);
return null;
}
+
+ public Material tryGetMaterial(String sessionToken, MaterialIdentifier materialIdentifier)
+ {
+ logAccess(sessionToken, "tryGetMaterial", "%s", materialIdentifier);
+ return null;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/MaterialHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/MaterialHelper.java
new file mode 100644
index 00000000000..7db559088f0
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/MaterialHelper.java
@@ -0,0 +1,273 @@
+/*
+ * 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.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import org.apache.log4j.Logger;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.openbis.generic.server.batch.BatchOperationExecutor;
+import ch.systemsx.cisd.openbis.generic.server.batch.IBatchOperation;
+import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IAbstractBussinessObjectFactory;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialTable;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.MaterialUpdateDTO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeConverter;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListMaterialCriteria;
+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.NewMaterial;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
+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.Session;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
+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.util.ServerUtils;
+
+/**
+ * @author Kaloyan Enimanev
+ */
+public class MaterialHelper
+{
+
+ private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ MaterialHelper.class);
+
+ private final Session session;
+
+ private final IAbstractBussinessObjectFactory businessObjectFactory;
+
+ private final IDAOFactory daoFactory;
+
+ private final IPropertiesBatchManager propertiesBatchManager;
+
+ public MaterialHelper(Session session,
+ IAbstractBussinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
+ IPropertiesBatchManager propertiesBatchManager)
+ {
+ this.session = session;
+ this.businessObjectFactory = businessObjectFactory;
+ this.daoFactory = daoFactory;
+ this.propertiesBatchManager = propertiesBatchManager;
+ }
+
+ public List<Material> registerMaterials(String materialTypeCode,
+ final List<NewMaterial> newMaterials)
+ {
+ assert materialTypeCode != null : "Unspecified material type.";
+ assert newMaterials != null : "Unspecified new materials.";
+
+ // Does nothing if material list is empty.
+ if (newMaterials.size() == 0)
+ {
+ return Collections.emptyList();
+ }
+ ServerUtils.prevalidate(newMaterials, "material");
+ final MaterialTypePE materialTypePE = findMaterialType(materialTypeCode);
+ final List<MaterialPE> registeredMaterials = new ArrayList<MaterialPE>();
+ propertiesBatchManager.manageProperties(materialTypePE, newMaterials,
+ session.tryGetPerson());
+ IBatchOperation<NewMaterial> strategy = new IBatchOperation<NewMaterial>()
+ {
+
+ public void execute(List<NewMaterial> entities)
+ {
+ final IMaterialTable materialTable =
+ businessObjectFactory.createMaterialTable(session);
+ materialTable.add(entities, materialTypePE);
+ materialTable.save();
+ registeredMaterials.addAll(materialTable.getMaterials());
+ }
+
+ public List<NewMaterial> getAllEntities()
+ {
+ return newMaterials;
+ }
+
+ public String getEntityName()
+ {
+ return "material";
+ }
+
+ public String getOperationName()
+ {
+ return "register";
+ }
+ };
+ BatchOperationExecutor.executeInBatches(strategy);
+
+ return MaterialTranslator.translate(registeredMaterials);
+ }
+
+ public int updateMaterials(String materialTypeCode,
+ final List<NewMaterial> newMaterials, final boolean ignoreUnregisteredMaterials)
+ throws UserFailureException
+ {
+ assert materialTypeCode != null : "Unspecified material type.";
+ assert newMaterials != null : "Unspecified new materials.";
+
+ // Does nothing if material list is empty.
+ if (newMaterials.size() == 0)
+ {
+ return 0;
+ }
+
+ ServerUtils.prevalidate(newMaterials, "material");
+
+ final AtomicInteger count = new AtomicInteger(0);
+ final Map<String/* code */, Material> existingMaterials = listMaterials(materialTypeCode);
+
+ final MaterialTypePE materialTypePE = findMaterialType(materialTypeCode);
+ propertiesBatchManager.manageProperties(materialTypePE, newMaterials,
+ session.tryGetPerson());
+ IBatchOperation<NewMaterial> strategy = new IBatchOperation<NewMaterial>()
+ {
+ public void execute(List<NewMaterial> entities)
+ {
+ List<MaterialUpdateDTO> materialUpdates = new ArrayList<MaterialUpdateDTO>();
+ for (NewMaterial material : entities)
+ {
+ Material existingMaterial =
+ existingMaterials.get(CodeConverter.tryToDatabase(material
+ .getCode()));
+ if (existingMaterial != null)
+ {
+ materialUpdates.add(createMaterialUpdate(existingMaterial, material));
+ count.incrementAndGet();
+ } else if (ignoreUnregisteredMaterials == false)
+ {
+ throw new UserFailureException("Can not update unregistered material '"
+ + material.getCode()
+ + "'. Please use checkbox for ignoring unregistered materials.");
+ }
+ }
+ updateMaterials(materialUpdates);
+ }
+
+ public List<NewMaterial> getAllEntities()
+ {
+ return newMaterials;
+ }
+
+ public String getEntityName()
+ {
+ return "material";
+ }
+
+ public String getOperationName()
+ {
+ return "update";
+ }
+ };
+ BatchOperationExecutor.executeInBatches(strategy);
+ return count.get();
+ }
+
+ public void registerOrUpdateMaterials(String materialTypeCode, List<NewMaterial> materials)
+ {
+ Map<String/* code */, Material> existingMaterials = listMaterials(materialTypeCode);
+ List<NewMaterial> materialsToRegister = new ArrayList<NewMaterial>();
+ List<MaterialUpdateDTO> materialUpdates = new ArrayList<MaterialUpdateDTO>();
+ for (NewMaterial material : materials)
+ {
+ Material existingMaterial =
+ existingMaterials.get(CodeConverter.tryToDatabase(material.getCode()));
+ if (existingMaterial != null)
+ {
+ materialUpdates.add(createMaterialUpdate(existingMaterial, material));
+ } else
+ {
+ materialsToRegister.add(material);
+ }
+ }
+ registerMaterials(materialTypeCode, materialsToRegister);
+ updateMaterials(materialUpdates);
+ operationLog.info(String.format("Number of newly registered materials: %d, "
+ + "number of existing materials which have been updated: %d",
+ materialsToRegister.size(), materialUpdates.size()));
+
+ }
+
+ private static MaterialUpdateDTO createMaterialUpdate(Material existingMaterial,
+ NewMaterial material)
+ {
+ return new MaterialUpdateDTO(new TechId(existingMaterial.getId()), Arrays.asList(material
+ .getProperties()), existingMaterial.getModificationDate());
+ }
+
+ private void updateMaterials(List<MaterialUpdateDTO> updates)
+ {
+ if (updates.isEmpty())
+ {
+ return;
+ }
+ IMaterialTable materialTable = businessObjectFactory.createMaterialTable(session);
+ materialTable.update(updates);
+ materialTable.save();
+ }
+
+ private Map<String/* code */, Material> listMaterials(String materialTypeCode)
+ {
+ EntityTypePE entityTypePE =
+ daoFactory.getEntityTypeDAO(EntityKind.MATERIAL).tryToFindEntityTypeByCode(
+ materialTypeCode);
+ MaterialType materialType = MaterialTypeTranslator.translateSimple(entityTypePE);
+
+ IMaterialLister materialLister = businessObjectFactory.createMaterialLister(session);
+ ListMaterialCriteria listByTypeCriteria = new ListMaterialCriteria(materialType);
+ List<Material> materials = materialLister.list(listByTypeCriteria, false);
+ return asCodeToMaterialMap(materials);
+ }
+
+ private static Map<String, Material> asCodeToMaterialMap(List<Material> materials)
+ {
+ Map<String, Material> map = new HashMap<String, Material>();
+ for (Material material : materials)
+ {
+ map.put(material.getCode(), material);
+ }
+ return map;
+ }
+
+ private MaterialTypePE findMaterialType(String materialTypeCode)
+ {
+ final MaterialTypePE materialTypePE =
+ (MaterialTypePE) daoFactory.getEntityTypeDAO(EntityKind.MATERIAL)
+ .tryToFindEntityTypeByCode(materialTypeCode);
+ if (materialTypePE == null)
+ {
+ throw UserFailureException.fromTemplate("Material type with code '%s' does not exist.",
+ materialTypeCode);
+ }
+ return materialTypePE;
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IAbstractBussinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IAbstractBussinessObjectFactory.java
new file mode 100644
index 00000000000..7eb0f58ccdf
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IAbstractBussinessObjectFactory.java
@@ -0,0 +1,35 @@
+/*
+ * 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.business.bo;
+
+import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+
+/**
+ * An abstract bussiness object factory.
+ *
+ * @author Kaloyan Enimanev
+ */
+public interface IAbstractBussinessObjectFactory
+{
+ public IMaterialTable createMaterialTable(Session session);
+
+ public IMaterialBO createMaterialBO(Session session);
+
+ public IMaterialLister createMaterialLister(Session session);
+
+}
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 dc1a3b9ee4c..a7478f32797 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
@@ -17,7 +17,6 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo;
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.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
@@ -28,7 +27,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
*
* @author Tomasz Pylak
*/
-public interface ICommonBusinessObjectFactory
+public interface ICommonBusinessObjectFactory extends IAbstractBussinessObjectFactory
{
public IAttachmentBO createAttachmentBO(final Session session);
@@ -63,12 +62,8 @@ public interface ICommonBusinessObjectFactory
public IProjectBO createProjectBO(final Session session);
- public IMaterialTable createMaterialTable(Session session);
-
public IEntityTypeBO createEntityTypeBO(Session session);
- public IMaterialBO createMaterialBO(Session session);
-
public IAuthorizationGroupBO createAuthorizationGroupBO(Session session);
public IGridCustomFilterOrColumnBO createGridCustomFilterBO(final Session session);
@@ -78,10 +73,8 @@ public interface ICommonBusinessObjectFactory
public IInvalidationBO createInvalidationBO(final Session session);
// Fast listing operations
-
public ISampleLister createSampleLister(Session session);
public IDatasetLister createDatasetLister(Session session);
- public IMaterialLister createMaterialLister(Session session);
}
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 2d773460d3d..cc540753cfe 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
@@ -57,6 +57,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
@@ -120,20 +122,11 @@ public interface IETLLIMSService extends IServer, ISessionProvider
throws UserFailureException;
/**
- * Gets a sample with the specified identifier. Sample is enriched with properties and the
- * experiment with properties.
- *
- * @param sessionToken the user authentication token. Must not be <code>null</code>.
- * @param sampleIdentifier an identifier which uniquely identifies the sample.
- * @return <code>null</code> if no sample attached to an experiment could be found for given
- * <var>sampleIdentifier</var>.
+ * For given {@link MaterialIdentifier} returns the corresponding {@link Material}.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
- public Sample tryGetSampleWithExperiment(
- final String sessionToken,
- @AuthorizationGuard(guardClass = ExistingSampleOwnerIdentifierPredicate.class) final SampleIdentifier sampleIdentifier)
- throws UserFailureException;
+ public Material tryGetMaterial(String sessionToken, MaterialIdentifier materialIdentifier);
/**
* Tries to get the identifier of sample with specified permanent ID.
@@ -154,6 +147,22 @@ public interface IETLLIMSService extends IServer, ISessionProvider
public ExperimentType getExperimentType(String sessionToken, String experimentTypeCode)
throws UserFailureException;
+ /**
+ * Gets a sample with the specified identifier. Sample is enriched with properties and the
+ * experiment with properties.
+ *
+ * @param sessionToken the user authentication token. Must not be <code>null</code>.
+ * @param sampleIdentifier an identifier which uniquely identifies the sample.
+ * @return <code>null</code> if no sample attached to an experiment could be found for given
+ * <var>sampleIdentifier</var>.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public Sample tryGetSampleWithExperiment(
+ final String sessionToken,
+ @AuthorizationGuard(guardClass = ExistingSampleOwnerIdentifierPredicate.class) final SampleIdentifier sampleIdentifier)
+ throws UserFailureException;
+
/**
* Returns a list of terms belonging to given vocabulary.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationDetails.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationDetails.java
index ab5f5ede932..e768b2523da 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationDetails.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationDetails.java
@@ -19,11 +19,14 @@ package ch.systemsx.cisd.openbis.generic.shared.dto;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
import org.apache.commons.lang.builder.ToStringBuilder;
import org.apache.commons.lang.builder.ToStringStyle;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
@@ -55,6 +58,8 @@ public class AtomicEntityOperationDetails implements Serializable
private final List<NewSample> sampleRegistrations;
+ private final Map<String /* material type */, List<NewMaterial>> materialRegistrations;
+
private final List<? extends NewExternalData> dataSetRegistrations;
private final List<DataSetUpdatesDTO> dataSetUpdates;
@@ -62,6 +67,7 @@ public class AtomicEntityOperationDetails implements Serializable
public AtomicEntityOperationDetails(String userIdOrNull, List<NewSpace> spaceRegistrations,
List<NewProject> projectRegistrations, List<NewExperiment> experimentRegistrations,
List<SampleUpdatesDTO> sampleUpdates, List<NewSample> sampleRegistrations,
+ Map<String, List<NewMaterial>> materialRegistrations,
List<? extends NewExternalData> dataSetRegistrations,
List<DataSetUpdatesDTO> dataSetUpdates)
{
@@ -72,6 +78,7 @@ public class AtomicEntityOperationDetails implements Serializable
this.experimentRegistrations = new ArrayList<NewExperiment>(experimentRegistrations);
this.sampleUpdates = new ArrayList<SampleUpdatesDTO>(sampleUpdates);
this.sampleRegistrations = new ArrayList<NewSample>(sampleRegistrations);
+ this.materialRegistrations = new TreeMap<String, List<NewMaterial>>(materialRegistrations);
this.dataSetRegistrations = new ArrayList<NewExternalData>(dataSetRegistrations);
this.dataSetUpdates = new ArrayList<DataSetUpdatesDTO>(dataSetUpdates);
}
@@ -121,6 +128,11 @@ public class AtomicEntityOperationDetails implements Serializable
return projectRegistrations;
}
+ public Map<String, List<NewMaterial>> getMaterialRegistrations()
+ {
+ return materialRegistrations;
+ }
+
@Override
public String toString()
{
@@ -132,8 +144,10 @@ public class AtomicEntityOperationDetails implements Serializable
sb.append("experimentRegistrations", experimentRegistrations);
sb.append("sampleUpdates", sampleUpdates);
sb.append("sampleRegistrations", sampleRegistrations);
+ sb.append("materialRegistrations", materialRegistrations);
sb.append("dataSetRegistrations", dataSetRegistrations);
sb.append("dataSetUpdates", dataSetUpdates);
return sb.toString();
}
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationResult.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationResult.java
index 1e7bf47897e..a085e4e32dc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationResult.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationResult.java
@@ -23,6 +23,7 @@ import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
@@ -48,6 +49,8 @@ public class AtomicEntityOperationResult implements Serializable
private final ArrayList<Sample> samplesCreated;
+ private final ArrayList<Material> materialsCreated;
+
private final ArrayList<ExternalData> dataSetsCreated;
private final ArrayList<ExternalData> dataSetsUpdated;
@@ -56,13 +59,15 @@ public class AtomicEntityOperationResult implements Serializable
{
this(Collections.<Space> emptyList(), Collections.<Project> emptyList(),
Collections.<Experiment> emptyList(), Collections.<Sample> emptyList(), Collections
- .<Sample> emptyList(), Collections.<ExternalData> emptyList(), Collections
+ .<Sample> emptyList(), Collections.<Material> emptyList(), Collections
+ .<ExternalData> emptyList(), Collections
.<ExternalData> emptyList());
}
public AtomicEntityOperationResult(List<Space> spacesCreated, List<Project> projectsCreated,
List<Experiment> experimentsCreated, List<Sample> samplesUpdated,
- List<Sample> samplesCreated, List<ExternalData> dataSetsCreated,
+ List<Sample> samplesCreated, List<Material> materialsCreated,
+ List<ExternalData> dataSetsCreated,
List<ExternalData> dataSetsUpdated)
{
this.spacesCreated = new ArrayList<Space>(spacesCreated);
@@ -71,6 +76,7 @@ public class AtomicEntityOperationResult implements Serializable
this.experimentsCreated = new ArrayList<Experiment>(experimentsCreated);
this.samplesUpdated = new ArrayList<Sample>(samplesUpdated);
this.samplesCreated = new ArrayList<Sample>(samplesCreated);
+ this.materialsCreated = new ArrayList<Material>(materialsCreated);
this.dataSetsCreated = new ArrayList<ExternalData>(dataSetsCreated);
this.dataSetsUpdated = new ArrayList<ExternalData>(dataSetsUpdated);
}
@@ -115,4 +121,9 @@ public class AtomicEntityOperationResult implements Serializable
return projectsCreated;
}
+ public ArrayList<Material> getMaterialsCreated()
+ {
+ return materialsCreated;
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericBusinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericBusinessObjectFactory.java
index 795344517a4..9ecaefa2c61 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericBusinessObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericBusinessObjectFactory.java
@@ -28,6 +28,8 @@ 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.ISampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleTable;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.MaterialLister;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.SampleLister;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
@@ -102,4 +104,10 @@ public final class GenericBusinessObjectFactory extends AbstractPluginBusinessOb
{
return SampleLister.create(getDaoFactory(), session.getBaseIndexURL());
}
+
+ public IMaterialLister createMaterialLister(Session session)
+ {
+ return MaterialLister.create(getDaoFactory(), session.getBaseIndexURL());
+ }
+
}
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 4ed12dc9945..cba34dec461 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
@@ -20,38 +20,31 @@ import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Date;
-import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
-import java.util.Map;
import java.util.Set;
import javax.annotation.Resource;
-import org.apache.log4j.Logger;
import org.springframework.stereotype.Component;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
+import ch.systemsx.cisd.openbis.generic.server.MaterialHelper;
import ch.systemsx.cisd.openbis.generic.server.batch.BatchOperationExecutor;
import ch.systemsx.cisd.openbis.generic.server.batch.IBatchOperation;
import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
-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.ISampleBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.MaterialUpdateDTO;
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.plugin.IDataSetTypeSlaveServerPlugin;
import ch.systemsx.cisd.openbis.generic.server.plugin.ISampleTypeSlaveServerPlugin;
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
-import ch.systemsx.cisd.openbis.generic.shared.basic.CodeConverter;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AttachmentWithContent;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
@@ -60,10 +53,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentUpdateResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListMaterialCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
-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.NewAttachment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewBasicExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewDataSet;
@@ -83,12 +73,10 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.UpdatedExperimentsWithT
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.UpdatedSample;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentBatchUpdatesDTO;
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.ExperimentUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleBatchUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
@@ -105,7 +93,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFa
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.translator.AttachmentTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.MaterialTypeTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
import ch.systemsx.cisd.openbis.generic.shared.util.ServerUtils;
import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
@@ -120,9 +107,6 @@ import ch.systemsx.cisd.openbis.plugin.generic.shared.ResourceNames;
public final class GenericServer extends AbstractServer<IGenericServer> implements
ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer
{
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
- GenericServer.class);
-
@Resource(name = ResourceNames.GENERIC_BUSINESS_OBJECT_FACTORY)
private IGenericBusinessObjectFactory businessObjectFactory;
@@ -516,46 +500,9 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
final List<NewMaterial> newMaterials)
{
assert sessionToken != null : "Unspecified session token.";
- assert materialTypeCode != null : "Unspecified material type.";
- assert newMaterials != null : "Unspecified new materials.";
+ Session session = getSession(sessionToken);
+ getMaterialHelper(session).registerMaterials(materialTypeCode, newMaterials);
- // Does nothing if material list is empty.
- if (newMaterials.size() == 0)
- {
- return;
- }
- ServerUtils.prevalidate(newMaterials, "material");
- final Session session = getSession(sessionToken);
- final MaterialTypePE materialTypePE = findMaterialType(materialTypeCode);
- getPropertiesBatchManager().manageProperties(materialTypePE, newMaterials,
- session.tryGetPerson());
- IBatchOperation<NewMaterial> strategy = new IBatchOperation<NewMaterial>()
- {
-
- public void execute(List<NewMaterial> entities)
- {
- final IMaterialTable materialTable =
- businessObjectFactory.createMaterialTable(session);
- materialTable.add(entities, materialTypePE);
- materialTable.save();
- }
-
- public List<NewMaterial> getAllEntities()
- {
- return newMaterials;
- }
-
- public String getEntityName()
- {
- return "material";
- }
-
- public String getOperationName()
- {
- return "register";
- }
- };
- BatchOperationExecutor.executeInBatches(strategy);
}
public int updateMaterials(String sessionToken, String materialTypeCode,
@@ -563,81 +510,9 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
throws UserFailureException
{
assert sessionToken != null : "Unspecified session token.";
- assert materialTypeCode != null : "Unspecified material type.";
- assert newMaterials != null : "Unspecified new materials.";
-
- // Does nothing if material list is empty.
- if (newMaterials.size() == 0)
- {
- return 0;
- }
- class Counter
- {
- int count;
- }
- final Counter counter = new Counter();
- ServerUtils.prevalidate(newMaterials, "material");
- final Map<String/* code */, Material> existingMaterials =
- listMaterials(sessionToken, materialTypeCode);
- final Session session = getSession(sessionToken);
-
- final MaterialTypePE materialTypePE = findMaterialType(materialTypeCode);
- getPropertiesBatchManager().manageProperties(materialTypePE, newMaterials,
- session.tryGetPerson());
- IBatchOperation<NewMaterial> strategy = new IBatchOperation<NewMaterial>()
- {
- public void execute(List<NewMaterial> entities)
- {
- List<MaterialUpdateDTO> materialUpdates = new ArrayList<MaterialUpdateDTO>();
- for (NewMaterial material : entities)
- {
- Material existingMaterial =
- existingMaterials.get(CodeConverter.tryToDatabase(material
- .getCode()));
- if (existingMaterial != null)
- {
- materialUpdates.add(createMaterialUpdate(existingMaterial, material));
- counter.count++;
- } else if (ignoreUnregisteredMaterials == false)
- {
- throw new UserFailureException("Can not update unregistered material '"
- + material.getCode()
- + "'. Please use checkbox for ignoring unregistered materials.");
- }
- }
- updateMaterials(session.getSessionToken(), materialUpdates);
- }
-
- public List<NewMaterial> getAllEntities()
- {
- return newMaterials;
- }
-
- public String getEntityName()
- {
- return "material";
- }
-
- public String getOperationName()
- {
- return "update";
- }
- };
- BatchOperationExecutor.executeInBatches(strategy);
- return counter.count;
- }
-
- private MaterialTypePE findMaterialType(String materialTypeCode)
- {
- final MaterialTypePE materialTypePE =
- (MaterialTypePE) getDAOFactory().getEntityTypeDAO(EntityKind.MATERIAL)
- .tryToFindEntityTypeByCode(materialTypeCode);
- if (materialTypePE == null)
- {
- throw UserFailureException.fromTemplate("Material type with code '%s' does not exist.",
- materialTypeCode);
- }
- return materialTypePE;
+ Session session = getSession(sessionToken);
+ return getMaterialHelper(session).updateMaterials(materialTypeCode, newMaterials,
+ ignoreUnregisteredMaterials);
}
public AttachmentWithContent getProjectFileAttachment(String sessionToken, TechId projectId,
@@ -707,71 +582,9 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
public void registerOrUpdateMaterials(String sessionToken, String materialTypeCode,
List<NewMaterial> materials)
{
- Map<String/* code */, Material> existingMaterials =
- listMaterials(sessionToken, materialTypeCode);
- List<NewMaterial> materialsToRegister = new ArrayList<NewMaterial>();
- List<MaterialUpdateDTO> materialUpdates = new ArrayList<MaterialUpdateDTO>();
- for (NewMaterial material : materials)
- {
- Material existingMaterial =
- existingMaterials.get(CodeConverter.tryToDatabase(material.getCode()));
- if (existingMaterial != null)
- {
- materialUpdates.add(createMaterialUpdate(existingMaterial, material));
- } else
- {
- materialsToRegister.add(material);
- }
- }
- registerMaterials(sessionToken, materialTypeCode, materialsToRegister);
- updateMaterials(sessionToken, materialUpdates);
- operationLog.info(String.format("Number of newly registered materials: %d, "
- + "number of existing materials which have been updated: %d",
- materialsToRegister.size(), materialUpdates.size()));
-
- }
-
- private static MaterialUpdateDTO createMaterialUpdate(Material existingMaterial,
- NewMaterial material)
- {
- return new MaterialUpdateDTO(new TechId(existingMaterial.getId()), Arrays.asList(material
- .getProperties()), existingMaterial.getModificationDate());
- }
-
- private void updateMaterials(String sessionToken, List<MaterialUpdateDTO> updates)
- {
- if (updates.size() == 0)
- {
- return;
- }
+ assert sessionToken != null : "Unspecified session token.";
final Session session = getSession(sessionToken);
- IMaterialTable materialTable = businessObjectFactory.createMaterialTable(session);
- materialTable.update(updates);
- materialTable.save();
- }
-
- private Map<String/* code */, Material> listMaterials(String sessionToken,
- String materialTypeCode)
- {
- checkSession(sessionToken);
- EntityTypePE entityTypePE =
- getDAOFactory().getEntityTypeDAO(EntityKind.MATERIAL).tryToFindEntityTypeByCode(
- materialTypeCode);
- MaterialType materialType = MaterialTypeTranslator.translateSimple(entityTypePE);
- List<Material> materials =
- commonServer.listMaterials(sessionToken, new ListMaterialCriteria(materialType),
- false);
- return asCodeToMaterialMap(materials);
- }
-
- private static Map<String, Material> asCodeToMaterialMap(List<Material> materials)
- {
- Map<String, Material> map = new HashMap<String, Material>();
- for (Material material : materials)
- {
- map.put(material.getCode(), material);
- }
- return map;
+ getMaterialHelper(session).registerOrUpdateMaterials(materialTypeCode, materials);
}
public void registerExperiments(String sessionToken, NewExperimentsWithType experiments)
@@ -888,4 +701,12 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
return experiments;
}
+ private MaterialHelper getMaterialHelper(final Session session)
+ {
+ final MaterialHelper materialHelper =
+ new MaterialHelper(session, businessObjectFactory, getDAOFactory(),
+ getPropertiesBatchManager());
+ return materialHelper;
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/IGenericBusinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/IGenericBusinessObjectFactory.java
index cd36a3b0985..eadeb1dd2ae 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/IGenericBusinessObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/IGenericBusinessObjectFactory.java
@@ -16,13 +16,12 @@
package ch.systemsx.cisd.openbis.plugin.generic.server;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IAbstractBussinessObjectFactory;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataSetTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IInvalidationBO;
-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.ISampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleTable;
@@ -34,7 +33,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
*
* @author Christian Ribeaud
*/
-public interface IGenericBusinessObjectFactory
+public interface IGenericBusinessObjectFactory extends IAbstractBussinessObjectFactory
{
/**
* Creates a {@link ISampleBO} <i>Business Object</i>.
@@ -56,11 +55,6 @@ public interface IGenericBusinessObjectFactory
*/
public IExperimentBO createExperimentBO(final Session session);
- /**
- * Creates a {@link IMaterialBO} <i>Business Object</i>.
- */
- public IMaterialBO createMaterialBO(final Session session);
-
/**
* Creates a {@link IDataBO} <i>Business Object</i>.
*/
@@ -71,11 +65,6 @@ public interface IGenericBusinessObjectFactory
*/
public ISampleTable createSampleTable(final Session session);
- /**
- * Creates a {@link IMaterialTable} <i>Business Object</i>.
- */
- public IMaterialTable createMaterialTable(Session session);
-
/**
* Creates a {@link IDataSetTable} <i>Business Object</i>.
*/
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 3ea32e1518a..2c63bb0434b 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
@@ -23,9 +23,11 @@ import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
+import java.util.Map;
import java.util.Set;
import org.hamcrest.BaseMatcher;
@@ -57,6 +59,7 @@ 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.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
@@ -81,6 +84,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DatastoreServiceDescriptions;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.InvalidationPE;
+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.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
@@ -93,6 +98,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePropertyTypePE;
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.builders.DatabaseInstancePEBuilder;
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;
@@ -914,6 +920,17 @@ public class ETLServiceTest extends AbstractServerTestCase
new SampleUpdatesDTO(CommonTestUtils.TECH_ID, null, null, attachments, version,
sampleIdentifier, null, null);
+ final MaterialPE material = new MaterialPE();
+ material.setCode("new-material");
+ final MaterialTypePE materialType = new MaterialTypePE();
+ materialType.setCode("new-material-type");
+ materialType.setDatabaseInstance(new DatabaseInstancePEBuilder().code("db")
+ .getDatabaseInstance());
+ final NewMaterial newMaterial = new NewMaterial(material.getCode());
+ Map<String, List<NewMaterial>> materialRegistrations =
+ new HashMap<String, List<NewMaterial>>();
+ materialRegistrations.put(materialType.getCode(), Arrays.asList(newMaterial));
+
final SamplePE newSamplePE = createSampleWithExperiment(experiment);
newSamplePE.setCode("sample code new");
final SampleIdentifier newSampleIdentifier = newSamplePE.getSampleIdentifier();
@@ -932,6 +949,30 @@ public class ETLServiceTest extends AbstractServerTestCase
dataSetUpdate.setModifiedContainedDatasetCodesOrNull(new String[]
{ "c1", "c2" });
+ context.checking(new Expectations()
+ {
+ {
+ allowing(daoFactory).getEntityTypeDAO(EntityKind.MATERIAL);
+ will(returnValue(entityTypeDAO));
+
+ allowing(entityTypeDAO).tryToFindEntityTypeByCode(
+ materialType.getCode());
+ will(returnValue(materialType));
+
+ final List<NewMaterial> newMaterials = Arrays.asList(newMaterial);
+ one(propertiesBatchManager).manageProperties(materialType, newMaterials, null);
+
+ one(boFactory).createMaterialTable(SESSION);
+ will(returnValue(materialTable));
+
+ one(materialTable).add(newMaterials, materialType);
+ one(materialTable).save();
+ one(materialTable).getMaterials();
+ will(returnValue(Arrays.asList(material)));
+
+ }
+ });
+
context.checking(new Expectations()
{
{
@@ -998,7 +1039,7 @@ public class ETLServiceTest extends AbstractServerTestCase
new AtomicEntityOperationDetails(null, new ArrayList<NewSpace>(),
new ArrayList<NewProject>(), new ArrayList<NewExperiment>(),
Collections.singletonList(sampleUpdate),
- Collections.singletonList(newSample),
+ Collections.singletonList(newSample), materialRegistrations,
Collections.singletonList(externalData),
Collections.singletonList(dataSetUpdate));
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 2d773460d3d..cc540753cfe 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
@@ -57,6 +57,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
@@ -120,20 +122,11 @@ public interface IETLLIMSService extends IServer, ISessionProvider
throws UserFailureException;
/**
- * Gets a sample with the specified identifier. Sample is enriched with properties and the
- * experiment with properties.
- *
- * @param sessionToken the user authentication token. Must not be <code>null</code>.
- * @param sampleIdentifier an identifier which uniquely identifies the sample.
- * @return <code>null</code> if no sample attached to an experiment could be found for given
- * <var>sampleIdentifier</var>.
+ * For given {@link MaterialIdentifier} returns the corresponding {@link Material}.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
- public Sample tryGetSampleWithExperiment(
- final String sessionToken,
- @AuthorizationGuard(guardClass = ExistingSampleOwnerIdentifierPredicate.class) final SampleIdentifier sampleIdentifier)
- throws UserFailureException;
+ public Material tryGetMaterial(String sessionToken, MaterialIdentifier materialIdentifier);
/**
* Tries to get the identifier of sample with specified permanent ID.
@@ -154,6 +147,22 @@ public interface IETLLIMSService extends IServer, ISessionProvider
public ExperimentType getExperimentType(String sessionToken, String experimentTypeCode)
throws UserFailureException;
+ /**
+ * Gets a sample with the specified identifier. Sample is enriched with properties and the
+ * experiment with properties.
+ *
+ * @param sessionToken the user authentication token. Must not be <code>null</code>.
+ * @param sampleIdentifier an identifier which uniquely identifies the sample.
+ * @return <code>null</code> if no sample attached to an experiment could be found for given
+ * <var>sampleIdentifier</var>.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public Sample tryGetSampleWithExperiment(
+ final String sessionToken,
+ @AuthorizationGuard(guardClass = ExistingSampleOwnerIdentifierPredicate.class) final SampleIdentifier sampleIdentifier)
+ throws UserFailureException;
+
/**
* Returns a list of terms belonging to given vocabulary.
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AtomicEntityOperationDetailsTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AtomicEntityOperationDetailsTest.java
index bcde99654f1..8dfee947408 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AtomicEntityOperationDetailsTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AtomicEntityOperationDetailsTest.java
@@ -17,7 +17,9 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import org.testng.AssertJUnit;
import org.testng.annotations.Test;
@@ -42,6 +44,16 @@ public class AtomicEntityOperationDetailsTest extends AssertJUnit
spaceRegistrations.add(new NewSpace("SPACE1", "description", "adminUser1"));
spaceRegistrations.add(new NewSpace("SPACE2", "description", "adminUser2"));
+ Map<String, List<NewMaterial>> materialRegistrations =
+ new HashMap<String, List<NewMaterial>>();
+ List<NewMaterial> newMaterials1 = new ArrayList<NewMaterial>();
+ newMaterials1.add(new NewMaterial("material-one"));
+ newMaterials1.add(new NewMaterial("material-two"));
+ List<NewMaterial> newMaterials2 = new ArrayList<NewMaterial>();
+ newMaterials2.add(new NewMaterial("material-three"));
+ materialRegistrations.put("material-type-1", newMaterials1);
+ materialRegistrations.put("material-type-2", newMaterials2);
+
ArrayList<NewProject> projectRegistrations = new ArrayList<NewProject>();
projectRegistrations.add(new NewProject("/SPACE/P1", "description"));
projectRegistrations.add(new NewProject("/SPACE/P2", "description"));
@@ -73,7 +85,7 @@ public class AtomicEntityOperationDetailsTest extends AssertJUnit
AtomicEntityOperationDetails details =
new AtomicEntityOperationDetails(null, spaceRegistrations, projectRegistrations,
experimentRegistrations, sampleUpdates, sampleRegistrations,
- dataSetRegistrations, dataSetUpdates);
+ materialRegistrations, dataSetRegistrations, dataSetUpdates);
assertEquals(
"AtomicEntityOperationDetails[userIdOrNull=<null>"
@@ -83,6 +95,7 @@ public class AtomicEntityOperationDetailsTest extends AssertJUnit
+ ",experimentRegistrations=[/SPACE/PROJECT/EXP-ID1, /SPACE/PROJECT/EXP-ID2]"
+ ",sampleUpdates=[]"
+ ",sampleRegistrations=[/SPACE/SAMPLE-ID1, /SPACE/SAMPLE-ID2]"
+ + ",materialRegistrations={material-type-1=[material-one, material-two], material-type-2=[material-three]}"
+ ",dataSetRegistrations=[NewExternalData[code=DATA-SET-CODE,type=<null>,fileFormat=<null>,properties=[]]]"
+ ",dataSetUpdates=[1]]",
details.toString());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java
index 4b01f7a5526..e41ed0567f8 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java
@@ -71,6 +71,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleRelationshipPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
@@ -461,6 +462,7 @@ public final class GenericServerTest extends AbstractServerTestCase
one(materialTable).add(newMaterials, materialTypePE);
one(materialTable).save();
+ one(materialTable).getMaterials();
}
});
createServer().registerMaterials(SESSION_TOKEN, typeCode, newMaterials);
@@ -564,8 +566,10 @@ public final class GenericServerTest extends AbstractServerTestCase
}
existingMaterials.add(createMaterial(createNewMaterial("A")));
- one(commonServer).listMaterials(with(SESSION_TOKEN),
- with(new BaseMatcher<ListMaterialCriteria>()
+ one(genericBusinessObjectFactory)
+ .createMaterialLister(with(any(Session.class)));
+ will(returnValue(materialLister));
+ one(materialLister).list(with(new BaseMatcher<ListMaterialCriteria>()
{
public boolean matches(Object item)
{
--
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