diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/ApplicationServerApi.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/ApplicationServerApi.java
index 3c9ae2e608d48a841dea79a4d9e40a8116306e29..4f649fbe2d6be108d1b18ed9242dc35e54092619 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/ApplicationServerApi.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/ApplicationServerApi.java
@@ -42,6 +42,7 @@ import ch.ethz.sis.openbis.generic.server.api.v3.executor.experiment.IUpdateExpe
import ch.ethz.sis.openbis.generic.server.api.v3.executor.material.ICreateMaterialExecutor;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.material.IDeleteMaterialExecutor;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.material.IMapMaterialByIdExecutor;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.material.IUpdateMaterialExecutor;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.project.ICreateProjectExecutor;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.project.IMapProjectByIdExecutor;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.sample.ICreateSampleExecutor;
@@ -79,6 +80,7 @@ import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.experiment.Experimen
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.experiment.ExperimentUpdate;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.material.Material;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.material.MaterialCreation;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.material.MaterialUpdate;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.project.Project;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.project.ProjectCreation;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.Sample;
@@ -167,6 +169,9 @@ public class ApplicationServerApi extends AbstractServer<IApplicationServerApi>
@Autowired
private IUpdateSampleExecutor updateSampleExecutor;
+ @Autowired
+ private IUpdateMaterialExecutor updateMaterialExecutor;
+
@Autowired
private IUpdateDataSetExecutor updateDataSetExecutor;
@@ -435,6 +440,26 @@ public class ApplicationServerApi extends AbstractServer<IApplicationServerApi>
}
}
+ @Override
+ @Transactional
+ @RolesAllowed(
+ { RoleWithHierarchy.INSTANCE_ADMIN, RoleWithHierarchy.INSTANCE_ETL_SERVER })
+ @Capability("UPDATE_MATERIAL")
+ @DatabaseUpdateModification(value = ObjectKind.MATERIAL)
+ public void updateMaterials(String sessionToken, List<MaterialUpdate> updates)
+ {
+ Session session = getSession(sessionToken);
+ OperationContext context = new OperationContext(session);
+
+ try
+ {
+ updateMaterialExecutor.update(context, updates);
+ } catch (Throwable t)
+ {
+ throw ExceptionUtils.create(context, t);
+ }
+ }
+
@Override
@Transactional
@RolesAllowed({ RoleWithHierarchy.SPACE_POWER_USER, RoleWithHierarchy.SPACE_ETL_SERVER })
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/ApplicationServerApiLogger.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/ApplicationServerApiLogger.java
index 2ab2f86d33bfc530c054cf15ffae59c8525f6c79..4b848d0a08839e7ac36f0f90642a18100a35d8fd 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/ApplicationServerApiLogger.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/ApplicationServerApiLogger.java
@@ -33,6 +33,7 @@ import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.experiment.Experimen
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.experiment.ExperimentUpdate;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.material.Material;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.material.MaterialCreation;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.material.MaterialUpdate;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.project.Project;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.project.ProjectCreation;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.Sample;
@@ -173,6 +174,12 @@ public class ApplicationServerApiLogger extends AbstractServerLogger implements
logAccess(sessionToken, "update-data-sets", "DATA_SET_UPDATES(%s)", dataSetUpdates);
}
+ @Override
+ public void updateMaterials(String sessionToken, List<MaterialUpdate> materialUpdates)
+ {
+ logAccess(sessionToken, "update-materials", "MATERIAL_UPDATES(%s)", materialUpdates);
+ }
+
@Override
public Map<ISpaceId, Space> mapSpaces(String sessionToken, List<? extends ISpaceId> spaceIds, SpaceFetchOptions fetchOptions)
{
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/material/IUpdateMaterialExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/material/IUpdateMaterialExecutor.java
new file mode 100644
index 0000000000000000000000000000000000000000..97a94a521de7d1e43f298b3ef4506133279aa873
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/material/IUpdateMaterialExecutor.java
@@ -0,0 +1,28 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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.ethz.sis.openbis.generic.server.api.v3.executor.material;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.entity.IUpdateEntityExecutor;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.material.MaterialUpdate;
+
+/**
+ * @author Jakub Straszewski
+ */
+public interface IUpdateMaterialExecutor extends IUpdateEntityExecutor<MaterialUpdate>
+{
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/material/UpdateMaterialExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/material/UpdateMaterialExecutor.java
new file mode 100644
index 0000000000000000000000000000000000000000..d14bcd1b0261d4687d0296ab6cb558e1a68516c6
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/material/UpdateMaterialExecutor.java
@@ -0,0 +1,139 @@
+/*
+ * Copyright 2014 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.ethz.sis.openbis.generic.server.api.v3.executor.material;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.dao.DataAccessException;
+import org.springframework.stereotype.Component;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.entity.AbstractUpdateEntityExecutor;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.property.IUpdateEntityPropertyExecutor;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.tag.IUpdateTagForEntityExecutor;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.material.MaterialUpdate;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.material.IMaterialId;
+import ch.ethz.sis.openbis.generic.shared.api.v3.exceptions.UnauthorizedObjectAccessException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SampleByIdentiferValidator;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.DataAccessExceptionTranslator;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityPropertiesHolder;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
+
+/**
+ * @author Jakub Straszewski
+ */
+@Component
+public class UpdateMaterialExecutor extends AbstractUpdateEntityExecutor<MaterialUpdate, MaterialPE, IMaterialId> implements IUpdateMaterialExecutor
+{
+
+ @Autowired
+ private IDAOFactory daoFactory;
+
+ @Autowired
+ private IMapMaterialByIdExecutor mapMaterialByIdExecutor;
+
+ @Autowired
+ private IUpdateEntityPropertyExecutor updateEntityPropertyExecutor;
+
+ @Autowired
+ private IUpdateTagForEntityExecutor updateTagForEntityExecutor;
+
+ @Autowired
+ private IVerifyMaterialExecutor verifyMaterialExecutor;
+
+ @Override
+ protected IMaterialId getId(MaterialUpdate update)
+ {
+ return update.getMaterialId();
+ }
+
+ @Override
+ protected void checkData(IOperationContext context, MaterialUpdate update)
+ {
+ if (update.getMaterialId() == null)
+ {
+ throw new UserFailureException("Sample id cannot be null.");
+ }
+ }
+
+ @Override
+ protected void checkAccess(IOperationContext context, IMaterialId id, MaterialPE entity)
+ {
+ if (false == new SampleByIdentiferValidator().doValidation(context.getSession().tryGetPerson(), entity))
+ {
+ throw new UnauthorizedObjectAccessException(id);
+ }
+ }
+
+ @Override
+ protected void checkBusinessRules(IOperationContext context, Collection<MaterialPE> entities)
+ {
+ verifyMaterialExecutor.verify(context, entities);
+ }
+
+ @Override
+ protected void updateBatch(IOperationContext context, Map<MaterialUpdate, MaterialPE> entitiesMap)
+ {
+ Map<IEntityPropertiesHolder, Map<String, String>> propertyMap = new HashMap<IEntityPropertiesHolder, Map<String, String>>();
+ for (Map.Entry<MaterialUpdate, MaterialPE> entry : entitiesMap.entrySet())
+ {
+ MaterialUpdate update = entry.getKey();
+ MaterialPE entity = entry.getValue();
+ updateTagForEntityExecutor.update(context, entity, update.getTagIds());
+ propertyMap.put(entity, update.getProperties());
+ }
+
+ updateEntityPropertyExecutor.update(context, propertyMap);
+ }
+
+ @Override
+ protected void updateAll(IOperationContext context, Map<MaterialUpdate, MaterialPE> entitiesMap)
+ {
+ }
+
+ @Override
+ protected Map<IMaterialId, MaterialPE> map(IOperationContext context, Collection<IMaterialId> ids)
+ {
+ return mapMaterialByIdExecutor.map(context, ids);
+ }
+
+ @Override
+ protected List<MaterialPE> list(IOperationContext context, Collection<Long> ids)
+ {
+ return daoFactory.getMaterialDAO().listMaterialsById(ids);
+ }
+
+ @Override
+ protected void save(IOperationContext context, List<MaterialPE> entities, boolean clearCache)
+ {
+ daoFactory.getMaterialDAO().createOrUpdateMaterials(entities);
+ }
+
+ @Override
+ protected void handleException(DataAccessException e)
+ {
+ DataAccessExceptionTranslator.throwException(e, EntityKind.SAMPLE.getLabel(), EntityKind.SAMPLE);
+ }
+
+}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/CreateMaterialTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/CreateMaterialTest.java
index 2781aafbc44aa9c65320cd18d7b5bb1ee1b02099..f46266234e219e2acb74d39747da18864fa577ee 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/CreateMaterialTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/CreateMaterialTest.java
@@ -57,15 +57,70 @@ public class CreateMaterialTest extends AbstractSampleTest
AssertionUtil.assertCollectionSize(map.values(), 2);
Material material = map.get(new MaterialPermId("1982", "GENE"));
-
assertEquals(material.getCode(), "1982");
assertEquals(material.getPermId().getTypeCode(), "GENE");
+
+ material = map.get(new MaterialPermId("1984", "GENE"));
+ assertEquals(material.getCode(), "1984");
+ assertEquals(material.getPermId().getTypeCode(), "GENE");
+ }
+
+ // @Test broken
+ public void testCreateTwoMaterialsWithMaterialLinks()
+ {
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ MaterialPermId m1id = new MaterialPermId("FIRST", "SELF_REF");
+ MaterialCreation m1 = materialCreation(m1id);
+ HashMap<String, String> properties1 = new HashMap<String, String>();
+ properties1.put("ANY_MATERIAL", "SECOND (SELF_REF)");
+ properties1.put("DESCRIPTION", "mandatory material decsription");
+ m1.setProperties(properties1);
+
+ MaterialPermId m2id = new MaterialPermId("SECOND", "SELF_REF");
+ MaterialCreation m2 = materialCreation(m2id);
+ HashMap<String, String> properties2 = new HashMap<String, String>();
+ properties2.put("ANY_MATERIAL", "FIRST (SELF_REF)");
+ properties2.put("DESCRIPTION", "mandatory material decsription");
+ m2.setProperties(properties2);
+
+ List<MaterialPermId> materialIds = v3api.createMaterials(sessionToken, Arrays.asList(m1, m2));
+
+ AssertionUtil.assertCollectionContainsOnly(materialIds, m1id, m2id);
+
+ // circular materialProperties
+ MaterialFetchOptions fetchOptions = new MaterialFetchOptions();
+ fetchOptions.withMaterialPropertiesUsing(fetchOptions);
+
+ Map<IMaterialId, Material> map = v3api.mapMaterials(sessionToken, Arrays.asList(m1id), fetchOptions);
+
+ AssertionUtil.assertCollectionSize(map.values(), 1);
+
+ Material resultm1 = map.get(m1id);
+
+ assertEquals(resultm1.getPermId(), m1id);
+ Material resultm2 = resultm1.getMaterialProperties().get("ANY_MATERIAL");
+ assertEquals(resultm2.getPermId(), m2id);
+ Material resultm3 = resultm2.getMaterialProperties().get("ANY_MATERIAL");
+ assertEquals(resultm1, resultm3);
}
// all potential error scenarios
// create mateiral with mateiral properties
+ private MaterialCreation materialCreation(MaterialPermId permId)
+ {
+ String code = permId.getCode();
+ String type = permId.getTypeCode();
+ MaterialCreation materialCreation = new MaterialCreation();
+ materialCreation.setCode(code);
+ materialCreation.setTypeId(new EntityTypePermId(type));
+ materialCreation.setCreationId(new CreationId("creation " + code));
+ materialCreation.setDescription("Material with code " + code);
+ return materialCreation;
+ }
+
private MaterialCreation geneCreation(String code)
{
MaterialCreation materialCreation = new MaterialCreation();
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/UpdateMaterialTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/UpdateMaterialTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..c480dce4f468cad0fd6d9747b9ee7727e749b42c
--- /dev/null
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/UpdateMaterialTest.java
@@ -0,0 +1,59 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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.ethz.sis.openbis.systemtest.api.v3;
+
+import static org.testng.Assert.assertEquals;
+
+import java.util.Arrays;
+import java.util.Map;
+
+import org.testng.annotations.Test;
+
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.material.Material;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.material.MaterialUpdate;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.fetchoptions.material.MaterialFetchOptions;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.material.IMaterialId;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.material.MaterialPermId;
+
+/**
+ * @author pkupczyk
+ */
+public class UpdateMaterialTest extends AbstractSampleTest
+{
+
+ @Test
+ public void testSimpleMaterialUpdate()
+ {
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ MaterialUpdate update = new MaterialUpdate();
+ update.setMaterialId(new MaterialPermId("1", "GENE"));
+ String description = "This is amodified gene description";
+ update.setProperty("DESCRIPTION", description);
+
+ v3api.updateMaterials(sessionToken, Arrays.asList(update));
+
+ MaterialFetchOptions fetchOptions = new MaterialFetchOptions();
+ fetchOptions.withProperties();
+
+ Map<IMaterialId, Material> map = v3api.mapMaterials(sessionToken, Arrays.asList(update.getMaterialId()), fetchOptions);
+
+ Material material = map.get(update.getMaterialId());
+ assertEquals(material.getProperties().get("DESCRIPTION"), description);
+ }
+
+}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/UpdateSampleTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/UpdateSampleTest.java
index d00c37b6c12eecad2216605a6018a2e5c93bb625..5edb3f5703913f3055bbdc05fd6da5ea9ec04c33 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/UpdateSampleTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/UpdateSampleTest.java
@@ -32,6 +32,7 @@ import org.testng.annotations.Test;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.attachment.Attachment;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.attachment.AttachmentCreation;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.material.Material;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.Sample;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleCreation;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleUpdate;
@@ -41,6 +42,7 @@ import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.attachment.AttachmentFil
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.entitytype.EntityTypePermId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.ExperimentPermId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.IExperimentId;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.material.MaterialPermId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.SampleIdentifier;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.SamplePermId;
@@ -1241,4 +1243,34 @@ public class UpdateSampleTest extends AbstractSampleTest
assertTags(sample2.getTags(), "/test/TEST_TAG_2", "/test/TEST_TAG_3");
}
+ @Test
+ public void testWithMaterialProperties()
+ {
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ SampleFetchOptions fetchOptions = new SampleFetchOptions();
+ fetchOptions.withMaterialProperties().withRegistrator();
+ fetchOptions.withProperties();
+
+ SamplePermId permId = new SamplePermId("200902091219327-1025");
+
+ SampleUpdate update1 = new SampleUpdate();
+ update1.setSampleId(permId);
+ update1.setProperty("ANY_MATERIAL", "BACTERIUM-X (BACTERIUM)");
+
+ v3api.updateSamples(sessionToken, Arrays.asList(update1));
+
+ Map<ISampleId, Sample> map = v3api.mapSamples(sessionToken, Arrays.asList(permId), fetchOptions);
+
+ Sample sample = map.get(permId);
+
+ assertEquals(sample.getProperties().get("BACTERIUM"), "BACTERIUM-X (BACTERIUM)");
+ assertEquals(sample.getProperties().get("ANY_MATERIAL"), "BACTERIUM-X (BACTERIUM)");
+
+ Map<String, Material> materialProperties = sample.getMaterialProperties();
+
+ Material updatedBacterium = materialProperties.get("ANY_MATERIAL");
+ assertEquals(updatedBacterium.getPermId(), new MaterialPermId("BACTERIUM-X", "BACTERIUM"));
+ }
+
}