/// <summary>
/// Take the HL7 message string and turn it into an HL7 object using NHAPI
/// </summary>
/// <param name="hl7Message">Raw HL7 string</param>
/// <returns>HL7 Object</returns>
private static ORU_R30 ParseMessage(string hl7Message)
{
// use NHapi to parse message if message complete:
PipeParser parser = new PipeParser();
ORU_R30 hl7 = new ORU_R30();
IMessage im = parser.Parse(hl7Message);
hl7 = im as ORU_R30;
// Device may send SPM which isn't officially part of ORU_R30, so we have to add it by hand
hl7.addNonstandardSegment("SPM");
ASCIIEncoding encoder = new ASCIIEncoding();
int spmStart = hl7Message.IndexOf("SPM");
int spmEnd = hl7Message.IndexOf(encoder.GetString(new byte[] { Constants.CR }), hl7Message.IndexOf("SPM"));
parser.Parse((NHapi.Model.V25.Segment.SPM)hl7.GetStructure("SPM"), hl7Message.Substring(spmStart, spmEnd - spmStart), new EncodingCharacters('|', hl7.MSH.EncodingCharacters.Value));
// Parse notes section
if (hl7Message.Contains("NTE") && hl7Message.Contains("OBX|2") && hl7Message.IndexOf("OBX|2") > hl7Message.IndexOf("NTE"))
{
parser.Parse((NHapi.Model.V25.Segment.NTE)hl7.GetStructure("NTE"), hl7Message.Substring(hl7Message.IndexOf("NTE"), hl7Message.IndexOf("OBX|2") - hl7Message.IndexOf("NTE")), new EncodingCharacters('|', hl7.MSH.EncodingCharacters.Value));
}
return(hl7);
}
/// <summary>
/// For debugging purposes: Gets raw messages from database that couldn't be parsed (testId = null) and tries parsing them again
/// </summary>
internal static void ReparseRawMessages()
{
var messages = DB.GetRawMessagesWithoutTestId();
Console.WriteLine("Reparsing " + messages.Count + " raw messages");
foreach (var msg in messages)
{
ORU_R30 hl7 = ParseMessage(msg.Message);
if (hl7 != null)
{
if (hl7.OBR.UniversalServiceIdentifier.Identifier.Value == "MTB-RIF")
{
var testId = DB.StoreParsedMessage(hl7, msg.Message, "192.168.1.110");
if (testId.HasValue)
{
DB.UpdateRawMessageTestId(msg.RawMessageId, testId.Value);
}
Console.WriteLine(testId);
}
else
{
Console.WriteLine("Non-Tb result");
}
}
}
Console.ReadLine();
}
/// <summary>
/// Returns a simple HL7 data item with all the data needed for the later HL7 ACK message
/// </summary>
/// <param name="hl7">HL7 object</param>
/// <returns>HL7 data item</returns>
private DataForHL7Acknowledgement GetDataForHL7Acknowledgement(ORU_R30 hl7)
{
DataForHL7Acknowledgement data = new DataForHL7Acknowledgement();
data.SendingApplicationNamespaceID = hl7.MSH.SendingApplication.NamespaceID.Value.ToString();
data.SendingApplicationUniversalID = hl7.MSH.SendingApplication.UniversalID.Value.ToString();
data.SendingApplicationUniversalIDType = hl7.MSH.SendingApplication.UniversalIDType.Value.ToString();
data.MessageControlID = hl7.MSH.MessageControlID.Value.ToString();
return(data);
}
/// <summary>
/// Take the HL7 message string and turn it into an HL7 object using NHAPI
/// </summary>
/// <param name="hl7Message">Raw HL7 string</param>
/// <param name="networkStream">Reference to the network stream so we can write to it.</param>
/// <returns>HL7 Object</returns>
private ORU_R30 ParseMessage(string hl7Message, ref NetworkStream networkStream)
{
// use NHapi to parse message if message complete:
PipeParser parser = new PipeParser();
ORU_R30 hl7 = new ORU_R30();
try
{
IMessage im = parser.Parse(hl7Message);
hl7 = im as ORU_R30;
}
catch (Exception e)
{
// send NAK for this frame
networkStream.WriteByte(Constants.EOT);
Logger.Log("Error converting message: " + e.Message, LogLevel.Error, hl7Message);
return(null);
}
try
{
// Device may send SPM which isn't officially part of ORU_R30, so we have to add it by hand
hl7.addNonstandardSegment("SPM");
int spmStart = hl7Message.IndexOf("SPM");
int spmEnd = hl7Message.IndexOf(this.encoder.GetString(new byte[] { Constants.CR }), hl7Message.IndexOf("SPM"));
parser.Parse((NHapi.Model.V25.Segment.SPM)hl7.GetStructure("SPM"), hl7Message.Substring(spmStart, spmEnd - spmStart), new EncodingCharacters('|', hl7.MSH.EncodingCharacters.Value));
}
catch (Exception e)
{
// send NAK for this frame
networkStream.WriteByte(Constants.EOT);
Logger.Log("Error parsing specimen part of message: " + e.Message, LogLevel.Error, hl7Message);
}
try
{
// Parse notes section
if (hl7Message.Contains("NTE") && hl7Message.Contains("OBX|2") && hl7Message.IndexOf("OBX|2") > hl7Message.IndexOf("NTE"))
{
parser.Parse((NHapi.Model.V25.Segment.NTE)hl7.GetStructure("NTE"), hl7Message.Substring(hl7Message.IndexOf("NTE"), hl7Message.IndexOf("OBX|2") - hl7Message.IndexOf("NTE")), new EncodingCharacters('|', hl7.MSH.EncodingCharacters.Value));
}
}
catch (Exception e)
{
// send NAK for this frame
networkStream.WriteByte(Constants.EOT);
Logger.Log("Error parsing notes part of message: " + e.Message, LogLevel.Error, hl7Message);
}
return(hl7);
}
/// <summary>
/// This is a thread for the client that has connected
/// </summary>
/// <param name="client">Client (GX-machine)</param>
private void HandleClientComm(object client)
{
//TCP client that connected
TcpClient tcpClient = (TcpClient)client;
//Get reference to stream for client so we can read/write data
NetworkStream networkStream = tcpClient.GetStream();
//log that new client connected
Logger.Log(string.Format("New client connected: {0}", tcpClient.Client.RemoteEndPoint.ToString()), LogLevel.Info);
//variable to keep track of the bytes we received in the client stream
int bytesRead;
//variable for constructing the message
string hl7Message = string.Empty;
//this will store all messages we receive for later ACK:
List <DataForHL7Acknowledgement> dataForAck = new List <DataForHL7Acknowledgement>();
bool awaitingHl7Ack = false;
//keep track of connection state:
ConnectionState connState = ConnectionState.Neutral;
while (true)
{
bytesRead = 0;
string message = string.Empty;
try
{
//blocks until a client sends a message
//bytesRead = networkStream.Read(message, 0, 1024 * 1024);
if (networkStream.CanRead)
{
byte[] msg = new byte[1];//TODO: set a higher value here or some other method to prevent reading lots of null-bytes/ Research: how to get perfect buffer size?
StringBuilder myCompleteMessage = new StringBuilder();
// Incoming message may be larger than the buffer size.
do
{
bytesRead = networkStream.Read(msg, 0, msg.Length);
myCompleteMessage.AppendFormat("{0}", Encoding.ASCII.GetString(msg, 0, msg.Length));
}while (networkStream.DataAvailable);
message = myCompleteMessage.ToString();
}
else
{
Console.WriteLine("Sorry. You cannot read from this NetworkStream.");
}
}
catch
{
//a socket error has occurred
break;
}
if (bytesRead == 0)
{
//the client has disconnected from the server
break;
}
//message has successfully been received
ASCIIEncoding encoder = new ASCIIEncoding();
//Logger.Log(encoder.GetString(message), LogLevel.Info);
//if we got an ENQ, respond with ACK:
if (message[0] == Constants.ENQ)
{
Logger.Log("Sending ACK in response to ENQ...", LogLevel.Info);
networkStream.WriteByte(Constants.ACK);
networkStream.Flush();
connState = ConnectionState.Receiving;
}
//if eot of full message, confirm end of receiving and start transmission of HL7 ack
else if (connState == ConnectionState.Receiving && message[0] == Constants.EOT)
{
//send enq to go from neutral state to transmission:
Logger.Log("Sending ENQ...", LogLevel.Info);
networkStream.WriteByte(Constants.ENQ);
networkStream.Flush();
connState = ConnectionState.Sending;
}
//did we get an eot in response to our hl7-eot?
else if (connState == ConnectionState.Sending && message[0] == Constants.EOT)
{
//do nothing (we're back in neutral state)
Logger.Log("Received EOT from GX", LogLevel.Info);
//set vars back to neutral
connState = ConnectionState.Neutral;
}
//did we receive an ack in response to our enq and do we have messages to send acks for?
else if (connState == ConnectionState.Sending && message[0] == Constants.ACK)
{
//GX acknowledged last message -> remove from list:
if (dataForAck.Any() && awaitingHl7Ack)
{
var data = dataForAck.First();
dataForAck.Remove(data);
}
if (!dataForAck.Any())
{
//send eot
Logger.Log("Sending EOT in response to ACK for HL7-ACK...", LogLevel.Info);
networkStream.WriteByte(Constants.EOT);
networkStream.Flush();
awaitingHl7Ack = false;
connState = ConnectionState.Neutral;
}
else
{
//get first data in list to acknowledge
var data = dataForAck.First();
awaitingHl7Ack = true;
PipeParser parser = new PipeParser();
//also need to send ack of complete message:
Logger.Log("Sending ack of entire message", LogLevel.Info);
NHapi.Model.V25.Message.ACK ack = new NHapi.Model.V25.Message.ACK();
//MSH-part of message acknowledgement:
ack.MSH.SendingApplication.NamespaceID.Value = "LIS";//TODO: set to "bigpicture"
ack.MSH.ReceivingApplication.NamespaceID.Value = data.SendingApplicationNamespaceID;
ack.MSH.ReceivingApplication.UniversalID.Value = data.SendingApplicationUniversalID;
ack.MSH.ReceivingApplication.UniversalIDType.Value = data.SendingApplicationUniversalIDType;
//ack.MSH.DateTimeOfMessage.Time.Set(DateTime.Now, "yyyyMMddHHmmss");
string guid = Guid.NewGuid().ToString();
ack.MSH.MessageControlID.Value = data.MessageControlID;
ack.MSH.ProcessingID.ProcessingID.Value = "P";
ack.MSH.AcceptAcknowledgmentType.Value = "NE";
ack.MSH.ApplicationAcknowledgmentType.Value = "NE";
//MSA-part
ack.MSA.AcknowledgmentCode.Value = "CA";
ack.MSA.MessageControlID.Value = data.MessageControlID;
//ack.MSA.TextMessage.Value = "Test";
PipeParser parserResponse = new PipeParser();
string hl7Response = parserResponse.Encode(ack);
//wrapping message in hl7 llp start and end chars?
//hl7Response = encoder.GetString(new byte[] { PIPE }) + hl7Response + encoder.GetString(new byte[] { SEPARATOR }) + encoder.GetString(new byte[] { CR });
//get checksum for sending:
byte[] hl7ResponseForChecksum = encoder.GetBytes("1" + hl7Response + encoder.GetString(new byte[1] {
Constants.ETX
}));
int checksum = 0;
for (int i = 0; i < hl7ResponseForChecksum.Length; i++)
{
checksum += hl7ResponseForChecksum[i];
}
//convert checksum to hex so we can get eight least significant bits:
string checksumHex = checksum.ToString("X");
//wrapping message in astm control chars
// "0" = Frame Number
hl7Response = encoder.GetString(new byte[1] {
Constants.STX
}) + "1" + hl7Response + encoder.GetString(new byte[1] {
Constants.ETX
}) + checksumHex.Substring(checksumHex.Length - 2, 1) + checksumHex.Substring(checksumHex.Length - 1, 1) + encoder.GetString(new byte[1] {
Constants.CR
}) + encoder.GetString(new byte[1] {
Constants.LF
});
//hl7Response = encoder.GetString(hl7Response );
byte[] response = encoder.GetBytes(hl7Response);
networkStream.Write(response, 0, response.Length);
networkStream.Flush();
}
}
else if (connState == ConnectionState.Receiving && message[0] == Constants.STX && (message.Any(m => m == Constants.ETX) || message.Any(m => m == Constants.ETB))) //we received a message frame
{
//TODO: verify that this is the frame number we expected, return nak if not
int frameNumber = Convert.ToInt32(message[1]) - 48;
bool isEndFrame = false;
Logger.Log(string.Format("Received {0}frame (Nr. {1})", isEndFrame ? "end" : "", frameNumber), LogLevel.Info);
//get text of message. It's the 2nd byte up until the ETB or ETX control character:
if (message.Any(m => m == Constants.ETX))
{
isEndFrame = true;
}
int indexOfEndMessage = message.IndexOf(isEndFrame ? Encoding.ASCII.GetString(new byte[] { Constants.ETX }) : Encoding.ASCII.GetString(new byte[] { Constants.ETB }));// Array.IndexOf(message, isEndFrame ? Constants.ETX : Constants.ETB);
//string encodedMessage = encoder.GetString(message, 2, indexOfEndMessage);
//TODO: verify checksum, send NAK if not correct
int cs1 = message[indexOfEndMessage + 1];
int cs2 = message[indexOfEndMessage + 2];
int checksum = 0;
for (int i = 1; i < indexOfEndMessage + 1; i++)
{
checksum += message[i];
}
//check checksum; send nak if not correct:
if (!checksum.ToString("X").EndsWith(message[indexOfEndMessage + 1].ToString() + message[indexOfEndMessage + 2].ToString()))
{
//send NAK for this frame
networkStream.WriteByte(Constants.NAK);
networkStream.Flush();
Logger.Log("Sent NAK because checksum incorrect", LogLevel.Warning);
}
else
{
hl7Message += message.Substring(2, indexOfEndMessage - 2);
//use nhapi to parse message if message complete:
if (isEndFrame)
{
PipeParser parser = new PipeParser();
ORU_R30 hl7 = new ORU_R30();
try
{
IMessage im = parser.Parse(hl7Message);
hl7 = im as ORU_R30;
}
catch (Exception e)
{
//send NAK for this frame
networkStream.WriteByte(Constants.EOT);
networkStream.Flush();
Logger.Log("Error converting message: " + e.Message, LogLevel.Error, hl7Message);
return;
}
try
{
//genexpert sends spm which isn't officially part of ORU_R30:
hl7.addNonstandardSegment("SPM");
//TODO: validate
parser.Parse((NHapi.Model.V25.Segment.SPM)hl7.GetStructure("SPM"), hl7Message.Substring(hl7Message.IndexOf("SPM"), 40), new EncodingCharacters('|', hl7.MSH.EncodingCharacters.Value));
}
catch (Exception e)
{
//send NAK for this frame
networkStream.WriteByte(Constants.EOT);
networkStream.Flush();
Logger.Log("Error parsing specimen part of message: " + e.Message, LogLevel.Error, hl7Message);
return;
}
//get all values that are of interest to us:
if (hl7 != null)
{
//make sure it's a Tb-result:
if (hl7.OBR.UniversalServiceIdentifier.Identifier.Value == "MTB-RIF")
{
//log message:
//Logger.Log(string.Format("HL7 Message: {0}", hl7Message), LogLevel.Info);
//try to store in db:
try
{
//store in database
using (BigPictureEntities bpe = new BigPictureEntities())
{
//first, see if we know this machine already and create it if we don't:
string instrumentSerial = ((NHapi.Model.V25.Datatype.EI)hl7.GetOBSERVATION(0).OBX.GetField(18).GetValue(4)).EntityIdentifier.Value;
device device = bpe.devices.FirstOrDefault(d => d.Serial == instrumentSerial);
//create device if we don't have it yet
if (device == null)
{
device = new device();
device.Serial = instrumentSerial;
device.InsertedBy = device.UpdatedBy = "BigPicture Listener";
device.InsertedOn = device.InsertedOn = DateTime.Now;
bpe.devices.Add(device);
}
//Add test to database if it doesn't exist already (=re-upload)
string cartridgeSerial = ((NHapi.Model.V25.Datatype.EI)hl7.GetOBSERVATION(0).OBX.GetField(18).GetValue(2)).EntityIdentifier.Value;
test test = bpe.tests.FirstOrDefault(t => t.CartridgeSerial == cartridgeSerial);
//create test if not already exists
if (test == null)
{
test = new test();
test.InsertedOn = DateTime.Now;
test.InsertedBy = "BigPicture Listener";
test.CartridgeSerial = cartridgeSerial;
bpe.tests.Add(test);
}
//fill test with new data we got:
test.AssayHostTestCode = hl7.OBR.UniversalServiceIdentifier.Identifier.Value;
test.AssayName = ((NHapi.Model.V25.Datatype.CE)hl7.GetOBSERVATION(0).OBX.GetField(3).GetValue(0)).Identifier.ExtraComponents.getComponent(1).Data.ToString();
test.AssayVersion = ((NHapi.Model.V25.Datatype.CE)hl7.GetOBSERVATION(0).OBX.GetField(3).GetValue(0)).Identifier.ExtraComponents.getComponent(2).Data.ToString();
test.CartridgeExpirationDate = DateTime.ParseExact(((NHapi.Model.V25.Datatype.EI)hl7.GetOBSERVATION(0).OBX.GetField(18).GetValue(0)).EntityIdentifier.Value.ToString(), "yyyyMMdd", CultureInfo.CurrentCulture);
test.ComputerName = ((NHapi.Model.V25.Datatype.EI)hl7.GetOBSERVATION(0).OBX.GetField(18).GetValue(5)).EntityIdentifier.Value.ToString();
test.SenderUser = ((NHapi.Model.V25.Datatype.XCN)hl7.GetOBSERVATION(0).OBX.GetField(16)[0]).FamilyName.Surname.ToString();
test.SenderVersion = hl7.MSH.SendingApplication.Components[2].ToString();
test.deployment = device.deployment;
test.MessageSentOn = hl7.MSH.DateTimeOfMessage.Time.GetAsDate();
test.ModuleSerial = ((NHapi.Model.V25.Datatype.EI)hl7.GetOBSERVATION(0).OBX.GetField(18).GetValue(3)).EntityIdentifier.Value.ToString();
//test.Notes = ;
//test.PatientId = ;
test.ReagentLotId = ((NHapi.Model.V25.Datatype.EI)hl7.GetOBSERVATION(0).OBX.GetField(18).GetValue(1)).EntityIdentifier.Value.ToString();
test.ResultText = ((NHapi.Base.Model.Varies)hl7.GetOBSERVATION(0).OBX.GetField(5).GetValue(0)).Data.ToString() + "|" + ((NHapi.Base.Model.Varies)hl7.GetOBSERVATION(19).OBX.GetField(5).GetValue(0)).Data.ToString() + "|";
test.SampleId = ((NHapi.Model.V25.Datatype.EI)(((NHapi.Model.V25.Datatype.EIP)((NHapi.Model.V25.Segment.SPM)hl7.GetStructure("SPM")).SpecimenID)[0])).EntityIdentifier.Value;
test.SystemName = hl7.MSH.SendingApplication.Components[0].ToString();
//test.TestEndedOn = ;
test.TestStartedOn = hl7.ORC.DateTimeOfTransaction.Time.GetAsDate();
test.UpdatedBy = "BigPicture Listener";
test.UpdatedOn = DateTime.Now;
//normalize test results. TODO: handle if not exits yet
//TB-result:
//TODO: Throw godo error/log when not present in db:
string resultTestCodeTb = ((NHapi.Model.V25.Datatype.CE)hl7.GetOBSERVATION(0).OBX.GetField(3).GetValue(0)).Identifier.ExtraComponents.getComponent(0).Data.ToString().Replace("4", "");
int resultTestCodeIdTb = bpe.resulttestcodes.First(r => r.ResultTestCode1 == resultTestCodeTb).ResultTestCodeId;
testresult testResultTb = new testresult();
testResultTb.InsertedBy = testResultTb.UpdatedBy = "BigPicture Listener";
testResultTb.InsertedOn = testResultTb.UpdatedOn = DateTime.Now;
testResultTb.Result = ((NHapi.Base.Model.Varies)hl7.GetOBSERVATION(0).OBX.GetField(5).GetValue(0)).Data == null || ((NHapi.Base.Model.Varies)hl7.GetOBSERVATION(0).OBX.GetField(5).GetValue(0)).Data.ToString() == null ? "" : ((NHapi.Base.Model.Varies)hl7.GetOBSERVATION(0).OBX.GetField(5).GetValue(0)).Data.ToString();
testResultTb.TestId = test.TestId;
testResultTb.ResultTestCodeId = resultTestCodeIdTb;
bpe.testresults.Add(testResultTb);
//Rif-resistance-result:
//TODO: Throw godo error/log when not present in db:
string resultTestCodeRif = ((NHapi.Model.V25.Datatype.CE)hl7.GetOBSERVATION(19).OBX.GetField(3).GetValue(0)).Identifier.ExtraComponents.getComponent(0).Data.ToString();
int resultTestCodeIdRif = bpe.resulttestcodes.First(r => r.ResultTestCode1 == resultTestCodeRif).ResultTestCodeId;
testresult testResultRif = new testresult();
testResultRif.InsertedBy = testResultRif.UpdatedBy = "BigPicture Listener";
testResultRif.InsertedOn = testResultRif.UpdatedOn = DateTime.Now;
testResultRif.Result = ((NHapi.Base.Model.Varies)hl7.GetOBSERVATION(19).OBX.GetField(5).GetValue(0)).Data == null || ((NHapi.Base.Model.Varies)hl7.GetOBSERVATION(19).OBX.GetField(5).GetValue(0)).Data.ToString() == null ? "" : ((NHapi.Base.Model.Varies)hl7.GetOBSERVATION(19).OBX.GetField(5).GetValue(0)).Data.ToString();
testResultRif.TestId = test.TestId;
testResultRif.ResultTestCodeId = resultTestCodeIdRif;
bpe.testresults.Add(testResultRif);
//finally, save everything to db:
bpe.SaveChanges();
}
}
catch (Exception e)
{
Logger.Log("Store in DB failed: " + e.Message, LogLevel.Error, hl7Message);
}
}
}
//add to list of received messages for later HL7 ACK:
DataForHL7Acknowledgement data = new DataForHL7Acknowledgement();
data.SendingApplicationNamespaceID = hl7.MSH.SendingApplication.NamespaceID.Value.ToString();
data.SendingApplicationUniversalID = hl7.MSH.SendingApplication.UniversalID.Value.ToString();
data.SendingApplicationUniversalIDType = hl7.MSH.SendingApplication.UniversalIDType.Value.ToString();
data.MessageControlID = hl7.MSH.MessageControlID.Value.ToString();
dataForAck.Add(data);
//empty message-var for the next message to be sent
hl7Message = string.Empty;
//for some reason, our system is too quick for GX. need a delay here (really!)
//TODO: Double-check that this is really necessary
//Thread.Sleep(1000);
//send ACK for this frame
networkStream.WriteByte(Constants.ACK);
networkStream.Flush();
Logger.Log("Sent ACK of endframe", LogLevel.Info);
}
else
{
//send ACK for this frame
networkStream.WriteByte(Constants.ACK);
networkStream.Flush();
Logger.Log("Sent ACK of regular frame", LogLevel.Info);
}
}
}
else
{
//send ACK in any other case
networkStream.WriteByte(Constants.ACK);
networkStream.Flush();
Logger.Log("Sent ACK for random frame", LogLevel.Info);
}
}
tcpClient.Close();
}
/// <summary>
/// Store the parsed HL7 object in the DB
/// </summary>
/// <param name="hl7">The HL7 object</param>
/// <param name="hl7Message">The raw HL7 message</param>
/// <param name="senderIp">IP that message was sent from.</param>
/// <returns>ID of test that was inserted into DB. Null if insert unsuccessful</returns>
internal static int?StoreParsedMessage(ORU_R30 hl7, string hl7Message, string senderIp)
{
// try to store in db:
try
{
// testId we'll return:
int?testId = null;
// store in database
using (GxAlertEntities bpe = new GxAlertEntities())
{
string deviceSerial = ((NHapi.Model.V25.Datatype.EI)hl7.GetOBSERVATION(0).OBX.GetField(18).GetValue(5)).EntityIdentifier.Value;
string hostId = hl7.MSH.ReceivingApplication.NamespaceID.Value.ToString();
// if we don't have a deployment for this device and hostId yet, create one:
deployment deployment = bpe.deployments.FirstOrDefault(l => l.HostId == hostId && l.devicedeploymenthistories.Any(h => h.device.Serial == deviceSerial));
if (deployment == null)
{
deployment = new deployment();
deployment.HostId = hostId;
deployment.Approved = false;
deployment.Insertedby = deployment.Updatedby = ConfigurationManager.AppSettings["appName"];
deployment.InsertedOn = deployment.UpdatedOn = DateTime.Now;
bpe.deployments.Add(deployment);
// notify admins of new machine:
new Notifications().SendNewDeploymentNotification(hostId, deviceSerial, senderIp);
}
// create device if we don't have it yet
device device = bpe.devices.FirstOrDefault(d => d.Serial == deviceSerial);
if (device == null)
{
//get device type id for GeneXpert
int deviceTypeId = bpe.devicetypes.First(d => d.Name.Contains("GeneXpert")).DeviceTypeId;
device = new device();
device.DeviceTypeId = deviceTypeId;
device.Serial = deviceSerial;
device.InsertedBy = device.UpdatedBy = ConfigurationManager.AppSettings["appName"];
device.InsertedOn = device.UpdatedOn = DateTime.Now;
bpe.devices.Add(device);
}
// keep device deployment history:
if (device.deployment != deployment)
{
device.deployment = deployment;
devicedeploymenthistory history = new devicedeploymenthistory();
history.device = device;
history.deployment = deployment;
history.InsertedBy = ConfigurationManager.AppSettings["appName"];
history.InsertedOn = DateTime.Now;
bpe.devicedeploymenthistories.Add(history);
}
// Add test to database if it doesn't exist already (=re-upload)
string cartridgeSerial = ((NHapi.Model.V25.Datatype.EI)hl7.GetOBSERVATION(0).OBX.GetField(18).GetValue(2)).EntityIdentifier.Value;
test test = bpe.tests.FirstOrDefault(t => t.CartridgeSerial == cartridgeSerial);
// create test if not already exists
if (test == null)
{
test = new test();
test.TestTypeId = 4;//GeneXpert TB/RIF Result
test.InsertedOn = DateTime.Now;
test.InsertedBy = ConfigurationManager.AppSettings["appName"];
test.CartridgeSerial = cartridgeSerial;
bpe.tests.Add(test);
}
// fill test with new data we got:
test.AssayHostTestCode = hl7.OBR.UniversalServiceIdentifier.Identifier.Value;
test.AssayName = ((NHapi.Model.V25.Datatype.CE)hl7.GetOBSERVATION(0).OBX.GetField(3).GetValue(0)).Identifier.ExtraComponents.getComponent(1).Data.ToString();
test.AssayVersion = ((NHapi.Model.V25.Datatype.CE)hl7.GetOBSERVATION(0).OBX.GetField(3).GetValue(0)).Identifier.ExtraComponents.getComponent(2).Data.ToString();
test.CartridgeExpirationDate = ((NHapi.Model.V25.Datatype.EI)hl7.GetOBSERVATION(0).OBX.GetField(18).GetValue(0)).EntityIdentifier.Value != null?DateTime.ParseExact(((NHapi.Model.V25.Datatype.EI)hl7.GetOBSERVATION(0).OBX.GetField(18).GetValue(0)).EntityIdentifier.Value.ToString(), "yyyyMMdd", CultureInfo.CurrentCulture) : new DateTime?();
test.ComputerName = ((NHapi.Model.V25.Datatype.EI)hl7.GetOBSERVATION(0).OBX.GetField(18).GetValue(5)).EntityIdentifier.Value.ToString();
test.SenderUser = ((NHapi.Model.V25.Datatype.XCN)hl7.GetOBSERVATION(0).OBX.GetField(16)[0]).FamilyName.Surname.ToString();
test.SenderVersion = hl7.MSH.SendingApplication.Components[2].ToString();
test.SenderIp = senderIp;
test.deployment = device.deployment;
test.MessageSentOn = hl7.MSH.DateTimeOfMessage.Time.GetAsDate();
test.ModuleSerial = ((NHapi.Model.V25.Datatype.EI)hl7.GetOBSERVATION(0).OBX.GetField(18).GetValue(3)).EntityIdentifier.Value.ToString();
test.InstrumentSerial = ((NHapi.Model.V25.Datatype.EI)hl7.GetOBSERVATION(0).OBX.GetField(18).GetValue(4)).EntityIdentifier.Value;
var notes1 = ((NHapi.Model.V25.Datatype.FT)hl7.GetNTE(0).GetComment(0)).ExtraComponents.getComponent(1).Data;
var notes2 = ((NHapi.Model.V25.Datatype.FT)hl7.GetNTE(0).GetComment(0)).ExtraComponents.getComponent(2).Data;
test.Notes = ((notes1 != null ? notes1.ToString() + " " : string.Empty) + (notes2 != null ? notes2.ToString() : string.Empty)).Trim();
test.Notes = string.IsNullOrWhiteSpace(test.Notes) ? null : test.Notes;
test.PatientId = hl7.PID.GetPatientIdentifierList(0).IDNumber.Value;
test.ReagentLotId = ((NHapi.Model.V25.Datatype.EI)hl7.GetOBSERVATION(0).OBX.GetField(18).GetValue(1)).EntityIdentifier.Value.ToString();
test.ResultText = ((NHapi.Base.Model.Varies)hl7.GetOBSERVATION(0).OBX.GetField(5).GetValue(0)).Data.ToString() + "|" + ((NHapi.Base.Model.Varies)hl7.GetOBSERVATION(19).OBX.GetField(5).GetValue(0)).Data.ToString() + "|";
test.SampleId = ((NHapi.Model.V25.Datatype.EI)((NHapi.Model.V25.Datatype.EIP)((NHapi.Model.V25.Segment.SPM)hl7.GetStructure("SPM")).SpecimenID)[0]).EntityIdentifier.Value;
test.SystemName = hl7.MSH.SendingApplication.Components[0].ToString();
test.TestStartedOn = hl7.GetTIMING_QTY(0).TQ1.StartDateTime.Time.GetAsDate();
// for some reason, we got a handful of results (we have over 10000 now) that have an invalid end date.
// we'll just use the start date for those
try
{
test.TestEndedOn = hl7.GetTIMING_QTY(0).TQ1.EndDateTime.Time.GetAsDate();
}
catch
{
test.TestEndedOn = test.TestStartedOn;
}
test.UpdatedBy = ConfigurationManager.AppSettings["appName"];
test.UpdatedOn = DateTime.Now;
// normalize test results.
// TB-result:
string resultTestCodeTb = ((NHapi.Model.V25.Datatype.CE)hl7.GetOBSERVATION(0).OBX.GetField(3).GetValue(0)).Identifier.ExtraComponents.getComponent(0).Data.ToString();
int resultTestCodeIdTb = bpe.resulttestcodes.First(r => r.ResultTestCode1 == resultTestCodeTb).ResultTestCodeId;
testresult resultTb = bpe.testresults.FirstOrDefault(t => t.TestId == test.TestId && t.ResultTestCodeId == resultTestCodeIdTb);
if (resultTb == null)
{
resultTb = new testresult();
resultTb.InsertedBy = ConfigurationManager.AppSettings["appName"];
resultTb.InsertedOn = DateTime.Now;
resultTb.TestId = test.TestId;
resultTb.ResultTestCodeId = resultTestCodeIdTb;
bpe.testresults.Add(resultTb);
}
resultTb.Result = ((NHapi.Base.Model.Varies)hl7.GetOBSERVATION(0).OBX.GetField(5).GetValue(0)).Data == null || ((NHapi.Base.Model.Varies)hl7.GetOBSERVATION(0).OBX.GetField(5).GetValue(0)).Data.ToString() == null ? string.Empty : ((NHapi.Base.Model.Varies)hl7.GetOBSERVATION(0).OBX.GetField(5).GetValue(0)).Data.ToString();
resultTb.UpdatedBy = ConfigurationManager.AppSettings["appName"];
resultTb.UpdatedOn = DateTime.Now;
// Rif-resistance-result:
string resultTestCodeRif = ((NHapi.Model.V25.Datatype.CE)hl7.GetOBSERVATION(19).OBX.GetField(3).GetValue(0)).Identifier.ExtraComponents.getComponent(0).Data.ToString();
int resultTestCodeIdRif = bpe.resulttestcodes.First(r => r.ResultTestCode1 == resultTestCodeRif).ResultTestCodeId;
testresult resultRif = bpe.testresults.FirstOrDefault(t => t.TestId == test.TestId && t.ResultTestCodeId == resultTestCodeIdRif);
if (resultRif == null)
{
resultRif = new testresult();
resultRif.InsertedBy = ConfigurationManager.AppSettings["appName"];
resultRif.InsertedOn = DateTime.Now;
resultRif.TestId = test.TestId;
resultRif.ResultTestCodeId = resultTestCodeIdRif;
bpe.testresults.Add(resultRif);
}
resultRif.Result = ((NHapi.Base.Model.Varies)hl7.GetOBSERVATION(19).OBX.GetField(5).GetValue(0)).Data == null || ((NHapi.Base.Model.Varies)hl7.GetOBSERVATION(19).OBX.GetField(5).GetValue(0)).Data.ToString() == null ? string.Empty : ((NHapi.Base.Model.Varies)hl7.GetOBSERVATION(19).OBX.GetField(5).GetValue(0)).Data.ToString();
resultRif.UpdatedBy = ConfigurationManager.AppSettings["appName"];
resultRif.UpdatedOn = DateTime.Now;
// finally, save everything to db:
bpe.SaveChanges();
testId = test.TestId;
}
return(testId);
}
catch (Exception e)
{
Logger.Log("Store in DB failed: " + e.Message, LogLevel.Error, hl7Message);
return(null);
}
}
/// <summary>
/// This is a thread for the client that has connected
/// </summary>
/// <param name="client">Client (medical device)</param>
private void HandleClientComm(object client)
{
#region Local Variables
// TCP client that connected
TcpClient tcpClient = (TcpClient)client;
// Get reference to stream for client so we can read/write data
NetworkStream networkStream = tcpClient.GetStream();
// log that new client connected
Logger.Log(string.Format("New client connected: {0}", tcpClient.Client.RemoteEndPoint.ToString()), LogLevel.Info);
// variable to keep track of the bytes we received in the client stream
int bytesRead;
// variable for constructing the message
string hl7Message = string.Empty;
// this will store all messages we receive for later ACK:
List <DataForHL7Acknowledgement> dataForAck = new List <DataForHL7Acknowledgement>();
// keep track of whether we're awaiting acknowledgement of our HL7-ACK
bool awaitingHl7Ack = false;
// keep track of connection state:
ConnectionState connState = ConnectionState.Neutral;
this.sendNotificationsDelegate = new SendNotificationsDelegate(new Notifications().SendNotifications);
#endregion
while (true)
{
#region Lower-level stuff (dealing with streams and receiving it as a message)
bytesRead = 0;
string message = string.Empty;
try
{
if (networkStream.CanRead)
{
byte[] messagePart = new byte[1024];
string completeMessage = string.Empty;
string lf = this.encoder.GetString(new byte[] { Constants.LF });
// Incoming message may be larger than the buffer size; keep reading until complete
do
{
bytesRead = networkStream.Read(messagePart, 0, messagePart.Length);
completeMessage = string.Concat(completeMessage, this.encoder.GetString(messagePart, 0, bytesRead));
}while (!completeMessage.EndsWith(lf) &&
completeMessage.Length != 1 &&
bytesRead != 0);
/* Read from the stream until we received everything.
* If we're reading an HL7 message, that means that the message ends with a line feed.
* If it's just the low-level ASTM stuff, the length will be one
* That way we can avoid the nasty workaround of putting a 10ms sleep in the read-loop*/
message = completeMessage;
}
else
{
Logger.Log("Cannot read from this NetworkStream.", LogLevel.Error);
}
}
catch (Exception e)
{
// a socket error has occurred
Logger.Log("A socket error has occurred: " + e.Message, LogLevel.Error);
break;
}
// did client disconnect?
if (bytesRead == 0)
{
Logger.Log(string.Format("Client disconnected (IP: {0})", tcpClient.Client.RemoteEndPoint.ToString()), LogLevel.Info);
tcpClient.Close();
Thread.CurrentThread.Abort();
break;
}
#endregion
// finally, handle the message itself:
if (message[0] == Constants.ENQ)
{
Logger.Log("Sending ACK in response to ENQ...", LogLevel.Info);
networkStream.WriteByte(Constants.ACK);
connState = ConnectionState.Receiving;
}
else if (connState == ConnectionState.Receiving && message[0] == Constants.EOT)
{
// if EOT of full message, confirm end of receiving and start transmission of HL7 ACK
Logger.Log("Sending ENQ...", LogLevel.Info);
networkStream.WriteByte(Constants.ENQ);
connState = ConnectionState.Sending;
}
else if (connState == ConnectionState.Sending && message[0] == Constants.EOT)
{
// We got an EOT in response to our hl7-EOT? - do nothing (we're back in neutral state)
Logger.Log("Received EOT from Device", LogLevel.Info);
connState = ConnectionState.Neutral;
}
else if (connState == ConnectionState.Sending && message[0] == Constants.ACK)
{
// Device acknowledged last message -> remove from list:
if (dataForAck.Any() && awaitingHl7Ack)
{
dataForAck.Remove(dataForAck.First());
}
// if no more messages to acknowledge, send EOT
if (!dataForAck.Any())
{
Logger.Log("Sending EOT in response to ACK for HL7-ACK...", LogLevel.Info);
networkStream.WriteByte(Constants.EOT);
awaitingHl7Ack = false;
connState = ConnectionState.Neutral;
}
else
{
Logger.Log("Sending ACK of entire message...", LogLevel.Info);
awaitingHl7Ack = true;
// build ACK-response from message data
string hl7Response = this.ConstructHL7Acknowledgement(dataForAck.First());
// get checksum in hexadecimal for sending:
string checksumHex = new Util().GetChecksum(this.encoder.GetBytes("1" + hl7Response + this.encoder.GetString(new byte[1] {
Constants.ETX
})), 0).ToString("X");
// wrapping message in astm control chars ("1" = Frame Number)
hl7Response = this.encoder.GetString(new byte[1] {
Constants.STX
}) + "1" + hl7Response +
this.encoder.GetString(new byte[1] {
Constants.ETX
}) +
checksumHex.Substring(checksumHex.Length - 2, 1) + checksumHex.Substring(checksumHex.Length - 1, 1) +
this.encoder.GetString(new byte[1] {
Constants.CR
}) + this.encoder.GetString(new byte[1] {
Constants.LF
});
// finally, convert message to byte array and write to stream
byte[] response = this.encoder.GetBytes(hl7Response);
networkStream.Write(response, 0, response.Length);
}
}
else if (connState == ConnectionState.Receiving &&
message[0] == Constants.STX &&
(message.Any(m => m == Constants.ETX) || message.Any(m => m == Constants.ETB)))
{
int frameNumber = Convert.ToInt32(message[1]) - 48; // TODO: verify that this is the frame number we expected, return NAK if not
bool isEndFrame = message.Any(m => m == Constants.ETX);
Logger.Log(string.Format("Received {0}frame (Nr. {1})", isEndFrame ? "end" : string.Empty, frameNumber), LogLevel.Info);
// get end index of actual message so we can calculate checksum
int indexOfEndMessage = message.IndexOf(isEndFrame ? Encoding.ASCII.GetString(new byte[] { Constants.ETX }) : Encoding.ASCII.GetString(new byte[] { Constants.ETB })); // Array.IndexOf(message, isEndFrame ? Constants.ETX : Constants.ETB);
int checksum = new Util().GetChecksum(message, 1, indexOfEndMessage + 1);
// check checksum; send NAK if not correct (the two bytes following the end of the message should equal the 2 least significant chars in the checksum in hex)
if (!checksum.ToString("X").EndsWith(message[indexOfEndMessage + 1].ToString() + message[indexOfEndMessage + 2].ToString()))
{
networkStream.WriteByte(Constants.NAK);
Logger.Log("Sent NAK because checksum incorrect", LogLevel.Warning);
}
else
{
hl7Message += message.Substring(2, indexOfEndMessage - 2);
// if we're dealing with an end frame, the message is complete -> parse and store in db
if (isEndFrame)
{
int? testId = null;
ORU_R30 hl7 = this.ParseMessage(hl7Message, ref networkStream);
if (hl7 != null)
{
if (hl7.OBR.UniversalServiceIdentifier.Identifier.Value == "MTB-RIF")
{
testId = DB.StoreParsedMessage(hl7, hl7Message, tcpClient.Client.RemoteEndPoint.ToString());
this.sendNotificationsDelegate.BeginInvoke(testId, null, null);
}
else
{
Logger.Log(string.Format("Received non-TB result. Assay Test Code: {0}", hl7.OBR.UniversalServiceIdentifier.Identifier.Value), LogLevel.Error);
}
// add to list of received messages for later HL7 ACK:
dataForAck.Add(this.GetDataForHL7Acknowledgement(hl7));
}
/* Not sure if we even have to handle this... should be enough to simply not send ACK
* else if (hl7Message.Contains("QCN"))
* {
* // did we receive a request for test orders?
* PipeParser parser = new PipeParser();
* IMessage im = parser.Parse(hl7Message);
* QCN_J01 qcn = im as QCN_J01;
*
* if (qcn != null)
* {
* // send NAK for this frame
* networkStream.WriteByte(Constants.NAK);
* Logger.Log("Sent NAK of QCN message", LogLevel.Warning);
* }
* }*/
DB.StoreRawMessage(hl7Message, testId);
// empty message-var for the next message to be sent
hl7Message = string.Empty;
// send ACK for this frame
networkStream.WriteByte(Constants.ACK);
Logger.Log("Sent ACK of endframe", LogLevel.Info);
}
else
{
// send ACK for this frame
networkStream.WriteByte(Constants.ACK);
Logger.Log("Sent ACK of regular frame", LogLevel.Info);
}
}
}
else
{
// send ACK in any other case
networkStream.WriteByte(Constants.ACK);
Logger.Log(string.Format("Sent ACK for random frame ({0})", message[0]), LogLevel.Info, message);
}
}
tcpClient.Close();
}
