Examples with ConceptName org.openmrs.ConceptName used on opensource projects

Example 41 with ConceptName

use of org.openmrs.ConceptName in project openmrs-core by openmrs.

the class ORUR01Handler method parseObs.

/**
 * Creates the Obs pojo from the OBX message
 *
 * @param encounter The Encounter object this Obs is a member of
 * @param obx The hl7 obx message
 * @param obr The parent hl7 or message
 * @param uid unique string for this message for any error reporting purposes
 * @return Obs pojo with all values filled in
 * @throws HL7Exception if there is a parsing exception
 * @throws ProposingConceptException if the answer to this obs is a proposed concept
 * @should add comments to an observation from NTE segments
 * @should add multiple comments for an observation as one comment
 * @should add comments to an observation group
 */
private Obs parseObs(Encounter encounter, OBX obx, OBR obr, String uid) throws HL7Exception, ProposingConceptException {
    if (log.isDebugEnabled()) {
        log.debug("parsing observation: " + obx);
    }
    Varies[] values = obx.getObservationValue();
    // bail out if no values were found
    if (values == null || values.length < 1) {
        return null;
    }
    String hl7Datatype = values[0].getName();
    if (log.isDebugEnabled()) {
        log.debug("  datatype = " + hl7Datatype);
    }
    Concept concept = getConcept(obx.getObservationIdentifier(), uid);
    if (log.isDebugEnabled()) {
        log.debug("  concept = " + concept.getConceptId());
    }
    ConceptName conceptName = getConceptName(obx.getObservationIdentifier());
    if (log.isDebugEnabled()) {
        log.debug("  concept-name = " + conceptName);
    }
    Date datetime = getDatetime(obx);
    if (log.isDebugEnabled()) {
        log.debug("  timestamp = " + datetime);
    }
    if (datetime == null) {
        datetime = encounter.getEncounterDatetime();
    }
    Obs obs = new Obs();
    obs.setPerson(encounter.getPatient());
    obs.setConcept(concept);
    obs.setEncounter(encounter);
    obs.setObsDatetime(datetime);
    obs.setLocation(encounter.getLocation());
    obs.setCreator(encounter.getCreator());
    obs.setDateCreated(encounter.getDateCreated());
    // set comments if there are any
    StringBuilder comments = new StringBuilder();
    ORU_R01_OBSERVATION parent = (ORU_R01_OBSERVATION) obx.getParent();
    // iterate over all OBX NTEs
    for (int i = 0; i < parent.getNTEReps(); i++) {
        for (FT obxComment : parent.getNTE(i).getComment()) {
            if (comments.length() > 0) {
                comments.append(" ");
            }
            comments = comments.append(obxComment.getValue());
        }
    }
    // only set comments if there are any
    if (StringUtils.hasText(comments.toString())) {
        obs.setComment(comments.toString());
    }
    Type obx5 = values[0].getData();
    if ("NM".equals(hl7Datatype)) {
        String value = ((NM) obx5).getValue();
        if (value == null || value.length() == 0) {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        } else if ("0".equals(value) || "1".equals(value)) {
            concept = concept.hydrate(concept.getConceptId().toString());
            obs.setConcept(concept);
            if (concept.getDatatype().isBoolean()) {
                obs.setValueBoolean("1".equals(value));
            } else if (concept.getDatatype().isNumeric()) {
                try {
                    obs.setValueNumeric(Double.valueOf(value));
                } catch (NumberFormatException e) {
                    throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.notnumericConcept", new Object[] { value, concept.getConceptId(), conceptName.getName(), uid }, null), e);
                }
            } else if (concept.getDatatype().isCoded()) {
                Concept answer = "1".equals(value) ? Context.getConceptService().getTrueConcept() : Context.getConceptService().getFalseConcept();
                boolean isValidAnswer = false;
                Collection<ConceptAnswer> conceptAnswers = concept.getAnswers();
                if (conceptAnswers != null && !conceptAnswers.isEmpty()) {
                    for (ConceptAnswer conceptAnswer : conceptAnswers) {
                        if (conceptAnswer.getAnswerConcept().getId().equals(answer.getId())) {
                            obs.setValueCoded(answer);
                            isValidAnswer = true;
                            break;
                        }
                    }
                }
                // answer the boolean answer concept was't found
                if (!isValidAnswer) {
                    throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.invalidAnswer", new Object[] { answer.toString(), uid }, null));
                }
            } else {
                // throw this exception to make sure that the handler doesn't silently ignore bad hl7 message
                throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.CannotSetBoolean", new Object[] { obs.getConcept().getConceptId() }, null));
            }
        } else {
            try {
                obs.setValueNumeric(Double.valueOf(value));
            } catch (NumberFormatException e) {
                throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.notnumericConcept", new Object[] { value, concept.getConceptId(), conceptName.getName(), uid }, null), e);
            }
        }
    } else if ("CWE".equals(hl7Datatype)) {
        log.debug("  CWE observation");
        CWE value = (CWE) obx5;
        String valueIdentifier = value.getIdentifier().getValue();
        log.debug("    value id = " + valueIdentifier);
        String valueName = value.getText().getValue();
        log.debug("    value name = " + valueName);
        if (isConceptProposal(valueIdentifier)) {
            if (log.isDebugEnabled()) {
                log.debug("Proposing concept");
            }
            throw new ProposingConceptException(concept, valueName);
        } else {
            log.debug("    not proposal");
            try {
                Concept valueConcept = getConcept(value, uid);
                obs.setValueCoded(valueConcept);
                if (HL7Constants.HL7_LOCAL_DRUG.equals(value.getNameOfAlternateCodingSystem().getValue())) {
                    Drug valueDrug = new Drug();
                    valueDrug.setDrugId(Integer.valueOf(value.getAlternateIdentifier().getValue()));
                    obs.setValueDrug(valueDrug);
                } else {
                    ConceptName valueConceptName = getConceptName(value);
                    if (valueConceptName != null) {
                        if (log.isDebugEnabled()) {
                            log.debug("    value concept-name-id = " + valueConceptName.getConceptNameId());
                            log.debug("    value concept-name = " + valueConceptName.getName());
                        }
                        obs.setValueCodedName(valueConceptName);
                    }
                }
            } catch (NumberFormatException e) {
                throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.InvalidConceptId", new Object[] { valueIdentifier, valueName }, null));
            }
        }
        if (log.isDebugEnabled()) {
            log.debug("  Done with CWE");
        }
    } else if ("CE".equals(hl7Datatype)) {
        CE value = (CE) obx5;
        String valueIdentifier = value.getIdentifier().getValue();
        String valueName = value.getText().getValue();
        if (isConceptProposal(valueIdentifier)) {
            throw new ProposingConceptException(concept, valueName);
        } else {
            try {
                obs.setValueCoded(getConcept(value, uid));
                obs.setValueCodedName(getConceptName(value));
            } catch (NumberFormatException e) {
                throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.InvalidConceptId", new Object[] { valueIdentifier, valueName }, null));
            }
        }
    } else if ("DT".equals(hl7Datatype)) {
        DT value = (DT) obx5;
        if (value != null) {
            Date valueDate = getDate(value.getYear(), value.getMonth(), value.getDay(), 0, 0, 0);
            obs.setValueDatetime(valueDate);
        } else {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        }
    } else if ("TS".equals(hl7Datatype)) {
        DTM value = ((TS) obx5).getTime();
        if (value != null) {
            Date valueDate = getDate(value.getYear(), value.getMonth(), value.getDay(), value.getHour(), value.getMinute(), value.getSecond());
            obs.setValueDatetime(valueDate);
        } else {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        }
    } else if ("TM".equals(hl7Datatype)) {
        TM value = (TM) obx5;
        if (value != null) {
            Date valueTime = getDate(0, 0, 0, value.getHour(), value.getMinute(), value.getSecond());
            obs.setValueDatetime(valueTime);
        } else {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        }
    } else if ("ST".equals(hl7Datatype)) {
        ST value = (ST) obx5;
        if (value == null || value.getValue() == null || value.getValue().trim().length() == 0) {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        }
        obs.setValueText(value.getValue());
    } else if ("ED".equals(hl7Datatype)) {
        ED value = (ED) obx5;
        if (value == null || value.getData() == null || !StringUtils.hasText(value.getData().getValue())) {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        }
        // we need to hydrate the concept so that the EncounterSaveHandler
        // doesn't fail since it needs to check if it is a concept numeric
        Concept c = Context.getConceptService().getConcept(obs.getConcept().getConceptId());
        obs.setConcept(c);
        String title = null;
        if (obs.getValueCodedName() != null) {
            title = obs.getValueCodedName().getName();
        }
        if (!StringUtils.hasText(title)) {
            title = c.getName().getName();
        }
        obs.setComplexData(new ComplexData(title, value.getData().getValue()));
    } else {
        // do we need to support BIT just in case it slips thru?
        throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.UpsupportedObsType", new Object[] { hl7Datatype }, null));
    }
    return obs;
}

Example 42 with ConceptName

use of org.openmrs.ConceptName in project openmrs-core by openmrs.

the class ORUR01Handler method getConceptName.

/**
 * Utility method to retrieve the openmrs ConceptName specified in an hl7 message observation
 * segment. This method assumes that the check for 99NAM has been done already and is being
 * given an openmrs conceptNameId
 *
 * @param hl7ConceptNameId internal ConceptNameId to look up
 * @return ConceptName from the database
 * @throws HL7Exception
 */
private ConceptName getConceptName(String hl7ConceptNameId) throws HL7Exception {
    ConceptName specifiedConceptName = null;
    if (hl7ConceptNameId != null) {
        // get the exact concept name specified by the id
        try {
            Integer conceptNameId = Integer.valueOf(hl7ConceptNameId);
            specifiedConceptName = new ConceptName();
            specifiedConceptName.setConceptNameId(conceptNameId);
        } catch (NumberFormatException e) {
            // if it is not a valid number, more than likely it is a bad hl7 message
            log.debug("Invalid concept name ID '" + hl7ConceptNameId + "'", e);
        }
    }
    return specifiedConceptName;
}

Example 43 with ConceptName

use of org.openmrs.ConceptName in project openmrs-core by openmrs.

the class ORUR01HandlerTest method processMessage_shouldCreateObsValueCodedName.

/**
 * @see ORUR01Handler#processMessage(Message)
 */
@Test
public void processMessage_shouldCreateObsValueCodedName() throws Exception {
    ObsService obsService = Context.getObsService();
    // the patient that is the focus of
    Patient patient = new Patient(3);
    // this hl7 message
    // the question concept for
    Concept concept = new Concept(21);
    // "Food assistance for entire family?"
    // sanity check to make sure this obs doesn't exist already
    Assert.assertEquals(0, obsService.getObservationsByPersonAndConcept(patient, concept).size());
    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" + "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";
    Message hl7message = parser.parse(hl7String);
    router.processMessage(hl7message);
    List<Obs> obss = obsService.getObservationsByPersonAndConcept(patient, concept);
    ConceptName name = obss.get(0).getValueCodedName();
    Assert.assertNotNull(name);
    Assert.assertEquals("The valueCodedName should be 2471", 2471, name.getId().intValue());
}

Example 44 with ConceptName

use of org.openmrs.ConceptName in project openmrs-core by openmrs.

the class HibernateConditionDAOTest method shouldSaveCondition.

@Test
public void shouldSaveCondition() {
    CodedOrFreeText codedOrFreeText = new CodedOrFreeText(new Concept(4), new ConceptName(5089), "non coded");
    ConditionClinicalStatus clinicalStatus = ConditionClinicalStatus.ACTIVE;
    ConditionVerificationStatus verificationStatus = ConditionVerificationStatus.CONFIRMED;
    Patient patient = new Patient(2);
    Date onsetDate = new Date();
    Date endDate = new Date();
    Condition previousVersion = dao.getConditionByUuid("2cc6880e-2c46-15e4-9038-a6c5e4d22fb7");
    String additionalDetail = "additionalDetail";
    int conditionId = 20;
    Condition condition = new Condition();
    condition.setConditionId(conditionId);
    condition.setCondition(codedOrFreeText);
    condition.setClinicalStatus(clinicalStatus);
    condition.setVerificationStatus(verificationStatus);
    condition.setPreviousVersion(previousVersion);
    condition.setAdditionalDetail(additionalDetail);
    condition.setOnsetDate(onsetDate);
    condition.setEndDate(endDate);
    condition.setPatient(patient);
    dao.saveCondition(condition);
    Condition savedCondition = dao.getCondition(conditionId);
    assertEquals(additionalDetail, savedCondition.getAdditionalDetail());
    assertEquals(conditionId, (int) savedCondition.getConditionId());
    assertEquals(onsetDate, savedCondition.getOnsetDate());
    assertEquals(endDate, savedCondition.getEndDate());
    assertEquals(clinicalStatus, savedCondition.getClinicalStatus());
    assertEquals(verificationStatus, savedCondition.getVerificationStatus());
    assertEquals(previousVersion, savedCondition.getPreviousVersion());
    assertEquals(patient, savedCondition.getPatient());
}

Example 45 with ConceptName

use of org.openmrs.ConceptName in project openmrs-module-coreapps by openmrs.

the class EncounterDiagnosesFragmentControllerTest method testController_createdProperPriorDiagnoses.

@Test
public void testController_createdProperPriorDiagnoses() throws Exception {
    EncounterDiagnosesFragmentController controller = new EncounterDiagnosesFragmentController();
    ConceptName specificName = new ConceptName("Specific Name", Context.getLocale());
    specificName.setId(1);
    specificName.setLocalePreferred(true);
    Concept conceptForSpecificName = new Concept();
    conceptForSpecificName.setId(2);
    conceptForSpecificName.addName(specificName);
    Concept nonSpecificConcept = new Concept();
    nonSpecificConcept.setId(3);
    ConceptName nonSpecificConceptName = new ConceptName("Non-specific concept", Context.getLocale());
    nonSpecificConceptName.setId(4);
    nonSpecificConceptName.setLocalePreferred(true);
    nonSpecificConcept.addName(nonSpecificConceptName);
    List<Diagnosis> diagnoses = new ArrayList<Diagnosis>();
    diagnoses.add(new Diagnosis(new CodedOrFreeTextAnswer(specificName), Diagnosis.Order.PRIMARY));
    diagnoses.add(new Diagnosis(new CodedOrFreeTextAnswer(nonSpecificConcept), Diagnosis.Order.SECONDARY));
    diagnoses.add(new Diagnosis(new CodedOrFreeTextAnswer("Unknown Disease"), Diagnosis.Order.SECONDARY));
    for (Diagnosis d : diagnoses) {
        d.setExistingObs(new Obs());
    }
    FragmentModel model = new FragmentModel();
    controller.controller(new TestUiUtils(), null, diagnoses, model);
    assertThat(((List<String>) model.getAttribute("jsForExisting")).size(), is(0));
    List<String> jsForPrior = (List<String>) model.getAttribute("jsForPrior");
    assertThat(jsForPrior.get(0), is("{ diagnosis: diagnoses.CodedOrFreeTextConceptAnswer({\"word\":null,\"conceptName\":{\"id\":1,\"uuid\":\"" + specificName.getUuid() + "\",\"conceptNameType\":\"FULLY_SPECIFIED\",\"name\":\"Specific Name\"},\"concept\":{\"id\":2,\"uuid\":\"" + conceptForSpecificName.getUuid() + "\",\"conceptMappings\":[],\"preferredName\":\"Specific Name\"}}), confirmed: false, primary: true, existingObs: null }"));
    assertThat(jsForPrior.get(1), is("{ diagnosis: diagnoses.CodedOrFreeTextConceptAnswer({\"word\":null,\"conceptName\":null,\"concept\":{\"id\":3,\"uuid\":\"" + nonSpecificConcept.getUuid() + "\",\"conceptMappings\":[],\"preferredName\":\"Non-specific concept\"}}), confirmed: false, primary: false, existingObs: null }"));
    assertThat(jsForPrior.get(2), is("{ diagnosis: diagnoses.CodedOrFreeTextConceptAnswer('Unknown Disease'), confirmed: false, primary: false, existingObs: null }"));
}