/// <summary>
/// Load the first instance from the first series of the StudyXml file for a study.
/// </summary>
/// <param name="location">The storage location of the study.</param>
/// <returns></returns>
protected static DicomFile LoadInstance(StudyStorageLocation location)
{
string studyXml = Path.Combine(location.GetStudyPath(), location.StudyInstanceUid + ".xml");
if (!File.Exists(studyXml))
{
return null;
}
FileStream stream = FileStreamOpener.OpenForRead(studyXml, FileMode.Open);
var theDoc = new XmlDocument();
StudyXmlIo.Read(theDoc, stream);
stream.Close();
stream.Dispose();
var xml = new StudyXml();
xml.SetMemento(theDoc);
IEnumerator<SeriesXml> seriesEnumerator = xml.GetEnumerator();
if (seriesEnumerator.MoveNext())
{
SeriesXml seriesXml = seriesEnumerator.Current;
IEnumerator<InstanceXml> instanceEnumerator = seriesXml.GetEnumerator();
if (instanceEnumerator.MoveNext())
{
InstanceXml instance = instanceEnumerator.Current;
var file = new DicomFile("file.dcm",new DicomAttributeCollection(), instance.Collection)
{TransferSyntax = instance.TransferSyntax};
return file;
}
}
return null;
}
public SaveXmlCommand(StudyXml stream, StudyStorageLocation storageLocation)
: base("Insert into Study XML", true)
{
Platform.CheckForNullReference(stream, "StudyStream object");
Platform.CheckForNullReference(storageLocation, "Study Storage Location");
_stream = stream;
_xmlPath = Path.Combine(storageLocation.GetStudyPath(), storageLocation.StudyInstanceUid + ".xml");
_gzPath = _xmlPath + ".gz";
}
private static StudyXml GetStudyXml(StudyStorageLocation storageLocation)
{
StudyXml studyXml = new StudyXml();
string studyXmlPath = Path.Combine(storageLocation.GetStudyPath(), storageLocation.StudyInstanceUid + ".xml");
using (Stream stream = FileStreamOpener.OpenForRead(studyXmlPath, FileMode.Open))
{
XmlDocument doc = new XmlDocument();
StudyXmlIo.Read(doc, stream);
studyXml.SetMemento(doc);
stream.Close();
}
return(studyXml);
}
protected override void OnExecute(CommandProcessor theProcessor)
{
if (_map == null)
{
return;// nothing to save
}
_path = Path.Combine(_studyLocation.GetStudyPath(), "UidMap.xml");
if (RequiresRollback)
{
Backup();
}
_map.Save(_path);
}
public void OnStudyDeleting()
{
if (!Enabled)
{
return;
}
StudyStorageLocation storage = _context.StorageLocation;
IList <ArchiveStudyStorage> archives = StudyStorageLocation.GetArchiveLocations(storage.GetKey());
if (archives != null && archives.Count > 0)
{
_archives = new DeletedStudyArchiveInfoCollection();
foreach (ArchiveStudyStorage archive in archives)
{
DeletedStudyArchiveInfo archiveInfo = new DeletedStudyArchiveInfo();
archiveInfo.ArchiveTime = archive.ArchiveTime;
archiveInfo.ArchiveXml = archive.ArchiveXml;
archiveInfo.PartitionArchiveRef = PartitionArchive.Load(archive.PartitionArchiveKey).GetKey().Key;
archiveInfo.TransferSyntaxUid = archive.ServerTransferSyntax.Uid;
_archives.Add(archiveInfo);
}
}
// only backup if study is manually deleted
if (_context.WorkQueueItem.WorkQueueTypeEnum == WorkQueueTypeEnum.WebDeleteStudy)
{
using (var processor = new ServerCommandProcessor("Backup deleted study"))
{
string path = _context.Filesystem.ResolveAbsolutePath(BackupSubPath);
Platform.Log(LogLevel.Info, "Saving a copy of the study to {0}...", path);
var mkdir = new CreateDirectoryCommand(path);
processor.AddCommand(mkdir);
var zip = new ZipStudyFolderCommand(storage.GetStudyPath(), BackupFullPath);
processor.AddCommand(zip);
if (!processor.Execute())
{
throw new ApplicationException(String.Format("Unable to backup study: {0}", processor.FailureReason));
}
}
}
}
/// <summary>
/// Estimate the folder size for a study
/// </summary>
/// <remarks>
/// This routine loads the StudyXml file and traverses through each series
/// for the study. It then looks at the size of the first image in the series,
/// and assumes the series size is equal to the first image size times the number
/// of images within the series. If the file sizes vary within the series, this
/// algorithm will fall down a bit.
/// </remarks>
/// <param name="location">The StudyStorageLocation object for the study.</param>
/// <returns></returns>
protected float EstimateFolderSizeFromStudyXml(StudyStorageLocation location)
{
float folderSize = 0.0f;
string studyFolder = location.GetStudyPath();
string file = Path.Combine(studyFolder, location.StudyInstanceUid + ".xml");
var finfo1 = new FileInfo(file);
if (finfo1.Exists)
{
folderSize += finfo1.Length;
}
file = Path.Combine(studyFolder, location.StudyInstanceUid + ".xml.gz");
var finfo2 = new FileInfo(file);
if (finfo2.Exists)
{
folderSize += finfo2.Length;
}
StudyXml study = LoadStudyXml(location);
foreach (SeriesXml series in study)
{
string seriesFolder = Path.Combine(studyFolder, series.SeriesInstanceUid);
foreach (InstanceXml instance in series)
{
if (instance.FileSize != 0)
{
folderSize += instance.FileSize;
}
else
{
file = Path.Combine(seriesFolder, String.Format("{0}.dcm", instance.SopInstanceUid));
var finfo = new FileInfo(file);
if (finfo.Exists)
{
folderSize += finfo.Length;
}
}
}
}
return(folderSize);
}
/// <summary>
/// Computes and returns the absolute path specified by this <see cref="FilesystemDynamicPath"/> for the <see cref="StudyStorageLocation"/>.
/// Note: The path may or may not be valid.
/// </summary>
/// <param name="studyStorage"></param>
/// <returns></returns>
public string ConvertToAbsolutePath(StudyStorageLocation studyStorage)
{
switch (_type)
{
case PathType.Absolute: return(_path);
case PathType.RelativeToReconcileFolder:
var basePath = studyStorage.GetReconcileRootPath();
return(Path.Combine(basePath, _path));
case PathType.RelativeToStudyFolder:
basePath = studyStorage.GetStudyPath();
return(Path.Combine(basePath, _path));
default:
return(_path);
}
}
/// <summary>
/// Helper method to load a <see cref="StudyXml"/> instance for a given study location.
/// </summary>
/// <param name="location"></param>
/// <returns></returns>
public static StudyXml LoadStudyXml(StudyStorageLocation location)
{
String streamFile = Path.Combine(location.GetStudyPath(), location.StudyInstanceUid + ".xml");
StudyXml theXml = new StudyXml();
if (File.Exists(streamFile))
{
// allocate the random number generator here, in case we need it below
Random rand = new Random();
// Go into a retry loop, to handle if the study is being processed right now
for (int i = 0; ; i++)
{
try
{
using (Stream fileStream = FileStreamOpener.OpenForRead(streamFile, FileMode.Open))
{
XmlDocument theDoc = new XmlDocument();
StudyXmlIo.Read(theDoc, fileStream);
theXml.SetMemento(theDoc);
fileStream.Close();
return(theXml);
}
}
catch (IOException)
{
if (i < 5)
{
Thread.Sleep(rand.Next(5, 50)); // Sleep 5-50 milliseconds
continue;
}
throw;
}
}
}
return(theXml);
}
protected void StudyStorageView_DataBound(object sender, EventArgs e)
{
StudyStorageLocation ssl = (StudyStorageViewControl.DataItem) as StudyStorageLocation;
if (ssl != null)
{
Label statusLabel = StudyStorageViewControl.FindControl("Status") as Label;
if (statusLabel != null)
{
statusLabel.Text = ServerEnumDescription.GetLocalizedDescription(ssl.StudyStatusEnum);
}
Label queueStateLable = StudyStorageViewControl.FindControl("QueueState") as Label;
if (queueStateLable != null)
{
queueStateLable.Text = ServerEnumDescription.GetLocalizedDescription(ssl.QueueStudyStateEnum);
}
Label studyFolder = StudyStorageViewControl.FindControl("StudyFolder") as Label;
if (studyFolder != null)
{
studyFolder.Text = ssl.GetStudyPath();
}
Label transferSyntaxUID = StudyStorageViewControl.FindControl("TransferSyntaxUID") as Label;
if (transferSyntaxUID != null)
{
transferSyntaxUID.Text = TransferSyntax.GetTransferSyntax(ssl.TransferSyntaxUid).Name;
}
Label tier = StudyStorageViewControl.FindControl("Tier") as Label;
if (tier != null)
{
tier.Text = ServerEnumDescription.GetLocalizedDescription(ssl.FilesystemTierEnum);
}
Label studySize = StudyStorageViewControl.FindControl("StudySize") as Label;
if (studySize != null)
{
ulong sizeInBytes = (ulong)(ssl.Study.StudySizeInKB * 1024);
studySize.Text = ByteCountFormatter.Format(sizeInBytes);
}
}
}
/// <summary>
/// Load a <see cref="StudyXml"/> file for a given <see cref="StudyStorageLocation"/>
/// </summary>
/// <param name="location">The location a study is stored.</param>
/// <returns>The <see cref="StudyXml"/> instance for <paramref name="location"/></returns>
protected virtual StudyXml LoadStudyXml(StudyStorageLocation location)
{
StudyXml theXml = new StudyXml();
String streamFile = Path.Combine(location.GetStudyPath(), location.StudyInstanceUid + ".xml");
if (File.Exists(streamFile))
{
using (Stream fileStream = FileStreamOpener.OpenForRead(streamFile, FileMode.Open))
{
XmlDocument theDoc = new XmlDocument();
StudyXmlIo.Read(theDoc, fileStream);
theXml.SetMemento(theDoc);
fileStream.Close();
}
}
return(theXml);
}
/// <summary>
/// Load the first instance from the first series of the StudyXml file for a study.
/// </summary>
/// <param name="location">The storage location of the study.</param>
/// <returns></returns>
protected static DicomFile LoadInstance(StudyStorageLocation location)
{
string studyXml = Path.Combine(location.GetStudyPath(), location.StudyInstanceUid + ".xml");
if (!File.Exists(studyXml))
{
return(null);
}
FileStream stream = FileStreamOpener.OpenForRead(studyXml, FileMode.Open);
var theMemento = new StudyXmlMemento();
StudyXmlIo.Read(theMemento, stream);
stream.Close();
stream.Dispose();
var xml = new StudyXml();
xml.SetMemento(theMemento);
IEnumerator <SeriesXml> seriesEnumerator = xml.GetEnumerator();
if (seriesEnumerator.MoveNext())
{
SeriesXml seriesXml = seriesEnumerator.Current;
IEnumerator <InstanceXml> instanceEnumerator = seriesXml.GetEnumerator();
if (instanceEnumerator.MoveNext())
{
InstanceXml instance = instanceEnumerator.Current;
var file = new DicomFile("file.dcm", new DicomAttributeCollection(), instance.Collection)
{
TransferSyntax = instance.TransferSyntax
};
return(file);
}
}
return(null);
}
protected static StudyXml LoadStudyXml(StudyStorageLocation location)
{
// This method should be combined with StudyStorageLocation.LoadStudyXml()
StudyXml theXml = new StudyXml(location.StudyInstanceUid);
String streamFile = Path.Combine(location.GetStudyPath(), location.StudyInstanceUid + ".xml");
if (File.Exists(streamFile))
{
using (Stream fileStream = FileStreamOpener.OpenForRead(streamFile, FileMode.Open))
{
var theMemento = new StudyXmlMemento();
StudyXmlIo.Read(theMemento, fileStream);
theXml.SetMemento(theMemento);
fileStream.Close();
}
}
return(theXml);
}
private void Initialize()
{
using (IPersistenceContext readContext = PersistentStoreRegistry.GetDefaultStore().OpenReadContext())
{
_backupDir = ServerExecutionContext.Current.BackupDirectory;
_oldStudyPath = _oldStudyLocation.GetStudyPath();
_oldStudyInstanceUid = _oldStudyLocation.StudyInstanceUid;
_oldStudyFolder = _oldStudyLocation.StudyFolder;
_newStudyInstanceUid = _oldStudyInstanceUid;
_study = _oldStudyLocation.LoadStudy(readContext);
_totalSopCount = _study.NumberOfStudyRelatedInstances;
_curPatient = _study.LoadPatient(readContext);
_oldPatientInfo = new PatientInfo
{
Name = _curPatient.PatientsName,
PatientId = _curPatient.PatientId,
IssuerOfPatientId = _curPatient.IssuerOfPatientId
};
_newPatientInfo = new PatientInfo(_oldPatientInfo);
Debug.Assert(_newPatientInfo.Equals(_oldPatientInfo));
foreach (BaseImageLevelUpdateCommand command in _commands)
{
ImageLevelUpdateEntry imageLevelUpdate = command.UpdateEntry;
if (imageLevelUpdate == null)
{
continue;
}
if (imageLevelUpdate.TagPath.Tag.TagValue == DicomTags.StudyInstanceUid)
{
_newStudyInstanceUid = imageLevelUpdate.GetStringValue();
}
else if (imageLevelUpdate.TagPath.Tag.TagValue == DicomTags.PatientId)
{
_newPatientInfo.PatientId = imageLevelUpdate.GetStringValue();
}
else if (imageLevelUpdate.TagPath.Tag.TagValue == DicomTags.IssuerOfPatientId)
{
_newPatientInfo.IssuerOfPatientId = imageLevelUpdate.GetStringValue();
}
else if (imageLevelUpdate.TagPath.Tag.TagValue == DicomTags.PatientsName)
{
_newPatientInfo.Name = imageLevelUpdate.GetStringValue();
}
}
Platform.CheckForNullReference(_newStudyInstanceUid, "_newStudyInstanceUid");
NewStudyPath = Path.Combine(_oldStudyLocation.FilesystemPath, _partition.PartitionFolder);
NewStudyPath = Path.Combine(NewStudyPath, _oldStudyFolder);
NewStudyPath = Path.Combine(NewStudyPath, _newStudyInstanceUid);
_newPatient = FindPatient(_newPatientInfo, readContext);
_patientInfoIsNotChanged = _newPatientInfo.Equals(_oldPatientInfo);
Statistics.InstanceCount = _study.NumberOfStudyRelatedInstances;
Statistics.StudySize = (ulong)_oldStudyLocation.LoadStudyXml().GetStudySize();
// The study path will be changed. We will need to delete the original folder at the end.
// May be too simple to test if two paths are the same. But let's assume it is good enough for 99% of the time.
_deleteOriginalFolder = NewStudyPath != _oldStudyPath;
_initialized = true;
}
}
/// <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
};
string 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
CopyDirectoryCommand 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);
}
/// <summary>
/// Do the restore.
/// </summary>
/// <param name="queueItem">The queue item to restore.</param>
public void Run(RestoreQueue queueItem)
{
using (RestoreProcessorContext context = new RestoreProcessorContext(queueItem))
{
try
{
// Load up related classes.
using (IReadContext readContext = _nasArchive.PersistentStore.OpenReadContext())
{
_archiveStudyStorage = ArchiveStudyStorage.Load(readContext, queueItem.ArchiveStudyStorageKey);
_serverSyntax = ServerTransferSyntax.Load(readContext, _archiveStudyStorage.ServerTransferSyntaxKey);
_syntax = TransferSyntax.GetTransferSyntax(_serverSyntax.Uid);
StudyStorageLocationQueryParameters parms = new StudyStorageLocationQueryParameters
{StudyStorageKey = queueItem.StudyStorageKey};
IQueryStudyStorageLocation broker = readContext.GetBroker<IQueryStudyStorageLocation>();
_location = broker.FindOne(parms);
if (_location == null)
{
_studyStorage = StudyStorage.Load(readContext, queueItem.StudyStorageKey);
if (_studyStorage==null)
{
DateTime scheduleTime = Platform.Time.AddMinutes(5);
Platform.Log(LogLevel.Error, "Unable to find storage location, rescheduling restore request to {0}",
scheduleTime);
queueItem.FailureDescription = "Unable to find storage location, rescheduling request.";
_nasArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Pending, scheduleTime);
return;
}
}
}
if (_location == null)
Platform.Log(LogLevel.Info, "Starting restore of nearline study: {0}", _studyStorage.StudyInstanceUid);
else
Platform.Log(LogLevel.Info, "Starting restore of online study: {0}", _location.StudyInstanceUid);
// If restoring a Nearline study, select a filesystem
string destinationFolder;
if (_location == null)
{
ServerFilesystemInfo fs = _nasArchive.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 request.";
_nasArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Pending, scheduleTime);
return;
}
destinationFolder = Path.Combine(fs.Filesystem.FilesystemPath, _nasArchive.ServerPartition.PartitionFolder);
}
else
destinationFolder = _location.GetStudyPath();
// Get the zip file path from the xml data in the ArchiveStudyStorage entry
// Also store the "StudyFolder" for use below
string studyFolder = String.Empty;
string filename = String.Empty;
string studyInstanceUid = String.Empty;
XmlElement element = _archiveStudyStorage.ArchiveXml.DocumentElement;
if (element!=null)
foreach (XmlElement node in element.ChildNodes)
if (node.Name.Equals("StudyFolder"))
studyFolder = node.InnerText;
else if (node.Name.Equals("Filename"))
filename = node.InnerText;
else if (node.Name.Equals("Uid"))
studyInstanceUid = node.InnerText;
string zipFile = Path.Combine(_nasArchive.NasPath, studyFolder);
zipFile = Path.Combine(zipFile, studyInstanceUid);
zipFile = Path.Combine(zipFile, filename);
// Do a test read of the zip file. If it succeeds, the file is available, if it
// fails, we just set back to pending and recheck.
try
{
FileStream stream = File.OpenRead(zipFile);
// Read a byte, just in case that makes a difference.
stream.ReadByte();
stream.Close();
stream.Dispose();
}
catch (Exception ex)
{
DateTime scheduledTime = Platform.Time.AddSeconds(NasSettings.Default.ReadFailRescheduleDelaySeconds);
Platform.Log(LogLevel.Error, ex, "Archive {0} for Study {1} is unreadable, rescheduling restore to {2}",
zipFile, _studyStorage == null ? (_location == null ? string.Empty : _location.StudyInstanceUid) : _studyStorage.StudyInstanceUid,
scheduledTime);
// Just reschedule in "Restoring" state, the file is unreadable.
_nasArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Restoring,
scheduledTime);
return;
}
if (_location == null)
RestoreNearlineStudy(queueItem, zipFile, destinationFolder, studyFolder);
else
RestoreOnlineStudy(queueItem, zipFile, destinationFolder);
}
catch (Exception e)
{
Platform.Log(LogLevel.Error, e, "Unexpected exception processing restore request for {0} on archive {1}",
_studyStorage == null ? (_location == null ? string.Empty : _location.StudyInstanceUid) : _studyStorage.StudyInstanceUid,
_nasArchive.PartitionArchive.Description);
queueItem.FailureDescription = e.Message;
_nasArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Failed, Platform.Time);
}
}
}
/// <summary>
/// Do the restore.
/// </summary>
/// <param name="queueItem">The queue item to restore.</param>
public void Run(RestoreQueue queueItem)
{
using (var context = new RestoreProcessorContext(queueItem))
{
try
{
// Load up related classes.
using (IReadContext readContext = _hsmArchive.PersistentStore.OpenReadContext())
{
_archiveStudyStorage = ArchiveStudyStorage.Load(readContext, queueItem.ArchiveStudyStorageKey);
_serverSyntax = ServerTransferSyntax.Load(readContext, _archiveStudyStorage.ServerTransferSyntaxKey);
_syntax = TransferSyntax.GetTransferSyntax(_serverSyntax.Uid);
var parms = new StudyStorageLocationQueryParameters
{
StudyStorageKey = queueItem.StudyStorageKey
};
var broker = readContext.GetBroker <IQueryStudyStorageLocation>();
_location = broker.FindOne(parms);
if (_location == null)
{
_studyStorage = StudyStorage.Load(readContext, queueItem.StudyStorageKey);
if (_studyStorage == null)
{
DateTime scheduleTime = Platform.Time.AddMinutes(5);
Platform.Log(LogLevel.Error, "Unable to find storage location, rescheduling restore request to {0}",
scheduleTime);
queueItem.FailureDescription = "Unable to find storage location, rescheduling request.";
_hsmArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Pending, scheduleTime);
return;
}
}
}
if (_location == null)
{
Platform.Log(LogLevel.Info, "Starting restore of nearline study: {0}",
_studyStorage.StudyInstanceUid);
// Get the zip file path from the xml data in the ArchiveStudyStorage entry
// Also store the "StudyFolder" for use below
string studyFolder;
string zipFile = GetZipFileName(out studyFolder);
// Do a test read of the zip file. If it succeeds, the file is available, if it
// fails, we just set back to pending and recheck.
if (!CanReadZip(zipFile, queueItem))
{
return;
}
RestoreNearlineStudy(queueItem, zipFile, studyFolder);
}
else
{
Platform.Log(LogLevel.Info, "Starting restore of online study: {0}", _location.StudyInstanceUid);
// Get the zip file path from the xml data in the ArchiveStudyStorage entry
// Also store the "StudyFolder" for use below
string studyFolder;
string zipFile = GetZipFileName(out studyFolder);
// Do a test read of the zip file. If it succeeds, the file is available, if it
// fails, we just set back to pending and recheck.
if (!CanReadZip(zipFile, queueItem))
{
return;
}
RestoreOnlineStudy(queueItem, zipFile, _location.GetStudyPath());
}
}
catch (Exception e)
{
Platform.Log(LogLevel.Error, e, "Unexpected exception processing restore request for {0} on archive {1}",
_studyStorage == null ? (_location == null ? string.Empty : _location.StudyInstanceUid) : _studyStorage.StudyInstanceUid,
_hsmArchive.PartitionArchive.Description);
queueItem.FailureDescription = e.Message;
_hsmArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Failed, Platform.Time);
}
}
}
/// <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);
}
/// <summary>
/// Loads the <see cref="Series"/> and instance mappings for the specified study.
/// </summary>
/// <param name="location"></param>
public void Load(StudyStorageLocation location)
{
Load(Path.Combine(location.GetStudyPath(), "UidMap.xml"));
}
/// <summary>
/// Do the restore.
/// </summary>
/// <param name="queueItem">The queue item to restore.</param>
public void Run(RestoreQueue queueItem)
{
using (var context = new RestoreProcessorContext(queueItem))
{
try
{
// Load up related classes.
using (IReadContext readContext = _hsmArchive.PersistentStore.OpenReadContext())
{
_archiveStudyStorage = ArchiveStudyStorage.Load(readContext, queueItem.ArchiveStudyStorageKey);
_serverSyntax = ServerTransferSyntax.Load(readContext, _archiveStudyStorage.ServerTransferSyntaxKey);
_syntax = TransferSyntax.GetTransferSyntax(_serverSyntax.Uid);
var parms = new StudyStorageLocationQueryParameters
{StudyStorageKey = queueItem.StudyStorageKey};
var broker = readContext.GetBroker<IQueryStudyStorageLocation>();
_location = broker.FindOne(parms);
if (_location == null)
{
_studyStorage = StudyStorage.Load(readContext, queueItem.StudyStorageKey);
if (_studyStorage==null)
{
DateTime scheduleTime = Platform.Time.AddMinutes(5);
Platform.Log(LogLevel.Error, "Unable to find storage location, rescheduling restore request to {0}",
scheduleTime);
queueItem.FailureDescription = "Unable to find storage location, rescheduling request.";
_hsmArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Pending, scheduleTime);
return;
}
}
}
if (_location == null)
{
Platform.Log(LogLevel.Info, "Starting restore of nearline study: {0}",
_studyStorage.StudyInstanceUid);
// Get the zip file path from the xml data in the ArchiveStudyStorage entry
// Also store the "StudyFolder" for use below
string studyFolder;
string zipFile = GetZipFileName(out studyFolder);
// Do a test read of the zip file. If it succeeds, the file is available, if it
// fails, we just set back to pending and recheck.
if (!CanReadZip(zipFile, queueItem))
return;
RestoreNearlineStudy(queueItem, zipFile, studyFolder);
}
else
{
Platform.Log(LogLevel.Info, "Starting restore of online study: {0}", _location.StudyInstanceUid);
// Get the zip file path from the xml data in the ArchiveStudyStorage entry
// Also store the "StudyFolder" for use below
string studyFolder;
string zipFile = GetZipFileName(out studyFolder);
// Do a test read of the zip file. If it succeeds, the file is available, if it
// fails, we just set back to pending and recheck.
if (!CanReadZip(zipFile, queueItem))
return;
RestoreOnlineStudy(queueItem, zipFile, _location.GetStudyPath());
}
}
catch (Exception e)
{
Platform.Log(LogLevel.Error, e, "Unexpected exception processing restore request for {0} on archive {1}",
_studyStorage == null ? (_location == null ? string.Empty : _location.StudyInstanceUid) : _studyStorage.StudyInstanceUid,
_hsmArchive.PartitionArchive.Description);
queueItem.FailureDescription = e.Message;
_hsmArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Failed, Platform.Time);
}
}
}
/// <summary>
/// Load a <see cref="StudyXml"/> file for a given <see cref="StudyStorageLocation"/>
/// </summary>
/// <param name="location">The location a study is stored.</param>
/// <returns>The <see cref="StudyXml"/> instance for <paramref name="location"/></returns>
protected virtual StudyXml LoadStudyXml(StudyStorageLocation location)
{
StudyXml theXml = new StudyXml();
String streamFile = Path.Combine(location.GetStudyPath(), location.StudyInstanceUid + ".xml");
if (File.Exists(streamFile))
{
using (Stream fileStream = FileStreamOpener.OpenForRead(streamFile, FileMode.Open))
{
var theMemento = new StudyXmlMemento();
StudyXmlIo.Read(theMemento, fileStream);
theXml.SetMemento(theMemento);
fileStream.Close();
}
}
return theXml;
}
/// <summary>
/// Do the restore.
/// </summary>
/// <param name="queueItem">The queue item to restore.</param>
public void Run(RestoreQueue queueItem)
{
using (RestoreProcessorContext context = new RestoreProcessorContext(queueItem))
{
try
{
// Load up related classes.
using (IReadContext readContext = _nasArchive.PersistentStore.OpenReadContext())
{
_archiveStudyStorage = ArchiveStudyStorage.Load(readContext, queueItem.ArchiveStudyStorageKey);
_serverSyntax = ServerTransferSyntax.Load(readContext, _archiveStudyStorage.ServerTransferSyntaxKey);
_syntax = TransferSyntax.GetTransferSyntax(_serverSyntax.Uid);
StudyStorageLocationQueryParameters parms = new StudyStorageLocationQueryParameters
{
StudyStorageKey = queueItem.StudyStorageKey
};
IQueryStudyStorageLocation broker = readContext.GetBroker <IQueryStudyStorageLocation>();
_location = broker.FindOne(parms);
if (_location == null)
{
_studyStorage = StudyStorage.Load(readContext, queueItem.StudyStorageKey);
if (_studyStorage == null)
{
DateTime scheduleTime = Platform.Time.AddMinutes(5);
Platform.Log(LogLevel.Error, "Unable to find storage location, rescheduling restore request to {0}",
scheduleTime);
queueItem.FailureDescription = "Unable to find storage location, rescheduling request.";
_nasArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Pending, scheduleTime);
return;
}
}
}
if (_location == null)
{
Platform.Log(LogLevel.Info, "Starting restore of nearline study: {0}", _studyStorage.StudyInstanceUid);
}
else
{
Platform.Log(LogLevel.Info, "Starting restore of online study: {0}", _location.StudyInstanceUid);
}
// If restoring a Nearline study, select a filesystem
string destinationFolder;
if (_location == null)
{
ServerFilesystemInfo fs = _nasArchive.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 request.";
_nasArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Pending, scheduleTime);
return;
}
destinationFolder = Path.Combine(fs.Filesystem.FilesystemPath, _nasArchive.ServerPartition.PartitionFolder);
}
else
{
destinationFolder = _location.GetStudyPath();
}
// Get the zip file path from the xml data in the ArchiveStudyStorage entry
// Also store the "StudyFolder" for use below
string studyFolder = String.Empty;
string filename = String.Empty;
string studyInstanceUid = String.Empty;
XmlElement element = _archiveStudyStorage.ArchiveXml.DocumentElement;
if (element != null)
{
foreach (XmlElement node in element.ChildNodes)
{
if (node.Name.Equals("StudyFolder"))
{
studyFolder = node.InnerText;
}
else if (node.Name.Equals("Filename"))
{
filename = node.InnerText;
}
else if (node.Name.Equals("Uid"))
{
studyInstanceUid = node.InnerText;
}
}
}
string zipFile = Path.Combine(_nasArchive.NasPath, studyFolder);
zipFile = Path.Combine(zipFile, studyInstanceUid);
zipFile = Path.Combine(zipFile, filename);
// Do a test read of the zip file. If it succeeds, the file is available, if it
// fails, we just set back to pending and recheck.
try
{
FileStream stream = File.OpenRead(zipFile);
// Read a byte, just in case that makes a difference.
stream.ReadByte();
stream.Close();
stream.Dispose();
}
catch (Exception ex)
{
DateTime scheduledTime = Platform.Time.AddSeconds(NasSettings.Default.ReadFailRescheduleDelaySeconds);
Platform.Log(LogLevel.Error, ex, "Archive {0} for Study {1} is unreadable, rescheduling restore to {2}",
zipFile, _studyStorage == null ? (_location == null ? string.Empty : _location.StudyInstanceUid) : _studyStorage.StudyInstanceUid,
scheduledTime);
// Just reschedule in "Restoring" state, the file is unreadable.
_nasArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Restoring,
scheduledTime);
return;
}
if (_location == null)
{
RestoreNearlineStudy(queueItem, zipFile, destinationFolder, studyFolder);
}
else
{
RestoreOnlineStudy(queueItem, zipFile, destinationFolder);
}
}
catch (Exception e)
{
Platform.Log(LogLevel.Error, e, "Unexpected exception processing restore request for {0} on archive {1}",
_studyStorage == null ? (_location == null ? string.Empty : _location.StudyInstanceUid) : _studyStorage.StudyInstanceUid,
_nasArchive.PartitionArchive.Description);
queueItem.FailureDescription = e.Message;
_nasArchive.UpdateRestoreQueue(queueItem, RestoreQueueStatusEnum.Failed, Platform.Time);
}
}
}
/// <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>
/// Estimate the folder size for a study
/// </summary>
/// <remarks>
/// This routine loads the StudyXml file and traverses through each series
/// for the study. It then looks at the size of the first image in the series,
/// and assumes the series size is equal to the first image size times the number
/// of images within the series. If the file sizes vary within the series, this
/// algorithm will fall down a bit.
/// </remarks>
/// <param name="location">The StudyStorageLocation object for the study.</param>
/// <returns></returns>
protected float EstimateFolderSizeFromStudyXml(StudyStorageLocation location)
{
float folderSize = 0.0f;
string studyFolder = location.GetStudyPath();
string file = Path.Combine(studyFolder, location.StudyInstanceUid + ".xml");
if (File.Exists(file))
{
FileInfo finfo = new FileInfo(file);
folderSize += finfo.Length;
}
file = Path.Combine(studyFolder, location.StudyInstanceUid + ".xml.gz");
if (File.Exists(file))
{
FileInfo finfo = new FileInfo(file);
folderSize += finfo.Length;
}
StudyXml study = LoadStudyXml(location);
foreach (SeriesXml series in study)
{
string seriesFolder = Path.Combine(studyFolder, series.SeriesInstanceUid);
foreach (InstanceXml instance in series)
{
if (instance.FileSize != 0)
{
folderSize += instance.FileSize;
}
else
{
file = Path.Combine(seriesFolder, String.Format("{0}.dcm", instance.SopInstanceUid));
if (File.Exists(file))
{
FileInfo finfo = new FileInfo(file);
folderSize += finfo.Length;
}
}
}
}
return folderSize;
}
/// <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);
}
}
}
private void DoStudyLevelValidation(StudyStorageLocation storageLocation, StudyXml studyXml, Study study, ServerPartition partition)
{
int xmlNumInstances = studyXml.NumberOfStudyRelatedInstances;
int xmlNumSeries = studyXml.NumberOfStudyRelatedSeries;
if (study.NumberOfStudyRelatedInstances != xmlNumInstances)
{
throw new StudyIntegrityValidationFailure(
ValidationErrors.InconsistentObjectCount,
new ValidationStudyInfo(study, partition),
String.Format("Number of study related instances in the database ({0}) does not match number of images in the filesystem ({1})",
study.NumberOfStudyRelatedInstances, xmlNumInstances));
}
if (study.NumberOfStudyRelatedSeries != xmlNumSeries)
{
throw new StudyIntegrityValidationFailure(ValidationErrors.InconsistentObjectCount,
new ValidationStudyInfo(study, partition),
String.Format("Number of study related series in the database ({0}) does not match number of series in the xml ({1})",
study.NumberOfStudyRelatedSeries, xmlNumSeries));
}
long dirFileCount = DirectoryUtility.Count(storageLocation.GetStudyPath(),
"*" + ServerPlatform.DicomFileExtension, true, null);
if (xmlNumInstances != dirFileCount)
{
throw new StudyIntegrityValidationFailure(ValidationErrors.InconsistentObjectCount,
new ValidationStudyInfo(study, partition),
String.Format("Number of instance in xml ({0}) does not match number of images in the filesystem ({1})",
xmlNumInstances, dirFileCount));
}
}
/// <summary>
/// Load a <see cref="StudyXml"/> file for a given <see cref="StudyStorageLocation"/>
/// </summary>
/// <param name="location">The location a study is stored.</param>
/// <returns>The <see cref="StudyXml"/> instance for <paramref name="location"/></returns>
protected virtual StudyXml LoadStudyXml(StudyStorageLocation location)
{
StudyXml theXml = new StudyXml();
StudyXmlLoadTime.Add(
delegate
{
String streamFile = Path.Combine(location.GetStudyPath(), location.StudyInstanceUid + ".xml");
if (File.Exists(streamFile))
{
using (Stream fileStream = FileStreamOpener.OpenForRead(streamFile, FileMode.Open))
{
XmlDocument theDoc = new XmlDocument();
StudyXmlIo.Read(theDoc, fileStream);
theXml.SetMemento(theDoc);
fileStream.Close();
}
}
}
);
return theXml;
}
/// <summary>
/// Computes and returns the absolute path specified by this <see cref="FilesystemDynamicPath"/> for the <see cref="StudyStorageLocation"/>.
/// Note: The path may or may not be valid.
/// </summary>
/// <param name="studyStorage"></param>
/// <returns></returns>
public string ConvertToAbsolutePath(StudyStorageLocation studyStorage)
{
switch (_type)
{
case PathType.Absolute: return _path;
case PathType.RelativeToReconcileFolder:
var basePath = studyStorage.GetReconcileRootPath();
return Path.Combine(basePath, _path);
case PathType.RelativeToStudyFolder:
basePath = studyStorage.GetStudyPath();
return Path.Combine(basePath, _path);
default:
return _path;
}
}
private static WorkQueueDetails CreateProcessDuplicateWorkQueueItemDetails(Model.WorkQueue item)
{
var detail = new WorkQueueDetails();
detail.Key = item.Key;
detail.ScheduledDateTime = item.ScheduledTime;
detail.ExpirationTime = item.ExpirationTime;
detail.InsertTime = item.InsertTime;
detail.FailureCount = item.FailureCount;
detail.Type = item.WorkQueueTypeEnum;
detail.Status = item.WorkQueueStatusEnum;
detail.Priority = item.WorkQueuePriorityEnum;
detail.FailureDescription = item.FailureDescription;
detail.ServerDescription = item.ProcessorID;
StudyStorageLocation storage = WorkQueueController.GetLoadStorageLocation(item);
detail.StorageLocationPath = storage.GetStudyPath();
XmlDocument doc = item.Data;
XmlNodeList nodeList = doc.GetElementsByTagName("DuplicateSopFolder");
detail.DuplicateStorageLocationPath = nodeList[0].InnerText;
// Fetch UIDs
var wqUidsAdaptor = new WorkQueueUidAdaptor();
var uidCriteria = new WorkQueueUidSelectCriteria();
uidCriteria.WorkQueueKey.EqualTo(item.GetKey());
IList <WorkQueueUid> uids = wqUidsAdaptor.Get(uidCriteria);
var mapSeries = new Hashtable();
foreach (WorkQueueUid uid in uids)
{
if (mapSeries.ContainsKey(uid.SeriesInstanceUid) == false)
{
mapSeries.Add(uid.SeriesInstanceUid, uid.SopInstanceUid);
}
}
detail.NumInstancesPending = uids.Count;
detail.NumSeriesPending = mapSeries.Count;
// Fetch the study and patient info
var ssAdaptor = new StudyStorageAdaptor();
StudyStorage storages = ssAdaptor.Get(item.StudyStorageKey);
var studyAdaptor = new StudyAdaptor();
var studycriteria = new StudySelectCriteria();
studycriteria.StudyInstanceUid.EqualTo(storages.StudyInstanceUid);
studycriteria.ServerPartitionKey.EqualTo(item.ServerPartitionKey);
Study study = studyAdaptor.GetFirst(studycriteria);
// Study may not be available until the images are processed.
if (study != null)
{
var studyAssembler = new StudyDetailsAssembler();
detail.Study = studyAssembler.CreateStudyDetail(study);
}
return(detail);
}
/// <summary>
/// Loads the <see cref="Series"/> and instance mappings for the specified study.
/// </summary>
/// <param name="location"></param>
public void Load(StudyStorageLocation location)
{
Load(Path.Combine(location.GetStudyPath(), "UidMap.xml"));
}
private static WorkQueueDetails CreateWebMoveStudyWorkQueueItemDetails(Model.WorkQueue item)
{
var deviceAdaptor = new DeviceDataAdapter();
var studyStorageAdaptor = new StudyStorageAdaptor();
StudyStorage studyStorage = studyStorageAdaptor.Get(item.StudyStorageKey);
var wqUidsAdaptor = new WorkQueueUidAdaptor();
var studyAdaptor = new StudyAdaptor();
Device dest = deviceAdaptor.Get(item.DeviceKey);
var detail = new WebMoveStudyWorkQueueDetails();
detail.Key = item.GetKey();
detail.DestinationAE = dest == null ? string.Empty : dest.AeTitle;
detail.StudyInstanceUid = studyStorage == null ? string.Empty : studyStorage.StudyInstanceUid;
detail.ScheduledDateTime = item.ScheduledTime;
detail.ExpirationTime = item.ExpirationTime;
detail.InsertTime = item.InsertTime;
detail.FailureCount = item.FailureCount;
detail.Type = item.WorkQueueTypeEnum;
detail.Status = item.WorkQueueStatusEnum;
detail.Priority = item.WorkQueuePriorityEnum;
detail.ServerDescription = item.ProcessorID;
detail.FailureDescription = item.FailureDescription;
StudyStorageLocation storage = WorkQueueController.GetLoadStorageLocation(item);
detail.StorageLocationPath = storage.GetStudyPath();
// Fetch UIDs
var uidCriteria = new WorkQueueUidSelectCriteria();
uidCriteria.WorkQueueKey.EqualTo(item.GetKey());
IList <WorkQueueUid> uids = wqUidsAdaptor.Get(uidCriteria);
var mapSeries = new Hashtable();
foreach (WorkQueueUid uid in uids)
{
if (mapSeries.ContainsKey(uid.SeriesInstanceUid) == false)
{
mapSeries.Add(uid.SeriesInstanceUid, uid.SopInstanceUid);
}
}
detail.NumInstancesPending = uids.Count;
detail.NumSeriesPending = mapSeries.Count;
// Fetch the study and patient info
if (studyStorage != null)
{
var studycriteria = new StudySelectCriteria();
studycriteria.StudyInstanceUid.EqualTo(studyStorage.StudyInstanceUid);
studycriteria.ServerPartitionKey.EqualTo(item.ServerPartitionKey);
Study study = studyAdaptor.GetFirst(studycriteria);
// Study may not be available until the images are processed.
if (study != null)
{
var studyAssembler = new StudyDetailsAssembler();
detail.Study = studyAssembler.CreateStudyDetail(study);
}
}
return(detail);
}
private static WorkQueueDetails CreateEditWorkQueueItemDetails(Model.WorkQueue item)
{
string studyPath;
try
{
StudyStorageLocation storage = WorkQueueController.GetLoadStorageLocation(item);
studyPath = storage.GetStudyPath();
}
catch (Exception)
{
studyPath = string.Empty;
}
var detail = new WorkQueueDetails
{
Key = item.Key,
ScheduledDateTime = item.ScheduledTime,
ExpirationTime = item.ExpirationTime,
InsertTime = item.InsertTime,
FailureCount = item.FailureCount,
Type = item.WorkQueueTypeEnum,
Status = item.WorkQueueStatusEnum,
Priority = item.WorkQueuePriorityEnum,
FailureDescription = item.FailureDescription,
ServerDescription = item.ProcessorID,
StorageLocationPath = studyPath
};
// Fetch UIDs
var wqUidsAdaptor = new WorkQueueUidAdaptor();
var uidCriteria = new WorkQueueUidSelectCriteria();
uidCriteria.WorkQueueKey.EqualTo(item.GetKey());
IList <WorkQueueUid> uids = wqUidsAdaptor.Get(uidCriteria);
var mapSeries = new Hashtable();
foreach (WorkQueueUid uid in uids)
{
if (mapSeries.ContainsKey(uid.SeriesInstanceUid) == false)
{
mapSeries.Add(uid.SeriesInstanceUid, uid.SopInstanceUid);
}
}
detail.NumInstancesPending = uids.Count;
detail.NumSeriesPending = mapSeries.Count;
// Fetch the study and patient info
var ssAdaptor = new StudyStorageAdaptor();
StudyStorage storages = ssAdaptor.Get(item.StudyStorageKey);
var studyAdaptor = new StudyAdaptor();
var studycriteria = new StudySelectCriteria();
studycriteria.StudyInstanceUid.EqualTo(storages.StudyInstanceUid);
studycriteria.ServerPartitionKey.EqualTo(item.ServerPartitionKey);
Study study = studyAdaptor.GetFirst(studycriteria);
// Study may not be available until the images are processed.
if (study != null)
{
var studyAssembler = new StudyDetailsAssembler();
detail.Study = studyAssembler.CreateStudyDetail(study);
}
var parser = new EditStudyWorkQueueDataParser();
EditStudyWorkQueueData data = parser.Parse(item.Data.DocumentElement);
detail.EditUpdateItems = data.EditRequest.UpdateEntries.ToArray();
return(detail);
}
/// <summary>
/// Archive the specified <see cref="ArchiveQueue"/> item.
/// </summary>
/// <param name="queueItem">The ArchiveQueue item to archive.</param>
public void Run(ArchiveQueue queueItem)
{
using (ArchiveProcessorContext executionContext = new ArchiveProcessorContext(queueItem))
{
try
{
if (!GetStudyStorageLocation(queueItem))
{
Platform.Log(LogLevel.Error,
"Unable to find readable study storage location for archival queue request {0}. Delaying request.",
queueItem.Key);
queueItem.FailureDescription = "Unable to find readable study storage location for archival queue request.";
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Pending, Platform.Time.AddMinutes(2));
return;
}
// First, check to see if we can lock the study, if not just reschedule the queue entry.
if (!_storageLocation.QueueStudyStateEnum.Equals(QueueStudyStateEnum.Idle))
{
Platform.Log(LogLevel.Info, "Study {0} on partition {1} is currently locked, delaying archival.", _storageLocation.StudyInstanceUid, _hsmArchive.ServerPartition.Description);
queueItem.FailureDescription = "Study is currently locked, delaying archival.";
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Pending, Platform.Time.AddMinutes(2));
return;
}
StudyIntegrityValidator validator = new StudyIntegrityValidator();
validator.ValidateStudyState("Archive", _storageLocation, StudyIntegrityValidationModes.Default);
using (IUpdateContext update = PersistentStoreRegistry.GetDefaultStore().OpenUpdateContext(UpdateContextSyncMode.Flush))
{
ILockStudy studyLock = update.GetBroker <ILockStudy>();
LockStudyParameters parms = new LockStudyParameters
{
StudyStorageKey = queueItem.StudyStorageKey,
QueueStudyStateEnum = QueueStudyStateEnum.ArchiveScheduled
};
bool retVal = studyLock.Execute(parms);
if (!parms.Successful || !retVal)
{
Platform.Log(LogLevel.Info, "Study {0} on partition {1} failed to lock, delaying archival.", _storageLocation.StudyInstanceUid, _hsmArchive.ServerPartition.Description);
queueItem.FailureDescription = "Study failed to lock, delaying archival.";
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Pending, Platform.Time.AddMinutes(2));
return;
}
update.Commit();
}
string studyFolder = _storageLocation.GetStudyPath();
string studyXmlFile = _storageLocation.GetStudyXmlPath();
// Load the study Xml file, this is used to generate the list of dicom files to archive.
LoadStudyXml(studyXmlFile);
DicomFile file = LoadFileFromStudyXml();
string patientsName = file.DataSet[DicomTags.PatientsName].GetString(0, string.Empty);
string patientId = file.DataSet[DicomTags.PatientId].GetString(0, string.Empty);
string accessionNumber = file.DataSet[DicomTags.AccessionNumber].GetString(0, string.Empty);
Platform.Log(LogLevel.Info,
"Starting archival of study {0} for Patient {1} (PatientId:{2} A#:{3}) on Partition {4} on archive {5}",
_storageLocation.StudyInstanceUid, patientsName, patientId,
accessionNumber, _hsmArchive.ServerPartition.Description,
_hsmArchive.PartitionArchive.Description);
// Use the command processor to do the archival.
using (ServerCommandProcessor commandProcessor = new ServerCommandProcessor("Archive"))
{
_archiveXml = new XmlDocument();
// Create the study date folder
string zipFilename = Path.Combine(_hsmArchive.HsmPath, _storageLocation.StudyFolder);
commandProcessor.AddCommand(new CreateDirectoryCommand(zipFilename));
// Create a folder for the study
zipFilename = Path.Combine(zipFilename, _storageLocation.StudyInstanceUid);
commandProcessor.AddCommand(new CreateDirectoryCommand(zipFilename));
// Save the archive data in the study folder, based on a filename with a date / time stamp
string filename = String.Format("{0}.zip", Platform.Time.ToString("yyyy-MM-dd-HHmm"));
zipFilename = Path.Combine(zipFilename, filename);
// Create the Xml data to store in the ArchiveStudyStorage table telling
// where the archived study is located.
XmlElement hsmArchiveElement = _archiveXml.CreateElement("HsmArchive");
_archiveXml.AppendChild(hsmArchiveElement);
XmlElement studyFolderElement = _archiveXml.CreateElement("StudyFolder");
hsmArchiveElement.AppendChild(studyFolderElement);
studyFolderElement.InnerText = _storageLocation.StudyFolder;
XmlElement filenameElement = _archiveXml.CreateElement("Filename");
hsmArchiveElement.AppendChild(filenameElement);
filenameElement.InnerText = filename;
XmlElement studyInstanceUidElement = _archiveXml.CreateElement("Uid");
hsmArchiveElement.AppendChild(studyInstanceUidElement);
studyInstanceUidElement.InnerText = _storageLocation.StudyInstanceUid;
// Create the Zip file
commandProcessor.AddCommand(
new CreateStudyZipCommand(zipFilename, _studyXml, studyFolder, executionContext.TempDirectory));
// Update the database.
commandProcessor.AddCommand(new InsertArchiveStudyStorageCommand(queueItem.StudyStorageKey, queueItem.PartitionArchiveKey, queueItem.GetKey(), _storageLocation.ServerTransferSyntaxKey, _archiveXml));
StudyRulesEngine studyEngine =
new StudyRulesEngine(_storageLocation, _hsmArchive.ServerPartition, _studyXml);
studyEngine.Apply(ServerRuleApplyTimeEnum.StudyArchived, commandProcessor);
if (!commandProcessor.Execute())
{
Platform.Log(LogLevel.Error,
"Unexpected failure archiving study ({0}) to archive {1}: {2}, zip filename: {3}",
_storageLocation.StudyInstanceUid, _hsmArchive.PartitionArchive.Description,
commandProcessor.FailureReason, zipFilename);
queueItem.FailureDescription = commandProcessor.FailureReason;
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Failed, Platform.Time);
}
else
{
Platform.Log(LogLevel.Info, "Successfully archived study {0} on {1} to zip {2}",
_storageLocation.StudyInstanceUid,
_hsmArchive.PartitionArchive.Description, zipFilename);
}
// Log the current FilesystemQueue settings
_storageLocation.LogFilesystemQueue();
}
}
catch (StudyIntegrityValidationFailure ex)
{
StringBuilder error = new StringBuilder();
error.AppendLine(String.Format("Partition : {0}", ex.ValidationStudyInfo.ServerAE));
error.AppendLine(String.Format("Patient : {0}", ex.ValidationStudyInfo.PatientsName));
error.AppendLine(String.Format("Study Uid : {0}", ex.ValidationStudyInfo.StudyInstaneUid));
error.AppendLine(String.Format("Accession# : {0}", ex.ValidationStudyInfo.AccessionNumber));
error.AppendLine(String.Format("Study Date : {0}", ex.ValidationStudyInfo.StudyDate));
queueItem.FailureDescription = error.ToString();
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Failed, Platform.Time);
}
catch (Exception e)
{
String msg = String.Format("Unexpected exception archiving study: {0} on {1}: {2}",
_storageLocation.StudyInstanceUid, _hsmArchive.PartitionArchive.Description, e.Message);
Platform.Log(LogLevel.Error, e, msg);
queueItem.FailureDescription = msg;
_hsmArchive.UpdateArchiveQueue(queueItem, ArchiveQueueStatusEnum.Failed, Platform.Time);
}
finally
{
// Unlock the Queue Entry
using (IUpdateContext update = PersistentStoreRegistry.GetDefaultStore().OpenUpdateContext(UpdateContextSyncMode.Flush))
{
ILockStudy studyLock = update.GetBroker <ILockStudy>();
LockStudyParameters parms = new LockStudyParameters
{
StudyStorageKey = queueItem.StudyStorageKey,
QueueStudyStateEnum = QueueStudyStateEnum.Idle
};
bool retVal = studyLock.Execute(parms);
if (!parms.Successful || !retVal)
{
Platform.Log(LogLevel.Info, "Study {0} on partition {1} is failed to unlock.", _storageLocation.StudyInstanceUid, _hsmArchive.ServerPartition.Description);
}
update.Commit();
}
}
}
}
