From ccca07de338fea0975724a2b122e7480f26735c4 Mon Sep 17 00:00:00 2001
From: jakubs <jakubs>
Date: Fri, 27 Jul 2012 13:29:36 +0000
Subject: [PATCH] BIS-102 SP-146 implement&test experiment updates from dss
SVN: 26247
---
.../server/ETLEntityOperationChecker.java | 7 ++++++
.../openbis/generic/server/ETLService.java | 25 +++++++++++++++++++
.../server/IETLEntityOperationChecker.java | 9 +++++++
.../dto/AtomicEntityOperationDetails.java | 12 +++++----
.../server/ETLServiceDatabaseTest.java | 21 ++++++++++------
.../generic/server/ETLServiceTest.java | 6 ++++-
.../dto/AtomicEntityOperationDetailsTest.java | 7 ++++--
.../systemtest/EntityOperationTest.java | 8 ++++--
8 files changed, 77 insertions(+), 18 deletions(-)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLEntityOperationChecker.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLEntityOperationChecker.java
index e3566a1e0eb..1a9e31f55ae 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLEntityOperationChecker.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLEntityOperationChecker.java
@@ -25,6 +25,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetBatchUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.IAuthSession;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialUpdateDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
@@ -101,4 +102,10 @@ public class ETLEntityOperationChecker implements IETLEntityOperationChecker
{
}
+ @Override
+ public void assertExperimentUpdateAllowed(IAuthSession session,
+ ExperimentUpdatesDTO experimentUpdates)
+ {
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
index 449aa349764..9d05783f58b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
@@ -149,6 +149,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.EntityOperationsLogEntryPE;
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.ExperimentUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataManagementSystemPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
@@ -1386,6 +1387,9 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
long experimentsCreated =
createExperiments(sessionForEntityOperation, operationDetails, progressListener);
+ long experimentsUpdates =
+ updateExperiments(sessionForEntityOperation, operationDetails, progressListener);
+
long samplesCreated =
createSamples(sessionForEntityOperation, operationDetails, progressListener);
@@ -1824,6 +1828,27 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
return index;
}
+ private void updateExperiment(Session session, ExperimentUpdatesDTO updates)
+ {
+ final IExperimentBO experimentBO = businessObjectFactory.createExperimentBO(session);
+ experimentBO.update(updates);
+ experimentBO.save();
+ }
+
+ private long updateExperiments(Session session, AtomicEntityOperationDetails operationDetails,
+ IProgressListener progress)
+ {
+ List<ExperimentUpdatesDTO> updates = operationDetails.getExperimentUpdates();
+
+ for (ExperimentUpdatesDTO update : updates)
+ {
+ entityOperationChecker.assertExperimentUpdateAllowed(session, update);
+ updateExperiment(session, update);
+ }
+
+ return updates.size();
+ }
+
private IDataBO registerDataSetInternal(final Session session,
SampleIdentifier sampleIdentifier, NewExternalData externalData)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/IETLEntityOperationChecker.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/IETLEntityOperationChecker.java
index 9bdd326b34b..5a7dadfca06 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/IETLEntityOperationChecker.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/IETLEntityOperationChecker.java
@@ -23,6 +23,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.Authoriz
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.Capability;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetUpdatesCollectionPredicate;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.ExperimentUpdatesPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.NewExperimentPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.NewExternalDataPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.NewProjectPredicate;
@@ -35,6 +36,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetBatchUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.IAuthSession;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialUpdateDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
@@ -73,6 +75,13 @@ public interface IETLEntityOperationChecker
@AuthorizationGuard(guardClass = NewExperimentPredicate.class)
List<NewExperiment> newExperiments);
+ @RolesAllowed(
+ { RoleWithHierarchy.SPACE_USER, RoleWithHierarchy.SPACE_ETL_SERVER })
+ @Capability("UPDATE_EXPERIMENTS_VIA_DSS")
+ public void assertExperimentUpdateAllowed(IAuthSession session,
+ @AuthorizationGuard(guardClass = ExperimentUpdatesPredicate.class)
+ ExperimentUpdatesDTO experimentUpdates);
+
@RolesAllowed(RoleWithHierarchy.INSTANCE_ETL_SERVER)
public void assertInstanceSampleCreationAllowed(IAuthSession session,
@AuthorizationGuard(guardClass = NewSamplePredicate.class)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationDetails.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationDetails.java
index 13fe13e235a..d973e68668a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationDetails.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationDetails.java
@@ -74,7 +74,8 @@ public class AtomicEntityOperationDetails implements Serializable
public AtomicEntityOperationDetails(TechId registrationId, String userIdOrNull,
List<NewSpace> spaceRegistrations, List<NewProject> projectRegistrations,
- List<NewExperiment> experimentRegistrations, List<SampleUpdatesDTO> sampleUpdates,
+ List<NewExperiment> experimentRegistrations,
+ List<ExperimentUpdatesDTO> experimentUpdates, List<SampleUpdatesDTO> sampleUpdates,
List<NewSample> sampleRegistrations,
Map<String, List<NewMaterial>> materialRegistrations,
List<MaterialUpdateDTO> materialUpdates,
@@ -85,7 +86,7 @@ public class AtomicEntityOperationDetails implements Serializable
this.userIdOrNull = userIdOrNull;
this.spaceRegistrations = new ArrayList<NewSpace>(spaceRegistrations);
this.projectRegistrations = new ArrayList<NewProject>(projectRegistrations);
- this.experimentUpdates = new ArrayList<ExperimentUpdatesDTO>();
+ this.experimentUpdates = new ArrayList<ExperimentUpdatesDTO>(experimentUpdates);
this.experimentRegistrations = new ArrayList<NewExperiment>(experimentRegistrations);
this.sampleUpdates = new ArrayList<SampleUpdatesDTO>(sampleUpdates);
this.sampleRegistrations = new ArrayList<NewSample>(sampleRegistrations);
@@ -97,7 +98,8 @@ public class AtomicEntityOperationDetails implements Serializable
public AtomicEntityOperationDetails(TechId registrationId, String userIdOrNull,
List<NewSpace> spaceRegistrations, List<NewProject> projectRegistrations,
- List<NewExperiment> experimentRegistrations, List<SampleUpdatesDTO> sampleUpdates,
+ List<NewExperiment> experimentRegistrations,
+ List<ExperimentUpdatesDTO> experimentUpdates, List<SampleUpdatesDTO> sampleUpdates,
List<NewSample> sampleRegistrations,
Map<String, List<NewMaterial>> materialRegistrations,
List<MaterialUpdateDTO> materialUpdates,
@@ -105,8 +107,8 @@ public class AtomicEntityOperationDetails implements Serializable
List<DataSetBatchUpdatesDTO> dataSetUpdates, Integer batchSizeOrNull)
{
this(registrationId, userIdOrNull, spaceRegistrations, projectRegistrations,
- experimentRegistrations, sampleUpdates, sampleRegistrations, materialRegistrations,
- materialUpdates, dataSetRegistrations, dataSetUpdates);
+ experimentRegistrations, experimentUpdates, sampleUpdates, sampleRegistrations,
+ materialRegistrations, materialUpdates, dataSetRegistrations, dataSetUpdates);
this.batchSizeOrNull = batchSizeOrNull;
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceDatabaseTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceDatabaseTest.java
index 4e7cd2fde5e..f1ca29e81e3 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceDatabaseTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceDatabaseTest.java
@@ -58,6 +58,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetBatchUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialUpdateDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
@@ -310,7 +311,8 @@ public class ETLServiceDatabaseTest extends AbstractDAOTest
List<NewSpace> spaceRegistrations = Collections.emptyList();
List<NewProject> projectRegistrations = Collections.emptyList();
List<NewExperiment> experimentRegistrations = Collections.emptyList();
-
+ List<ExperimentUpdatesDTO> experimentUpdates =
+ Collections.<ExperimentUpdatesDTO> emptyList();
List<SampleUpdatesDTO> sampleUpdates = Collections.emptyList();
List<NewSample> sampleRegistrations = Collections.emptyList();
Map<String, List<NewMaterial>> materialRegistrations = Collections.emptyMap();
@@ -318,8 +320,8 @@ public class ETLServiceDatabaseTest extends AbstractDAOTest
List<? extends NewExternalData> dataSetRegistrations = Collections.emptyList();
AtomicEntityOperationDetails details =
new AtomicEntityOperationDetails(registrationid, null, spaceRegistrations,
- projectRegistrations, experimentRegistrations, sampleUpdates,
- sampleRegistrations, materialRegistrations, materialUpdates,
+ projectRegistrations, experimentRegistrations, experimentUpdates,
+ sampleUpdates, sampleRegistrations, materialRegistrations, materialUpdates,
dataSetRegistrations, dataSetUpdates, batchSizeOrNull);
service.performEntityOperations(sessionToken, details);
}
@@ -330,6 +332,8 @@ public class ETLServiceDatabaseTest extends AbstractDAOTest
List<NewSpace> spaceRegistrations = Collections.emptyList();
List<NewProject> projectRegistrations = Collections.emptyList();
List<NewExperiment> experimentRegistrations = Collections.emptyList();
+ List<ExperimentUpdatesDTO> experimentUpdates =
+ Collections.<ExperimentUpdatesDTO> emptyList();
List<NewSample> sampleRegistrations = Collections.emptyList();
Map<String, List<NewMaterial>> materialRegistrations = Collections.emptyMap();
@@ -338,8 +342,8 @@ public class ETLServiceDatabaseTest extends AbstractDAOTest
List<DataSetBatchUpdatesDTO> dataSetUpdates = Collections.emptyList();
AtomicEntityOperationDetails details =
new AtomicEntityOperationDetails(registrationid, null, spaceRegistrations,
- projectRegistrations, experimentRegistrations, sampleUpdates,
- sampleRegistrations, materialRegistrations, materialUpdates,
+ projectRegistrations, experimentRegistrations, experimentUpdates,
+ sampleUpdates, sampleRegistrations, materialRegistrations, materialUpdates,
dataSetRegistrations, dataSetUpdates, batchSizeOrNull);
service.performEntityOperations(sessionToken, details);
}
@@ -402,7 +406,8 @@ public class ETLServiceDatabaseTest extends AbstractDAOTest
List<NewSpace> spaceRegistrations = Collections.emptyList();
List<NewProject> projectRegistrations = Collections.emptyList();
List<NewExperiment> experimentRegistrations = Collections.emptyList();
-
+ List<ExperimentUpdatesDTO> experimentUpdates =
+ Collections.<ExperimentUpdatesDTO> emptyList();
List<SampleUpdatesDTO> sampleUpdates = Collections.emptyList();
List<NewSample> sampleRegistrations = Arrays.asList(sampleToCreate);
Map<String, List<NewMaterial>> materialRegistrations = Collections.emptyMap();
@@ -411,8 +416,8 @@ public class ETLServiceDatabaseTest extends AbstractDAOTest
List<DataSetBatchUpdatesDTO> dataSetUpdates = Collections.emptyList();
AtomicEntityOperationDetails details =
new AtomicEntityOperationDetails(registrationid, null, spaceRegistrations,
- projectRegistrations, experimentRegistrations, sampleUpdates,
- sampleRegistrations, materialRegistrations, materialUpdates,
+ projectRegistrations, experimentRegistrations, experimentUpdates,
+ sampleUpdates, sampleRegistrations, materialRegistrations, materialUpdates,
dataSetRegistrations, dataSetUpdates);
service.performEntityOperations(sessionToken, details);
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java
index 44ae0acb74c..69e03816c38 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java
@@ -84,6 +84,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DataTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatastoreServiceDescriptions;
import ch.systemsx.cisd.openbis.generic.shared.dto.DeletionPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialTypePE;
@@ -969,6 +970,8 @@ public class ETLServiceTest extends AbstractServerTestCase
final Date version = new Date();
final Collection<NewAttachment> attachments = Collections.<NewAttachment> emptyList();
+ List<ExperimentUpdatesDTO> experimentUpdates = new ArrayList<ExperimentUpdatesDTO>();
+
final SampleUpdatesDTO sampleUpdate =
new SampleUpdatesDTO(CommonTestUtils.TECH_ID, null, null, attachments, version,
sampleIdentifier, null, null);
@@ -1011,7 +1014,7 @@ public class ETLServiceTest extends AbstractServerTestCase
AtomicEntityOperationDetails details =
new AtomicEntityOperationDetails(null, null, new ArrayList<NewSpace>(),
new ArrayList<NewProject>(), new ArrayList<NewExperiment>(),
- Collections.singletonList(sampleUpdate),
+ experimentUpdates, Collections.singletonList(sampleUpdate),
Collections.singletonList(newSample), materialRegistrations,
materialUpdates, Collections.singletonList(externalData),
Collections.singletonList(dataSetUpdate));
@@ -1194,6 +1197,7 @@ public class ETLServiceTest extends AbstractServerTestCase
AtomicEntityOperationDetails details =
new AtomicEntityOperationDetails(new TechId(1), null, new ArrayList<NewSpace>(),
new ArrayList<NewProject>(), new ArrayList<NewExperiment>(),
+ new ArrayList<ExperimentUpdatesDTO>(),
Collections.singletonList(sampleUpdate),
Collections.singletonList(newSample), materialRegistrations,
materialUpdates, Collections.singletonList(externalData),
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AtomicEntityOperationDetailsTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AtomicEntityOperationDetailsTest.java
index 8cd7c35e4b5..8f0c7de0243 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AtomicEntityOperationDetailsTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AtomicEntityOperationDetailsTest.java
@@ -27,6 +27,7 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetBatchUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialUpdateDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
@@ -65,6 +66,8 @@ public class AtomicEntityOperationDetailsTest extends AssertJUnit
experimentRegistrations.add(new NewExperiment("/SPACE/PROJECT/EXP-ID1", "EXP-TYPE"));
experimentRegistrations.add(new NewExperiment("/SPACE/PROJECT/EXP-ID2", "EXP-TYPE"));
+ List<ExperimentUpdatesDTO> experimentUpdates = new ArrayList<ExperimentUpdatesDTO>();
+
ArrayList<SampleUpdatesDTO> sampleUpdates = new ArrayList<SampleUpdatesDTO>();
ArrayList<NewSample> sampleRegistrations = new ArrayList<NewSample>();
@@ -89,8 +92,8 @@ public class AtomicEntityOperationDetailsTest extends AssertJUnit
AtomicEntityOperationDetails details =
new AtomicEntityOperationDetails(null, null, spaceRegistrations,
- projectRegistrations, experimentRegistrations, sampleUpdates,
- sampleRegistrations, materialRegistrations, materialUpdates,
+ projectRegistrations, experimentRegistrations, experimentUpdates,
+ sampleUpdates, sampleRegistrations, materialRegistrations, materialUpdates,
dataSetRegistrations, dataSetUpdates);
assertEquals(
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/EntityOperationTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/EntityOperationTest.java
index 1e566a706fb..bdfefadab95 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/EntityOperationTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/EntityOperationTest.java
@@ -55,6 +55,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.SampleBuilder;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationResult;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetBatchUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialUpdateDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
@@ -99,6 +100,9 @@ public class EntityOperationTest extends SystemTestCase
private final List<NewExperiment> experiments = new ArrayList<NewExperiment>();
+ private final List<ExperimentUpdatesDTO> experimentUpdates =
+ new ArrayList<ExperimentUpdatesDTO>();
+
private final List<NewSample> samples = new ArrayList<NewSample>();
private final List<SampleUpdatesDTO> sampleUpdates = new ArrayList<SampleUpdatesDTO>();
@@ -272,8 +276,8 @@ public class EntityOperationTest extends SystemTestCase
AtomicEntityOperationDetails create()
{
return new AtomicEntityOperationDetails(registrationID, userID, spaces, projects,
- experiments, sampleUpdates, samples, materials, materialUpdates, dataSets,
- dataSetUpdates);
+ experiments, experimentUpdates, sampleUpdates, samples, materials,
+ materialUpdates, dataSets, dataSetUpdates);
}
}
--
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