From 13daf6b96e18b1f2a862261a8f18b36829bcbdd4 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Tue, 22 May 2012 11:34:44 +0000
Subject: [PATCH] SP-45 BIS-21 : Log invocations to performEntityOperations
SVN: 25335
---
.../openbis/generic/server/ETLService.java | 40 +++--
.../generic/server/ETLServiceLogger.java | 7 +
.../business/bo/AbstractBusinessObject.java | 6 +
.../server/dataaccess/IDAOFactory.java | 3 +
.../dataaccess/IEntityOperationsLogDAO.java | 17 ++
.../server/dataaccess/db/DAOFactory.java | 9 +
.../dataaccess/db/DatabaseVersionHolder.java | 2 +-
.../dataaccess/db/EntityOperationsLogDAO.java | 60 +++++++
.../generic/shared/IETLLIMSService.java | 157 +++++++-----------
.../dto/AtomicEntityOperationDetails.java | 22 ++-
.../generic/shared/dto/ColumnNames.java | 2 +
.../dto/EntityOperationsLogEntryPE.java | 61 +++++++
.../generic/shared/dto/SequenceNames.java | 2 +
.../generic/shared/dto/TableNames.java | 2 +
.../shared/dto/ValidationMessages.java | 3 +
openbis/source/java/hibernateContext.xml | 1 +
openbis/source/sql/generic/105/schema-105.sql | 8 +-
.../source/sql/postgresql/105/grants-105.sql | 2 +
.../migration/migration-104-105.sql | 10 +-
.../generic/server/ETLServiceTest.java | 97 ++++++++++-
.../shared/AbstractServerTestCase.java | 6 +
.../shared/IETLLIMSService.java.expected | 157 +++++++-----------
.../dto/AtomicEntityOperationDetailsTest.java | 10 +-
.../sql/postgresql/105/finish-105.sql | 3 +
.../sql/postgresql/105/schema-105.sql | 11 ++
25 files changed, 481 insertions(+), 217 deletions(-)
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IEntityOperationsLogDAO.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityOperationsLogDAO.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityOperationsLogEntryPE.java
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 b6358c8fcc2..c3e014040a7 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
@@ -125,6 +125,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatastoreServiceDescriptions;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityCollectionForCreationOrUpdate;
+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;
@@ -1250,19 +1251,16 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
public AtomicEntityOperationResult performEntityOperations(String sessionToken,
AtomicEntityOperationDetails operationDetails)
{
- return this.performEntityOperations(sessionToken, operationDetails,
- new ProgressListener()
- {
+ return this.performEntityOperations(sessionToken, operationDetails, new ProgressListener()
+ {
- public void update(String label, int totalItemsToProcess,
- int numItemsProcessed)
- {
- }
- });
+ public void update(String label, int totalItemsToProcess, int numItemsProcessed)
+ {
+ }
+ });
}
- public AtomicEntityOperationResult performEntityOperations(
- String sessionToken,
+ public AtomicEntityOperationResult performEntityOperations(String sessionToken,
AtomicEntityOperationDetails operationDetails, ProgressListener progressListener)
{
@@ -1288,10 +1286,31 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
List<ExternalData> dataSetsUpdated =
updateDataSets(session, operationDetails, progressListener);
+ // If the id is not null, the caller wants to persist the fact that the operation was
+ // invoked and completed;
+ // if the id is null, the caller does not care.
+ TechId registrationId = operationDetails.getRegistrationIdOrNull();
+ if (null != registrationId)
+ {
+ daoFactory.getEntityOperationsLogDAO().addLogEntry(registrationId.getId());
+ }
+
return new AtomicEntityOperationResult(spacesCreated, projectsCreated, experimentsCreated,
samplesUpdated, samplesCreated, materialsCreated, dataSetsCreated, dataSetsUpdated);
}
+ public Boolean didEntityOperationsSucceed(String token, TechId registrationId)
+ {
+ if (registrationId == null)
+ {
+ return false;
+ }
+
+ EntityOperationsLogEntryPE logEntry =
+ daoFactory.getEntityOperationsLogDAO().tryFindLogEntry(registrationId.getId());
+ return logEntry != null;
+ }
+
private List<Space> createSpaces(Session session,
AtomicEntityOperationDetails operationDetails, ProgressListener progress)
{
@@ -1715,5 +1734,4 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
}
return result;
}
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
index 25d9d77f383..e0c3493135f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
@@ -581,4 +581,11 @@ public class ETLServiceLogger extends AbstractServerLogger implements IETLLIMSSe
return null;
}
+ public Boolean didEntityOperationsSucceed(String token, TechId registrationId)
+ {
+ logAccess(Level.DEBUG, token, "didEntityOperationsSucceed", "REGISTRATION_ID(%s)",
+ registrationId);
+ return null;
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBusinessObject.java
index 85b364db4ce..f0844d35307 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBusinessObject.java
@@ -33,6 +33,7 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataSetTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataStoreDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDatabaseInstanceDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDeletionDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityOperationsLogDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityPropertyHistoryDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityPropertyTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
@@ -390,4 +391,9 @@ abstract class AbstractBusinessObject implements IDAOFactory
{
return daoFactory.getPostRegistrationDAO();
}
+
+ public IEntityOperationsLogDAO getEntityOperationsLogDAO()
+ {
+ return daoFactory.getEntityOperationsLogDAO();
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDAOFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDAOFactory.java
index fc467a310c9..1cbac222b2f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDAOFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDAOFactory.java
@@ -109,4 +109,7 @@ public interface IDAOFactory extends IAuthorizationDAOFactory
/** Returns an implementation of {@link IPostRegistrationDAO}. */
public IPostRegistrationDAO getPostRegistrationDAO();
+ /** Returns an implementation of {@link IEntityOperationsLogDAO}. */
+ public IEntityOperationsLogDAO getEntityOperationsLogDAO();
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IEntityOperationsLogDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IEntityOperationsLogDAO.java
new file mode 100644
index 00000000000..bf336f2ac08
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IEntityOperationsLogDAO.java
@@ -0,0 +1,17 @@
+package ch.systemsx.cisd.openbis.generic.server.dataaccess;
+
+import ch.systemsx.cisd.openbis.generic.shared.dto.EntityOperationsLogEntryPE;
+
+public interface IEntityOperationsLogDAO
+{
+ /**
+ * Adds an entry to the log for the given registrationId.
+ */
+ public void addLogEntry(Long registrationId);
+
+ /**
+ * Return the entry with the given registrationId or null if none exists
+ */
+ public EntityOperationsLogEntryPE tryFindLogEntry(Long registrationId);
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DAOFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DAOFactory.java
index 20051f169cc..42ba37ac55f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DAOFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DAOFactory.java
@@ -30,6 +30,7 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataSetTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataStoreDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDynamicPropertyEvaluationScheduler;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityOperationsLogDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityPropertyHistoryDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityPropertyTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
@@ -108,6 +109,8 @@ public final class DAOFactory extends AuthorizationDAOFactory implements IDAOFac
private final IPostRegistrationDAO postRegistrationDAO;
+ private final IEntityOperationsLogDAO entityOperationsLogDAO;
+
private EntityPropertyHistoryDAO entityPropertyHistoryDAO;
public DAOFactory(final DatabaseConfigurationContext context,
@@ -138,6 +141,7 @@ public final class DAOFactory extends AuthorizationDAOFactory implements IDAOFac
scriptDAO = new ScriptDAO(sessionFactory, databaseInstance);
corePluginDAO = new CorePluginDAO(sessionFactory, databaseInstance);
postRegistrationDAO = new PostRegistrationDAO(sessionFactory, databaseInstance);
+ entityOperationsLogDAO = new EntityOperationsLogDAO(sessionFactory, databaseInstance);
final EntityKind[] entityKinds = EntityKind.values();
for (final EntityKind entityKind : entityKinds)
{
@@ -269,4 +273,9 @@ public final class DAOFactory extends AuthorizationDAOFactory implements IDAOFac
{
return postRegistrationDAO;
}
+
+ public IEntityOperationsLogDAO getEntityOperationsLogDAO()
+ {
+ return entityOperationsLogDAO;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DatabaseVersionHolder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DatabaseVersionHolder.java
index 7027d79c1c8..87775343efd 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DatabaseVersionHolder.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DatabaseVersionHolder.java
@@ -24,7 +24,7 @@ package ch.systemsx.cisd.openbis.generic.server.dataaccess.db;
public final class DatabaseVersionHolder
{
/** Current version of the database. */
- private static final String DATABASE_VERSION = "105"; // S131
+ private static final String DATABASE_VERSION = "105"; // S132
private DatabaseVersionHolder()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityOperationsLogDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityOperationsLogDAO.java
new file mode 100644
index 00000000000..2e7b12ddea5
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityOperationsLogDAO.java
@@ -0,0 +1,60 @@
+package ch.systemsx.cisd.openbis.generic.server.dataaccess.db;
+
+import org.apache.log4j.Logger;
+import org.hibernate.Criteria;
+import org.hibernate.SessionFactory;
+import org.hibernate.criterion.Restrictions;
+import org.springframework.orm.hibernate3.HibernateTemplate;
+
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityOperationsLogDAO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ColumnNames;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EntityOperationsLogEntryPE;
+
+public class EntityOperationsLogDAO extends AbstractGenericEntityDAO<EntityOperationsLogEntryPE>
+ implements IEntityOperationsLogDAO
+{
+ private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ EntityOperationsLogDAO.class);
+
+ protected EntityOperationsLogDAO(SessionFactory sessionFactory,
+ DatabaseInstancePE databaseInstance)
+ {
+ super(sessionFactory, databaseInstance, EntityOperationsLogEntryPE.class);
+ }
+
+ public void addLogEntry(Long registrationId)
+ {
+ EntityOperationsLogEntryPE logEntry = new EntityOperationsLogEntryPE();
+ logEntry.setRegistrationId(registrationId);
+
+ HibernateTemplate template = getHibernateTemplate();
+ template.persist(logEntry);
+ template.flush();
+
+ operationLog.info(String.format("Add entity operation log entry for registration id '%d'.",
+ registrationId));
+ }
+
+ public EntityOperationsLogEntryPE tryFindLogEntry(Long registrationId)
+ {
+ assert registrationId != null : "Unspecified registration id.";
+
+ final Criteria criteria = getSession().createCriteria(getEntityClass());
+ criteria.add(Restrictions.eq(ColumnNames.REGISTRATION_ID, registrationId));
+ EntityOperationsLogEntryPE result = (EntityOperationsLogEntryPE) criteria.uniqueResult();
+ if (null != result)
+ {
+ operationLog.info(String.format("Found a log entry for registration id '%d'.",
+ registrationId));
+ } else
+ {
+ operationLog.info(String.format("Did not find a log entry for registration id '%d'.",
+ registrationId));
+ }
+ return result;
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
index e033fecd653..e52fbe8991e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
@@ -121,11 +121,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
- public Experiment tryToGetExperiment(
- String sessionToken,
+ public Experiment tryToGetExperiment(String sessionToken,
@AuthorizationGuard(guardClass = ExistingSpaceIdentifierPredicate.class)
- ExperimentIdentifier experimentIdentifier)
- throws UserFailureException;
+ ExperimentIdentifier experimentIdentifier) throws UserFailureException;
/**
* For given {@link MaterialIdentifier} returns the corresponding {@link Material}.
@@ -164,11 +162,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
- public Sample tryGetSampleWithExperiment(
- final String sessionToken,
+ public Sample tryGetSampleWithExperiment(final String sessionToken,
@AuthorizationGuard(guardClass = ExistingSampleOwnerIdentifierPredicate.class)
- final SampleIdentifier sampleIdentifier)
- throws UserFailureException;
+ final SampleIdentifier sampleIdentifier) throws UserFailureException;
/**
* Returns a list of terms belonging to given vocabulary.
@@ -203,11 +199,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
- public List<ExternalData> listDataSetsByExperimentID(
- final String sessionToken,
+ public List<ExternalData> listDataSetsByExperimentID(final String sessionToken,
@AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class)
- final TechId experimentID)
- throws UserFailureException;
+ final TechId experimentID) throws UserFailureException;
/**
* For given sample {@link TechId} returns the corresponding list of {@link ExternalData}.
@@ -219,8 +213,8 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
public List<ExternalData> listDataSetsBySampleID(final String sessionToken,
@AuthorizationGuard(guardClass = SampleTechIdPredicate.class)
- final TechId sampleId,
- final boolean showOnlyDirectlyConnected) throws UserFailureException;
+ final TechId sampleId, final boolean showOnlyDirectlyConnected)
+ throws UserFailureException;
/**
* Returns all data sets found for specified data set codes.
@@ -230,11 +224,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
- public List<ExternalData> listDataSetsByCode(
- String sessionToken,
+ public List<ExternalData> listDataSetsByCode(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class)
- List<String> dataSetCodes)
- throws UserFailureException;
+ List<String> dataSetCodes) throws UserFailureException;
/**
* Lists samples using given configuration.
@@ -245,8 +237,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@RolesAllowed(
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
@ReturnValueFilter(validatorClass = SampleValidator.class)
- public List<Sample> listSamples(
- final String sessionToken,
+ public List<Sample> listSamples(final String sessionToken,
@AuthorizationGuard(guardClass = ListSampleCriteriaPredicate.class)
final ListSampleCriteria criteria);
@@ -262,11 +253,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
- public IEntityProperty[] tryToGetPropertiesOfTopSampleRegisteredFor(
- final String sessionToken,
+ public IEntityProperty[] tryToGetPropertiesOfTopSampleRegisteredFor(final String sessionToken,
@AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class)
- final SampleIdentifier sampleIdentifier)
- throws UserFailureException;
+ final SampleIdentifier sampleIdentifier) throws UserFailureException;
/**
* Registers/updates various entities in one transaction.
@@ -286,8 +275,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@DatabaseCreateOrDeleteModification(value = ObjectKind.EXPERIMENT)
public long registerExperiment(String sessionToken,
@AuthorizationGuard(guardClass = NewExperimentPredicate.class)
- NewExperiment experiment)
- throws UserFailureException;
+ NewExperiment experiment) throws UserFailureException;
/**
* Registers samples in batches.
@@ -295,11 +283,10 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseUpdateModification(value = ObjectKind.SAMPLE)
- public void registerSamples(
- final String sessionToken,
+ public void registerSamples(final String sessionToken,
@AuthorizationGuard(guardClass = NewSamplesWithTypePredicate.class)
- final List<NewSamplesWithTypes> newSamplesWithType,
- String userIdOrNull) throws UserFailureException;
+ final List<NewSamplesWithTypes> newSamplesWithType, String userIdOrNull)
+ throws UserFailureException;
/**
* Registers a new sample.
@@ -309,8 +296,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@DatabaseCreateOrDeleteModification(value = ObjectKind.SAMPLE)
public long registerSample(final String sessionToken,
@AuthorizationGuard(guardClass = NewSamplePredicate.class)
- final NewSample newSample,
- String userIDOrNull) throws UserFailureException;
+ final NewSample newSample, String userIDOrNull) throws UserFailureException;
/**
* Saves changed sample.
@@ -336,11 +322,10 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseCreateOrDeleteModification(value = ObjectKind.DATA_SET)
- public void registerDataSet(
- final String sessionToken,
+ public void registerDataSet(final String sessionToken,
@AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class)
- final SampleIdentifier sampleIdentifier,
- final NewExternalData externalData) throws UserFailureException;
+ final SampleIdentifier sampleIdentifier, final NewExternalData externalData)
+ throws UserFailureException;
/**
* Registers the specified data connected to an experiment.
@@ -356,11 +341,10 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseCreateOrDeleteModification(value = ObjectKind.DATA_SET)
- public void registerDataSet(
- final String sessionToken,
+ public void registerDataSet(final String sessionToken,
@AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class)
- final ExperimentIdentifier experimentIdentifier,
- final NewExternalData externalData) throws UserFailureException;
+ final ExperimentIdentifier experimentIdentifier, final NewExternalData externalData)
+ throws UserFailureException;
/**
* Checks that the user of specified session has INSTANCE_ADMIN access rights.
@@ -384,8 +368,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public void checkDataSetAccess(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class)
- String dataSetCode)
- throws UserFailureException;
+ String dataSetCode) throws UserFailureException;
/**
* Check if the current user can access all the data sets in the list
@@ -395,8 +378,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
- public void checkDataSetCollectionAccess(
- String sessionToken,
+ public void checkDataSetCollectionAccess(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class)
List<String> dataSetCodes);
@@ -408,8 +390,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
public ExternalData tryGetDataSet(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class)
- String dataSetCode)
- throws UserFailureException;
+ String dataSetCode) throws UserFailureException;
/**
* Creates and returns a unique code for a new data set. TODO KE: 2011-04-19 remove this method.
@@ -441,11 +422,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
- public List<Sample> listSamplesByCriteria(
- final String sessionToken,
+ public List<Sample> listSamplesByCriteria(final String sessionToken,
@AuthorizationGuard(guardClass = ListSamplesByPropertyPredicate.class)
- final ListSamplesByPropertyCriteria criteria)
- throws UserFailureException;
+ final ListSamplesByPropertyCriteria criteria) throws UserFailureException;
/**
* Lists share ids of all data sets belonging to chosen data store (even the ones in trash!).
@@ -493,8 +472,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
- public List<Experiment> listExperiments(
- String sessionToken,
+ public List<Experiment> listExperiments(String sessionToken,
@AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class)
ProjectIdentifier projectIdentifier);
@@ -504,8 +482,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
- public List<Experiment> listExperiments(
- String sessionToken,
+ public List<Experiment> listExperiments(String sessionToken,
@AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class)
List<ExperimentIdentifier> experimentIdentifiers,
ExperimentFetchOptions experimentFetchOptions);
@@ -516,8 +493,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
- public List<Experiment> listExperimentsForProjects(
- String sessionToken,
+ public List<Experiment> listExperimentsForProjects(String sessionToken,
@AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class)
List<ProjectIdentifier> projectIdentifiers,
ExperimentFetchOptions experimentFetchOptions);
@@ -548,13 +524,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseUpdateModification(value = ObjectKind.DATA_SET)
- public void addPropertiesToDataSet(
- String sessionToken,
- List<NewProperty> properties,
- String dataSetCode,
- @AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class)
- final SpaceIdentifier identifier)
- throws UserFailureException;
+ public void addPropertiesToDataSet(String sessionToken, List<NewProperty> properties,
+ String dataSetCode, @AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class)
+ final SpaceIdentifier identifier) throws UserFailureException;
/**
* Updates share id and size of specified data set.
@@ -564,8 +536,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@DatabaseUpdateModification(value = ObjectKind.DATA_SET)
public void updateShareIdAndSize(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class)
- String dataSetCode,
- String shareId, long size) throws UserFailureException;
+ String dataSetCode, String shareId, long size) throws UserFailureException;
/**
* Updates status of given data sets.
@@ -573,12 +544,10 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseUpdateModification(value = ObjectKind.DATA_SET)
- public void updateDataSetStatuses(
- String sessionToken,
+ public void updateDataSetStatuses(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class)
- List<String> dataSetCodes,
- final DataSetArchivingStatus newStatus, boolean presentInArchive)
- throws UserFailureException;
+ List<String> dataSetCodes, final DataSetArchivingStatus newStatus,
+ boolean presentInArchive) throws UserFailureException;
/**
* Set the status for a given dataset to the given new status value if the current status equals
@@ -604,11 +573,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseUpdateModification(value = ObjectKind.DATA_SET)
- public int archiveDatasets(
- String sessionToken,
+ public int archiveDatasets(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class)
- List<String> datasetCodes,
- boolean removeFromDataStore);
+ List<String> datasetCodes, boolean removeFromDataStore);
/**
* Schedules unarchiving of specified data sets.
@@ -618,8 +585,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseUpdateModification(value = ObjectKind.DATA_SET)
- public int unarchiveDatasets(
- String sessionToken,
+ public int unarchiveDatasets(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class)
List<String> datasetCodes);
@@ -642,8 +608,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
public ExternalData tryGetDataSetForServer(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class)
- String dataSetCode)
- throws UserFailureException;
+ String dataSetCode) throws UserFailureException;
/**
* Returns a list of unique codes.
@@ -685,8 +650,8 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
{ ObjectKind.SAMPLE, ObjectKind.DATA_SET })
public Sample registerSampleAndDataSet(final String sessionToken,
@AuthorizationGuard(guardClass = NewSamplePredicate.class)
- final NewSample newSample,
- final NewExternalData externalData, String userIdOrNull) throws UserFailureException;
+ final NewSample newSample, final NewExternalData externalData, String userIdOrNull)
+ throws UserFailureException;
/**
* Updates a sample and registers a data set connected to that sample in one transaction.
@@ -703,11 +668,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseUpdateModification(value = ObjectKind.SAMPLE)
@DatabaseCreateOrDeleteModification(value = ObjectKind.DATA_SET)
- public Sample updateSampleAndRegisterDataSet(
- String sessionToken,
+ public Sample updateSampleAndRegisterDataSet(String sessionToken,
@AuthorizationGuard(guardClass = SampleUpdatesPredicate.class)
- SampleUpdatesDTO updates,
- NewExternalData externalData);
+ SampleUpdatesDTO updates, NewExternalData externalData);
/**
* Updates a sample and registers a data set connected to that sample in one transaction.
@@ -724,8 +687,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@DatabaseCreateOrDeleteModification(value =
{ ObjectKind.SPACE, ObjectKind.PROJECT, ObjectKind.SAMPLE, ObjectKind.EXPERIMENT,
ObjectKind.DATA_SET })
- public AtomicEntityOperationResult performEntityOperations(
- String sessionToken,
+ public AtomicEntityOperationResult performEntityOperations(String sessionToken,
@AuthorizationGuard(guardClass = AtomicOperationsPredicate.class)
AtomicEntityOperationDetails operationDetails);
@@ -735,8 +697,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER })
- public Space tryGetSpace(
- String sessionToken,
+ public Space tryGetSpace(String sessionToken,
@AuthorizationGuard(guardClass = ExistingSpaceIdentifierPredicate.class)
SpaceIdentifier spaceIdentifier);
@@ -746,8 +707,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER })
- public Project tryGetProject(
- String sessionToken,
+ public Project tryGetProject(String sessionToken,
@AuthorizationGuard(guardClass = ExistingSpaceIdentifierPredicate.class)
ProjectIdentifier projectIdentifier);
@@ -782,11 +742,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
{ ObjectKind.SAMPLE, ObjectKind.EXPERIMENT })
@DatabaseCreateOrDeleteModification(value =
{ ObjectKind.DATA_SET })
- public void removeDataSetsPermanently(
- String sessionToken,
+ public void removeDataSetsPermanently(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class)
- List<String> dataSetCodes,
- String reason);
+ List<String> dataSetCodes, String reason);
/**
* updates a data set.
@@ -795,8 +753,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseUpdateModification(value =
{ ObjectKind.EXPERIMENT, ObjectKind.SAMPLE, ObjectKind.DATA_SET })
- public void updateDataSet(
- String sessionToken,
+ public void updateDataSet(String sessionToken,
@AuthorizationGuard(guardClass = DataSetUpdatesPredicate.class)
DataSetUpdatesDTO dataSetUpdates);
@@ -837,4 +794,12 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
public List<ExternalData> listDataSetsForPostRegistration(String token, String dataStoreCode);
+
+ /**
+ * Return true if the log indicates that the performEntityOperations invocation for the given
+ * registrationId succeeded.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public Boolean didEntityOperationsSucceed(String token, TechId registrationId);
}
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 e768b2523da..6d2d710fa65 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
@@ -25,6 +25,7 @@ import java.util.TreeMap;
import org.apache.commons.lang.builder.ToStringBuilder;
import org.apache.commons.lang.builder.ToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
@@ -41,6 +42,9 @@ public class AtomicEntityOperationDetails implements Serializable
{
private static final long serialVersionUID = 1L;
+ // The unique identifier for this registration
+ private final TechId registrationIdOrNull;
+
// The userid on whose behalf the operations are done.
private final String userIdOrNull;
@@ -63,14 +67,16 @@ public class AtomicEntityOperationDetails implements Serializable
private final List<? extends NewExternalData> dataSetRegistrations;
private final List<DataSetUpdatesDTO> dataSetUpdates;
-
- public AtomicEntityOperationDetails(String userIdOrNull, List<NewSpace> spaceRegistrations,
- List<NewProject> projectRegistrations, List<NewExperiment> experimentRegistrations,
- List<SampleUpdatesDTO> sampleUpdates, List<NewSample> sampleRegistrations,
+
+ public AtomicEntityOperationDetails(TechId registrationId, String userIdOrNull,
+ List<NewSpace> spaceRegistrations, List<NewProject> projectRegistrations,
+ List<NewExperiment> experimentRegistrations, List<SampleUpdatesDTO> sampleUpdates,
+ List<NewSample> sampleRegistrations,
Map<String, List<NewMaterial>> materialRegistrations,
List<? extends NewExternalData> dataSetRegistrations,
List<DataSetUpdatesDTO> dataSetUpdates)
{
+ this.registrationIdOrNull = registrationId;
this.userIdOrNull = userIdOrNull;
this.spaceRegistrations = new ArrayList<NewSpace>(spaceRegistrations);
this.projectRegistrations = new ArrayList<NewProject>(projectRegistrations);
@@ -83,6 +89,11 @@ public class AtomicEntityOperationDetails implements Serializable
this.dataSetUpdates = new ArrayList<DataSetUpdatesDTO>(dataSetUpdates);
}
+ public TechId getRegistrationIdOrNull()
+ {
+ return registrationIdOrNull;
+ }
+
public String tryUserIdOrNull()
{
return userIdOrNull;
@@ -117,7 +128,7 @@ public class AtomicEntityOperationDetails implements Serializable
{
return dataSetUpdates;
}
-
+
public List<NewSpace> getSpaceRegistrations()
{
return spaceRegistrations;
@@ -137,6 +148,7 @@ public class AtomicEntityOperationDetails implements Serializable
public String toString()
{
ToStringBuilder sb = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
+ sb.append("registrationIdOrNull", registrationIdOrNull);
sb.append("userIdOrNull", userIdOrNull);
sb.append("spaceRegistrations", spaceRegistrations);
sb.append("projectRegistrations", projectRegistrations);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ColumnNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ColumnNames.java
index 65f08fc800d..93394a69693 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ColumnNames.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ColumnNames.java
@@ -298,6 +298,8 @@ public final class ColumnNames
public static final String DELETION_DISALLOW = "deletion_disallow";
+ public static final String REGISTRATION_ID = "registration_id";
+
private ColumnNames()
{
// Can not be instantiated.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityOperationsLogEntryPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityOperationsLogEntryPE.java
new file mode 100644
index 00000000000..1cf09e37672
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/EntityOperationsLogEntryPE.java
@@ -0,0 +1,61 @@
+package ch.systemsx.cisd.openbis.generic.shared.dto;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.validation.constraints.NotNull;
+
+import ch.systemsx.cisd.openbis.generic.server.ETLService;
+import ch.systemsx.cisd.openbis.generic.shared.IServer;
+import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
+
+/**
+ * Persistent entity representing an invocation of the
+ * {@link ETLService#performEntityOperations(String, AtomicEntityOperationDetails)} method. This
+ * table is used to check if the results of an invocation of this method made it into the database.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+
+@Entity
+@Table(name = TableNames.ENTITY_OPERATIONS_LOG_TABLE)
+public class EntityOperationsLogEntryPE implements IIdHolder, Serializable
+{
+ private static final long serialVersionUID = IServer.VERSION;
+
+ private Long id;
+
+ private Long registrationId;
+
+ @SequenceGenerator(name = SequenceNames.ENTITY_OPERATIONS_LOG_SEQUENCE, sequenceName = SequenceNames.ENTITY_OPERATIONS_LOG_SEQUENCE, allocationSize = 1)
+ @Id
+ @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.ENTITY_OPERATIONS_LOG_SEQUENCE)
+ public final Long getId()
+ {
+ return id;
+ }
+
+ public void setId(Long id)
+ {
+ this.id = id;
+ }
+
+ @NotNull(message = ValidationMessages.REGISTRATION_ID_NOT_NULL_MESSAGE)
+ @Column(name = ColumnNames.REGISTRATION_ID)
+ public Long getRegistrationId()
+ {
+ return registrationId;
+ }
+
+ public void setRegistrationId(Long registrationId)
+ {
+ this.registrationId = registrationId;
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SequenceNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SequenceNames.java
index e1edbd93807..fead77eccb6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SequenceNames.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SequenceNames.java
@@ -124,6 +124,8 @@ public final class SequenceNames
public static final String POST_REGISTRATION_DATASET_QUEUE_SEQUENCE =
"POST_REGISTRATION_DATASET_QUEUE_ID_SEQ";
+ public static final String ENTITY_OPERATIONS_LOG_SEQUENCE = "ENTITY_OPERATIONS_LOG_ID_SEQ";
+
private SequenceNames()
{
// Can not be instantiated.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TableNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TableNames.java
index f486a6ebfb2..e6bd958a9d0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TableNames.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/TableNames.java
@@ -150,6 +150,8 @@ public final class TableNames
public static final String POST_REGISTRATION_DATASET_QUEUE_TABLE =
"post_registration_dataset_queue";
+ public static final String ENTITY_OPERATIONS_LOG_TABLE = "entity_operations_log";
+
private TableNames()
{
// This class can not be instantiated.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ValidationMessages.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ValidationMessages.java
index ce3d1d1508f..12b44c211fe 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ValidationMessages.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ValidationMessages.java
@@ -230,6 +230,9 @@ public final class ValidationMessages
public static final String SCRIPT_TYPE_NOT_NULL_MESSAGE = "Script Type" + CAN_NOT_BE_NULL;
+ public static final String REGISTRATION_ID_NOT_NULL_MESSAGE = "Regirtation id"
+ + CAN_NOT_BE_NULL;
+
private ValidationMessages()
{
// Can not be instantiated.
diff --git a/openbis/source/java/hibernateContext.xml b/openbis/source/java/hibernateContext.xml
index f5db7f2e970..4dfb4c1eef0 100644
--- a/openbis/source/java/hibernateContext.xml
+++ b/openbis/source/java/hibernateContext.xml
@@ -97,6 +97,7 @@
<value>ch.systemsx.cisd.openbis.generic.shared.dto.CorePluginPE</value>
<value>ch.systemsx.cisd.openbis.generic.shared.dto.DataSetRelationshipPE</value>
<value>ch.systemsx.cisd.openbis.generic.shared.dto.PostRegistrationPE</value>
+ <value>ch.systemsx.cisd.openbis.generic.shared.dto.EntityOperationsLogEntryPE</value>
</list>
</property>
diff --git a/openbis/source/sql/generic/105/schema-105.sql b/openbis/source/sql/generic/105/schema-105.sql
index e82f5ff0e33..e92d4a4c7c0 100644
--- a/openbis/source/sql/generic/105/schema-105.sql
+++ b/openbis/source/sql/generic/105/schema-105.sql
@@ -56,7 +56,9 @@ CREATE TABLE scripts (ID TECH_ID NOT NULL,DBIN_ID TECH_ID NOT NULL,NAME VARCHAR(
CREATE TABLE CORE_PLUGINS (ID TECH_ID NOT NULL, NAME VARCHAR(200) NOT NULL, VERSION INTEGER NOT NULL, REGISTRATION_TIMESTAMP TIME_STAMP_DFL NOT NULL DEFAULT CURRENT_TIMESTAMP, MASTER_REG_SCRIPT TEXT_VALUE);
-CREATE TABLE POST_REGISTRATION_DATASET_QUEUE (ID TECH_ID NOT NULL, DS_ID TECH_ID NOT NULL);
+CREATE TABLE POST_REGISTRATION_DATASET_QUEUE (ID TECH_ID NOT NULL, DS_ID TECH_ID NOT NULL);
+
+CREATE TABLE ENTITY_OPERATIONS_LOG (ID TECH_ID NOT NULL, REGISTRATION_ID TECH_ID NOT NULL);
-- Creating views - copied from schema generated for tests, '*' can't be used because of PgDiffViews limitation in view comparison
@@ -145,6 +147,7 @@ CREATE SEQUENCE SAMPLE_RELATIONSHIP_ID_SEQ;
CREATE SEQUENCE SCRIPT_ID_SEQ;
CREATE SEQUENCE CORE_PLUGIN_ID_SEQ;
CREATE SEQUENCE POST_REGISTRATION_DATASET_QUEUE_ID_SEQ;
+CREATE SEQUENCE ENTITY_OPERATIONS_LOG_ID_SEQ;
-- Creating primary key constraints
@@ -195,6 +198,7 @@ ALTER TABLE relationship_types ADD CONSTRAINT rety_pk PRIMARY KEY (id);
ALTER TABLE sample_relationships_all ADD CONSTRAINT sare_pk PRIMARY KEY (id);
ALTER TABLE SCRIPTS ADD CONSTRAINT SCRI_PK PRIMARY KEY(ID);
ALTER TABLE POST_REGISTRATION_DATASET_QUEUE ADD CONSTRAINT PRDQ_PK PRIMARY KEY(ID);
+ALTER TABLE ENTITY_OPERATIONS_LOG ADD CONSTRAINT EOL_PK PRIMARY KEY(ID);
-- Creating unique constraints
@@ -247,6 +251,7 @@ ALTER TABLE sample_relationships_all ADD CONSTRAINT sare_bk_uk UNIQUE(sample_id_
ALTER TABLE relationship_types ADD CONSTRAINT rety_uk UNIQUE(code,dbin_id);
ALTER TABLE SCRIPTS ADD CONSTRAINT SCRI_UK UNIQUE(NAME,DBIN_ID);
ALTER TABLE CORE_PLUGINS ADD CONSTRAINT COPL_NAME_VER_UK UNIQUE(NAME,VERSION);
+ALTER TABLE ENTITY_OPERATIONS_LOG ADD CONSTRAINT EOL_REG_ID_UK UNIQUE(REGISTRATION_ID);
-- Creating foreign key constraints
@@ -543,3 +548,4 @@ CREATE INDEX GRID_CUSTOM_COLUMNS_PERS_FK_I ON GRID_CUSTOM_COLUMNS (PERS_ID_REGIS
CREATE INDEX GRID_CUSTOM_COLUMNS_DBIN_FK_I ON GRID_CUSTOM_COLUMNS (DBIN_ID);
CREATE INDEX SCRIPT_PERS_FK_I ON SCRIPTS (PERS_ID_REGISTERER);
CREATE INDEX SCRIPT_DBIN_FK_I ON SCRIPTS (DBIN_ID);
+CREATE INDEX ENTITY_OPERATIONS_LOG_RID_I ON ENTITY_OPERATIONS_LOG(REGISTRATION_ID);
diff --git a/openbis/source/sql/postgresql/105/grants-105.sql b/openbis/source/sql/postgresql/105/grants-105.sql
index 58e6a28f7ab..efed69b5ad8 100644
--- a/openbis/source/sql/postgresql/105/grants-105.sql
+++ b/openbis/source/sql/postgresql/105/grants-105.sql
@@ -41,6 +41,7 @@ GRANT SELECT ON SEQUENCE authorization_group_id_seq TO GROUP OPENBIS_READONLY;
GRANT SELECT ON SEQUENCE filter_id_seq TO GROUP OPENBIS_READONLY;
GRANT SELECT ON SEQUENCE query_id_seq TO GROUP OPENBIS_READONLY;
GRANT SELECT ON SEQUENCE POST_REGISTRATION_DATASET_QUEUE_ID_SEQ TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE ENTITY_OPERATIONS_LOG_ID_SEQ TO GROUP OPENBIS_READONLY;
GRANT SELECT ON TABLE attachment_contents TO GROUP OPENBIS_READONLY;
GRANT SELECT ON TABLE attachments TO GROUP OPENBIS_READONLY;
GRANT SELECT ON TABLE controlled_vocabularies TO GROUP OPENBIS_READONLY;
@@ -98,3 +99,4 @@ GRANT SELECT ON TABLE filters TO GROUP OPENBIS_READONLY;
GRANT SELECT ON TABLE queries TO GROUP OPENBIS_READONLY;
GRANT SELECT ON TABLE scripts TO GROUP OPENBIS_READONLY;
GRANT SELECT ON TABLE POST_REGISTRATION_DATASET_QUEUE TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE ENTITY_OPERATIONS_LOG TO GROUP OPENBIS_READONLY;
diff --git a/openbis/source/sql/postgresql/migration/migration-104-105.sql b/openbis/source/sql/postgresql/migration/migration-104-105.sql
index 4a68c04938a..9eca380426f 100644
--- a/openbis/source/sql/postgresql/migration/migration-104-105.sql
+++ b/openbis/source/sql/postgresql/migration/migration-104-105.sql
@@ -1,3 +1,11 @@
-- Migration from 104 to 105
ALTER DOMAIN DATA_STORE_SERVICE_REPORTING_PLUGIN_TYPE DROP CONSTRAINT DATA_STORE_SERVICE_REPORTING_PLUGIN_TYPE_CHECK;
-ALTER DOMAIN DATA_STORE_SERVICE_REPORTING_PLUGIN_TYPE ADD CONSTRAINT DATA_STORE_SERVICE_REPORTING_PLUGIN_TYPE_CHECK CHECK (VALUE IN ('TABLE_MODEL', 'DSS_LINK', 'AGGREGATION_TABLE_MODEL'));
\ No newline at end of file
+ALTER DOMAIN DATA_STORE_SERVICE_REPORTING_PLUGIN_TYPE ADD CONSTRAINT DATA_STORE_SERVICE_REPORTING_PLUGIN_TYPE_CHECK CHECK (VALUE IN ('TABLE_MODEL', 'DSS_LINK', 'AGGREGATION_TABLE_MODEL'));
+
+CREATE TABLE ENTITY_OPERATIONS_LOG (ID TECH_ID NOT NULL, REGISTRATION_ID TECH_ID NOT NULL);
+CREATE SEQUENCE ENTITY_OPERATIONS_LOG_ID_SEQ;
+ALTER TABLE ENTITY_OPERATIONS_LOG ADD CONSTRAINT EOL_PK PRIMARY KEY(ID);
+ALTER TABLE ENTITY_OPERATIONS_LOG ADD CONSTRAINT EOL_REG_ID_UK UNIQUE(REGISTRATION_ID);
+CREATE INDEX ENTITY_OPERATIONS_LOG_RID_I ON ENTITY_OPERATIONS_LOG(REGISTRATION_ID);
+GRANT SELECT ON SEQUENCE ENTITY_OPERATIONS_LOG_ID_SEQ TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE ENTITY_OPERATIONS_LOG TO GROUP OPENBIS_READONLY;
\ No newline at end of file
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 f737c2e1998..061fe17ca45 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
@@ -50,6 +50,7 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
@@ -975,7 +976,7 @@ public class ETLServiceTest extends AbstractServerTestCase
}
@Test
- public void testPerformOperations()
+ public void testPerformOperationsWithoutRegistrationId()
{
prepareGetSession();
@@ -1019,6 +1020,41 @@ public class ETLServiceTest extends AbstractServerTestCase
dataSetUpdate.setModifiedContainedDatasetCodesOrNull(new String[]
{ "c1", "c2" });
+ prepareEntityOperationsExpectations(samplePE, sampleUpdate, material, materialType,
+ newMaterial, newSamplePE, newSampleIdentifier, newSample, externalData,
+ updatedDataSetCode, dataSetUpdate);
+
+ AtomicEntityOperationDetails details =
+ new AtomicEntityOperationDetails(null, null, new ArrayList<NewSpace>(),
+ new ArrayList<NewProject>(), new ArrayList<NewExperiment>(),
+ Collections.singletonList(sampleUpdate),
+ Collections.singletonList(newSample), materialRegistrations,
+ Collections.singletonList(externalData),
+ Collections.singletonList(dataSetUpdate));
+
+ AtomicEntityOperationResult result =
+ createService().performEntityOperations(SESSION_TOKEN, details);
+ assertNotNull(result);
+ assertEquals(sampleUpdate.getSampleIdentifier().toString(),
+ result.getSamplesUpdated().get(0).getIdentifier());
+ assertEquals(experiment.getIdentifier(), result.getSamplesUpdated().get(0).getExperiment()
+ .getIdentifier());
+
+ assertEquals(newSample.getIdentifier(), result.getSamplesCreated().get(0).getIdentifier());
+ assertEquals(experiment.getIdentifier(), result.getSamplesCreated().get(0).getExperiment()
+ .getIdentifier());
+ assertEquals(updatedDataSetCode, result.getDataSetsUpdated().get(0).getCode());
+
+ context.assertIsSatisfied();
+ }
+
+ private void prepareEntityOperationsExpectations(final SamplePE samplePE,
+ final SampleUpdatesDTO sampleUpdate, final MaterialPE material,
+ final MaterialTypePE materialType, final NewMaterial newMaterial,
+ final SamplePE newSamplePE, final SampleIdentifier newSampleIdentifier,
+ final NewSample newSample, final NewExternalData externalData,
+ final String updatedDataSetCode, final DataSetUpdatesDTO dataSetUpdate)
+ {
context.checking(new Expectations()
{
{
@@ -1106,9 +1142,66 @@ public class ETLServiceTest extends AbstractServerTestCase
will(returnValue(updatedDataSet));
}
});
+ }
+
+ @Test
+ public void testPerformOperations()
+ {
+ prepareGetSession();
+
+ final ExperimentPE experiment = createExperiment("TYPE", "EXP1", "G1");
+ final SamplePE samplePE = createSampleWithExperiment(experiment);
+ final SampleIdentifier sampleIdentifier = samplePE.getSampleIdentifier();
+
+ final Date version = new Date();
+ final Collection<NewAttachment> attachments = Collections.<NewAttachment> emptyList();
+
+ final SampleUpdatesDTO sampleUpdate =
+ new SampleUpdatesDTO(CommonTestUtils.TECH_ID, null, null, attachments, version,
+ sampleIdentifier, null, null);
+
+ final MaterialPE material = new MaterialPE();
+ material.setCode("new-material");
+ final MaterialTypePE materialType = new MaterialTypePE();
+ materialType.setCode("new-material-type");
+ materialType.setDatabaseInstance(new DatabaseInstancePEBuilder().code("DB")
+ .getDatabaseInstance());
+ final NewMaterial newMaterial = new NewMaterial(material.getCode());
+ Map<String, List<NewMaterial>> materialRegistrations =
+ new HashMap<String, List<NewMaterial>>();
+ materialRegistrations.put(materialType.getCode(), Arrays.asList(newMaterial));
+
+ final SamplePE newSamplePE = createSampleWithExperiment(experiment);
+ newSamplePE.setCode("SAMPLE_CODE_NEW");
+ final SampleIdentifier newSampleIdentifier = newSamplePE.getSampleIdentifier();
+ final NewSample newSample = new NewSample();
+ newSample.setIdentifier(newSampleIdentifier.toString());
+
+ final NewExternalData externalData = new NewExternalData();
+ externalData.setCode("dc");
+ externalData.setMeasured(true);
+ externalData.setSampleIdentifierOrNull(newSampleIdentifier);
+
+ final String updatedDataSetCode = "updateDataSetCode";
+ final DataSetUpdatesDTO dataSetUpdate = new DataSetUpdatesDTO();
+ dataSetUpdate.setDatasetId(CommonTestUtils.TECH_ID);
+ dataSetUpdate.setFileFormatTypeCode("new-file-format");
+ dataSetUpdate.setModifiedContainedDatasetCodesOrNull(new String[]
+ { "c1", "c2" });
+
+ prepareEntityOperationsExpectations(samplePE, sampleUpdate, material, materialType,
+ newMaterial, newSamplePE, newSampleIdentifier, newSample, externalData,
+ updatedDataSetCode, dataSetUpdate);
+
+ context.checking(new Expectations()
+ {
+ {
+ one(entityOperationsLogDAO).addLogEntry(new Long(1));
+ }
+ });
AtomicEntityOperationDetails details =
- new AtomicEntityOperationDetails(null, new ArrayList<NewSpace>(),
+ new AtomicEntityOperationDetails(new TechId(1), null, new ArrayList<NewSpace>(),
new ArrayList<NewProject>(), new ArrayList<NewExperiment>(),
Collections.singletonList(sampleUpdate),
Collections.singletonList(newSample), materialRegistrations,
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
index fcad72be014..2ca9c55e4e5 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
@@ -60,6 +60,7 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataSetTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataStoreDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDatabaseInstanceDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDeletionDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityOperationsLogDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IFileFormatTypeDAO;
@@ -197,6 +198,8 @@ public abstract class AbstractServerTestCase extends AssertJUnit
protected IHibernateSearchDAO hibernateSearchDAO;
+ protected IEntityOperationsLogDAO entityOperationsLogDAO;
+
@BeforeMethod
@SuppressWarnings("unchecked")
public void setUp()
@@ -229,6 +232,7 @@ public abstract class AbstractServerTestCase extends AssertJUnit
queryDAO = context.mock(IQueryDAO.class);
deletionDAO = context.mock(IDeletionDAO.class);
hibernateSearchDAO = context.mock(IHibernateSearchDAO.class);
+ entityOperationsLogDAO = context.mock(IEntityOperationsLogDAO.class);
// BO
groupBO = context.mock(IGroupBO.class);
entityTypeBO = context.mock(IEntityTypeBO.class);
@@ -288,6 +292,8 @@ public abstract class AbstractServerTestCase extends AssertJUnit
will(returnValue(deletionDAO));
allowing(daoFactory).getHibernateSearchDAO();
will(returnValue(hibernateSearchDAO));
+ allowing(daoFactory).getEntityOperationsLogDAO();
+ will(returnValue(entityOperationsLogDAO));
}
});
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
index e033fecd653..e52fbe8991e 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
@@ -121,11 +121,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
- public Experiment tryToGetExperiment(
- String sessionToken,
+ public Experiment tryToGetExperiment(String sessionToken,
@AuthorizationGuard(guardClass = ExistingSpaceIdentifierPredicate.class)
- ExperimentIdentifier experimentIdentifier)
- throws UserFailureException;
+ ExperimentIdentifier experimentIdentifier) throws UserFailureException;
/**
* For given {@link MaterialIdentifier} returns the corresponding {@link Material}.
@@ -164,11 +162,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
- public Sample tryGetSampleWithExperiment(
- final String sessionToken,
+ public Sample tryGetSampleWithExperiment(final String sessionToken,
@AuthorizationGuard(guardClass = ExistingSampleOwnerIdentifierPredicate.class)
- final SampleIdentifier sampleIdentifier)
- throws UserFailureException;
+ final SampleIdentifier sampleIdentifier) throws UserFailureException;
/**
* Returns a list of terms belonging to given vocabulary.
@@ -203,11 +199,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
- public List<ExternalData> listDataSetsByExperimentID(
- final String sessionToken,
+ public List<ExternalData> listDataSetsByExperimentID(final String sessionToken,
@AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class)
- final TechId experimentID)
- throws UserFailureException;
+ final TechId experimentID) throws UserFailureException;
/**
* For given sample {@link TechId} returns the corresponding list of {@link ExternalData}.
@@ -219,8 +213,8 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
public List<ExternalData> listDataSetsBySampleID(final String sessionToken,
@AuthorizationGuard(guardClass = SampleTechIdPredicate.class)
- final TechId sampleId,
- final boolean showOnlyDirectlyConnected) throws UserFailureException;
+ final TechId sampleId, final boolean showOnlyDirectlyConnected)
+ throws UserFailureException;
/**
* Returns all data sets found for specified data set codes.
@@ -230,11 +224,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
- public List<ExternalData> listDataSetsByCode(
- String sessionToken,
+ public List<ExternalData> listDataSetsByCode(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class)
- List<String> dataSetCodes)
- throws UserFailureException;
+ List<String> dataSetCodes) throws UserFailureException;
/**
* Lists samples using given configuration.
@@ -245,8 +237,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@RolesAllowed(
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
@ReturnValueFilter(validatorClass = SampleValidator.class)
- public List<Sample> listSamples(
- final String sessionToken,
+ public List<Sample> listSamples(final String sessionToken,
@AuthorizationGuard(guardClass = ListSampleCriteriaPredicate.class)
final ListSampleCriteria criteria);
@@ -262,11 +253,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
- public IEntityProperty[] tryToGetPropertiesOfTopSampleRegisteredFor(
- final String sessionToken,
+ public IEntityProperty[] tryToGetPropertiesOfTopSampleRegisteredFor(final String sessionToken,
@AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class)
- final SampleIdentifier sampleIdentifier)
- throws UserFailureException;
+ final SampleIdentifier sampleIdentifier) throws UserFailureException;
/**
* Registers/updates various entities in one transaction.
@@ -286,8 +275,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@DatabaseCreateOrDeleteModification(value = ObjectKind.EXPERIMENT)
public long registerExperiment(String sessionToken,
@AuthorizationGuard(guardClass = NewExperimentPredicate.class)
- NewExperiment experiment)
- throws UserFailureException;
+ NewExperiment experiment) throws UserFailureException;
/**
* Registers samples in batches.
@@ -295,11 +283,10 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseUpdateModification(value = ObjectKind.SAMPLE)
- public void registerSamples(
- final String sessionToken,
+ public void registerSamples(final String sessionToken,
@AuthorizationGuard(guardClass = NewSamplesWithTypePredicate.class)
- final List<NewSamplesWithTypes> newSamplesWithType,
- String userIdOrNull) throws UserFailureException;
+ final List<NewSamplesWithTypes> newSamplesWithType, String userIdOrNull)
+ throws UserFailureException;
/**
* Registers a new sample.
@@ -309,8 +296,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@DatabaseCreateOrDeleteModification(value = ObjectKind.SAMPLE)
public long registerSample(final String sessionToken,
@AuthorizationGuard(guardClass = NewSamplePredicate.class)
- final NewSample newSample,
- String userIDOrNull) throws UserFailureException;
+ final NewSample newSample, String userIDOrNull) throws UserFailureException;
/**
* Saves changed sample.
@@ -336,11 +322,10 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseCreateOrDeleteModification(value = ObjectKind.DATA_SET)
- public void registerDataSet(
- final String sessionToken,
+ public void registerDataSet(final String sessionToken,
@AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class)
- final SampleIdentifier sampleIdentifier,
- final NewExternalData externalData) throws UserFailureException;
+ final SampleIdentifier sampleIdentifier, final NewExternalData externalData)
+ throws UserFailureException;
/**
* Registers the specified data connected to an experiment.
@@ -356,11 +341,10 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseCreateOrDeleteModification(value = ObjectKind.DATA_SET)
- public void registerDataSet(
- final String sessionToken,
+ public void registerDataSet(final String sessionToken,
@AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class)
- final ExperimentIdentifier experimentIdentifier,
- final NewExternalData externalData) throws UserFailureException;
+ final ExperimentIdentifier experimentIdentifier, final NewExternalData externalData)
+ throws UserFailureException;
/**
* Checks that the user of specified session has INSTANCE_ADMIN access rights.
@@ -384,8 +368,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public void checkDataSetAccess(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class)
- String dataSetCode)
- throws UserFailureException;
+ String dataSetCode) throws UserFailureException;
/**
* Check if the current user can access all the data sets in the list
@@ -395,8 +378,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
- public void checkDataSetCollectionAccess(
- String sessionToken,
+ public void checkDataSetCollectionAccess(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class)
List<String> dataSetCodes);
@@ -408,8 +390,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
public ExternalData tryGetDataSet(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class)
- String dataSetCode)
- throws UserFailureException;
+ String dataSetCode) throws UserFailureException;
/**
* Creates and returns a unique code for a new data set. TODO KE: 2011-04-19 remove this method.
@@ -441,11 +422,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
- public List<Sample> listSamplesByCriteria(
- final String sessionToken,
+ public List<Sample> listSamplesByCriteria(final String sessionToken,
@AuthorizationGuard(guardClass = ListSamplesByPropertyPredicate.class)
- final ListSamplesByPropertyCriteria criteria)
- throws UserFailureException;
+ final ListSamplesByPropertyCriteria criteria) throws UserFailureException;
/**
* Lists share ids of all data sets belonging to chosen data store (even the ones in trash!).
@@ -493,8 +472,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
- public List<Experiment> listExperiments(
- String sessionToken,
+ public List<Experiment> listExperiments(String sessionToken,
@AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class)
ProjectIdentifier projectIdentifier);
@@ -504,8 +482,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
- public List<Experiment> listExperiments(
- String sessionToken,
+ public List<Experiment> listExperiments(String sessionToken,
@AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class)
List<ExperimentIdentifier> experimentIdentifiers,
ExperimentFetchOptions experimentFetchOptions);
@@ -516,8 +493,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
- public List<Experiment> listExperimentsForProjects(
- String sessionToken,
+ public List<Experiment> listExperimentsForProjects(String sessionToken,
@AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class)
List<ProjectIdentifier> projectIdentifiers,
ExperimentFetchOptions experimentFetchOptions);
@@ -548,13 +524,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseUpdateModification(value = ObjectKind.DATA_SET)
- public void addPropertiesToDataSet(
- String sessionToken,
- List<NewProperty> properties,
- String dataSetCode,
- @AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class)
- final SpaceIdentifier identifier)
- throws UserFailureException;
+ public void addPropertiesToDataSet(String sessionToken, List<NewProperty> properties,
+ String dataSetCode, @AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class)
+ final SpaceIdentifier identifier) throws UserFailureException;
/**
* Updates share id and size of specified data set.
@@ -564,8 +536,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@DatabaseUpdateModification(value = ObjectKind.DATA_SET)
public void updateShareIdAndSize(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class)
- String dataSetCode,
- String shareId, long size) throws UserFailureException;
+ String dataSetCode, String shareId, long size) throws UserFailureException;
/**
* Updates status of given data sets.
@@ -573,12 +544,10 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseUpdateModification(value = ObjectKind.DATA_SET)
- public void updateDataSetStatuses(
- String sessionToken,
+ public void updateDataSetStatuses(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class)
- List<String> dataSetCodes,
- final DataSetArchivingStatus newStatus, boolean presentInArchive)
- throws UserFailureException;
+ List<String> dataSetCodes, final DataSetArchivingStatus newStatus,
+ boolean presentInArchive) throws UserFailureException;
/**
* Set the status for a given dataset to the given new status value if the current status equals
@@ -604,11 +573,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseUpdateModification(value = ObjectKind.DATA_SET)
- public int archiveDatasets(
- String sessionToken,
+ public int archiveDatasets(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class)
- List<String> datasetCodes,
- boolean removeFromDataStore);
+ List<String> datasetCodes, boolean removeFromDataStore);
/**
* Schedules unarchiving of specified data sets.
@@ -618,8 +585,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseUpdateModification(value = ObjectKind.DATA_SET)
- public int unarchiveDatasets(
- String sessionToken,
+ public int unarchiveDatasets(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class)
List<String> datasetCodes);
@@ -642,8 +608,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
public ExternalData tryGetDataSetForServer(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class)
- String dataSetCode)
- throws UserFailureException;
+ String dataSetCode) throws UserFailureException;
/**
* Returns a list of unique codes.
@@ -685,8 +650,8 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
{ ObjectKind.SAMPLE, ObjectKind.DATA_SET })
public Sample registerSampleAndDataSet(final String sessionToken,
@AuthorizationGuard(guardClass = NewSamplePredicate.class)
- final NewSample newSample,
- final NewExternalData externalData, String userIdOrNull) throws UserFailureException;
+ final NewSample newSample, final NewExternalData externalData, String userIdOrNull)
+ throws UserFailureException;
/**
* Updates a sample and registers a data set connected to that sample in one transaction.
@@ -703,11 +668,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseUpdateModification(value = ObjectKind.SAMPLE)
@DatabaseCreateOrDeleteModification(value = ObjectKind.DATA_SET)
- public Sample updateSampleAndRegisterDataSet(
- String sessionToken,
+ public Sample updateSampleAndRegisterDataSet(String sessionToken,
@AuthorizationGuard(guardClass = SampleUpdatesPredicate.class)
- SampleUpdatesDTO updates,
- NewExternalData externalData);
+ SampleUpdatesDTO updates, NewExternalData externalData);
/**
* Updates a sample and registers a data set connected to that sample in one transaction.
@@ -724,8 +687,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@DatabaseCreateOrDeleteModification(value =
{ ObjectKind.SPACE, ObjectKind.PROJECT, ObjectKind.SAMPLE, ObjectKind.EXPERIMENT,
ObjectKind.DATA_SET })
- public AtomicEntityOperationResult performEntityOperations(
- String sessionToken,
+ public AtomicEntityOperationResult performEntityOperations(String sessionToken,
@AuthorizationGuard(guardClass = AtomicOperationsPredicate.class)
AtomicEntityOperationDetails operationDetails);
@@ -735,8 +697,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER })
- public Space tryGetSpace(
- String sessionToken,
+ public Space tryGetSpace(String sessionToken,
@AuthorizationGuard(guardClass = ExistingSpaceIdentifierPredicate.class)
SpaceIdentifier spaceIdentifier);
@@ -746,8 +707,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional(readOnly = true)
@RolesAllowed(value =
{ RoleWithHierarchy.SPACE_ETL_SERVER })
- public Project tryGetProject(
- String sessionToken,
+ public Project tryGetProject(String sessionToken,
@AuthorizationGuard(guardClass = ExistingSpaceIdentifierPredicate.class)
ProjectIdentifier projectIdentifier);
@@ -782,11 +742,9 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
{ ObjectKind.SAMPLE, ObjectKind.EXPERIMENT })
@DatabaseCreateOrDeleteModification(value =
{ ObjectKind.DATA_SET })
- public void removeDataSetsPermanently(
- String sessionToken,
+ public void removeDataSetsPermanently(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class)
- List<String> dataSetCodes,
- String reason);
+ List<String> dataSetCodes, String reason);
/**
* updates a data set.
@@ -795,8 +753,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@DatabaseUpdateModification(value =
{ ObjectKind.EXPERIMENT, ObjectKind.SAMPLE, ObjectKind.DATA_SET })
- public void updateDataSet(
- String sessionToken,
+ public void updateDataSet(String sessionToken,
@AuthorizationGuard(guardClass = DataSetUpdatesPredicate.class)
DataSetUpdatesDTO dataSetUpdates);
@@ -837,4 +794,12 @@ public interface IETLLIMSService extends IServer, ISessionProvider, Conversation
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
public List<ExternalData> listDataSetsForPostRegistration(String token, String dataStoreCode);
+
+ /**
+ * Return true if the log indicates that the performEntityOperations invocation for the given
+ * registrationId succeeded.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public Boolean didEntityOperationsSucceed(String token, TechId registrationId);
}
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 881f36d23e1..e65ac36460e 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
@@ -85,12 +85,14 @@ public class AtomicEntityOperationDetailsTest extends AssertJUnit
dataSetUpdates.add(dataSetUpdate);
AtomicEntityOperationDetails details =
- new AtomicEntityOperationDetails(null, spaceRegistrations, projectRegistrations,
- experimentRegistrations, sampleUpdates, sampleRegistrations,
- materialRegistrations, dataSetRegistrations, dataSetUpdates);
+ new AtomicEntityOperationDetails(null, null, spaceRegistrations,
+ projectRegistrations, experimentRegistrations, sampleUpdates,
+ sampleRegistrations, materialRegistrations, dataSetRegistrations,
+ dataSetUpdates);
assertEquals(
- "AtomicEntityOperationDetails[userIdOrNull=<null>"
+ "AtomicEntityOperationDetails[registrationIdOrNull=<null>"
+ + ",userIdOrNull=<null>"
+ ",spaceRegistrations=[SPACE1, SPACE2]"
+ ",projectRegistrations=[/SPACE/P1, /SPACE/P2]"
+ ",experimentUpdates=[]"
diff --git a/openbis/sourceTest/sql/postgresql/105/finish-105.sql b/openbis/sourceTest/sql/postgresql/105/finish-105.sql
index 7ac24414201..ed0c554c585 100644
--- a/openbis/sourceTest/sql/postgresql/105/finish-105.sql
+++ b/openbis/sourceTest/sql/postgresql/105/finish-105.sql
@@ -64,6 +64,8 @@ ALTER TABLE ONLY data_set_types
ADD CONSTRAINT dsty_bk_uk UNIQUE (code, dbin_id);
ALTER TABLE ONLY data_set_types
ADD CONSTRAINT dsty_pk PRIMARY KEY (id);
+ALTER TABLE ONLY entity_operations_log
+ ADD CONSTRAINT eol_pk PRIMARY KEY (id);
ALTER TABLE ONLY experiment_type_property_types
ADD CONSTRAINT etpt_bk_uk UNIQUE (exty_id, prty_id);
ALTER TABLE ONLY experiment_type_property_types
@@ -219,6 +221,7 @@ CREATE INDEX dsse_ds_fk_i ON data_store_services USING btree (data_store_id);
CREATE INDEX dstpt_dsty_fk_i ON data_set_type_property_types USING btree (dsty_id);
CREATE INDEX dstpt_pers_fk_i ON data_set_type_property_types USING btree (pers_id_registerer);
CREATE INDEX dstpt_prty_fk_i ON data_set_type_property_types USING btree (prty_id);
+CREATE INDEX entity_operations_log_rid_i ON entity_operations_log USING btree (registration_id);
CREATE INDEX etpt_exty_fk_i ON experiment_type_property_types USING btree (exty_id);
CREATE INDEX etpt_pers_fk_i ON experiment_type_property_types USING btree (pers_id_registerer);
CREATE INDEX etpt_prty_fk_i ON experiment_type_property_types USING btree (prty_id);
diff --git a/openbis/sourceTest/sql/postgresql/105/schema-105.sql b/openbis/sourceTest/sql/postgresql/105/schema-105.sql
index 1eeb638af13..81a91f14ed0 100644
--- a/openbis/sourceTest/sql/postgresql/105/schema-105.sql
+++ b/openbis/sourceTest/sql/postgresql/105/schema-105.sql
@@ -745,6 +745,17 @@ CREATE SEQUENCE dstpt_id_seq
NO MAXVALUE
CACHE 1;
SELECT pg_catalog.setval('dstpt_id_seq', 4, true);
+CREATE TABLE entity_operations_log (
+ id tech_id NOT NULL,
+ registration_id tech_id NOT NULL
+);
+CREATE SEQUENCE entity_operations_log_id_seq
+ START WITH 1
+ INCREMENT BY 1
+ NO MINVALUE
+ NO MAXVALUE
+ CACHE 1;
+SELECT pg_catalog.setval('entity_operations_log_id_seq', 1, false);
CREATE SEQUENCE etpt_id_seq
START WITH 1
INCREMENT BY 1
--
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