Examples with IS ca.uhn.hl7v2.model.v25.datatype.IS used on opensource projects

Example 26 with IS

use of ca.uhn.hl7v2.model.v25.datatype.IS in project openmrs-core by openmrs.

the class ORUR01Handler method processNK1.

/**
 * process an NK1 segment and add relationships if needed
 *
 * @param patient
 * @param nk1
 * @throws HL7Exception
 * @should create a relationship from a NK1 segment
 * @should not create a relationship if one exists
 * @should create a person if the relative is not found
 * @should fail if the coding system is not 99REL
 * @should fail if the relationship identifier is formatted improperly
 * @should fail if the relationship type is not found
 */
protected void processNK1(Patient patient, NK1 nk1) throws HL7Exception {
    // guarantee we are working with our custom coding system
    String relCodingSystem = nk1.getRelationship().getNameOfCodingSystem().getValue();
    if (!relCodingSystem.equals(HL7Constants.HL7_LOCAL_RELATIONSHIP)) {
        throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.relationshipCoding", new Object[] { relCodingSystem }, null));
    }
    // get the relationship type identifier
    String relIdentifier = nk1.getRelationship().getIdentifier().getValue();
    // validate the format of the relationship identifier
    if (!Pattern.matches("[0-9]+[AB]", relIdentifier)) {
        throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.relationshipType", new Object[] { relIdentifier }, null));
    }
    // get the type ID
    Integer relTypeId;
    try {
        relTypeId = Integer.parseInt(relIdentifier.substring(0, relIdentifier.length() - 1));
    } catch (NumberFormatException e) {
        throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.relationshipType", new Object[] { relIdentifier }, null));
    }
    // find the relationship type
    RelationshipType relType = Context.getPersonService().getRelationshipType(relTypeId);
    if (relType == null) {
        throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.relationshipTypeNotFound", new Object[] { relTypeId }, null));
    }
    // find the relative
    Person relative = getRelative(nk1);
    // determine if the patient is person A or B; the relIdentifier indicates
    // the relative's side of the relationship, so the patient is the inverse
    boolean patientIsPersonA = relIdentifier.endsWith("B");
    boolean patientCanBeEitherPerson = relType.getbIsToA().equals(relType.getaIsToB());
    // look at existing relationships to determine if a new one is needed
    Set<Relationship> rels = new HashSet<>();
    if (relative != null) {
        if (patientCanBeEitherPerson || patientIsPersonA) {
            rels.addAll(Context.getPersonService().getRelationships(patient, relative, relType));
        }
        if (patientCanBeEitherPerson || !patientIsPersonA) {
            rels.addAll(Context.getPersonService().getRelationships(relative, patient, relType));
        }
    }
    // create a relationship if none is found
    if (rels.isEmpty()) {
        // check the relative's existence
        if (relative == null) {
            // create one based on NK1 information
            relative = Context.getHL7Service().createPersonFromNK1(nk1);
            if (relative == null) {
                throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.relativeNotCreated"));
            }
        }
        // create the relationship
        Relationship relation = new Relationship();
        if (patientCanBeEitherPerson || patientIsPersonA) {
            relation.setPersonA(patient);
            relation.setPersonB(relative);
        } else {
            relation.setPersonA(relative);
            relation.setPersonB(patient);
        }
        relation.setRelationshipType(relType);
        Context.getPersonService().saveRelationship(relation);
    }
}

Example 27 with IS

use of ca.uhn.hl7v2.model.v25.datatype.IS 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;
}

Example 28 with IS

use of ca.uhn.hl7v2.model.v25.datatype.IS in project openmrs-core by openmrs.

the class ORUR01Handler method updateHealthCenter.

private void updateHealthCenter(Patient patient, PV1 pv1) {
    // Update patient's location if it has changed
    if (log.isDebugEnabled()) {
        log.debug("Checking for discharge to location");
    }
    DLD dld = pv1.getDischargedToLocation();
    log.debug("DLD = " + dld);
    if (dld == null) {
        return;
    }
    IS hl7DischargeToLocation = dld.getDischargeLocation();
    log.debug("is = " + hl7DischargeToLocation);
    if (hl7DischargeToLocation == null) {
        return;
    }
    String dischargeToLocation = hl7DischargeToLocation.getValue();
    log.debug("dischargeToLocation = " + dischargeToLocation);
    if (dischargeToLocation != null && dischargeToLocation.length() > 0) {
        if (log.isDebugEnabled()) {
            log.debug("Patient discharged to " + dischargeToLocation);
        }
        // delimiter
        for (int i = 0; i < dischargeToLocation.length(); i++) {
            char ch = dischargeToLocation.charAt(i);
            if (ch == '&' || ch == '^') {
                dischargeToLocation = dischargeToLocation.substring(0, i);
                break;
            }
        }
        Integer newLocationId = Integer.parseInt(dischargeToLocation);
        // Hydrate a full patient object from patient object containing only
        // identifier
        patient = Context.getPatientService().getPatient(patient.getPatientId());
        PersonAttributeType healthCenterAttrType = Context.getPersonService().getPersonAttributeTypeByName("Health Center");
        if (healthCenterAttrType == null) {
            log.error("A person attribute type with name 'Health Center' is not defined but patient " + patient.getPatientId() + " is trying to change their health center to " + newLocationId);
            return;
        }
        PersonAttribute currentHealthCenter = patient.getAttribute("Health Center");
        if (currentHealthCenter == null || !newLocationId.toString().equals(currentHealthCenter.getValue())) {
            PersonAttribute newHealthCenter = new PersonAttribute(healthCenterAttrType, newLocationId.toString());
            log.debug("Updating patient's location from " + currentHealthCenter + " to " + newLocationId);
            // add attribute (and void old if there is one)
            patient.addAttribute(newHealthCenter);
            // save the patient and their new attribute
            Context.getPatientService().savePatient(patient);
        }
    }
    log.debug("finished discharge to location method");
}

Example 29 with IS

use of ca.uhn.hl7v2.model.v25.datatype.IS in project openmrs-core by openmrs.

the class HL7ServiceImpl method processHL7InQueue.

/**
 * @see org.openmrs.hl7.HL7Service#processHL7InQueue(org.openmrs.hl7.HL7InQueue)
 */
@Override
public HL7InQueue processHL7InQueue(HL7InQueue hl7InQueue) throws HL7Exception {
    if (hl7InQueue == null) {
        throw new HL7Exception("hl7InQueue argument cannot be null");
    }
    // mark this queue object as processing so that it isn't processed twice
    if (OpenmrsUtil.nullSafeEquals(HL7Constants.HL7_STATUS_PROCESSING, hl7InQueue.getMessageState())) {
        throw new HL7Exception("The hl7InQueue message with id: " + hl7InQueue.getHL7InQueueId() + " is already processing. " + ",key=" + hl7InQueue.getHL7SourceKey() + ")");
    } else {
        hl7InQueue.setMessageState(HL7Constants.HL7_STATUS_PROCESSING);
    }
    if (log.isDebugEnabled()) {
        log.debug("Processing HL7 inbound queue (id=" + hl7InQueue.getHL7InQueueId() + ",key=" + hl7InQueue.getHL7SourceKey() + ")");
    }
    // Parse the HL7 into an HL7Message or abort with failure
    String hl7Message = hl7InQueue.getHL7Data();
    try {
        // Parse the inbound HL7 message using the parser
        // NOT making a direct call here so that AOP can happen around this
        // method
        Message parsedMessage = Context.getHL7Service().parseHL7String(hl7Message);
        // Send the parsed message to our receiver routine for processing
        // into db
        // NOT making a direct call here so that AOP can happen around this
        // method
        Context.getHL7Service().processHL7Message(parsedMessage);
        // Move HL7 inbound queue entry into the archive before exiting
        log.debug("Archiving HL7 inbound queue entry");
        Context.getHL7Service().saveHL7InArchive(new HL7InArchive(hl7InQueue));
        log.debug("Removing HL7 message from inbound queue");
        Context.getHL7Service().purgeHL7InQueue(hl7InQueue);
    } catch (HL7Exception e) {
        boolean skipError = false;
        log.debug("Unable to process hl7inqueue: " + hl7InQueue.getHL7InQueueId(), e);
        log.debug("Hl7inqueue source: " + hl7InQueue.getHL7Source());
        log.debug("hl7_processor.ignore_missing_patient_non_local? " + Context.getAdministrationService().getGlobalProperty(OpenmrsConstants.GLOBAL_PROPERTY_IGNORE_MISSING_NONLOCAL_PATIENTS, "false"));
        if (e.getCause() != null && "Could not resolve patient".equals(e.getCause().getMessage()) && !"local".equals(hl7InQueue.getHL7Source().getName()) && "true".equals(Context.getAdministrationService().getGlobalProperty(OpenmrsConstants.GLOBAL_PROPERTY_IGNORE_MISSING_NONLOCAL_PATIENTS, "false"))) {
            skipError = true;
        }
        if (!skipError) {
            setFatalError(hl7InQueue, "Trouble parsing HL7 message (" + hl7InQueue.getHL7SourceKey() + ")", e);
        }
    } catch (Exception e) {
        setFatalError(hl7InQueue, "Exception while attempting to process HL7 In Queue (" + hl7InQueue.getHL7SourceKey() + ")", e);
    }
    return hl7InQueue;
}

Example 30 with IS

use of ca.uhn.hl7v2.model.v25.datatype.IS in project openmrs-core by openmrs.

the class ORUR01HandlerTest method parseObs_shouldAddCommentsToAnObservationFromNTESegments.

/**
 * @see ORUR01Handler#parseObs(Encounter,OBX,OBR,String)
 */
@Test
public void parseObs_shouldAddCommentsToAnObservationFromNTESegments() throws Exception {
    ObsService os = Context.getObsService();
    String hl7string = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20080226102656||ORU^R01|JqnfhKKtouEz8kzTk6Zo|P|2.5|1||||||||16^AMRS.ELD.FORMID\r" + "PID|||7^^^^||Collet^Test^Chebaskwony||\r" + "PV1||O|1^Unknown Location||||1^Super User (1-8)|||||||||||||||||||||||||||||||||||||20080212|||||||V\r" + "ORC|RE||||||||20080226102537|1^Super User\r" + "OBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\r" + "OBX|1|NM|5497^CD4, BY FACS^99DCT||1|||||||||20080206\r" + "NTE|1|L|This is a comment";
    // the expected question for the obs in the hl7 message has to be
    // numeric
    Assert.assertEquals("Numeric", Context.getConceptService().getConcept(5497).getDatatype().getName());
    List<Obs> oldList = os.getObservationsByPersonAndConcept(new Person(7), new Concept(5497));
    Message hl7message = parser.parse(hl7string);
    router.processMessage(hl7message);
    List<Obs> newList = os.getObservationsByPersonAndConcept(new Person(7), new Concept(5497));
    Obs newObservation = null;
    for (Obs newObs : newList) {
        if (!oldList.contains(newObs) && !newObs.isObsGrouping()) {
            newObservation = newObs;
        }
    }
    Assert.assertEquals("This is a comment", newObservation.getComment());
}