ca.uhn.hl7v2.parser.PipeParser Java Examples

/**
 * Adds a ORU_R01 observation result
 * 
 * @param oru
 * @param patient
 * @param labItem
 * @param labwert
 * @param initial
 * @return
 */
private String addResultInternal(final ORU_R01 oru, final HL7Patient patient,
	final HL7LaborItem labItem, final HL7LaborWert labwert, int orderObservationIndex)
	throws DataTypeException, HL7Exception{
	
	// Observation
	ORU_R01_ORDER_OBSERVATION orderObservation =
		(ORU_R01_ORDER_OBSERVATION) oru.getPATIENT_RESULT().getORDER_OBSERVATION(
			orderObservationIndex);
	fillOBR(orderObservation.getOBR(), orderObservationIndex, labItem);
	fillOBX(orderObservation.getOBSERVATION().getOBX(), patient, labItem, labwert);
	if (labwert.getKommentar() != null && labwert.getKommentar().length() > 0) {
		fillNTE(orderObservation.getNTE(), labwert);
	}
	// Now, let's encode the message and look at the output
	Parser parser = new PipeParser();
	return parser.encode(oru);
}
 

/**
 * Creates an ORU_R01 message
 * 
 * @param patient
 * @param labItem
 * @param labwert
 * 
 * @return
 */
public String createText(final HL7Patient patient, final HL7LaborItem labItem,
	final HL7LaborWert labwert) throws DataTypeException, HL7Exception{
	
	ORU_R01 oru = new ORU_R01();
	// Message
	fillMSH(oru.getMSH(), "ORU", "R01", mandant, this.uniqueMessageControlID, //$NON-NLS-1$ //$NON-NLS-2$
		this.uniqueProcessingID, patient); //$NON-NLS-1$ //$NON-NLS-2$
	
	// Patient
	PID pid = oru.getPATIENT_RESULT().getPATIENT().getPID();
	fillPID(pid, patient);
	
	ORU_R01_ORDER_OBSERVATION orderObservation = oru.getPATIENT_RESULT().getORDER_OBSERVATION();
	fillORC(orderObservation.getORC(), "RE", null); //$NON-NLS-1$
	
	addResultInternal(oru, patient, labItem, labwert, 0);
	
	// Now, let's encode the message and look at the output
	Parser parser = new PipeParser();
	return parser.encode(oru);
}
 

/**
 * Creates an OMG_O19 message
 * 
 * @param patient
 * @param kostentraeger
 * @param rechnungsempfaenger
 * @param auftragsNummer
 * @param plan
 *            Abrechnungssystem (MV, UVG, VVG, KVG, usw)
 * @param beginDate
 * @param vnr
 *            Versicherungs-, Fall- oder Unfallnr
 * @return
 */
public String createText(final HL7Patient patient, final HL7Kostentraeger rechnungsempfaenger,
	final HL7Kostentraeger kostentraeger, final String plan, final Date beginDate,
	final String fallNr, final long auftragsNummer) throws DataTypeException, HL7Exception{
	
	OML_O21 omg = new OML_O21();
	fillMSH(omg.getMSH(), "OML", "O21", mandant, this.uniqueMessageControlID, //$NON-NLS-1$ //$NON-NLS-2$
		this.uniqueProcessingID, patient); //$NON-NLS-1$ //$NON-NLS-2$
	fillPID(omg.getPATIENT().getPID(), patient);
	fillNK1(omg.getPATIENT().getNK1(), rechnungsempfaenger);
	fillPV1(omg.getPATIENT().getPATIENT_VISIT().getPV1(), patient, beginDate);
	fillIN1(omg.getPATIENT().getINSURANCE().getIN1(), patient, kostentraeger, plan, fallNr);
	fillORC(omg.getORDER().getORC(), "1", auftragsNummer); //$NON-NLS-1$
	
	// Now, let's encode the message and look at the output
	Parser parser = new PipeParser();
	return parser.encode(omg);
}
 

/**
 * {@inheritDoc}
 */
public Message processMessage(Message theIn) throws ApplicationException, HL7Exception {

    String encodedMessage = new PipeParser().encode(theIn);
    System.out.println("Received message:\n" + encodedMessage + "\n\n");

    // Now we need to generate a message to return. This will generally be an ACK message.
    Segment msh = (Segment) theIn.get("MSH");
    Message retVal;
    try {
        // This method takes in the MSH segment of an incoming message, and generates an
        // appropriate ACK
        retVal = DefaultApplication.makeACK(msh);
    } catch (IOException e) {
        throw new HL7Exception(e);
    }

    return retVal;
}
 

/**
 * Reads an ORU_R01 HL7 file
 * 
 * @param text
 *            ISO-8559-1 String
 * @param readWithValidation
 *            True for parsing with validation, False for parsing without validation
 * @return The ORU_R01 message
 * @throws HL7Exception
 */
public ORU_R01 read(String text, boolean readWithValidation) throws HL7Exception{
	Parser p = new PipeParser();
	if (readWithValidation) {
		p.setValidationContext(new ElexisValidation());
	} else {
		p.setValidationContext(new NoValidation());
	}
	Message hl7Msg = p.parse(text);
	if (hl7Msg instanceof ORU_R01) {
		return (ORU_R01) hl7Msg;
	} else {
		addError(
			MessageFormat.format(Messages.HL7_ORU_R01_Error_WrongMsgType, hl7Msg.getName()));
	}
	return null;
}
 

/**
* Starts a PIX Registry Server to accept PIX Feed messages. 
* 
   * @return <code>true</code> if the initialization is successful; 
   * 		   otherwise <code>false</code>.
*/
  private boolean initPixRegistry() {
boolean isSuccess = false;
try {
       LowerLayerProtocol llp = LowerLayerProtocol.makeLLP(); // The transport protocol
       pixServer = new HL7Server(pixRegistryConnection, llp, new PipeParser());
       Application pixFeed  = new PixFeedHandler(this);
       
       //Admission of in-patient into a facility
       pixServer.registerApplication("ADT", "A01", pixFeed);  
       //Registration of an out-patient for a visit of the facility
       pixServer.registerApplication("ADT", "A04", pixFeed);  
       //Pre-admission of an in-patient
       pixServer.registerApplication("ADT", "A05", pixFeed);   
       //Update patient information
       pixServer.registerApplication("ADT", "A08", pixFeed);  
       //Merge patients
       pixServer.registerApplication("ADT", "A40", pixFeed);  
       //now start the Pix Registry Server
       pixServer.start();
       isSuccess = true;
}catch(Exception e) {
      	log.fatal("Failed to start the PIX Registry server", e);			
}
      return isSuccess;
  }
 

protected void createPatient(String patientId) throws Exception {
	if (!validatePatient)
		return ;
	
	patientId = patientId.replace("&", "&");
	//If it is a valid patient, then no need to re-create.
	if (isValidPatient(patientId))
		return; 
	
	String msg = "MSH|^~\\&|OTHER_KIOSK|HIMSSSANDIEGO|PAT_IDENTITY_X_REF_MGR_MISYS|ALLSCRIPTS|20090512132906-0300||ADT^A04^ADT_A01|7723510070655179915|P|2.3.1\r" + 
      "EVN||20090512132906-0300\r" +
      "PID|||"+ patientId +"||FARNSWORTH^STEVE||19781208|M|||820 JORIE BLVD^^CHICAGO^IL^60523\r" +
      "PV1||O|";
	PipeParser pipeParser = new PipeParser();
	Message adt = pipeParser.parse(msg);
	ConnectionHub connectionHub = ConnectionHub.getInstance();
	Connection connection = connectionHub.attach(hostName, pixRegistryPort, new PipeParser(), MinLowerLayerProtocol.class);
	Initiator initiator = connection.getInitiator();
	Message response = initiator.sendAndReceive(adt);
	String responseString = pipeParser.encode(response);	        
	System.out.println("Received response:\n" + responseString);
		MSA msa = (MSA)response.get("MSA");
	assertEquals("AA", msa.getAcknowledgementCode().getValue());
}
 

private void SendPIX(String msg) throws Exception {
PipeParser pipeParser = new PipeParser();
Message adt = pipeParser.parse(msg);
ConnectionHub connectionHub = ConnectionHub.getInstance();
Connection connection = connectionHub.attach(hostName, pixRegistryPort, new PipeParser(), MinLowerLayerProtocol.class);
Initiator initiator = connection.getInitiator();
Message response = initiator.sendAndReceive(adt);
String responseString = pipeParser.encode(response);	        
System.out.println("Received response:\n" + responseString);
MSA msa = (MSA)response.get("MSA");
assertEquals("AA", msa.getAcknowledgementCode().getValue());    	
  }
 

/**
 * Reads an ORU_R01 HL7 file
 * 
 * @param text
 *            ISO-8559-1 String
 * @return
 * @throws HL7Exception
 */
public ORU_R01 read(String text) throws HL7Exception{
	Parser p = new PipeParser();
	p.setValidationContext(new ElexisValidation());
	Message hl7Msg = p.parse(text);
	if (hl7Msg instanceof ORU_R01) {
		return (ORU_R01) hl7Msg;
	} else {
		addError(MessageFormat.format(
			Messages.HL7_ORU_R01_Error_WrongMsgType, hl7Msg.getName())); //$NON-NLS-1$
	}
	return null;
}
 

private HL7Message createMessage(final String msgText) throws HL7Exception, IOException {
    final HapiContext hapiContext = new DefaultHapiContext();
    hapiContext.setValidationContext(ValidationContextFactory.noValidation());

    final PipeParser parser = hapiContext.getPipeParser();
    final Message message = parser.parse(msgText);
    return new HapiMessage(message);
}
 

public HapiField(final Type type) {
    this.value = PipeParser.encode(type, EncodingCharacters.defaultInstance());

    final List<HL7Component> componentList = new ArrayList<>();
    if (type instanceof Composite) {
        final Composite composite = (Composite) type;

        for (final Type component : composite.getComponents()) {
            componentList.add(new HapiField(component));
        }
    }

    final ExtraComponents extra = type.getExtraComponents();
    if (extra != null && extra.numComponents() > 0) {
        final String singleFieldValue;
        if (type instanceof Primitive) {
            singleFieldValue = ((Primitive) type).getValue();
        } else {
            singleFieldValue = this.value;
        }
        componentList.add(new SingleValueField(singleFieldValue));

        for (int i = 0; i < extra.numComponents(); i++) {
            componentList.add(new HapiField(extra.getComponent(i)));
        }
    }

    this.components = Collections.unmodifiableList(componentList);
}
 

public HapiField(final Type type) {
    this.value = PipeParser.encode(type, EncodingCharacters.defaultInstance());

    final List<HL7Component> componentList = new ArrayList<>();
    if (type instanceof Composite) {
        final Composite composite = (Composite) type;

        for (final Type component : composite.getComponents()) {
            componentList.add(new HapiField(component));
        }
    }

    final ExtraComponents extra = type.getExtraComponents();
    if (extra != null && extra.numComponents() > 0) {
        final String singleFieldValue;
        if (type instanceof Primitive) {
            singleFieldValue = ((Primitive) type).getValue();
        } else {
            singleFieldValue = this.value;
        }
        componentList.add(new SingleValueField(singleFieldValue));

        for (int i = 0; i < extra.numComponents(); i++) {
            final Varies varies = extra.getComponent(i);
            componentList.add(new HapiField(varies));
        }
    }

    this.components = Collections.unmodifiableList(componentList);
}
 

private HL7Message createMessage(final File file) throws HL7Exception, IOException {
    final byte[] bytes = Files.readAllBytes(file.toPath());
    final String msgText = new String(bytes, "UTF-8");

    final HapiContext hapiContext = new DefaultHapiContext();
    hapiContext.setValidationContext(ValidationContextFactory.noValidation());

    final PipeParser parser = hapiContext.getPipeParser();
    final Message message = parser.parse(msgText);
    return new HapiMessage(message);
}
 

@Override
public void onTrigger(final ProcessContext context, final ProcessSession session) throws ProcessException {
    FlowFile flowFile = session.get();
    if (flowFile == null) {
        return;
    }

    final Charset charset = Charset.forName(context.getProperty(CHARACTER_SET).evaluateAttributeExpressions(flowFile).getValue());

    final byte[] buffer = new byte[(int) flowFile.getSize()];
    session.read(flowFile, new InputStreamCallback() {
        @Override
        public void process(final InputStream in) throws IOException {
            StreamUtils.fillBuffer(in, buffer);
        }
    });

    @SuppressWarnings("resource")
    final HapiContext hapiContext = new DefaultHapiContext();
    hapiContext.setValidationContext((ca.uhn.hl7v2.validation.ValidationContext) ValidationContextFactory.noValidation());

    final PipeParser parser = hapiContext.getPipeParser();
    final String hl7Text = new String(buffer, charset);
    final HL7Message message;
    try {
        final Message hapiMessage = parser.parse(hl7Text);
        message = new HapiMessage(hapiMessage);
    } catch (final Exception e) {
        getLogger().error("Failed to parse {} as HL7 due to {}; routing to failure", new Object[]{flowFile, e});
        session.transfer(flowFile, REL_FAILURE);
        return;
    }

    final Set<String> matchingRels = new HashSet<>();
    final Map<Relationship, HL7Query> queryMap = queries;
    for (final Map.Entry<Relationship, HL7Query> entry : queryMap.entrySet()) {
        final Relationship relationship = entry.getKey();
        final HL7Query query = entry.getValue();

        final QueryResult result = query.evaluate(message);
        if (result.isMatch()) {
            FlowFile clone = session.clone(flowFile);
            clone = session.putAttribute(clone, "RouteHL7.Route", relationship.getName());
            session.transfer(clone, relationship);
            session.getProvenanceReporter().route(clone, relationship);
            matchingRels.add(relationship.getName());
        }
    }

    session.transfer(flowFile, REL_ORIGINAL);
    getLogger().info("Routed a copy of {} to {} relationships: {}", new Object[]{flowFile, matchingRels.size(), matchingRels});
}
 

@Override
public void onTrigger(final ProcessContext context, final ProcessSession session) throws ProcessException {
    FlowFile flowFile = session.get();
    if (flowFile == null) {
        return;
    }

    final Charset charset = Charset.forName(context.getProperty(CHARACTER_SET).evaluateAttributeExpressions(flowFile).getValue());
    final Boolean useSegmentNames = context.getProperty(USE_SEGMENT_NAMES).asBoolean();
    final Boolean parseSegmentFields = context.getProperty(PARSE_SEGMENT_FIELDS).asBoolean();
    final Boolean skipValidation = context.getProperty(SKIP_VALIDATION).asBoolean();
    final String inputVersion = context.getProperty(HL7_INPUT_VERSION).getValue();

    final byte[] buffer = new byte[(int) flowFile.getSize()];
    session.read(flowFile, new InputStreamCallback() {
        @Override
        public void process(final InputStream in) throws IOException {
            StreamUtils.fillBuffer(in, buffer);
        }
    });

    @SuppressWarnings("resource")
    final HapiContext hapiContext = new DefaultHapiContext();
    if (!inputVersion.equals("autodetect")) {
        hapiContext.setModelClassFactory(new CanonicalModelClassFactory(inputVersion));
    }
    if (skipValidation) {
        hapiContext.setValidationContext((ValidationContext) ValidationContextFactory.noValidation());
    }

    final PipeParser parser = hapiContext.getPipeParser();
    final String hl7Text = new String(buffer, charset);
    try {
        final Message message = parser.parse(hl7Text);
        final Map<String, String> attributes = getAttributes(message, useSegmentNames, parseSegmentFields);
        flowFile = session.putAllAttributes(flowFile, attributes);
        getLogger().debug("Added the following attributes for {}: {}", new Object[]{flowFile, attributes});
    } catch (final HL7Exception e) {
        getLogger().error("Failed to extract attributes from {} due to {}", new Object[]{flowFile, e});
        session.transfer(flowFile, REL_FAILURE);
        return;
    }

    session.transfer(flowFile, REL_SUCCESS);
}
 

public Message getOULMessage() throws HL7Exception {
    PipeParser parser = new PipeParser();
    return parser.parse(OULMessage);
}
 

public HL7Server(int port) {
	LowerLayerProtocol llp = LowerLayerProtocol.makeLLP(); // The transport
														   // protocol
	PipeParser parser = new PipeParser();
	server = new SimpleServer(port, llp, parser);
}
 

@Override
public void onTrigger(final ProcessContext context, final ProcessSession session) throws ProcessException {
    FlowFile flowFile = session.get();
    if (flowFile == null) {
        return;
    }

    final Charset charset = Charset.forName(context.getProperty(CHARACTER_SET).evaluateAttributeExpressions(flowFile).getValue());
    final Boolean useSegmentNames = context.getProperty(USE_SEGMENT_NAMES).asBoolean();
    final Boolean parseSegmentFields = context.getProperty(PARSE_SEGMENT_FIELDS).asBoolean();
    final Boolean skipValidation = context.getProperty(SKIP_VALIDATION).asBoolean();
    final String inputVersion = context.getProperty(HL7_INPUT_VERSION).getValue();

    final byte[] buffer = new byte[(int) flowFile.getSize()];
    session.read(flowFile, new InputStreamCallback() {
        @Override
        public void process(final InputStream in) throws IOException {
            StreamUtils.fillBuffer(in, buffer);
        }
    });

    @SuppressWarnings("resource")
    final HapiContext hapiContext = new DefaultHapiContext();
    if (!inputVersion.equals("autodetect")) {
        hapiContext.setModelClassFactory(new CanonicalModelClassFactory(inputVersion));
    }
    if (skipValidation) {
        hapiContext.setValidationContext((ValidationContext) ValidationContextFactory.noValidation());
    }

    final PipeParser parser = hapiContext.getPipeParser();
    final String hl7Text = new String(buffer, charset);
    try {
        final Message message = parser.parse(hl7Text);
        final Map<String, String> attributes = getAttributes(message, useSegmentNames, parseSegmentFields);
        flowFile = session.putAllAttributes(flowFile, attributes);
        getLogger().debug("Added the following attributes for {}: {}", new Object[]{flowFile, attributes});
    } catch (final HL7Exception e) {
        getLogger().error("Failed to extract attributes from {} due to {}", new Object[]{flowFile, e});
        session.transfer(flowFile, REL_FAILURE);
        return;
    }

    session.transfer(flowFile, REL_SUCCESS);
}
 

@Override
public void onTrigger(final ProcessContext context, final ProcessSession session) throws ProcessException {
    FlowFile flowFile = session.get();
    if (flowFile == null) {
        return;
    }

    final Charset charset = Charset.forName(context.getProperty(CHARACTER_SET).evaluateAttributeExpressions(flowFile).getValue());

    final byte[] buffer = new byte[(int) flowFile.getSize()];
    session.read(flowFile, new InputStreamCallback() {
        @Override
        public void process(final InputStream in) throws IOException {
            StreamUtils.fillBuffer(in, buffer);
        }
    });

    @SuppressWarnings("resource")
    final HapiContext hapiContext = new DefaultHapiContext();
    hapiContext.setValidationContext((ca.uhn.hl7v2.validation.ValidationContext) ValidationContextFactory.noValidation());

    final PipeParser parser = hapiContext.getPipeParser();
    final String hl7Text = new String(buffer, charset);
    final HL7Message message;
    try {
        final Message hapiMessage = parser.parse(hl7Text);
        message = new HapiMessage(hapiMessage);
    } catch (final Exception e) {
        getLogger().error("Failed to parse {} as HL7 due to {}; routing to failure", new Object[]{flowFile, e});
        session.transfer(flowFile, REL_FAILURE);
        return;
    }

    final Set<String> matchingRels = new HashSet<>();
    final Map<Relationship, HL7Query> queryMap = queries;
    for (final Map.Entry<Relationship, HL7Query> entry : queryMap.entrySet()) {
        final Relationship relationship = entry.getKey();
        final HL7Query query = entry.getValue();

        final QueryResult result = query.evaluate(message);
        if (result.isMatch()) {
            FlowFile clone = session.clone(flowFile);
            clone = session.putAttribute(clone, "RouteHL7.Route", relationship.getName());
            session.transfer(clone, relationship);
            session.getProvenanceReporter().route(clone, relationship);
            matchingRels.add(relationship.getName());
        }
    }

    session.transfer(flowFile, REL_ORIGINAL);
    getLogger().info("Routed a copy of {} to {} relationships: {}", new Object[]{flowFile, matchingRels.size(), matchingRels});
}