From 7d442e2290411e858a4be2818a17fe0be130b5f3 Mon Sep 17 00:00:00 2001
From: pkupczyk <pkupczyk>
Date: Thu, 16 Oct 2014 14:16:47 +0000
Subject: [PATCH] SSDM-942 : V3 AS API - authorization predicates
SVN: 32620
---
.../server/api/v3/ApplicationServerApi.java | 19 ++-
.../ListExperimentCreationPredicate.java | 89 ----------
.../AbstractListObjectByIdExecutor.java | 42 +++++
.../common/AbstractMapObjectByIdExecutor.java | 51 ++++++
.../common/IListObjectByIdExecutor.java | 33 ++++
.../common/IMapObjectByIdExecutor.java | 33 ++++
.../entity/MapEntityTypeByIdExecutor.java | 30 +---
.../experiment/CreateExperimentExecutor.java | 12 +-
.../IListExperimentByIdExecutor.java | 9 +-
.../IMapExperimentByIdExecutor.java | 9 +-
.../ListExperimentByIdExecutor.java | 15 +-
.../experiment/MapExperimentByIdExecutor.java | 51 ++----
.../experiment/UpdateExperimentExecutor.java | 10 ++
.../project/IListProjectByIdExecutor.java | 29 ++++
.../project/IMapProjectByIdExecutor.java | 29 ++++
.../project/ListProjectByIdExecutor.java | 53 ++++++
.../project/MapProjectByIdExecutor.java | 70 ++++++++
.../project/TryGetProjectByIdExecutor.java | 37 ++---
...stractSetSampleRelatedSamplesExecutor.java | 39 ++---
...actUpdateSampleRelatedSamplesExecutor.java | 68 ++++----
.../executor/sample/CreateSampleExecutor.java | 146 ++++++----------
.../sample/IListSampleByIdExecutor.java | 9 +-
.../sample/IMapSampleByIdExecutor.java | 29 ++++
.../sample/ISetSampleChildrenExecutor.java | 2 +-
.../sample/ISetSampleContainedExecutor.java | 2 +-
.../sample/ISetSampleContainerExecutor.java | 2 +-
.../sample/ISetSampleExperimentExecutor.java | 33 ++++
.../sample/ISetSampleParentsExecutor.java | 2 +-
.../sample/ISetSampleSpaceExecutor.java | 33 ++++
.../sample/ISetSampleTypeExecutor.java | 33 ++++
.../sample/IUpdateSampleChildrenExecutor.java | 2 +-
.../IUpdateSampleContainedExecutor.java | 2 +-
.../IUpdateSampleContainerExecutor.java | 2 +-
.../sample/IUpdateSampleParentsExecutor.java | 2 +-
.../sample/ListSampleByIdExecutor.java | 36 +---
.../sample/MapSampleByIdExecutor.java | 75 +++++++++
.../sample/SetSampleChildrenExecutor.java | 43 ++---
.../sample/SetSampleContainedExecutor.java | 27 +--
.../sample/SetSampleContainerExecutor.java | 33 ++--
.../sample/SetSampleExperimentExecutor.java | 87 ++++++++++
.../sample/SetSampleParentsExecutor.java | 44 ++---
.../SetSampleRelatedSamplesExecutor.java | 45 +++--
.../sample/SetSampleSpaceExecutor.java | 87 ++++++++++
.../sample/SetSampleTypeExecutor.java | 85 ++++++++++
.../sample/UpdateSampleChildrenExecutor.java | 75 +++++----
.../sample/UpdateSampleContainedExecutor.java | 89 ++++++++--
.../sample/UpdateSampleContainerExecutor.java | 43 ++---
.../executor/sample/UpdateSampleExecutor.java | 10 ++
.../UpdateSampleExperimentExecutor.java | 12 ++
.../sample/UpdateSampleParentsExecutor.java | 75 +++++----
.../UpdateSampleRelatedSamplesExecutor.java | 38 ++---
.../sample/UpdateSampleSpaceExecutor.java | 12 ++
.../space/IListSpaceByIdExecutor.java | 9 +-
.../executor/space/IMapSpaceByIdExecutor.java | 9 +-
.../executor/space/ListSpaceByIdExecutor.java | 15 +-
.../executor/space/MapSpaceByIdExecutor.java | 49 ++----
.../v3/helper/common/IListObjectById.java} | 12 +-
.../api/v3/helper/common/MapObjectById.java} | 76 +++++----
.../entity/ListEntityTypeByPermId.java} | 22 +--
.../experiment/ListExperimentByPermId.java} | 25 ++-
.../project/ListProjectByIdentifier.java | 67 ++++++++
.../helper/project/ListProjectByPermId.java | 65 ++++++++
.../sample/ListSampleByIdentifier.java} | 39 +++--
.../v3/helper/sample/ListSampleByPermId.java} | 25 ++-
.../v3/helper/space/ListSpaceByPermId.java} | 25 ++-
.../EntityTypePermIdTranslator.java | 35 ----
.../entitytype/IEntityTypeIdTranslator.java | 43 -----
.../ExperimentIdentifierIdTranslator.java | 35 ----
.../ExperimentPermIdTranslator.java | 35 ----
.../experiment/IExperimentIdTranslator.java | 48 ------
.../id/sample/ISampleIdTranslator.java | 48 ------
.../sample/SampleIdentifierIdTranslator.java | 35 ----
.../id/sample/SamplePermIdTranslator.java | 35 ----
.../id/space/ISpaceIdTranslator.java | 44 -----
.../id/space/SpacePermIdTranslator.java | 35 ----
.../experiment/ExperimentValidator.java | 46 -----
.../api/v3/validator/entity/sample/.gitignore | 0
.../ListerByExperimentTechIdId.java | 66 --------
.../id/sample/ListerBySampleTechIdId.java | 66 --------
.../server/dataaccess/IExperimentDAO.java | 21 ++-
.../server/dataaccess/IProjectDAO.java | 11 ++
.../server/dataaccess/db/ProjectDAO.java | 29 ++++
.../openbis/generic/shared/dto/SamplePE.java | 3 +-
.../MapExperimentByIdExecutorTest.java | 5 +-
.../project/MapProjectByIdExecutorTest.java | 157 ++++++++++++++++++
.../TryGetProjectByIdExecutorTest.java | 75 ++-------
.../api/v3/ExperimentCreateTest.java | 15 +-
.../api/v3/ExperimentUpdateTest.java | 46 ++++-
.../systemtest/api/v3/SampleCreateTest.java | 157 +++++++++++++++++-
.../systemtest/api/v3/SampleUpdateTest.java | 147 +++++++++++++++-
.../exceptions/ObjectNotFoundException.java | 35 ++++
91 files changed, 2198 insertions(+), 1455 deletions(-)
delete mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/authorization/predicate/ListExperimentCreationPredicate.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/common/AbstractListObjectByIdExecutor.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/common/AbstractMapObjectByIdExecutor.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/common/IListObjectByIdExecutor.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/common/IMapObjectByIdExecutor.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/IListProjectByIdExecutor.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/IMapProjectByIdExecutor.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/ListProjectByIdExecutor.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/MapProjectByIdExecutor.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IMapSampleByIdExecutor.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleExperimentExecutor.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleSpaceExecutor.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleTypeExecutor.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/MapSampleByIdExecutor.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleExperimentExecutor.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleSpaceExecutor.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleTypeExecutor.java
rename openbis/source/java/ch/{systemsx/cisd/openbis/generic/server/business/search/id/IListerById.java => ethz/sis/openbis/generic/server/api/v3/helper/common/IListObjectById.java} (68%)
rename openbis/source/java/ch/{systemsx/cisd/openbis/generic/server/business/search/id/ListerById.java => ethz/sis/openbis/generic/server/api/v3/helper/common/MapObjectById.java} (51%)
rename openbis/source/java/ch/{systemsx/cisd/openbis/generic/server/business/search/id/entitytype/ListerByEntityTypePermIdId.java => ethz/sis/openbis/generic/server/api/v3/helper/entity/ListEntityTypeByPermId.java} (64%)
rename openbis/source/java/ch/{systemsx/cisd/openbis/generic/server/business/search/id/experiment/ListerByExperimentPermIdId.java => ethz/sis/openbis/generic/server/api/v3/helper/experiment/ListExperimentByPermId.java} (56%)
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/project/ListProjectByIdentifier.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/project/ListProjectByPermId.java
rename openbis/source/java/ch/{systemsx/cisd/openbis/generic/server/business/search/id/sample/ListerBySampleIdentifierId.java => ethz/sis/openbis/generic/server/api/v3/helper/sample/ListSampleByIdentifier.java} (81%)
rename openbis/source/java/ch/{systemsx/cisd/openbis/generic/server/business/search/id/sample/ListerBySamplePermIdId.java => ethz/sis/openbis/generic/server/api/v3/helper/sample/ListSampleByPermId.java} (58%)
rename openbis/source/java/ch/{systemsx/cisd/openbis/generic/server/business/search/id/space/ListerBySpacePermIdId.java => ethz/sis/openbis/generic/server/api/v3/helper/space/ListSpaceByPermId.java} (59%)
delete mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/entitytype/EntityTypePermIdTranslator.java
delete mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/entitytype/IEntityTypeIdTranslator.java
delete mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/experiment/ExperimentIdentifierIdTranslator.java
delete mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/experiment/ExperimentPermIdTranslator.java
delete mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/experiment/IExperimentIdTranslator.java
delete mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/sample/ISampleIdTranslator.java
delete mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/sample/SampleIdentifierIdTranslator.java
delete mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/sample/SamplePermIdTranslator.java
delete mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/space/ISpaceIdTranslator.java
delete mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/space/SpacePermIdTranslator.java
delete mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/validator/entity/experiment/ExperimentValidator.java
delete mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/validator/entity/sample/.gitignore
delete mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/experiment/ListerByExperimentTechIdId.java
delete mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/sample/ListerBySampleTechIdId.java
create mode 100644 openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/MapProjectByIdExecutorTest.java
create mode 100644 openbis_api/source/java/ch/ethz/sis/openbis/generic/shared/api/v3/exceptions/ObjectNotFoundException.java
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 f9a0d185643..b4b206954d5 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
@@ -16,8 +16,8 @@
package ch.ethz.sis.openbis.generic.server.api.v3;
+import java.util.ArrayList;
import java.util.Collection;
-import java.util.LinkedList;
import java.util.List;
import javax.annotation.Resource;
@@ -26,7 +26,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import org.springframework.transaction.annotation.Transactional;
-import ch.ethz.sis.openbis.generic.server.api.v3.authorization.predicate.ListExperimentCreationPredicate;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.OperationContext;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.experiment.ICreateExperimentExecutor;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.experiment.IListExperimentByIdExecutor;
@@ -63,7 +62,6 @@ import ch.ethz.sis.openbis.generic.shared.api.v3.dto.search.SampleSearchCriterio
import ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
import ch.systemsx.cisd.openbis.generic.server.ComponentNames;
-import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.AuthorizationGuard;
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.RolesAllowed;
import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
import ch.systemsx.cisd.openbis.generic.server.business.IRelationshipService;
@@ -167,7 +165,6 @@ public class ApplicationServerApi extends AbstractServer<IApplicationServerApi>
{ RoleWithHierarchy.SPACE_USER })
@DatabaseCreateOrDeleteModification(value = ObjectKind.EXPERIMENT)
public List<ExperimentPermId> createExperiments(String sessionToken,
- @AuthorizationGuard(guardClass = ListExperimentCreationPredicate.class)
List<ExperimentCreation> creations)
{
// REPLACES:
@@ -187,7 +184,11 @@ public class ApplicationServerApi extends AbstractServer<IApplicationServerApi>
@Override
@Transactional
- public List<SamplePermId> createSamples(String sessionToken, List<SampleCreation> creations)
+ @RolesAllowed(
+ { RoleWithHierarchy.SPACE_USER })
+ @DatabaseCreateOrDeleteModification(value = ObjectKind.SAMPLE)
+ public List<SamplePermId> createSamples(String sessionToken,
+ List<SampleCreation> creations)
{
Session session = getSession(sessionToken);
OperationContext context = new OperationContext(session);
@@ -265,7 +266,7 @@ public class ApplicationServerApi extends AbstractServer<IApplicationServerApi>
List<ExperimentPE> experiments = listExperimentByIdExecutor.list(context, experimentIds);
- return new LinkedList<Experiment>(
+ return new ArrayList<Experiment>(
new ExperimentTranslator(new TranslationContext(session), managedPropertyEvaluatorFactory, fetchOptions).translate(experiments));
}
@@ -280,7 +281,7 @@ public class ApplicationServerApi extends AbstractServer<IApplicationServerApi>
List<SamplePE> samples = listSampleByIdExecutor.list(context, sampleIds);
- return new LinkedList<Sample>(
+ return new ArrayList<Sample>(
new SampleTranslator(new TranslationContext(session), managedPropertyEvaluatorFactory, fetchOptions).translate(samples));
}
@@ -305,7 +306,7 @@ public class ApplicationServerApi extends AbstractServer<IApplicationServerApi>
List<ExperimentPE> experiments = getDAOFactory().getExperimentDAO().listByIDs(experimentIds);
- return new LinkedList<Experiment>(
+ return new ArrayList<Experiment>(
new ExperimentTranslator(new TranslationContext(session), managedPropertyEvaluatorFactory, fetchOptions).translate(experiments));
}
@@ -329,7 +330,7 @@ public class ApplicationServerApi extends AbstractServer<IApplicationServerApi>
List<SamplePE> samples = getDAOFactory().getSampleDAO().listByIDs(sampleIds);
- return new LinkedList<Sample>(
+ return new ArrayList<Sample>(
new SampleTranslator(new TranslationContext(session), managedPropertyEvaluatorFactory, fetchOptions).translate(samples));
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/authorization/predicate/ListExperimentCreationPredicate.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/authorization/predicate/ListExperimentCreationPredicate.java
deleted file mode 100644
index 42dac1ad6b3..00000000000
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/authorization/predicate/ListExperimentCreationPredicate.java
+++ /dev/null
@@ -1,89 +0,0 @@
-package ch.ethz.sis.openbis.generic.server.api.v3.authorization.predicate;
-
-/*
- * 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.
- */
-
-import java.util.List;
-
-import ch.ethz.sis.openbis.generic.server.api.v3.executor.OperationContext;
-import ch.ethz.sis.openbis.generic.server.api.v3.executor.project.TryGetProjectByIdExecutor;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.experiment.ExperimentCreation;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.IProjectId;
-import ch.systemsx.cisd.common.exceptions.Status;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.server.authorization.IAuthorizationDataProvider;
-import ch.systemsx.cisd.openbis.generic.server.authorization.RoleWithIdentifier;
-import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.ShouldFlattenCollections;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.AbstractPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.ProjectPEPredicate;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
-
-/**
- * @author Jakub Straszewski
- * @author Franz-Josef Elmer
- */
-@ShouldFlattenCollections(value = false)
-public class ListExperimentCreationPredicate extends AbstractPredicate<List<ExperimentCreation>>
-{
- private IAuthorizationDataProvider provider;
-
- private ProjectPEPredicate projectPredicate;
-
- public ListExperimentCreationPredicate()
- {
- projectPredicate = new ProjectPEPredicate();
- }
-
- @Override
- public void init(IAuthorizationDataProvider dataProvider)
- {
- this.provider = dataProvider;
- projectPredicate.init(provider);
- }
-
- @Override
- public String getCandidateDescription()
- {
- return "experiment creation";
- }
-
- @Override
- protected Status doEvaluation(PersonPE person, List<RoleWithIdentifier> allowedRoles,
- List<ExperimentCreation> experimentCreations)
- {
-
- for (ExperimentCreation experimentCreation : experimentCreations)
- {
- IProjectId projectId = experimentCreation.getProjectId();
- if (projectId == null)
- {
- throw new UserFailureException(
- "Unspecified project for experiment to registered with code '"
- + experimentCreation.getCode() + "'.");
- }
- ProjectPE project =
- new TryGetProjectByIdExecutor(provider.getDaoFactory().getProjectDAO()).tryGet(new OperationContext(null), projectId);
- Status status = projectPredicate.evaluate(person, allowedRoles, project);
- if (status.isError())
- {
- return status;
- }
- }
- return Status.OK;
- }
-
-}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/common/AbstractListObjectByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/common/AbstractListObjectByIdExecutor.java
new file mode 100644
index 00000000000..fdd475ea421
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/common/AbstractListObjectByIdExecutor.java
@@ -0,0 +1,42 @@
+/*
+ * 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.common;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.IObjectId;
+
+/**
+ * @author pkupczyk
+ */
+public abstract class AbstractListObjectByIdExecutor<ID extends IObjectId, OBJECT> implements IListObjectByIdExecutor<ID, OBJECT>
+{
+
+ @Override
+ public List<OBJECT> list(IOperationContext context, Collection<? extends ID> ids)
+ {
+ Map<ID, OBJECT> map = getMapExecutor().map(context, ids);
+ return new ArrayList<OBJECT>(map.values());
+ }
+
+ protected abstract IMapObjectByIdExecutor<ID, OBJECT> getMapExecutor();
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/common/AbstractMapObjectByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/common/AbstractMapObjectByIdExecutor.java
new file mode 100644
index 00000000000..582edf7da02
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/common/AbstractMapObjectByIdExecutor.java
@@ -0,0 +1,51 @@
+/*
+ * 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.common;
+
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.IListObjectById;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.MapObjectById;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.IObjectId;
+
+/**
+ * @author pkupczyk
+ */
+public abstract class AbstractMapObjectByIdExecutor<ID extends IObjectId, OBJECT> implements IMapObjectByIdExecutor<ID, OBJECT>
+{
+
+ @Override
+ public Map<ID, OBJECT> map(IOperationContext context, Collection<? extends ID> ids)
+ {
+ if (ids == null)
+ {
+ throw new IllegalArgumentException("Ids were null");
+ }
+ if (ids.isEmpty())
+ {
+ return Collections.emptyMap();
+ }
+ return new MapObjectById<ID, OBJECT>().map(createListers(context), ids);
+ }
+
+ protected abstract List<IListObjectById<? extends ID, OBJECT>> createListers(IOperationContext context);
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/common/IListObjectByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/common/IListObjectByIdExecutor.java
new file mode 100644
index 00000000000..76d43077412
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/common/IListObjectByIdExecutor.java
@@ -0,0 +1,33 @@
+/*
+ * 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.common;
+
+import java.util.Collection;
+import java.util.List;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.IObjectId;
+
+/**
+ * @author pkupczyk
+ */
+public interface IListObjectByIdExecutor<ID extends IObjectId, OBJECT>
+{
+
+ public List<OBJECT> list(IOperationContext context, Collection<? extends ID> ids);
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/common/IMapObjectByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/common/IMapObjectByIdExecutor.java
new file mode 100644
index 00000000000..26aa2c63956
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/common/IMapObjectByIdExecutor.java
@@ -0,0 +1,33 @@
+/*
+ * 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.common;
+
+import java.util.Collection;
+import java.util.Map;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.IObjectId;
+
+/**
+ * @author pkupczyk
+ */
+public interface IMapObjectByIdExecutor<ID extends IObjectId, OBJECT>
+{
+
+ public Map<ID, OBJECT> map(IOperationContext context, Collection<? extends ID> ids);
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/entity/MapEntityTypeByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/entity/MapEntityTypeByIdExecutor.java
index 94d4b2b248b..1fb8c8418ae 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/entity/MapEntityTypeByIdExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/entity/MapEntityTypeByIdExecutor.java
@@ -17,7 +17,6 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.entity;
import java.util.Collection;
-import java.util.LinkedHashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
@@ -26,12 +25,10 @@ import org.springframework.beans.factory.annotation.Autowired;
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.translator.collection.ListTranslator;
-import ch.ethz.sis.openbis.generic.server.api.v3.translator.id.entitytype.IEntityTypeIdTranslator;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.IListObjectById;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.MapObjectById;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.entity.ListEntityTypeByPermId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.entitytype.IEntityTypeId;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.IListerById;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.ListerById;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.entitytype.ListerByEntityTypePermIdId;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
@@ -59,24 +56,11 @@ public class MapEntityTypeByIdExecutor implements IMapEntityTypeByIdExecutor
@Override
public Map<IEntityTypeId, EntityTypePE> map(IOperationContext context, EntityKind entityKind, Collection<? extends IEntityTypeId> entityTypeIds)
{
- List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.entitytype.IEntityTypeId> entityTypeIdsCore =
- new ListTranslator().translate(entityTypeIds, new IEntityTypeIdTranslator());
+ List<IListObjectById<? extends IEntityTypeId, EntityTypePE>> listers =
+ new LinkedList<IListObjectById<? extends IEntityTypeId, EntityTypePE>>();
+ listers.add(new ListEntityTypeByPermId(daoFactory, entityKind));
- @SuppressWarnings("rawtypes")
- List<IListerById> listers = new LinkedList<IListerById>();
- listers.add(new ListerByEntityTypePermIdId(daoFactory, entityKind));
-
- List<EntityTypePE> list = new ListerById(listers).list(entityTypeIdsCore);
- Map<IEntityTypeId, EntityTypePE> map = new LinkedHashMap<IEntityTypeId, EntityTypePE>();
- int index = 0;
-
- for (IEntityTypeId entityTypeId : entityTypeIds)
- {
- map.put(entityTypeId, list.get(index));
- index++;
- }
-
- return map;
+ return new MapObjectById<IEntityTypeId, EntityTypePE>().map(listers, entityTypeIds);
}
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/CreateExperimentExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/CreateExperimentExecutor.java
index a12565f46b2..6312387aeae 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/CreateExperimentExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/CreateExperimentExecutor.java
@@ -31,10 +31,13 @@ import ch.ethz.sis.openbis.generic.server.api.v3.executor.tag.IAddTagToEntityExe
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.experiment.ExperimentCreation;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.entitytype.IEntityTypeId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.ExperimentPermId;
+import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
+import ch.systemsx.cisd.openbis.generic.server.authorization.validator.ProjectByIdentiferValidator;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
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.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.util.RelationshipUtils;
@@ -114,7 +117,14 @@ public class CreateExperimentExecutor implements ICreateExperimentExecutor
updateEntityPropertyExecutor.update(context, experiment, entityType, experimentCreation.getProperties());
- experiment.setProject(getProjectByIdExecutor.get(context, experimentCreation.getProjectId()));
+ ProjectPE project = getProjectByIdExecutor.get(context, experimentCreation.getProjectId());
+
+ if (false == new ProjectByIdentiferValidator().doValidation(context.getSession().tryGetPerson(), project))
+ {
+ throw new AuthorizationFailureException("Cannot access project " + experimentCreation.getProjectId());
+ }
+
+ experiment.setProject(project);
String createdPermId = daoFactory.getPermIdDAO().createPermId();
experiment.setPermId(createdPermId);
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/IListExperimentByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/IListExperimentByIdExecutor.java
index 6ac0499fd42..c1289dd2836 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/IListExperimentByIdExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/IListExperimentByIdExecutor.java
@@ -16,19 +16,14 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.experiment;
-import java.util.Collection;
-import java.util.List;
-
-import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.IListObjectByIdExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.IExperimentId;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
/**
* @author pkupczyk
*/
-public interface IListExperimentByIdExecutor
+public interface IListExperimentByIdExecutor extends IListObjectByIdExecutor<IExperimentId, ExperimentPE>
{
- public List<ExperimentPE> list(IOperationContext context, Collection<? extends IExperimentId> experimentIds);
-
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/IMapExperimentByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/IMapExperimentByIdExecutor.java
index a24a1f54854..9cfcea6dcb8 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/IMapExperimentByIdExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/IMapExperimentByIdExecutor.java
@@ -16,19 +16,14 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.experiment;
-import java.util.Collection;
-import java.util.Map;
-
-import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.IMapObjectByIdExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.IExperimentId;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
/**
* @author pkupczyk
*/
-public interface IMapExperimentByIdExecutor
+public interface IMapExperimentByIdExecutor extends IMapObjectByIdExecutor<IExperimentId, ExperimentPE>
{
- public Map<IExperimentId, ExperimentPE> map(IOperationContext context, Collection<? extends IExperimentId> experimentIds);
-
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/ListExperimentByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/ListExperimentByIdExecutor.java
index 91071f9ccbd..56c960d5051 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/ListExperimentByIdExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/ListExperimentByIdExecutor.java
@@ -16,15 +16,11 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.experiment;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import java.util.Map;
-
import org.springframework.beans.factory.annotation.Autowired;
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.common.AbstractListObjectByIdExecutor;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.IMapObjectByIdExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.IExperimentId;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
@@ -32,7 +28,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
* @author pkupczyk
*/
@Component
-public class ListExperimentByIdExecutor implements IListExperimentByIdExecutor
+public class ListExperimentByIdExecutor extends AbstractListObjectByIdExecutor<IExperimentId, ExperimentPE> implements IListExperimentByIdExecutor
{
@Autowired
@@ -49,10 +45,9 @@ public class ListExperimentByIdExecutor implements IListExperimentByIdExecutor
}
@Override
- public List<ExperimentPE> list(IOperationContext context, Collection<? extends IExperimentId> experimentIds)
+ protected IMapObjectByIdExecutor<IExperimentId, ExperimentPE> getMapExecutor()
{
- Map<IExperimentId, ExperimentPE> map = mapExperimentByIdExecutor.map(context, experimentIds);
- return new ArrayList<ExperimentPE>(map.values());
+ return mapExperimentByIdExecutor;
}
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/MapExperimentByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/MapExperimentByIdExecutor.java
index 447feba1ac9..7e7e2e5e545 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/MapExperimentByIdExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/MapExperimentByIdExecutor.java
@@ -16,68 +16,53 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.experiment;
-import java.util.Collection;
-import java.util.LinkedHashMap;
import java.util.LinkedList;
import java.util.List;
-import java.util.Map;
import org.springframework.beans.factory.annotation.Autowired;
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.translator.collection.ListTranslator;
-import ch.ethz.sis.openbis.generic.server.api.v3.translator.id.experiment.IExperimentIdTranslator;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.AbstractMapObjectByIdExecutor;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.IListObjectById;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.experiment.ListExperimentByPermId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.IExperimentId;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.IListerById;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.ListerById;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.experiment.ListerByExperimentPermIdId;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.experiment.ListerByExperimentTechIdId;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
/**
* @author pkupczyk
*/
@Component
-public class MapExperimentByIdExecutor implements IMapExperimentByIdExecutor
+public class MapExperimentByIdExecutor extends AbstractMapObjectByIdExecutor<IExperimentId, ExperimentPE> implements IMapExperimentByIdExecutor
{
- @Autowired
- private IDAOFactory daoFactory;
+ private IExperimentDAO experimentDAO;
@SuppressWarnings("unused")
private MapExperimentByIdExecutor()
{
}
- public MapExperimentByIdExecutor(IDAOFactory daoFactory)
+ public MapExperimentByIdExecutor(IExperimentDAO experimentDAO)
{
- this.daoFactory = daoFactory;
+ this.experimentDAO = experimentDAO;
}
@Override
- public Map<IExperimentId, ExperimentPE> map(IOperationContext context, Collection<? extends IExperimentId> experimentIds)
+ protected List<IListObjectById<? extends IExperimentId, ExperimentPE>> createListers(IOperationContext context)
{
- List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.experiment.IExperimentId> experimentIdsCore =
- new ListTranslator().translate(experimentIds, new IExperimentIdTranslator());
-
- @SuppressWarnings("rawtypes")
- List<IListerById> listers = new LinkedList<IListerById>();
- listers.add(new ListerByExperimentTechIdId(daoFactory));
- listers.add(new ListerByExperimentPermIdId(daoFactory));
-
- List<ExperimentPE> list = new ListerById(listers).list(experimentIdsCore);
- Map<IExperimentId, ExperimentPE> map = new LinkedHashMap<IExperimentId, ExperimentPE>();
- int index = 0;
-
- for (IExperimentId experimentId : experimentIds)
- {
- map.put(experimentId, list.get(index));
- index++;
- }
+ List<IListObjectById<? extends IExperimentId, ExperimentPE>> listers =
+ new LinkedList<IListObjectById<? extends IExperimentId, ExperimentPE>>();
+ listers.add(new ListExperimentByPermId(experimentDAO));
+ return listers;
+ }
- return map;
+ @Autowired
+ private void setDAOFactory(IDAOFactory daoFactory)
+ {
+ experimentDAO = daoFactory.getExperimentDAO();
}
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/UpdateExperimentExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/UpdateExperimentExecutor.java
index 355a52f3e89..058194026e4 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/UpdateExperimentExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/UpdateExperimentExecutor.java
@@ -35,6 +35,8 @@ import ch.ethz.sis.openbis.generic.server.api.v3.executor.property.IUpdateEntity
import ch.ethz.sis.openbis.generic.server.api.v3.executor.tag.IUpdateTagForEntityExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.experiment.ExperimentUpdate;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.IExperimentId;
+import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
+import ch.systemsx.cisd.openbis.generic.server.authorization.validator.ExperimentByIdentiferValidator;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.util.RelationshipUtils;
@@ -110,6 +112,14 @@ public class UpdateExperimentExecutor implements IUpdateExperimentExecutor
assert experimentIds.size() == experiments.size();
+ for (ExperimentPE experiment : experiments)
+ {
+ if (false == new ExperimentByIdentiferValidator().doValidation(context.getSession().tryGetPerson(), experiment))
+ {
+ throw new AuthorizationFailureException("Cannot access experiment " + experiment.getIdentifier());
+ }
+ }
+
Map<ExperimentUpdate, ExperimentPE> result = new HashMap<ExperimentUpdate, ExperimentPE>();
Iterator<ExperimentUpdate> it1 = updates.iterator();
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/IListProjectByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/IListProjectByIdExecutor.java
new file mode 100644
index 00000000000..ac6ee7adfab
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/IListProjectByIdExecutor.java
@@ -0,0 +1,29 @@
+/*
+ * 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.project;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.IListObjectByIdExecutor;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.IProjectId;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
+
+/**
+ * @author pkupczyk
+ */
+public interface IListProjectByIdExecutor extends IListObjectByIdExecutor<IProjectId, ProjectPE>
+{
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/IMapProjectByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/IMapProjectByIdExecutor.java
new file mode 100644
index 00000000000..6f50828b9c0
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/IMapProjectByIdExecutor.java
@@ -0,0 +1,29 @@
+/*
+ * 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.project;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.IMapObjectByIdExecutor;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.IProjectId;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
+
+/**
+ * @author pkupczyk
+ */
+public interface IMapProjectByIdExecutor extends IMapObjectByIdExecutor<IProjectId, ProjectPE>
+{
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/ListProjectByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/ListProjectByIdExecutor.java
new file mode 100644
index 00000000000..28d883b88b9
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/ListProjectByIdExecutor.java
@@ -0,0 +1,53 @@
+/*
+ * 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.project;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.AbstractListObjectByIdExecutor;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.IMapObjectByIdExecutor;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.IProjectId;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
+
+/**
+ * @author pkupczyk
+ */
+@Component
+public class ListProjectByIdExecutor extends AbstractListObjectByIdExecutor<IProjectId, ProjectPE> implements IListProjectByIdExecutor
+{
+
+ @Autowired
+ private IMapProjectByIdExecutor mapProjectByIdExecutor;
+
+ @SuppressWarnings("unused")
+ private ListProjectByIdExecutor()
+ {
+ }
+
+ public ListProjectByIdExecutor(IMapProjectByIdExecutor mapProjectByIdExecutor)
+ {
+ this.mapProjectByIdExecutor = mapProjectByIdExecutor;
+ }
+
+ @Override
+ protected IMapObjectByIdExecutor<IProjectId, ProjectPE> getMapExecutor()
+ {
+ return mapProjectByIdExecutor;
+ }
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/MapProjectByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/MapProjectByIdExecutor.java
new file mode 100644
index 00000000000..4e0a84a5092
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/MapProjectByIdExecutor.java
@@ -0,0 +1,70 @@
+/*
+ * 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.project;
+
+import java.util.LinkedList;
+import java.util.List;
+
+import org.springframework.beans.factory.annotation.Autowired;
+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.common.AbstractMapObjectByIdExecutor;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.IListObjectById;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.project.ListProjectByIdentifier;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.project.ListProjectByPermId;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.IProjectId;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProjectDAO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
+
+/**
+ * @author pkupczyk
+ */
+@Component
+public class MapProjectByIdExecutor extends AbstractMapObjectByIdExecutor<IProjectId, ProjectPE> implements IMapProjectByIdExecutor
+{
+
+ private IProjectDAO projectDAO;
+
+ @SuppressWarnings("unused")
+ private MapProjectByIdExecutor()
+ {
+ }
+
+ public MapProjectByIdExecutor(IProjectDAO projectDAO)
+ {
+ this.projectDAO = projectDAO;
+ }
+
+ @Override
+ protected List<IListObjectById<? extends IProjectId, ProjectPE>> createListers(IOperationContext context)
+ {
+ List<IListObjectById<? extends IProjectId, ProjectPE>> listers =
+ new LinkedList<IListObjectById<? extends IProjectId, ProjectPE>>();
+ listers.add(new ListProjectByIdentifier(projectDAO));
+ listers.add(new ListProjectByPermId(projectDAO));
+ return listers;
+ }
+
+ @Autowired
+ private void setDAOFactory(IDAOFactory daoFactory)
+ {
+ projectDAO = daoFactory.getProjectDAO();
+ }
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/TryGetProjectByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/TryGetProjectByIdExecutor.java
index 31349b6b47e..d624801387c 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/TryGetProjectByIdExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/TryGetProjectByIdExecutor.java
@@ -16,18 +16,16 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.project;
+import java.util.Collections;
+import java.util.Map;
+
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.IProjectId;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.ProjectIdentifier;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.ProjectPermId;
-import ch.ethz.sis.openbis.generic.shared.api.v3.exceptions.UnsupportedObjectIdException;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProjectDAO;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
/**
* @author pkupczyk
@@ -36,40 +34,29 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierF
public class TryGetProjectByIdExecutor implements ITryGetProjectByIdExecutor
{
- private IProjectDAO projectDAO;
+ @Autowired
+ private IMapProjectByIdExecutor mapProjectByIdExecutor;
@SuppressWarnings("unused")
private TryGetProjectByIdExecutor()
{
}
- public TryGetProjectByIdExecutor(IProjectDAO projectDAO)
+ public TryGetProjectByIdExecutor(IMapProjectByIdExecutor mapProjectByIdExecutor)
{
- this.projectDAO = projectDAO;
+ this.mapProjectByIdExecutor = mapProjectByIdExecutor;
}
@Override
public ProjectPE tryGet(IOperationContext context, IProjectId projectId)
{
- if (projectId instanceof ProjectPermId)
- {
- ProjectPermId projectPermId = (ProjectPermId) projectId;
- return projectDAO.tryGetByPermID(projectPermId.getPermId());
- }
- if (projectId instanceof ProjectIdentifier)
+ if (projectId == null)
{
- ProjectIdentifier projectIdentifier = (ProjectIdentifier) projectId;
- ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier pid =
- ProjectIdentifierFactory.parse(projectIdentifier.getIdentifier());
- return projectDAO.tryFindProject(pid.getSpaceCode(), pid.getProjectCode());
+ throw new UserFailureException("Unspecified project id.");
}
- throw new UnsupportedObjectIdException(projectId);
- }
- @Autowired
- private void setDAOFactory(IDAOFactory daoFactory)
- {
- projectDAO = daoFactory.getProjectDAO();
+ Map<IProjectId, ProjectPE> projects = mapProjectByIdExecutor.map(context, Collections.singletonList(projectId));
+ return projects.get(projectId);
}
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/AbstractSetSampleRelatedSamplesExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/AbstractSetSampleRelatedSamplesExecutor.java
index 51902b3fb00..71bc3306394 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/AbstractSetSampleRelatedSamplesExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/AbstractSetSampleRelatedSamplesExecutor.java
@@ -20,12 +20,9 @@ import java.util.Collection;
import java.util.LinkedList;
import java.util.Map;
-import org.springframework.beans.factory.annotation.Autowired;
-
import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleCreation;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
/**
@@ -34,46 +31,32 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public abstract class AbstractSetSampleRelatedSamplesExecutor
{
- @Autowired
- private IDAOFactory daoFactory;
-
- protected AbstractSetSampleRelatedSamplesExecutor()
- {
- }
-
- public AbstractSetSampleRelatedSamplesExecutor(IDAOFactory daoFactory)
- {
- this.daoFactory = daoFactory;
- }
-
- public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap, Map<ISampleId, Long> techIdMap)
+ public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap, Map<ISampleId, SamplePE> sampleMap)
{
for (SampleCreation creation : creationsMap.keySet())
{
SamplePE sample = creationsMap.get(creation);
- Collection<? extends ISampleId> sampleIds = getRelatedSamplesIds(context, creation);
+ Collection<? extends ISampleId> relatedSampleIds = getRelatedSamplesIds(context, creation);
- if (sampleIds != null)
+ if (relatedSampleIds != null)
{
- Collection<Long> sampleTechIds = new LinkedList<Long>();
+ Collection<SamplePE> relatedSamples = new LinkedList<SamplePE>();
- for (ISampleId sampleId : sampleIds)
+ for (ISampleId relatedSampleId : relatedSampleIds)
{
- sampleTechIds.add(techIdMap.get(sampleId));
+ relatedSamples.add(sampleMap.get(relatedSampleId));
}
- setRelatedSamples(context, sample, sampleTechIds);
+ if (false == relatedSamples.isEmpty())
+ {
+ setRelatedSamples(context, sample, relatedSamples);
+ }
}
}
}
protected abstract Collection<? extends ISampleId> getRelatedSamplesIds(IOperationContext context, SampleCreation creation);
- protected abstract void setRelatedSamples(IOperationContext context, SamplePE sample, Collection<Long> relatedSamplesTechIds);
-
- public IDAOFactory getDaoFactory()
- {
- return daoFactory;
- }
+ protected abstract void setRelatedSamples(IOperationContext context, SamplePE sample, Collection<SamplePE> relatedSamples);
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/AbstractUpdateSampleRelatedSamplesExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/AbstractUpdateSampleRelatedSamplesExecutor.java
index 1e2bd7fd317..7f6be89010c 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/AbstractUpdateSampleRelatedSamplesExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/AbstractUpdateSampleRelatedSamplesExecutor.java
@@ -20,8 +20,6 @@ import java.util.Collection;
import java.util.LinkedList;
import java.util.Map;
-import org.springframework.beans.factory.annotation.Autowired;
-
import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.ListUpdateValue;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.ListUpdateValue.ListUpdateAction;
@@ -30,7 +28,7 @@ import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.ListUpdateValue.List
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.ListUpdateValue.ListUpdateActionSet;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleUpdate;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.ethz.sis.openbis.generic.shared.api.v3.exceptions.ObjectNotFoundException;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
/**
@@ -39,19 +37,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public abstract class AbstractUpdateSampleRelatedSamplesExecutor
{
- @Autowired
- private IDAOFactory daoFactory;
-
- protected AbstractUpdateSampleRelatedSamplesExecutor()
- {
- }
-
- public AbstractUpdateSampleRelatedSamplesExecutor(IDAOFactory daoFactory)
- {
- this.daoFactory = daoFactory;
- }
-
- public void update(IOperationContext context, Map<SampleUpdate, SamplePE> updateMap, Map<ISampleId, Long> techIdMap)
+ public void update(IOperationContext context, Map<SampleUpdate, SamplePE> updateMap, Map<ISampleId, SamplePE> samplesMap)
{
for (SampleUpdate update : updateMap.keySet())
{
@@ -63,22 +49,37 @@ public abstract class AbstractUpdateSampleRelatedSamplesExecutor
for (ListUpdateAction<? extends ISampleId> action : listUpdate.getActions())
{
- Collection<Long> relatedTechIds = new LinkedList<Long>();
+ Collection<SamplePE> relatedSamples = new LinkedList<SamplePE>();
- for (ISampleId relatedId : action.getIds())
+ if (action instanceof ListUpdateActionSet<?> || action instanceof ListUpdateActionAdd<?>)
{
- relatedTechIds.add(techIdMap.get(relatedId));
- }
-
- if (action instanceof ListUpdateActionSet<?>)
- {
- setRelatedSamples(context, sample, relatedTechIds);
- } else if (action instanceof ListUpdateActionAdd<?>)
- {
- addRelatedSamples(context, sample, relatedTechIds);
+ for (ISampleId relatedId : action.getIds())
+ {
+ SamplePE relatedSample = samplesMap.get(relatedId);
+ if (relatedSample == null)
+ {
+ throw new ObjectNotFoundException(relatedId);
+ }
+ relatedSamples.add(relatedSample);
+ }
+ if (action instanceof ListUpdateActionSet<?>)
+ {
+ setRelatedSamples(context, sample, relatedSamples);
+ } else
+ {
+ addRelatedSamples(context, sample, relatedSamples);
+ }
} else if (action instanceof ListUpdateActionRemove<?>)
{
- removeRelatedSamples(context, sample, relatedTechIds);
+ for (ISampleId relatedId : action.getIds())
+ {
+ SamplePE relatedSample = samplesMap.get(relatedId);
+ if (relatedSample != null)
+ {
+ relatedSamples.add(relatedSample);
+ }
+ }
+ removeRelatedSamples(context, sample, relatedSamples);
}
}
}
@@ -88,15 +89,10 @@ public abstract class AbstractUpdateSampleRelatedSamplesExecutor
protected abstract ListUpdateValue<? extends ISampleId> getRelatedSamplesUpdate(IOperationContext context, SampleUpdate update);
- protected abstract void setRelatedSamples(IOperationContext context, SamplePE sample, Collection<Long> relatedSamplesIds);
+ protected abstract void setRelatedSamples(IOperationContext context, SamplePE sample, Collection<SamplePE> relatedSamples);
- protected abstract void addRelatedSamples(IOperationContext context, SamplePE sample, Collection<Long> relatedSamplesIds);
+ protected abstract void addRelatedSamples(IOperationContext context, SamplePE sample, Collection<SamplePE> relatedSamples);
- protected abstract void removeRelatedSamples(IOperationContext context, SamplePE sample, Collection<Long> relatedSamplesIds);
-
- public IDAOFactory getDaoFactory()
- {
- return daoFactory;
- }
+ protected abstract void removeRelatedSamples(IOperationContext context, SamplePE sample, Collection<SamplePE> relatedSamples);
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/CreateSampleExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/CreateSampleExecutor.java
index 3220c6b3096..c84fe0f29ac 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/CreateSampleExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/CreateSampleExecutor.java
@@ -16,37 +16,27 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.sample;
+import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
+import java.util.LinkedHashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
-import java.util.Set;
import org.springframework.beans.factory.annotation.Autowired;
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.attachment.ICreateAttachmentExecutor;
-import ch.ethz.sis.openbis.generic.server.api.v3.executor.entity.IMapEntityTypeByIdExecutor;
-import ch.ethz.sis.openbis.generic.server.api.v3.executor.experiment.IMapExperimentByIdExecutor;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.property.IUpdateEntityPropertyExecutor;
-import ch.ethz.sis.openbis.generic.server.api.v3.executor.space.IMapSpaceByIdExecutor;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.tag.IAddTagToEntityExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleCreation;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.entitytype.IEntityTypeId;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.IExperimentId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.SamplePermId;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.space.ISpaceId;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.util.RelationshipUtils;
/**
@@ -60,13 +50,13 @@ public class CreateSampleExecutor implements ICreateSampleExecutor
private IDAOFactory daoFactory;
@Autowired
- private IMapEntityTypeByIdExecutor mapEntityTypeByIdExecutor;
+ private ISetSampleTypeExecutor setSampleTypeExecutor;
@Autowired
- private IMapSpaceByIdExecutor mapSpaceByIdExecutor;
+ private ISetSampleSpaceExecutor setSampleSpaceExecutor;
@Autowired
- private IMapExperimentByIdExecutor mapExperimentByIdExecutor;
+ private ISetSampleExperimentExecutor setSampleExperimentExecutor;
@Autowired
private ISetSampleRelatedSamplesExecutor setSampleRelatedSamplesExecutor;
@@ -88,16 +78,16 @@ public class CreateSampleExecutor implements ICreateSampleExecutor
{
}
- public CreateSampleExecutor(IDAOFactory daoFactory, IMapEntityTypeByIdExecutor mapEntityTypeByIdExecutor,
- IMapSpaceByIdExecutor mapSpaceByIdExecutor, IMapExperimentByIdExecutor mapExperimentByIdExecutor,
+ public CreateSampleExecutor(IDAOFactory daoFactory, ISetSampleTypeExecutor setSampleTypeExecutor,
+ ISetSampleSpaceExecutor setSampleSpaceExecutor, ISetSampleExperimentExecutor setSampleExperimentExecutor,
ISetSampleRelatedSamplesExecutor setSampleRelatedSamplesExecutor, IUpdateEntityPropertyExecutor updateEntityPropertyExecutor,
ICreateAttachmentExecutor createAttachmentExecutor, IAddTagToEntityExecutor addTagToEntityExecutor,
IVerifySampleExecutor verifySampleExecutor)
{
this.daoFactory = daoFactory;
- this.mapEntityTypeByIdExecutor = mapEntityTypeByIdExecutor;
- this.mapSpaceByIdExecutor = mapSpaceByIdExecutor;
- this.mapExperimentByIdExecutor = mapExperimentByIdExecutor;
+ this.setSampleTypeExecutor = setSampleTypeExecutor;
+ this.setSampleSpaceExecutor = setSampleSpaceExecutor;
+ this.setSampleExperimentExecutor = setSampleExperimentExecutor;
this.setSampleRelatedSamplesExecutor = setSampleRelatedSamplesExecutor;
this.updateEntityPropertyExecutor = updateEntityPropertyExecutor;
this.createAttachmentExecutor = createAttachmentExecutor;
@@ -108,8 +98,9 @@ public class CreateSampleExecutor implements ICreateSampleExecutor
@Override
public List<SamplePermId> create(IOperationContext context, List<SampleCreation> creations)
{
+ // TODO split this method
List<SamplePermId> permIdsAll = new LinkedList<SamplePermId>();
- HashMap<SampleCreation, SamplePE> samplesAll = new HashMap<SampleCreation, SamplePE>();
+ Map<SampleCreation, SamplePE> samplesAll = new LinkedHashMap<SampleCreation, SamplePE>();
int batchSize = 1000;
int batchStart = 0;
@@ -117,28 +108,34 @@ public class CreateSampleExecutor implements ICreateSampleExecutor
while (batchStart < creations.size())
{
List<SampleCreation> creationsBatch = creations.subList(batchStart, Math.min(batchStart + batchSize, creations.size()));
- List<SamplePE> samplesBatch = new LinkedList<SamplePE>();
+ Map<SampleCreation, SamplePE> batchMap = new LinkedHashMap<SampleCreation, SamplePE>();
daoFactory.setBatchUpdateMode(true);
- Map<IEntityTypeId, EntityTypePE> typeMap = getTypeMap(context, creationsBatch);
- Map<ISpaceId, SpacePE> spaceMap = getSpaceMap(context, creationsBatch);
- Map<IExperimentId, ExperimentPE> experimentMap = getExperimentMap(context, creationsBatch);
-
for (SampleCreation creation : creationsBatch)
{
context.pushContextDescription("register sample " + creation.getCode());
- SamplePE sample = createSamplePE(context, creation, typeMap, spaceMap, experimentMap);
+ SamplePE sample = createSamplePE(context, creation);
permIdsAll.add(new SamplePermId(sample.getPermId()));
samplesAll.put(creation, sample);
- samplesBatch.add(sample);
+ batchMap.put(creation, sample);
context.popContextDescription();
}
- daoFactory.getSampleDAO().createOrUpdateSamples(samplesBatch, context.getSession().tryGetPerson(), false);
+ setSampleSpaceExecutor.set(context, batchMap);
+ setSampleExperimentExecutor.set(context, batchMap);
+ setSampleTypeExecutor.set(context, batchMap);
+
+ for (Map.Entry<SampleCreation, SamplePE> batchEntry : batchMap.entrySet())
+ {
+ updateEntityPropertyExecutor.update(context, batchEntry.getValue(), batchEntry.getValue().getEntityType(), batchEntry.getKey()
+ .getProperties());
+ }
+
+ daoFactory.getSampleDAO().createOrUpdateSamples(new ArrayList<SamplePE>(batchMap.values()), context.getSession().tryGetPerson(), false);
daoFactory.setBatchUpdateMode(false);
for (SampleCreation creation : creationsBatch)
@@ -154,53 +151,18 @@ public class CreateSampleExecutor implements ICreateSampleExecutor
batchStart += batchSize;
}
- setSampleRelatedSamplesExecutor.set(context, samplesAll);
- verifySamples(context, samplesAll.values());
-
- return permIdsAll;
- }
+ reloadSamples(samplesAll);
- private Map<IEntityTypeId, EntityTypePE> getTypeMap(IOperationContext context, List<SampleCreation> creations)
- {
- Set<IEntityTypeId> ids = new HashSet<IEntityTypeId>();
- for (SampleCreation creation : creations)
- {
- if (creation.getTypeId() != null)
- {
- ids.add(creation.getTypeId());
- }
- }
- return mapEntityTypeByIdExecutor.map(context, EntityKind.SAMPLE, ids);
- }
+ setSampleRelatedSamplesExecutor.set(context, samplesAll);
+ verifySampleExecutor.verify(context, samplesAll.values());
- private Map<ISpaceId, SpacePE> getSpaceMap(IOperationContext context, List<SampleCreation> creations)
- {
- Set<ISpaceId> ids = new HashSet<ISpaceId>();
- for (SampleCreation creation : creations)
- {
- if (creation.getSpaceId() != null)
- {
- ids.add(creation.getSpaceId());
- }
- }
- return mapSpaceByIdExecutor.map(context, ids);
- }
+ daoFactory.getSessionFactory().getCurrentSession().flush();
+ daoFactory.getSessionFactory().getCurrentSession().clear();
- private Map<IExperimentId, ExperimentPE> getExperimentMap(IOperationContext context, List<SampleCreation> creations)
- {
- Set<IExperimentId> ids = new HashSet<IExperimentId>();
- for (SampleCreation creation : creations)
- {
- if (creation.getExperimentId() != null)
- {
- ids.add(creation.getExperimentId());
- }
- }
- return mapExperimentByIdExecutor.map(context, ids);
+ return permIdsAll;
}
- private SamplePE createSamplePE(IOperationContext context, SampleCreation sampleCreation, Map<IEntityTypeId, EntityTypePE> typeMap,
- Map<ISpaceId, SpacePE> spaceMap, Map<IExperimentId, ExperimentPE> experimentMap)
+ private SamplePE createSamplePE(IOperationContext context, SampleCreation sampleCreation)
{
SamplePE sample = new SamplePE();
@@ -214,45 +176,35 @@ public class CreateSampleExecutor implements ICreateSampleExecutor
String createdPermId = daoFactory.getPermIdDAO().createPermId();
sample.setPermId(createdPermId);
+ sample.setRegistrator(context.getSession().tryGetPerson());
+ RelationshipUtils.updateModificationDateAndModifier(sample, context.getSession().tryGetPerson());
- IEntityTypeId typeId = sampleCreation.getTypeId();
- EntityTypePE entityType = typeMap.get(typeId);
- sample.setSampleType((SampleTypePE) entityType);
+ return sample;
+ }
- IExperimentId experimentId = sampleCreation.getExperimentId();
- if (experimentId != null)
- {
- sample.setExperiment(experimentMap.get(experimentId));
- }
+ private void reloadSamples(Map<SampleCreation, SamplePE> creationToSampleMap)
+ {
+ Collection<Long> ids = new HashSet<Long>();
- ISpaceId spaceId = sampleCreation.getSpaceId();
- if (spaceId != null)
+ for (SamplePE sample : creationToSampleMap.values())
{
- SpacePE space = spaceMap.get(spaceId);
- sample.setSpace(space);
+ ids.add(sample.getId());
}
- updateEntityPropertyExecutor.update(context, sample, entityType, sampleCreation.getProperties());
- sample.setRegistrator(context.getSession().tryGetPerson());
- RelationshipUtils.updateModificationDateAndModifier(sample, context.getSession().tryGetPerson());
+ List<SamplePE> samples = daoFactory.getSampleDAO().listByIDs(ids);
- return sample;
- }
+ Map<Long, SamplePE> idToSampleMap = new HashMap<Long, SamplePE>();
- private void verifySamples(IOperationContext context, Collection<SamplePE> samples)
- {
- Set<Long> techIds = new HashSet<Long>();
for (SamplePE sample : samples)
{
- techIds.add(sample.getId());
+ idToSampleMap.put(sample.getId(), sample);
}
- daoFactory.getSessionFactory().getCurrentSession().flush();
- daoFactory.getSessionFactory().getCurrentSession().clear();
-
- Collection<SamplePE> freshSamples = daoFactory.getSampleDAO().listByIDs(techIds);
+ for (Map.Entry<SampleCreation, SamplePE> entry : creationToSampleMap.entrySet())
+ {
+ entry.setValue(idToSampleMap.get(entry.getValue().getId()));
+ }
- verifySampleExecutor.verify(context, freshSamples);
}
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IListSampleByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IListSampleByIdExecutor.java
index cc02c18b202..72ae7222bb7 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IListSampleByIdExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IListSampleByIdExecutor.java
@@ -16,19 +16,14 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.sample;
-import java.util.Collection;
-import java.util.List;
-
-import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.IListObjectByIdExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
/**
* @author pkupczyk
*/
-public interface IListSampleByIdExecutor
+public interface IListSampleByIdExecutor extends IListObjectByIdExecutor<ISampleId, SamplePE>
{
- public List<SamplePE> list(IOperationContext context, Collection<? extends ISampleId> sampleIds);
-
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IMapSampleByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IMapSampleByIdExecutor.java
new file mode 100644
index 00000000000..617de604058
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IMapSampleByIdExecutor.java
@@ -0,0 +1,29 @@
+/*
+ * 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.sample;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.IMapObjectByIdExecutor;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+
+/**
+ * @author pkupczyk
+ */
+public interface IMapSampleByIdExecutor extends IMapObjectByIdExecutor<ISampleId, SamplePE>
+{
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleChildrenExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleChildrenExecutor.java
index 71a0ffebe1e..b274a242dfc 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleChildrenExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleChildrenExecutor.java
@@ -29,6 +29,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public interface ISetSampleChildrenExecutor
{
- public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap, Map<ISampleId, Long> techIdMap);
+ public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap, Map<ISampleId, SamplePE> sampleMap);
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleContainedExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleContainedExecutor.java
index 58713cd4803..6da84732aa1 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleContainedExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleContainedExecutor.java
@@ -29,6 +29,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public interface ISetSampleContainedExecutor
{
- public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap, Map<ISampleId, Long> techIdMap);
+ public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap, Map<ISampleId, SamplePE> sampleMap);
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleContainerExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleContainerExecutor.java
index 97e74506f95..ea7de4bae7c 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleContainerExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleContainerExecutor.java
@@ -29,6 +29,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public interface ISetSampleContainerExecutor
{
- public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap, Map<ISampleId, Long> techIdMap);
+ public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap, Map<ISampleId, SamplePE> sampleMap);
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleExperimentExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleExperimentExecutor.java
new file mode 100644
index 00000000000..a0e32ca0a64
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleExperimentExecutor.java
@@ -0,0 +1,33 @@
+/*
+ * 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.sample;
+
+import java.util.Map;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleCreation;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+
+/**
+ * @author pkupczyk
+ */
+public interface ISetSampleExperimentExecutor
+{
+
+ public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap);
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleParentsExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleParentsExecutor.java
index c0e457b94ac..32b8b3e483d 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleParentsExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleParentsExecutor.java
@@ -29,6 +29,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public interface ISetSampleParentsExecutor
{
- public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap, Map<ISampleId, Long> techIdMap);
+ public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap, Map<ISampleId, SamplePE> sampleMap);
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleSpaceExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleSpaceExecutor.java
new file mode 100644
index 00000000000..9f12fa6976d
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleSpaceExecutor.java
@@ -0,0 +1,33 @@
+/*
+ * 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.sample;
+
+import java.util.Map;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleCreation;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+
+/**
+ * @author pkupczyk
+ */
+public interface ISetSampleSpaceExecutor
+{
+
+ public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap);
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleTypeExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleTypeExecutor.java
new file mode 100644
index 00000000000..0fd492f847f
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ISetSampleTypeExecutor.java
@@ -0,0 +1,33 @@
+/*
+ * 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.sample;
+
+import java.util.Map;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleCreation;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+
+/**
+ * @author pkupczyk
+ */
+public interface ISetSampleTypeExecutor
+{
+
+ public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap);
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IUpdateSampleChildrenExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IUpdateSampleChildrenExecutor.java
index 59264477583..345e832c94a 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IUpdateSampleChildrenExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IUpdateSampleChildrenExecutor.java
@@ -29,6 +29,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public interface IUpdateSampleChildrenExecutor
{
- public void update(IOperationContext context, Map<SampleUpdate, SamplePE> updateMap, Map<ISampleId, Long> techIdMap);
+ public void update(IOperationContext context, Map<SampleUpdate, SamplePE> updateMap, Map<ISampleId, SamplePE> sampleMap);
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IUpdateSampleContainedExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IUpdateSampleContainedExecutor.java
index 2cac239d099..77818e909f9 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IUpdateSampleContainedExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IUpdateSampleContainedExecutor.java
@@ -29,6 +29,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public interface IUpdateSampleContainedExecutor
{
- public void update(IOperationContext context, Map<SampleUpdate, SamplePE> updateMap, Map<ISampleId, Long> techIdMap);
+ public void update(IOperationContext context, Map<SampleUpdate, SamplePE> updateMap, Map<ISampleId, SamplePE> sampleMap);
}
\ No newline at end of file
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IUpdateSampleContainerExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IUpdateSampleContainerExecutor.java
index 4335d25893a..56c119272d4 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IUpdateSampleContainerExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IUpdateSampleContainerExecutor.java
@@ -29,6 +29,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public interface IUpdateSampleContainerExecutor
{
- public void update(IOperationContext context, Map<SampleUpdate, SamplePE> updateMap, Map<ISampleId, Long> techIdMap);
+ public void update(IOperationContext context, Map<SampleUpdate, SamplePE> updateMap, Map<ISampleId, SamplePE> sampleMap);
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IUpdateSampleParentsExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IUpdateSampleParentsExecutor.java
index dd6574b6af6..88f3fcec9eb 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IUpdateSampleParentsExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IUpdateSampleParentsExecutor.java
@@ -29,6 +29,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public interface IUpdateSampleParentsExecutor
{
- public void update(IOperationContext context, Map<SampleUpdate, SamplePE> updateMap, Map<ISampleId, Long> techIdMap);
+ public void update(IOperationContext context, Map<SampleUpdate, SamplePE> updateMap, Map<ISampleId, SamplePE> sampleMap);
}
\ No newline at end of file
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ListSampleByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ListSampleByIdExecutor.java
index 15677f34daa..0d6535e100b 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ListSampleByIdExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ListSampleByIdExecutor.java
@@ -16,58 +16,38 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.sample;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
import org.springframework.beans.factory.annotation.Autowired;
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.translator.collection.ListTranslator;
-import ch.ethz.sis.openbis.generic.server.api.v3.translator.id.sample.ISampleIdTranslator;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.AbstractListObjectByIdExecutor;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.IMapObjectByIdExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.IListerById;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.ListerById;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.sample.ListerBySampleIdentifierId;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.sample.ListerBySamplePermIdId;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.sample.ListerBySampleTechIdId;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
/**
* @author pkupczyk
*/
@Component
-public class ListSampleByIdExecutor implements IListSampleByIdExecutor
+public class ListSampleByIdExecutor extends AbstractListObjectByIdExecutor<ISampleId, SamplePE> implements IListSampleByIdExecutor
{
@Autowired
- private IDAOFactory daoFactory;
+ private IMapSampleByIdExecutor mapSampleByIdExecutor;
@SuppressWarnings("unused")
private ListSampleByIdExecutor()
{
}
- public ListSampleByIdExecutor(IDAOFactory daoFactory)
+ public ListSampleByIdExecutor(IMapSampleByIdExecutor mapSampleByIdExecutor)
{
- this.daoFactory = daoFactory;
+ this.mapSampleByIdExecutor = mapSampleByIdExecutor;
}
@Override
- public List<SamplePE> list(IOperationContext context, Collection<? extends ISampleId> sampleIds)
+ protected IMapObjectByIdExecutor<ISampleId, SamplePE> getMapExecutor()
{
- List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.sample.ISampleId> sampleIdsCore =
- new ListTranslator().translate(sampleIds, new ISampleIdTranslator());
-
- @SuppressWarnings("rawtypes")
- List<IListerById> listers = new ArrayList<IListerById>();
- listers.add(new ListerBySamplePermIdId(daoFactory));
- listers.add(new ListerBySampleTechIdId(daoFactory));
- listers.add(new ListerBySampleIdentifierId(daoFactory, context.getSession().tryGetPerson().getHomeSpace()));
-
- return new ListerById(listers).list(sampleIdsCore);
+ return mapSampleByIdExecutor;
}
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/MapSampleByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/MapSampleByIdExecutor.java
new file mode 100644
index 00000000000..e9eb72dd69e
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/MapSampleByIdExecutor.java
@@ -0,0 +1,75 @@
+/*
+ * 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.sample;
+
+import java.util.LinkedList;
+import java.util.List;
+
+import org.springframework.beans.factory.annotation.Autowired;
+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.common.AbstractMapObjectByIdExecutor;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.IListObjectById;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.sample.ListSampleByIdentifier;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.sample.ListSampleByPermId;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISpaceDAO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+
+/**
+ * @author pkupczyk
+ */
+@Component
+public class MapSampleByIdExecutor extends AbstractMapObjectByIdExecutor<ISampleId, SamplePE> implements IMapSampleByIdExecutor
+{
+
+ private ISpaceDAO spaceDAO;
+
+ private ISampleDAO sampleDAO;
+
+ @SuppressWarnings("unused")
+ private MapSampleByIdExecutor()
+ {
+ }
+
+ public MapSampleByIdExecutor(ISpaceDAO spaceDAO, ISampleDAO sampleDAO)
+ {
+ this.spaceDAO = spaceDAO;
+ this.sampleDAO = sampleDAO;
+ }
+
+ @Override
+ protected List<IListObjectById<? extends ISampleId, SamplePE>> createListers(IOperationContext context)
+ {
+ List<IListObjectById<? extends ISampleId, SamplePE>> listers =
+ new LinkedList<IListObjectById<? extends ISampleId, SamplePE>>();
+ listers.add(new ListSampleByPermId(sampleDAO));
+ listers.add(new ListSampleByIdentifier(spaceDAO, sampleDAO, context.getSession().tryGetHomeGroup()));
+ return listers;
+ }
+
+ @Autowired
+ private void setDAOFactory(IDAOFactory daoFactory)
+ {
+ spaceDAO = daoFactory.getSpaceDAO();
+ sampleDAO = daoFactory.getSampleDAO();
+ }
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleChildrenExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleChildrenExecutor.java
index 85d8cdce47e..7aa4a125a65 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleChildrenExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleChildrenExecutor.java
@@ -17,15 +17,18 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.sample;
import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.annotation.Resource;
-import org.springframework.beans.factory.annotation.Autowired;
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.relationship.IGetParentChildRelationshipIdExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleCreation;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.ComponentNames;
+import ch.systemsx.cisd.openbis.generic.server.business.IRelationshipService;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
/**
@@ -35,19 +38,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public class SetSampleChildrenExecutor extends AbstractSetSampleRelatedSamplesExecutor implements ISetSampleChildrenExecutor
{
- @Autowired
- private IGetParentChildRelationshipIdExecutor getParentChildRelationshipIdExecutor;
-
- @SuppressWarnings("unused")
- private SetSampleChildrenExecutor()
- {
- }
-
- public SetSampleChildrenExecutor(IDAOFactory daoFactory, IGetParentChildRelationshipIdExecutor getParentChildRelationshipIdExecutor)
- {
- super(daoFactory);
- this.getParentChildRelationshipIdExecutor = getParentChildRelationshipIdExecutor;
- }
+ @Resource(name = ComponentNames.RELATIONSHIP_SERVICE)
+ private IRelationshipService relationshipService;
@Override
protected Collection<? extends ISampleId> getRelatedSamplesIds(IOperationContext context, SampleCreation creation)
@@ -56,11 +48,22 @@ public class SetSampleChildrenExecutor extends AbstractSetSampleRelatedSamplesEx
}
@Override
- protected void setRelatedSamples(IOperationContext context, SamplePE sample, Collection<Long> relatedSamplesTechIds)
+ protected void setRelatedSamples(IOperationContext context, SamplePE parent, Collection<SamplePE> children)
{
- getDaoFactory().getSampleDAO().setSampleRelationshipChildren(sample.getId(), relatedSamplesTechIds,
- getParentChildRelationshipIdExecutor.get(context),
- context.getSession().tryGetPerson());
+ Set<SamplePE> existingChildren = new HashSet<SamplePE>(parent.getChildren());
+
+ context.pushContextDescription("set children for sample " + parent.getCode());
+
+ for (SamplePE child : children)
+ {
+ if (false == existingChildren.contains(child))
+ {
+ relationshipService.addParentToSample(context.getSession(), child, parent);
+ existingChildren.add(child);
+ }
+ }
+
+ context.popContextDescription();
}
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleContainedExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleContainedExecutor.java
index 6273c1b558c..27c8dc60547 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleContainedExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleContainedExecutor.java
@@ -18,12 +18,15 @@ package ch.ethz.sis.openbis.generic.server.api.v3.executor.sample;
import java.util.Collection;
+import javax.annotation.Resource;
+
import org.springframework.stereotype.Component;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleCreation;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.ComponentNames;
+import ch.systemsx.cisd.openbis.generic.server.business.IRelationshipService;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
/**
@@ -33,15 +36,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public class SetSampleContainedExecutor extends AbstractSetSampleRelatedSamplesExecutor implements ISetSampleContainedExecutor
{
- @SuppressWarnings("unused")
- private SetSampleContainedExecutor()
- {
- }
-
- public SetSampleContainedExecutor(IDAOFactory daoFactory)
- {
- super(daoFactory);
- }
+ @Resource(name = ComponentNames.RELATIONSHIP_SERVICE)
+ private IRelationshipService relationshipService;
@Override
protected Collection<? extends ISampleId> getRelatedSamplesIds(IOperationContext context, SampleCreation creation)
@@ -50,9 +46,16 @@ public class SetSampleContainedExecutor extends AbstractSetSampleRelatedSamplesE
}
@Override
- protected void setRelatedSamples(IOperationContext context, SamplePE sample, Collection<Long> relatedSamplesTechIds)
+ protected void setRelatedSamples(IOperationContext context, SamplePE container, Collection<SamplePE> contained)
{
- getDaoFactory().getSampleDAO().setSampleContained(sample.getId(), relatedSamplesTechIds);
+ context.pushContextDescription("set contained for sample " + container.getCode());
+
+ for (SamplePE aContained : contained)
+ {
+ relationshipService.assignSampleToContainer(context.getSession(), aContained, container);
+ }
+
+ context.popContextDescription();
}
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleContainerExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleContainerExecutor.java
index 9660e759cd5..78d674b4ab8 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleContainerExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleContainerExecutor.java
@@ -18,14 +18,15 @@ package ch.ethz.sis.openbis.generic.server.api.v3.executor.sample;
import java.util.Map;
-import org.springframework.beans.factory.annotation.Autowired;
+import javax.annotation.Resource;
+
import org.springframework.stereotype.Component;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleCreation;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
+import ch.systemsx.cisd.openbis.generic.server.ComponentNames;
+import ch.systemsx.cisd.openbis.generic.server.business.IRelationshipService;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
/**
@@ -35,33 +36,25 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public class SetSampleContainerExecutor implements ISetSampleContainerExecutor
{
- @Autowired
- private IDAOFactory daoFactory;
-
- @SuppressWarnings("unused")
- private SetSampleContainerExecutor()
- {
- }
-
- public SetSampleContainerExecutor(IDAOFactory daoFactory)
- {
- this.daoFactory = daoFactory;
- }
+ @Resource(name = ComponentNames.RELATIONSHIP_SERVICE)
+ private IRelationshipService relationshipService;
@Override
- public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap, Map<ISampleId, Long> techIdMap)
+ public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap, Map<ISampleId, SamplePE> sampleMap)
{
- ISampleDAO sampleDAO = daoFactory.getSampleDAO();
-
for (SampleCreation creation : creationsMap.keySet())
{
+ context.pushContextDescription("set container for sample " + creation.getCode());
+
SamplePE sample = creationsMap.get(creation);
ISampleId containerId = creation.getContainerId();
if (containerId != null)
{
- Long containerTechId = techIdMap.get(containerId);
- sampleDAO.setSampleContainer(sample.getId(), containerTechId);
+ SamplePE container = sampleMap.get(containerId);
+ relationshipService.assignSampleToContainer(context.getSession(), sample, container);
}
+
+ context.popContextDescription();
}
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleExperimentExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleExperimentExecutor.java
new file mode 100644
index 00000000000..33a3070b427
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleExperimentExecutor.java
@@ -0,0 +1,87 @@
+/*
+ * 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.sample;
+
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+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.experiment.IMapExperimentByIdExecutor;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleCreation;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.IExperimentId;
+import ch.ethz.sis.openbis.generic.shared.api.v3.exceptions.ObjectNotFoundException;
+import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
+import ch.systemsx.cisd.openbis.generic.server.authorization.validator.ExperimentByIdentiferValidator;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+
+/**
+ * @author pkupczyk
+ */
+@Component
+public class SetSampleExperimentExecutor implements ISetSampleExperimentExecutor
+{
+
+ @Autowired
+ private IMapExperimentByIdExecutor mapExperimentByIdExecutor;
+
+ @Override
+ public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap)
+ {
+ List<IExperimentId> experimentIds = new LinkedList<IExperimentId>();
+
+ for (SampleCreation creation : creationsMap.keySet())
+ {
+ if (creation.getExperimentId() != null)
+ {
+ experimentIds.add(creation.getExperimentId());
+ }
+ }
+
+ Map<IExperimentId, ExperimentPE> experimentMap = mapExperimentByIdExecutor.map(context, experimentIds);
+
+ for (Map.Entry<SampleCreation, SamplePE> creationEntry : creationsMap.entrySet())
+ {
+ SampleCreation creation = creationEntry.getKey();
+ SamplePE sample = creationEntry.getValue();
+
+ context.pushContextDescription("set experiment for sample " + creation.getCode());
+
+ if (creation.getExperimentId() != null)
+ {
+ ExperimentPE experiment = experimentMap.get(creation.getExperimentId());
+ if (experiment == null)
+ {
+ throw new ObjectNotFoundException(creation.getExperimentId());
+ }
+
+ if (false == new ExperimentByIdentiferValidator().doValidation(context.getSession().tryGetPerson(), experiment))
+ {
+ throw new AuthorizationFailureException("Cannot access experiment " + creation.getExperimentId());
+ }
+
+ sample.setExperiment(experiment);
+ }
+
+ context.popContextDescription();
+ }
+ }
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleParentsExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleParentsExecutor.java
index c086f643af5..b6d01fe5230 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleParentsExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleParentsExecutor.java
@@ -17,15 +17,18 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.sample;
import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.annotation.Resource;
-import org.springframework.beans.factory.annotation.Autowired;
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.relationship.IGetParentChildRelationshipIdExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleCreation;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.ComponentNames;
+import ch.systemsx.cisd.openbis.generic.server.business.IRelationshipService;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
/**
@@ -35,19 +38,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public class SetSampleParentsExecutor extends AbstractSetSampleRelatedSamplesExecutor implements ISetSampleParentsExecutor
{
- @Autowired
- private IGetParentChildRelationshipIdExecutor getParentChildRelationshipIdExecutor;
-
- @SuppressWarnings("unused")
- private SetSampleParentsExecutor()
- {
- }
-
- public SetSampleParentsExecutor(IDAOFactory daoFactory, IGetParentChildRelationshipIdExecutor getParentChildRelationshipIdExecutor)
- {
- super(daoFactory);
- this.getParentChildRelationshipIdExecutor = getParentChildRelationshipIdExecutor;
- }
+ @Resource(name = ComponentNames.RELATIONSHIP_SERVICE)
+ private IRelationshipService relationshipService;
@Override
protected Collection<? extends ISampleId> getRelatedSamplesIds(IOperationContext context, SampleCreation creation)
@@ -56,11 +48,21 @@ public class SetSampleParentsExecutor extends AbstractSetSampleRelatedSamplesExe
}
@Override
- protected void setRelatedSamples(IOperationContext context, SamplePE sample, Collection<Long> relatedSamplesTechIds)
+ protected void setRelatedSamples(IOperationContext context, SamplePE child, Collection<SamplePE> parents)
{
- getDaoFactory().getSampleDAO().setSampleRelationshipParents(sample.getId(), relatedSamplesTechIds,
- getParentChildRelationshipIdExecutor.get(context),
- context.getSession().tryGetPerson());
- }
+ Set<SamplePE> existingParents = new HashSet<SamplePE>(child.getParents());
+
+ context.pushContextDescription("set parents for sample " + child.getCode());
+ for (SamplePE parent : parents)
+ {
+ if (false == existingParents.contains(parent))
+ {
+ relationshipService.addParentToSample(context.getSession(), child, parent);
+ existingParents.add(parent);
+ }
+ }
+
+ context.popContextDescription();
+ }
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleRelatedSamplesExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleRelatedSamplesExecutor.java
index d567c9e0e8a..a4b43a11438 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleRelatedSamplesExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleRelatedSamplesExecutor.java
@@ -19,7 +19,6 @@ package ch.ethz.sis.openbis.generic.server.api.v3.executor.sample;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
-import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
@@ -33,6 +32,7 @@ import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleCreation;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.CreationId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
+import ch.ethz.sis.openbis.generic.shared.api.v3.exceptions.ObjectNotFoundException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
@@ -44,7 +44,7 @@ public class SetSampleRelatedSamplesExecutor implements ISetSampleRelatedSamples
{
@Autowired
- private IListSampleTechIdByIdExecutor listSampleTechIdByIdExecutor;
+ private IMapSampleByIdExecutor mapSampleByIdExecutor;
@Autowired
private ISetSampleContainerExecutor setSampleContainerExecutor;
@@ -63,11 +63,11 @@ public class SetSampleRelatedSamplesExecutor implements ISetSampleRelatedSamples
{
}
- public SetSampleRelatedSamplesExecutor(IListSampleTechIdByIdExecutor listSampleTechIdByIdExecutor,
+ public SetSampleRelatedSamplesExecutor(IMapSampleByIdExecutor mapSampleByIdExecutor,
ISetSampleContainerExecutor setSampleContainerExecutor, ISetSampleContainedExecutor setSampleContainedExecutor,
ISetSampleParentsExecutor setSampleParentsExecutor, ISetSampleChildrenExecutor setSampleChildrenExecutor)
{
- this.listSampleTechIdByIdExecutor = listSampleTechIdByIdExecutor;
+ this.mapSampleByIdExecutor = mapSampleByIdExecutor;
this.setSampleContainerExecutor = setSampleContainerExecutor;
this.setSampleContainedExecutor = setSampleContainedExecutor;
this.setSampleParentsExecutor = setSampleParentsExecutor;
@@ -77,7 +77,7 @@ public class SetSampleRelatedSamplesExecutor implements ISetSampleRelatedSamples
@Override
public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap)
{
- Map<ISampleId, Long> relatedSamplesMap = getRelatedSamplesMap(context, creationsMap);
+ Map<ISampleId, SamplePE> relatedSamplesMap = getRelatedSamplesMap(context, creationsMap);
setSampleContainerExecutor.set(context, creationsMap, relatedSamplesMap);
setSampleContainedExecutor.set(context, creationsMap, relatedSamplesMap);
@@ -85,12 +85,12 @@ public class SetSampleRelatedSamplesExecutor implements ISetSampleRelatedSamples
setSampleChildrenExecutor.set(context, creationsMap, relatedSamplesMap);
}
- private Map<ISampleId, Long> getRelatedSamplesMap(IOperationContext context, Map<SampleCreation, SamplePE> createdSamples)
+ private Map<ISampleId, SamplePE> getRelatedSamplesMap(IOperationContext context, Map<SampleCreation, SamplePE> createdSamples)
{
- context.pushContextDescription("register samples - verify relationships");
+ context.pushContextDescription("load related samples");
- Collection<ISampleId> relatedSamples = getRelatedSamplesIds(createdSamples.keySet());
- HashMap<ISampleId, Long> sampleIdToTechIdMap = new HashMap<ISampleId, Long>();
+ Collection<ISampleId> relatedSamplesIds = getRelatedSamplesIds(createdSamples.keySet());
+ HashMap<ISampleId, SamplePE> relatedSamplesMap = new HashMap<ISampleId, SamplePE>();
for (Entry<SampleCreation, SamplePE> entry : createdSamples.entrySet())
{
@@ -99,41 +99,40 @@ public class SetSampleRelatedSamplesExecutor implements ISetSampleRelatedSamples
if (sampleCreation.getCreationId() != null)
{
- sampleIdToTechIdMap.put(sampleCreation.getCreationId(), sample.getId());
+ relatedSamplesMap.put(sampleCreation.getCreationId(), sample);
}
}
- List<ISampleId> knownSampleIds = new LinkedList<ISampleId>();
+ List<ISampleId> samplesToLoadIds = new LinkedList<ISampleId>();
- for (ISampleId relatedSample : relatedSamples)
+ for (ISampleId relatedSample : relatedSamplesIds)
{
if (relatedSample instanceof CreationId)
{
- if (false == sampleIdToTechIdMap.containsKey(relatedSample))
+ if (false == relatedSamplesMap.containsKey(relatedSample))
{
throw new UserFailureException("Unknown sample creation id: " + relatedSample);
}
}
else
{
- knownSampleIds.add(relatedSample);
+ samplesToLoadIds.add(relatedSample);
}
}
- Collection<Long> techIds = listSampleTechIdByIdExecutor.list(context, knownSampleIds);
+ Map<ISampleId, SamplePE> loadedSamplesMap = mapSampleByIdExecutor.map(context, samplesToLoadIds);
+ relatedSamplesMap.putAll(loadedSamplesMap);
- assert knownSampleIds.size() == techIds.size();
-
- Iterator<ISampleId> it1 = knownSampleIds.iterator();
- Iterator<Long> it2 = techIds.iterator();
-
- while (it1.hasNext())
+ for (ISampleId relatedSampleId : relatedSamplesIds)
{
- sampleIdToTechIdMap.put(it1.next(), it2.next());
+ if (false == relatedSamplesMap.containsKey(relatedSampleId))
+ {
+ throw new ObjectNotFoundException(relatedSampleId);
+ }
}
context.popContextDescription();
- return sampleIdToTechIdMap;
+ return relatedSamplesMap;
}
private Set<ISampleId> getRelatedSamplesIds(Collection<SampleCreation> sampleCreations)
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleSpaceExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleSpaceExecutor.java
new file mode 100644
index 00000000000..5da74234aa1
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleSpaceExecutor.java
@@ -0,0 +1,87 @@
+/*
+ * 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.sample;
+
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+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.space.IMapSpaceByIdExecutor;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleCreation;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.space.ISpaceId;
+import ch.ethz.sis.openbis.generic.shared.api.v3.exceptions.ObjectNotFoundException;
+import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
+import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SimpleSpaceValidator;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
+
+/**
+ * @author pkupczyk
+ */
+@Component
+public class SetSampleSpaceExecutor implements ISetSampleSpaceExecutor
+{
+
+ @Autowired
+ private IMapSpaceByIdExecutor mapSpaceByIdExecutor;
+
+ @Override
+ public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap)
+ {
+ List<ISpaceId> spaceIds = new LinkedList<ISpaceId>();
+
+ for (SampleCreation creation : creationsMap.keySet())
+ {
+ if (creation.getSpaceId() != null)
+ {
+ spaceIds.add(creation.getSpaceId());
+ }
+ }
+
+ Map<ISpaceId, SpacePE> spaceMap = mapSpaceByIdExecutor.map(context, spaceIds);
+
+ for (Map.Entry<SampleCreation, SamplePE> creationEntry : creationsMap.entrySet())
+ {
+ SampleCreation creation = creationEntry.getKey();
+ SamplePE sample = creationEntry.getValue();
+
+ context.pushContextDescription("set space for sample " + creation.getCode());
+
+ if (creation.getSpaceId() != null)
+ {
+ SpacePE space = spaceMap.get(creation.getSpaceId());
+ if (space == null)
+ {
+ throw new ObjectNotFoundException(creation.getSpaceId());
+ }
+
+ if (false == new SimpleSpaceValidator().doValidation(context.getSession().tryGetPerson(), space))
+ {
+ throw new AuthorizationFailureException("Cannot access space " + creation.getSpaceId());
+ }
+
+ sample.setSpace(space);
+ }
+
+ context.popContextDescription();
+ }
+ }
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleTypeExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleTypeExecutor.java
new file mode 100644
index 00000000000..1efccea22df
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleTypeExecutor.java
@@ -0,0 +1,85 @@
+/*
+ * 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.sample;
+
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+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.IMapEntityTypeByIdExecutor;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleCreation;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.entitytype.IEntityTypeId;
+import ch.ethz.sis.openbis.generic.shared.api.v3.exceptions.ObjectNotFoundException;
+import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
+
+/**
+ * @author pkupczyk
+ */
+@Component
+public class SetSampleTypeExecutor implements ISetSampleTypeExecutor
+{
+
+ @Autowired
+ private IMapEntityTypeByIdExecutor mapEntityTypeByIdExecutor;
+
+ @Override
+ public void set(IOperationContext context, Map<SampleCreation, SamplePE> creationsMap)
+ {
+ List<IEntityTypeId> typeIds = new LinkedList<IEntityTypeId>();
+
+ for (SampleCreation creation : creationsMap.keySet())
+ {
+ if (creation.getTypeId() != null)
+ {
+ typeIds.add(creation.getTypeId());
+ }
+ }
+
+ Map<IEntityTypeId, EntityTypePE> typeMap = mapEntityTypeByIdExecutor.map(context, EntityKind.SAMPLE, typeIds);
+
+ for (Map.Entry<SampleCreation, SamplePE> creationEntry : creationsMap.entrySet())
+ {
+ SampleCreation creation = creationEntry.getKey();
+ SamplePE sample = creationEntry.getValue();
+
+ context.pushContextDescription("set type for sample " + creation.getCode());
+
+ if (creation.getTypeId() == null)
+ {
+ throw new UserFailureException("No type for sample provided");
+ } else
+ {
+ EntityTypePE type = typeMap.get(creation.getTypeId());
+ if (type == null)
+ {
+ throw new ObjectNotFoundException(creation.getTypeId());
+ }
+ sample.setSampleType((SampleTypePE) type);
+ }
+
+ context.popContextDescription();
+ }
+ }
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleChildrenExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleChildrenExecutor.java
index a011fe971a4..54cdc8198fd 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleChildrenExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleChildrenExecutor.java
@@ -17,16 +17,19 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.sample;
import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.annotation.Resource;
-import org.springframework.beans.factory.annotation.Autowired;
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.relationship.IGetParentChildRelationshipIdExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.ListUpdateValue;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleUpdate;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.ComponentNames;
+import ch.systemsx.cisd.openbis.generic.server.business.IRelationshipService;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
/**
@@ -36,19 +39,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public class UpdateSampleChildrenExecutor extends AbstractUpdateSampleRelatedSamplesExecutor implements IUpdateSampleChildrenExecutor
{
- @Autowired
- private IGetParentChildRelationshipIdExecutor getParentChildRelationshipIdExecutor;
-
- @SuppressWarnings("unused")
- private UpdateSampleChildrenExecutor()
- {
- }
-
- public UpdateSampleChildrenExecutor(IDAOFactory daoFactory, IGetParentChildRelationshipIdExecutor getParentChildRelationshipIdExecutor)
- {
- super(daoFactory);
- this.getParentChildRelationshipIdExecutor = getParentChildRelationshipIdExecutor;
- }
+ @Resource(name = ComponentNames.RELATIONSHIP_SERVICE)
+ private IRelationshipService relationshipService;
@Override
protected ListUpdateValue<? extends ISampleId> getRelatedSamplesUpdate(IOperationContext context, SampleUpdate update)
@@ -57,27 +49,54 @@ public class UpdateSampleChildrenExecutor extends AbstractUpdateSampleRelatedSam
}
@Override
- protected void setRelatedSamples(IOperationContext context, SamplePE sample, Collection<Long> relatedSamplesIds)
+ protected void setRelatedSamples(IOperationContext context, SamplePE parent, Collection<SamplePE> children)
{
- getDaoFactory().getSampleDAO().setSampleRelationshipChildren(sample.getId(), relatedSamplesIds,
- getParentChildRelationshipIdExecutor.get(context),
- context.getSession().tryGetPerson());
+ Set<SamplePE> existingChildren = new HashSet<SamplePE>(parent.getChildren());
+ Set<SamplePE> newChildren = new HashSet<SamplePE>(children);
+
+ for (SamplePE anExistingChild : existingChildren)
+ {
+ if (false == newChildren.contains(anExistingChild))
+ {
+ relationshipService.removeParentFromSample(context.getSession(), anExistingChild, parent);
+ }
+ }
+
+ for (SamplePE aNewChild : newChildren)
+ {
+ if (false == existingChildren.contains(aNewChild))
+ {
+ relationshipService.addParentToSample(context.getSession(), aNewChild, parent);
+ }
+ }
}
@Override
- protected void addRelatedSamples(IOperationContext context, SamplePE sample, Collection<Long> relatedSamplesIds)
+ protected void addRelatedSamples(IOperationContext context, SamplePE parent, Collection<SamplePE> children)
{
- getDaoFactory().getSampleDAO().addSampleRelationshipChildren(sample.getId(), relatedSamplesIds,
- getParentChildRelationshipIdExecutor.get(context),
- context.getSession().tryGetPerson());
+ Set<SamplePE> existingChildren = new HashSet<SamplePE>(parent.getChildren());
+
+ for (SamplePE aChild : children)
+ {
+ if (false == existingChildren.contains(aChild))
+ {
+ relationshipService.addParentToSample(context.getSession(), aChild, parent);
+ }
+ }
}
@Override
- protected void removeRelatedSamples(IOperationContext context, SamplePE sample, Collection<Long> relatedSamplesIds)
+ protected void removeRelatedSamples(IOperationContext context, SamplePE parent, Collection<SamplePE> children)
{
- getDaoFactory().getSampleDAO().removeSampleRelationshipChildren(sample.getId(), relatedSamplesIds,
- getParentChildRelationshipIdExecutor.get(context),
- context.getSession().tryGetPerson());
+ Set<SamplePE> existingChildren = new HashSet<SamplePE>(parent.getChildren());
+
+ for (SamplePE aChild : children)
+ {
+ if (existingChildren.contains(aChild))
+ {
+ relationshipService.removeParentFromSample(context.getSession(), aChild, parent);
+ }
+ }
}
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleContainedExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleContainedExecutor.java
index 7222cd60ab7..ab187ac72aa 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleContainedExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleContainedExecutor.java
@@ -16,7 +16,12 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.sample;
+import java.util.ArrayList;
import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.annotation.Resource;
import org.springframework.stereotype.Component;
@@ -24,7 +29,8 @@ import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.ListUpdateValue;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleUpdate;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.ComponentNames;
+import ch.systemsx.cisd.openbis.generic.server.business.IRelationshipService;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
/**
@@ -34,38 +40,91 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public class UpdateSampleContainedExecutor extends AbstractUpdateSampleRelatedSamplesExecutor implements IUpdateSampleContainedExecutor
{
- @SuppressWarnings("unused")
- private UpdateSampleContainedExecutor()
+ @Resource(name = ComponentNames.RELATIONSHIP_SERVICE)
+ private IRelationshipService relationshipService;
+
+ @Override
+ protected ListUpdateValue<? extends ISampleId> getRelatedSamplesUpdate(IOperationContext context, SampleUpdate update)
{
+ return update.getContainedIds();
}
- public UpdateSampleContainedExecutor(IDAOFactory daoFactory)
+ @Override
+ protected void setRelatedSamples(IOperationContext context, SamplePE container, Collection<SamplePE> contained)
{
- super(daoFactory);
+ Set<SamplePE> existingContained = new HashSet<SamplePE>(container.getContained());
+ Set<SamplePE> newContained = new HashSet<SamplePE>(contained);
+
+ for (SamplePE anExistingContained : existingContained)
+ {
+ if (false == newContained.contains(existingContained))
+ {
+ removeFromContainer(relationshipService, context, anExistingContained, container);
+ }
+ }
+
+ for (SamplePE aNewContained : newContained)
+ {
+ if (false == existingContained.contains(aNewContained))
+ {
+ assignToContainer(relationshipService, context, aNewContained, container);
+ }
+ }
}
@Override
- protected ListUpdateValue<? extends ISampleId> getRelatedSamplesUpdate(IOperationContext context, SampleUpdate update)
+ protected void addRelatedSamples(IOperationContext context, SamplePE container, Collection<SamplePE> contained)
{
- return update.getContainedIds();
+ for (SamplePE aContained : contained)
+ {
+ assignToContainer(relationshipService, context, aContained, container);
+ }
}
@Override
- protected void setRelatedSamples(IOperationContext context, SamplePE sample, Collection<Long> relatedSamplesIds)
+ protected void removeRelatedSamples(IOperationContext context, SamplePE container, Collection<SamplePE> contained)
{
- getDaoFactory().getSampleDAO().setSampleContained(sample.getId(), relatedSamplesIds);
+ for (SamplePE aContained : contained)
+ {
+ removeFromContainer(relationshipService, context, aContained, container);
+ }
}
- @Override
- protected void addRelatedSamples(IOperationContext context, SamplePE sample, Collection<Long> relatedSamplesIds)
+ static void assignToContainer(IRelationshipService service, IOperationContext context, SamplePE sample, SamplePE container)
{
- getDaoFactory().getSampleDAO().addSampleContained(sample.getId(), relatedSamplesIds);
+ SamplePE previousContainer = sample.getContainer();
+
+ if (previousContainer != null)
+ {
+ if (previousContainer.equals(container))
+ {
+ // nothing to do
+ return;
+ } else
+ {
+ removeFromContainer(service, context, sample, previousContainer);
+ }
+ }
+
+ Set<SamplePE> contained = new HashSet<SamplePE>(container.getContained());
+ contained.add(sample);
+ container.setContained(new ArrayList<SamplePE>(contained));
+
+ service.assignSampleToContainer(context.getSession(), sample, container);
}
- @Override
- protected void removeRelatedSamples(IOperationContext context, SamplePE sample, Collection<Long> relatedSamplesIds)
+ static void removeFromContainer(IRelationshipService service, IOperationContext context, SamplePE sample, SamplePE container)
{
- getDaoFactory().getSampleDAO().removeSampleContained(sample.getId(), relatedSamplesIds);
+ SamplePE previousContainer = sample.getContainer();
+
+ if (previousContainer != null && previousContainer.equals(container))
+ {
+ Set<SamplePE> contained = new HashSet<SamplePE>(container.getContained());
+ contained.remove(sample);
+ container.setContained(new ArrayList<SamplePE>(contained));
+
+ service.removeSampleFromContainer(context.getSession(), sample);
+ }
}
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleContainerExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleContainerExecutor.java
index 3dcf79e6368..fedbbc1a0d8 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleContainerExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleContainerExecutor.java
@@ -18,15 +18,17 @@ package ch.ethz.sis.openbis.generic.server.api.v3.executor.sample;
import java.util.Map;
-import org.springframework.beans.factory.annotation.Autowired;
+import javax.annotation.Resource;
+
import org.springframework.stereotype.Component;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.FieldUpdateValue;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleUpdate;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
+import ch.ethz.sis.openbis.generic.shared.api.v3.exceptions.ObjectNotFoundException;
+import ch.systemsx.cisd.openbis.generic.server.ComponentNames;
+import ch.systemsx.cisd.openbis.generic.server.business.IRelationshipService;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
/**
@@ -36,24 +38,12 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public class UpdateSampleContainerExecutor implements IUpdateSampleContainerExecutor
{
- @Autowired
- private IDAOFactory daoFactory;
-
- @SuppressWarnings("unused")
- private UpdateSampleContainerExecutor()
- {
- }
-
- public UpdateSampleContainerExecutor(IDAOFactory daoFactory)
- {
- this.daoFactory = daoFactory;
- }
+ @Resource(name = ComponentNames.RELATIONSHIP_SERVICE)
+ private IRelationshipService relationshipService;
@Override
- public void update(IOperationContext context, Map<SampleUpdate, SamplePE> updateMap, Map<ISampleId, Long> techIdMap)
+ public void update(IOperationContext context, Map<SampleUpdate, SamplePE> updateMap, Map<ISampleId, SamplePE> samplesMap)
{
- ISampleDAO sampleDAO = daoFactory.getSampleDAO();
-
for (SampleUpdate update : updateMap.keySet())
{
SamplePE sample = updateMap.get(update);
@@ -61,8 +51,21 @@ public class UpdateSampleContainerExecutor implements IUpdateSampleContainerExec
if (containerUpdate != null && containerUpdate.isModified())
{
- Long containerTechId = techIdMap.get(containerUpdate.getValue());
- sampleDAO.setSampleContainer(sample.getId(), containerTechId);
+ if (containerUpdate.getValue() == null)
+ {
+ if (sample.getContainer() != null)
+ {
+ UpdateSampleContainedExecutor.removeFromContainer(relationshipService, context, sample, sample.getContainer());
+ }
+ } else
+ {
+ SamplePE container = samplesMap.get(containerUpdate.getValue());
+ if (container == null)
+ {
+ throw new ObjectNotFoundException(containerUpdate.getValue());
+ }
+ UpdateSampleContainedExecutor.assignToContainer(relationshipService, context, sample, container);
+ }
}
}
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleExecutor.java
index 8b4f8d2c137..2dafdcdc337 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleExecutor.java
@@ -35,6 +35,8 @@ import ch.ethz.sis.openbis.generic.server.api.v3.executor.property.IUpdateEntity
import ch.ethz.sis.openbis.generic.server.api.v3.executor.tag.IUpdateTagForEntityExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleUpdate;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
+import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
+import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SampleByIdentiferValidator;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.util.RelationshipUtils;
@@ -121,6 +123,14 @@ public class UpdateSampleExecutor implements IUpdateSampleExecutor
assert sampleIds.size() == samples.size();
+ for (SamplePE sample : samples)
+ {
+ if (false == new SampleByIdentiferValidator().doValidation(context.getSession().tryGetPerson(), sample))
+ {
+ throw new AuthorizationFailureException("Cannot access sample " + sample.getIdentifier());
+ }
+ }
+
Map<SampleUpdate, SamplePE> result = new HashMap<SampleUpdate, SamplePE>();
Iterator<SampleUpdate> it1 = updates.iterator();
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleExperimentExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleExperimentExecutor.java
index 66ffd719435..6ddc179fc0f 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleExperimentExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleExperimentExecutor.java
@@ -23,6 +23,8 @@ import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.experiment.IGetExperimentByIdExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.FieldUpdateValue;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.IExperimentId;
+import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
+import ch.systemsx.cisd.openbis.generic.server.authorization.validator.ExperimentByIdentiferValidator;
import ch.systemsx.cisd.openbis.generic.server.business.IRelationshipService;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
@@ -60,6 +62,7 @@ public class UpdateSampleExperimentExecutor implements IUpdateSampleExperimentEx
{
if (sample.getExperiment() != null)
{
+ checkExperiment(context, sample.getExperiment());
relationshipService.unassignSampleFromExperiment(context.getSession(), sample);
}
}
@@ -68,10 +71,19 @@ public class UpdateSampleExperimentExecutor implements IUpdateSampleExperimentEx
ExperimentPE experiment = getExperimentByIdExecutor.get(context, update.getValue());
if (false == experiment.equals(sample.getExperiment()))
{
+ checkExperiment(context, experiment);
relationshipService.assignSampleToExperiment(context.getSession(), sample, experiment);
}
}
}
}
+ private void checkExperiment(IOperationContext context, ExperimentPE experiment)
+ {
+ if (false == new ExperimentByIdentiferValidator().doValidation(context.getSession().tryGetPerson(), experiment))
+ {
+ throw new AuthorizationFailureException("Cannot access experiment " + experiment.getIdentifier());
+ }
+ }
+
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleParentsExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleParentsExecutor.java
index 676b2911193..e3f7175125c 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleParentsExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleParentsExecutor.java
@@ -17,16 +17,19 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.sample;
import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.annotation.Resource;
-import org.springframework.beans.factory.annotation.Autowired;
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.relationship.IGetParentChildRelationshipIdExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.ListUpdateValue;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleUpdate;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.ComponentNames;
+import ch.systemsx.cisd.openbis.generic.server.business.IRelationshipService;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
/**
@@ -36,19 +39,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
public class UpdateSampleParentsExecutor extends AbstractUpdateSampleRelatedSamplesExecutor implements IUpdateSampleParentsExecutor
{
- @Autowired
- private IGetParentChildRelationshipIdExecutor getParentChildRelationshipIdExecutor;
-
- @SuppressWarnings("unused")
- private UpdateSampleParentsExecutor()
- {
- }
-
- public UpdateSampleParentsExecutor(IDAOFactory daoFactory, IGetParentChildRelationshipIdExecutor getParentChildRelationshipIdExecutor)
- {
- super(daoFactory);
- this.getParentChildRelationshipIdExecutor = getParentChildRelationshipIdExecutor;
- }
+ @Resource(name = ComponentNames.RELATIONSHIP_SERVICE)
+ private IRelationshipService relationshipService;
@Override
protected ListUpdateValue<? extends ISampleId> getRelatedSamplesUpdate(IOperationContext context, SampleUpdate update)
@@ -57,27 +49,54 @@ public class UpdateSampleParentsExecutor extends AbstractUpdateSampleRelatedSamp
}
@Override
- protected void setRelatedSamples(IOperationContext context, SamplePE sample, Collection<Long> relatedSamplesIds)
+ protected void setRelatedSamples(IOperationContext context, SamplePE child, Collection<SamplePE> parents)
{
- getDaoFactory().getSampleDAO().setSampleRelationshipParents(sample.getId(), relatedSamplesIds,
- getParentChildRelationshipIdExecutor.get(context),
- context.getSession().tryGetPerson());
+ Set<SamplePE> existingParents = new HashSet<SamplePE>(child.getParents());
+ Set<SamplePE> newParents = new HashSet<SamplePE>(parents);
+
+ for (SamplePE anExistingParent : existingParents)
+ {
+ if (false == newParents.contains(anExistingParent))
+ {
+ relationshipService.removeParentFromSample(context.getSession(), child, anExistingParent);
+ }
+ }
+
+ for (SamplePE aNewParent : newParents)
+ {
+ if (false == existingParents.contains(aNewParent))
+ {
+ relationshipService.addParentToSample(context.getSession(), child, aNewParent);
+ }
+ }
}
@Override
- protected void addRelatedSamples(IOperationContext context, SamplePE sample, Collection<Long> relatedSamplesIds)
+ protected void addRelatedSamples(IOperationContext context, SamplePE child, Collection<SamplePE> parents)
{
- getDaoFactory().getSampleDAO().addSampleRelationshipParents(sample.getId(), relatedSamplesIds,
- getParentChildRelationshipIdExecutor.get(context),
- context.getSession().tryGetPerson());
+ Set<SamplePE> existingParents = new HashSet<SamplePE>(child.getParents());
+
+ for (SamplePE aParent : parents)
+ {
+ if (false == existingParents.contains(aParent))
+ {
+ relationshipService.addParentToSample(context.getSession(), child, aParent);
+ }
+ }
}
@Override
- protected void removeRelatedSamples(IOperationContext context, SamplePE sample, Collection<Long> relatedSamplesIds)
+ protected void removeRelatedSamples(IOperationContext context, SamplePE child, Collection<SamplePE> parents)
{
- getDaoFactory().getSampleDAO().removeSampleRelationshipParents(sample.getId(), relatedSamplesIds,
- getParentChildRelationshipIdExecutor.get(context),
- context.getSession().tryGetPerson());
+ Set<SamplePE> existingParents = new HashSet<SamplePE>(child.getParents());
+
+ for (SamplePE aParent : parents)
+ {
+ if (existingParents.contains(aParent))
+ {
+ relationshipService.removeParentFromSample(context.getSession(), child, aParent);
+ }
+ }
}
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleRelatedSamplesExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleRelatedSamplesExecutor.java
index d57df7f2ab8..a6e8c0f4923 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleRelatedSamplesExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleRelatedSamplesExecutor.java
@@ -17,9 +17,7 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.sample;
import java.util.Collection;
-import java.util.HashMap;
import java.util.HashSet;
-import java.util.Iterator;
import java.util.Map;
import java.util.Set;
@@ -41,7 +39,7 @@ public class UpdateSampleRelatedSamplesExecutor implements IUpdateSampleRelatedS
{
@Autowired
- private IListSampleTechIdByIdExecutor listSampleTechIdByIdExecutor;
+ private IMapSampleByIdExecutor mapSampleByIdExecutor;
@Autowired
private IUpdateSampleContainerExecutor updateSampleContainerExecutor;
@@ -60,11 +58,11 @@ public class UpdateSampleRelatedSamplesExecutor implements IUpdateSampleRelatedS
{
}
- public UpdateSampleRelatedSamplesExecutor(IListSampleTechIdByIdExecutor listSampleTechIdByIdExecutor,
+ public UpdateSampleRelatedSamplesExecutor(IMapSampleByIdExecutor mapSampleByIdExecutor,
IUpdateSampleContainerExecutor updateSampleContainerExecutor, IUpdateSampleContainedExecutor updateSampleContainedExecutor,
IUpdateSampleParentsExecutor updateSampleParentsExecutor, IUpdateSampleChildrenExecutor updateSampleChildrenExecutor)
{
- this.listSampleTechIdByIdExecutor = listSampleTechIdByIdExecutor;
+ this.mapSampleByIdExecutor = mapSampleByIdExecutor;
this.updateSampleContainerExecutor = updateSampleContainerExecutor;
this.updateSampleContainedExecutor = updateSampleContainedExecutor;
this.updateSampleParentsExecutor = updateSampleParentsExecutor;
@@ -74,35 +72,23 @@ public class UpdateSampleRelatedSamplesExecutor implements IUpdateSampleRelatedS
@Override
public void update(IOperationContext context, Map<SampleUpdate, SamplePE> updateMap)
{
- Map<ISampleId, Long> techIdMap = getRelatedSamplesMap(context, updateMap.keySet());
- updateSampleContainerExecutor.update(context, updateMap, techIdMap);
- updateSampleContainedExecutor.update(context, updateMap, techIdMap);
- updateSampleParentsExecutor.update(context, updateMap, techIdMap);
- updateSampleChildrenExecutor.update(context, updateMap, techIdMap);
+ Map<ISampleId, SamplePE> samplesMap = getRelatedSamplesMap(context, updateMap.keySet());
+ updateSampleContainerExecutor.update(context, updateMap, samplesMap);
+ updateSampleContainedExecutor.update(context, updateMap, samplesMap);
+ updateSampleParentsExecutor.update(context, updateMap, samplesMap);
+ updateSampleChildrenExecutor.update(context, updateMap, samplesMap);
}
- private HashMap<ISampleId, Long> getRelatedSamplesMap(IOperationContext context, Collection<SampleUpdate> updates)
+ private Map<ISampleId, SamplePE> getRelatedSamplesMap(IOperationContext context, Collection<SampleUpdate> updates)
{
context.pushContextDescription("update samples - verify related entities exist");
- Collection<ISampleId> relatedSamples = getRelatedSamplesIds(updates);
- HashMap<ISampleId, Long> sampleIdToTechIdMap = new HashMap<ISampleId, Long>();
-
- Collection<Long> techIds = listSampleTechIdByIdExecutor.list(context, relatedSamples);
-
- assert relatedSamples.size() == techIds.size();
-
- Iterator<ISampleId> it1 = relatedSamples.iterator();
- Iterator<Long> it2 = techIds.iterator();
-
- while (it1.hasNext())
- {
- sampleIdToTechIdMap.put(it1.next(), it2.next());
- }
+ Collection<ISampleId> relatedSamplesIds = getRelatedSamplesIds(updates);
+ Map<ISampleId, SamplePE> relatedSamplesMap = mapSampleByIdExecutor.map(context, relatedSamplesIds);
context.popContextDescription();
- return sampleIdToTechIdMap;
+ return relatedSamplesMap;
}
private Set<ISampleId> getRelatedSamplesIds(Collection<SampleUpdate> updates)
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleSpaceExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleSpaceExecutor.java
index 5989cc61741..0d95bcc3963 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleSpaceExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleSpaceExecutor.java
@@ -23,6 +23,8 @@ import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.space.IGetSpaceByIdExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.FieldUpdateValue;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.space.ISpaceId;
+import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
+import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SimpleSpaceValidator;
import ch.systemsx.cisd.openbis.generic.server.business.IRelationshipService;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
@@ -60,12 +62,14 @@ public class UpdateSampleSpaceExecutor implements IUpdateSampleSpaceExecutor
{
if (sample.getSpace() != null)
{
+ checkSpace(context, sample.getSpace());
relationshipService.shareSample(context.getSession(), sample);
}
}
else
{
SpacePE space = getSpaceByIdExecutor.get(context, update.getValue());
+ checkSpace(context, space);
if (sample.getSpace() == null)
{
@@ -78,4 +82,12 @@ public class UpdateSampleSpaceExecutor implements IUpdateSampleSpaceExecutor
}
}
+ private void checkSpace(IOperationContext context, SpacePE space)
+ {
+ if (false == new SimpleSpaceValidator().doValidation(context.getSession().tryGetPerson(), space))
+ {
+ throw new AuthorizationFailureException("Cannot access space " + space.getCode());
+ }
+ }
+
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/space/IListSpaceByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/space/IListSpaceByIdExecutor.java
index 2f0ae3f6461..0df20a394fa 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/space/IListSpaceByIdExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/space/IListSpaceByIdExecutor.java
@@ -16,19 +16,14 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.space;
-import java.util.Collection;
-import java.util.List;
-
-import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.IListObjectByIdExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.space.ISpaceId;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
/**
* @author pkupczyk
*/
-public interface IListSpaceByIdExecutor
+public interface IListSpaceByIdExecutor extends IListObjectByIdExecutor<ISpaceId, SpacePE>
{
- public List<SpacePE> list(IOperationContext context, Collection<? extends ISpaceId> spaceIds);
-
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/space/IMapSpaceByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/space/IMapSpaceByIdExecutor.java
index 0b6072a140a..63af0686733 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/space/IMapSpaceByIdExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/space/IMapSpaceByIdExecutor.java
@@ -16,19 +16,14 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.space;
-import java.util.Collection;
-import java.util.Map;
-
-import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.IMapObjectByIdExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.space.ISpaceId;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
/**
* @author pkupczyk
*/
-public interface IMapSpaceByIdExecutor
+public interface IMapSpaceByIdExecutor extends IMapObjectByIdExecutor<ISpaceId, SpacePE>
{
- public Map<ISpaceId, SpacePE> map(IOperationContext context, Collection<? extends ISpaceId> spaceIds);
-
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/space/ListSpaceByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/space/ListSpaceByIdExecutor.java
index 44eb78d7fd6..297c21cbec2 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/space/ListSpaceByIdExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/space/ListSpaceByIdExecutor.java
@@ -16,15 +16,11 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.space;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import java.util.Map;
-
import org.springframework.beans.factory.annotation.Autowired;
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.common.AbstractListObjectByIdExecutor;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.IMapObjectByIdExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.space.ISpaceId;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
@@ -32,7 +28,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
* @author pkupczyk
*/
@Component
-public class ListSpaceByIdExecutor implements IListSpaceByIdExecutor
+public class ListSpaceByIdExecutor extends AbstractListObjectByIdExecutor<ISpaceId, SpacePE> implements IListSpaceByIdExecutor
{
@Autowired
@@ -49,10 +45,9 @@ public class ListSpaceByIdExecutor implements IListSpaceByIdExecutor
}
@Override
- public List<SpacePE> list(IOperationContext context, Collection<? extends ISpaceId> spaceIds)
+ protected IMapObjectByIdExecutor<ISpaceId, SpacePE> getMapExecutor()
{
- Map<ISpaceId, SpacePE> map = mapSpaceByIdExecutor.map(context, spaceIds);
- return new ArrayList<SpacePE>(map.values());
+ return mapSpaceByIdExecutor;
}
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/space/MapSpaceByIdExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/space/MapSpaceByIdExecutor.java
index 6d375101c52..12df18578a2 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/space/MapSpaceByIdExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/space/MapSpaceByIdExecutor.java
@@ -16,66 +16,53 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.space;
-import java.util.Collection;
-import java.util.LinkedHashMap;
import java.util.LinkedList;
import java.util.List;
-import java.util.Map;
import org.springframework.beans.factory.annotation.Autowired;
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.translator.collection.ListTranslator;
-import ch.ethz.sis.openbis.generic.server.api.v3.translator.id.space.ISpaceIdTranslator;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.AbstractMapObjectByIdExecutor;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.IListObjectById;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.space.ListSpaceByPermId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.space.ISpaceId;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.IListerById;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.ListerById;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.space.ListerBySpacePermIdId;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISpaceDAO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
/**
* @author pkupczyk
*/
@Component
-public class MapSpaceByIdExecutor implements IMapSpaceByIdExecutor
+public class MapSpaceByIdExecutor extends AbstractMapObjectByIdExecutor<ISpaceId, SpacePE> implements IMapSpaceByIdExecutor
{
- @Autowired
- private IDAOFactory daoFactory;
+ private ISpaceDAO spaceDAO;
@SuppressWarnings("unused")
private MapSpaceByIdExecutor()
{
}
- public MapSpaceByIdExecutor(IDAOFactory daoFactory)
+ public MapSpaceByIdExecutor(ISpaceDAO spaceDAO)
{
- this.daoFactory = daoFactory;
+ this.spaceDAO = spaceDAO;
}
@Override
- public Map<ISpaceId, SpacePE> map(IOperationContext context, Collection<? extends ISpaceId> spaceIds)
+ protected List<IListObjectById<? extends ISpaceId, SpacePE>> createListers(IOperationContext context)
{
- List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.space.ISpaceId> spaceIdsCore =
- new ListTranslator().translate(spaceIds, new ISpaceIdTranslator());
-
- @SuppressWarnings("rawtypes")
- List<IListerById> listers = new LinkedList<IListerById>();
- listers.add(new ListerBySpacePermIdId(daoFactory));
-
- List<SpacePE> list = new ListerById(listers).list(spaceIdsCore);
- Map<ISpaceId, SpacePE> map = new LinkedHashMap<ISpaceId, SpacePE>();
- int index = 0;
-
- for (ISpaceId spaceId : spaceIds)
- {
- map.put(spaceId, list.get(index));
- index++;
- }
+ List<IListObjectById<? extends ISpaceId, SpacePE>> listers =
+ new LinkedList<IListObjectById<? extends ISpaceId, SpacePE>>();
+ listers.add(new ListSpaceByPermId(spaceDAO));
+ return listers;
+ }
- return map;
+ @Autowired
+ private void setDAOFactory(IDAOFactory daoFactory)
+ {
+ spaceDAO = daoFactory.getSpaceDAO();
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/IListerById.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/common/IListObjectById.java
similarity index 68%
rename from openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/IListerById.java
rename to openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/common/IListObjectById.java
index 984c74cff54..dd628a61dc3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/IListerById.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/common/IListObjectById.java
@@ -1,5 +1,5 @@
/*
- * Copyright 2013 ETH Zuerich, CISD
+ * 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.
@@ -14,20 +14,20 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.generic.server.business.search.id;
+package ch.ethz.sis.openbis.generic.server.api.v3.helper.common;
import java.util.List;
/**
* @author pkupczyk
*/
-public interface IListerById<I, O>
+public interface IListObjectById<ID, OBJECT>
{
- public Class<I> getIdClass();
+ public Class<ID> getIdClass();
- public I createId(O object);
+ public ID createId(OBJECT entity);
- public List<O> listByIds(List<I> ids);
+ public List<OBJECT> listByIds(List<ID> ids);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/ListerById.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/common/MapObjectById.java
similarity index 51%
rename from openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/ListerById.java
rename to openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/common/MapObjectById.java
index 411c1ff996a..8ba3cc25da0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/ListerById.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/common/MapObjectById.java
@@ -14,33 +14,25 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.generic.server.business.search.id;
+package ch.ethz.sis.openbis.generic.server.api.v3.helper.common;
import java.util.Collection;
import java.util.HashMap;
-import java.util.HashSet;
+import java.util.LinkedHashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
-import java.util.Set;
-import ch.systemsx.cisd.common.collection.CollectionUtils;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.IObjectId;
+import ch.ethz.sis.openbis.generic.shared.api.v3.exceptions.UnsupportedObjectIdException;
/**
* @author pkupczyk
*/
@SuppressWarnings({ "rawtypes", "unchecked" })
-public class ListerById
+public class MapObjectById<ID, OBJECT>
{
- private List<IListerById> listers;
-
- public ListerById(List<IListerById> listers)
- {
- this.listers = listers;
- }
-
private Map<Class, List> groupIdsByClass(Collection ids)
{
Map<Class, List> idClassToIdListMap =
@@ -48,11 +40,16 @@ public class ListerById
for (Object id : ids)
{
- List<Object> idList = idClassToIdListMap.get(id.getClass());
+ if (id == null)
+ {
+ continue;
+ }
+
+ List idList = idClassToIdListMap.get(id.getClass());
if (idList == null)
{
- idList = new LinkedList<Object>();
+ idList = new LinkedList<ID>();
idClassToIdListMap.put(id.getClass(), idList);
}
@@ -61,44 +58,59 @@ public class ListerById
return idClassToIdListMap;
}
- private Map<Object, Object> listByIds(Map<Class, List> idClassToIdListMap)
+ private Map mapByIds(List<IListObjectById<? extends ID, OBJECT>> listers, Map<Class, List> idClassToIdListMap)
{
- final Map<Object, Object> idToObject = new HashMap<Object, Object>();
-
- final Set unmatchedIds = new HashSet();
+ final Map idToObject = new HashMap();
for (Class idClass : idClassToIdListMap.keySet())
{
List idList = idClassToIdListMap.get(idClass);
+ IListObjectById listerForIdClass = null;
- for (IListerById lister : listers)
+ for (IListObjectById lister : listers)
{
if (lister.getIdClass().equals(idClass))
{
- HashSet idSet = new HashSet(idList);
+ listerForIdClass = lister;
+ }
+ }
- List objects = lister.listByIds(idList);
+ if (listerForIdClass == null)
+ {
+ throw new UnsupportedObjectIdException((IObjectId) idList.iterator().next());
+ } else
+ {
+ List objects = listerForIdClass.listByIds(idList);
+ if (objects != null)
+ {
for (Object object : objects)
{
- Object createId = lister.createId(object);
+ Object createId = listerForIdClass.createId(object);
idToObject.put(createId, object);
- idSet.remove(createId);
}
- unmatchedIds.addAll(idSet);
}
}
}
- if (unmatchedIds.isEmpty() == false)
- {
- throw new UserFailureException("Unknown ids " + CollectionUtils.abbreviate(unmatchedIds, 200));
- }
+
return idToObject;
}
- public <T> List<T> list(Collection ids)
+ public Map<ID, OBJECT> map(List<IListObjectById<? extends ID, OBJECT>> listers, Collection<? extends ID> ids)
{
Map<Class, List> idClassToIdListMap = groupIdsByClass(ids);
- Map<Object, Object> idToObjectMap = listByIds(idClassToIdListMap);
- return CollectionUtils.map(ids, idToObjectMap);
+ Map idToObjectMap = mapByIds(listers, idClassToIdListMap);
+ Map orderedMap = new LinkedHashMap();
+
+ for (ID id : ids)
+ {
+ Object object = idToObjectMap.get(id);
+ if (object != null)
+ {
+ orderedMap.put(id, object);
+ }
+ }
+
+ return orderedMap;
}
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/entitytype/ListerByEntityTypePermIdId.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/entity/ListEntityTypeByPermId.java
similarity index 64%
rename from openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/entitytype/ListerByEntityTypePermIdId.java
rename to openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/entity/ListEntityTypeByPermId.java
index 6bb26478615..9a18acaec2a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/entitytype/ListerByEntityTypePermIdId.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/entity/ListEntityTypeByPermId.java
@@ -14,49 +14,49 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.generic.server.business.search.id.entitytype;
+package ch.ethz.sis.openbis.generic.server.api.v3.helper.entity;
import java.util.LinkedList;
import java.util.List;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.IListerById;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.IListObjectById;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.entitytype.EntityTypePermId;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.entitytype.EntityTypePermIdId;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
/**
* @author pkupczyk
*/
-public class ListerByEntityTypePermIdId implements IListerById<EntityTypePermIdId, EntityTypePE>
+public class ListEntityTypeByPermId implements IListObjectById<EntityTypePermId, EntityTypePE>
{
private IEntityTypeDAO entityTypeDAO;
- public ListerByEntityTypePermIdId(IDAOFactory daoFactory, EntityKind entityKind)
+ public ListEntityTypeByPermId(IDAOFactory daoFactory, EntityKind entityKind)
{
this.entityTypeDAO = daoFactory.getEntityTypeDAO(entityKind);
}
@Override
- public Class<EntityTypePermIdId> getIdClass()
+ public Class<EntityTypePermId> getIdClass()
{
- return EntityTypePermIdId.class;
+ return EntityTypePermId.class;
}
@Override
- public EntityTypePermIdId createId(EntityTypePE entityType)
+ public EntityTypePermId createId(EntityTypePE entityType)
{
- return new EntityTypePermIdId(entityType.getCode());
+ return new EntityTypePermId(entityType.getCode());
}
@Override
- public List<EntityTypePE> listByIds(List<EntityTypePermIdId> ids)
+ public List<EntityTypePE> listByIds(List<EntityTypePermId> ids)
{
List<String> permIds = new LinkedList<String>();
- for (EntityTypePermIdId id : ids)
+ for (EntityTypePermId id : ids)
{
permIds.add(id.getPermId());
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/experiment/ListerByExperimentPermIdId.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/experiment/ListExperimentByPermId.java
similarity index 56%
rename from openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/experiment/ListerByExperimentPermIdId.java
rename to openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/experiment/ListExperimentByPermId.java
index 7e6213f8d07..3879590d418 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/experiment/ListerByExperimentPermIdId.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/experiment/ListExperimentByPermId.java
@@ -14,48 +14,47 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.generic.server.business.search.id.experiment;
+package ch.ethz.sis.openbis.generic.server.api.v3.helper.experiment;
import java.util.LinkedList;
import java.util.List;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.IListerById;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.IListObjectById;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.ExperimentPermId;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.experiment.ExperimentPermIdId;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
/**
* @author pkupczyk
*/
-public class ListerByExperimentPermIdId implements IListerById<ExperimentPermIdId, ExperimentPE>
+public class ListExperimentByPermId implements IListObjectById<ExperimentPermId, ExperimentPE>
{
private IExperimentDAO experimentDAO;
- public ListerByExperimentPermIdId(IDAOFactory daoFactory)
+ public ListExperimentByPermId(IExperimentDAO experimentDAO)
{
- this.experimentDAO = daoFactory.getExperimentDAO();
+ this.experimentDAO = experimentDAO;
}
@Override
- public Class<ExperimentPermIdId> getIdClass()
+ public Class<ExperimentPermId> getIdClass()
{
- return ExperimentPermIdId.class;
+ return ExperimentPermId.class;
}
@Override
- public ExperimentPermIdId createId(ExperimentPE experiment)
+ public ExperimentPermId createId(ExperimentPE experiment)
{
- return new ExperimentPermIdId(experiment.getPermId());
+ return new ExperimentPermId(experiment.getPermId());
}
@Override
- public List<ExperimentPE> listByIds(List<ExperimentPermIdId> ids)
+ public List<ExperimentPE> listByIds(List<ExperimentPermId> ids)
{
List<String> permIds = new LinkedList<String>();
- for (ExperimentPermIdId id : ids)
+ for (ExperimentPermId id : ids)
{
permIds.add(id.getPermId());
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/project/ListProjectByIdentifier.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/project/ListProjectByIdentifier.java
new file mode 100644
index 00000000000..48b330470b5
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/project/ListProjectByIdentifier.java
@@ -0,0 +1,67 @@
+/*
+ * 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.helper.project;
+
+import java.util.LinkedList;
+import java.util.List;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.IListObjectById;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.ProjectIdentifier;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProjectDAO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
+
+/**
+ * @author pkupczyk
+ */
+public class ListProjectByIdentifier implements IListObjectById<ProjectIdentifier, ProjectPE>
+{
+
+ private IProjectDAO projectDAO;
+
+ public ListProjectByIdentifier(IProjectDAO projectDAO)
+ {
+ this.projectDAO = projectDAO;
+ }
+
+ @Override
+ public Class<ProjectIdentifier> getIdClass()
+ {
+ return ProjectIdentifier.class;
+ }
+
+ @Override
+ public ProjectIdentifier createId(ProjectPE project)
+ {
+ return new ProjectIdentifier(project.getIdentifier());
+ }
+
+ @Override
+ public List<ProjectPE> listByIds(List<ProjectIdentifier> ids)
+ {
+ List<ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier> identifiers =
+ new LinkedList<ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier>();
+
+ for (ProjectIdentifier id : ids)
+ {
+ identifiers.add(ProjectIdentifierFactory.parse(id.getIdentifier()));
+ }
+
+ return projectDAO.tryFindProjects(identifiers);
+ }
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/project/ListProjectByPermId.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/project/ListProjectByPermId.java
new file mode 100644
index 00000000000..41d853fdf5f
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/project/ListProjectByPermId.java
@@ -0,0 +1,65 @@
+/*
+ * Copyright 2013 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.helper.project;
+
+import java.util.LinkedList;
+import java.util.List;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.IListObjectById;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.ProjectPermId;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProjectDAO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
+
+/**
+ * @author pkupczyk
+ */
+public class ListProjectByPermId implements IListObjectById<ProjectPermId, ProjectPE>
+{
+
+ private IProjectDAO projectDAO;
+
+ public ListProjectByPermId(IProjectDAO projectDAO)
+ {
+ this.projectDAO = projectDAO;
+ }
+
+ @Override
+ public Class<ProjectPermId> getIdClass()
+ {
+ return ProjectPermId.class;
+ }
+
+ @Override
+ public ProjectPermId createId(ProjectPE project)
+ {
+ return new ProjectPermId(project.getPermId());
+ }
+
+ @Override
+ public List<ProjectPE> listByIds(List<ProjectPermId> ids)
+ {
+ List<String> permIds = new LinkedList<String>();
+
+ for (ProjectPermId id : ids)
+ {
+ permIds.add(id.getPermId());
+ }
+
+ return projectDAO.listByPermID(permIds);
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/sample/ListerBySampleIdentifierId.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/sample/ListSampleByIdentifier.java
similarity index 81%
rename from openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/sample/ListerBySampleIdentifierId.java
rename to openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/sample/ListSampleByIdentifier.java
index c87599280f7..d2419e79d44 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/sample/ListerBySampleIdentifierId.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/sample/ListSampleByIdentifier.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.generic.server.business.search.id.sample;
+package ch.ethz.sis.openbis.generic.server.api.v3.helper.sample;
import java.util.ArrayList;
import java.util.HashMap;
@@ -23,14 +23,12 @@ import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.IListerById;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.IListObjectById;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISpaceDAO;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.sample.SampleIdentifierId;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
@@ -38,41 +36,41 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
* @author Franz-Josef Elmer
*/
// TODO: neds unit tests
-public class ListerBySampleIdentifierId implements IListerById<SampleIdentifierId, SamplePE>
+public class ListSampleByIdentifier implements IListObjectById<SampleIdentifier, SamplePE>
{
- private ISampleDAO sampleDAO;
-
private ISpaceDAO spaceDAO;
+ private ISampleDAO sampleDAO;
+
private SpacePE homeSpaceOrNull;
- public ListerBySampleIdentifierId(IDAOFactory daoFactory, SpacePE homeSpaceOrNull)
+ public ListSampleByIdentifier(ISpaceDAO spaceDAO, ISampleDAO sampleDAO, SpacePE homeSpaceOrNull)
{
- this.spaceDAO = daoFactory.getSpaceDAO();
- this.sampleDAO = daoFactory.getSampleDAO();
+ this.spaceDAO = spaceDAO;
+ this.sampleDAO = sampleDAO;
this.homeSpaceOrNull = homeSpaceOrNull;
}
@Override
- public Class<SampleIdentifierId> getIdClass()
+ public Class<SampleIdentifier> getIdClass()
{
- return SampleIdentifierId.class;
+ return SampleIdentifier.class;
}
@Override
- public SampleIdentifierId createId(SamplePE sample)
+ public SampleIdentifier createId(SamplePE sample)
{
- return new SampleIdentifierId(sample.getIdentifier());
+ return new SampleIdentifier(sample.getIdentifier());
}
@Override
- public List<SamplePE> listByIds(List<SampleIdentifierId> ids)
+ public List<SamplePE> listByIds(List<SampleIdentifier> ids)
{
- Map<Key, List<String>> sampleCodesBySpaceAndContainer = new HashMap<ListerBySampleIdentifierId.Key, List<String>>();
- for (SampleIdentifierId id : ids)
+ Map<Key, List<String>> sampleCodesBySpaceAndContainer = new HashMap<ListSampleByIdentifier.Key, List<String>>();
+ for (SampleIdentifier id : ids)
{
- SampleIdentifier sid = SampleIdentifierFactory.parse(id.getIdentifier());
+ ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier sid = SampleIdentifierFactory.parse(id.getIdentifier());
if (sid.isDatabaseInstanceLevel())
{
addToMap(sampleCodesBySpaceAndContainer, null, sid);
@@ -116,7 +114,8 @@ public class ListerBySampleIdentifierId implements IListerById<SampleIdentifierI
return result;
}
- private void addToMap(Map<Key, List<String>> sampleCodesBySpaceAndContainer, SpacePE space, SampleIdentifier sampleIdentifier)
+ private void addToMap(Map<Key, List<String>> sampleCodesBySpaceAndContainer, SpacePE space,
+ ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier sampleIdentifier)
{
Key key = new Key(space, sampleIdentifier.tryGetContainerCode());
List<String> list = sampleCodesBySpaceAndContainer.get(key);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/sample/ListerBySamplePermIdId.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/sample/ListSampleByPermId.java
similarity index 58%
rename from openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/sample/ListerBySamplePermIdId.java
rename to openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/sample/ListSampleByPermId.java
index 478e6186928..3465a85b474 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/sample/ListerBySamplePermIdId.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/sample/ListSampleByPermId.java
@@ -14,48 +14,47 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.generic.server.business.search.id.sample;
+package ch.ethz.sis.openbis.generic.server.api.v3.helper.sample;
import java.util.LinkedList;
import java.util.List;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.IListerById;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.IListObjectById;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.SamplePermId;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.sample.SamplePermIdId;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
/**
* @author pkupczyk
*/
-public class ListerBySamplePermIdId implements IListerById<SamplePermIdId, SamplePE>
+public class ListSampleByPermId implements IListObjectById<SamplePermId, SamplePE>
{
private ISampleDAO sampleDAO;
- public ListerBySamplePermIdId(IDAOFactory daoFactory)
+ public ListSampleByPermId(ISampleDAO sampleDAO)
{
- this.sampleDAO = daoFactory.getSampleDAO();
+ this.sampleDAO = sampleDAO;
}
@Override
- public Class<SamplePermIdId> getIdClass()
+ public Class<SamplePermId> getIdClass()
{
- return SamplePermIdId.class;
+ return SamplePermId.class;
}
@Override
- public SamplePermIdId createId(SamplePE sample)
+ public SamplePermId createId(SamplePE sample)
{
- return new SamplePermIdId(sample.getPermId());
+ return new SamplePermId(sample.getPermId());
}
@Override
- public List<SamplePE> listByIds(List<SamplePermIdId> ids)
+ public List<SamplePE> listByIds(List<SamplePermId> ids)
{
List<String> permIds = new LinkedList<String>();
- for (SamplePermIdId id : ids)
+ for (SamplePermId id : ids)
{
permIds.add(id.getPermId());
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/space/ListerBySpacePermIdId.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/space/ListSpaceByPermId.java
similarity index 59%
rename from openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/space/ListerBySpacePermIdId.java
rename to openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/space/ListSpaceByPermId.java
index c406e07bb9b..d4531e3edc3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/space/ListerBySpacePermIdId.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/helper/space/ListSpaceByPermId.java
@@ -14,48 +14,47 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.generic.server.business.search.id.space;
+package ch.ethz.sis.openbis.generic.server.api.v3.helper.space;
import java.util.LinkedList;
import java.util.List;
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.IListerById;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.IListObjectById;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.space.SpacePermId;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISpaceDAO;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.space.SpacePermIdId;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
/**
* @author pkupczyk
*/
-public class ListerBySpacePermIdId implements IListerById<SpacePermIdId, SpacePE>
+public class ListSpaceByPermId implements IListObjectById<SpacePermId, SpacePE>
{
private ISpaceDAO spaceDAO;
- public ListerBySpacePermIdId(IDAOFactory daoFactory)
+ public ListSpaceByPermId(ISpaceDAO spaceDAO)
{
- this.spaceDAO = daoFactory.getSpaceDAO();
+ this.spaceDAO = spaceDAO;
}
@Override
- public Class<SpacePermIdId> getIdClass()
+ public Class<SpacePermId> getIdClass()
{
- return SpacePermIdId.class;
+ return SpacePermId.class;
}
@Override
- public SpacePermIdId createId(SpacePE space)
+ public SpacePermId createId(SpacePE space)
{
- return new SpacePermIdId(space.getCode());
+ return new SpacePermId(space.getCode());
}
@Override
- public List<SpacePE> listByIds(List<SpacePermIdId> ids)
+ public List<SpacePE> listByIds(List<SpacePermId> ids)
{
List<String> permIds = new LinkedList<String>();
- for (SpacePermIdId id : ids)
+ for (SpacePermId id : ids)
{
permIds.add(id.getPermId());
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/entitytype/EntityTypePermIdTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/entitytype/EntityTypePermIdTranslator.java
deleted file mode 100644
index 667b1d96a25..00000000000
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/entitytype/EntityTypePermIdTranslator.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2013 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.translator.id.entitytype;
-
-import ch.ethz.sis.openbis.generic.server.api.v3.translator.AbstractTranslator;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.entitytype.EntityTypePermId;
-
-/**
- * @author pkupczyk
- */
-public class EntityTypePermIdTranslator extends
- AbstractTranslator<EntityTypePermId, ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.entitytype.EntityTypePermIdId>
-{
-
- @Override
- protected ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.entitytype.EntityTypePermIdId doTranslate(EntityTypePermId id)
- {
- return new ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.entitytype.EntityTypePermIdId(id.getPermId());
- }
-
-}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/entitytype/IEntityTypeIdTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/entitytype/IEntityTypeIdTranslator.java
deleted file mode 100644
index e8496fdbd64..00000000000
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/entitytype/IEntityTypeIdTranslator.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Copyright 2013 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.translator.id.entitytype;
-
-import ch.ethz.sis.openbis.generic.server.api.v3.translator.AbstractTranslator;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.entitytype.EntityTypePermId;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.entitytype.IEntityTypeId;
-import ch.ethz.sis.openbis.generic.shared.api.v3.exceptions.UnsupportedObjectIdException;
-
-/**
- * @author pkupczyk
- */
-public class IEntityTypeIdTranslator extends
- AbstractTranslator<IEntityTypeId, ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.entitytype.IEntityTypeId>
-{
-
- @Override
- protected ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.entitytype.IEntityTypeId doTranslate(IEntityTypeId id)
- {
- if (id instanceof EntityTypePermId)
- {
- return new EntityTypePermIdTranslator().translate((EntityTypePermId) id);
- } else
- {
- throw new UnsupportedObjectIdException(id);
- }
- }
-
-}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/experiment/ExperimentIdentifierIdTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/experiment/ExperimentIdentifierIdTranslator.java
deleted file mode 100644
index 908d09a8343..00000000000
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/experiment/ExperimentIdentifierIdTranslator.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2013 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.translator.id.experiment;
-
-import ch.ethz.sis.openbis.generic.server.api.v3.translator.AbstractTranslator;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.ExperimentIdentifier;
-
-/**
- * @author pkupczyk
- */
-public class ExperimentIdentifierIdTranslator extends
- AbstractTranslator<ExperimentIdentifier, ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.experiment.ExperimentIdentifierId>
-{
-
- @Override
- protected ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.experiment.ExperimentIdentifierId doTranslate(ExperimentIdentifier id)
- {
- return new ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.experiment.ExperimentIdentifierId(id.getIdentifier());
- }
-
-}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/experiment/ExperimentPermIdTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/experiment/ExperimentPermIdTranslator.java
deleted file mode 100644
index 392927a720d..00000000000
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/experiment/ExperimentPermIdTranslator.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2013 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.translator.id.experiment;
-
-import ch.ethz.sis.openbis.generic.server.api.v3.translator.AbstractTranslator;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.ExperimentPermId;
-
-/**
- * @author pkupczyk
- */
-public class ExperimentPermIdTranslator extends
- AbstractTranslator<ExperimentPermId, ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.experiment.ExperimentPermIdId>
-{
-
- @Override
- protected ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.experiment.ExperimentPermIdId doTranslate(ExperimentPermId id)
- {
- return new ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.experiment.ExperimentPermIdId(id.getPermId());
- }
-
-}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/experiment/IExperimentIdTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/experiment/IExperimentIdTranslator.java
deleted file mode 100644
index 0820261ab30..00000000000
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/experiment/IExperimentIdTranslator.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * Copyright 2013 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.translator.id.experiment;
-
-import ch.ethz.sis.openbis.generic.server.api.v3.translator.AbstractTranslator;
-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.ExperimentIdentifier;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.IExperimentId;
-import ch.ethz.sis.openbis.generic.shared.api.v3.exceptions.UnsupportedObjectIdException;
-
-/**
- * @author pkupczyk
- */
-public class IExperimentIdTranslator extends
- AbstractTranslator<IExperimentId, ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.experiment.IExperimentId>
-{
-
- @Override
- protected ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.experiment.IExperimentId doTranslate(
- IExperimentId id)
- {
- if (id instanceof ExperimentPermId)
- {
- return new ExperimentPermIdTranslator().translate((ExperimentPermId) id);
- } else if (id instanceof ExperimentIdentifier)
- {
- return new ExperimentIdentifierIdTranslator().translate((ExperimentIdentifier) id);
- } else
- {
- throw new UnsupportedObjectIdException(id);
- }
- }
-
-}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/sample/ISampleIdTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/sample/ISampleIdTranslator.java
deleted file mode 100644
index 57472b974b7..00000000000
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/sample/ISampleIdTranslator.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * Copyright 2013 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.translator.id.sample;
-
-import ch.ethz.sis.openbis.generic.server.api.v3.translator.AbstractTranslator;
-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.SamplePermId;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.SampleIdentifier;
-import ch.ethz.sis.openbis.generic.shared.api.v3.exceptions.UnsupportedObjectIdException;
-
-/**
- * @author pkupczyk
- */
-public class ISampleIdTranslator extends
- AbstractTranslator<ISampleId, ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.sample.ISampleId>
-{
-
- @Override
- protected ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.sample.ISampleId doTranslate(
- ISampleId id)
- {
- if (id instanceof SamplePermId)
- {
- return new SamplePermIdTranslator().translate((SamplePermId) id);
- } else if (id instanceof SampleIdentifier)
- {
- return new SampleIdentifierIdTranslator().translate((SampleIdentifier) id);
- } else
- {
- throw new UnsupportedObjectIdException(id);
- }
- }
-
-}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/sample/SampleIdentifierIdTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/sample/SampleIdentifierIdTranslator.java
deleted file mode 100644
index 6c67eab9d8e..00000000000
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/sample/SampleIdentifierIdTranslator.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2013 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.translator.id.sample;
-
-import ch.ethz.sis.openbis.generic.server.api.v3.translator.AbstractTranslator;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.SampleIdentifier;
-
-/**
- * @author pkupczyk
- */
-public class SampleIdentifierIdTranslator extends
- AbstractTranslator<SampleIdentifier, ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.sample.SampleIdentifierId>
-{
-
- @Override
- protected ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.sample.SampleIdentifierId doTranslate(SampleIdentifier id)
- {
- return new ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.sample.SampleIdentifierId(id.getIdentifier());
- }
-
-}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/sample/SamplePermIdTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/sample/SamplePermIdTranslator.java
deleted file mode 100644
index 674aaf48ba6..00000000000
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/sample/SamplePermIdTranslator.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2013 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.translator.id.sample;
-
-import ch.ethz.sis.openbis.generic.server.api.v3.translator.AbstractTranslator;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.SamplePermId;
-
-/**
- * @author pkupczyk
- */
-public class SamplePermIdTranslator extends
- AbstractTranslator<SamplePermId, ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.sample.SamplePermIdId>
-{
-
- @Override
- protected ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.sample.SamplePermIdId doTranslate(SamplePermId id)
- {
- return new ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.sample.SamplePermIdId(id.getPermId());
- }
-
-}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/space/ISpaceIdTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/space/ISpaceIdTranslator.java
deleted file mode 100644
index ea431e4f56a..00000000000
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/space/ISpaceIdTranslator.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * Copyright 2013 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.translator.id.space;
-
-import ch.ethz.sis.openbis.generic.server.api.v3.translator.AbstractTranslator;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.space.ISpaceId;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.space.SpacePermId;
-import ch.ethz.sis.openbis.generic.shared.api.v3.exceptions.UnsupportedObjectIdException;
-
-/**
- * @author pkupczyk
- */
-public class ISpaceIdTranslator extends
- AbstractTranslator<ISpaceId, ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.space.ISpaceId>
-{
-
- @Override
- protected ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.space.ISpaceId doTranslate(
- ISpaceId id)
- {
- if (id instanceof SpacePermId)
- {
- return new SpacePermIdTranslator().translate((SpacePermId) id);
- } else
- {
- throw new UnsupportedObjectIdException(id);
- }
- }
-
-}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/space/SpacePermIdTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/space/SpacePermIdTranslator.java
deleted file mode 100644
index d5e55ab91fd..00000000000
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/translator/id/space/SpacePermIdTranslator.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2013 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.translator.id.space;
-
-import ch.ethz.sis.openbis.generic.server.api.v3.translator.AbstractTranslator;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.space.SpacePermId;
-
-/**
- * @author pkupczyk
- */
-public class SpacePermIdTranslator extends
- AbstractTranslator<SpacePermId, ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.space.SpacePermIdId>
-{
-
- @Override
- protected ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.space.SpacePermIdId doTranslate(SpacePermId id)
- {
- return new ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.space.SpacePermIdId(id.getPermId());
- }
-
-}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/validator/entity/experiment/ExperimentValidator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/validator/entity/experiment/ExperimentValidator.java
deleted file mode 100644
index 728c5c451ba..00000000000
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/validator/entity/experiment/ExperimentValidator.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * Copyright 2013 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.validator.entity.experiment;
-
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.experiment.Experiment;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.AbstractValidator;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.ExperimentByIdentiferValidator;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IIdentifierHolder;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
-
-/**
- * @author pkupczyk
- */
-public class ExperimentValidator extends AbstractValidator<Experiment>
-{
-
- private ExperimentByIdentiferValidator validator = new ExperimentByIdentiferValidator();
-
- @Override
- public boolean doValidation(final PersonPE person, final Experiment experiment)
- {
- return validator.doValidation(person, new IIdentifierHolder()
- {
- @Override
- public String getIdentifier()
- {
- return experiment.getIdentifier().getIdentifier();
- }
- });
- }
-
-}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/validator/entity/sample/.gitignore b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/validator/entity/sample/.gitignore
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/experiment/ListerByExperimentTechIdId.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/experiment/ListerByExperimentTechIdId.java
deleted file mode 100644
index 7fe3bc8c8fb..00000000000
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/experiment/ListerByExperimentTechIdId.java
+++ /dev/null
@@ -1,66 +0,0 @@
-/*
- * Copyright 2013 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.search.id.experiment;
-
-import java.util.LinkedList;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.IListerById;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.experiment.ExperimentTechIdId;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-
-/**
- * @author pkupczyk
- */
-public class ListerByExperimentTechIdId implements IListerById<ExperimentTechIdId, ExperimentPE>
-{
-
- private IExperimentDAO experimentDAO;
-
- public ListerByExperimentTechIdId(IDAOFactory daoFactory)
- {
- this.experimentDAO = daoFactory.getExperimentDAO();
- }
-
- @Override
- public Class<ExperimentTechIdId> getIdClass()
- {
- return ExperimentTechIdId.class;
- }
-
- @Override
- public ExperimentTechIdId createId(ExperimentPE experiment)
- {
- return new ExperimentTechIdId(experiment.getId());
- }
-
- @Override
- public List<ExperimentPE> listByIds(List<ExperimentTechIdId> ids)
- {
- List<Long> techIds = new LinkedList<Long>();
-
- for (ExperimentTechIdId id : ids)
- {
- techIds.add(id.getTechId());
- }
-
- return experimentDAO.listByIDs(techIds);
- }
-
-}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/sample/ListerBySampleTechIdId.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/sample/ListerBySampleTechIdId.java
deleted file mode 100644
index f1ec0c54bb7..00000000000
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/id/sample/ListerBySampleTechIdId.java
+++ /dev/null
@@ -1,66 +0,0 @@
-/*
- * Copyright 2013 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.search.id.sample;
-
-import java.util.LinkedList;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.server.business.search.id.IListerById;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.id.sample.SampleTechIdId;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
-
-/**
- * @author pkupczyk
- */
-public class ListerBySampleTechIdId implements IListerById<SampleTechIdId, SamplePE>
-{
-
- private ISampleDAO sampleDAO;
-
- public ListerBySampleTechIdId(IDAOFactory daoFactory)
- {
- this.sampleDAO = daoFactory.getSampleDAO();
- }
-
- @Override
- public Class<SampleTechIdId> getIdClass()
- {
- return SampleTechIdId.class;
- }
-
- @Override
- public SampleTechIdId createId(SamplePE sample)
- {
- return new SampleTechIdId(sample.getId());
- }
-
- @Override
- public List<SamplePE> listByIds(List<SampleTechIdId> ids)
- {
- List<Long> techIds = new LinkedList<Long>();
-
- for (SampleTechIdId id : ids)
- {
- techIds.add(id.getTechId());
- }
-
- return sampleDAO.listByIDs(techIds);
- }
-
-}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExperimentDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExperimentDAO.java
index 2341a183ab9..23db41cb42b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExperimentDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExperimentDAO.java
@@ -54,16 +54,16 @@ public interface IExperimentDAO extends IGenericDAO<ExperimentPE>
throws DataAccessException;
/**
- * Lists experiments of specified type, project and space. All criteria are optional. If no
- * criteria is specified all experiments are returned. Fetches also properties.
+ * Lists experiments of specified type, project and space. All criteria are optional. If no criteria is specified all experiments are returned.
+ * Fetches also properties.
*/
public List<ExperimentPE> listExperimentsWithProperties(
final ExperimentTypePE experimentTypeOrNull, final ProjectPE projectOrNull,
final SpacePE spaceOrNull) throws DataAccessException;
/**
- * Lists experiments of specified type, project and space. All criteria are optional. If no
- * criteria is specified all experiments are returned. Fetches also properties.
+ * Lists experiments of specified type, project and space. All criteria are optional. If no criteria is specified all experiments are returned.
+ * Fetches also properties.
*/
public List<ExperimentPE> listExperimentsWithProperties(
final ExperimentTypePE experimentTypeOrNull, final List<ProjectPE> projectsOrNull,
@@ -81,8 +81,8 @@ public interface IExperimentDAO extends IGenericDAO<ExperimentPE>
public ExperimentPE tryFindByCodeAndProject(ProjectPE project, String experimentCode);
/**
- * Lists experiments (with minimal additional information) belonging to the given
- * <code>project</code> and having a property with the specified value.
+ * Lists experiments (with minimal additional information) belonging to the given <code>project</code> and having a property with the specified
+ * value.
*/
public List<ExperimentPE> listExperimentsByProjectAndProperty(final String propertyCode,
final String propertyValue, final ProjectPE project) throws DataAccessException;
@@ -99,13 +99,18 @@ public interface IExperimentDAO extends IGenericDAO<ExperimentPE>
public List<String> getSampleCodes(ExperimentPE experiment);
/**
- * Try to obtain the experiment for the given <var>permId</var>. Returns <code>null</code>, if
- * no experiment with the given perm id exists.
+ * Try to obtain the experiment for the given <var>permId</var>. Returns <code>null</code>, if no experiment with the given perm id exists.
*/
public ExperimentPE tryGetByPermID(String permId);
+ /**
+ * List experiments by perm ids.
+ */
public List<ExperimentPE> listByPermID(Collection<String> permId);
+ /**
+ * List experiments by ids.
+ */
public List<ExperimentPE> listByIDs(Collection<Long> ids);
/**
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IProjectDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IProjectDAO.java
index eccc6445312..255f21b5bf6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IProjectDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IProjectDAO.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.generic.server.dataaccess;
+import java.util.Collection;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
@@ -41,6 +42,16 @@ public interface IProjectDAO extends IGenericDAO<ProjectPE>
*/
public List<ProjectPE> listProjects(SpacePE space);
+ /**
+ * Lists projects by ids.
+ */
+ public List<ProjectPE> listByIDs(Collection<Long> ids);
+
+ /**
+ * Lists projects by perm ids.
+ */
+ public List<ProjectPE> listByPermID(Collection<String> permIds);
+
/**
* Returns project for given perm id or null if such a project does not exist.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ProjectDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ProjectDAO.java
index 8d8dd19b646..0b432f01fea 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ProjectDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ProjectDAO.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.generic.server.dataaccess.db;
+import java.util.ArrayList;
+import java.util.Collection;
import java.util.Date;
import java.util.HashSet;
import java.util.LinkedList;
@@ -135,6 +137,33 @@ public class ProjectDAO extends AbstractGenericEntityDAO<ProjectPE> implements I
return matchingProjects;
}
+ @Override
+ public List<ProjectPE> listByPermID(Collection<String> values)
+ {
+ return listByIDsOfName("permId", values);
+ }
+
+ @Override
+ public List<ProjectPE> listByIDs(Collection<Long> values)
+ {
+ return listByIDsOfName("id", values);
+ }
+
+ private List<ProjectPE> listByIDsOfName(String idName, Collection<?> values)
+ {
+ if (values == null || values.isEmpty())
+ {
+ return new ArrayList<ProjectPE>();
+ }
+ final List<ProjectPE> list =
+ DAOUtils.listByCollection(getHibernateTemplate(), ProjectPE.class, idName, values);
+ if (operationLog.isDebugEnabled())
+ {
+ operationLog.debug(String.format("%d projects(s) have been found.", list.size()));
+ }
+ return list;
+ }
+
@Override
public void createProject(ProjectPE project, PersonPE modifier)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePE.java
index 899fd31ec71..261b2e81def 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SamplePE.java
@@ -811,8 +811,7 @@ public class SamplePE extends AttachmentHolderPE implements IIdAndCodeHolder, Co
return contained;
}
- @SuppressWarnings("unused")
- private void setContained(List<SamplePE> contained)
+ public void setContained(List<SamplePE> contained)
{
this.contained = contained;
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/MapExperimentByIdExecutorTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/MapExperimentByIdExecutorTest.java
index fed01f37867..81ffba2879f 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/MapExperimentByIdExecutorTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/MapExperimentByIdExecutorTest.java
@@ -67,9 +67,6 @@ public class MapExperimentByIdExecutorTest extends AbstractExecutorTest
context.checking(new Expectations()
{
{
- allowing(daoFactory).getExperimentDAO();
- will(returnValue(experimentDao));
-
one(experimentDao).listByPermID(Arrays.asList(permId1.getPermId(), permId2.getPermId(), permId3.getPermId()));
will(returnValue(Arrays.asList(experiment2, experiment1, experiment3)));
}
@@ -85,7 +82,7 @@ public class MapExperimentByIdExecutorTest extends AbstractExecutorTest
private Map<IExperimentId, ExperimentPE> execute(IExperimentId... experimentIds)
{
- MapExperimentByIdExecutor executor = new MapExperimentByIdExecutor(daoFactory);
+ MapExperimentByIdExecutor executor = new MapExperimentByIdExecutor(experimentDao);
return executor.map(operationContext, Arrays.asList(experimentIds));
}
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/MapProjectByIdExecutorTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/MapProjectByIdExecutorTest.java
new file mode 100644
index 00000000000..445916d0662
--- /dev/null
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/MapProjectByIdExecutorTest.java
@@ -0,0 +1,157 @@
+/*
+ * 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.project;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Map;
+
+import junit.framework.Assert;
+
+import org.jmock.Expectations;
+import org.testng.annotations.Test;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.AbstractExecutorTest;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.IProjectId;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.ProjectIdentifier;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.ProjectPermId;
+import ch.ethz.sis.openbis.generic.shared.api.v3.exceptions.UnsupportedObjectIdException;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProjectDAO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
+
+/**
+ * @author pkupczyk
+ */
+public class MapProjectByIdExecutorTest extends AbstractExecutorTest
+{
+
+ private IProjectDAO projectDao;
+
+ @Override
+ protected void init()
+ {
+ projectDao = context.mock(IProjectDAO.class);
+ }
+
+ @Test
+ public void testGetByPermId()
+ {
+ final ProjectPE project = new ProjectPE();
+ project.setId(123L);
+ project.setPermId("TEST_PERM_ID");
+ final ProjectPermId permId = new ProjectPermId(project.getPermId());
+
+ context.checking(new Expectations()
+ {
+ {
+ one(projectDao).listByPermID(Collections.singletonList(project.getPermId()));
+ will(returnValue(Collections.singletonList(project)));
+ }
+ });
+
+ Map<IProjectId, ProjectPE> result = execute(permId);
+ Assert.assertEquals(1, result.size());
+ Assert.assertEquals(Long.valueOf(123L), result.get(permId).getId());
+ }
+
+ @Test
+ public void testGetByPermIdNonexistent()
+ {
+ final ProjectPermId permId = new ProjectPermId("NONEXISTENT_PROJECT");
+
+ context.checking(new Expectations()
+ {
+ {
+ one(projectDao).listByPermID(Collections.singletonList(permId.getPermId()));
+ will(returnValue(null));
+ }
+ });
+
+ Map<IProjectId, ProjectPE> result = execute(permId);
+ Assert.assertNotNull(result);
+ Assert.assertEquals(0, result.size());
+ }
+
+ @Test
+ public void testGetByIdentifier()
+ {
+ final SpacePE space = new SpacePE();
+ space.setCode("TEST_SPACE");
+
+ final ProjectPE project = new ProjectPE();
+ project.setId(123L);
+ project.setCode("TEST_PROJECT");
+ project.setSpace(space);
+
+ final ProjectIdentifier identifier = new ProjectIdentifier("/" + space.getCode() + "/" + project.getCode());
+
+ context.checking(new Expectations()
+ {
+ {
+ one(projectDao).tryFindProjects(
+ Collections.singletonList(new ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier(space.getCode(),
+ project.getCode())));
+ will(returnValue(Collections.singletonList(project)));
+ }
+ });
+
+ Map<IProjectId, ProjectPE> result = execute(identifier);
+ Assert.assertEquals(1, result.size());
+ Assert.assertEquals(Long.valueOf(123L), result.get(identifier).getId());
+ }
+
+ @Test
+ public void testGetByIdentifierNonexistent()
+ {
+ final String spaceCode = "TEST_SPACE";
+ final String projectCode = "NONEXISTENT_PROJECT";
+ final ProjectIdentifier identifier = new ProjectIdentifier("/" + spaceCode + "/" + projectCode);
+
+ context.checking(new Expectations()
+ {
+ {
+ one(projectDao).tryFindProjects(
+ Collections.singletonList(new ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier(spaceCode,
+ projectCode)));
+ will(returnValue(Collections.emptyList()));
+ }
+ });
+
+ Map<IProjectId, ProjectPE> result = execute(identifier);
+ Assert.assertNotNull(result);
+ Assert.assertEquals(0, result.size());
+ }
+
+ @Test(expectedExceptions = { UnsupportedObjectIdException.class })
+ public void testGetByUnknownId()
+ {
+ final IProjectId unknownId = new IProjectId()
+ {
+
+ private static final long serialVersionUID = 1L;
+
+ };
+ execute(unknownId);
+ }
+
+ private Map<IProjectId, ProjectPE> execute(IProjectId... projectIds)
+ {
+ IMapProjectByIdExecutor executor = new MapProjectByIdExecutor(projectDao);
+ return executor.map(operationContext, Arrays.asList(projectIds));
+ }
+}
\ No newline at end of file
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/TryGetProjectByIdExecutorTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/TryGetProjectByIdExecutorTest.java
index 5ca31ad800a..2c35c8d705b 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/TryGetProjectByIdExecutorTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/project/TryGetProjectByIdExecutorTest.java
@@ -16,18 +16,16 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.project;
+import java.util.Collections;
+
import junit.framework.Assert;
import org.jmock.Expectations;
import org.testng.annotations.Test;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.AbstractExecutorTest;
-import ch.ethz.sis.openbis.generic.server.api.v3.executor.project.TryGetProjectByIdExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.IProjectId;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.ProjectIdentifier;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.ProjectPermId;
-import ch.ethz.sis.openbis.generic.shared.api.v3.exceptions.UnsupportedObjectIdException;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProjectDAO;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
/**
@@ -36,16 +34,16 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
public class TryGetProjectByIdExecutorTest extends AbstractExecutorTest
{
- private IProjectDAO projectDao;
+ private IMapProjectByIdExecutor mapExecutor;
@Override
protected void init()
{
- projectDao = context.mock(IProjectDAO.class);
+ mapExecutor = context.mock(IMapProjectByIdExecutor.class);
}
@Test
- public void testGetByPermId()
+ public void testGetExisting()
{
final ProjectPermId permId = new ProjectPermId("TEST_PERM_ID");
final ProjectPE project = new ProjectPE();
@@ -54,8 +52,8 @@ public class TryGetProjectByIdExecutorTest extends AbstractExecutorTest
context.checking(new Expectations()
{
{
- one(projectDao).tryGetByPermID(permId.getPermId());
- will(returnValue(project));
+ one(mapExecutor).map(operationContext, Collections.singletonList(permId));
+ will(returnValue(Collections.singletonMap(permId, project)));
}
});
@@ -64,15 +62,15 @@ public class TryGetProjectByIdExecutorTest extends AbstractExecutorTest
}
@Test
- public void testGetByPermIdNonexistent()
+ public void testGetNonexistent()
{
final ProjectPermId permId = new ProjectPermId("NONEXISTENT_PROJECT");
context.checking(new Expectations()
{
{
- one(projectDao).tryGetByPermID("NONEXISTENT_PROJECT");
- will(returnValue(null));
+ one(mapExecutor).map(operationContext, Collections.singletonList(permId));
+ will(returnValue(Collections.emptyMap()));
}
});
@@ -80,60 +78,9 @@ public class TryGetProjectByIdExecutorTest extends AbstractExecutorTest
Assert.assertNull(result);
}
- @Test
- public void testGetByIdentifier()
- {
- final ProjectIdentifier identifier = new ProjectIdentifier("/TEST_SPACE/TEST_PROJECT");
- final ProjectPE project = new ProjectPE();
- project.setId(123L);
-
- context.checking(new Expectations()
- {
- {
- one(projectDao).tryFindProject("TEST_SPACE", "TEST_PROJECT");
- will(returnValue(project));
- }
- });
-
- ProjectPE result = execute(identifier);
- Assert.assertEquals(Long.valueOf(123L), result.getId());
- }
-
- @Test
- public void testGetByIdentifierNonexistent()
- {
- final ProjectIdentifier identifier = new ProjectIdentifier("/TEST_SPACE/NONEXISTENT_PROJECT");
-
- context.checking(new Expectations()
- {
- {
- one(projectDao).tryFindProject("TEST_SPACE", "NONEXISTENT_PROJECT");
- will(returnValue(null));
- }
- });
-
- ProjectPE result = execute(identifier);
- Assert.assertNull(result);
- }
-
- @Test(expectedExceptions = { UnsupportedObjectIdException.class })
- public void testGetByUnknownId()
- {
- final IProjectId unknownId = new IProjectId()
- {
-
- private static final long serialVersionUID = 1L;
-
- };
- final ProjectPE project = new ProjectPE();
- project.setId(123L);
-
- execute(unknownId);
- }
-
private ProjectPE execute(IProjectId projectId)
{
- TryGetProjectByIdExecutor executor = new TryGetProjectByIdExecutor(projectDao);
+ TryGetProjectByIdExecutor executor = new TryGetProjectByIdExecutor(mapExecutor);
return executor.tryGet(operationContext, projectId);
}
}
\ No newline at end of file
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/ExperimentCreateTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/ExperimentCreateTest.java
index 15443aae166..af6458be30d 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/ExperimentCreateTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/ExperimentCreateTest.java
@@ -40,7 +40,8 @@ import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.ProjectIdentifie
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.ProjectPermId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.tag.ITagId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.tag.TagPermId;
-import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.test.AssertionUtil;
/**
* @author pkupczyk
@@ -48,8 +49,8 @@ import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
public class ExperimentCreateTest extends AbstractExperimentTest
{
- @Test(expectedExceptions = AuthorizationFailureException.class)
- public void testCreateExperimentWithFailedAuthorization()
+ @Test
+ public void testCreateExperimentWithUnauthorizedProject()
{
String sessionToken = v3api.login(TEST_POWER_USER_CISD, PASSWORD);
@@ -58,7 +59,13 @@ public class ExperimentCreateTest extends AbstractExperimentTest
experiment.setTypeId(new EntityTypePermId("SIRNA_HCS"));
experiment.setProjectId(new ProjectIdentifier("/TESTGROUP/TESTPROJ"));
- v3api.createExperiments(sessionToken, Arrays.asList(experiment));
+ try
+ {
+ v3api.createExperiments(sessionToken, Arrays.asList(experiment));
+ } catch (UserFailureException e)
+ {
+ AssertionUtil.assertContains("Authorization failure", e.getMessage());
+ }
}
@Test
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/ExperimentUpdateTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/ExperimentUpdateTest.java
index c4a52205f0f..760f1ca8fa7 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/ExperimentUpdateTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/ExperimentUpdateTest.java
@@ -17,6 +17,7 @@
package ch.ethz.sis.openbis.systemtest.api.v3;
import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.fail;
import java.util.Arrays;
import java.util.List;
@@ -31,6 +32,7 @@ import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.entitytype.EntityTypePer
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.ExperimentPermId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.ProjectIdentifier;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.tag.TagNameId;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.test.AssertionUtil;
/**
@@ -66,10 +68,48 @@ public class ExperimentUpdateTest extends AbstractExperimentTest
Experiment experiment = experiments.get(0);
assertEquals(experiment.getIdentifier().getIdentifier(), "/CISD/NOE/TEST_EXPERIMENT");
}
-
+
+ @Test
+ public void testUpdateExperimentWithUnauthorizedExperiment()
+ {
+ String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ ExperimentUpdate update = new ExperimentUpdate();
+ update.setExperimentId(new ExperimentPermId("200811050951882-1028"));
+
+ try
+ {
+ v3api.updateExperiments(sessionToken, Arrays.asList(update));
+ fail("Expected user failure exception");
+ } catch (UserFailureException e)
+ {
+ AssertionUtil.assertContains("Authorization failure: Cannot access experiment /CISD/NEMO/EXP1", e.getMessage());
+ }
+ }
+
@Test
- public void samplesAreUpdatedWhenNewProjectOfExperimentIsInAnotherSpace() {
-
+ public void testUpdateExperimentWithUnauthorizedProject()
+ {
+ String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ ExperimentUpdate update = new ExperimentUpdate();
+ update.setExperimentId(new ExperimentPermId("200902091255058-1037"));
+ update.setProjectId(new ProjectIdentifier("/CISD/NEMO"));
+
+ try
+ {
+ v3api.updateExperiments(sessionToken, Arrays.asList(update));
+ fail("Expected user failure exception");
+ } catch (UserFailureException e)
+ {
+ AssertionUtil.assertContains("Authorization failure", e.getMessage());
+ }
+ }
+
+ @Test
+ public void samplesAreUpdatedWhenNewProjectOfExperimentIsInAnotherSpace()
+ {
+
}
@Test
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/SampleCreateTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/SampleCreateTest.java
index 5d87bd1857d..ba48fce1f2b 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/SampleCreateTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/SampleCreateTest.java
@@ -38,6 +38,7 @@ import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.tag.Tag;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.fetchoptions.sample.SampleFetchOptions;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.CreationId;
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.sample.SampleIdentifier;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.SamplePermId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.space.SpacePermId;
@@ -393,8 +394,8 @@ public class SampleCreateTest extends AbstractSampleTest
{
String sessionToken = v3api.login(TEST_USER, PASSWORD);
- SampleCreation sc1 = createSimpleSample("SAMPLE_1");
- SampleCreation sc2 = createSimpleSample("SAMPLE_2");
+ SampleCreation sc1 = sampleCreation("SAMPLE_1");
+ SampleCreation sc2 = sampleCreation("SAMPLE_2");
sc2.setContainerId(new SampleIdentifier("/CISD/SAMPLE_1"));
@@ -418,8 +419,8 @@ public class SampleCreateTest extends AbstractSampleTest
{
String sessionToken = v3api.login(TEST_USER, PASSWORD);
- SampleCreation sc1 = createSimpleSample("SAMPLE_1");
- SampleCreation sc2 = createSimpleSample("SAMPLE_2");
+ SampleCreation sc1 = sampleCreation("SAMPLE_1");
+ SampleCreation sc2 = sampleCreation("SAMPLE_2");
sc2.setContainerId(sc1.getCreationId());
@@ -443,9 +444,9 @@ public class SampleCreateTest extends AbstractSampleTest
{
String sessionToken = v3api.login(TEST_USER, PASSWORD);
- SampleCreation sample1 = createSimpleSample("SAMPLE_1");
- SampleCreation sample2 = createSimpleSample("SAMPLE_2");
- SampleCreation sample3 = createSimpleSample("SAMPLE_3");
+ SampleCreation sample1 = sampleCreation("SAMPLE_1");
+ SampleCreation sample2 = sampleCreation("SAMPLE_2");
+ SampleCreation sample3 = sampleCreation("SAMPLE_3");
sample2.setContainerId(sample1.getCreationId());
sample3.setContainerId(sample2.getCreationId());
@@ -465,7 +466,7 @@ public class SampleCreateTest extends AbstractSampleTest
public void testCreateSampleWithoutCode()
{
String sessionToken = v3api.login(TEST_USER, PASSWORD);
- SampleCreation sample = createSimpleSample(null);
+ SampleCreation sample = sampleCreation(null);
try
{
v3api.createSamples(sessionToken, Arrays.asList(sample));
@@ -476,7 +477,126 @@ public class SampleCreateTest extends AbstractSampleTest
}
}
- private SampleCreation createSimpleSample(String code)
+ @Test
+ public void testCreateSampleWithUnauthorizedSpace()
+ {
+ String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ SampleCreation creation = new SampleCreation();
+ creation.setCode("UNAUTHORIZED_SPACE");
+ creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
+ creation.setSpaceId(new SpacePermId("CISD"));
+
+ try
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ fail("Expected user failure exception");
+ } catch (UserFailureException e)
+ {
+ AssertionUtil.assertContains("Authorization failure", e.getMessage());
+ AssertionUtil.assertContains("set space for sample UNAUTHORIZED_SPACE", e.getMessage());
+ }
+ }
+
+ @Test
+ public void testCreateSampleWithUnauthorizedExperiment()
+ {
+ String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ SampleCreation creation = new SampleCreation();
+ creation.setCode("UNAUTHORIZED_EXPERIMENT");
+ creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
+ creation.setSpaceId(new SpacePermId("TEST-SPACE"));
+ creation.setExperimentId(new ExperimentPermId("200811050951882-1028"));
+
+ try
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ fail("Expected user failure exception");
+ } catch (UserFailureException e)
+ {
+ AssertionUtil.assertContains("Authorization failure", e.getMessage());
+ AssertionUtil.assertContains("set experiment for sample UNAUTHORIZED_EXPERIMENT", e.getMessage());
+ }
+ }
+
+ @Test
+ public void testCreateSampleWithUnauthorizedParent()
+ {
+ String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ SampleCreation creation = sampleCreation("TEST-SPACE", "UNAUTHORIZED_PARENT");
+ creation.setParentIds(Collections.singletonList(createCisdSample("PARENT_SAMPLE")));
+
+ try
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ fail("Expected user failure exception");
+ } catch (UserFailureException e)
+ {
+ AssertionUtil.assertContains("Authorization failure", e.getMessage());
+ AssertionUtil.assertContains("set parents for sample UNAUTHORIZED_PARENT", e.getMessage());
+ }
+ }
+
+ @Test
+ public void testCreateSampleWithUnauthorizedChild()
+ {
+ String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ SampleCreation creation = sampleCreation("TEST-SPACE", "UNAUTHORIZED_CHILD");
+ creation.setChildIds(Collections.singletonList(createCisdSample("CHILD_SAMPLE")));
+
+ try
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ fail("Expected user failure exception");
+ } catch (UserFailureException e)
+ {
+ AssertionUtil.assertContains("Authorization failure", e.getMessage());
+ AssertionUtil.assertContains("set children for sample UNAUTHORIZED_CHILD", e.getMessage());
+ }
+ }
+
+ @Test
+ public void testCreateSampleWithUnauthorizedContainer()
+ {
+ String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ SampleCreation creation = sampleCreation("TEST-SPACE", "UNAUTHORIZED_CONTAINER");
+ creation.setContainerId(createCisdSample("CONTAINER_SAMPLE"));
+
+ try
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ fail("Expected user failure exception");
+ } catch (UserFailureException e)
+ {
+ AssertionUtil.assertContains("Authorization failure", e.getMessage());
+ AssertionUtil.assertContains("set container for sample UNAUTHORIZED_CONTAINER", e.getMessage());
+ }
+ }
+
+ @Test
+ public void testCreateSampleWithUnauthorizedContained()
+ {
+ String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ SampleCreation creation = sampleCreation("TEST-SPACE", "UNAUTHORIZED_CONTAINED");
+ creation.setContainedIds(Collections.singletonList(createCisdSample("CONTAINED_SAMPLE")));
+
+ try
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ fail("Expected user failure exception");
+ } catch (UserFailureException e)
+ {
+ AssertionUtil.assertContains("Authorization failure", e.getMessage());
+ AssertionUtil.assertContains("set contained for sample UNAUTHORIZED_CONTAINED", e.getMessage());
+ }
+ }
+
+ private SampleCreation sampleCreation(String code)
{
SampleCreation sampleParent = new SampleCreation();
sampleParent.setCode(code);
@@ -486,4 +606,23 @@ public class SampleCreateTest extends AbstractSampleTest
return sampleParent;
}
+ private SampleCreation sampleCreation(String spaceCode, String code)
+ {
+ SampleCreation sampleParent = new SampleCreation();
+ sampleParent.setCode(code);
+ sampleParent.setTypeId(new EntityTypePermId("CELL_PLATE"));
+ sampleParent.setSpaceId(new SpacePermId(spaceCode));
+ sampleParent.setCreationId(new CreationId("creation " + code));
+ return sampleParent;
+ }
+
+ private SamplePermId createCisdSample(String code)
+ {
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+ SampleCreation creation = sampleCreation("CISD", code);
+ List<SamplePermId> ids = v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ v3api.logout(sessionToken);
+ return ids.get(0);
+ }
+
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/SampleUpdateTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/SampleUpdateTest.java
index 874310207f3..1414317d1d6 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/SampleUpdateTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/SampleUpdateTest.java
@@ -19,6 +19,7 @@ package ch.ethz.sis.openbis.systemtest.api.v3;
import static ch.systemsx.cisd.common.test.AssertionUtil.assertCollectionContainsOnly;
import static ch.systemsx.cisd.common.test.AssertionUtil.assertCollectionSize;
import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.fail;
import java.util.Arrays;
import java.util.HashMap;
@@ -564,9 +565,10 @@ public class SampleUpdateTest extends AbstractSampleTest
assertIdentifier(sample2, "/CISD/SAMPLE_2_WITH_TAGS");
assertTags(sample2.getTags(), "TEST_TAG_2", "TEST_TAG_3");
}
-
+
@Test
- public void updateSampleRemoveSpace() {
+ public void updateSampleRemoveSpace()
+ {
String sessionToken = v3api.login(TEST_USER, PASSWORD);
SampleCreation creation = new SampleCreation();
@@ -597,9 +599,10 @@ public class SampleUpdateTest extends AbstractSampleTest
assertEquals(sample.getExperiment(), null);
assertIdentifier(sample, "/SAMPLE");
}
-
+
@Test
- public void updateSharedSampleSetSpace() {
+ public void updateSharedSampleSetSpace()
+ {
String sessionToken = v3api.login(TEST_USER, PASSWORD);
SampleCreation creation = new SampleCreation();
@@ -627,7 +630,139 @@ public class SampleUpdateTest extends AbstractSampleTest
assertEquals(sample.getSpace().getCode(), "TEST-SPACE");
assertEquals(sample.getExperiment().getIdentifier().getIdentifier(), "/TEST-SPACE/TEST-PROJECT/EXP-SPACE-TEST");
assertIdentifier(sample, "/TEST-SPACE/SAMPLE");
-
+
}
-
+
+ @Test
+ public void testUpdateSampleWithUnauthorizedSample()
+ {
+ String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ SampleUpdate update = new SampleUpdate();
+ update.setSampleId(new SamplePermId("200902091219327-1025"));
+
+ try
+ {
+ v3api.updateSamples(sessionToken, Arrays.asList(update));
+ fail("Expected user failure exception");
+ } catch (UserFailureException e)
+ {
+ AssertionUtil.assertContains("Authorization failure: Cannot access sample /CISD/CP-TEST-1", e.getMessage());
+ }
+ }
+
+ @Test
+ public void testUpdateSampleWithUnauthorizedSpace()
+ {
+ String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ SampleUpdate update = new SampleUpdate();
+ update.setSampleId(new SamplePermId("200902091250077-1060"));
+ update.setSpaceId(new SpacePermId("CISD"));
+
+ try
+ {
+ v3api.updateSamples(sessionToken, Arrays.asList(update));
+ fail("Expected user failure exception");
+ } catch (UserFailureException e)
+ {
+ AssertionUtil.assertContains("Authorization failure: Cannot access space CISD", e.getMessage());
+ }
+ }
+
+ @Test
+ public void testUpdateSampleWithUnauthorizedExperiment()
+ {
+ String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ SampleUpdate update = new SampleUpdate();
+ update.setSampleId(new SamplePermId("200902091250077-1060"));
+ update.setExperimentId(new ExperimentPermId("200811050951882-1028"));
+
+ try
+ {
+ v3api.updateSamples(sessionToken, Arrays.asList(update));
+ fail("Expected user failure exception");
+ } catch (UserFailureException e)
+ {
+ AssertionUtil.assertContains("Authorization failure: Cannot access experiment /CISD/NEMO/EXP1", e.getMessage());
+ }
+ }
+
+ @Test
+ public void testUpdateSampleWithUnauthorizedContainer()
+ {
+ String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ SampleUpdate update = new SampleUpdate();
+ update.setSampleId(new SamplePermId("200902091250077-1060"));
+ update.setContainerId(new SamplePermId("200902091219327-1025"));
+
+ try
+ {
+ v3api.updateSamples(sessionToken, Arrays.asList(update));
+ fail("Expected user failure exception");
+ } catch (UserFailureException e)
+ {
+ AssertionUtil.assertContains("Authorization failure", e.getMessage());
+ }
+ }
+
+ @Test
+ public void testUpdateSampleWithUnauthorizedContained()
+ {
+ String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ SampleUpdate update = new SampleUpdate();
+ update.setSampleId(new SamplePermId("200902091250077-1060"));
+ update.getContainedIds().add(new SamplePermId("200902091219327-1025"));
+
+ try
+ {
+ v3api.updateSamples(sessionToken, Arrays.asList(update));
+ fail("Expected user failure exception");
+ } catch (UserFailureException e)
+ {
+ AssertionUtil.assertContains("Authorization failure", e.getMessage());
+ }
+ }
+
+ @Test
+ public void testUpdateSampleWithUnauthorizedParent()
+ {
+ String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ SampleUpdate update = new SampleUpdate();
+ update.setSampleId(new SamplePermId("200902091250077-1060"));
+ update.getParentIds().add(new SamplePermId("200902091219327-1025"));
+
+ try
+ {
+ v3api.updateSamples(sessionToken, Arrays.asList(update));
+ fail("Expected user failure exception");
+ } catch (UserFailureException e)
+ {
+ AssertionUtil.assertContains("Authorization failure", e.getMessage());
+ }
+ }
+
+ @Test
+ public void testUpdateSampleWithUnauthorizedChild()
+ {
+ String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ SampleUpdate update = new SampleUpdate();
+ update.setSampleId(new SamplePermId("200902091250077-1060"));
+ update.getChildIds().add(new SamplePermId("200902091219327-1025"));
+
+ try
+ {
+ v3api.updateSamples(sessionToken, Arrays.asList(update));
+ fail("Expected user failure exception");
+ } catch (UserFailureException e)
+ {
+ AssertionUtil.assertContains("Authorization failure", e.getMessage());
+ }
+ }
+
}
diff --git a/openbis_api/source/java/ch/ethz/sis/openbis/generic/shared/api/v3/exceptions/ObjectNotFoundException.java b/openbis_api/source/java/ch/ethz/sis/openbis/generic/shared/api/v3/exceptions/ObjectNotFoundException.java
new file mode 100644
index 00000000000..93753fc65ff
--- /dev/null
+++ b/openbis_api/source/java/ch/ethz/sis/openbis/generic/shared/api/v3/exceptions/ObjectNotFoundException.java
@@ -0,0 +1,35 @@
+/*
+ * 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.shared.api.v3.exceptions;
+
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.IObjectId;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+/**
+ * @author pkupczyk
+ */
+public class ObjectNotFoundException extends UserFailureException
+{
+
+ private static final long serialVersionUID = 1L;
+
+ public ObjectNotFoundException(IObjectId id)
+ {
+ super("Object with id [" + id + "] has not been found.");
+ }
+
+}
--
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