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Signed-off-by: Buddhika Ariyaratne <[email protected]>
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@buddhika75
buddhika75 committed Sep 3, 2024
1 parent 6e9f45f commit 2628bfb
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Showing 3 changed files with 282 additions and 16 deletions.
18 changes: 13 additions & 5 deletions pom.xml
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Expand Up @@ -34,12 +34,20 @@
<dependency>
<groupId>com.github.hmislk</groupId>
<artifactId>lims-middleware-libraries</artifactId>
<version>1.1.3</version>
<version>1.1.4</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi</groupId>
<artifactId>hapi-base</artifactId>
<version>2.3</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>ca.uhn.hapi</groupId>
<artifactId>hapi-structures-v25</artifactId>
<version>2.3</version>
<type>jar</type>
</dependency>




</dependencies>

<repositories>
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2 changes: 1 addition & 1 deletion src/main/java/org/carecode/mw/lims/mw/MaglumiX3/MaglumiX3.java
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Expand Up @@ -33,7 +33,7 @@ public static void main(String[] args) {

pdb.setPatientRecord(patientRecord);

ResultsRecord r1 = new ResultsRecord(1, "GLU", 112.0, "mg/dl", "202408172147", "Indigo", "0010");
ResultsRecord r1 = new ResultsRecord(1, "GLU", "112.0", "mg/dl", "202408172147", "Indigo", "0010");
pdb.getResultsRecords().add(r1);

QueryRecord qr = new QueryRecord(0, "1101", "1101", "");
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278 changes: 268 additions & 10 deletions src/main/java/org/carecode/mw/lims/mw/MaglumiX3/MaglumiX3Server.java
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@@ -1,5 +1,7 @@
package org.carecode.mw.lims.mw.MaglumiX3;

import ca.uhn.hl7v2.DefaultHapiContext;
import ca.uhn.hl7v2.HapiContext;
import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.IOException;
Expand All @@ -19,6 +21,17 @@
import org.carecode.lims.libraries.PatientRecord;
import org.carecode.lims.libraries.QueryRecord;
import org.carecode.lims.libraries.ResultsRecord;
import ca.uhn.hl7v2.model.Message;
import ca.uhn.hl7v2.model.Segment;
import ca.uhn.hl7v2.parser.Parser;
import ca.uhn.hl7v2.parser.PipeParser;
import ca.uhn.hl7v2.model.v25.message.ORU_R01;
import ca.uhn.hl7v2.model.v25.segment.MSH;
import ca.uhn.hl7v2.model.v25.segment.PID;
import ca.uhn.hl7v2.model.v25.segment.OBR;
import ca.uhn.hl7v2.model.v25.segment.OBX;
import java.util.ArrayList;
import java.util.logging.Level;

public class MaglumiX3Server {

Expand Down Expand Up @@ -100,7 +113,7 @@ private void handleClient(Socket clientSocket) {
case CARRIAGE_RETURN: // Handle CR as potential end of message
String message = messageBuilder.toString();
System.out.println("Complete HL7 message received: " + message);
processHL7Message(message);
processHL7Messages(message);
out.write(ACKNOWLEDGEMENT);
out.flush();
System.out.println("Sent ACK after message processing");
Expand Down Expand Up @@ -131,10 +144,261 @@ private void handleClient(Socket clientSocket) {
}
}

// Process the individual HL7 messages received
public void processHL7Messages(String combinedMessages) {
String[] individualMessages = splitHL7Messages(combinedMessages);
for (String message : individualMessages) {
if (!message.trim().isEmpty()) {
processIndividualHL7Message(message);
}
}
}

// Split the combined string of HL7 messages into individual messages
private String[] splitHL7Messages(String combinedMessages) {
return combinedMessages.split("(?<=\\r)\\n");
}

// Process each individual HL7 message and determine action based on message type
private void processIndividualHL7Message(String message) {
HapiContext context = new DefaultHapiContext();
Parser parser = context.getPipeParser();

try {
Message hl7Message = parser.parse(message);
MSH msh = (MSH) hl7Message.get("MSH");
String messageType = msh.getMessageType().getMessageCode().getValue();

switch (messageType) {
case "OUL^R22":
handleResultMessage(hl7Message);
break;
case "QRY^R02":
handleQueryMessage(hl7Message);
break;
default:
System.err.println("Unhandled message type: " + messageType);
break;
}
} catch (Exception e) {
System.err.println("Error processing individual HL7 message: " + e.getMessage());
} finally {
try {
context.close();
} catch (IOException ex) {
java.util.logging.Logger.getLogger(MaglumiX3Server.class.getName()).log(Level.SEVERE, null, ex);
}
}
}

// Create a QueryRecord from a parsed HL7 message
private void handleQueryMessage(Message hl7Message) {
// Assume we extract sampleId and create a QueryRecord accordingly
String sampleId = extractSampleId(hl7Message); // Implement this method based on your message structure
QueryRecord qr = new QueryRecord(0, sampleId, "universalTestId", "queryType");
LISCommunicator.pullTestOrdersForSampleRequests(queryRecord);
}

public String extractSampleId(Message hl7Message) {
try {
// Extracting the MSH segment to access message details
MSH msh = (MSH) hl7Message.get("MSH");

// We will manually parse the field from the MSH segment since QPD-like data is actually here
String messageType = msh.getMessageType().getMessageCode().getValue();
if (!"TSREQ".equals(messageType)) {
throw new IllegalArgumentException("Unsupported message type for sample ID extraction: " + messageType);
}

// The field index might vary; you need to confirm the index from a sample message
// Assuming the structure of the QPD-like data is in MSH-9 field
String fieldContent = msh.getField(9, 0).encode();

// Assuming the structure is `215698^^NA003^1` and we want the first part before the first '^'
String[] parts = fieldContent.split("\\^");
if (parts.length > 0) {
return parts[0]; // Returns '215698' as the sample ID
} else {
return "Sample ID not found"; // Handling case where no data is available
}
} catch (Exception e) {
e.printStackTrace();
return "Error extracting sample ID: " + e.getMessage();
}
}

// private void handleResultMessage(Message hl7Message) {
// ORU_R01 message = (ORU_R01) hl7Message;
// DataBundle dataBundle = new DataBundle();
// dataBundle.setMiddlewareSettings(SettingsLoader.getSettings());
//
// // Patient information
// PID pid = message.getPATIENT_RESULT().getPATIENT().getPID();
// String patientId = pid.getPatientIdentifierList(0).getIDNumber().getValue();
// String additionalId = pid.getPatientIdentifierList(0).getIdentifierTypeCode().getValue();
// String patientName = pid.getPatientName(0).getFamilyName().getSurname().getValue();
// String patientSecondName = pid.getPatientName(0).getGivenName().getValue();
// String patientSex = pid.getAdministrativeSex().getValue();
// String race = pid.getRace(0).getIdentifier().getValue();
// String dob = "";
// String patientAddress = pid.getPatientAddress(0).getStreetAddress().getStreetOrMailingAddress().getValue();
// String patientPhoneNumber = "";
// String attendingDoctor = message.getPATIENT_RESULT().getPATIENT().getVISIT().getPV1().getAttendingDoctor(0).getFamilyName().getSurname().getValue();
//
// PatientRecord pr = new PatientRecord(0,
// patientId,
// additionalId,
// patientName,
// patientSecondName,
// patientSex,
// race,
// dob,
// patientAddress,
// patientPhoneNumber,
// attendingDoctor);
// dataBundle.setPatientRecord(pr);
//
// // Iterate over all OBX segments within the first OBR segment
// OBR obr = message.getPATIENT_RESULT().getORDER_OBSERVATION().getOBR();
// int obxCount = message.getPATIENT_RESULT().getORDER_OBSERVATION().getOBSERVATIONReps();
//
// for (int i = 0; i < obxCount; i++) {
// OBX obx = message.getPATIENT_RESULT().getORDER_OBSERVATION().getOBSERVATION(i).getOBX();
// String testCode = obx.getObservationIdentifier().getIdentifier().getValue();
// String resultValueString = obx.getObservationValue(0).getData().toString();
// String resultUnits = obx.getUnits().getIdentifier().getValue();
// String resultDateTime = "";
// String instrumentName = SettingsLoader.getSettings().getAnalyzerDetails().getAnalyzerName();
// String sampleId = obr.getFillerOrderNumber().getEntityIdentifier().getValue();
//
// ResultsRecord rr = new ResultsRecord(testCode, resultValueString, resultUnits, resultDateTime, instrumentName, sampleId);
//
// LISCommunicator.pushResults(patientDataBundle);
//
// dataBundle.getResultsRecords().add(rr);
// }
//
// logger.info("Handling Result Message: " + hl7Message.toString());
// }
private void processHL7Message(String message) {
// Process the HL7 message here
// This method should be defined to handle parsing and further processing of the HL7 message
logger.info("Processing HL7 Message: " + message);

// Create a parser instance (HAPI library)
Parser parser = new PipeParser();

try {
// Parse the message string into a Message object
Message hl7Message = parser.parse(message);

// Extract MSH segment
Segment mshSegment = (Segment) hl7Message.get("MSH");

// Extract message type and trigger event (e.g., ADT^A01)
String messageType = mshSegment.getField(9, 0).toString();
String triggerEvent = mshSegment.getField(10, 0).toString();

// Log the extracted values
logger.info("Message Type: " + messageType);
logger.info("Trigger Event: " + triggerEvent);

// Route based on type and event
switch (messageType) {
case "OUL^R22":
handleResultMessage(hl7Message);
break;
// Add more cases as needed for other types
default:
logger.warn("Unhandled message type: " + messageType);
}
} catch (Exception e) {
logger.error("Failed to parse HL7 message", e);
}
}

public List<QueryRecord> createQueryRecordsFromMessages(String combinedMessages) throws IOException {
List<QueryRecord> records = new ArrayList<>();
String[] individualMessages = combinedMessages.split("MSH");

HapiContext context = new DefaultHapiContext();
Parser parser = context.getPipeParser();

try {
for (String rawMessage : individualMessages) {
if (!rawMessage.trim().isEmpty()) {
// Prepend "MSH" as it's removed by the split operation
String message = "MSH" + rawMessage;

try {
Message hl7Message = parser.parse(message);
// Manually navigate to the right segment and field to extract the sample ID
String sampleId = extractSampleId(hl7Message);
QueryRecord qr = new QueryRecord(0, sampleId, "universalTestId", "queryType");
records.add(qr);
} catch (Exception e) {
System.err.println("Error parsing message: " + e.getMessage());
}
}
}
} finally {
context.close();
}

return records;
}

// Example handler method for result messages
private void handleResultMessage(Message hl7Message) {
ORU_R01 message = (ORU_R01) hl7Message;
DataBundle dataBundle = new DataBundle();
dataBundle.setMiddlewareSettings(SettingsLoader.getSettings());

// Patient information
PID pid = message.getPATIENT_RESULT().getPATIENT().getPID();
String patientId = pid.getPatientIdentifierList(0).getIDNumber().getValue();
String additionalId = pid.getPatientIdentifierList(0).getIdentifierTypeCode().getValue();
String patientName = pid.getPatientName(0).getFamilyName().getSurname().getValue();
String patientSecondName = pid.getPatientName(0).getGivenName().getValue();
String patientSex = pid.getAdministrativeSex().getValue();
String race = pid.getRace(0).getIdentifier().getValue();
String dob = "";
String patientAddress = pid.getPatientAddress(0).getStreetAddress().getStreetOrMailingAddress().getValue();
String patientPhoneNumber = "";
String attendingDoctor = message.getPATIENT_RESULT().getPATIENT().getVISIT().getPV1().getAttendingDoctor(0).getFamilyName().getSurname().getValue();

PatientRecord pr = new PatientRecord(0,
patientId,
additionalId,
patientName,
patientSecondName,
patientSex,
race,
dob,
patientAddress,
patientPhoneNumber,
attendingDoctor);
dataBundle.setPatientRecord(pr);

// Iterate over all OBX segments within the first OBR segment
OBR obr = message.getPATIENT_RESULT().getORDER_OBSERVATION().getOBR();
int obxCount = message.getPATIENT_RESULT().getORDER_OBSERVATION().getOBSERVATIONReps();

for (int i = 0; i < obxCount; i++) {
OBX obx = message.getPATIENT_RESULT().getORDER_OBSERVATION().getOBSERVATION(i).getOBX();
String testCode = obx.getObservationIdentifier().getIdentifier().getValue();
String resultValueString = obx.getObservationValue(0).getData().toString();
String resultUnits = obx.getUnits().getIdentifier().getValue();
String resultDateTime = "";
String instrumentName = SettingsLoader.getSettings().getAnalyzerDetails().getAnalyzerName();
String sampleId = obr.getFillerOrderNumber().getEntityIdentifier().getValue();

ResultsRecord rr = new ResultsRecord(testCode, resultValueString, resultUnits, resultDateTime, instrumentName, sampleId);

LISCommunicator.pushResults(patientDataBundle);

dataBundle.getResultsRecords().add(rr);
}

logger.info("Handling Result Message: " + hl7Message.toString());
}

public void start(int port) {
Expand Down Expand Up @@ -640,13 +904,7 @@ public static ResultsRecord parseResultsRecord(String resultSegment) {
logger.debug("Test code extracted: {}", testCode);

// Result value parsing assumes the result is in the fourth field
double resultValue = 0.0;
try {
resultValue = Double.parseDouble(fields[3]);
logger.debug("Result value extracted: {}", resultValue);
} catch (NumberFormatException e) {
logger.error("Failed to parse result value from segment: {}", resultSegment, e);
}
String resultValue = fields[3];

// Units and other details
String resultUnits = fields[4];
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