Examples with Application ca.uhn.hl7v2.app.Application used on opensource projects

Example 1 with Application

use of ca.uhn.hl7v2.app.Application in project jmonkeyengine by jMonkeyEngine.

the class TestGhostObject method main.

public static void main(String[] args) {
    Application app = new TestGhostObject();
    app.start();
}

Example 2 with Application

use of ca.uhn.hl7v2.app.Application in project openmrs-core by openmrs.

the class ADTA28Handler method processADT_A28.

private Message processADT_A28(ADT_A05 adt) throws HL7Exception {
    // validate HL7 version
    validate(adt);
    // extract segments for convenient use below
    MSH msh = getMSH(adt);
    PID pid = getPID(adt);
    // Obtain message control id (unique ID for message from sending
    // application). Eventually avoid replaying the same message.
    String messageControlId = msh.getMessageControlID().getValue();
    log.debug("Found HL7 message in inbound queue with control id = " + messageControlId);
    // Add creator of the patient to application
    String sendingApp = msh.getSendingApplication().getComponent(0).toString();
    log.debug("SendingApplication = " + sendingApp);
    // Search for the patient
    Integer patientId = findPatientId(pid);
    // Create new patient if the patient id doesn't exist yet
    if (patientId == null) {
        log.info("Creating new patient in response to ADT_A28 " + messageControlId);
        Patient patient = createPatient(pid, sendingApp);
        if (patient == null) {
            throw new HL7Exception("Couldn't create Patient object from PID");
        }
        Context.getPatientService().savePatient(patient);
    } else {
        log.info("Ignoring ADT_A28 message because patient (" + patientId + ") already exists.");
    }
    return adt;
}

Example 3 with Application

use of ca.uhn.hl7v2.app.Application in project openmrs-core by openmrs.

the class HL7ServiceTest method processHL7Message_shouldParseMessageTypeSuppliedByModule.

/**
 * @see HL7Service#processHL7Message(Message)
 */
@Test
@Ignore("TRUNK-3945")
public void processHL7Message_shouldParseMessageTypeSuppliedByModule() throws Exception {
    Properties props = super.getRuntimeProperties();
    props.setProperty(ModuleConstants.RUNTIMEPROPERTY_MODULE_LIST_TO_LOAD, "org/openmrs/hl7/include/examplehl7handlers-0.1.omod");
    // the above module provides a handler for messages of type "ADR" with trigger "A19"
    ModuleUtil.startup(props);
    // the application context cannot restart here to load in the moduleApplicationContext that
    // calls the setHL7Handlers method so we're doing it manually here
    Class<Application> c = (Class<Application>) Context.loadClass("org.openmrs.module.examplehl7handlers.ADRHandler");
    Application classInstance = c.newInstance();
    HashMap<String, Application> map = new HashMap<>();
    map.put("ADR_A19", classInstance);
    HL7ServiceImpl.getInstance().setHL7Handlers(map);
    HL7Service hl7service = Context.getHL7Service();
    Message message = hl7service.parseHL7String("MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20080226102656||ADR^A19|JqnfhKKtouEz8kzTk6Zo|P|2.5|1||||||||16^AMRS.ELD.FORMID\r" + "PID|||3^^^^||John3^Doe^||\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\r" + "OBX|2|DT|5096^RETURN VISIT DATE^99DCT||20080229|||||||||20080212");
    Assert.assertNotNull(message);
    try {
        hl7service.processHL7Message(message);
        Assert.fail("Should not be here. The ADR_A19 parser provided by the module throws an ApplicationException.");
    } catch (HL7Exception e) {
        if (e.getCause() != null)
            Assert.assertEquals("In ADR A19 parser", e.getCause().getMessage());
        else {
            log.error("unable to parse message", e);
            Assert.fail("something bad happened, check the log statement 1 line up");
        }
    }
    ModuleUtil.shutdown();
}

Example 4 with Application

use of ca.uhn.hl7v2.app.Application 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 5 with Application

use of ca.uhn.hl7v2.app.Application in project openmrs-core by openmrs.

the class HL7ServiceTest method processHL7InQueue_shouldParseOruR01MessageUsingOverriddenParserProvidedByAModule.

/**
 * @see HL7Service#processHL7InQueue(HL7InQueue)
 */
@Test
@Ignore("TRUNK-3945")
public void processHL7InQueue_shouldParseOruR01MessageUsingOverriddenParserProvidedByAModule() throws Exception {
    executeDataSet("org/openmrs/hl7/include/ORUTest-initialData.xml");
    Properties props = super.getRuntimeProperties();
    props.setProperty(ModuleConstants.RUNTIMEPROPERTY_MODULE_LIST_TO_LOAD, "org/openmrs/hl7/include/examplehl7handlers-0.1.omod");
    // the above module provides a handler for messages of type "ADR" with trigger "A19"
    ModuleUtil.startup(props);
    // the application context cannot restart here to load in the moduleApplicationContext that
    // calls the setHL7Handlers method so we're doing it manually here
    Class<Application> c = (Class<Application>) Context.loadClass("org.openmrs.module.examplehl7handlers.AlternateORUR01Handler");
    Application classInstance = c.newInstance();
    HashMap<String, Application> map = new HashMap<>();
    map.put("ORU_R01", classInstance);
    HL7ServiceImpl.getInstance().setHL7Handlers(map);
    HL7Service hl7service = Context.getHL7Service();
    // a valid ORU_R01
    HL7InQueue queueItem = hl7service.getHL7InQueue(1);
    // this will create 1 HL7InError item
    hl7service.processHL7InQueue(queueItem);
    List<HL7InError> errors = hl7service.getAllHL7InErrors();
    // get the last error, the one made by this test presumably
    HL7InError error = errors.get(errors.size() - 1);
    Assert.assertTrue(error.getErrorDetails().contains("In alternate oru r01 parser"));
    ModuleUtil.shutdown();
}