static void Main(string[] args)
{
Console.WriteLine("NetworkMessageBuilder run");
string outputDir = "./";
if (args.Length > 0)
{
outputDir = args[0];
}
string includeFile = null;
if (args.Length > 1)
{
includeFile = args[1];
}
Console.WriteLine(outputDir);
Console.WriteLine(includeFile);
AppDomain.CurrentDomain.Load("NetworkMessage");
SchemaBox.Parse();
var groupWriter = new GroupWriter();
groupWriter.GenerateCode(outputDir, includeFile);
var groupHandlerWriter = new GroupHandlerWriter();
groupHandlerWriter.GenerateCode(outputDir, includeFile);
}
private static void WriteGroupHistory(List <Commit> history)
{
var groupWriter = new GroupWriter("history-grouped.html");
var items = CommitsToHistoryItem.Transform(history);
groupWriter.Write(items);
}
public GroupApiController(
GroupReader groupReader,
GroupWriter groupWriter,
IUserContext userContext) : base(userContext)
{
_groupReader = groupReader;
_groupWriter = groupWriter;
}
public CMoveResponse(CMoveRequest req, Status status)
{
this.CommandField = (ushort)C.C_MOVE_RP;
this.AffectedSOPClassUID = req.AffectedSOPClassUID;
this.MessageIDBeingRespondedTo = req.MessageID;
this.DataSetType = (ushort)257;
this.Status = (ushort)status;
this.GroupLength = (uint)GroupWriter.WriteGroupBytes(new DICOMObject(this.Elements.Skip <IDICOMElement>(1).Take <IDICOMElement>(6).ToList <IDICOMElement>()), new DICOMIOSettings(), "0000").Length;
}
public CStoreResponse(CStoreRequest req, Status status)
{
AffectedSOPClassUID = req.AffectedSOPClassUID;
CommandField = (ushort)C.C_STORE_RP;
MessageIDBeingResponsedTo = req.MessageID;
DataSetType = _dataSet;
AffectedSOPInstanceUID = req.AffectedSOPInstanceUID;
Status = (ushort)status;
GroupLength = (uint)GroupWriter.WriteGroupBytes(new DICOMObject(Elements.Skip(1).Take(6).ToList()),
new DICOMWriteSettings(), "0000").Length;
}
public CCancel(AbstractDIMSERequest req)
{
this.AffectedSOPClassUID = req.AffectedSOPClassUID;
this.MessageIDBeingResponsedTo = req.MessageID;
this.DataSetType = 257; // No data
this.CommandField = (ushort)C.C_CANCEL;
GroupLength = (uint)GroupWriter.WriteGroupBytes(new DICOMObject(Elements.Skip(1).Take(5).ToList()),
new DICOMWriteSettings {
TransferSyntax = TransferSyntax.IMPLICIT_VR_LITTLE_ENDIAN
}, "0000").Length;
}
/// <summary>
/// Used to generate a new Echo Response from an Echo Request
/// </summary>
/// <param name="req">the request that is being responded to</param>
/// <param name="status">the status of the echo</param>
/// <param name="presContext">the presentation context with which to write the data</param>
public CEchoResponse(CEchoRequest req, Status status)
{
AffectedSOPClassUID = req.AffectedSOPClassUID;
CommandField = (ushort)C.C_ECHO_RP;
MessageIDBeingRespondedTo = req.MessageID;
DataSetType = _dataSet;
Status = (ushort)status;
GroupLength = (uint)GroupWriter.WriteGroupBytes(new DICOMObject(Elements.Skip(1).Take(5).ToList()),
new DICOMWriteSettings {
TransferSyntax = TransferSyntax.IMPLICIT_VR_LITTLE_ENDIAN
}, "0000").Length;
}
public override void WriteToFile(string fileName, IIdentifiedResult identifiedResult)
{
CheckFormat(identifiedResult);
var groups = GetValidGroups(identifiedResult);
int totalSpectraCount = (from g in groups
select g[0].Peptides.Count).Sum();
Progress.SetRange(0, totalSpectraCount);
using (StreamWriter sw = new StreamWriter(fileName))
{
sw.WriteLine(ProteinFormat.Headers);
WritePeptideHeader(sw);
foreach (IIdentifiedProteinGroup mpg in groups)
{
GroupWriter.WriteToStream(sw, mpg);
var spectra = GetValidSpectra(mpg.GetSortedPeptides());
foreach (var p in spectra)
{
WritePeptide(sw, p);
}
Progress.Increment(mpg[0].Peptides.Count);
}
}
using (StreamWriter sw = new StreamWriter(fileName + ".summary"))
{
WriteSummary(sw, identifiedResult);
}
if (identifiedResult.Count > 0 && identifiedResult[0][0].Sequence != null)
{
string fastaFilename = fileName + ".fasta";
WriteFastaFile(fastaFilename, identifiedResult);
}
}
public void OnRequestRecieved(CFindRequest req, Association asc)
{
asc.Logger.LogInformation("<-- DIMSE" + req.GetLogString());
req.LogData(asc);
asc.LastActive = DateTime.Now;
asc.IdleClock.Restart();
asc.State = NetworkState.TRANSPORT_CONNECTION_OPEN;
var resp = new CFindResponse(req, Status.SUCCESS);
dms.RaiseDIMSERequestReceived(req, asc);
var results = RetrieveResults(req);
if (results != null)
{
foreach (var result in results)
{
resp.Data = new DICOMObject(result.Elements);
resp.Status = (ushort)Status.PENDING;
resp.GroupLength = (uint)GroupWriter.WriteGroupBytes(new DICOMObject(resp.Elements.Skip(1).ToList()),
new DICOMIOSettings(), "0000").Length;
PDataMessenger.Send(resp, asc,
asc.PresentationContexts.First(p => p.Id == req.DataPresentationContextId));
}
//Finish
resp.Status = results.Any() ? (ushort)Status.SUCCESS : (ushort)Status.FAILURE_UNABLE_TO_FIND;
resp.Data = null;
resp.GroupLength = (uint)GroupWriter.WriteGroupBytes(new DICOMObject(resp.Elements.Skip(1).ToList()),
new DICOMIOSettings(), "0000").Length;
PDataMessenger.Send(resp, asc);
}
else
{
resp.Status = (ushort)Status.FAILURE;
resp.Data = null;
resp.GroupLength = (uint)GroupWriter.WriteGroupBytes(new DICOMObject(resp.Elements.Skip(1).ToList()),
new DICOMIOSettings(), "0000").Length;
PDataMessenger.Send(resp, asc);
}
}
public void SetGroupLength()
{
var bytes = GroupWriter.WriteGroupBytes(new DICOMObject(Elements), DICOMIOSettings.Default(), "0000");
GroupLength = (uint)bytes.Length;
}
public GroupController(GroupWriter groupWriter)
{
_groupWriter = groupWriter;
}
public override void WriteToFile(string fileName, IIdentifiedResult identifiedResult)
{
CheckFormat(identifiedResult);
List <IIdentifiedSpectrum> allSpectra = identifiedResult.GetSpectra();
for (int i = 0; i < allSpectra.Count; i++)
{
allSpectra[i].Id = i.ToString();
}
string linkFilename = GetLinkFileName(fileName);
HashSet <IIdentifiedSpectrum> spectra = new HashSet <IIdentifiedSpectrum>();
using (var linkWriter = new StreamWriter(linkFilename))
{
linkWriter.WriteLine("PeptideId\tGroupId");
using (var sw = new StreamWriter(fileName))
{
sw.WriteLine(ProteinFormat.GetHeader());
var groups = GetValidGroups(identifiedResult);
foreach (IIdentifiedProteinGroup mpg in groups)
{
GroupWriter.WriteToStream(sw, mpg);
var validSpectra = GetValidSpectra(mpg.GetSortedPeptides());
foreach (var spectrum in validSpectra)
{
linkWriter.WriteLine(spectrum.Id + "\t" + mpg.Index);
}
spectra.UnionWith(validSpectra);
}
}
}
var finalSpectra = from s in spectra
orderby s.Id
select s;
string peptideFile = GetPeptideFileName(fileName);
if (!PeptideFormat.GetHeader().Contains("Id\t"))
{
PeptideFormat = new PeptideLineFormat("Id\t" + PeptideFormat.GetHeader());
}
using (var sw = new StreamWriter(peptideFile))
{
WritePeptideHeader(sw);
foreach (IIdentifiedSpectrum mph in finalSpectra)
{
WritePeptide(sw, mph);
}
}
if (identifiedResult.Count > 0 && identifiedResult[0][0].Sequence != null)
{
string fastaFilename = fileName + ".fasta";
WriteFastaFile(fastaFilename, identifiedResult);
}
}
