private void WriteStudyStream(string streamFile, string gzStreamFile, StudyXml theStream)
{
XmlDocument doc = theStream.GetMemento(_outputSettings);
// allocate the random number generator here, in case we need it below
var rand = new Random();
string tmpStreamFile = streamFile + "_tmp";
string tmpGzStreamFile = gzStreamFile + "_tmp";
for (int i = 0; ; i++)
{
try
{
if (File.Exists(tmpStreamFile))
{
FileUtils.Delete(tmpStreamFile);
}
if (File.Exists(tmpGzStreamFile))
{
FileUtils.Delete(tmpGzStreamFile);
}
_fileSaved = true;
using (FileStream xmlStream = FileStreamOpener.OpenForSoleUpdate(tmpStreamFile, FileMode.CreateNew),
gzipStream = FileStreamOpener.OpenForSoleUpdate(tmpGzStreamFile, FileMode.CreateNew))
{
StudyXmlIo.WriteXmlAndGzip(doc, xmlStream, gzipStream);
xmlStream.Close();
gzipStream.Close();
}
if (File.Exists(streamFile))
{
FileUtils.Delete(streamFile);
}
File.Move(tmpStreamFile, streamFile);
if (File.Exists(_gzPath))
{
FileUtils.Delete(_gzPath);
}
File.Move(tmpGzStreamFile, _gzPath);
return;
}
catch (IOException)
{
if (i < 5)
{
Thread.Sleep(rand.Next(5, 50)); // Sleep 5-50 milliseconds
continue;
}
throw;
}
}
}
private void SaveStudyXml(StudyXml studyXml)
{
XmlDocument doc = studyXml.GetMemento(new StudyXmlOutputSettings());
using (FileStream xmlStream = FileStreamOpener.OpenForSoleUpdate(StorageLocation.GetStudyXmlPath(), FileMode.Create),
gzipStream = FileStreamOpener.OpenForSoleUpdate(StorageLocation.GetCompressedStudyXmlPath(), FileMode.Create))
{
StudyXmlIo.WriteXmlAndGzip(doc, xmlStream, gzipStream);
xmlStream.Close();
gzipStream.Close();
}
}
protected override void OnExecute(CommandProcessor theProcessor)
{
// Make sure the directory exists where we're storing the file.
var p = Path.GetDirectoryName(_path);
if (string.IsNullOrEmpty(p) || !Directory.Exists(p))
{
if (!theProcessor.ExecuteSubCommand(this, new CreateDirectoryCommand(Path.GetDirectoryName(_path))))
{
throw new ApplicationException(theProcessor.FailureReason);
}
}
if (RequiresRollback)
{
Backup();
}
string path = GetTempPath();
using (FileStream stream = FileStreamOpener.OpenForSoleUpdate(path,
_failOnExists
? FileMode.CreateNew
: FileMode.Create))
{
_file.Save(stream, DicomWriteOptions.Default);
stream.Flush();
stream.Close();
}
if (_failOnExists && File.Exists(_path))
{
// Do this test after creating the temp folder in case another thread is receiving the file at the same
// time.
try
{
// Delete the temp file we saved
FileUtils.Delete(path);
}
catch (Exception x)
{
throw new ApplicationException(String.Format("DICOM File unexpectedly already exists: {0}", _path),
x);
}
throw new ApplicationException(String.Format("DICOM File unexpectedly already exists: {0}", _path));
}
FileUtils.Copy(path, _path, true);
_fileCreated = true;
FileUtils.Delete(path);
}
/// <summary>
/// Save the <see cref="StudyXml"/> file for a study.
/// </summary>
/// <param name="studyXml">The <see cref="StudyXml"/> file to save.</param>
/// <param name="fileCreated">flag set to true if the file was created</param>
public void SaveStudyXml(StudyXml studyXml, out bool fileCreated)
{
var settings = new StudyXmlOutputSettings
{
IncludePrivateValues = StudyXmlTagInclusion.IgnoreTag,
IncludeUnknownTags = StudyXmlTagInclusion.IgnoreTag,
IncludeLargeTags = StudyXmlTagInclusion.IncludeTagExclusion,
MaxTagLength = 2048,
IncludeSourceFileName = true
};
var doc = studyXml.GetMemento(settings);
string streamFile = GetStudyXmlPath();
// allocate the random number generator here, in case we need it below
var rand = new Random();
string tmpStreamFile = streamFile + "_tmp";
for (int i = 0; ; i++)
{
try
{
if (File.Exists(tmpStreamFile))
{
FileUtils.Delete(tmpStreamFile);
}
using (FileStream xmlStream = FileStreamOpener.OpenForSoleUpdate(tmpStreamFile, FileMode.CreateNew))
{
StudyXmlIo.Write(doc, xmlStream);
xmlStream.Close();
}
File.Copy(tmpStreamFile, streamFile, true);
fileCreated = true;
FileUtils.Delete(tmpStreamFile);
return;
}
catch (IOException)
{
if (i < 5)
{
Thread.Sleep(rand.Next(5, 50)); // Sleep 5-50 milliseconds
continue;
}
throw;
}
}
}
private void UpdateFilesystem()
{
Platform.Log(LogLevel.Info, "Updating filesystem...");
StudyXml studyXml = _oldStudyLocation.LoadStudyXml();
StudyXmlOutputSettings outputSettings = ImageServerCommonConfiguration.DefaultStudyXmlOutputSettings;
StudyXml newStudyXml = new StudyXml();
foreach (SeriesXml seriesXml in studyXml)
{
foreach (InstanceXml instanceXml in seriesXml)
{
string path = Path.Combine(_oldStudyPath, seriesXml.SeriesInstanceUid);
path = Path.Combine(path, instanceXml.SopInstanceUid);
path += ServerPlatform.DicomFileExtension;
if (!File.Exists(path))
{
Platform.Log(LogLevel.Info, "SOP {0} is referenced in study xml but does not exist. It will be removed");
continue; // file was removed but xml was not updated?
}
try
{
DicomFile file = new DicomFile(path);
file.Load();
InstanceInfo instance = new InstanceInfo
{
SeriesInstanceUid = file.DataSet[DicomTags.SeriesInstanceUid].GetString(0, String.Empty),
SopInstanceUid = file.DataSet[DicomTags.SopInstanceUid].GetString(0, String.Empty)
};
UpdateDicomFile(file);
// Add into the temporary study xml
long fileSize = 0;
if (File.Exists(file.Filename))
{
FileInfo finfo = new FileInfo(file.Filename);
fileSize = finfo.Length;
}
newStudyXml.AddFile(file, fileSize, outputSettings);
_updatedSopList.Add(instance);
Platform.Log(ServerPlatform.InstanceLogLevel, "SOP {0} has been updated [{1} of {2}].", instance.SopInstanceUid, _updatedSopList.Count, _totalSopCount);
}
catch (Exception)
{
File.Delete(Path.Combine(_backupDir, instanceXml.SopInstanceUid) + ".bak"); //dont' need to restore this file
throw;
}
}
}
// Log any study-level warnings
if (_updatedSopList.Count != _totalSopCount)
{
Platform.Log(LogLevel.Warn, "Inconsistent data: expected {0} instances to be updated / Found {1}.", _totalSopCount, _updatedSopList.Count);
}
// update the header
Platform.Log(LogLevel.Info, "Generating new study header...");
string newStudyXmlPath = Path.Combine(NewStudyPath, _newStudyInstanceUid + ".xml");
string gzipStudyXmlPath = Path.Combine(NewStudyPath, _newStudyInstanceUid + ".xml.gz");
using (FileStream xmlStream = FileStreamOpener.OpenForSoleUpdate(newStudyXmlPath, FileMode.Create),
gzipStream = FileStreamOpener.OpenForSoleUpdate(gzipStudyXmlPath, FileMode.Create))
{
StudyXmlIo.WriteXmlAndGzip(newStudyXml.GetMemento(outputSettings), xmlStream, gzipStream);
xmlStream.Close();
gzipStream.Close();
}
}
protected override void OnExecute(CommandProcessor theProcessor)
{
if (_path == null)
{
String seriesUid = _file.DataSet[DicomTags.SeriesInstanceUid].GetString(0, String.Empty);
String sopUid = _file.DataSet[DicomTags.SopInstanceUid].GetString(0, String.Empty);
_path = _storageLocation.GetSopInstancePath(seriesUid, sopUid);
}
// Make sure the directory exists where we're storing the file.
var p = Path.GetDirectoryName(_path);
if (string.IsNullOrEmpty(p) || !Directory.Exists(p))
{
if (!theProcessor.ExecuteSubCommand(this, new CreateDirectoryCommand(Path.GetDirectoryName(_path))))
{
throw new ApplicationException(theProcessor.FailureReason);
}
}
if (RequiresRollback)
{
Backup();
}
string path = _saveTemp ? GetTempPath() : _path;
using (FileStream stream = FileStreamOpener.OpenForSoleUpdate(path, FileMode.Create))
{
// Set _fileCreated here, because the file has been opened.
if (!_saveTemp)
{
_fileCreated = true;
}
_saveSpeed.Start();
_file.Save(stream, DicomWriteOptions.Default);
stream.Flush();
stream.Close();
_saveSpeed.End();
var fi = new FileInfo(path);
_saveSpeed.SetData(fi.Length);
}
if (_saveTemp)
{
if (File.Exists(_path))
{
if (_failOnExists)
{
try
{
FileUtils.Delete(path);
}
catch (Exception x)
{
throw new ApplicationException(String.Format("DICOM File unexpectedly already exists: {0}", _path), x);
}
throw new ApplicationException(String.Format("DICOM File unexpectedly already exists: {0}", _path));
}
FileUtils.Delete(_path);
}
File.Move(path, _path);
_fileCreated = true;
}
}
