diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/MultiDataSetArchiverOrphanFinderTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/MultiDataSetArchiverOrphanFinderTask.java
index 0b67e117d09af486a66fd15037b4249def08d126..62bf27811556cdff695ed8747a321e4be181ac32 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/MultiDataSetArchiverOrphanFinderTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/MultiDataSetArchiverOrphanFinderTask.java
@@ -21,6 +21,9 @@ import ch.systemsx.cisd.openbis.dss.generic.server.DataStoreServer;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.archiver.dataaccess.IMultiDataSetArchiverReadonlyQueryDAO;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.archiver.dataaccess.MultiDataSetArchiverContainerDTO;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.archiver.dataaccess.MultiDataSetArchiverDataSourceUtil;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
public class MultiDataSetArchiverOrphanFinderTask implements IMaintenanceTask
{
@@ -49,64 +52,69 @@ public class MultiDataSetArchiverOrphanFinderTask implements IMaintenanceTask
{
operationLog.info(MultiDataSetArchiverOrphanFinderTask.class.getSimpleName() + " Started");
- // 1.Database, obtain a list of the containers on the database.
- operationLog.info("1.Database, obtain a list of the containers on the database.");
+ // 1.Directories
+ operationLog.info("1.Directories, obtain archiver directory.");
+ String destination = DataStoreServer.getConfigParameters().getProperties().getProperty("archiver.final-destination", null);
+ if (destination == null)
+ {
+ destination = DataStoreServer.getConfigParameters().getProperties().getProperty("archiver.destination", null);
+ }
+
+ if (destination == null)
+ {
+ operationLog.info("No destination directory found, this task can't execute.");
+ return;
+ }
+
+ // 2.Database
+ operationLog.info("2.1 Database, obtain a list of the multi dataset containers on the database.");
IMultiDataSetArchiverReadonlyQueryDAO readonlyQuery = MultiDataSetArchiverDataSourceUtil.getReadonlyQueryDAO();
List<MultiDataSetArchiverContainerDTO> containerDTOs = readonlyQuery.listContainers();
- Set<String> containersOnDB = new HashSet<String>();
+ Set<String> multiDatasetsContainersOnDB = new HashSet<String>();
for (MultiDataSetArchiverContainerDTO containerDTO : containerDTOs)
{
- containersOnDB.add(containerDTO.getPath());
+ multiDatasetsContainersOnDB.add(containerDTO.getPath());
}
- // 2.Directories, obtain a list of the files into the directory.
- operationLog.info("2.Directories, obtain a list of the files into the directory.");
- // String tempFolder = DataStoreServer.getConfigParameters().getProperties().getProperty("archiver.temp-folder", null);
- String finalDestination = DataStoreServer.getConfigParameters().getProperties().getProperty("archiver.final-destination", null);
- // String replicatedDestination = DataStoreServer.getConfigParameters().getProperties().getProperty("archiver.replicated-destination", null);
- File[] containersOnDisk = new File(finalDestination).listFiles();
-
- // 3.Verify if the files are on the database containers
- operationLog.info("3.Verify if the files are on the database containers.");
- List<File> notFound = new ArrayList<File>();
- for (File file : containersOnDisk)
+ operationLog.info("2.2 Database, obtain a list of the archived datasets on the database.");
+ IEncapsulatedOpenBISService service = ServiceProvider.getOpenBISService();
+ List<SimpleDataSetInformationDTO> presentDTOs = service.listPhysicalDataSetsByArchivingStatus(null, Boolean.TRUE);
+ Set<String> presentInArchiveOnDB = new HashSet<String>();
+ for (SimpleDataSetInformationDTO presentDTO : presentDTOs)
{
- if (containersOnDB.contains(file.getName()))
- {
- operationLog.info("Found container: " + file.getName());
- } else
- {
- notFound.add(file);
- operationLog.info("Not Found file: " + file.getName());
- }
+ presentInArchiveOnDB.add(presentDTO.getDataSetCode());
}
- // 4.Verify if the non found files follow the format needed to qualify as Multi DataSet Archiver containers.
- operationLog.info("4.Verify if the non found files follow the format needed to qualify as Multi DataSet Archiver containers.");
- List<File> notFoundFilesAndMDAFormat = new ArrayList<File>();
- for (File file : notFound)
+ // 3.Verify if the files on destination are on multi dataset archiver containers or a normal archived dataset
+ operationLog.info("3.Verify if the files on destination are on multi dataset archiver containers or a normal archived dataset.");
+ File[] filesOnDisk = new File(destination).listFiles();
+ List<File> notFounds = new ArrayList<File>();
+ for (File file : filesOnDisk)
{
- String name = file.getName();
- String[] nameParts = name.split("-");
- if (nameParts.length == 4 && name.endsWith(".tar"))
+ if (multiDatasetsContainersOnDB.contains(file.getName()))
+ {
+ operationLog.info("Found multi dataset archiver container: " + file.getName());
+ } else if ((file.getName().toLowerCase().endsWith(".tar") ||
+ file.getName().toLowerCase().endsWith(".zip"))
+ && presentInArchiveOnDB.contains(file.getName().substring(0, file.getName().length() - 4)))
{
- notFoundFilesAndMDAFormat.add(file);
- operationLog.info("Not Found file, MDA format: " + file.getName());
+ operationLog.info("Found archived dataset: " + file.getName());
} else
{
- operationLog.info("Not Found file, not MDA format: " + file.getName());
+ notFounds.add(file);
+ operationLog.info("Not Found file: " + file.getName());
}
}
- // 5.Send email with not found files with MDA format.
- operationLog.info("Send email with not found files with MDA format.");
- if (notFoundFilesAndMDAFormat.size() > 0)
+ // 4.Send email with not found files.
+ operationLog.info("4.Send email with not found files.");
+ if (notFounds.size() > 0)
{
String subject = "openBIS MultiDataSetArchiverOrphanFinderTask found files";
- String content = "Found " + notFoundFilesAndMDAFormat.size() + " files by MultiDataSetArchiverOrphanFinderTask:\n";
- for (File notFoundFileAndMDAFormat : notFoundFilesAndMDAFormat)
+ String content = "Found " + notFounds.size() + " files by MultiDataSetArchiverOrphanFinderTask:\n";
+ for (File notFound : notFounds)
{
- content += notFoundFileAndMDAFormat.getName() + "\t" + notFoundFileAndMDAFormat.length() + "\n";
+ content += notFound.getName() + "\t" + notFound.length() + "\n";
}
for (EMailAddress recipient : emailAddresses)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/ResetArchivePendingTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/ResetArchivePendingTask.java
index d6fd57f93a13d9e2f46125057c17466e79c81f79..9fce18e0c34b6d7e9c9488677107af76b0dd40c3 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/ResetArchivePendingTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/ResetArchivePendingTask.java
@@ -57,7 +57,7 @@ public class ResetArchivePendingTask implements IMaintenanceTask
operationLog.info(ResetArchivePendingTask.class.getSimpleName() + " Started");
// 1. Find datasets with DataSetArchivingStatus.ARCHIVE_PENDING
IEncapsulatedOpenBISService service = ServiceProvider.getOpenBISService();
- List<SimpleDataSetInformationDTO> inArchivePendings = service.listPhysicalDataSetsByArchivingStatus(DataSetArchivingStatus.ARCHIVE_PENDING);
+ List<SimpleDataSetInformationDTO> inArchivePendings = service.listPhysicalDataSetsByArchivingStatus(DataSetArchivingStatus.ARCHIVE_PENDING, null);
if (inArchivePendings.isEmpty() == false)
{
operationLog.info("Found " + inArchivePendings.size() + " datasets in " + DataSetArchivingStatus.ARCHIVE_PENDING.name() + " status.");
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
index 48c4b4fbfdfa6db28f59e292e5f7e21ea5f5d4fe..ea2fb19f317ca8caf326ef0f9e5b888bd8d8292d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
@@ -692,11 +692,11 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
}
@Override
- public List<SimpleDataSetInformationDTO> listPhysicalDataSetsByArchivingStatus(DataSetArchivingStatus archivingStatus)
+ public List<SimpleDataSetInformationDTO> listPhysicalDataSetsByArchivingStatus(DataSetArchivingStatus archivingStatus, Boolean presentInArchive)
throws UserFailureException
{
List<SimpleDataSetInformationDTO> dataSets = service.listPhysicalDataSetsByArchivingStatus(session.getSessionToken(),
- session.getDataStoreCode(), archivingStatus);
+ session.getDataStoreCode(), archivingStatus, presentInArchive);
return injectDefaultShareIdIfMissing(dataSets);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
index 28ea7a3d5f171d0c2a527f1fda924f4ed9c45da8..eb9aadde38907162abdd318fc58cc641b5e0b7b4 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
@@ -292,7 +292,7 @@ public interface IEncapsulatedOpenBISService extends IEncapsulatedBasicOpenBISSe
* Returns informations about physical data sets with certain archiving status
*/
@ManagedAuthentication
- public List<SimpleDataSetInformationDTO> listPhysicalDataSetsByArchivingStatus(DataSetArchivingStatus archivingStatus)
+ public List<SimpleDataSetInformationDTO> listPhysicalDataSetsByArchivingStatus(DataSetArchivingStatus archivingStatus, Boolean presentInArchive)
throws UserFailureException;
/**
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServer.java
index 3be2a21633a0b82fee05e5a40e6ae5049ade0c50..61e8f1abf38018cea1bf4eab3c350ca85851df4b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServer.java
@@ -605,7 +605,7 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
@RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
public Experiment tryGetExperiment(String sessionToken,
@AuthorizationGuard(guardClass = ExistingSpaceIdentifierPredicate.class) ExperimentIdentifier experimentIdentifier)
- throws UserFailureException
+ throws UserFailureException
{
assert sessionToken != null : "Unspecified session token.";
assert experimentIdentifier != null : "Unspecified experiment identifier.";
@@ -650,7 +650,7 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
@ReturnValueFilter(validatorClass = SampleValidator.class)
public List<Sample> listSamples(final String sessionToken,
@AuthorizationGuard(guardClass = ListSampleCriteriaPredicate.class)
- final ListSampleCriteria criteria)
+ final ListSampleCriteria criteria)
{
final Session session = getSession(sessionToken);
final ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
@@ -661,7 +661,7 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
public Sample tryGetSampleWithExperiment(final String sessionToken,
@AuthorizationGuard(guardClass = ExistingSampleOwnerIdentifierPredicate.class)
- final SampleIdentifier sampleIdentifier) throws UserFailureException
+ final SampleIdentifier sampleIdentifier) throws UserFailureException
{
assert sessionToken != null : "Unspecified session token.";
assert sampleIdentifier != null : "Unspecified sample identifier.";
@@ -860,7 +860,7 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
@RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
public List<AbstractExternalData> listDataSetsByExperimentID(final String sessionToken,
@AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class)
- final TechId experimentID) throws UserFailureException
+ final TechId experimentID) throws UserFailureException
{
Session session = getSession(sessionToken);
IDatasetLister datasetLister = createDatasetLister(session);
@@ -874,7 +874,7 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
@RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
public List<AbstractExternalData> listDataSetsBySampleID(final String sessionToken,
@AuthorizationGuard(guardClass = SampleTechIdPredicate.class)
- final TechId sampleId, final boolean showOnlyDirectlyConnected)
+ final TechId sampleId, final boolean showOnlyDirectlyConnected)
throws UserFailureException
{
final Session session = getSession(sessionToken);
@@ -935,7 +935,7 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
@RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
public IEntityProperty[] tryGetPropertiesOfTopSample(final String sessionToken,
@AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class)
- final SampleIdentifier sampleIdentifier) throws UserFailureException
+ final SampleIdentifier sampleIdentifier) throws UserFailureException
{
assert sessionToken != null : "Unspecified session token.";
assert sampleIdentifier != null : "Unspecified sample identifier.";
@@ -1020,7 +1020,7 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
public void registerSamples(final String sessionToken,
@AuthorizationGuard(guardClass = NewSamplesWithTypePredicate.class)
- final List<NewSamplesWithTypes> newSamplesWithType, String userIDOrNull)
+ final List<NewSamplesWithTypes> newSamplesWithType, String userIDOrNull)
throws UserFailureException
{
assert sessionToken != null : "Unspecified session token.";
@@ -1037,7 +1037,7 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
public long registerSample(final String sessionToken,
@AuthorizationGuard(guardClass = NewSamplePredicate.class)
- final NewSample newSample, String userIDOrNull) throws UserFailureException
+ final NewSample newSample, String userIDOrNull) throws UserFailureException
{
assert sessionToken != null : "Unspecified session token.";
assert newSample != null : "Unspecified new sample.";
@@ -1071,7 +1071,7 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
public void registerDataSet(final String sessionToken,
@AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class)
- final SampleIdentifier sampleIdentifier, final NewExternalData externalData)
+ final SampleIdentifier sampleIdentifier, final NewExternalData externalData)
throws UserFailureException
{
assert sessionToken != null : "Unspecified session token.";
@@ -1085,7 +1085,7 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
public void registerDataSet(final String sessionToken,
@AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class)
- final ExperimentIdentifier experimentIdentifier, final NewExternalData externalData)
+ final ExperimentIdentifier experimentIdentifier, final NewExternalData externalData)
throws UserFailureException
{
assert sessionToken != null : "Unspecified session token.";
@@ -1099,7 +1099,7 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
public void addPropertiesToDataSet(String sessionToken, List<NewProperty> properties,
String dataSetCode, @AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class)
- final SpaceIdentifier identifier) throws UserFailureException
+ final SpaceIdentifier identifier) throws UserFailureException
{
assert sessionToken != null : "Unspecified session token.";
final Session session = getSession(sessionToken);
@@ -1334,7 +1334,7 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
@RolesAllowed({ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
public List<Sample> listSamplesByCriteria(final String sessionToken,
@AuthorizationGuard(guardClass = ListSamplesByPropertyPredicate.class)
- final ListSamplesByPropertyCriteria criteria) throws UserFailureException
+ final ListSamplesByPropertyCriteria criteria) throws UserFailureException
{
assert sessionToken != null : "Unspecified session token.";
assert criteria != null : "Unspecified criteria.";
@@ -1410,13 +1410,13 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
public List<SimpleDataSetInformationDTO> listPhysicalDataSetsByArchivingStatus(String sessionToken, String dataStoreCode,
- DataSetArchivingStatus archivingStatus)
+ DataSetArchivingStatus archivingStatus, Boolean presentInArchive)
{
final Session session = getSession(sessionToken);
final DataStorePE dataStore = loadDataStore(session, dataStoreCode);
final IDatasetLister datasetLister = businessObjectFactory.createDatasetLister(session);
final List<AbstractExternalData> dataSets =
- datasetLister.listByArchivingStatus(dataStore.getId(), archivingStatus,
+ datasetLister.listByArchivingStatus(dataStore.getId(), archivingStatus, presentInArchive,
DATASET_FETCH_OPTIONS_FILE_DATASETS);
return SimpleDataSetHelper.filterAndTranslate(dataSets);
}
@@ -1600,7 +1600,7 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
public Sample registerSampleAndDataSet(final String sessionToken,
@AuthorizationGuard(guardClass = NewSamplePredicate.class)
- final NewSample newSample, final NewExternalData externalData, String userIdOrNull)
+ final NewSample newSample, final NewExternalData externalData, String userIdOrNull)
throws UserFailureException
{
assert sessionToken != null : "Unspecified session token.";
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServerLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServerLogger.java
index 7971e8826149110c7fd926935be41db5d793ac0d..b6185a3fe850265e5f7babb061ae5b2af79da24d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServerLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServerLogger.java
@@ -420,9 +420,9 @@ public class ServiceForDataStoreServerLogger extends AbstractServerLogger implem
@Override
public List<SimpleDataSetInformationDTO> listPhysicalDataSetsByArchivingStatus(String sessionToken, String dataStoreCode,
- DataSetArchivingStatus archivingStatus) throws UserFailureException
+ DataSetArchivingStatus archivingStatus, Boolean presentInArchive) throws UserFailureException
{
- logAccess(sessionToken, "listPhysicalDataSetsByArchivingStatus", "DATA_STORE(%s) STATUS(%s)", dataStoreCode, archivingStatus);
+ logAccess(sessionToken, "listPhysicalDataSetsByArchivingStatus", "DATA_STORE(%s) STATUS(%s) PRESENT(%s)", dataStoreCode, archivingStatus, presentInArchive);
return null;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
index f6d89c414a4443f42da33d9289b082f88c89c0dd..e2749b5f011bd9c2075b630413c69e3bdf2429a6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
@@ -532,12 +532,23 @@ public class DatasetLister extends AbstractLister implements IDatasetLister
}
@Override
- public List<AbstractExternalData> listByArchivingStatus(long dataStoreID, DataSetArchivingStatus archivingStatus,
+ public List<AbstractExternalData> listByArchivingStatus(long dataStoreID, DataSetArchivingStatus archivingStatus, Boolean presentInArchive,
EnumSet<DataSetFetchOption> datasetFetchOptions)
{
checkFetchOptions(datasetFetchOptions);
- List<DatasetRecord> dataSets = query.getDatasetsByDataStoreIdWithArchivingStatus(dataStoreID, archivingStatus.name());
+ List<DatasetRecord> dataSets = null;
+
+ if (archivingStatus != null && presentInArchive != null)
+ {
+ dataSets = query.getDatasetsByDataStoreIdWithArchivingStatusAndPressentInArchive(dataStoreID, archivingStatus.name(), presentInArchive);
+ } else if (archivingStatus == null)
+ {
+ dataSets = query.getDatasetsByDataStoreIdWithPressentInArchive(dataStoreID, presentInArchive);
+ } else if (presentInArchive == null)
+ {
+ dataSets = query.getDatasetsByDataStoreIdWithArchivingStatus(dataStoreID, archivingStatus.name());
+ }
return orderByCode(enrichDatasets(dataSets, datasetFetchOptions));
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java
index 64ef8d8962294db04293384ae03a4f237261ee27..28b14a6887839eeb192f78c02bbddd48e0f2bfac 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java
@@ -142,7 +142,7 @@ public interface IDatasetLister
/**
* Lists physical datasets by archiving status of the specified data store.
*/
- List<AbstractExternalData> listByArchivingStatus(long dataStoreID, DataSetArchivingStatus archivingStatus,
+ List<AbstractExternalData> listByArchivingStatus(long dataStoreID, DataSetArchivingStatus archivingStatus, Boolean presentInArchive,
EnumSet<DataSetFetchOption> datasetFetchOptions);
/**
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
index b60c471bea37efa7c95b6d5531e707aa1a8d0875..b9a8e953c9122ce8de1289a560db1c2b71ad2c81 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
@@ -270,9 +270,15 @@ public interface IDatasetListingQuery extends BaseQuery, IPropertyListingQuery
+ " where data.dast_id = ?{1} and size is null and data.code > ?{3}"
+ " order by data.code limit ?{2}", fetchSize = FETCH_SIZE)
public List<DatasetRecord> getDatasetsByDataStoreIdWithUnknownSize(long dataStoreID, int limit, String dataSetCodeLowerLimit);
-
+
@Select(sql = SELECT_ALL_EXTERNAL_DATAS + " where data.dast_id = ?{1} and external_data.status = ?{2}", fetchSize = FETCH_SIZE)
public List<DatasetRecord> getDatasetsByDataStoreIdWithArchivingStatus(long dataStoreID, String archivingStatus);
+
+ @Select(sql = SELECT_ALL_EXTERNAL_DATAS + " where data.dast_id = ?{1} and external_data.present_in_archive = ?{2}", fetchSize = FETCH_SIZE)
+ public List<DatasetRecord> getDatasetsByDataStoreIdWithPressentInArchive(long dataStoreID, Boolean presentInArchive);
+
+ @Select(sql = SELECT_ALL_EXTERNAL_DATAS + " where data.dast_id = ?{1} and external_data.status = ?{2} and external_data.present_in_archive = ?{3}", fetchSize = FETCH_SIZE)
+ public List<DatasetRecord> getDatasetsByDataStoreIdWithArchivingStatusAndPressentInArchive(long dataStoreID, String archivingStatus, Boolean presentInArchive);
// NOTE: we list ALL data sets (even those in trash) using data_all table here
@Select(sql = "SELECT code, share_id FROM data_all LEFT OUTER JOIN external_data "
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IServiceForDataStoreServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IServiceForDataStoreServer.java
index 31a7f890d5343fe23e851db75ba9c72a4d0a33f1..0f34c083d3a912a8d2a051108fa0a1cfea79f089 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IServiceForDataStoreServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IServiceForDataStoreServer.java
@@ -256,8 +256,7 @@ public interface IServiceForDataStoreServer extends IServer, ISessionProvider
* Registers/updates various entities in one transaction.
*/
@Transactional
- @DatabaseCreateOrDeleteModification(value =
- { ObjectKind.EXPERIMENT, ObjectKind.SAMPLE, ObjectKind.DATA_SET })
+ @DatabaseCreateOrDeleteModification(value = { ObjectKind.EXPERIMENT, ObjectKind.SAMPLE, ObjectKind.DATA_SET })
public void registerEntities(String sessionToken, EntityCollectionForCreationOrUpdate collection)
throws UserFailureException;
@@ -431,8 +430,8 @@ public interface IServiceForDataStoreServer extends IServer, ISessionProvider
*/
@Transactional(readOnly = true)
public List<SimpleDataSetInformationDTO> listPhysicalDataSetsByArchivingStatus(String sessionToken, String dataStoreCode,
- DataSetArchivingStatus archivingStatus);
-
+ DataSetArchivingStatus archivingStatus, Boolean presentInArchive);
+
/**
* Lists the <var>limit</var> oldest physical data sets younger than <var>youngerThan</var> belonging to specified data store.
* <p>
@@ -618,8 +617,7 @@ public interface IServiceForDataStoreServer extends IServer, ISessionProvider
* @throws UserFailureException if given data set code could not be found in the persistence layer.
*/
@Transactional
- @DatabaseCreateOrDeleteModification(value =
- { ObjectKind.SAMPLE, ObjectKind.DATA_SET })
+ @DatabaseCreateOrDeleteModification(value = { ObjectKind.SAMPLE, ObjectKind.DATA_SET })
public Sample registerSampleAndDataSet(final String sessionToken, final NewSample newSample,
final NewExternalData externalData, String userIdOrNull) throws UserFailureException;
@@ -647,10 +645,8 @@ public interface IServiceForDataStoreServer extends IServer, ISessionProvider
*/
@Transactional
@Conversational(progress = Progress.MANUAL)
- @DatabaseUpdateModification(value =
- { ObjectKind.SAMPLE, ObjectKind.EXPERIMENT, ObjectKind.DATA_SET })
- @DatabaseCreateOrDeleteModification(value =
- { ObjectKind.SPACE, ObjectKind.PROJECT, ObjectKind.SAMPLE, ObjectKind.EXPERIMENT,
+ @DatabaseUpdateModification(value = { ObjectKind.SAMPLE, ObjectKind.EXPERIMENT, ObjectKind.DATA_SET })
+ @DatabaseCreateOrDeleteModification(value = { ObjectKind.SPACE, ObjectKind.PROJECT, ObjectKind.SAMPLE, ObjectKind.EXPERIMENT,
ObjectKind.DATA_SET })
public AtomicEntityOperationResult performEntityOperations(String sessionToken,
AtomicEntityOperationDetails operationDetails);
@@ -702,10 +698,8 @@ public interface IServiceForDataStoreServer extends IServer, ISessionProvider
* permanently deletes a list of data sets.
*/
@Transactional
- @DatabaseUpdateModification(value =
- { ObjectKind.SAMPLE, ObjectKind.EXPERIMENT })
- @DatabaseCreateOrDeleteModification(value =
- { ObjectKind.DATA_SET })
+ @DatabaseUpdateModification(value = { ObjectKind.SAMPLE, ObjectKind.EXPERIMENT })
+ @DatabaseCreateOrDeleteModification(value = { ObjectKind.DATA_SET })
public void removeDataSetsPermanently(String sessionToken, List<String> dataSetCodes,
String reason);
@@ -713,8 +707,7 @@ public interface IServiceForDataStoreServer extends IServer, ISessionProvider
* updates a data set.
*/
@Transactional
- @DatabaseUpdateModification(value =
- { ObjectKind.EXPERIMENT, ObjectKind.SAMPLE, ObjectKind.DATA_SET })
+ @DatabaseUpdateModification(value = { ObjectKind.EXPERIMENT, ObjectKind.SAMPLE, ObjectKind.DATA_SET })
public void updateDataSet(String sessionToken, DataSetUpdatesDTO dataSetUpdates);
/**