@Test
public void testTerserGetPrimitive_VariesCompositeFirstComponent() throws HL7Exception {
final Varies variesField = new Varies(mshOnly);
final Primitive comp1Sub1 = Terser.getPrimitive(variesField, 1, 1);
comp1Sub1.setValue("comp1Sub1");
final Primitive comp1Sub2 = Terser.getPrimitive(variesField, 1, 2);
comp1Sub2.setValue("comp1Sub2");
final Primitive comp2Sub1 = Terser.getPrimitive(variesField, 2, 1);
comp2Sub1.setValue("comp2Sub1");
assertEquals(GenericComposite.class, variesField.getData().getClass());
final GenericComposite field = (GenericComposite) variesField.getData();
final Type typeComp1 = field.getComponent(0);
assertEquals(typeComp1.getClass(), Varies.class);
final Varies variesComp1 = (Varies) typeComp1;
assertEquals(GenericComposite.class, variesComp1.getData().getClass());
final GenericComposite comp1 = (GenericComposite) variesComp1.getData();
final Type typeSub1 = comp1.getComponent(1);
assertEquals(typeSub1.getClass(), Varies.class);
final Varies variesSub1 = (Varies) typeSub1;
assertEquals(GenericPrimitive.class, variesSub1.getData().getClass());
assertEquals("comp1Sub1&comp1Sub2^comp2Sub1", PipeParser.encode(variesField, encoders));
}
public String getOBXResult(int i, int j) {
try {
return (getString(
Terser.get(
msg.getRESPONSE().getORDER_OBSERVATION(i).getOBSERVATION(j).getOBX(), 5, 0, 1, 1)));
} catch (Exception e) {
return ("");
}
}
private Message doProcess(Message theArg0) throws HL7Exception, ApplicationException {
String encodedMessage = theArg0.encode();
Terser terser = new Terser(theArg0);
String msgType = terser.get("/MSH-9-1");
String msgTrigger = terser.get("/MSH-9-2");
MSH msh = (MSH) theArg0.get("MSH");
ourLog.info("Message is of type " + msgType + "^" + msgTrigger);
List<Failure> failures;
try {
String msgSourceOrg = terser.get("/MSH-3-1");
String sourceOrg =
myContributorConfig.getContributorConfig().getNameOfHspId9004(msgSourceOrg);
ourLog.info("Sending organization from message is {} - {}", msgSourceOrg, sourceOrg);
} catch (Exception e) {
// ignore
}
Converter converter;
try {
converter = new Converter(true);
} catch (JAXBException e2) {
ourLog.error("Failed to convert message: Could not initialize converter", e2);
throw new HL7Exception(e2);
}
String outcome = null;
if ("ORU".equals(msgType) && "R01".equals(msgTrigger)) {
final ORU_R01 oru = (ORU_R01) theArg0;
final List<ClinicalDocumentGroup> documents = converter.convertClinicalDocument(oru);
try {
outcome =
"ORU^R01 message evaluated (containing " + documents.size() + " documents/results)";
// outcome = Persister.persist(documents);
} catch (final Exception e1) {
throw new HL7Exception(e1);
}
} else if ("ADT".equals(msgType)) {
ADT_A01 adt = new ADT_A01();
adt.setParser(myParser);
adt.parse(encodedMessage);
PatientWithVisits pwv = converter.convertPatientWithVisits(adt);
try {
if (pwv != null) {
outcome = "ADT^" + msgTrigger + " message evaluated";
// outcome = Persister.persist(pwv);
} else {
outcome = PROCESSING_FAILED_OUTCOME;
}
} catch (final Exception e1) {
throw new HL7Exception(e1);
}
} else if ("RDE".equals(msgType) && "O11".equals(msgTrigger)) {
RDE_O11 rde = new RDE_O11();
rde.setParser(myParser);
rde.parse(encodedMessage);
List<MedicationOrder> medOrders = converter.convertMedicationOrder(rde);
try {
outcome =
"RDE^O11 message evaluated (containing " + medOrders.size() + " medication orders)";
// outcome = Persister.persistMedicationOrders(medOrders);
} catch (final Exception e1) {
throw new HL7Exception(e1);
}
} else if ("RAS".equals(msgType) && "O17".equals(msgTrigger)) {
RAS_O17 ras = new RAS_O17();
ras.setParser(myParser);
ras.parse(encodedMessage);
List<MedicationOrderWithAdmins> medOrdersWithAdmins = converter.convertMedicationAdmin(ras);
try {
outcome =
"RAS^O17 message evaluated (containing administration data for "
+ medOrdersWithAdmins.size()
+ " medication orders)";
// outcome = Persister.persistMedicationAdmins(medOrdersWithAdmins);
} catch (final Exception e1) {
throw new HL7Exception(e1);
}
} else {
/*
* Note: If adding processors for additional message types, make
* sure to update the description for F098!!
*/
converter.validateMsh(msh);
converter.addFailure("/MSH-9", FailureCode.F098, msgType + "^" + msgTrigger);
outcome = PROCESSING_FAILED_OUTCOME;
}
if (StringUtils.isBlank(outcome)) {
outcome = PROCESSING_FAILED_OUTCOME;
}
// These are determined from the IDs in the message
SendingSystem sendingSystem = converter.getSendingSystem();
Contributor contributor = converter.getContributorConfig();
// if (contributor == null) {
// contributor = myContributor;
// } else if (contributor != myContributor) {
// converter.addFailure("MSH-3-1", FailureCode.F112,
// msh.getMsh3_SendingApplication().getHd1_NamespaceID().getValue());
// contributor = myContributor;
// }
if (sendingSystem == null) {
throw new ApplicationException(
"Failed to determine sender from message. Please check MSH-3 value");
}
// if (sendingSystem == null ||
// contributor.getSendingSystem9008WithOid(sendingSystem.getCode()) == null) {
// converter.addFailure("MSH-3-2", FailureCode.F113,
// msh.getMsh3_SendingApplication().getHd2_UniversalID().getValue());
// sendingSystem = contributor.getSendingSystem().get(0);
// ourLog.info("Defaulting to first sending system {} because MSH-3-2 was {}",
// sendingSystem.getDescription(),
// msh.getMsh3_SendingApplication().getHd2_UniversalID().getValue());
// }
ourLog.info(
"Converted message from {} - {}", contributor.getName(), sendingSystem.getDescription());
String orgId = sendingSystem.getManagementConsoleOrgId();
if (StringUtils.isBlank(orgId)) {
orgId = contributor.getManagementConsoleOrgId();
}
final CanonicalHl7V2Message canon =
AbstractPojo.createNewCanonicalMessageHl7V2(
encodedMessage,
orgId,
sendingSystem.getManagementConsoleSystemId(),
Listener.INTERFACE_ID,
MessagePhase.INCOMING,
Listener.class,
java.util.logging.Logger.getLogger(Listener.class.getName()));
failures = converter.getFailures();
if (failures.size() > 0) {
String problemDescription = createHtmlProblemDescription(converter);
if (problemDescription.length() > 0) {
canon.setValidationOutcomeDescription(problemDescription);
}
ourLog.info("Message has {} failures", converter.getFailures().size());
} else {
ourLog.info("Message has no validation failures! Outstanding.");
canon.setValidationOutcomeDescription("No issues");
}
if (outcome != null) {
canon.setValidationOutcomeDescription(
canon.getValidationOutcomeDescription() + "<br>Outcome: " + outcome);
} else {
canon.setValidationOutcomeDescription(canon.getValidationOutcomeDescription());
}
// Journal for the source
ourLog.info("Journalling message");
final JournalMessageRequest request = new JournalMessageRequest();
request.setCanonicalHl7V2Message(canon);
try {
AbstractPojo.tryToJournalMessage(myJournalSvc, request);
} catch (InvalidInputException e) {
ourLog.error("Failed to send message to journal", e);
throw new HL7Exception("Failed to process message");
} catch (final sail.wsdl.infrastructure.journalling.UnexpectedErrorException e) {
ourLog.error("Failed to send message to dead letter", e);
throw new HL7Exception("Failed to process message");
} catch (Exception e) {
ourLog.error("Failed to journal message. Moving on", e);
StringWriter w = new StringWriter();
JAXB.marshal(request, w);
ourLog.error("Request was: " + w.toString());
}
// // Journal again for the destination
// canon.setDestination(new OutboundInterface());
// canon.getDestination().setBoxId(canon.getSource().getBoxId());
// canon.getDestination().setDomainId(canon.getSource().getDomainId());
// canon.getDestination().setInterfaceDirection("O");
// canon.getDestination().setOrgId("SIMS");
// canon.getDestination().setSystemId("CGTA_Interim_CDR");
// canon.getDestination().setInterfaceId("All");
// canon.setCurrentMessagePhase(MessagePhase.OUTGOING);
// try {
// myJournalSvc.journalMessage(request);
// } catch (final InvalidInputException e) {
// ourLog.error("Failed to send message to journal", e);
// } catch (final
// sail.wsdl.infrastructure.journalling.UnexpectedErrorException e)
// {
// ourLog.error("Failed to send message to dead letter", e);
// }
try {
ACK ack = (ACK) theArg0.generateACK();
for (final Failure next : converter.getFailures()) {
ERR err = ack.getERR(ack.getERRReps());
err.getErr1_ErrorCodeAndLocation(0).getEld1_SegmentID().setValue(next.getTerserPath());
err.getErr3_HL7ErrorCode().getCwe1_Identifier().setValue(next.getFailureCode().name());
err.getErr6_ApplicationErrorParameter(0).setValue(next.getFieldVal());
err.getErr7_DiagnosticInformation().setValue(next.getMessage());
}
return ack;
} catch (final IOException e) {
throw new HL7Exception(e);
}
}
/** Accumulates fragments and passes the "big" message to the processing route. */
@Override
public void process(Exchange exchange) throws Exception {
String requestString = exchange.getIn().getBody(String.class);
Parser parser = getEndpoint().getHl7v2TransactionConfiguration().getParser();
Message requestMessage = parser.parse(requestString);
Terser requestTerser = new Terser(requestMessage);
String msh14 = requestTerser.get("MSH-14");
String dsc1 = null;
try {
if (!"I".equals(requestTerser.get("DSC-2"))) {
dsc1 = requestTerser.get("DSC-1");
}
} catch (HL7Exception e) {
// segment DSC does not exist in cancel requests
}
// pass when the message is not fragmented
if (isEmpty(msh14) && isEmpty(dsc1)) {
getWrappedProcessor().process(exchange);
return;
}
// get pieces of the accumulator's key
String msh31 = requestTerser.get("MSH-3-1");
String msh32 = requestTerser.get("MSH-3-2");
String msh33 = requestTerser.get("MSH-3-3");
// create an accumulator (on the arrival of the first fragment)
// or get an existing one (on the arrival of fragments 2..n)
StringBuilder accumulator;
if (isEmpty(msh14)) {
accumulator = new StringBuilder();
} else {
accumulator = storage.getAndRemove(keyString(msh14, msh31, msh32, msh33));
if (accumulator == null) {
LOG.warn("Pass unknown fragment with MSH-14=={} to the route", msh14);
getWrappedProcessor().process(exchange);
return;
}
}
// append current fragment to the accumulator
int beginIndex = isEmpty(msh14) ? 0 : requestString.indexOf('\r');
int endIndex = isEmpty(dsc1) ? requestString.length() : (requestString.indexOf("\rDSC") + 1);
accumulator.append(requestString, beginIndex, endIndex);
// DSC-1 is empty -- finish accumulation, pass message to the marshaller
if (isEmpty(dsc1)) {
LOG.debug("Finished fragment chain {}", msh14);
exchange.getIn().setBody(accumulator.toString());
getWrappedProcessor().process(exchange);
return;
}
// DSC-1 is not empty -- update accumulators map, request the next fragment
LOG.debug("Processed fragment {} requesting {}", msh14, dsc1);
storage.put(keyString(dsc1, msh31, msh32, msh33), accumulator);
Message ack = MessageUtils.response(requestMessage, "ACK", requestTerser.get("MSH-9-2"));
Terser ackTerser = new Terser(ack);
ackTerser.set("MSA-1", "CA");
ackTerser.set("MSA-2", requestTerser.get("MSH-10"));
Exchanges.resultMessage(exchange).setBody(parser.encode(ack));
}