protected override void OnExecute(CommandProcessor theProcessor)
{
Platform.CheckForNullReference(Context, "Context");
Platform.CheckForNullReference(Context.ReconcileWorkQueueData, "Context.ReconcileWorkQueueData");
foreach (WorkQueueUid uid in Context.WorkQueueUidList)
{
string imagePath = GetReconcileUidPath(uid);
try
{
using (var processor = new ServerCommandProcessor(String.Format("Deleting {0}", uid.SopInstanceUid)))
{
var deleteFile = new FileDeleteCommand(imagePath, true);
var deleteUid = new DeleteWorkQueueUidCommand(uid);
processor.AddCommand(deleteFile);
processor.AddCommand(deleteUid);
Platform.Log(ServerPlatform.InstanceLogLevel, deleteFile.ToString());
if (!processor.Execute())
{
throw new Exception(String.Format("Unable to discard image {0}", uid.SopInstanceUid));
}
}
}
catch (Exception e)
{
Platform.Log(LogLevel.Error, e, "Unexpected exception discarding file: {0}", imagePath);
SopInstanceProcessor.FailUid(uid, true);
}
}
}
/// <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>
/// Creates an instance of <see cref="SopInstanceProcessorContext"/>
/// </summary>
/// <param name="commandProcessor">The <see cref="ServerCommandProcessor"/> used in the context</param>
/// <param name="studyLocation">The <see cref="StudyStorageLocation"/> of the study being processed</param>
/// <param name="uidGroup">A String value respresenting the group of SOP instances which are being processed.</param>
/// <param name="request">An external request that may have triggered this item.</param>
public SopInstanceProcessorContext(ServerCommandProcessor commandProcessor, StudyStorageLocation studyLocation,
string uidGroup, ExternalRequestQueue request = null)
{
_commandProcessor = commandProcessor;
_studyLocation = studyLocation;
_group = uidGroup;
_request = request;
}
private void HandleNonDuplicateFile(string seriesInstanceUid, string sopInstanceUid, StudyStorageLocation studyLocation, ServerCommandProcessor commandProcessor, DicomMessageBase message, string sourcePath, string path, bool dupImage, StudyProcessWorkQueueData data)
{
commandProcessor.AddCommand(new CreateDirectoryCommand(path));
path = Path.Combine(path, studyLocation.PartitionFolder);
commandProcessor.AddCommand(new CreateDirectoryCommand(path));
path = Path.Combine(path, studyLocation.StudyFolder);
commandProcessor.AddCommand(new CreateDirectoryCommand(path));
path = Path.Combine(path, studyLocation.StudyInstanceUid);
commandProcessor.AddCommand(new CreateDirectoryCommand(path));
path = Path.Combine(path, seriesInstanceUid);
commandProcessor.AddCommand(new CreateDirectoryCommand(path));
path = Path.Combine(path, sopInstanceUid);
path += ServerPlatform.DicomFileExtension;
commandProcessor.AddCommand(new RenameFileCommand(sourcePath, path, true));
WorkQueueUidData uidData = null;
if (_context.Request != null && !string.IsNullOrEmpty(_context.Request.OperationToken))
{
uidData = new WorkQueueUidData
{
OperationToken = _context.Request.OperationToken
};
}
commandProcessor.AddCommand(
new UpdateWorkQueueCommand(message, studyLocation, dupImage, data, uidData, _context.Request));
#region SPECIAL CODE FOR TESTING
if (Diagnostics.Settings.SimulateFileCorruption)
{
commandProcessor.AddCommand(new CorruptDicomFileCommand(path));
}
#endregion
}
private static bool SaveToFolder(string folder, string sopInstanceUid, string studyInstanceUid, DicomFile file)
{
using (var commandProcessor =
new ServerCommandProcessor(String.Format("Saving Sop Instance to Incoming {0}", sopInstanceUid)))
{
string path = Path.Combine(folder, studyInstanceUid);
commandProcessor.AddCommand(new CreateDirectoryCommand(path));
path = Path.Combine(path, sopInstanceUid);
path += ServerPlatform.DicomFileExtension;
if (File.Exists(path))
return false;
commandProcessor.AddCommand(new SaveDicomFileCommand(path, file, true));
return commandProcessor.Execute();
}
}
private void InsertInstance(DicomFile file, StudyXml stream, WorkQueueUid uid, string deleteFile, SopInstanceProcessorSopType sopType)
{
using (var processor = new ServerCommandProcessor("Processing WorkQueue DICOM file"))
{
EventsHelper.Fire(OnInsertingSop, this, new SopInsertingEventArgs {Processor = processor });
InsertInstanceCommand insertInstanceCommand = null;
InsertStudyXmlCommand insertStudyXmlCommand = null;
String patientsName = file.DataSet[DicomTags.PatientsName].GetString(0, String.Empty);
_modality = file.DataSet[DicomTags.Modality].GetString(0, String.Empty);
if (_context.UpdateCommands.Count > 0)
{
foreach (BaseImageLevelUpdateCommand command in _context.UpdateCommands)
{
command.File = file;
processor.AddCommand(command);
}
}
try
{
// Create a context for applying actions from the rules engine
ServerActionContext context =
new ServerActionContext(file, _context.StorageLocation.FilesystemKey, _context.Partition, _context.StorageLocation.Key);
context.CommandProcessor = processor;
_context.SopCompressionRulesEngine.Execute(context);
String seriesUid = file.DataSet[DicomTags.SeriesInstanceUid].GetString(0, String.Empty);
String sopUid = file.DataSet[DicomTags.SopInstanceUid].GetString(0, String.Empty);
String finalDest = _context.StorageLocation.GetSopInstancePath(seriesUid, sopUid);
if (_context.UpdateCommands.Count > 0)
{
processor.AddCommand(new SaveDicomFileCommand(_context.StorageLocation, file, file.Filename != finalDest));
}
else if (file.Filename != finalDest || processor.CommandCount > 0)
{
// Have to be careful here about failure on exists vs. not failing on exists
// because of the different use cases of the importer.
// save the file in the study folder, or if its been compressed
processor.AddCommand(new SaveDicomFileCommand(finalDest, file, file.Filename != finalDest));
}
// Update the StudyStream object
insertStudyXmlCommand = new InsertStudyXmlCommand(file, stream, _context.StorageLocation);
processor.AddCommand(insertStudyXmlCommand);
// Have the rules applied during the command processor, and add the objects.
processor.AddCommand(new ApplySopRulesCommand(context,_context.SopProcessedRulesEngine));
// If specified, delete the file
if (deleteFile != null)
processor.AddCommand(new FileDeleteCommand(deleteFile, true));
// Insert into the database, but only if its not a duplicate so the counts don't get off
insertInstanceCommand = new InsertInstanceCommand(file, _context.StorageLocation);
processor.AddCommand(insertInstanceCommand);
// Do a check if the StudyStatus value should be changed in the StorageLocation. This
// should only occur if the object has been compressed in the previous steps.
processor.AddCommand(new UpdateStudyStatusCommand(_context.StorageLocation, file));
if (uid!=null)
processor.AddCommand(new DeleteWorkQueueUidCommand(uid));
// Do the actual processing
if (!processor.Execute())
{
Platform.Log(LogLevel.Error, "Failure processing command {0} for SOP: {1}", processor.Description, file.MediaStorageSopInstanceUid);
Platform.Log(LogLevel.Error, "File that failed processing: {0}", file.Filename);
throw new ApplicationException("Unexpected failure (" + processor.FailureReason + ") executing command for SOP: " + file.MediaStorageSopInstanceUid, processor.FailureException);
}
Platform.Log(ServerPlatform.InstanceLogLevel, "Processed SOP: {0} for Patient {1}", file.MediaStorageSopInstanceUid, patientsName);
// Fire NewSopEventArgs or UpdateSopEventArgs Event
// Know its a duplicate if we have to delete the duplicate object
if (sopType == SopInstanceProcessorSopType.NewSop)
EventManager.FireEvent(this, new NewSopEventArgs { File = file, ServerPartitionEntry = _context.Partition, WorkQueueUidEntry = uid, WorkQueueEntry = _context.WorkQueueEntry, FileLength = InstanceStats.FileSize });
else if (sopType == SopInstanceProcessorSopType.UpdatedSop)
EventManager.FireEvent(this, new UpdateSopEventArgs {File = file,ServerPartitionEntry = _context.Partition,WorkQueueUidEntry = uid, WorkQueueEntry = _context.WorkQueueEntry, FileLength = InstanceStats.FileSize});
}
catch (Exception e)
{
Platform.Log(LogLevel.Error, e, "Unexpected exception when {0}. Rolling back operation.",
processor.Description);
processor.Rollback();
if (sopType == SopInstanceProcessorSopType.NewSop)
EventManager.FireEvent(this, new FailedNewSopEventArgs { File = file, ServerPartitionEntry = _context.Partition, WorkQueueUidEntry = uid, WorkQueueEntry = _context.WorkQueueEntry, FileLength = InstanceStats.FileSize, FailureMessage = e.Message });
else
EventManager.FireEvent(this, new FailedUpdateSopEventArgs { File = file, ServerPartitionEntry = _context.Partition, WorkQueueUidEntry = uid, WorkQueueEntry = _context.WorkQueueEntry, FileLength = InstanceStats.FileSize, FailureMessage = e.Message });
throw new ApplicationException("Unexpected exception when processing file.", e);
}
finally
{
if (insertInstanceCommand != null && insertInstanceCommand.Statistics.IsSet)
_instanceStats.InsertDBTime.Add(insertInstanceCommand.Statistics);
if (insertStudyXmlCommand != null && insertStudyXmlCommand.Statistics.IsSet)
_instanceStats.InsertStreamTime.Add(insertStudyXmlCommand.Statistics);
}
}
}
public void RestoreNearlineStudy(RestoreQueue queueItem, string zipFile, string studyFolder)
{
ServerFilesystemInfo fs = _hsmArchive.Selector.SelectFilesystem();
if (fs == null)
{
DateTime scheduleTime = Platform.Time.AddMinutes(5);
Platform.Log(LogLevel.Error, "No writeable filesystem for restore, rescheduling restore request to {0}", scheduleTime);
queueItem.FailureDescription = "No writeable filesystem for restore, rescheduling restore request";
_hsmArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Pending, scheduleTime);
return;
}
string destinationFolder = Path.Combine(fs.Filesystem.FilesystemPath, _hsmArchive.ServerPartition.PartitionFolder);
StudyStorageLocation restoredLocation = null;
try
{
using (var processor = new ServerCommandProcessor("HSM Restore Offline Study"))
{
processor.AddCommand(new CreateDirectoryCommand(destinationFolder));
destinationFolder = Path.Combine(destinationFolder, studyFolder);
processor.AddCommand(new CreateDirectoryCommand(destinationFolder));
destinationFolder = Path.Combine(destinationFolder, _studyStorage.StudyInstanceUid);
processor.AddCommand(new CreateDirectoryCommand(destinationFolder));
processor.AddCommand(new ExtractZipCommand(zipFile, destinationFolder));
// We rebuild the StudyXml, in case any settings or issues have happened since archival
processor.AddCommand(new RebuildStudyXmlCommand(_studyStorage.StudyInstanceUid, destinationFolder));
// Apply the rules engine.
var context =
new ServerActionContext(null, fs.Filesystem.GetKey(), _hsmArchive.ServerPartition,
queueItem.StudyStorageKey, processor);
processor.AddCommand(
new ApplyRulesCommand(destinationFolder, _studyStorage.StudyInstanceUid, context));
// Do the actual insert into the DB
var insertStorageCommand = new InsertFilesystemStudyStorageCommand(
_hsmArchive.PartitionArchive.ServerPartitionKey,
_studyStorage.StudyInstanceUid,
studyFolder,
fs.Filesystem.GetKey(), _syntax);
processor.AddCommand(insertStorageCommand);
if (!processor.Execute())
{
Platform.Log(LogLevel.Error, "Unexpected error processing restore request for {0} on archive {1}",
_studyStorage.StudyInstanceUid, _hsmArchive.PartitionArchive.Description);
queueItem.FailureDescription = processor.FailureReason;
_hsmArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Failed, Platform.Time);
}
else
{
restoredLocation = insertStorageCommand.Location;
// Unlock the Queue Entry
using (
IUpdateContext update = PersistentStoreRegistry.GetDefaultStore().OpenUpdateContext(UpdateContextSyncMode.Flush))
{
bool retVal = _hsmArchive.UpdateRestoreQueue(update, queueItem, RestoreQueueStatusEnum.Completed, Platform.Time.AddSeconds(60));
var studyLock = update.GetBroker<ILockStudy>();
var parms = new LockStudyParameters
{
StudyStorageKey = queueItem.StudyStorageKey,
QueueStudyStateEnum = QueueStudyStateEnum.Idle
};
retVal = retVal && studyLock.Execute(parms);
if (!parms.Successful || !retVal)
{
string message =
String.Format("Study {0} on partition {1} failed to unlock.", _studyStorage.StudyInstanceUid,
_hsmArchive.ServerPartition.Description);
Platform.Log(LogLevel.Info, message);
throw new ApplicationException(message);
}
update.Commit();
Platform.Log(LogLevel.Info, "Successfully restored study: {0} on archive {1}", _studyStorage.StudyInstanceUid,
_hsmArchive.PartitionArchive.Description);
OnStudyRestored(restoredLocation);
}
}
}
}
catch(StudyIntegrityValidationFailure ex)
{
Debug.Assert(restoredLocation != null);
// study has been restored but it seems corrupted. Need to reprocess it.
ReprocessStudy(restoredLocation, ex.Message);
}
catch (Exception e)
{
Platform.Log(LogLevel.Error, e, "Unexpected exception processing restore request for {0} on archive {1}",
_studyStorage.StudyInstanceUid, _hsmArchive.PartitionArchive.Description);
_hsmArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Failed, Platform.Time);
}
}
private void RestoreOnlineStudy(RestoreQueue queueItem, string zipFile, string destinationFolder)
{
try
{
using (var processor = new ServerCommandProcessor("HSM Restore Online Study"))
{
var zipService = Platform.GetService<IZipService>();
using (var zipWriter = zipService.OpenWrite(zipFile))
{
foreach (string file in zipWriter.EntryFileNames)
{
processor.AddCommand(new ExtractZipFileAndReplaceCommand(zipFile, file, destinationFolder));
}
}
// We rebuild the StudyXml, in case any settings or issues have happened since archival
processor.AddCommand(new RebuildStudyXmlCommand(_location.StudyInstanceUid, destinationFolder));
StudyStatusEnum status;
if (_syntax.Encapsulated && _syntax.LosslessCompressed)
status = StudyStatusEnum.OnlineLossless;
else if (_syntax.Encapsulated && _syntax.LossyCompressed)
status = StudyStatusEnum.OnlineLossy;
else
status = StudyStatusEnum.Online;
processor.AddCommand(new UpdateStudyStateCommand(_location, status, _serverSyntax));
// Apply the rules engine.
var context =
new ServerActionContext(null, _location.FilesystemKey, _hsmArchive.ServerPartition,
queueItem.StudyStorageKey, processor);
processor.AddCommand(
new ApplyRulesCommand(destinationFolder, _location.StudyInstanceUid, context));
if (!processor.Execute())
{
Platform.Log(LogLevel.Error, "Unexpected error processing restore request for {0} on archive {1}",
_location.StudyInstanceUid, _hsmArchive.PartitionArchive.Description);
queueItem.FailureDescription = processor.FailureReason;
_hsmArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Failed, Platform.Time);
}
else
{
// Unlock the Queue Entry and set to complete
using (IUpdateContext update = PersistentStoreRegistry.GetDefaultStore().OpenUpdateContext(UpdateContextSyncMode.Flush))
{
_hsmArchive.UpdateRestoreQueue(update, queueItem, RestoreQueueStatusEnum.Completed, Platform.Time.AddSeconds(60));
var studyLock = update.GetBroker<ILockStudy>();
var 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} failed to unlock.", _location.StudyInstanceUid,
_hsmArchive.ServerPartition.Description);
}
update.Commit();
Platform.Log(LogLevel.Info, "Successfully restored study: {0} on archive {1}", _location.StudyInstanceUid,
_hsmArchive.PartitionArchive.Description);
_location = ReloadStorageLocation();
OnStudyRestored(_location);
}
}
}
}
catch (StudyIntegrityValidationFailure ex)
{
// study has been restored but it seems corrupted. Need to reprocess it.
ReprocessStudy(_location, ex.Message);
}
catch (Exception e)
{
Platform.Log(LogLevel.Error, e, "Unexpected exception processing restore request for {0} on archive {1}",
_location.StudyInstanceUid, _hsmArchive.PartitionArchive.Description);
queueItem.FailureDescription = e.Message;
_hsmArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Failed, Platform.Time);
}
}
private static void RemoveWorkQueueUid(WorkQueueUid uid, string fileToDelete)
{
using (var processor = new ServerCommandProcessor("Remove Work Queue Uid"))
{
processor.AddCommand(new DeleteWorkQueueUidCommand(uid));
if (String.IsNullOrEmpty(fileToDelete) == false)
{
processor.AddCommand(new FileDeleteCommand(fileToDelete, true));
}
if (!processor.Execute())
{
String error = String.Format("Unable to delete Work Queue Uid {0}: {1}", uid.Key, processor.FailureReason);
Platform.Log(LogLevel.Error, error);
throw new ApplicationException(error, processor.FailureException);
}
}
}
/// <summary>
/// Removes all WorkQueueUids from the database and delete the corresponding DICOM files from the filesystem.
/// </summary>
private void ProcessWorkQueueUids()
{
if (Study == null)
Platform.Log(LogLevel.Info, "Begin StudyProcess Cleanup (Study has not been created): Attempt #{0}. {1} unprocessed files will be removed",
WorkQueueItem.FailureCount + 1,
WorkQueueUidList.Count);
else
Platform.Log(LogLevel.Info,
"Begin StudyProcess Cleanup for study {0}, Patient {1} (PatientId:{2} A#:{3}) on Partition {4}. Attempt #{5}. {6} unprocessed files will be removed",
Study.StudyInstanceUid, Study.PatientsName, Study.PatientId,
Study.AccessionNumber, ServerPartition.Description,
WorkQueueItem.FailureCount + 1,
WorkQueueUidList.Count
);
foreach (WorkQueueUid sop in WorkQueueUidList)
{
string path = GetFileStoredPath(sop);
Platform.Log(LogLevel.Info, "Cleaning up {0}", path);
using (ServerCommandProcessor processor = new ServerCommandProcessor(String.Format("Deleting {0}", sop.SopInstanceUid)))
{
// delete the file
FileDeleteCommand deleteFile = new FileDeleteCommand(path, true);
processor.AddCommand(deleteFile);
// delete the WorkQueueUID from the database
DeleteWorkQueueUidCommand deleteUid = new DeleteWorkQueueUidCommand(sop);
processor.AddCommand(deleteUid);
try
{
// delete the directory (if empty)
var fileInfo = new FileInfo(path);
ClearCanvas.ImageServer.Core.Command.DeleteDirectoryCommand deleteDir = new ClearCanvas.ImageServer.Core.Command.DeleteDirectoryCommand(fileInfo.Directory.FullName, false, true);
processor.AddCommand(deleteDir);
}
catch (DirectoryNotFoundException)
{
// ignore
}
if (!processor.Execute())
{
throw new Exception(String.Format("Unable to delete SOP {0}", sop.SopInstanceUid), processor.FailureException);
}
}
// Delete the base directory if it's empty
var baseDir = GetBaseDirectory(sop);
if (Directory.Exists(baseDir))
{
using (ServerCommandProcessor processor = new ServerCommandProcessor(String.Format("Deleting {0}", sop.SopInstanceUid)))
{
ClearCanvas.ImageServer.Core.Command.DeleteDirectoryCommand deleteDir = new ClearCanvas.ImageServer.Core.Command.DeleteDirectoryCommand(baseDir, false, true);
processor.AddCommand(deleteDir);
if (!processor.Execute())
{
throw new Exception(String.Format("Unable to delete {0}", baseDir), processor.FailureException);
}
}
}
}
}
private void DeleteDuplicate(WorkQueueUid uid)
{
using (ServerCommandProcessor processor = new ServerCommandProcessor("Delete Received Duplicate"))
{
FileInfo duplicateFile = GetDuplicateSopFile(uid);
processor.AddCommand(new FileDeleteCommand(duplicateFile.FullName,true));
processor.AddCommand(new DeleteWorkQueueUidCommand(uid));
if (!processor.Execute())
{
throw new ApplicationException(processor.FailureReason, processor.FailureException);
}
Platform.Log(ServerPlatform.InstanceLogLevel, "Discard duplicate SOP {0} in {1}", uid.SopInstanceUid, duplicateFile.FullName);
}
}
/// <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"))
{
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();
}
}
}
/// <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>
/// Create Duplicate SIQ Entry
/// </summary>
/// <param name="file"></param>
/// <param name="location"></param>
/// <param name="sourcePath"></param>
/// <param name="queue"></param>
/// <param name="uid"></param>
/// <param name="data"></param>
public static void CreateDuplicateSIQEntry(DicomFile file, StudyStorageLocation location, string sourcePath,
WorkQueue queue, WorkQueueUid uid, StudyProcessWorkQueueData data)
{
Platform.Log(LogLevel.Info, "Creating Work Queue Entry for duplicate...");
String uidGroup = queue.GroupID ?? queue.GetKey().Key.ToString();
using (var commandProcessor = new ServerCommandProcessor("Insert Work Queue entry for duplicate"))
{
commandProcessor.AddCommand(new FileDeleteCommand(sourcePath, true));
var sopProcessingContext = new SopInstanceProcessorContext(commandProcessor, location, uidGroup);
DicomProcessingResult result = Process(sopProcessingContext, file, data);
if (!result.Successful)
{
FailUid(uid, true);
return;
}
commandProcessor.AddCommand(new DeleteWorkQueueUidCommand(uid));
if (!commandProcessor.Execute())
{
Platform.Log(LogLevel.Error, "Unexpected error when creating duplicate study integrity queue entry: {0}",
commandProcessor.FailureReason);
FailUid(uid, true);
}
}
}
private void Purge(StudyItem study)
{
Task.Factory.StartNew(() =>
{
var archive = SelectPartitionArchive(study);
if (archive == null)
{
MessageBox.Show("Please add an archive in the partition where this study is located");
return;
}
if (study.IsArchivingScheduled())
{
if (
MessageBox.Show(
"This study is scheduled in the Archive Queue. Do you want to remove it from the queue before purging?",
"Study is scheduled for archiving",
MessageBoxButtons.YesNo) == System.Windows.Forms.DialogResult.Yes)
{
using (var processor = new ServerCommandProcessor("archive"))
{
processor.AddCommand(new DeleteAllArchiveQueueItemCommand(study.StudyStorage, archive));
processor.Execute();
}
}
}
if (study.StudyStorageLocation.ArchiveLocations == null || !study.StudyStorageLocation.ArchiveLocations.Any())
{
var i = 0;
using (var processor = new ServerCommandProcessor("archive"))
{
var archiveCommand = new ArchiveStudyCommand(study.StudyStorageLocation, GetArchivePath(archive), @"C:\temp", archive);
archiveCommand.ProgressUpdated += (s, e) =>
{
study.OperationProgress = new OperationProgress()
{
Status = e.Percentage == 100 ? "Archived" : e.Status,
Percentage = (int)e.Percentage
};
};
processor.AddCommand(archiveCommand);
if (!processor.Execute())
MessageBox.Show(string.Format("Unable to archive study: {0}", processor.FailureException.Message));
}
}
using (var processor = new ServerCommandProcessor("archive"))
{
processor.AddCommand(new PurgeStudyCommand(study.StudyStorage));
if (!processor.Execute())
MessageBox.Show(string.Format("Unable to purge study: {0}", processor.FailureException.Message));
else
{
MessageBox.Show("Study has been succesfully purged");
study.Status = "Nearline";
}
}
});
}
private void ProcessInstanceLevelDelete(Model.WorkQueue item)
{
// ensure the Study is loaded.
Study study = StorageLocation.Study;
Platform.CheckForNullReference(study, "Study record doesn't exist");
Platform.Log(LogLevel.Info, "Processing Instance Level Deletion for Study {0}, A#: {1}",
study.StudyInstanceUid, study.AccessionNumber);
bool completed = false;
try
{
// Load the list of Sop Instances to be deleted from the WorkQueueUid
LoadUids(item);
// Go through the list of series and add commands
// to delete each of them. It's all or nothing.
using (var processor = new ServerCommandProcessor(String.Format("Deleting Series from study {0}, A#:{1}, Patient: {2}, ID:{3}", study.StudyInstanceUid, study.AccessionNumber, study.PatientsName, study.PatientId)))
{
StudyXml studyXml = StorageLocation.LoadStudyXml();
IDictionary<string, Series> existingSeries = StorageLocation.Study.Series;
// Add commands to delete the folders and update the xml
foreach (WorkQueueUid uid in WorkQueueUidList)
{
// Delete from study XML
if (studyXml.Contains(uid.SeriesInstanceUid, uid.SopInstanceUid))
{
//Note: DeleteDirectoryCommand doesn't throw exception if the folder doesn't exist
var xmlUpdate = new RemoveInstanceFromStudyXmlCommand(StorageLocation, studyXml, uid.SeriesInstanceUid, uid.SopInstanceUid);
processor.AddCommand(xmlUpdate);
}
// Delete from filesystem
string path = StorageLocation.GetSopInstancePath(uid.SeriesInstanceUid, uid.SopInstanceUid);
if (File.Exists(path))
{
var delDir = new FileDeleteCommand(path, true);
processor.AddCommand(delDir);
}
}
// flush the updated xml to disk
processor.AddCommand(new SaveXmlCommand(studyXml, StorageLocation));
// Update the db.. NOTE: these commands are executed at the end.
foreach (WorkQueueUid uid in WorkQueueUidList)
{
// Delete from DB
if (studyXml.Contains(uid.SeriesInstanceUid, uid.SopInstanceUid))
{
var delInstance = new UpdateInstanceCountCommand(StorageLocation, uid.SeriesInstanceUid, uid.SopInstanceUid);
processor.AddCommand(delInstance);
delInstance.Executing += DeleteSeriesFromDbExecuting;
}
else
{
// SOP doesn't exist
Platform.Log(LogLevel.Info, "SOP {0} is invalid or no longer exists", uid.SopInstanceUid);
}
// The WorkQueueUid must be cleared before the entry can be removed from the queue
var deleteUid = new DeleteWorkQueueUidCommand(uid);
processor.AddCommand(deleteUid);
// Force a re-archival if necessary
processor.AddCommand(new InsertArchiveQueueCommand(item.ServerPartitionKey, item.StudyStorageKey));
}
if (!processor.Execute())
throw new ApplicationException(
String.Format("Error occurred when series from Study {0}, A#: {1}",
study.StudyInstanceUid, study.AccessionNumber), processor.FailureException);
}
completed = true;
}
finally
{
if (completed)
{
OnCompleted();
PostProcessing(item, WorkQueueProcessorStatus.Complete, WorkQueueProcessorDatabaseUpdate.ResetQueueState);
}
else
{
PostProcessing(item, WorkQueueProcessorStatus.Pending, WorkQueueProcessorDatabaseUpdate.None);
}
}
}
private DicomProcessingResult HandleDuplicateFile(string sopInstanceUid, StudyStorageLocation studyLocation, ServerCommandProcessor commandProcessor, DicomMessageBase message, string sourceFilename, StudyProcessWorkQueueData data)
{
Study study = studyLocation.Study ??
studyLocation.LoadStudy(ServerExecutionContext.Current.PersistenceContext);
if (study != null)
Platform.Log(LogLevel.Info, "Received duplicate SOP {0} (A#:{1} StudyUid:{2} Patient: {3} ID:{4})",
sopInstanceUid,
study.AccessionNumber, study.StudyInstanceUid,
study.PatientsName, study.PatientId);
else
Platform.Log(LogLevel.Info,
"Received duplicate SOP {0} (StudyUid:{1}). Existing files haven't been processed.",
sopInstanceUid, studyLocation.StudyInstanceUid);
var sopProcessingContext = new SopInstanceProcessorContext(commandProcessor, studyLocation, _context.ContextID,
_context.Request)
{
DuplicateProcessing = _context.DuplicateProcessing
};
DicomProcessingResult result = DuplicateSopProcessorHelper.Process(sopProcessingContext, message, data,
sourceFilename);
return result;
}
/// <summary>
/// Apply the Rules engine.
/// </summary>
/// <remarks>
/// <para>
/// This method applies the rules engine to the first image in each series within a study.
/// The assumption is that the actions generated by the engine can handle being applied more
/// than once for the same study. This is also done to handle the case of multi-modality
/// studies where you may want the rules to be run against each series, because they may
/// apply differently.
/// </para>
/// <para>
/// Note that we are still applying series level moves, although there currently are not
/// any series level rules. We've somewhat turned the study level rules into series
/// level rules.
/// </para>
/// </remarks>
public void Apply(ServerRuleApplyTimeEnum applyTime)
{
using(var theProcessor = new ServerCommandProcessor("Study Rule Processor")
{
PrimaryServerPartitionKey = _partition.GetKey(),
PrimaryStudyKey = _location.Study.GetKey()
})
{
Apply(applyTime, theProcessor);
if (false == theProcessor.Execute())
{
Platform.Log(LogLevel.Error,
"Unexpected failure processing Study level rules for study {0} on partition {1} for {2} apply time",
_location.StudyInstanceUid, _partition.Description, applyTime.Description);
}
}
}
private void UpdateStudyOrDuplicates()
{
// StorageLocation object must be reloaded if we are overwriting the study
// with info in the duplicates.
bool needReload = false;
switch (_processDuplicateEntry.QueueData.Action)
{
case ProcessDuplicateAction.OverwriteUseDuplicates:
if (_processDuplicateEntry.QueueData.State.ExistingStudyUpdated)
Platform.Log(LogLevel.Info, "Existing Study has been updated before");
else
{
Platform.Log(LogLevel.Info, "Update Existing Study w/ Duplicate Info");
_studyUpdateCommands = BuildUpdateStudyCommandsFromDuplicate();
using (ServerCommandProcessor processor = new ServerCommandProcessor("Update Existing Study w/ Duplicate Info"))
{
processor.AddCommand(new UpdateStudyCommand(ServerPartition, StorageLocation, _studyUpdateCommands, ServerRuleApplyTimeEnum.SopProcessed, WorkQueueItem));
if (!processor.Execute())
{
throw new ApplicationException(processor.FailureReason, processor.FailureException);
}
needReload = true;
_processDuplicateEntry.QueueData.State.ExistingStudyUpdated = true;
}
}
break;
case ProcessDuplicateAction.OverwriteUseExisting:
ImageUpdateCommandBuilder commandBuilder = new ImageUpdateCommandBuilder();
_duplicateUpdateCommands = new List<BaseImageLevelUpdateCommand>();
_duplicateUpdateCommands.AddRange(commandBuilder.BuildCommands<StudyMatchingMap>(StorageLocation));
PrintCommands(_duplicateUpdateCommands);
break;
}
if (needReload)
{
StudyStorageLocation updatedStorageLocation;
//NOTE: Make sure we are loading the storage location fro the database instead of the cache.
if (!FilesystemMonitor.Instance.GetWritableStudyStorageLocation(WorkQueueItem.StudyStorageKey, out updatedStorageLocation))
{
// this is odd.. we just updated it and now it's no longer writable?
throw new ApplicationException("Filesystem is not writable");
}
StorageLocation = updatedStorageLocation;
}
}
private ProcessDuplicateResult OverwriteAndUpdateDuplicate(DicomFile dupFile, WorkQueueUid uid, StudyXml studyXml)
{
Platform.Log(LogLevel.Info, "Overwriting duplicate SOP {0}", uid.SopInstanceUid);
var result = new ProcessDuplicateResult();
result.ActionTaken = DuplicateProcessResultAction.Accept;
using (var processor = new ServerCommandProcessor("Overwrite duplicate instance"))
{
var destination = Context.StorageLocation.GetSopInstancePath(uid.SeriesInstanceUid, uid.SopInstanceUid);
processor.AddCommand(new RenameFileCommand(dupFile.Filename, destination, false));
// Do so that the FileSize calculation inInsertStudyXmlCommand works
dupFile.Filename = destination;
// Update the StudyStream object
var insertStudyXmlCommand = new InsertStudyXmlCommand(dupFile, studyXml, Context.StorageLocation);
processor.AddCommand(insertStudyXmlCommand);
// Ideally we don't need to insert the instance into the database since it's a duplicate.
// However, we need to do so to ensure the Study record is recreated if we are dealing with an orphan study.
// For other cases, this will cause the instance count in the DB to be out of sync with the filesystem.
// But it will be corrected at the end of the processing when the study verification is executed.
processor.AddCommand(new UpdateInstanceCommand(Context.StorageLocation.ServerPartition,Context.StorageLocation,dupFile));
processor.AddCommand(new DeleteWorkQueueUidCommand(uid));
if (!processor.Execute())
{
EventManager.FireEvent(this, new FailedUpdateSopEventArgs { File = dupFile, ServerPartitionEntry = Context.StorageLocation.ServerPartition, WorkQueueUidEntry = uid, WorkQueueEntry = WorkQueueItem, FileLength = (ulong)insertStudyXmlCommand.FileSize, FailureMessage = processor.FailureReason });
// cause the item to fail
throw new Exception(string.Format("Error occurred when trying to overwrite duplicate in the filesystem."), processor.FailureException);
}
EventManager.FireEvent(this, new UpdateSopEventArgs { File = dupFile, ServerPartitionEntry = Context.StorageLocation.ServerPartition, WorkQueueUidEntry = uid, WorkQueueEntry = WorkQueueItem, FileLength = (ulong)insertStudyXmlCommand.FileSize });
}
return result;
}
private void RemoveExistingImage(WorkQueueUid uid)
{
string path = StorageLocation.GetSopInstancePath(uid.SeriesInstanceUid, uid.SopInstanceUid);
if (!File.Exists(path))
return;
StudyXml studyXml = StorageLocation.LoadStudyXml();
var file = new DicomFile(path);
file.Load(DicomReadOptions.DoNotStorePixelDataInDataSet | DicomReadOptions.Default); // don't need to load pixel data cause we will delete it
#if DEBUG
int originalInstanceCountInXml = studyXml.NumberOfStudyRelatedInstances;
int originalStudyInstanceCount = Study.NumberOfStudyRelatedInstances;
int originalSeriesInstanceCount = Study.Series[uid.SeriesInstanceUid].NumberOfSeriesRelatedInstances;
#endif
using (var processor = new ServerCommandProcessor("Delete Existing Image"))
{
var seriesInstanceUid = file.DataSet[DicomTags.SeriesInstanceUid].ToString();
var sopInstanceUid = file.DataSet[DicomTags.SopInstanceUid].ToString();
processor.AddCommand(new FileDeleteCommand(path,true));
processor.AddCommand(new RemoveInstanceFromStudyXmlCommand(StorageLocation, studyXml, seriesInstanceUid, sopInstanceUid));
processor.AddCommand(new UpdateInstanceCountCommand(StorageLocation, seriesInstanceUid,sopInstanceUid));
if (!processor.Execute())
{
throw new ApplicationException(String.Format("Unable to remove existing image {0}", file.Filename), processor.FailureException);
}
}
#if DEBUG
Debug.Assert(!File.Exists(path));
Debug.Assert(studyXml.NumberOfStudyRelatedInstances == originalInstanceCountInXml - 1);
Debug.Assert(Study.Load(Study.Key).NumberOfStudyRelatedInstances == originalStudyInstanceCount - 1);
Debug.Assert(Study.Load(Study.Key).Series[uid.SeriesInstanceUid].NumberOfSeriesRelatedInstances == originalSeriesInstanceCount - 1);
#endif
}
private static void OnStudyRestored(StudyStorageLocation location)
{
ValidateStudy(location);
using(var processor = new ServerCommandProcessor("Update Study Size In DB"))
{
processor.AddCommand(new UpdateStudySizeInDBCommand(location));
if (!processor.Execute())
{
Platform.Log(LogLevel.Error, "Unexpected error when trying to update the study size in DB:", processor.FailureReason);
}
}
}
void SaveDuplicateReport(WorkQueueUid uid, string sourceFile, string destinationFile, DicomFile dupFile, StudyXml studyXml)
{
using (var processor = new ServerCommandProcessor("Save duplicate report"))
{
processor.AddCommand(new RenameFileCommand(sourceFile, destinationFile, false));
// Update the StudyStream object
processor.AddCommand( new InsertStudyXmlCommand(dupFile, studyXml, Context.StorageLocation));
processor.AddCommand(new DeleteWorkQueueUidCommand(uid));
processor.Execute();
}
}
/// <summary>
/// Migrates the study to new tier
/// </summary>
/// <param name="storage"></param>
/// <param name="newFilesystem"></param>
private void DoMigrateStudy(StudyStorageLocation storage, ServerFilesystemInfo newFilesystem)
{
Platform.CheckForNullReference(storage, "storage");
Platform.CheckForNullReference(newFilesystem, "newFilesystem");
TierMigrationStatistics stat = new TierMigrationStatistics {StudyInstanceUid = storage.StudyInstanceUid};
stat.ProcessSpeed.Start();
StudyXml studyXml = storage.LoadStudyXml();
stat.StudySize = (ulong) studyXml.GetStudySize();
Platform.Log(LogLevel.Info, "About to migrate study {0} from {1} to {2}",
storage.StudyInstanceUid, storage.FilesystemTierEnum, newFilesystem.Filesystem.Description);
string newPath = Path.Combine(newFilesystem.Filesystem.FilesystemPath, storage.PartitionFolder);
DateTime startTime = Platform.Time;
DateTime lastLog = Platform.Time;
int fileCounter = 0;
ulong bytesCopied = 0;
long instanceCountInXml = studyXml.NumberOfStudyRelatedInstances;
using (ServerCommandProcessor processor = new ServerCommandProcessor("Migrate Study"))
{
TierMigrationContext context = new TierMigrationContext
{
OriginalStudyLocation = storage,
Destination = newFilesystem
};
// The multiple CreateDirectoryCommands are done so that rollback of the directories being created happens properly if either of the directories already exist.
var origFolder = context.OriginalStudyLocation.GetStudyPath();
processor.AddCommand(new CreateDirectoryCommand(newPath));
newPath = Path.Combine(newPath, context.OriginalStudyLocation.StudyFolder);
processor.AddCommand(new CreateDirectoryCommand(newPath));
newPath = Path.Combine(newPath, context.OriginalStudyLocation.StudyInstanceUid);
// don't create this directory so that it won't be backed up by MoveDirectoryCommand
var copyDirCommand = new CopyDirectoryCommand(origFolder, newPath,
delegate (string path)
{
// Update the progress. This is useful if the migration takes long time to complete.
FileInfo file = new FileInfo(path);
bytesCopied += (ulong)file.Length;
fileCounter++;
if (file.Extension != null && file.Extension.Equals(ServerPlatform.DicomFileExtension, StringComparison.InvariantCultureIgnoreCase))
{
TimeSpan elapsed = Platform.Time - lastLog;
TimeSpan totalElapsed = Platform.Time - startTime;
double speedInMBPerSecond = 0;
if (totalElapsed.TotalSeconds > 0)
{
speedInMBPerSecond = (bytesCopied / 1024f / 1024f) / totalElapsed.TotalSeconds;
}
if (elapsed > TimeSpan.FromSeconds(WorkQueueSettings.Instance.TierMigrationProgressUpdateInSeconds))
{
#region Log Progress
StringBuilder stats = new StringBuilder();
if (instanceCountInXml != 0)
{
float pct = (float)fileCounter / instanceCountInXml;
stats.AppendFormat("{0} files moved [{1:0.0}MB] since {2} ({3:0}% completed). Speed={4:0.00}MB/s",
fileCounter, bytesCopied / 1024f / 1024f, startTime, pct * 100, speedInMBPerSecond);
}
else
{
stats.AppendFormat("{0} files moved [{1:0.0}MB] since {2}. Speed={3:0.00}MB/s",
fileCounter, bytesCopied / 1024f / 1024f, startTime, speedInMBPerSecond);
}
Platform.Log(LogLevel.Info, "Tier migration for study {0}: {1}", storage.StudyInstanceUid, stats.ToString());
try
{
using (IUpdateContext ctx = PersistentStoreRegistry.GetDefaultStore().OpenUpdateContext(UpdateContextSyncMode.Flush))
{
IWorkQueueEntityBroker broker = ctx.GetBroker<IWorkQueueEntityBroker>();
WorkQueueUpdateColumns parameters = new WorkQueueUpdateColumns
{FailureDescription = stats.ToString()};
broker.Update(WorkQueueItem.GetKey(), parameters);
ctx.Commit();
}
}
catch
{
// can't log the progress so far... just ignore it
}
finally
{
lastLog = DateTime.Now;
}
#endregion
}
}
});
processor.AddCommand(copyDirCommand);
DeleteDirectoryCommand delDirCommand = new DeleteDirectoryCommand(origFolder, false)
{RequiresRollback = false};
processor.AddCommand(delDirCommand);
TierMigrateDatabaseUpdateCommand updateDbCommand = new TierMigrateDatabaseUpdateCommand(context);
processor.AddCommand(updateDbCommand);
Platform.Log(LogLevel.Info, "Start migrating study {0}.. expecting {1} to be moved", storage.StudyInstanceUid, ByteCountFormatter.Format(stat.StudySize));
if (!processor.Execute())
{
if (processor.FailureException != null)
throw processor.FailureException;
throw new ApplicationException(processor.FailureReason);
}
stat.DBUpdate = updateDbCommand.Statistics;
stat.CopyFiles = copyDirCommand.CopySpeed;
stat.DeleteDirTime = delDirCommand.Statistics;
}
stat.ProcessSpeed.SetData(bytesCopied);
stat.ProcessSpeed.End();
Platform.Log(LogLevel.Info, "Successfully migrated study {0} from {1} to {2} in {3} [ {4} files, {5} @ {6}, DB Update={7}, Remove Dir={8}]",
storage.StudyInstanceUid,
storage.FilesystemTierEnum,
newFilesystem.Filesystem.FilesystemTierEnum,
TimeSpanFormatter.Format(stat.ProcessSpeed.ElapsedTime),
fileCounter,
ByteCountFormatter.Format(bytesCopied),
stat.CopyFiles.FormattedValue,
stat.DBUpdate.FormattedValue,
stat.DeleteDirTime.FormattedValue);
string originalPath = storage.GetStudyPath();
if (Directory.Exists(storage.GetStudyPath()))
{
Platform.Log(LogLevel.Info, "Original study folder could not be deleted. It must be cleaned up manually: {0}", originalPath);
ServerPlatform.Alert(AlertCategory.Application, AlertLevel.Warning, WorkQueueItem.WorkQueueTypeEnum.ToString(), 1000, GetWorkQueueContextData(WorkQueueItem), TimeSpan.Zero,
"Study has been migrated to a new tier. Original study folder must be cleaned up manually: {0}", originalPath);
}
UpdateAverageStatistics(stat);
}
void CreateDuplicateSIQEntry(WorkQueueUid uid, DicomFile file, List<DicomAttributeComparisonResult> differences)
{
Platform.Log(LogLevel.Info, "Duplicate SOP is different from existing copy. Creating duplicate SIQ entry. SOP: {0}", uid.SopInstanceUid);
using (var processor = new ServerCommandProcessor("Create Duplicate SIQ Entry"))
{
var insertCommand = new InsertOrUpdateEntryCommand(
uid.GroupID, StorageLocation, file,
ServerHelper.GetDuplicateGroupPath(StorageLocation, uid),
string.IsNullOrEmpty(uid.RelativePath)
? Path.Combine(StorageLocation.StudyInstanceUid, uid.SopInstanceUid + "." + uid.Extension)
: uid.RelativePath,
differences);
processor.AddCommand(insertCommand);
processor.AddCommand(new DeleteWorkQueueUidCommand(uid));
processor.Execute();
}
}
private void SaveFile(DicomFile file)
{
String seriesInstanceUid = file.DataSet[DicomTags.SeriesInstanceUid].GetString(0, String.Empty);
String sopInstanceUid = file.DataSet[DicomTags.SopInstanceUid].GetString(0, String.Empty);
String destPath = _oldStudyLocation.FilesystemPath;
using (ServerCommandProcessor filesystemUpdateProcessor = new ServerCommandProcessor("Update Study"))
{
filesystemUpdateProcessor.AddCommand(new CreateDirectoryCommand(destPath));
destPath = Path.Combine(destPath, _partition.PartitionFolder);
filesystemUpdateProcessor.AddCommand(new CreateDirectoryCommand(destPath));
destPath = Path.Combine(destPath, _oldStudyFolder);
filesystemUpdateProcessor.AddCommand(new CreateDirectoryCommand(destPath));
destPath = Path.Combine(destPath, _newStudyInstanceUid);
filesystemUpdateProcessor.AddCommand(new CreateDirectoryCommand(destPath));
destPath = Path.Combine(destPath, seriesInstanceUid);
filesystemUpdateProcessor.AddCommand(new CreateDirectoryCommand(destPath));
destPath = Path.Combine(destPath, sopInstanceUid);
destPath += ServerPlatform.DicomFileExtension;
// Overwrite the prior file
SaveDicomFileCommand saveCommand = new SaveDicomFileCommand(destPath, file, false);
filesystemUpdateProcessor.AddCommand(saveCommand);
if (_rulesEngine != null)
{
ServerActionContext context = new ServerActionContext(file, _oldStudyLocation.FilesystemKey, _partition, _oldStudyLocation.Key, filesystemUpdateProcessor);
_rulesEngine.Execute(context);
}
if (!filesystemUpdateProcessor.Execute())
{
throw new ApplicationException(String.Format("Unable to update image {0} : {1}", file.Filename, filesystemUpdateProcessor.FailureReason));
}
}
}
/// <summary>
/// Process a specific DICOM file related to a <see cref="WorkQueue"/> request.
/// </summary>
/// <remarks>
/// <para>
/// On success and if <see cref="uid"/> is set, the <see cref="WorkQueueUid"/> field is deleted.
/// </para>
/// </remarks>
/// <param name="stream">The <see cref="StudyXml"/> file to update with information from the file.</param>
/// <param name="group">A group the sop is associated with.</param>
/// <param name="file">The file to process.</param>
/// <param name="compare">Flag to compare the demographics of <see cref="file"/> with the demographics in the database</param>
/// <param name="retry">Flag telling if the item should be retried on failure. Note that if the item is a duplicate, the WorkQueueUid item is not failed. </param>
/// <param name="uid">An optional WorkQueueUid associated with the entry, that will be deleted upon success or failed on failure.</param>
/// <param name="deleteFile">An option file to delete as part of the process</param>
/// <param name="sopType">Flag telling if the SOP is a new or updated SOP</param>
/// <exception cref="Exception"/>
/// <exception cref="DicomDataException"/>
public ProcessingResult ProcessFile(string group, DicomFile file, StudyXml stream, bool compare, bool retry, WorkQueueUid uid, string deleteFile, SopInstanceProcessorSopType sopType)
{
Platform.CheckForNullReference(file, "file");
try
{
CheckDataLength(file);
_instanceStats.ProcessTime.Start();
ProcessingResult result = new ProcessingResult
{
Status = ProcessingStatus.Success
};
using (ServerCommandProcessor processor = new ServerCommandProcessor("Process File"))
{
SopInstanceProcessorContext processingContext = new SopInstanceProcessorContext(processor,
_context.StorageLocation, group);
if (EnforceNameRules)
{
_patientNameRules.Apply(file);
}
if (compare && ShouldReconcile(_context.StorageLocation, file))
{
ScheduleReconcile(processingContext, file, uid);
result.Status = ProcessingStatus.Reconciled;
}
else
{
InsertInstance(file, stream, uid, deleteFile,sopType);
result.Status = ProcessingStatus.Success;
}
}
_instanceStats.ProcessTime.End();
if (_context.SopProcessedRulesEngine.Statistics.LoadTime.IsSet)
_instanceStats.SopRulesLoadTime.Add(_context.SopProcessedRulesEngine.Statistics.LoadTime);
if (_context.SopProcessedRulesEngine.Statistics.ExecutionTime.IsSet)
_instanceStats.SopEngineExecutionTime.Add(_context.SopProcessedRulesEngine.Statistics.ExecutionTime);
_context.SopProcessedRulesEngine.Statistics.Reset();
//TODO: Should throw exception if result is failed?
return result;
}
catch (Exception e)
{
// If its a duplicate, ignore the exception, and just throw it
if (deleteFile != null && (e is InstanceAlreadyExistsException
|| e.InnerException is InstanceAlreadyExistsException))
throw;
if (uid != null)
FailUid(uid, retry);
throw;
}
}
public bool GetStreamedFileStorageFolder(DicomMessageBase message, out string folder, out string filesystemStreamingFolder)
{
var location = GetWritableOnlineStorage(message);
using (
var commandProcessor =
new ServerCommandProcessor(String.Format("Streaming folder for Study Instance {0}", location.StudyInstanceUid)))
{
String path = Path.Combine(location.FilesystemPath, location.PartitionFolder);
commandProcessor.AddCommand(new CreateDirectoryCommand(path));
filesystemStreamingFolder = path = Path.Combine(path, ServerPlatform.StreamingStorageFolder);
commandProcessor.AddCommand(new CreateDirectoryCommand(path));
path = Path.Combine(path, _context.ContextID /* the AE title + timestamp */);
commandProcessor.AddCommand(new CreateDirectoryCommand(path));
path = Path.Combine(path, location.StudyInstanceUid);
commandProcessor.AddCommand(new CreateDirectoryCommand(path));
if (!commandProcessor.Execute())
{
folder = null;
Platform.Log(LogLevel.Warn, "Unable to create directory to store study: {0}: {1}", path,
commandProcessor.FailureReason);
return false;
}
folder = path;
return true;
}
}
/// <summary>
/// Move the file specified in the path to the incoming folder so that it will be imported again
/// </summary>
/// <param name="path"></param>
private void MoveFileToIncomingFolder(string path)
{
Platform.Log(LogLevel.Debug, "Moving file {0} to incoming folder", path);
// should not proceed because it may mean incomplete study
if (!File.Exists(path))
throw new FileNotFoundException(string.Format("File is missing: {0}", path));
// move the file to the Incoming folder to reprocess
using (var processor = new ServerCommandProcessor("Move file back to incoming folder"))
{
var fileInfo = new FileInfo(path);
var incomingPath = GetServerPartitionIncomingFolder();
incomingPath = Path.Combine(incomingPath, "FromWorkQueue");
incomingPath = Path.Combine(incomingPath, StorageLocation.StudyInstanceUid);
var createDirCommand = new CreateDirectoryCommand(incomingPath);
processor.AddCommand(createDirCommand);
incomingPath = Path.Combine(incomingPath, fileInfo.Name);
var move = new RenameFileCommand(path, incomingPath, true);
processor.AddCommand(move);
if (!processor.Execute())
{
throw new Exception("Unexpected error happened when trying to move file back to the incoming folder for reprocess", processor.FailureException);
}
Platform.Log(LogLevel.Info, "File {0} has been moved to the incoming folder.", path);
}
}
/// <summary>
/// Imports the specified <see cref="DicomMessageBase"/> object into the system.
/// The object will be inserted into the <see cref="WorkQueue"/> for processing and
/// if it's a duplicate, proper checks will be done and depending on the policy, it will be
/// ignored, rejected or inserted into the <see cref="StudyIntegrityQueue"/> for manual intervention.
/// </summary>
/// <param name="message">The DICOM object to be imported.</param>
/// <returns>An instance of <see cref="DicomProcessingResult"/> that describes the result of the processing.</returns>
/// <exception cref="DicomDataException">Thrown when the DICOM object contains invalid data</exception>
public DicomProcessingResult Import(DicomMessageBase message)
{
Platform.CheckForNullReference(message, "message");
String studyInstanceUid;
String seriesInstanceUid;
String sopInstanceUid;
String accessionNumber;
String patientsName;
LoadMessageUids(message, out studyInstanceUid, out seriesInstanceUid, out sopInstanceUid,
out accessionNumber, out patientsName);
DicomFile file = null;
// Scrub the name for invalid characters.
string newName = XmlUtils.XmlCharacterScrub(patientsName);
if (!newName.Equals(patientsName))
message.DataSet[DicomTags.PatientsName].SetStringValue(newName);
var result = new DicomProcessingResult
{
Successful = true,
StudyInstanceUid = studyInstanceUid,
SeriesInstanceUid = seriesInstanceUid,
SopInstanceUid = sopInstanceUid,
AccessionNumber = accessionNumber
};
try
{
Validate(message);
}
catch (DicomDataException e)
{
result.SetError(DicomStatuses.ProcessingFailure, e.Message);
return result;
}
// Use the command processor for rollback capabilities.
using (var commandProcessor = new ServerCommandProcessor(String.Format("Processing Sop Instance {0}", sopInstanceUid)))
{
try
{
string failureMessage;
StudyStorageLocation studyLocation = GetWritableOnlineStorage(message);
// GetWritableOnlineStorage should throw an exception if the study location cannot be found.
Platform.CheckForNullReference(studyLocation, "studyLocation");
if (!studyLocation.QueueStudyStateEnum.Equals(QueueStudyStateEnum.Idle)
&& (!studyLocation.QueueStudyStateEnum.Equals(QueueStudyStateEnum.ProcessingScheduled)))
{
failureMessage = String.Format("Study {0} on partition {1} is being processed: {2}, can't accept new images.",
studyLocation.StudyInstanceUid, _context.Partition.Description, studyLocation.QueueStudyStateEnum.Description);
result.SetError(DicomStatuses.StorageStorageOutOfResources, failureMessage);
return result;
}
if (studyLocation.StudyStatusEnum.Equals(StudyStatusEnum.OnlineLossy))
{
if (studyLocation.IsLatestArchiveLossless)
{
result.DicomStatus = DicomStatuses.StorageStorageOutOfResources;
failureMessage = String.Format("Study {0} on partition {1} can't accept new images due to lossy compression of the study. Restoring study.",
studyLocation.StudyInstanceUid, _context.Partition.Description);
Platform.Log(LogLevel.Error, failureMessage);
if (ServerHelper.InsertRestoreRequest(studyLocation) == null)
{
Platform.Log(LogLevel.Warn, "Unable to insert Restore Request for Study");
}
result.SetError(DicomStatuses.StorageStorageOutOfResources, failureMessage);
result.RestoreRequested = true;
return result;
}
}
String path = studyLocation.FilesystemPath;
String finalDest = studyLocation.GetSopInstancePath(seriesInstanceUid, sopInstanceUid);
file = ConvertToDicomFile(message, finalDest, _context.SourceAE);
if (HasUnprocessedCopy(studyLocation.Key, seriesInstanceUid, sopInstanceUid))
{
var accept = false;
// This is a special case: #10569
// Allow user to revive an orphaned study by reprocessing the files found in the filesystem
if (File.Exists(finalDest))
{
accept = DuplicatePolicy.IsParitionDuplicatePolicyOverridden(studyLocation);
}
if (!accept)
{
failureMessage = string.Format("Another copy of the SOP Instance was received but has not been processed: {0}", sopInstanceUid);
result.SetError(DicomStatuses.DuplicateSOPInstance, failureMessage);
return result;
}
}
var data = new StudyProcessWorkQueueData
{
ReceivingAeTitle = _context.AlternateAe == null
? _context.Partition.AeTitle
: _context.AlternateAe.AeTitle
};
if (File.Exists(finalDest))
{
result = HandleDuplicate(sopInstanceUid, studyLocation, commandProcessor, file, data);
if (!result.Successful)
return result;
}
else
{
HandleNonDuplicate(seriesInstanceUid, sopInstanceUid, studyLocation, commandProcessor, file, path,
false, data);
}
if (commandProcessor.Execute())
{
result.DicomStatus = DicomStatuses.Success;
}
else
{
failureMessage =
String.Format("Failure processing message: {0}. Sending failure status.",
commandProcessor.FailureReason);
result.SetError(DicomStatuses.ProcessingFailure, failureMessage);
// processor already rolled back
return result;
}
}
catch(NoWritableFilesystemException)
{
String failureMessage = String.Format("Unable to process image, no writable filesystem found for Study UID {0}.", sopInstanceUid);
commandProcessor.Rollback();
result.SetError(DicomStatuses.StorageStorageOutOfResources, failureMessage);
}
catch(StudyIsNearlineException e)
{
String failureMessage = e.RestoreRequested
? String.Format("{0}. Restore has been requested.", e.Message)
: e.Message;
Platform.Log(LogLevel.Error, failureMessage);
commandProcessor.Rollback();
result.SetError(DicomStatuses.ProcessingFailure, failureMessage);
}
catch (FilesystemNotWritableException)
{
commandProcessor.Rollback();
string folder;
if (!FilesystemMonitor.Instance.GetWriteableIncomingFolder(_context.Partition, out folder))
{
String failureMessage =
String.Format("Unable to process image, study storage location is missing or not writeable: {0}.", sopInstanceUid);
result.SetError(DicomStatuses.StorageStorageOutOfResources, failureMessage);
return result;
}
if (file == null)
file = ConvertToDicomFile(message, string.Empty, _context.SourceAE);
if (!SaveToFolder(folder, sopInstanceUid, studyInstanceUid, file))
{
String failureMessage =
String.Format("Study storage location not writeable and no writeable incoming folder: {0}.", sopInstanceUid);
result.SetError(DicomStatuses.StorageStorageOutOfResources, failureMessage);
return result;
}
Platform.Log(LogLevel.Info, "Saved existing SOP without writeable storage location to {0} folder: {1}",
FilesystemMonitor.ImportDirectorySuffix, sopInstanceUid);
result.DicomStatus = DicomStatuses.Success;
return result;
}
catch (Exception e)
{
Platform.Log(LogLevel.Error, e, "Unexpected exception when {0}. Rolling back operation.", commandProcessor.Description);
commandProcessor.Rollback();
result.SetError(result.DicomStatus ?? DicomStatuses.ProcessingFailure, e.Message);
}
}
return result;
}
