/// <summary>
///
/// </summary>
/// <param name="reason"></param>
/// <param name="key"></param>
/// <exception cref="InvalidStudyStateOperationException">Study is in a state that reprocessing is not allowed</exception>
public void ReprocessStudy(String reason, ServerEntityKey key)
{
StudyStorageAdaptor adaptor = new StudyStorageAdaptor();
StudyStorage storage = adaptor.Get(key);
StudyStorageLocation storageLocation = StudyStorageLocation.FindStorageLocations(storage)[0];
StudyReprocessor reprocessor = new StudyReprocessor();
reprocessor.ReprocessStudy(reason, storageLocation, Platform.Time);
}
/// <summary>
/// Do the actual rebuild. On error, will attempt to reprocess the study.
/// </summary>
public void RebuildXml()
{
string rootStudyPath = _location.GetStudyPath();
try
{
using (ServerCommandProcessor processor = new ServerCommandProcessor("Rebuild XML"))
{
var command = new RebuildStudyXmlCommand(_location.StudyInstanceUid, rootStudyPath);
processor.AddCommand(command);
var updateCommand = new UpdateStudySizeInDBCommand(_location, command);
processor.AddCommand(updateCommand);
if (!processor.Execute())
{
throw new ApplicationException(processor.FailureReason, processor.FailureException);
}
Study theStudy = _location.Study;
if (theStudy.NumberOfStudyRelatedInstances != command.StudyXml.NumberOfStudyRelatedInstances)
{
// We rebuilt, but the counts don't match.
throw new StudyIntegrityValidationFailure(ValidationErrors.InconsistentObjectCount,
new ValidationStudyInfo(theStudy,
_location.ServerPartition),
string.Format(
"Database study count {0} does not match study xml {1}",
theStudy.NumberOfStudyRelatedInstances,
command.StudyXml.NumberOfStudyRelatedInstances));
}
Platform.Log(LogLevel.Info, "Completed reprocessing Study XML file for study {0}", _location.StudyInstanceUid);
}
}
catch (Exception e)
{
Platform.Log(LogLevel.Error, e, "Unexpected error when rebuilding study XML for directory: {0}",
_location.FilesystemPath);
StudyReprocessor reprocessor = new StudyReprocessor();
try
{
WorkQueue reprocessEntry = reprocessor.ReprocessStudy("Rebuild StudyXml", _location, Platform.Time);
if (reprocessEntry != null)
{
Platform.Log(LogLevel.Error, "Failure attempting to reprocess study: {0}",
_location.StudyInstanceUid);
}
else
Platform.Log(LogLevel.Error, "Inserted reprocess request for study: {0}",
_location.StudyInstanceUid);
}
catch(InvalidStudyStateOperationException ex)
{
Platform.Log(LogLevel.Error, "Failure attempting to reprocess study {0}: {1}",
_location.StudyInstanceUid, ex.Message);
}
}
}
/// <summary>
///
/// </summary>
/// <param name="item"></param>
/// <param name="reason"></param>
/// <returns></returns>
/// <exception cref="InvalidStudyStateOperationException">Study is in a state that reprocessing is not allowed</exception>
protected static AutoRecoveryResult PerformAutoRecovery(Model.WorkQueue item, string reason)
{
AutoRecoveryResult result;
//Note: need to reload the storage location because it may have changed after the processing (eg, tier migration)
IList<StudyStorageLocation> storageLocations = StudyStorageLocation.FindStorageLocations(StudyStorage.Load(item.StudyStorageKey));
// storageLocations cannot be null for this operation
Platform.CheckForNullReference(storageLocations, "storageLocations");
Platform.CheckTrue(storageLocations.Count >= 1, "storageLocations.Count>=1");
StudyStorageLocation storageLocation = storageLocations[0];
Study study = storageLocation.LoadStudy(ServerExecutionContext.Current.PersistenceContext);
Platform.Log(LogLevel.Info, "{4} failed. Reason:{5}. Attempting to perform auto-recovery for Study:{0}, A#:{1}, Patient:{2}, ID:{3}",
study.StudyInstanceUid, study.AccessionNumber, study.PatientsName, study.PatientId, item.WorkQueueTypeEnum.ToString(), reason);
StudyXml studyXml = storageLocation.LoadStudyXml();
Platform.CheckForNullReference(studyXml, "studyXml does not exist");
// Do a secondary check on the filesystem vs. the Study Xml.
// If these match, then the DB is just update to reflect the valid counts.
// If they don't match, a Reprocess entry is inserted into the WorkQueue.
String studyFolder = storageLocation.GetStudyPath();
long fileCounter = DirectoryUtility.Count(studyFolder, "*.dcm", true, null);
// cache these values to avoid looping again
int numStudyRelatedSeriesInXml = studyXml.NumberOfStudyRelatedSeries;
int numStudyRelatedInstancesInXml = studyXml.NumberOfStudyRelatedInstances;
if (fileCounter != numStudyRelatedInstancesInXml)
{
// reprocess the study
Log(LogLevel.Info, "AUTO-RECOVERY", "# of study related instances in study Xml ({0}) appears incorrect. Study needs to be reprocessed.", numStudyRelatedInstancesInXml);
StudyReprocessor reprocessor = new StudyReprocessor();
String reprocessReason = String.Format("Auto-recovery from {0}. {1}", item.WorkQueueTypeEnum, reason);
Model.WorkQueue reprocessEntry = reprocessor.ReprocessStudy(reprocessReason, storageLocation, Platform.Time);
result = new AutoRecoveryResult
{
Successful = reprocessEntry!=null,
ReprocessWorkQueueEntry=reprocessEntry
};
return result;
}
Log(LogLevel.Info, "AUTO-RECOVERY", "# of study related instances in study Xml ({0}) appears correct. Update database based on study xml", numStudyRelatedInstancesInXml);
// update the counts in db to match the study xml
// Update count for each series
IDictionary<string, Series> seriesList = storageLocation.Study.Series;
foreach (Series series in seriesList.Values)
{
SeriesXml seriesXml = studyXml[series.SeriesInstanceUid];
if (seriesXml != null)
{
int numInstancesInSeriesXml = seriesXml.NumberOfSeriesRelatedInstances;
if (numInstancesInSeriesXml != series.NumberOfSeriesRelatedInstances)
{
// Update the count in the series table. Assuming the stored procedure
// will also update the count in the Study/Patient tables based on
// the new value.
Log(LogLevel.Info, "AUTO-RECOVERY", "Update series in the db. UID:{0}, #Instance:{1}==>{2}", series.SeriesInstanceUid, series.NumberOfSeriesRelatedInstances, numInstancesInSeriesXml);
using (IUpdateContext updateContext = PersistentStoreRegistry.GetDefaultStore().OpenUpdateContext(UpdateContextSyncMode.Flush))
{
ISetSeriesRelatedInstanceCount broker = updateContext.GetBroker<ISetSeriesRelatedInstanceCount>();
SetSeriesRelatedInstanceCountParameters criteria = new SetSeriesRelatedInstanceCountParameters(storageLocation.GetKey(), series.SeriesInstanceUid)
{
SeriesRelatedInstanceCount = numInstancesInSeriesXml
};
if (!broker.Execute(criteria))
{
throw new ApplicationException("Unable to update series related instance count in db");
}
updateContext.Commit();
}
}
}
else
{
// TODO: series in the db doesn't exist in the xml... the series was deleted from the study?
// For now we just reprocess the study. Can we delete the series? If so, we need to take care of the counts.
Log(LogLevel.Info, "AUTO-RECOVERY", "Found series in the db which does not exist in the study xml. Force to reprocess the study.");
StudyReprocessor reprocessor = new StudyReprocessor();
String reprocessReason = String.Format("Auto-recovery from {0}. {1}", item.WorkQueueTypeEnum, reason);
Model.WorkQueue reprocessEntry = reprocessor.ReprocessStudy(reprocessReason, storageLocation, Platform.Time);
result = new AutoRecoveryResult
{
Successful = reprocessEntry != null,
ReprocessWorkQueueEntry = reprocessEntry
};
return result;
}
}
if (numStudyRelatedSeriesInXml != storageLocation.Study.NumberOfStudyRelatedSeries ||
numStudyRelatedInstancesInXml != storageLocation.Study.NumberOfStudyRelatedInstances)
{
Log(LogLevel.Info, "AUTO-RECOVERY", "Updating study related series and instance counts in the db. #Series: {0} ==> {1}. #Instances: {2}==>{3}",
storageLocation.Study.NumberOfStudyRelatedSeries, numStudyRelatedSeriesInXml,
storageLocation.Study.NumberOfStudyRelatedInstances, numStudyRelatedInstancesInXml);
using (IUpdateContext updateContext = PersistentStoreRegistry.GetDefaultStore().OpenUpdateContext(UpdateContextSyncMode.Flush))
{
var broker = updateContext.GetBroker<ISetStudyRelatedInstanceCount>();
var criteria = new SetStudyRelatedInstanceCountParameters(storageLocation.GetKey())
{
StudyRelatedSeriesCount = numStudyRelatedSeriesInXml,
StudyRelatedInstanceCount = numStudyRelatedInstancesInXml
};
if (!broker.Execute(criteria))
{
throw new ApplicationException("Unable to update study related instance count in db");
}
updateContext.Commit();
}
}
Log(LogLevel.Info, "AUTO-RECOVERY", "Object count in the db have been corrected.");
result = new AutoRecoveryResult
{
Successful = true
};
return result;
}
public bool ReprocessWorkQueueItem(WorkQueue item)
{
// #10620: Get a list of remaining WorkQueueUids which need to be reprocess
// Note: currently only WorkQueueUIDs in failed StudyProcess will be reprocessed
var remainingWorkQueueUidPaths = item.GetAllWorkQueueUidPaths();
IPersistentStore store = PersistentStoreRegistry.GetDefaultStore();
using (IUpdateContext ctx = store.OpenUpdateContext(UpdateContextSyncMode.Flush))
{
// delete current workqueue
IWorkQueueUidEntityBroker uidBroker = ctx.GetBroker<IWorkQueueUidEntityBroker>();
WorkQueueUidSelectCriteria criteria = new WorkQueueUidSelectCriteria();
criteria.WorkQueueKey.EqualTo(item.GetKey());
if (uidBroker.Delete(criteria) >= 0)
{
IWorkQueueEntityBroker workQueueBroker = ctx.GetBroker<IWorkQueueEntityBroker>();
if (workQueueBroker.Delete(item.GetKey()))
{
IList<StudyStorageLocation> locations = item.LoadStudyLocations(ctx);
if (locations!=null && locations.Count>0)
{
StudyReprocessor reprocessor = new StudyReprocessor();
String reason = String.Format("User reprocesses failed {0}", item.WorkQueueTypeEnum);
WorkQueue reprocessEntry = reprocessor.ReprocessStudy(ctx, reason, locations[0], remainingWorkQueueUidPaths, Platform.Time);
if (reprocessEntry!=null)
ctx.Commit();
return reprocessEntry!=null;
}
}
}
}
return false;
}
private void ReprocessStudy(StudyStorageLocation restoredLocation, string reason)
{
StudyReprocessor reprocessor = new StudyReprocessor();
String reprocessReason = String.Format("Restore Validation Error: {0}", reason);
reprocessor.ReprocessStudy(reprocessReason, restoredLocation, Platform.Time);
string message = string.Format("Study {0} has been restored but failed the validation. Reprocess Study has been triggerred. Reason for validation failure: {1}", restoredLocation.StudyInstanceUid, reason);
Platform.Log(LogLevel.Warn, message);
ServerPlatform.Alert(AlertCategory.Application, AlertLevel.Informational, "Restore", 0, null, TimeSpan.Zero, message);
}