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

Example 16 with ID

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

the class ORUR01HandlerTest method processMessage_shouldCreateObsGroupForOBRs.

/**
 * This method checks that obs grouping is happening correctly when processing an ORUR01
 *
 * @see ORUR01Handler#processMessage(Message)
 */
@Test
public void processMessage_shouldCreateObsGroupForOBRs() throws Exception {
    ObsService obsService = Context.getObsService();
    String hl7string = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20080226103553||ORU^R01|OD9PWqcD9g0NKn81rvSD|P|2.5|1||||||||66^AMRS.ELD.FORMID\r" + "PID|||3^^^^||John^Doe^||\r" + "PV1||O|1^Unknown Location||||1^Super User (1-8)|||||||||||||||||||||||||||||||||||||20080205|||||||V\r" + "ORC|RE||||||||20080226103428|1^Super User\r" + "OBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\r" + "OBX|1|DT|1592^MISSED RETURNED VISIT DATE^99DCT||20080201|||||||||20080205\r" + "OBR|2|||1726^FOLLOW-UP ACTION^99DCT\r" + "OBX|1|CWE|1558^PATIENT CONTACT METHOD^99DCT|1|1555^PHONE^99DCT|||||||||20080205\r" + "OBX|2|NM|1553^NUMBER OF ATTEMPTS^99DCT|1|1|||||||||20080205\r" + "OBX|3|NM|1554^SUCCESSFUL^99DCT|1|1|||||||||20080205";
    Message hl7message = parser.parse(hl7string);
    router.processMessage(hl7message);
    Patient patient = new Patient(3);
    Context.clearSession();
    // check for any obs
    List<Obs> obsForPatient2 = obsService.getObservationsByPerson(patient);
    assertNotNull(obsForPatient2);
    assertTrue("There should be some obs created for #3", obsForPatient2.size() > 0);
    // check for the missed return visit date obs
    Concept returnVisitDateConcept = new Concept(1592);
    Calendar cal = new GregorianCalendar();
    cal.set(2008, Calendar.FEBRUARY, 1, 0, 0, 0);
    Date returnVisitDate = cal.getTime();
    List<Obs> returnVisitDateObsForPatient2 = obsService.getObservationsByPersonAndConcept(patient, returnVisitDateConcept);
    assertEquals("There should be a return visit date", 1, returnVisitDateObsForPatient2.size());
    Obs firstObs = (Obs) returnVisitDateObsForPatient2.toArray()[0];
    cal.setTime(firstObs.getValueDatetime());
    cal.clear(Calendar.HOUR);
    cal.clear(Calendar.MINUTE);
    cal.clear(Calendar.SECOND);
    cal.clear(Calendar.MILLISECOND);
    assertEquals("The date should be the 1st", returnVisitDate.toString(), cal.getTime().toString());
    // check for the grouped obs
    Concept contactMethod = new Concept(1558);
    Concept phoneContact = Context.getConceptService().getConcept(1555);
    List<Obs> contactMethodObsForPatient2 = obsService.getObservationsByPersonAndConcept(patient, contactMethod);
    assertEquals("There should be a contact method", 1, contactMethodObsForPatient2.size());
    Obs firstContactMethodObs = (Obs) contactMethodObsForPatient2.toArray()[0];
    assertEquals("The contact method should be phone", phoneContact, firstContactMethodObs.getValueCoded());
    // check that there is a group id
    Obs obsGroup = firstContactMethodObs.getObsGroup();
    assertNotNull("Their should be a grouping obs", obsGroup);
    assertNotNull("Their should be an associated encounter", firstContactMethodObs.getEncounter());
    // check that the obs that are grouped have the same group id
    List<Integer> groupedConceptIds = new ArrayList<>();
    groupedConceptIds.add(1558);
    groupedConceptIds.add(1553);
    groupedConceptIds.add(1554);
    // total obs should be 5
    assertEquals(5, obsForPatient2.size());
    int groupedObsCount = 0;
    for (Obs obs : obsForPatient2) {
        if (groupedConceptIds.contains(obs.getConcept().getConceptId())) {
            groupedObsCount += 1;
            assertEquals("All of the parent groups should match", obsGroup, obs.getObsGroup());
        }
    }
    // the number of obs that were grouped
    assertEquals(3, groupedObsCount);
}

Example 17 with ID

use of ca.uhn.hl7v2.model.v25.datatype.ID 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 18 with ID

use of ca.uhn.hl7v2.model.v25.datatype.ID 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 19 with ID

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

the class ORUR01Handler method getConceptName.

/**
 * Derive a concept name from the CWE component of an hl7 message.
 *
 * @param cwe
 * @return
 * @throws HL7Exception
 */
private ConceptName getConceptName(CWE cwe) throws HL7Exception {
    ST altIdentifier = cwe.getAlternateIdentifier();
    ID altCodingSystem = cwe.getNameOfAlternateCodingSystem();
    return getConceptName(altIdentifier, altCodingSystem);
}

Example 20 with ID

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

the class ORUR01Handler method getConceptName.

/**
 * Derive a concept name from the CE component of an hl7 message.
 *
 * @param ce
 * @return
 * @throws HL7Exception
 */
private ConceptName getConceptName(CE ce) throws HL7Exception {
    ST altIdentifier = ce.getAlternateIdentifier();
    ID altCodingSystem = ce.getNameOfAlternateCodingSystem();
    return getConceptName(altIdentifier, altCodingSystem);
}