use of ca.uhn.hl7v2.model.v25.group.ORU_R01_PATIENT_RESULT in project streamsx.health by IBMStreams.
the class ObxToSplMapper method messageToModel.
@SuppressWarnings("unchecked")
public <T> Iterable<T> messageToModel(Message message) {
ArrayList<Observation> observations = new ArrayList<Observation>();
if (message instanceof ORU_R01) {
ORU_R01 oruMsg = (ORU_R01) message;
String obxTs = "";
String obxLocation = "";
String sendingApp = "";
String sendingFacility = "";
try {
MSH msh = oruMsg.getMSH();
sendingApp = msh.getSendingApplication().encode();
sendingFacility = msh.getSendingFacility().encode();
List<ORU_R01_PATIENT_RESULT> patient_RESULTAll = ((ORU_R01) message).getPATIENT_RESULTAll();
for (ORU_R01_PATIENT_RESULT result : patient_RESULTAll) {
ORU_R01_ORDER_OBSERVATION order_OBSERVATION = result.getORDER_OBSERVATION();
OBR obr = order_OBSERVATION.getOBR();
DTM ts = obr.getObservationDateTime();
obxTs = ts.getValue();
ORU_R01_PATIENT patient = result.getPATIENT();
ORU_R01_VISIT visit = patient.getVISIT();
PL location = visit.getPV1().getAssignedPatientLocation();
obxLocation = location.encode();
List<ORU_R01_OBSERVATION> observationAll = order_OBSERVATION.getOBSERVATIONAll();
for (ORU_R01_OBSERVATION oru_R01_OBSERVATION : observationAll) {
parseOBX(observations, obxTs, obxLocation, oru_R01_OBSERVATION.getOBX(), sendingApp, sendingFacility);
}
}
} catch (HL7Exception e) {
if (TRACE.isDebugEnabled())
TRACE.log(TraceLevel.WARN, e);
}
try {
OBR obr = (OBR) oruMsg.get("OBR");
DTM ts = obr.getObservationDateTime();
obxTs = ts.getValue();
Structure tmp = oruMsg.get("PV1");
if (tmp != null) {
PV1 pv1 = (PV1) tmp;
PL location = pv1.getAssignedPatientLocation();
obxLocation = location.encode();
}
Structure[] structures = oruMsg.getAll("OBX");
for (Structure structure : structures) {
parseOBX(observations, obxTs, obxLocation, (OBX) structure, sendingApp, sendingFacility);
}
} catch (HL7Exception e) {
if (TRACE.isDebugEnabled())
TRACE.log(TraceLevel.WARN, e);
}
}
return (Iterable<T>) observations;
}
use of ca.uhn.hl7v2.model.v25.group.ORU_R01_PATIENT_RESULT in project openmrs-core by openmrs.
the class ORUR01Handler method processORU_R01.
/**
* Bulk of the processing done here. Called by the main processMessage method
*
* @param oru the message to process
* @return the processed message
* @throws HL7Exception
* @should process multiple NK1 segments
*/
private Message processORU_R01(ORU_R01 oru) throws HL7Exception {
// TODO: ideally, we would branch or alter our behavior based on the
// sending application.
// validate message
validate(oru);
// extract segments for convenient use below
MSH msh = getMSH(oru);
PID pid = getPID(oru);
List<NK1> nk1List = getNK1List(oru);
PV1 pv1 = getPV1(oru);
// we're using the ORC assoc with first OBR to
ORC orc = getORC(oru);
// hold data enterer and date entered for now
// Obtain message control id (unique ID for message from sending
// application)
String messageControlId = msh.getMessageControlID().getValue();
if (log.isDebugEnabled()) {
log.debug("Found HL7 message in inbound queue with control id = " + messageControlId);
}
// create the encounter
Patient patient = getPatient(pid);
if (log.isDebugEnabled()) {
log.debug("Processing HL7 message for patient " + patient.getPatientId());
}
Encounter encounter = createEncounter(msh, patient, pv1, orc);
// do the discharge to location logic
try {
updateHealthCenter(patient, pv1);
} catch (Exception e) {
log.error("Error while processing Discharge To Location (" + messageControlId + ")", e);
}
// process NK1 (relationship) segments
for (NK1 nk1 : nk1List) {
processNK1(patient, nk1);
}
// list of concepts proposed in the obs of this encounter.
// these proposals need to be created after the encounter
// has been created
List<ConceptProposal> conceptProposals = new ArrayList<>();
// create observations
if (log.isDebugEnabled()) {
log.debug("Creating observations for message " + messageControlId + "...");
}
// we ignore all MEDICAL_RECORD_OBSERVATIONS that are OBRs. We do not
// create obs_groups for them
List<Integer> ignoredConceptIds = new ArrayList<>();
String obrConceptId = Context.getAdministrationService().getGlobalProperty(OpenmrsConstants.GLOBAL_PROPERTY_MEDICAL_RECORD_OBSERVATIONS, "1238");
if (StringUtils.hasLength(obrConceptId)) {
ignoredConceptIds.add(Integer.valueOf(obrConceptId));
}
// we also ignore all PROBLEM_LIST that are OBRs
String obrProblemListConceptId = Context.getAdministrationService().getGlobalProperty(OpenmrsConstants.GLOBAL_PROPERTY_PROBLEM_LIST, "1284");
if (StringUtils.hasLength(obrProblemListConceptId)) {
ignoredConceptIds.add(Integer.valueOf(obrProblemListConceptId));
}
ORU_R01_PATIENT_RESULT patientResult = oru.getPATIENT_RESULT();
int numObr = patientResult.getORDER_OBSERVATIONReps();
for (int i = 0; i < numObr; i++) {
if (log.isDebugEnabled()) {
log.debug("Processing OBR (" + i + " of " + numObr + ")");
}
ORU_R01_ORDER_OBSERVATION orderObs = patientResult.getORDER_OBSERVATION(i);
// the parent obr
OBR obr = orderObs.getOBR();
if (!StringUtils.hasText(obr.getUniversalServiceIdentifier().getIdentifier().getValue())) {
throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.errorInvalidOBR ", new Object[] { messageControlId }, null));
}
// if we're not ignoring this obs group, create an
// Obs grouper object that the underlying obs objects will use
Obs obsGrouper = null;
Concept obrConcept = getConcept(obr.getUniversalServiceIdentifier(), messageControlId);
if (obrConcept != null && !ignoredConceptIds.contains(obrConcept.getId())) {
// maybe check for a parent obs group from OBR-29 Parent ?
// create an obs for this obs group too
obsGrouper = new Obs();
obsGrouper.setConcept(obrConcept);
obsGrouper.setPerson(encounter.getPatient());
obsGrouper.setEncounter(encounter);
Date datetime = getDatetime(obr);
if (datetime == null) {
datetime = encounter.getEncounterDatetime();
}
obsGrouper.setObsDatetime(datetime);
obsGrouper.setLocation(encounter.getLocation());
obsGrouper.setCreator(encounter.getCreator());
// set comments if there are any
StringBuilder comments = new StringBuilder();
ORU_R01_ORDER_OBSERVATION parent = (ORU_R01_ORDER_OBSERVATION) obr.getParent();
int totalNTEs = parent.getNTEReps();
for (int iNTE = 0; iNTE < totalNTEs; iNTE++) {
for (FT obxComment : parent.getNTE(iNTE).getComment()) {
if (comments.length() > 0) {
comments.append(" ");
}
comments.append(obxComment.getValue());
}
}
// only set comments if there are any
if (StringUtils.hasText(comments.toString())) {
obsGrouper.setComment(comments.toString());
}
// add this obs as another row in the obs table
encounter.addObs(obsGrouper);
}
// loop over the obs and create each object, adding it to the encounter
int numObs = orderObs.getOBSERVATIONReps();
HL7Exception errorInHL7Queue = null;
for (int j = 0; j < numObs; j++) {
if (log.isDebugEnabled()) {
log.debug("Processing OBS (" + j + " of " + numObs + ")");
}
OBX obx = orderObs.getOBSERVATION(j).getOBX();
try {
log.debug("Parsing observation");
Obs obs = parseObs(encounter, obx, obr, messageControlId);
if (obs != null) {
// the creator/dateCreated from the encounter
if (encounter.getEncounterId() != null) {
obs.setCreator(getEnterer(orc));
obs.setDateCreated(new Date());
}
// set the obsGroup on this obs
if (obsGrouper != null) {
// set the obs to the group. This assumes the group is already
// on the encounter and that when the encounter is saved it will
// propagate to the children obs
obsGrouper.addGroupMember(obs);
} else {
// set this obs on the encounter object that we
// will be saving later
log.debug("Obs is not null. Adding to encounter object");
encounter.addObs(obs);
log.debug("Done with this obs");
}
}
} catch (ProposingConceptException proposingException) {
Concept questionConcept = proposingException.getConcept();
String value = proposingException.getValueName();
// if the sender never specified any text for the proposed concept
if (!StringUtils.isEmpty(value)) {
conceptProposals.add(createConceptProposal(encounter, questionConcept, value));
} else {
errorInHL7Queue = new HL7Exception(Context.getMessageSourceService().getMessage("Hl7.proposed.concept.name.empty"), proposingException);
// stop any further processing of current message
break;
}
} catch (HL7Exception e) {
errorInHL7Queue = e;
} finally {
// Handle obs-level exceptions
if (errorInHL7Queue != null) {
throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.improperlyFormattedOBX", new Object[] { PipeParser.encode(obx, new EncodingCharacters('|', "^~\\&")) }, null), HL7Exception.DATA_TYPE_ERROR, errorInHL7Queue);
}
}
}
}
if (log.isDebugEnabled()) {
log.debug("Finished creating observations");
log.debug("Current thread: " + Thread.currentThread());
log.debug("Creating the encounter object");
}
Context.getEncounterService().saveEncounter(encounter);
// now that the encounter is saved
for (ConceptProposal proposal : conceptProposals) {
Context.getConceptService().saveConceptProposal(proposal);
}
return oru;
}
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