/// <summary>
/// Inserts a move request to move one or more series in a study.
/// </summary>
/// <param name="context">The persistence context used for database connection.</param>
/// <param name="partition">The <see cref="ServerPartition"/> where the study resides</param>
/// <param name="studyInstanceUid">The Study Instance Uid of the study</param>
/// <param name="deviceKey">The Key of the device to move the series to.</param>
/// <param name="seriesInstanceUids">The Series Instance Uid of the series to be move.</param>
/// <returns>A MoveSeries <see cref="WorkQueue"/> entry inserted into the system.</returns>
/// <exception cref="InvalidStudyStateOperationException"></exception>
public static IList <WorkQueue> MoveSeries(IUpdateContext context, ServerPartition partition, string studyInstanceUid, ServerEntityKey deviceKey, List <string> seriesInstanceUids)
{
// Find all location of the study in the system and insert series delete request
IList <StudyStorageLocation> storageLocations = StudyStorageLocation.FindStorageLocations(partition.Key, studyInstanceUid);
IList <WorkQueue> entries = new List <WorkQueue>();
foreach (StudyStorageLocation location in storageLocations)
{
try
{
// insert a move series request
WorkQueue request = InsertMoveSeriesRequest(context, location, seriesInstanceUids, deviceKey);
Debug.Assert(request.WorkQueueTypeEnum.Equals(WorkQueueTypeEnum.WebMoveStudy));
entries.Add(request);
}
catch (Exception ex)
{
Platform.Log(LogLevel.Error, ex, "Errors occurred when trying to insert move request");
if (!ServerHelper.UnlockStudy(location.Key))
{
throw new ApplicationException("Unable to unlock the study");
}
}
}
return(entries);
}
/// <summary>
/// Inserts delete request(s) to delete a series in a study.
/// </summary>
/// <param name="context">The persistence context used for database connection.</param>
/// <param name="partition">The <see cref="ServerPartition"/> where the study resides</param>
/// <param name="studyInstanceUid">The Study Instance Uid of the study</param>
/// <param name="seriesInstanceUids">The Series Instance Uid of the series to be deleted.</param>
/// <param name="reason">The reason for deleting the series.</param>
/// <returns>A list of DeleteSeries <see cref="WorkQueue"/> entries inserted into the system.</returns>
/// <exception cref="InvalidStudyStateOperationException"></exception>
public static IList <WorkQueue> DeleteSeries(IUpdateContext context, ServerPartition partition, string studyInstanceUid, List <string> seriesInstanceUids, string reason)
{
// Find all location of the study in the system and insert series delete request
IList <StudyStorageLocation> storageLocations = StudyStorageLocation.FindStorageLocations(partition.Key, studyInstanceUid);
IList <WorkQueue> entries = new List <WorkQueue>();
foreach (StudyStorageLocation location in storageLocations)
{
try
{
string failureReason;
if (ServerHelper.LockStudy(location.Key, QueueStudyStateEnum.WebDeleteScheduled, out failureReason))
{
// insert a delete series request
WorkQueue request = InsertDeleteSeriesRequest(context, location, seriesInstanceUids, reason);
Debug.Assert(request.WorkQueueTypeEnum.Equals(WorkQueueTypeEnum.WebDeleteStudy));
entries.Add(request);
}
else
{
throw new ApplicationException(String.Format("Unable to lock storage location {0} for deletion : {1}", location.Key, failureReason));
}
}
catch (Exception ex)
{
Platform.Log(LogLevel.Error, ex, "Errors occurred when trying to insert delete request");
if (!ServerHelper.UnlockStudy(location.Key))
{
throw new ApplicationException("Unable to unlock the study");
}
}
}
return(entries);
}
protected override string GetTemporaryPath()
{
StudyStorageLocation storage = StudyStorageLocation.FindStorageLocations(StudyStorage.Load(_item.StudyStorageKey))[0];
if (storage == null)
{
return(base.GetTemporaryPath());
}
else
{
String basePath = GetTempPathRoot();
if (String.IsNullOrEmpty(basePath))
{
basePath = Path.Combine(storage.FilesystemPath, "temp");
}
String tempDirectory = Path.Combine(basePath, String.Format("ArchiveQueue-{0}", _item.GetKey()));
for (int i = 2; i < 1000; i++)
{
if (!Directory.Exists(tempDirectory))
{
break;
}
tempDirectory = Path.Combine(basePath, String.Format("ArchiveQueue-{0}({1})", _item.GetKey(), i));
}
if (!Directory.Exists(tempDirectory))
{
Directory.CreateDirectory(tempDirectory);
}
return(tempDirectory);
}
}
public override void DataBind()
{
ExistingPatientSeriesGridView.DataSource = ReconcileDetails.ExistingStudy.Series;
ConflictingPatientSeriesGridView.DataSource = ReconcileDetails.ConflictingStudyInfo.Series;
StudyStorage storage =
StudyStorage.Load(HttpContextData.Current.ReadContext, StudyIntegrityQueueItem.StudyStorageKey);
IList <StudyStorageLocation> studyLocations = StudyStorageLocation.FindStorageLocations(storage);
StudyStorageLocation location = studyLocations[0];
StudyLocation.Text = location.GetStudyPath();
ConflictingStudyLocation.Text = ReconcileDetails != null
? ReconcileDetails.GetFolderPath()
: SR.NotSpecified;
string reason;
CanReconcile = _controller.CanReconcile(location, out reason);
MessagePanel.Visible = !CanReconcile;
AlertMessage.Text = reason;
OKButton.Enabled = CanReconcile;
OptionRow.Visible = CanReconcile;
base.DataBind();
}
public StudyItem(Study study)
{
_study = study;
StudyStorage = StudyStorage.Load(_study.StudyStorageKey);
StudyStorageLocation = StudyStorageLocation.FindStorageLocations(StudyStorage).FirstOrDefault();
_status = StudyStorage.StudyStatusEnum.Description;
}
public string GetFolderPath()
{
if (_location == null)
{
if (_studyStorage == null)
{
using (IReadContext context = PersistentStoreRegistry.GetDefaultStore().OpenReadContext())
{
_studyStorage = StudyStorage.Load(context, _item.StudyStorageKey);
}
}
_location = StudyStorageLocation.FindStorageLocations(_studyStorage)[0];
}
String path = Path.Combine(_location.FilesystemPath, _location.PartitionFolder);
path = Path.Combine(path, ServerPlatform.ReconcileStorageFolder);
if (!string.IsNullOrEmpty(_item.GroupID))
{
path = Path.Combine(path, _item.GroupID);
}
path = Path.Combine(path, _location.StudyInstanceUid);
return(path);
}
private void LoadStorageLocation()
{
if (_storageLocation == null)
{
var studyStorage = StudyStorage.Load(HttpContextData.Current.ReadContext, TheStudyIntegrityQueueItem.StudyStorageKey);
_storageLocation = StudyStorageLocation.FindStorageLocations(studyStorage)[0];
}
}
private void LoadStorageLocation()
{
if (_storageLocation == null)
{
var studyStorage = StudyStorage.Load(HttpContext.Current.GetSharedPersistentContext(), TheStudyIntegrityQueueItem.StudyStorageKey);
_storageLocation = StudyStorageLocation.FindStorageLocations(studyStorage)[0];
}
}
/// <summary>
///
/// </summary>
/// <param name="reason"></param>
/// <param name="key"></param>
/// <exception cref="InvalidStudyStateOperationException">Study is in a state that reprocessing is not allowed</exception>
public void ReprocessStudy(String reason, ServerEntityKey key)
{
StudyStorageAdaptor adaptor = new StudyStorageAdaptor();
StudyStorage storage = adaptor.Get(key);
StudyStorageLocation storageLocation = StudyStorageLocation.FindStorageLocations(storage)[0];
StudyReprocessor reprocessor = new StudyReprocessor();
reprocessor.ReprocessStudy(reason, storageLocation, Platform.Time);
}
/// <summary>
/// Builds a list of <see cref="BaseImageLevelUpdateCommand"/> for the specified study using the specified mapping template.
/// </summary>
/// <typeparam name="TMappingObject"></typeparam>
/// <param name="storage"></param>
/// <returns></returns>
/// <remarks>
/// This method generates a list of <see cref="BaseImageLevelUpdateCommand"/> based on the mapping in <see cref="TMappingObject"/>.
/// <see cref="TMappingObject"/> specifies which Dicom fields the application is interested in, using <see cref="DicomFieldAttribute"/>.
/// For example, if the application needs to update the study instance uid and study date in an image with what's in the database,
/// it will define the mapping class as:
/// <code>
/// class StudyInfoMapping
/// {
/// [DicomField(DicomTags.StudyInstanceUid)]
/// public String StudyInstanceUid{
/// get{ ... }
/// set{ ... }
/// }
///
/// [DicomField(DicomTags.StudyDate)]
/// public String StudyDate{
/// get{ ... }
/// set{ ... }
/// }
/// }
///
/// ImageUpdateCommandBuilder builder = new ImageUpdateCommandBuilder();
/// IList<BaseImageLevelUpdateCommand> commandList = builder.BuildCommands<StudyInfoMapping>(studystorage);
///
/// DicomFile file = new DicomFile("file.dcm");
/// foreach(BaseImageUpdateCommand command in commandList)
/// {
/// command.Apply(file);
/// }
///
///
/// </code>
///
/// </remarks>
public IList <BaseImageLevelUpdateCommand> BuildCommands <TMappingObject>(StudyStorage storage, IDicomAttributeProvider originalDicomAttributeProvider)
{
IList <StudyStorageLocation> storageLocationList = StudyStorageLocation.FindStorageLocations(storage);
Debug.Assert(storageLocationList != null && storageLocationList.Count > 0);
StudyStorageLocation storageLocation = storageLocationList[0];
return(BuildCommands <TMappingObject>(storageLocation, originalDicomAttributeProvider));
}
protected override void OnExecute(CommandProcessor theProcessor)
{
var locations = StudyStorageLocation.FindStorageLocations(_storage);
if (locations.Any(location => location.ArchiveLocations.Any()))
{
return;
}
throw new ApplicationException("Cannot purge study which has not been archived");
}
private void DetermineTargetLocation()
{
if (Context.History.DestStudyStorageKey != null)
{
_destinationStudyStorage =
StudyStorageLocation.FindStorageLocations(StudyStorage.Load(Context.History.DestStudyStorageKey))[0];
}
else
{
_destinationStudyStorage = Context.WorkQueueItemStudyStorage;
Context.History.DestStudyStorageKey = _destinationStudyStorage.Key;
}
}
public PurgeStudyCommand(StudyStorage studyStorage) : base()
{
var storageLocations = StudyStorageLocation.FindStorageLocations(studyStorage);
AddSubCommand(new VerifyStudyHasBeenArchivedCommand(studyStorage));
foreach (var location in storageLocations)
{
string path = location.GetStudyPath();
AddSubCommand(new Dicom.Utilities.Command.DeleteDirectoryCommand(path, false));
}
AddSubCommand(new SetStudyStatusNearlineCommand(studyStorage));
}
public static ReconcileHistoryRecord ReadReconcileRecord(StudyHistory historyRecord)
{
Platform.CheckTrue(historyRecord.StudyHistoryTypeEnum == StudyHistoryTypeEnum.StudyReconciled,
"History record has invalid history record type");
ReconcileHistoryRecord record = new ReconcileHistoryRecord();
record.InsertTime = historyRecord.InsertTime;
record.StudyStorageLocation = StudyStorageLocation.FindStorageLocations(StudyStorage.Load(historyRecord.StudyStorageKey))[0];
StudyReconcileDescriptorParser parser = new StudyReconcileDescriptorParser();
record.UpdateDescription = parser.Parse(historyRecord.ChangeDescription);
return(record);
}
protected override string GetTemporaryPath()
{
IList <StudyStorageLocation> storages =
StudyStorageLocation.FindStorageLocations(StudyStorage.Load(_item.StudyStorageKey));
if (storages == null || storages.Count == 0)
{
// ???
return(base.GetTemporaryPath());
}
ServerFilesystemInfo filesystem = FilesystemMonitor.Instance.GetFilesystemInfo(storages[0].FilesystemKey);
if (filesystem == null)
{
// not ready?
return(base.GetTemporaryPath());
}
string basePath = GetTempPathRoot();
if (String.IsNullOrEmpty(basePath))
{
basePath = Path.Combine(filesystem.Filesystem.FilesystemPath, "temp");
}
String tempDirectory = Path.Combine(basePath,
String.Format("{0}-{1}", _item.WorkQueueTypeEnum.Lookup, _item.GetKey()));
for (int i = 2; i < 1000; i++)
{
if (!Directory.Exists(tempDirectory))
{
break;
}
tempDirectory = Path.Combine(basePath, String.Format("{0}-{1}({2})",
_item.WorkQueueTypeEnum.Lookup, _item.GetKey(), i));
}
if (!Directory.Exists(tempDirectory))
{
Directory.CreateDirectory(tempDirectory);
}
return(tempDirectory);
}
public override void DataBind()
{
ExistingPatientSeriesGridView.DataSource = DuplicateEntryDetails.ExistingStudy.Series;
ConflictingPatientSeriesGridView.DataSource = DuplicateEntryDetails.ConflictingImageSet.StudyInfo.Series;
StudyStorage storage =
StudyStorage.Load(HttpContext.Current.GetSharedPersistentContext(), StudyIntegrityQueueItem.StudyStorageKey);
IList <StudyStorageLocation> studyLocations = StudyStorageLocation.FindStorageLocations(storage);
StudyLocation.Text = studyLocations[0].GetStudyPath();
var entry = new DuplicateSopReceivedQueue(StudyIntegrityQueueItem);
DuplicateSopLocation.Text = entry.GetFolderPath(HttpContext.Current.GetSharedPersistentContext());
ComparisonResultGridView.DataSource = DuplicateEntryDetails.QueueData.ComparisonResults;
base.DataBind();
}
private void CreateDestinationStudyStorage()
{
// This really should never happen;
if (Context.History.DestStudyStorageKey != null)
{
_destinationStudyStorage =
StudyStorageLocation.FindStorageLocations(StudyStorage.Load(Context.History.DestStudyStorageKey))[0];
return;
}
string newStudyInstanceUid = string.Empty;
// Get the new Study Instance Uid by looking through the update commands
foreach (BaseImageLevelUpdateCommand command in Commands)
{
SetTagCommand setTag = command as SetTagCommand;
if (setTag != null && setTag.Tag.TagValue.Equals(DicomTags.StudyInstanceUid))
{
newStudyInstanceUid = setTag.Value;
break;
}
}
if (string.IsNullOrEmpty(newStudyInstanceUid))
{
throw new ApplicationException("Unexpectedly could not find new Study Instance Uid value for Create Study");
}
using (ServerCommandProcessor processor = new ServerCommandProcessor("Reconciling image processor"))
{
// Assign new series and instance uid
InitializeStorageCommand command = new InitializeStorageCommand(Context, newStudyInstanceUid, Context.WorkQueueItemStudyStorage.StudyFolder,
TransferSyntax.GetTransferSyntax(Context.WorkQueueItemStudyStorage.TransferSyntaxUid));
processor.AddCommand(command);
if (!processor.Execute())
{
throw new ApplicationException(String.Format("Unable to create Study Storage for study: {0}", newStudyInstanceUid), processor.FailureException);
}
_destinationStudyStorage = command.Location;
}
}
public static WebEditStudyHistoryRecord ReadEditRecord(StudyHistory historyRecord)
{
Platform.CheckTrue(historyRecord.StudyHistoryTypeEnum == StudyHistoryTypeEnum.WebEdited ||
historyRecord.StudyHistoryTypeEnum == StudyHistoryTypeEnum.ExternalEdit,
"History record has invalid history record type");
WebEditStudyHistoryRecord record = new WebEditStudyHistoryRecord
{
InsertTime = historyRecord.InsertTime,
StudyStorageLocation =
StudyStorageLocation.FindStorageLocations(
StudyStorage.Load(historyRecord.StudyStorageKey))[0],
UpdateDescription =
XmlUtils.Deserialize <WebEditStudyHistoryChangeDescription>(
historyRecord.ChangeDescription)
};
return(record);
}
/// <summary>
/// Inserts edit request(s) to update a study.
/// </summary>
/// <param name="context">The persistence context used for database connection.</param>
/// <param name="studyStorageKey">The StudyStorage record key</param>
/// <param name="reason">The reason the study is being editted</param>
/// <param name="userId">The ID of the user requesting the study edit</param>
/// <param name="editType">The request is a web edit request</param>
/// <exception cref="InvalidStudyStateOperationException"></exception>
/// <param name="updateItems"></param>
public static IList <WorkQueue> EditStudy(IUpdateContext context, ServerEntityKey studyStorageKey, List <UpdateItem> updateItems, string reason, string userId, EditType editType)
{
// Find all location of the study in the system and insert series delete request
IList <StudyStorageLocation> storageLocations = StudyStorageLocation.FindStorageLocations(studyStorageKey);
IList <WorkQueue> entries = new List <WorkQueue>();
foreach (StudyStorageLocation location in storageLocations)
{
if (location.StudyStatusEnum.Equals(StudyStatusEnum.OnlineLossy))
{
if (location.IsLatestArchiveLossless)
{
throw new InvalidStudyStateOperationException("Study is lossy but was archived as lossless. It must be restored before editing.");
}
}
try
{
string failureReason;
if (ServerHelper.LockStudy(location.Key, QueueStudyStateEnum.EditScheduled, out failureReason))
{
// insert an edit request
WorkQueue request = InsertEditStudyRequest(context, location.Key, location.ServerPartitionKey, WorkQueueTypeEnum.WebEditStudy, updateItems, reason, userId, editType);
entries.Add(request);
}
else
{
throw new ApplicationException(String.Format("Unable to lock storage location {0} for edit : {1}", location.Key, failureReason));
}
}
catch (Exception ex)
{
Platform.Log(LogLevel.Error, ex, "Errors occured when trying to insert edit request");
if (!ServerHelper.UnlockStudy(location.Key))
{
throw new ApplicationException("Unable to unlock the study");
}
}
}
return(entries);
}
protected override void OnExecute(CommandProcessor theProcessor)
{
Platform.CheckForNullReference(Context, "Context");
_destinationStudyStorage = Context.History.DestStudyStorageKey != null
? StudyStorageLocation.FindStorageLocations(StudyStorage.Load(Context.History.DestStudyStorageKey))[0]
: Context.WorkQueueItemStudyStorage;
EnsureStudyCanBeUpdated(_destinationStudyStorage);
if (_updateDestination)
{
UpdateExistingStudy();
}
LoadMergedStudyEntities();
try
{
LoadUidMappings();
if (Context.WorkQueueUidList.Count > 0)
{
ProcessUidList();
LogResult();
}
}
finally
{
UpdateHistory(_destinationStudyStorage);
}
if (_complete)
{
StudyRulesEngine engine = new StudyRulesEngine(_destinationStudyStorage, Context.Partition);
engine.Apply(ServerRuleApplyTimeEnum.StudyProcessed, theProcessor);
}
}
private static WorkQueueAlertContextData GetWorkQueueContextData(Model.WorkQueue item)
{
Platform.CheckForNullReference(item, "item");
WorkQueueAlertContextData contextData = new WorkQueueAlertContextData
{
WorkQueueItemKey = item.Key.Key.ToString()
};
StudyStorage storage = StudyStorage.Load(item.StudyStorageKey);
IList <StudyStorageLocation> locations = StudyStorageLocation.FindStorageLocations(storage);
if (locations != null && locations.Count > 0)
{
StudyStorageLocation location = locations[0];
if (location != null)
{
contextData.ValidationStudyInfo = new ValidationStudyInfo
{
StudyInstaneUid = location.StudyInstanceUid
};
// study info is not always available (eg, when all images failed to process)
if (location.Study != null)
{
contextData.ValidationStudyInfo.AccessionNumber = location.Study.AccessionNumber;
contextData.ValidationStudyInfo.PatientsId = location.Study.PatientId;
contextData.ValidationStudyInfo.PatientsName = location.Study.PatientsName;
contextData.ValidationStudyInfo.ServerAE = location.ServerPartition.AeTitle;
contextData.ValidationStudyInfo.StudyDate = location.Study.StudyDate;
}
}
}
return(contextData);
}
private void LoadMergedStudyEntities()
{
StudyStorage storage = StudyStorage.Load(_destinationStudyStorage.Key);
_destinationStudyStorage = StudyStorageLocation.FindStorageLocations(storage)[0];
}
protected override void ProcessItem(Model.WorkQueue item)
{
Platform.CheckForNullReference(item, "item");
Platform.CheckForNullReference(item.StudyStorageKey, "item.StudyStorageKey");
bool successful = true;
string failureDescription = null;
// The processor stores its state in the Data column
ReadQueueData(item);
if (_queueData.State == null || !_queueData.State.ExecuteAtLeastOnce)
{
// Added for ticket #9673:
// If the study folder does not exist and the study has been archived, trigger a restore and we're done
if (!Directory.Exists(StorageLocation.GetStudyPath()))
{
if (StorageLocation.ArchiveLocations.Count > 0)
{
Platform.Log(LogLevel.Info,
"Reprocessing archived study {0} for Patient {1} (PatientId:{2} A#:{3}) on Partition {4} without study data on the filesystem. Inserting Restore Request.",
Study.StudyInstanceUid, Study.PatientsName, Study.PatientId,
Study.AccessionNumber, ServerPartition.Description);
PostProcessing(item, WorkQueueProcessorStatus.Complete, WorkQueueProcessorDatabaseUpdate.ResetQueueState);
// Post process had to be done first so the study is unlocked so the RestoreRequest can be inserted.
ServerHelper.InsertRestoreRequest(StorageLocation);
RaiseAlert(WorkQueueItem, AlertLevel.Warning,
string.Format(
"Found study {0} for Patient {1} (A#:{2})on Partition {3} without storage folder, restoring study.",
Study.StudyInstanceUid, Study.PatientsName, Study.AccessionNumber, ServerPartition.Description));
return;
}
}
if (Study == null)
{
Platform.Log(LogLevel.Info,
"Reprocessing study {0} on Partition {1}", StorageLocation.StudyInstanceUid,
ServerPartition.Description);
}
else
{
Platform.Log(LogLevel.Info,
"Reprocessing study {0} for Patient {1} (PatientId:{2} A#:{3}) on Partition {4}",
Study.StudyInstanceUid, Study.PatientsName, Study.PatientId,
Study.AccessionNumber, ServerPartition.Description);
}
CleanupDatabase();
}
else
{
if (_queueData.State.Completed)
{
#region SAFE-GUARD CODE: PREVENT INFINITE LOOP
// The processor indicated it had completed reprocessing in previous run. The entry should have been removed and this block of code should never be called.
// However, we have seen ReprocessStudy entries that mysterously contain rows in the WorkQueueUid table.
// The rows prevent the entry from being removed from the database and the ReprocessStudy keeps repeating itself.
// update the state first, increment the CompleteAttemptCount
_queueData.State.ExecuteAtLeastOnce = true;
_queueData.State.Completed = true;
_queueData.State.CompleteAttemptCount++;
SaveState(item, _queueData);
if (_queueData.State.CompleteAttemptCount < 10)
{
// maybe there was db error in previous attempt to remove the entry. Let's try again.
Platform.Log(LogLevel.Info, "Resuming Reprocessing study {0} but it was already completed!!!", StorageLocation.StudyInstanceUid);
PostProcessing(item, WorkQueueProcessorStatus.Complete, WorkQueueProcessorDatabaseUpdate.ResetQueueState);
}
else
{
// we are definitely stuck.
Platform.Log(LogLevel.Error, "ReprocessStudy {0} for study {1} appears stuck. Aborting it.", item.Key, StorageLocation.StudyInstanceUid);
item.FailureDescription = "This entry had completed but could not be removed.";
PostProcessingFailure(item, WorkQueueProcessorFailureType.Fatal);
}
return;
#endregion
}
if (Study == null)
{
Platform.Log(LogLevel.Info,
"Resuming Reprocessing study {0} on Partition {1}", StorageLocation.StudyInstanceUid,
ServerPartition.Description);
}
else
{
Platform.Log(LogLevel.Info,
"Resuming Reprocessing study {0} for Patient {1} (PatientId:{2} A#:{3}) on Partition {4}",
Study.StudyInstanceUid, Study.PatientsName, Study.PatientId,
Study.AccessionNumber, ServerPartition.Description);
}
}
// As per #12583, Creation of the SopInstanceProcessor should occur after the CleanupDatabase() call.
var context = new StudyProcessorContext(StorageLocation, WorkQueueItem);
// TODO: Should we enforce the patient's name rule?
// If we do, the Study record will have the new patient's name
// but how should we handle the name in the Patient record?
const bool enforceNameRules = false;
var processor = new SopInstanceProcessor(context)
{
EnforceNameRules = enforceNameRules
};
var seriesMap = new Dictionary <string, List <string> >();
StudyXml studyXml = LoadStudyXml();
var reprocessedCounter = 0;
var skippedCount = 0;
var removedFiles = new List <FileInfo>();
try
{
// Traverse the directories, process 500 files at a time
var isCancelled = FileProcessor.Process(StorageLocation.GetStudyPath(), "*.*",
delegate(string path, out bool cancel)
{
#region Reprocess File
var file = new FileInfo(path);
// ignore all files except those ending ".dcm"
// ignore "bad(0).dcm" files too
if (Regex.IsMatch(file.Name.ToUpper(), "[0-9]+\\.DCM$"))
{
try
{
var dicomFile = new DicomFile(path);
dicomFile.Load(DicomReadOptions.StorePixelDataReferences | DicomReadOptions.Default);
string seriesUid = dicomFile.DataSet[DicomTags.SeriesInstanceUid].GetString(0, string.Empty);
string instanceUid = dicomFile.DataSet[DicomTags.SopInstanceUid].GetString(0, string.Empty);
if (studyXml.Contains(seriesUid, instanceUid))
{
if (!seriesMap.ContainsKey(seriesUid))
{
seriesMap.Add(seriesUid, new List <string>());
}
if (!seriesMap[seriesUid].Contains(instanceUid))
{
seriesMap[seriesUid].Add(instanceUid);
}
else
{
Platform.Log(LogLevel.Warn, "SOP Instance UID in {0} appears more than once in the study.", path);
}
skippedCount++;
}
else
{
Platform.Log(ServerPlatform.InstanceLogLevel, "Reprocessing SOP {0} for study {1}", instanceUid, StorageLocation.StudyInstanceUid);
string groupId = ServerHelper.GetUidGroup(dicomFile, StorageLocation.ServerPartition, WorkQueueItem.InsertTime);
ProcessingResult result = processor.ProcessFile(groupId, dicomFile, studyXml, true, false, null, null, SopInstanceProcessorSopType.ReprocessedSop);
switch (result.Status)
{
case ProcessingStatus.Success:
reprocessedCounter++;
if (!seriesMap.ContainsKey(seriesUid))
{
seriesMap.Add(seriesUid, new List <string>());
}
if (!seriesMap[seriesUid].Contains(instanceUid))
{
seriesMap[seriesUid].Add(instanceUid);
}
else
{
Platform.Log(LogLevel.Warn, "SOP Instance UID in {0} appears more than once in the study.", path);
}
break;
case ProcessingStatus.Reconciled:
Platform.Log(LogLevel.Warn, "SOP was unexpectedly reconciled on reprocess SOP {0} for study {1}. It will be removed from the folder.", instanceUid, StorageLocation.StudyInstanceUid);
failureDescription = String.Format("SOP Was reconciled: {0}", instanceUid);
// Added for #10620 (Previously we didn't do anything here)
// Because we are reprocessing files in the study folder, when file needs to be reconciled it is copied to the reconcile folder
// Therefore, we need to delete the one in the study folder. Otherwise, there will be problem when the SIQ entry is reconciled.
// InstanceAlreadyExistsException will also be thrown by the SOpInstanceProcessor if this ReprocessStudy WQI
// resumes and reprocesses the same file again.
// Note: we are sure that the file has been copied to the Reconcile folder and there's no way back.
// We must get rid of this file in the study folder.
FileUtils.Delete(path);
// Special handling: if the file is one which we're supposed to reprocess at the end (see ProcessAdditionalFiles), we must remove the file from the list
if (_additionalFilesToProcess != null && _additionalFilesToProcess.Contains(path))
{
_additionalFilesToProcess.Remove(path);
}
break;
}
}
}
catch (DicomException ex)
{
// TODO : should we fail the reprocess instead? Deleting an dicom file can lead to incomplete study.
removedFiles.Add(file);
Platform.Log(LogLevel.Warn, "Skip reprocessing and delete {0}: Not readable.", path);
FileUtils.Delete(path);
failureDescription = ex.Message;
}
}
else if (!file.Extension.Equals(".xml") && !file.Extension.Equals(".gz"))
{
// not a ".dcm" or header file, delete it
removedFiles.Add(file);
FileUtils.Delete(path);
}
#endregion
if (reprocessedCounter > 0 && reprocessedCounter % 200 == 0)
{
Platform.Log(LogLevel.Info, "Reprocessed {0} files for study {1}", reprocessedCounter + skippedCount, StorageLocation.StudyInstanceUid);
}
cancel = reprocessedCounter >= 5000;
}, true);
if (studyXml != null)
{
EnsureConsistentObjectCount(studyXml, seriesMap);
SaveStudyXml(studyXml);
}
// Completed if either all files have been reprocessed
// or no more dicom files left that can be reprocessed.
_completed = reprocessedCounter == 0 || !isCancelled;
}
catch (Exception e)
{
successful = false;
failureDescription = e.Message;
Platform.Log(LogLevel.Error, e, "Unexpected exception when reprocessing study: {0}", StorageLocation.StudyInstanceUid);
Platform.Log(LogLevel.Error, "Study may be in invalid unprocessed state. Study location: {0}", StorageLocation.GetStudyPath());
throw;
}
finally
{
LogRemovedFiles(removedFiles);
// Update the state
_queueData.State.ExecuteAtLeastOnce = true;
_queueData.State.Completed = _completed;
_queueData.State.CompleteAttemptCount++;
SaveState(item, _queueData);
if (!successful)
{
FailQueueItem(item, failureDescription);
}
else
{
if (!_completed)
{
// Put it back to Pending
PostProcessing(item, WorkQueueProcessorStatus.Pending, WorkQueueProcessorDatabaseUpdate.None);
}
else
{
// Reload the record from the database because referenced entities have been modified since the beginning.
// Need to reload because we are passing the location to the rule engine.
StorageLocation = CollectionUtils.FirstElement <StudyStorageLocation>(StudyStorageLocation.FindStorageLocations(item.ServerPartitionKey, StorageLocation.StudyInstanceUid), null);
LogHistory();
// Run Study / Series Rules Engine.
var engine = new StudyRulesEngine(StorageLocation, ServerPartition);
engine.Apply(ServerRuleApplyTimeEnum.StudyProcessed);
// Log the FilesystemQueue related entries
StorageLocation.LogFilesystemQueue();
PostProcessing(item, WorkQueueProcessorStatus.Complete, WorkQueueProcessorDatabaseUpdate.ResetQueueState);
Platform.Log(LogLevel.Info, "Completed reprocessing of study {0} on partition {1}", StorageLocation.StudyInstanceUid, ServerPartition.Description);
}
}
}
}
/// <summary>
/// Perform the edit.
/// </summary>
/// <param name="actionXml">A serialized XML representation of <see cref="SetTagCommand"/> objects</param>
/// <returns></returns>
public bool Edit(XmlElement actionXml)
{
Platform.Log(LogLevel.Info,
"Starting Edit of study {0} for Patient {1} (PatientId:{2} A#:{3}) on Partition {4}",
Study.StudyInstanceUid, Study.PatientsName, Study.PatientId,
Study.AccessionNumber, ServerPartition.Description);
LoadExtensions();
EditStudyWorkQueueDataParser parser = new EditStudyWorkQueueDataParser();
EditStudyWorkQueueData data = parser.Parse(actionXml);
using (ServerCommandProcessor processor = new ServerCommandProcessor("Web Edit Study"))
{
// Convert UpdateItem in the request into BaseImageLevelUpdateCommand
List <BaseImageLevelUpdateCommand> updateCommands = null;
if (data != null)
{
updateCommands = CollectionUtils.Map <Edit.UpdateItem, BaseImageLevelUpdateCommand>(
data.EditRequest.UpdateEntries,
delegate(Edit.UpdateItem item)
{
// Note: For edit, we assume each UpdateItem is equivalent to SetTagCommand
return(new SetTagCommand(item.DicomTag.TagValue, item.OriginalValue, item.Value));
}
);
}
UpdateStudyCommand updateStudyCommand =
new UpdateStudyCommand(ServerPartition, StorageLocation, updateCommands,
ServerRuleApplyTimeEnum.SopEdited);
processor.AddCommand(updateStudyCommand);
// Note, this command will only insert the ArchiveQueue command if a delete doesn't exist
processor.AddCommand(new InsertArchiveQueueCommand(ServerPartition.Key, StorageLocation.Key));
var context = new WebEditStudyContext
{
CommandProcessor = processor,
EditType = data.EditRequest.EditType,
OriginalStudyStorageLocation = StorageLocation,
EditCommands = updateCommands,
OriginalStudy = Study,
OrginalPatient = Patient,
UserId = data.EditRequest.UserId,
Reason = data.EditRequest.Reason
};
OnStudyUpdating(context);
if (!processor.Execute())
{
Platform.Log(LogLevel.Error, processor.FailureException, "Unexpected failure editing study: {0}",
processor.FailureReason);
FailureReason = processor.FailureReason;
return(false);
}
// reload the StudyStorageLocation
NewStorageLocation = StudyStorageLocation.FindStorageLocations(StorageLocation.StudyStorage)[0];
context.NewStudystorageLocation = NewStorageLocation;
OnStudyUpdated(context);
if (updateStudyCommand.Statistics != null)
{
StatisticsLogger.Log(LogLevel.Info, updateStudyCommand.Statistics);
}
return(true);
}
}
