public void Insert(Guid Guid, Guid WorkQueueGUID, string SeriesInstanceUid, string SopInstanceUid, bool Failed,
bool Duplicate, string Extension, short FailureCount, string GroupID, string RelativePath)
{
var item = new WorkQueueUid();
item.Guid = Guid;
item.WorkQueueGUID = WorkQueueGUID;
item.SeriesInstanceUid = SeriesInstanceUid;
item.SopInstanceUid = SopInstanceUid;
item.Failed = Failed;
item.Duplicate = Duplicate;
item.Extension = Extension;
item.FailureCount = FailureCount;
item.GroupID = GroupID;
item.RelativePath = RelativePath;
item.Save(UserName);
}
private void ProcessUid(WorkQueueUid uid)
{
Platform.CheckForNullReference(uid, "uid");
string imagePath = GetUidPath(uid);
using (ServerCommandProcessor processor = new ServerCommandProcessor(String.Format("Deleting {0}", uid.SopInstanceUid)))
{
// If the file for some reason doesn't exist, we just ignore it
if (File.Exists(imagePath))
{
Platform.Log(ServerPlatform.InstanceLogLevel, "Deleting {0}", imagePath);
FileDeleteCommand deleteFile = new FileDeleteCommand(imagePath, true);
processor.AddCommand(deleteFile);
}
else
{
Platform.Log(LogLevel.Warn, "WARNING {0} is missing.", imagePath);
}
DeleteWorkQueueUidCommand deleteUid = new DeleteWorkQueueUidCommand(uid);
processor.AddCommand(deleteUid);
if (!processor.Execute())
{
throw new Exception(String.Format("Unable to delete image {0}", uid.SopInstanceUid));
}
}
}
/// <summary>
/// Helper method to return the path to the duplicate image (in the Reconcile folder)
/// </summary>
/// <param name="studyStorage"></param>
/// <param name="sop"></param>
/// <returns></returns>
public static String GetDuplicateUidPath(StudyStorageLocation studyStorage, WorkQueueUid sop)
{
string dupPath = GetDuplicateGroupPath(studyStorage, sop);
dupPath = string.IsNullOrEmpty(sop.RelativePath)
? Path.Combine(dupPath,
Path.Combine(studyStorage.StudyInstanceUid, sop.SopInstanceUid + "." + sop.Extension))
: Path.Combine(dupPath, sop.RelativePath);
#region BACKWARD_COMPATIBILTY_CODE
if (string.IsNullOrEmpty(sop.RelativePath) && !File.Exists(dupPath))
{
string basePath = Path.Combine(studyStorage.GetStudyPath(), sop.SeriesInstanceUid);
basePath = Path.Combine(basePath, sop.SopInstanceUid);
if (sop.Extension != null)
{
dupPath = basePath + "." + sop.Extension;
}
else
{
dupPath = basePath + ".dcm";
}
}
#endregion
return(dupPath);
}
/// <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);
}
}
}
/// <summary>
/// Gets the path to DICOM file referenced by the <see cref="WorkQueueUid"/>. This is either the study folder or the reconcile folder.
/// </summary>
/// <param name="sop"></param>
/// <returns></returns>
protected string GetFileStoredPath(WorkQueueUid uid)
{
Platform.CheckForNullReference(uid, "uid");
if (!uid.Duplicate)
{
return(StorageLocation.GetSopInstancePath(uid.SeriesInstanceUid, uid.SopInstanceUid));
}
else
{
// For StudyProcess (which this processor is designed to clean up), duplicates are stored in the Reconcile folder (see SopInstanceImporter)
string path = Path.Combine(StorageLocation.FilesystemPath, StorageLocation.PartitionFolder);
path = Path.Combine(path, ServerPlatform.ReconcileStorageFolder);
path = Path.Combine(path, uid.GroupID);
if (string.IsNullOrEmpty(uid.RelativePath))
{
path = Path.Combine(path, StorageLocation.StudyInstanceUid);
var extension = uid.Extension ?? ServerPlatform.DicomFileExtension;
path = Path.Combine(path, uid.SopInstanceUid + "." + extension);
}
else
{
path = Path.Combine(path, uid.RelativePath);
}
return(path);
}
}
private ProcessDuplicateResult OverwriteDuplicate(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));
// 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 InsertInstanceCommand(dupFile, Context.StorageLocation));
// Update the StudyStream object
processor.AddCommand(new InsertStudyXmlCommand(dupFile, studyXml, Context.StorageLocation));
processor.AddCommand(new DeleteWorkQueueUidCommand(uid));
if (!processor.Execute())
{
// cause the item to fail
throw new Exception(string.Format("Error occurred when trying to overwrite duplicate in the filesystem."), processor.FailureException);
}
}
return(result);
}
protected string GetReconcileUidPath(WorkQueueUid sop)
{
// In 2.0: Path = \\Filesystem Path\Reconcile\GroupID\StudyInstanceUid\*.dcm
WorkQueue workqueueItem = Context.WorkQueueItem;
if (!String.IsNullOrEmpty(workqueueItem.GroupID))
{
StudyStorageLocation storageLocation = Context.WorkQueueItemStudyStorage;
string path = Path.Combine(storageLocation.FilesystemPath, storageLocation.PartitionFolder);
path = Path.Combine(path, ServerPlatform.ReconcileStorageFolder);
path = Path.Combine(path, workqueueItem.GroupID);
path = Path.Combine(path, storageLocation.StudyInstanceUid);
path = Path.Combine(path, sop.SopInstanceUid + ServerPlatform.DicomFileExtension);
return(path);
}
else
{
#region BACKWARD-COMPATIBLE CODE
// 1.5 SP1, RelativePath is NOT populated for Reconcile Study entry
// Path = \\Filesystem Path\Reconcile\GUID\*.dcm
// where \\Filesystem Path\Reconcile\GUID = Context.ReconcileWorkQueueData.StoragePath
if (String.IsNullOrEmpty(sop.RelativePath))
{
string path = Context.ReconcileWorkQueueData.StoragePath;
path = Path.Combine(path, sop.SopInstanceUid + ServerPlatform.DicomFileExtension);
return(path);
}
// will this ever happen?
return(Path.Combine(Context.ReconcileWorkQueueData.StoragePath, sop.RelativePath));
#endregion
}
}
private void AddDuplicateToStudy(DicomFile duplicateDicomFile, WorkQueueUid uid, ProcessDuplicateAction action)
{
var context = new StudyProcessorContext(StorageLocation, WorkQueueItem);
var sopInstanceProcessor = new SopInstanceProcessor(context)
{
EnforceNameRules = true
};
string group = uid.GroupID ?? ServerHelper.GetUidGroup(duplicateDicomFile, ServerPartition, WorkQueueItem.InsertTime);
StudyXml studyXml = StorageLocation.LoadStudyXml();
int originalInstanceCount = studyXml.NumberOfStudyRelatedInstances;
bool compare = action != ProcessDuplicateAction.OverwriteAsIs;
// NOTE: "compare" has no effect for OverwriteUseExisting or OverwriteUseDuplicate
// because in both cases, the study and the duplicates are modified to be the same.
ProcessingResult result = sopInstanceProcessor.ProcessFile(group, duplicateDicomFile, studyXml, compare, true, uid, duplicateDicomFile.Filename, SopInstanceProcessorSopType.UpdatedSop);
if (result.Status == ProcessingStatus.Reconciled)
{
throw new ApplicationException("Unexpected status of Reconciled image in duplicate handling!");
}
Debug.Assert(studyXml.NumberOfStudyRelatedInstances == originalInstanceCount + 1);
Debug.Assert(File.Exists(StorageLocation.GetSopInstancePath(uid.SeriesInstanceUid, uid.SopInstanceUid)));
}
public static void FailUid(WorkQueueUid sop, bool retry)
{
using (IUpdateContext updateContext = PersistentStoreRegistry.GetDefaultStore().OpenUpdateContext(UpdateContextSyncMode.Flush))
{
IWorkQueueUidEntityBroker uidUpdateBroker = updateContext.GetBroker <IWorkQueueUidEntityBroker>();
WorkQueueUidUpdateColumns columns = new WorkQueueUidUpdateColumns();
if (!retry)
{
columns.Failed = true;
}
else
{
if (sop.FailureCount >= ImageServerCommonConfiguration.WorkQueueMaxFailureCount)
{
columns.Failed = true;
}
else
{
columns.FailureCount = ++sop.FailureCount;
}
}
uidUpdateBroker.Update(sop.GetKey(), columns);
updateContext.Commit();
}
}
private void ProcessUid(WorkQueueUid uid)
{
switch (_processDuplicateEntry.QueueData.Action)
{
case ProcessDuplicateAction.Delete:
DeleteDuplicate(uid);
break;
case ProcessDuplicateAction.OverwriteUseDuplicates:
OverwriteExistingInstance(uid, ProcessDuplicateAction.OverwriteUseDuplicates);
break;
case ProcessDuplicateAction.OverwriteUseExisting:
OverwriteExistingInstance(uid, ProcessDuplicateAction.OverwriteUseExisting);
break;
case ProcessDuplicateAction.OverwriteAsIs:
OverwriteExistingInstance(uid, ProcessDuplicateAction.OverwriteAsIs);
break;
default:
throw new NotSupportedException(
String.Format("Not supported action: {0}", _processDuplicateEntry.QueueData.Action));
}
}
private string GetUidPath(WorkQueueUid sop)
{
string imagePath = Path.Combine(_reconcileQueueData.StoragePath, sop.SopInstanceUid + ServerPlatform.DicomFileExtension);
Debug.Assert(String.IsNullOrEmpty(imagePath) == false);
return(imagePath);
}
private DicomFile LoadDuplicateDicomFile(WorkQueueUid uid, bool skipPixelData)
{
FileInfo duplicateFile = GetDuplicateSopFile(uid);
Platform.CheckTrue(duplicateFile.Exists, String.Format("Duplicate SOP doesn't exist at {0}", uid.SopInstanceUid));
DicomFile file = new DicomFile(duplicateFile.FullName);
file.Load(skipPixelData ? DicomReadOptions.StorePixelDataReferences | DicomReadOptions.Default : DicomReadOptions.Default);
return(file);
}
private void OverwriteExistingInstance(WorkQueueUid uid, ProcessDuplicateAction action)
{
if (ExistsInStudy(uid))
{
// remove the existing image and update the count
RemoveExistingImage(uid);
}
DicomFile duplicateDicomFile = LoadDuplicateDicomFile(uid, false);
PreprocessDuplicate(duplicateDicomFile, action);
AddDuplicateToStudy(duplicateDicomFile, uid, action);
}
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();
}
}
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);
}
}
private ProcessDuplicateResult OverwriteDuplicate(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 context = new ServerActionContext(dupFile, Context.StorageLocation.FilesystemKey, Context.StorageLocation.ServerPartition, Context.StorageLocation.Key, processor);
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 InsertInstanceCommand(dupFile, Context.StorageLocation));
processor.AddCommand(new DeleteWorkQueueUidCommand(uid));
processor.AddCommand(new ApplySopRulesCommand(context, Context.SopProcessedRulesEngine));
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 bool ExistsInStudy(WorkQueueUid uid)
{
String path = StorageLocation.GetSopInstancePath(uid.SeriesInstanceUid, uid.SopInstanceUid);
if (File.Exists(path))
{
return(true);
}
// check the study xml
StudyXml studyXml = StorageLocation.LoadStudyXml();
return(studyXml[uid.SeriesInstanceUid] != null &&
studyXml[uid.SeriesInstanceUid][uid.SopInstanceUid] != null);
}
private FileInfo GetDuplicateSopFile(WorkQueueUid uid)
{
string path = DuplicateFolder;
if (string.IsNullOrEmpty(uid.RelativePath))
{
path = Path.Combine(path, StorageLocation.StudyInstanceUid);
path = Path.Combine(path, uid.SopInstanceUid + "." + uid.Extension);
}
else
{
path = Path.Combine(path, uid.RelativePath);
}
return(new FileInfo(path));
}
/// <summary>
/// Gets the base directory for the <see cref="WorkQueueUid"/> where the corresponding file is stored (see
/// <see cref="GetFileStoredPath"/>)
/// </summary>
/// <param name="sop"></param>
/// <returns></returns>
protected string GetBaseDirectory(WorkQueueUid sop)
{
if (!sop.Duplicate)
{
return(StorageLocation.GetStudyPath());
}
else
{
string path = Path.Combine(StorageLocation.FilesystemPath, StorageLocation.PartitionFolder);
path = Path.Combine(path, ServerPlatform.ReconcileStorageFolder);
path = Path.Combine(path, sop.GroupID);
Debug.Assert(GetFileStoredPath(sop).IndexOf(path) == 0, "Should be consistent with what GetFileStoredPath() returns");
return(path);
}
}
/// <summary>
/// Called after the specified <see cref="WorkQueueUid"/> has been processed
/// </summary>
/// <param name="item">The <see cref="WorkQueue"/> item being processed</param>
/// <param name="uid">The <see cref="WorkQueueUid"/> being processed</param>
protected virtual void OnProcessUidEnd(Model.WorkQueue item, WorkQueueUid uid)
{
Platform.CheckForNullReference(item, "item");
Platform.CheckForNullReference(uid, "uid");
if (uid.Duplicate)
{
String dupPath = ServerPlatform.GetDuplicateUidPath(StorageLocation, uid);
// Delete the container if it's empty
var f = new FileInfo(dupPath);
if (f.Directory != null && DirectoryUtility.DeleteIfEmpty(f.Directory.FullName))
{
DirectoryUtility.DeleteIfEmpty(ServerPlatform.GetDuplicateGroupPath(StorageLocation, uid));
}
}
}
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);
}
}
}
private ProcessDuplicateResult ProcessDuplicate(DicomFile dupFile, WorkQueueUid uid, StudyXml studyXml)
{
var result = new ProcessDuplicateResult();
var data = uid.SerializeWorkQueueUidData;
var basePath = StorageLocation.GetSopInstancePath(uid.SeriesInstanceUid, uid.SopInstanceUid);
if (!File.Exists(basePath))
{
// NOTE: This is special case. The file which caused dicom service to think this sop is a duplicate
// no longer exists in the study folder. Perhaps it has been moved to another folder during auto reconciliation.
// We have nothing to compare against so let's just throw it into the SIQ queue.
CreateDuplicateSIQEntry(uid, dupFile, null);
result.ActionTaken = DuplicateProcessResultAction.Reconcile;
}
else
{
var duplicateEnum = data.DuplicateProcessing.HasValue ? data.DuplicateProcessing.Value : DuplicateProcessingEnum.Compare;
switch (duplicateEnum)
{
case DuplicateProcessingEnum.OverwriteSop:
// Note: There's actually no difference between OverwriteDuplicate and OverwriteAndUpdateDuplicate. But decided to leave it as is.
return(OverwriteDuplicate(dupFile, uid, studyXml));
case DuplicateProcessingEnum.OverwriteSopAndUpdateDatabase:
return(OverwriteAndUpdateDuplicate(dupFile, uid, studyXml));
case DuplicateProcessingEnum.OverwriteReport:
var file = new DicomFile(basePath);
return(ProcessDuplicateReport(dupFile, file, uid, studyXml));
case DuplicateProcessingEnum.Compare:
var baseFile = new DicomFile(basePath);
return(CompareDuplicates(dupFile, baseFile, uid));
default:
throw new InvalidOperationException("");
}
}
return(result);
}
private FileInfo GetDuplicateSopFile(WorkQueueUid uid)
{
string path = Path.Combine(StorageLocation.FilesystemPath, StorageLocation.PartitionFolder);
path = Path.Combine(path, ServerPlatform.ReconcileStorageFolder);
path = Path.Combine(path, WorkQueueItem.GroupID);
if (string.IsNullOrEmpty(uid.RelativePath))
{
path = Path.Combine(path, StorageLocation.StudyInstanceUid);
path = Path.Combine(path, uid.SopInstanceUid + "." + uid.Extension);
}
else
{
path = Path.Combine(path, uid.RelativePath);
}
return(new FileInfo(path));
}
/// <summary>
/// Gets the path of the specified <see cref="WorkQueueUid"/>.
/// Note: only StudyProcess is currently supported. Other type of WQI will cause InvalidOperationException
/// </summary>
/// <param name="item"></param>
/// <param name="uid"></param>
/// <returns></returns>
public static FilesystemDynamicPath GetWorkQueueUidPath(this WorkQueue item, WorkQueueUid uid)
{
// Check for invalid use of this method
if (!uid.WorkQueueKey.Equals(item.Key))
{
throw new InvalidOperationException("uid.WorkQueueKey and item.Key do not match");
}
var studyStorage = item.StudyStorage;
// Logic for determining WorkQueueUid path for StudyProcess WQI
#region Logic forStudyProcess
if (item.WorkQueueTypeEnum == WorkQueueTypeEnum.StudyProcess)
{
if (!uid.Duplicate)
{
var path = Path.Combine(uid.SeriesInstanceUid, uid.SopInstanceUid + ServerPlatform.DicomFileExtension);
return(new FilesystemDynamicPath(path, FilesystemDynamicPath.PathType.RelativeToStudyFolder));
}
else
{
// full path = \\FS\Partition\Reconcile\UidGroup\sopUID.ext
// relative path = UidGroup\sopUID.ext
var ext = string.IsNullOrEmpty(uid.Extension) ? ServerPlatform.DicomFileExtension : uid.Extension;
var path = uid.GroupID;
if (string.IsNullOrEmpty(uid.RelativePath))
{
path = Path.Combine(path, studyStorage.StudyInstanceUid);
path = Path.Combine(path, uid.SopInstanceUid + "." + ext);
}
else
{
path = Path.Combine(path, uid.RelativePath);
}
return(new FilesystemDynamicPath(path, FilesystemDynamicPath.PathType.RelativeToReconcileFolder));
}
}
#endregion
throw new InvalidOperationException(string.Format("GetWorkQueueUidPath should not be used for {0} WQI", item.WorkQueueTypeEnum));
}
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
}
/// <summary>
/// Gets the commands to update the study
/// </summary>
/// <returns></returns>
private List <BaseImageLevelUpdateCommand> BuildUpdateStudyCommandsFromDuplicate()
{
List <BaseImageLevelUpdateCommand> commands = new List <BaseImageLevelUpdateCommand>();
if (WorkQueueUidList.Count > 0)
{
WorkQueueUid uid = WorkQueueUidList[0];
DicomFile file = LoadDuplicateDicomFile(uid, true);
ImageUpdateCommandBuilder commandBuilder = new ImageUpdateCommandBuilder();
// Create a list of commands to update the existing study based on what's defined in StudyMatchingMap
// The value will be taken from the content of the duplicate image.
commands.AddRange(commandBuilder.BuildCommands <StudyMatchingMap>(file.DataSet,
new[] {
new ServerEntityAttributeProvider(StorageLocation.Study),
new ServerEntityAttributeProvider(StorageLocation.Patient)
}));
}
return(commands);
}
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,
ServerPlatform.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();
}
}
void SaveDuplicateReport(WorkQueueUid uid, string sourceFile, string destinationFile, DicomFile dupFile, StudyXml studyXml)
{
using (var processor = new ServerCommandProcessor("Save duplicate report"))
{
var sopContext = new ServerActionContext(dupFile, Context.StorageLocation.FilesystemKey, Context.StorageLocation.ServerPartition, Context.StorageLocation.Key, processor);
processor.AddCommand(new RenameFileCommand(sourceFile, destinationFile, false));
// Update the StudyStream object
processor.AddCommand(new InsertStudyXmlCommand(dupFile, studyXml, Context.StorageLocation));
// Update the series
processor.AddCommand(new UpdateSeriesCommand(Context.StorageLocation, sopContext));
processor.AddCommand(new DeleteWorkQueueUidCommand(uid));
processor.AddCommand(new ApplySopRulesCommand(sopContext, Context.SopProcessedRulesEngine));
processor.Execute();
}
}
/// <summary>
/// Process a specific DICOM file related to a <see cref="WorkQueue"/> request.
/// </summary>
/// <param name="queueUid"></param>
/// <param name="stream">The <see cref="StudyXml"/> file to update with information from the file.</param>
/// <param name="file">The file being processed.</param>
/// <param name="compare">Indicates whether to compare the DICOM file against the study in the system.</param>
protected virtual void ProcessFile(WorkQueueUid queueUid, DicomFile file, StudyXml stream, bool compare)
{
var processor = new SopInstanceProcessor(Context)
{
EnforceNameRules = true
};
var fileInfo = new FileInfo(file.Filename);
long fileSize = fileInfo.Length;
processor.InstanceStats.FileLoadTime.Start();
processor.InstanceStats.FileLoadTime.End();
processor.InstanceStats.FileSize = (ulong)fileSize;
string sopInstanceUid = file.DataSet[DicomTags.SopInstanceUid].GetString(0, "File:" + fileInfo.Name);
processor.InstanceStats.Description = sopInstanceUid;
string group = queueUid.GroupID ?? ServerHelper.GetUidGroup(file, ServerPartition, WorkQueueItem.InsertTime);
ProcessingResult result = processor.ProcessFile(group, file, stream, compare, true, queueUid, null);
if (result.Status == ProcessingStatus.Reconciled)
{
// file has been saved by SopInstanceProcessor in another place for reconcilation
// Note: SopInstanceProcessor has removed the WorkQueueUid so we
// only need to delete the file here.
FileUtils.Delete(fileInfo.FullName);
}
Statistics.StudyInstanceUid = StorageLocation.StudyInstanceUid;
if (String.IsNullOrEmpty(processor.Modality) == false)
{
Statistics.Modality = processor.Modality;
}
// Update the statistics
Statistics.NumInstances++;
Statistics.AddSubStats(processor.InstanceStats);
}
/// <summary>
/// Apply changes to the file prior to processing it.
/// </summary>
/// <param name="uid"></param>
/// <param name="file"></param>
protected virtual InstancePreProcessingResult PreProcessFile(WorkQueueUid uid, DicomFile file)
{
String contextID = uid.GroupID ?? String.Format("{0}_{1}",
String.IsNullOrEmpty(file.SourceApplicationEntityTitle) ? ServerPartition.AeTitle : file.SourceApplicationEntityTitle,
WorkQueueItem.InsertTime.ToString("yyyyMMddHHmmss"));
var result = new InstancePreProcessingResult();
var patientNameRules = new PatientNameRules(Study);
UpdateItem updateItem = patientNameRules.Apply(file);
result.Modified = updateItem != null;
var autoBaseReconciler = new AutoReconciler(contextID, StorageLocation);
InstancePreProcessingResult reconcileResult = autoBaseReconciler.Process(file);
result.AutoReconciled = reconcileResult != null;
result.Modified |= reconcileResult != null;
if (reconcileResult != null && reconcileResult.DiscardImage)
{
result.DiscardImage = true;
}
// if the studyuid is modified, the file will be deleted by the caller.
if (file.DataSet[DicomTags.StudyInstanceUid].ToString().Equals(StorageLocation.StudyInstanceUid))
{
if (result.Modified)
{
file.Save();
}
}
return(result);
}
private void InsertInstance(DicomFile file, StudyXml stream, WorkQueueUid uid, string deleteFile)
{
using (ServerCommandProcessor 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);
}
catch (Exception e)
{
Platform.Log(LogLevel.Error, e, "Unexpected exception when {0}. Rolling back operation.",
processor.Description);
processor.Rollback();
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);
}
}
}
}
