protected override void OnExecute(CommandProcessor theProcessor)
{
Platform.CheckForNullReference(Context, "Context");
DetermineTargetLocation();
EnsureStudyCanBeUpdated(_destinationStudyStorage);
try
{
if (Context.WorkQueueUidList.Count > 0)
{
ProcessUidList();
}
}
finally
{
UpdateHistory(_destinationStudyStorage);
}
if (_complete)
{
StudyRulesEngine engine = new StudyRulesEngine(_destinationStudyStorage, Context.Partition);
engine.Apply(ServerRuleApplyTimeEnum.StudyProcessed, theProcessor);
}
}
protected override void OnExecute(CommandProcessor theProcessor)
{
Platform.CheckForNullReference(Context, "Context");
Platform.CheckForNullReference(Context.WorkQueueItem, "Context.WorkQueueItem");
Platform.CheckForNullReference(Context.WorkQueueUidList, "Context.WorkQueueUidList");
// Create or Load the Destination StorageLocation. Note that this may cause
// issues with orphan StorageLocations if none of the images below are actually
// processed. This must be done becasue the SopInstanceProcessor requires the
// destination location.
CreateDestinationStudyStorage();
try
{
if (Context.WorkQueueUidList.Count > 0)
{
CreateOrLoadUidMappings();
PrintChangeList();
ProcessUidList();
}
}
finally
{
UpdateHistory(_destinationStudyStorage);
}
if (_complete)
{
var engine = new StudyRulesEngine(_destinationStudyStorage, Context.Partition);
engine.Apply(ServerRuleApplyTimeEnum.StudyProcessed, theProcessor);
}
}
protected override void OnExecute(CommandProcessor theProcessor)
{
Platform.CheckForNullReference(Context, "Context");
_destinationStudyStorage = Context.History.DestStudyStorageKey != null
? StudyStorageLocation.FindStorageLocations(StudyStorage.Load(Context.History.DestStudyStorageKey))[0]
: Context.WorkQueueItemStudyStorage;
EnsureStudyCanBeUpdated(_destinationStudyStorage);
if (_updateDestination)
{
UpdateExistingStudy();
}
LoadMergedStudyEntities();
try
{
LoadUidMappings();
if (Context.WorkQueueUidList.Count > 0)
{
ProcessUidList();
LogResult();
}
}
finally
{
UpdateHistory(_destinationStudyStorage);
}
if (_complete)
{
StudyRulesEngine engine = new StudyRulesEngine(_destinationStudyStorage, Context.Partition);
engine.Apply(ServerRuleApplyTimeEnum.StudyProcessed, theProcessor);
}
}
/// <summary>
/// Called when all WorkQueue UIDs have been processed
/// </summary>
private void OnAllWorkQueueUidsProcessed()
{
if (Study != null)
{
Platform.Log(LogLevel.Info,
"StudyProcess Cleanup completed for study {0} for Patient {1} (PatientId:{2} A#:{3}) on Partition {4}",
Study.StudyInstanceUid, Study.PatientsName, Study.PatientId,
Study.AccessionNumber, ServerPartition.Description);
Platform.Log(LogLevel.Info, "Applying rules engine to study being cleaned up to ensure disk management is applied.");
// Run Study / Series Rules Engine.
var engine = new StudyRulesEngine(StorageLocation, ServerPartition);
engine.Apply(ServerRuleApplyTimeEnum.StudyProcessed);
StorageLocation.LogFilesystemQueue();
PostProcessing(WorkQueueItem,
WorkQueueProcessorStatus.Complete,
WorkQueueProcessorDatabaseUpdate.ResetQueueState);
}
else
{
Platform.Log(LogLevel.Info, "StudyProcess Cleanup completed. Performing final checks..");
// Study is never processed
if (EnsureNoOrphanFiles())
{
DeleteStudyStorage(WorkQueueItem);
Platform.Log(LogLevel.Info, "StudyProcess Cleanup completed. Study no longer exists in the system");
PostProcessing(WorkQueueItem,
WorkQueueProcessorStatus.Complete,
WorkQueueProcessorDatabaseUpdate.ResetQueueState);
}
}
}
protected override void ProcessItem(Model.WorkQueue item)
{
Platform.CheckForNullReference(item, "item");
Platform.CheckForNullReference(StorageLocation, "StorageLocation");
// Verify the study is not lossy online and lossless in the archive.
// This could happen if the images were received WHILE the study was being lossy compressed.
// The study state would not be set until the compression was completed or partially completed.
CheckIfStudyIsLossy();
Statistics.TotalProcessTime.Start();
bool successful;
bool idle = false;
//Load the specific UIDs that need to be processed.
LoadUids(item);
int totalUidCount = WorkQueueUidList.Count;
if (totalUidCount == 0)
{
successful = true;
idle = true;
}
else
{
try
{
Context = new StudyProcessorContext(StorageLocation);
// Load the rules engine
_sopProcessedRulesEngine = new ServerRulesEngine(ServerRuleApplyTimeEnum.SopProcessed, item.ServerPartitionKey);
_sopProcessedRulesEngine.AddOmittedType(ServerRuleTypeEnum.SopCompress);
_sopProcessedRulesEngine.Load();
Statistics.SopProcessedEngineLoadTime.Add(_sopProcessedRulesEngine.Statistics.LoadTime);
Context.SopProcessedRulesEngine = _sopProcessedRulesEngine;
if (Study != null)
{
Platform.Log(LogLevel.Info, "Processing study {0} for Patient {1} (PatientId:{2} A#:{3}), {4} objects",
Study.StudyInstanceUid, Study.PatientsName, Study.PatientId,
Study.AccessionNumber, WorkQueueUidList.Count);
}
else
{
Platform.Log(LogLevel.Info, "Processing study {0}, {1} objects",
StorageLocation.StudyInstanceUid, WorkQueueUidList.Count);
}
// Process the images in the list
successful = ProcessUidList(item) > 0;
}
catch (StudyIsNearlineException ex)
{
// delay until the target is restored
// NOTE: If the study could not be restored after certain period of time, this entry will be failed.
if (ex.RestoreRequested)
{
PostponeItem(string.Format("Unable to auto-reconcile at this time: the target study {0} is not online yet. Restore has been requested.", ex.StudyInstanceUid));
return;
}
// fail right away
FailQueueItem(item, string.Format("Unable to auto-reconcile at this time: the target study {0} is not nearline and could not be restored.", ex.StudyInstanceUid));
return;
}
}
Statistics.TotalProcessTime.End();
if (successful)
{
if (idle && item.ExpirationTime <= Platform.Time)
{
// Run Study / Series Rules Engine.
var engine = new StudyRulesEngine(StorageLocation, ServerPartition);
engine.Apply(ServerRuleApplyTimeEnum.StudyProcessed);
// Log the FilesystemQueue related entries
StorageLocation.LogFilesystemQueue();
// Delete the queue entry.
PostProcessing(item,
WorkQueueProcessorStatus.Complete,
WorkQueueProcessorDatabaseUpdate.ResetQueueState);
}
else if (idle)
{
PostProcessing(item,
WorkQueueProcessorStatus.IdleNoDelete, // Don't delete, so we ensure the rules engine is run later.
WorkQueueProcessorDatabaseUpdate.ResetQueueState);
}
else
{
PostProcessing(item,
WorkQueueProcessorStatus.Pending,
WorkQueueProcessorDatabaseUpdate.ResetQueueState);
}
}
else
{
bool allFailedDuplicate = CollectionUtils.TrueForAll(WorkQueueUidList, uid => uid.Duplicate && uid.Failed);
if (allFailedDuplicate)
{
Platform.Log(LogLevel.Error, "All entries are duplicates");
PostProcessingFailure(item, WorkQueueProcessorFailureType.Fatal);
return;
}
PostProcessingFailure(item, WorkQueueProcessorFailureType.NonFatal);
}
}
/// <summary>
/// Archive the specified <see cref="ArchiveQueue"/> item.
/// </summary>
/// <param name="queueItem">The ArchiveQueue item to archive.</param>
public void Run(ArchiveQueue queueItem)
{
using (ArchiveProcessorContext executionContext = new ArchiveProcessorContext(queueItem))
{
try
{
if (!GetStudyStorageLocation(queueItem))
{
Platform.Log(LogLevel.Error,
"Unable to find readable study storage location for archival queue request {0}. Delaying request.",
queueItem.Key);
queueItem.FailureDescription = "Unable to find readable study storage location for archival queue request.";
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Pending, Platform.Time.AddMinutes(2));
return;
}
// First, check to see if we can lock the study, if not just reschedule the queue entry.
if (!_storageLocation.QueueStudyStateEnum.Equals(QueueStudyStateEnum.Idle))
{
Platform.Log(LogLevel.Info, "Study {0} on partition {1} is currently locked, delaying archival.", _storageLocation.StudyInstanceUid, _hsmArchive.ServerPartition.Description);
queueItem.FailureDescription = "Study is currently locked, delaying archival.";
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Pending, Platform.Time.AddMinutes(2));
return;
}
StudyIntegrityValidator validator = new StudyIntegrityValidator();
validator.ValidateStudyState("Archive", _storageLocation, StudyIntegrityValidationModes.Default);
using (IUpdateContext update = PersistentStoreRegistry.GetDefaultStore().OpenUpdateContext(UpdateContextSyncMode.Flush))
{
ILockStudy studyLock = update.GetBroker <ILockStudy>();
LockStudyParameters parms = new LockStudyParameters
{
StudyStorageKey = queueItem.StudyStorageKey,
QueueStudyStateEnum = QueueStudyStateEnum.ArchiveScheduled
};
bool retVal = studyLock.Execute(parms);
if (!parms.Successful || !retVal)
{
Platform.Log(LogLevel.Info, "Study {0} on partition {1} failed to lock, delaying archival.", _storageLocation.StudyInstanceUid, _hsmArchive.ServerPartition.Description);
queueItem.FailureDescription = "Study failed to lock, delaying archival.";
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Pending, Platform.Time.AddMinutes(2));
return;
}
update.Commit();
}
string studyXmlFile = _storageLocation.GetStudyXmlPath();
// Load the study Xml file, this is used to generate the list of dicom files to archive.
LoadStudyXml(studyXmlFile);
DicomFile file = LoadFileFromStudyXml();
string patientsName = file.DataSet[DicomTags.PatientsName].GetString(0, string.Empty);
string patientId = file.DataSet[DicomTags.PatientId].GetString(0, string.Empty);
string accessionNumber = file.DataSet[DicomTags.AccessionNumber].GetString(0, string.Empty);
Platform.Log(LogLevel.Info,
"Starting archival of study {0} for Patient {1} (PatientId:{2} A#:{3}) on Partition {4} on archive {5}",
_storageLocation.StudyInstanceUid, patientsName, patientId,
accessionNumber, _hsmArchive.ServerPartition.Description,
_hsmArchive.PartitionArchive.Description);
// Use the command processor to do the archival.
using (ServerCommandProcessor commandProcessor = new ServerCommandProcessor("Archive"))
{
var archiveStudyCmd = new ArchiveStudyCommand(_storageLocation, _hsmArchive.HsmPath, executionContext.TempDirectory, _hsmArchive.PartitionArchive)
{
ForceCompress = HsmSettings.Default.CompressZipFiles
};
commandProcessor.AddCommand(archiveStudyCmd);
commandProcessor.AddCommand(new UpdateArchiveQueueItemCommand(queueItem.GetKey(), _storageLocation.GetKey(), ArchiveQueueStatusEnum.Completed));
StudyRulesEngine studyEngine = new StudyRulesEngine(_storageLocation, _hsmArchive.ServerPartition, _studyXml);
studyEngine.Apply(ServerRuleApplyTimeEnum.StudyArchived, commandProcessor);
if (!commandProcessor.Execute())
{
Platform.Log(LogLevel.Error,
"Unexpected failure archiving study ({0}) to archive {1}: {2}, zip filename: {3}",
_storageLocation.StudyInstanceUid, _hsmArchive.PartitionArchive.Description,
commandProcessor.FailureReason, archiveStudyCmd.OutputZipFilePath);
queueItem.FailureDescription = commandProcessor.FailureReason;
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Failed, Platform.Time);
}
else
{
Platform.Log(LogLevel.Info, "Successfully archived study {0} on {1} to zip {2}",
_storageLocation.StudyInstanceUid,
_hsmArchive.PartitionArchive.Description, archiveStudyCmd.OutputZipFilePath);
}
// Log the current FilesystemQueue settings
_storageLocation.LogFilesystemQueue();
}
}
catch (StudyIntegrityValidationFailure ex)
{
StringBuilder error = new StringBuilder();
error.AppendLine(String.Format("Partition : {0}", ex.ValidationStudyInfo.ServerAE));
error.AppendLine(String.Format("Patient : {0}", ex.ValidationStudyInfo.PatientsName));
error.AppendLine(String.Format("Study Uid : {0}", ex.ValidationStudyInfo.StudyInstaneUid));
error.AppendLine(String.Format("Accession# : {0}", ex.ValidationStudyInfo.AccessionNumber));
error.AppendLine(String.Format("Study Date : {0}", ex.ValidationStudyInfo.StudyDate));
queueItem.FailureDescription = error.ToString();
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Failed, Platform.Time);
}
catch (Exception e)
{
String msg = String.Format("Unexpected exception archiving study: {0} on {1}: {2}",
_storageLocation.StudyInstanceUid, _hsmArchive.PartitionArchive.Description, e.Message);
Platform.Log(LogLevel.Error, e, msg);
queueItem.FailureDescription = msg;
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Failed, Platform.Time);
}
finally
{
// Unlock the Queue Entry
using (IUpdateContext update = PersistentStoreRegistry.GetDefaultStore().OpenUpdateContext(UpdateContextSyncMode.Flush))
{
ILockStudy studyLock = update.GetBroker <ILockStudy>();
LockStudyParameters parms = new LockStudyParameters
{
StudyStorageKey = queueItem.StudyStorageKey,
QueueStudyStateEnum = QueueStudyStateEnum.Idle
};
bool retVal = studyLock.Execute(parms);
if (!parms.Successful || !retVal)
{
Platform.Log(LogLevel.Info, "Study {0} on partition {1} is failed to unlock.", _storageLocation.StudyInstanceUid, _hsmArchive.ServerPartition.Description);
}
update.Commit();
}
}
}
}
/// <summary>
/// Reprocess a specific study.
/// </summary>
/// <param name="partition">The ServerPartition the study is on.</param>
/// <param name="location">The storage location of the study to process.</param>
/// <param name="engine">The rules engine to use when processing the study.</param>
/// <param name="postArchivalEngine">The rules engine used for studies that have been archived.</param>
/// <param name="dataAccessEngine">The rules engine strictly used for setting data acess.</param>
protected static void ProcessStudy(ServerPartition partition, StudyStorageLocation location, ServerRulesEngine engine, ServerRulesEngine postArchivalEngine, ServerRulesEngine dataAccessEngine)
{
if (!location.QueueStudyStateEnum.Equals(QueueStudyStateEnum.Idle) || !location.AcquireWriteLock())
{
Platform.Log(LogLevel.Error, "Unable to lock study {0}. The study is being processed. (Queue State: {1})", location.StudyInstanceUid, location.QueueStudyStateEnum.Description);
}
else
{
try
{
DicomFile msg = LoadInstance(location);
if (msg == null)
{
Platform.Log(LogLevel.Error, "Unable to load file for study {0}", location.StudyInstanceUid);
return;
}
bool archiveQueueExists;
bool archiveStudyStorageExists;
bool filesystemDeleteExists;
using (IReadContext read = PersistentStoreRegistry.GetDefaultStore().OpenReadContext())
{
// Check for existing archive queue entries
var archiveQueueBroker = read.GetBroker <IArchiveQueueEntityBroker>();
var archiveQueueCriteria = new ArchiveQueueSelectCriteria();
archiveQueueCriteria.StudyStorageKey.EqualTo(location.Key);
archiveQueueExists = archiveQueueBroker.Count(archiveQueueCriteria) > 0;
var archiveStorageBroker = read.GetBroker <IArchiveStudyStorageEntityBroker>();
var archiveStudyStorageCriteria = new ArchiveStudyStorageSelectCriteria();
archiveStudyStorageCriteria.StudyStorageKey.EqualTo(location.Key);
archiveStudyStorageExists = archiveStorageBroker.Count(archiveStudyStorageCriteria) > 0;
var filesystemQueueBroker = read.GetBroker <IFilesystemQueueEntityBroker>();
var filesystemQueueCriteria = new FilesystemQueueSelectCriteria();
filesystemQueueCriteria.StudyStorageKey.EqualTo(location.Key);
filesystemQueueCriteria.FilesystemQueueTypeEnum.EqualTo(FilesystemQueueTypeEnum.DeleteStudy);
filesystemDeleteExists = filesystemQueueBroker.Count(filesystemQueueCriteria) > 0;
}
using (var commandProcessor = new ServerCommandProcessor("Study Rule Processor")
{
PrimaryServerPartitionKey = partition.GetKey(),
PrimaryStudyKey = location.Study.GetKey()
})
{
var context = new ServerActionContext(msg, location.FilesystemKey, partition, location.Key, commandProcessor);
// Check if the Study has been archived
if (archiveStudyStorageExists && !archiveQueueExists && !filesystemDeleteExists)
{
// Add a command to delete the current filesystemQueue entries, so that they can
// be reinserted by the rules engine.
context.CommandProcessor.AddCommand(new DeleteFilesystemQueueCommand(location.Key, ServerRuleApplyTimeEnum.StudyArchived));
// How to deal with exiting FilesystemQueue entries is problematic here. If the study
// has been migrated off tier 1, we probably don't want to modify the tier migration
// entries. Compression entries may have been entered when the Study was initially
// processed, we don't want to delete them, because they might still be valid.
// We just re-run the rules engine at this point, and delete only the StudyPurge entries,
// since those we know at least would only be applied for archived studies.
var studyRulesEngine = new StudyRulesEngine(postArchivalEngine, location, location.ServerPartition, location.LoadStudyXml());
studyRulesEngine.Apply(ServerRuleApplyTimeEnum.StudyArchived, commandProcessor);
// Post Archive doesn't allow data access rules. Force Data Access rules to be reapplied
// to these studies also.
dataAccessEngine.Execute(context);
}
else
{
// Add a command to delete the current filesystemQueue entries, so that they can
// be reinserted by the rules engine.
context.CommandProcessor.AddCommand(new DeleteFilesystemQueueCommand(location.Key, ServerRuleApplyTimeEnum.StudyProcessed));
// Execute the rules engine, insert commands to update the database into the command processor.
// Due to ticket #11673, we create a new rules engine instance for each study, since the Study QC rules
// don't work right now with a single rules engine.
//TODO CR (Jan 2014) - Check if we can go back to caching the rules engine to reduce database hits on the rules
var studyRulesEngine = new StudyRulesEngine(location, location.ServerPartition, location.LoadStudyXml());
studyRulesEngine.Apply(ServerRuleApplyTimeEnum.StudyProcessed, commandProcessor);
}
// Do the actual database updates.
if (false == context.CommandProcessor.Execute())
{
Platform.Log(LogLevel.Error, "Unexpected failure processing Study level rules for study {0}", location.StudyInstanceUid);
}
// Log the FilesystemQueue related entries
location.LogFilesystemQueue();
}
}
finally
{
location.ReleaseWriteLock();
}
}
}
protected override void ProcessItem(Model.WorkQueue item)
{
Platform.CheckForNullReference(item, "item");
Platform.CheckForNullReference(item.StudyStorageKey, "item.StudyStorageKey");
var context = new StudyProcessorContext(StorageLocation);
// TODO: Should we enforce the patient's name rule?
// If we do, the Study record will have the new patient's name
// but how should we handle the name in the Patient record?
bool enforceNameRules = false;
var processor = new SopInstanceProcessor(context)
{
EnforceNameRules = enforceNameRules
};
var seriesMap = new Dictionary <string, List <string> >();
bool successful = true;
string failureDescription = null;
// The processor stores its state in the Data column
ReadQueueData(item);
if (_queueData.State == null || !_queueData.State.ExecuteAtLeastOnce)
{
// Added for ticket #9673:
// If the study folder does not exist and the study has been archived, trigger a restore and we're done
if (!Directory.Exists(StorageLocation.GetStudyPath()))
{
if (StorageLocation.ArchiveLocations.Count > 0)
{
Platform.Log(LogLevel.Info,
"Reprocessing archived study {0} for Patient {1} (PatientId:{2} A#:{3}) on Partition {4} without study data on the filesystem. Inserting Restore Request.",
Study.StudyInstanceUid, Study.PatientsName, Study.PatientId,
Study.AccessionNumber, ServerPartition.Description);
PostProcessing(item, WorkQueueProcessorStatus.Complete, WorkQueueProcessorDatabaseUpdate.ResetQueueState);
// Post process had to be done first so the study is unlocked so the RestoreRequest can be inserted.
ServerHelper.InsertRestoreRequest(StorageLocation);
RaiseAlert(WorkQueueItem, AlertLevel.Warning,
string.Format(
"Found study {0} for Patient {1} (A#:{2})on Partition {3} without storage folder, restoring study.",
Study.StudyInstanceUid, Study.PatientsName, Study.AccessionNumber, ServerPartition.Description));
return;
}
}
if (Study == null)
{
Platform.Log(LogLevel.Info,
"Reprocessing study {0} on Partition {1}", StorageLocation.StudyInstanceUid,
ServerPartition.Description);
}
else
{
Platform.Log(LogLevel.Info,
"Reprocessing study {0} for Patient {1} (PatientId:{2} A#:{3}) on Partition {4}",
Study.StudyInstanceUid, Study.PatientsName, Study.PatientId,
Study.AccessionNumber, ServerPartition.Description);
}
CleanupDatabase();
}
else
{
if (_queueData.State.Completed)
{
#region SAFE-GUARD CODE: PREVENT INFINITE LOOP
// The processor indicated it had completed reprocessing in previous run. The entry should have been removed and this block of code should never be called.
// However, we have seen ReprocessStudy entries that mysterously contain rows in the WorkQueueUid table.
// The rows prevent the entry from being removed from the database and the ReprocessStudy keeps repeating itself.
// update the state first, increment the CompleteAttemptCount
_queueData.State.ExecuteAtLeastOnce = true;
_queueData.State.Completed = true;
_queueData.State.CompleteAttemptCount++;
SaveState(item, _queueData);
if (_queueData.State.CompleteAttemptCount < 10)
{
// maybe there was db error in previous attempt to remove the entry. Let's try again.
Platform.Log(LogLevel.Info, "Resuming Reprocessing study {0} but it was already completed!!!", StorageLocation.StudyInstanceUid);
PostProcessing(item, WorkQueueProcessorStatus.Complete, WorkQueueProcessorDatabaseUpdate.ResetQueueState);
}
else
{
// we are definitely stuck.
Platform.Log(LogLevel.Error, "ReprocessStudy {0} for study {1} appears stuck. Aborting it.", item.Key, StorageLocation.StudyInstanceUid);
item.FailureDescription = "This entry had completed but could not be removed.";
PostProcessingFailure(item, WorkQueueProcessorFailureType.Fatal);
}
return;
#endregion
}
if (Study == null)
{
Platform.Log(LogLevel.Info,
"Resuming Reprocessing study {0} on Partition {1}", StorageLocation.StudyInstanceUid,
ServerPartition.Description);
}
else
{
Platform.Log(LogLevel.Info,
"Resuming Reprocessing study {0} for Patient {1} (PatientId:{2} A#:{3}) on Partition {4}",
Study.StudyInstanceUid, Study.PatientsName, Study.PatientId,
Study.AccessionNumber, ServerPartition.Description);
}
}
StudyXml studyXml = LoadStudyXml();
int reprocessedCounter = 0;
var removedFiles = new List <FileInfo>();
try
{
// Traverse the directories, process 500 files at a time
FileProcessor.Process(StorageLocation.GetStudyPath(), "*.*",
delegate(string path, out bool cancel)
{
#region Reprocess File
var file = new FileInfo(path);
// ignore all files except those ending ".dcm"
// ignore "bad(0).dcm" files too
if (Regex.IsMatch(file.Name.ToUpper(), "[0-9]+\\.DCM$"))
{
try
{
var dicomFile = new DicomFile(path);
dicomFile.Load(DicomReadOptions.StorePixelDataReferences | DicomReadOptions.Default);
string seriesUid = dicomFile.DataSet[DicomTags.SeriesInstanceUid].GetString(0, string.Empty);
string instanceUid = dicomFile.DataSet[DicomTags.SopInstanceUid].GetString(0, string.Empty);
if (studyXml.Contains(seriesUid, instanceUid))
{
if (!seriesMap.ContainsKey(seriesUid))
{
seriesMap.Add(seriesUid, new List <string>());
}
if (!seriesMap[seriesUid].Contains(instanceUid))
{
seriesMap[seriesUid].Add(instanceUid);
}
else
{
Platform.Log(LogLevel.Warn, "SOP Instance UID in {0} appears more than once in the study.", path);
}
}
else
{
Platform.Log(ServerPlatform.InstanceLogLevel, "Reprocessing SOP {0} for study {1}", instanceUid, StorageLocation.StudyInstanceUid);
string groupId = ServerHelper.GetUidGroup(dicomFile, StorageLocation.ServerPartition, WorkQueueItem.InsertTime);
ProcessingResult result = processor.ProcessFile(groupId, dicomFile, studyXml, true, false, null, null);
switch (result.Status)
{
case ProcessingStatus.Success:
reprocessedCounter++;
if (!seriesMap.ContainsKey(seriesUid))
{
seriesMap.Add(seriesUid, new List <string>());
}
if (!seriesMap[seriesUid].Contains(instanceUid))
{
seriesMap[seriesUid].Add(instanceUid);
}
else
{
Platform.Log(LogLevel.Warn, "SOP Instance UID in {0} appears more than once in the study.", path);
}
break;
case ProcessingStatus.Reconciled:
Platform.Log(LogLevel.Warn, "SOP was unexpectedly reconciled on reprocess SOP {0} for study {1}. It will be removed from the folder.", instanceUid, StorageLocation.StudyInstanceUid);
failureDescription = String.Format("SOP Was reconciled: {0}", instanceUid);
// Added for #10620 (Previously we didn't do anything here)
// Because we are reprocessing files in the study folder, when file needs to be reconciled it is copied to the reconcile folder
// Therefore, we need to delete the one in the study folder. Otherwise, there will be problem when the SIQ entry is reconciled.
// InstanceAlreadyExistsException will also be thrown by the SOpInstanceProcessor if this ReprocessStudy WQI
// resumes and reprocesses the same file again.
// Note: we are sure that the file has been copied to the Reconcile folder and there's no way back.
// We must get rid of this file in the study folder.
FileUtils.Delete(path);
// Special handling: if the file is one which we're supposed to reprocess at the end (see ProcessAdditionalFiles), we must remove the file from the list
if (_additionalFilesToProcess != null && _additionalFilesToProcess.Contains(path))
{
_additionalFilesToProcess.Remove(path);
}
break;
}
}
}
catch (DicomException ex)
{
// TODO : should we fail the reprocess instead? Deleting an dicom file can lead to incomplete study.
removedFiles.Add(file);
Platform.Log(LogLevel.Warn, "Skip reprocessing and delete {0}: Not readable.", path);
FileUtils.Delete(path);
failureDescription = ex.Message;
}
}
else if (!file.Extension.Equals(".xml") && !file.Extension.Equals(".gz"))
{
// not a ".dcm" or header file, delete it
removedFiles.Add(file);
FileUtils.Delete(path);
}
#endregion
cancel = reprocessedCounter >= 500;
}, true);
if (studyXml != null)
{
EnsureConsistentObjectCount(studyXml, seriesMap);
SaveStudyXml(studyXml);
}
// Completed if either all files have been reprocessed
// or no more dicom files left that can be reprocessed.
_completed = reprocessedCounter == 0;
}
catch (Exception e)
{
successful = false;
failureDescription = e.Message;
Platform.Log(LogLevel.Error, e, "Unexpected exception when reprocessing study: {0}", StorageLocation.StudyInstanceUid);
Platform.Log(LogLevel.Error, "Study may be in invalid unprocessed state. Study location: {0}", StorageLocation.GetStudyPath());
throw;
}
finally
{
LogRemovedFiles(removedFiles);
// Update the state
_queueData.State.ExecuteAtLeastOnce = true;
_queueData.State.Completed = _completed;
_queueData.State.CompleteAttemptCount++;
SaveState(item, _queueData);
if (!successful)
{
FailQueueItem(item, failureDescription);
}
else
{
if (!_completed)
{
// Put it back to Pending
PostProcessing(item, WorkQueueProcessorStatus.Pending, WorkQueueProcessorDatabaseUpdate.None);
}
else
{
LogHistory();
// Run Study / Series Rules Engine.
var engine = new StudyRulesEngine(StorageLocation, ServerPartition);
engine.Apply(ServerRuleApplyTimeEnum.StudyProcessed);
// Log the FilesystemQueue related entries
StorageLocation.LogFilesystemQueue();
PostProcessing(item, WorkQueueProcessorStatus.Complete, WorkQueueProcessorDatabaseUpdate.ResetQueueState);
Platform.Log(LogLevel.Info, "Completed reprocessing of study {0} on partition {1}", StorageLocation.StudyInstanceUid, ServerPartition.Description);
}
}
}
}
/// <summary>
/// Archive the specified <see cref="ArchiveQueue"/> item.
/// </summary>
/// <param name="queueItem">The ArchiveQueue item to archive.</param>
public void Run(ArchiveQueue queueItem)
{
using (ArchiveProcessorContext executionContext = new ArchiveProcessorContext(queueItem))
{
try
{
if (!GetStudyStorageLocation(queueItem))
{
Platform.Log(LogLevel.Error,
"Unable to find readable study storage location for archival queue request {0}. Delaying request.",
queueItem.Key);
queueItem.FailureDescription = "Unable to find readable study storage location for archival queue request.";
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Pending, Platform.Time.AddMinutes(2));
return;
}
// First, check to see if we can lock the study, if not just reschedule the queue entry.
if (!_storageLocation.QueueStudyStateEnum.Equals(QueueStudyStateEnum.Idle))
{
Platform.Log(LogLevel.Info, "Study {0} on partition {1} is currently locked, delaying archival.", _storageLocation.StudyInstanceUid, _hsmArchive.ServerPartition.Description);
queueItem.FailureDescription = "Study is currently locked, delaying archival.";
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Pending, Platform.Time.AddMinutes(2));
return;
}
StudyIntegrityValidator validator = new StudyIntegrityValidator();
validator.ValidateStudyState("Archive", _storageLocation, StudyIntegrityValidationModes.Default);
using (IUpdateContext update = PersistentStoreRegistry.GetDefaultStore().OpenUpdateContext(UpdateContextSyncMode.Flush))
{
ILockStudy studyLock = update.GetBroker <ILockStudy>();
LockStudyParameters parms = new LockStudyParameters
{
StudyStorageKey = queueItem.StudyStorageKey,
QueueStudyStateEnum = QueueStudyStateEnum.ArchiveScheduled
};
bool retVal = studyLock.Execute(parms);
if (!parms.Successful || !retVal)
{
Platform.Log(LogLevel.Info, "Study {0} on partition {1} failed to lock, delaying archival.", _storageLocation.StudyInstanceUid, _hsmArchive.ServerPartition.Description);
queueItem.FailureDescription = "Study failed to lock, delaying archival.";
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Pending, Platform.Time.AddMinutes(2));
return;
}
update.Commit();
}
string studyFolder = _storageLocation.GetStudyPath();
string studyXmlFile = _storageLocation.GetStudyXmlPath();
// Load the study Xml file, this is used to generate the list of dicom files to archive.
LoadStudyXml(studyXmlFile);
DicomFile file = LoadFileFromStudyXml();
string patientsName = file.DataSet[DicomTags.PatientsName].GetString(0, string.Empty);
string patientId = file.DataSet[DicomTags.PatientId].GetString(0, string.Empty);
string accessionNumber = file.DataSet[DicomTags.AccessionNumber].GetString(0, string.Empty);
Platform.Log(LogLevel.Info,
"Starting archival of study {0} for Patient {1} (PatientId:{2} A#:{3}) on Partition {4} on archive {5}",
_storageLocation.StudyInstanceUid, patientsName, patientId,
accessionNumber, _hsmArchive.ServerPartition.Description,
_hsmArchive.PartitionArchive.Description);
// Use the command processor to do the archival.
using (ServerCommandProcessor commandProcessor = new ServerCommandProcessor("Archive"))
{
_archiveXml = new XmlDocument();
// Create the study date folder
string zipFilename = Path.Combine(_hsmArchive.HsmPath, _storageLocation.StudyFolder);
commandProcessor.AddCommand(new CreateDirectoryCommand(zipFilename));
// Create a folder for the study
zipFilename = Path.Combine(zipFilename, _storageLocation.StudyInstanceUid);
commandProcessor.AddCommand(new CreateDirectoryCommand(zipFilename));
// Save the archive data in the study folder, based on a filename with a date / time stamp
string filename = String.Format("{0}.zip", Platform.Time.ToString("yyyy-MM-dd-HHmm"));
zipFilename = Path.Combine(zipFilename, filename);
// Create the Xml data to store in the ArchiveStudyStorage table telling
// where the archived study is located.
XmlElement hsmArchiveElement = _archiveXml.CreateElement("HsmArchive");
_archiveXml.AppendChild(hsmArchiveElement);
XmlElement studyFolderElement = _archiveXml.CreateElement("StudyFolder");
hsmArchiveElement.AppendChild(studyFolderElement);
studyFolderElement.InnerText = _storageLocation.StudyFolder;
XmlElement filenameElement = _archiveXml.CreateElement("Filename");
hsmArchiveElement.AppendChild(filenameElement);
filenameElement.InnerText = filename;
XmlElement studyInstanceUidElement = _archiveXml.CreateElement("Uid");
hsmArchiveElement.AppendChild(studyInstanceUidElement);
studyInstanceUidElement.InnerText = _storageLocation.StudyInstanceUid;
// Create the Zip file
commandProcessor.AddCommand(
new CreateStudyZipCommand(zipFilename, _studyXml, studyFolder, executionContext.TempDirectory));
// Update the database.
commandProcessor.AddCommand(new InsertArchiveStudyStorageCommand(queueItem.StudyStorageKey, queueItem.PartitionArchiveKey, queueItem.GetKey(), _storageLocation.ServerTransferSyntaxKey, _archiveXml));
StudyRulesEngine studyEngine =
new StudyRulesEngine(_storageLocation, _hsmArchive.ServerPartition, _studyXml);
studyEngine.Apply(ServerRuleApplyTimeEnum.StudyArchived, commandProcessor);
if (!commandProcessor.Execute())
{
Platform.Log(LogLevel.Error,
"Unexpected failure archiving study ({0}) to archive {1}: {2}, zip filename: {3}",
_storageLocation.StudyInstanceUid, _hsmArchive.PartitionArchive.Description,
commandProcessor.FailureReason, zipFilename);
queueItem.FailureDescription = commandProcessor.FailureReason;
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Failed, Platform.Time);
}
else
{
Platform.Log(LogLevel.Info, "Successfully archived study {0} on {1} to zip {2}",
_storageLocation.StudyInstanceUid,
_hsmArchive.PartitionArchive.Description, zipFilename);
}
// Log the current FilesystemQueue settings
_storageLocation.LogFilesystemQueue();
}
}
catch (StudyIntegrityValidationFailure ex)
{
StringBuilder error = new StringBuilder();
error.AppendLine(String.Format("Partition : {0}", ex.ValidationStudyInfo.ServerAE));
error.AppendLine(String.Format("Patient : {0}", ex.ValidationStudyInfo.PatientsName));
error.AppendLine(String.Format("Study Uid : {0}", ex.ValidationStudyInfo.StudyInstaneUid));
error.AppendLine(String.Format("Accession# : {0}", ex.ValidationStudyInfo.AccessionNumber));
error.AppendLine(String.Format("Study Date : {0}", ex.ValidationStudyInfo.StudyDate));
queueItem.FailureDescription = error.ToString();
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Failed, Platform.Time);
}
catch (Exception e)
{
String msg = String.Format("Unexpected exception archiving study: {0} on {1}: {2}",
_storageLocation.StudyInstanceUid, _hsmArchive.PartitionArchive.Description, e.Message);
Platform.Log(LogLevel.Error, e, msg);
queueItem.FailureDescription = msg;
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Failed, Platform.Time);
}
finally
{
// Unlock the Queue Entry
using (IUpdateContext update = PersistentStoreRegistry.GetDefaultStore().OpenUpdateContext(UpdateContextSyncMode.Flush))
{
ILockStudy studyLock = update.GetBroker <ILockStudy>();
LockStudyParameters parms = new LockStudyParameters
{
StudyStorageKey = queueItem.StudyStorageKey,
QueueStudyStateEnum = QueueStudyStateEnum.Idle
};
bool retVal = studyLock.Execute(parms);
if (!parms.Successful || !retVal)
{
Platform.Log(LogLevel.Info, "Study {0} on partition {1} is failed to unlock.", _storageLocation.StudyInstanceUid, _hsmArchive.ServerPartition.Description);
}
update.Commit();
}
}
}
}
