From 8077d7b4aa4597bf4abe3237280d144421d60327 Mon Sep 17 00:00:00 2001
From: gakin <gakin>
Date: Wed, 28 Sep 2016 14:12:03 +0000
Subject: [PATCH] SSDM-4141 : Implement corner case: delete and re-create
entity with the permId of already synced entity.
SVN: 37135
---
.../dss/plugins/DataSetRegistrationTask.java | 40 +++++++++++++++++--
1 file changed, 37 insertions(+), 3 deletions(-)
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/DataSetRegistrationTask.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/DataSetRegistrationTask.java
index fb5784acd2c..b6400471077 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/DataSetRegistrationTask.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/DataSetRegistrationTask.java
@@ -116,6 +116,7 @@ import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.Status;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.http.JettyHttpClientFactory;
+import ch.systemsx.cisd.common.logging.Log4jSimpleLogger;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.mail.EMailAddress;
@@ -130,13 +131,18 @@ import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetRegistrationTransac
import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetUpdatable;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.IngestionService;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.PluginTaskInfoProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetDirectoryProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IConfigProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IDataSetDirectoryProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IShareIdManager;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.SegmentedStoreUtils;
import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IMasterDataRegistrationTransaction;
import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl.EncapsulatedCommonServer;
import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl.MasterDataRegistrationService;
@@ -152,6 +158,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterialWithType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PhysicalDataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
@@ -575,7 +582,6 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
mailClient = ServiceProvider.getDataStoreService().createEMailClient();
String configFileProperty = properties.getProperty(HARVESTER_CONFIG_FILE_PROPERTY_NAME);
-
if (configFileProperty == null)
{
harvesterConfigFile =
@@ -807,7 +813,7 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
} catch (Exception e)
{
- operationLog.error("Sync failed: " + e.getMessage());
+ operationLog.error("Sync failed: ", e);
sendErrorEmail("Synchronization failed");
}
}
@@ -861,7 +867,7 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
config.setLogFilePath(reader.getString(DEFAULT_DATA_SOURCE_SECTION, LOG_FILE_PROPERTY_NAME, DEFAULT_LOG_FILE_NAME, false));
if (config.getLogFilePath() != null)
{
- // configureFileAppender();
+ configureFileAppender();
}
config.setDataSourceURI(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_URL_PROPERTY_NAME, null, true));
@@ -903,6 +909,7 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
List<DataSetPermId> dsPermIds = new ArrayList<DataSetPermId>();
List<MaterialPermId> matPermIds = new ArrayList<MaterialPermId>();
+ Set<PhysicalDataSet> physicalDataSetsDelete = new HashSet<PhysicalDataSet>();
// first find out the entities to be deleted
for (String harvesterSpaceId : spaceMappings.values())
{
@@ -959,6 +966,7 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
boolean sameDS = true;
// if (ds.getKind() == DataSetKind.PHYSICAL && ds.lastModificationDate.after(lastSyncDate))
String typeCodeOrNull = entity.getTypeCodeOrNull();
+
DataSetWithConnections dsWithConns = data.datasetsToProcess.get(entity.getPermId());
NewExternalData ds = dsWithConns.getDataSet();
if (typeCodeOrNull.equals(ds.getDataSetType().getCode()) == false)
@@ -969,7 +977,10 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
{
if (dsWithConns.getKind() == DataSetKind.PHYSICAL && dsWithConns.getLastModificationDate().after(lastSyncTimestamp))
{
+ PhysicalDataSet physicalDS = service.tryGetDataSet(entity.getPermId()).tryGetAsDataSet();
sameDS = deepCompareDataSets(entity.getPermId());
+ if (sameDS == false)
+ physicalDataSetsDelete.add(physicalDS);
}
}
if (sameDS == false)
@@ -1023,6 +1034,29 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
// confirm deletions
v3Api.confirmDeletions(sessionToken, Arrays.asList(expDeletionId, dsDeletionId, smpDeletionId));
+
+ for (PhysicalDataSet physicalDS : physicalDataSetsDelete)
+ {
+ operationLog.info("Is going to delete the location: " + physicalDS.getLocation());
+ File datasetDir =
+ getDirectoryProvider().getDataSetDirectory(physicalDS);
+ SegmentedStoreUtils.deleteDataSetInstantly(physicalDS.getCode(), datasetDir, new Log4jSimpleLogger(operationLog));
+ }
+ }
+
+ private IDataSetDirectoryProvider getDirectoryProvider()
+ {
+ return new DataSetDirectoryProvider(getConfigProvider().getStoreRoot(), getShareIdManager());
+ }
+
+ private IConfigProvider getConfigProvider()
+ {
+ return ServiceProvider.getConfigProvider();
+ }
+
+ private IShareIdManager getShareIdManager()
+ {
+ return ServiceProvider.getShareIdManager();
}
private boolean deepCompareDataSets(String dataSetCode)
--
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