Examples with OBR ca.uhn.hl7v2.model.v26.segment.OBR used on opensource projects

Example 36 with OBR

use of ca.uhn.hl7v2.model.v26.segment.OBR in project openmrs-core by openmrs.

the class ORUR01HandlerTest method processMessage_shouldSetValue_NumericForObsIfQuestionDatatypeIsNumeric.

/**
 * @see ORUR01Handler#processMessage(Message)
 */
@Test
public void processMessage_shouldSetValue_NumericForObsIfQuestionDatatypeIsNumeric() 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||450|||||||||20080206";
    // 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(450, newObservation.getValueNumeric().intValue());
}

Example 37 with OBR

use of ca.uhn.hl7v2.model.v26.segment.OBR in project openmrs-core by openmrs.

the class ORUR01HandlerTest method processNK1_shouldFailIfTheRelationshipIdentifierIsFormattedImproperly.

/**
 * @see ORUR01Handler#processNK1(Patient,NK1)
 */
@Test(expected = HL7Exception.class)
public void processNK1_shouldFailIfTheRelationshipIdentifierIsFormattedImproperly() throws Exception {
    // process a message with an invalid relationship identifier format
    // the patient that is the focus of
    Patient patient = new Patient(3);
    // this hl7 message
    String hl7String = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20090728170332||ORU^R01|gu99yBh4loLX2mh9cHaV|P|2.5|1||||||||4^AMRS.ELD.FORMID\r" + "PID|||3^^^^||Beren^John^Bondo||\r" + "NK1|1|Jones^Jane^Lee^^RN|3C^Parent^99REL||||||||||||F|19751016|||||||||||||||||2^^^L^PI\r" + "PV1||O|1^Unknown||||1^Super User (admin)|||||||||||||||||||||||||||||||||||||20090714|||||||V\r" + "ORC|RE||||||||20090728165937|1^Super User\r" + "OBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\r" + "OBX|2|NM|5497^CD4 COUNT^99DCT||123|||||||||20090714\r" + "OBR|3|||23^FOOD CONSTRUCT^99DCT\r" + "OBX|1|CWE|21^FOOD ASSISTANCE FOR ENTIRE FAMILY^99DCT||22^UNKNOWN^99DCT^2471^UNKNOWN^99NAM|||||||||20090714";
    ORUR01Handler oruHandler = new ORUR01Handler();
    Message hl7message = parser.parse(hl7String);
    ORU_R01 oru = (ORU_R01) hl7message;
    List<NK1> nk1List = oruHandler.getNK1List(oru);
    for (NK1 nk1 : nk1List) oruHandler.processNK1(patient, nk1);
}

Example 38 with OBR

use of ca.uhn.hl7v2.model.v26.segment.OBR in project openmrs-core by openmrs.

the class ORUR01HandlerTest method processMessage_shouldCreateAnEncounterAndFindTheProviderByUuid.

/**
 * @see ORUR01Handler#processMessage(Message)
 */
@Test
public void processMessage_shouldCreateAnEncounterAndFindTheProviderByUuid() throws Exception {
    executeDataSet("org/openmrs/api/include/ProviderServiceTest-initial.xml");
    int patientId = 2;
    Patient patient = new Patient(patientId);
    List<Encounter> encForPatient1 = Context.getEncounterService().getEncountersByPatient(patient);
    ProviderService ps = Context.getProviderService();
    Provider provider = ps.getProviderByIdentifier("8a760");
    String hl7string = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20080226102656||ORU^R01|JqnfhKKtouEz8kzTk6Zo|P|2.5|1||||||||16^AMRS.ELD.FORMID\r" + "PID|||" + patientId + "^^^^||Hornblower^Horatio^Test||\r" + "PV1||O|1^Unknown Location||||ba4781f4-6b94-11e0-93c3-18a905e044dc^name^^^^^^^&" + HL7Constants.PROVIDER_ASSIGNING_AUTH_PROV_UUID + "&L|||||||||||||||||||||||||||||||||||||20080212|||||||V\r" + "ORC|RE||||||||20080226102537|1^Super User\r" + "OBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT";
    Message hl7message = parser.parse(hl7string);
    router.processMessage(hl7message);
    // check for the new encounter
    List<Encounter> encForPatient2 = Context.getEncounterService().getEncountersByPatient(patient);
    encForPatient2.removeAll(encForPatient1);
    Assert.assertTrue(encForPatient2.size() == 1);
    Provider newProvider = encForPatient2.get(0).getProvidersByRole(Context.getEncounterService().getEncounterRoleByUuid(EncounterRole.UNKNOWN_ENCOUNTER_ROLE_UUID)).iterator().next();
    Assert.assertEquals(4, newProvider.getId().intValue());
}

Example 39 with OBR

use of ca.uhn.hl7v2.model.v26.segment.OBR 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 40 with OBR

use of ca.uhn.hl7v2.model.v26.segment.OBR in project openmrs-core by openmrs.

the class HL7ServiceTest method resolveLocationId_shouldReturnInternalIdentifierOfLocationIfOnlyLocationIdIsSpecified.

/**
 * @throws HL7Exception
 * @see HL7Service#resolveLocationId(ca.uhn.hl7v2.model.v25.datatype.PL)
 */
@Test
public void resolveLocationId_shouldReturnInternalIdentifierOfLocationIfOnlyLocationIdIsSpecified() throws HL7Exception {
    executeDataSet("org/openmrs/hl7/include/ORUTest-initialData.xml");
    HL7Service hl7service = Context.getHL7Service();
    Message message = hl7service.parseHL7String("MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20080226102656||ORU^R01|JqnfhKKtouEz8kzTk6Zo|P|2.5|1||||||||16^AMRS.ELD.FORMID\r" + "PID|||3^^^^||John3^Doe^||\r" + "NK1|1|Hornblower^Horatio^L|2B^Sibling^99REL||||||||||||M|19410501|||||||||||||||||1000^^^L^PN||||\r" + "PV1||O|1^0^0^0&Test Location&0||||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||450|||||||||20080206\r" + "OBX|2|DT|5096^RETURN VISIT DATE^99DCT||20080229|||||||||20080212");
    ORU_R01 oru = (ORU_R01) message;
    PV1 pv1 = oru.getPATIENT_RESULT().getPATIENT().getVISIT().getPV1();
    Assert.assertNotNull("PV1 parsed as null", pv1);
    PL hl7Location = pv1.getAssignedPatientLocation();
    Integer locationId = hl7service.resolveLocationId(hl7Location);
    Assert.assertEquals("Resolved and given locationId shoud be equals", Integer.valueOf(1), locationId);
}