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

Example 6 with ConceptAnswer

use of org.openmrs.ConceptAnswer 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 7 with ConceptAnswer

use of org.openmrs.ConceptAnswer in project openmrs-module-pihcore by PIH.

the class ConceptDictionaryExportTest method exportData.

/**
 * Intentional issues currently with this, in order to isolate away known issues.  These should be removed as appropriate:
 * - Normalizes concept source name, due to known issue needed in OCL to facilitate source matching
 * - Excludes voided concept names (which are really retired names that may have references), as these are not provided by ocl
 * - Converts answer sort weight from null -> 1.0 if only one answer exists for the concept
 */
@Test
public void exportData() throws Exception {
    // Only run this test if it is being run alone.  This ensures this test will not run in normal build.
    if (props == null) {
        return;
    }
    if (!Context.isSessionOpen()) {
        Context.openSession();
    }
    authenticate();
    List<Map<String, Object>> concepts = new ArrayList<>();
    System.out.println("Pulling concepts");
    int i = 0;
    List<Concept> conceptList = Context.getConceptService().getAllConcepts();
    conceptList.sort(Comparator.comparing(t -> t.getUuid().toUpperCase()));
    List<Concept> conceptsToIgnore = getConceptsToIgnore();
    conceptList.removeAll(conceptsToIgnore);
    for (Concept concept : conceptList) {
        System.out.println(i++ + ": Pulling concept: " + concept.getUuid());
        Map<String, Object> c = new LinkedHashMap<>();
        concepts.add(c);
        c.put("uuid", concept.getUuid());
        c.put("concept_class", concept.getConceptClass().getName());
        c.put("concept_datatype", concept.getDatatype().getName());
        c.put("is_set", BooleanUtils.isTrue(concept.getSet()) ? "true" : "false");
        c.put("version", concept.getVersion() == null ? "" : concept.getVersion());
        c.put("retired", BooleanUtils.isTrue(concept.getRetired()) ? "true" : "false");
        c.put("retireReason", concept.getRetireReason() == null ? "" : concept.getRetireReason());
        if (concept instanceof ConceptNumeric) {
            ConceptNumeric cn = (ConceptNumeric) concept;
            c.put("hi_absolute", cn.getHiAbsolute() == null ? "" : cn.getHiAbsolute().toString());
            c.put("hi_critical", cn.getLowAbsolute() == null ? "" : cn.getLowAbsolute().toString());
            c.put("hi_normal", cn.getHiNormal() == null ? "" : cn.getHiNormal().toString());
            c.put("low_absolute", cn.getLowAbsolute() == null ? "" : cn.getLowAbsolute().toString());
            c.put("low_critical", cn.getLowCritical() == null ? "" : cn.getLowCritical().toString());
            c.put("low_normal", cn.getLowNormal() == null ? "" : cn.getLowNormal().toString());
            c.put("units", cn.getUnits() == null ? "" : cn.getUnits());
            c.put("allow_decimal", BooleanUtils.isTrue(cn.getAllowDecimal()) ? "true" : "false");
            c.put("display_precision", cn.getHiAbsolute() == null ? "" : cn.getHiAbsolute().toString());
        }
        if (concept instanceof ConceptComplex) {
            ConceptComplex cc = (ConceptComplex) concept;
            c.put("handler", cc.getHandler());
        }
        List<ConceptName> names = new ArrayList<>(concept.getNames(true));
        names.sort(Comparator.comparing(ConceptName::getName).thenComparing(cn -> cn.getConceptNameType() == null ? "" : cn.getConceptNameType().name()).thenComparing(cn -> cn.getLocale().toString()).thenComparing(ConceptName::getLocalePreferred));
        List<Map<String, Object>> nameList = new ArrayList<>();
        for (ConceptName name : names) {
            if (BooleanUtils.isNotTrue(name.getVoided())) {
                Map<String, Object> n = new LinkedHashMap<>();
                n.put("name", name.getName());
                n.put("locale", name.getLocale().toString());
                n.put("locale_preferred", BooleanUtils.isTrue(name.getLocalePreferred()) ? "true" : "false");
                n.put("type", name.getConceptNameType() == null ? "" : name.getConceptNameType().name());
                n.put("voided", BooleanUtils.isTrue(name.getVoided()) ? "true" : "false");
                nameList.add(n);
            }
        }
        c.put("names", nameList);
        List<ConceptDescription> descriptions = new ArrayList<>(concept.getDescriptions());
        descriptions.sort(Comparator.comparing(ConceptDescription::getDescription));
        List<Map<String, Object>> descriptionList = new ArrayList<>();
        for (ConceptDescription description : descriptions) {
            Map<String, Object> n = new LinkedHashMap<>();
            n.put("description", description.getDescription());
            n.put("locale", description.getLocale().toString());
            descriptionList.add(n);
        }
        c.put("descriptions", descriptionList);
        List<ConceptAnswer> answers = new ArrayList<>(concept.getAnswers(true));
        answers.sort(Comparator.comparingDouble(ConceptAnswer::getSortWeight).thenComparing(ca -> ca.getAnswerConcept().getUuid()));
        List<Map<String, Object>> answerList = new ArrayList<>();
        for (ConceptAnswer ca : answers) {
            if (!conceptsToIgnore.contains(ca.getAnswerConcept())) {
                Map<String, Object> n = new LinkedHashMap<>();
                n.put("answerConcept", ca.getAnswerConcept().getUuid());
                n.put("sortWeight", ca.getSortWeight() == null ? (answers.size() == 1 ? "1.0" : "") : ca.getSortWeight().toString());
                answerList.add(n);
            }
        }
        c.put("answers", answerList);
        List<ConceptSet> setMembers = new ArrayList<>(concept.getConceptSets());
        setMembers.sort(Comparator.comparingDouble(ConceptSet::getSortWeight).thenComparing(cs -> cs.getConcept().getUuid()));
        List<Map<String, Object>> setMemberList = new ArrayList<>();
        for (ConceptSet cs : setMembers) {
            if (!conceptsToIgnore.contains(cs.getConcept())) {
                Map<String, Object> n = new LinkedHashMap<>();
                n.put("concept", cs.getConcept().getUuid());
                n.put("sortWeight", cs.getSortWeight() == null ? "" : cs.getSortWeight().toString());
                setMemberList.add(n);
            }
        }
        c.put("setMembers", setMemberList);
        List<ConceptMap> mappings = new ArrayList<>(concept.getConceptMappings());
        mappings.sort(Comparator.comparing((ConceptMap m) -> m.getConceptReferenceTerm().getConceptSource().getName()).thenComparing(m -> m.getConceptMapType().getName()).thenComparing(m -> m.getConceptReferenceTerm().getCode()));
        List<Map<String, Object>> mappingList = new ArrayList<>();
        for (ConceptMap cm : mappings) {
            Map<String, Object> n = new LinkedHashMap<>();
            n.put("source", normalizeSourceName(cm.getConceptReferenceTerm().getConceptSource().getName()));
            n.put("type", cm.getConceptMapType().getName());
            n.put("code", cm.getConceptReferenceTerm().getCode());
            mappingList.add(n);
        }
        c.put("mappings", mappingList);
    }
    File exportFile = new File(EXPORT_DIR, EXPORT_FILENAME);
    System.out.println("Writing concepts to: " + exportFile);
    ObjectMapper objectMapper = new ObjectMapper();
    objectMapper.writerWithDefaultPrettyPrinter().writeValue(exportFile, concepts);
    System.out.println("Concepts exported successfully");
}

Example 8 with ConceptAnswer

use of org.openmrs.ConceptAnswer in project openmrs-module-mirebalais by PIH.

the class PatientRegistrationApp method populateDropdownWithConceptAnswers.

protected void populateDropdownWithConceptAnswers(DropdownWidget d, Concept questionConcept) {
    List<ConceptAnswer> conceptAnswers = new ArrayList<ConceptAnswer>(questionConcept.getAnswers());
    Collections.sort(conceptAnswers, new Comparator<ConceptAnswer>() {

        @Override
        public int compare(ConceptAnswer answer1, ConceptAnswer answer2) {
            return answer1.getAnswerConcept().getName().toString().compareTo(answer2.getAnswerConcept().getName().toString());
        }
    });
    for (ConceptAnswer conceptAnswer : conceptAnswers) {
        d.getConfig().addOption(conceptAnswer.getAnswerConcept().getId().toString(), conceptAnswer.getAnswerConcept().getName().toString());
    }
}

Example 9 with ConceptAnswer

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

the class EncounterDispositionTagHandlerComponentTest method testFormOnlyShowsDispositionsInDescriptor.

@Test
public void testFormOnlyShowsDispositionsInDescriptor() throws Exception {
    ConceptClass misc = conceptService.getConceptClassByName("Misc");
    ConceptDatatype naDatatype = conceptService.getConceptDatatypeByName("N/A");
    Concept dispositionConcept = dispositionService.getDispositionDescriptor().getDispositionConcept();
    dispositionConcept.addAnswer(new ConceptAnswer(new ConceptBuilder(conceptService, naDatatype, misc).addName("Should not be in option list").saveAndGet()));
    new RegressionTestHelper() {

        @Override
        public void testBlankFormHtml(String html) {
            assertThat(html, containsString("disposition.admission"));
            assertThat(html, containsString("disposition.transfer"));
            assertThat(html, containsString("disposition.discharge"));
            assertThat(html, not(containsString("Should not be in option list")));
        }

        @Override
        public String getXmlDatasetPath() {
            return "";
        }

        @Override
        public String getFormName() {
            return "encounterDispositionSimpleForm";
        }

        @Override
        public Map<String, Object> getFormEntrySessionAttributes() {
            Map<String, Object> attributes = new HashMap<String, Object>();
            attributes.put("uiUtils", new TestUiUtils());
            return attributes;
        }

        @Override
        public String[] widgetLabels() {
            return new String[] { "Date:", "Location:", "Provider:", "Disposition:", "Encounter Type:" };
        }
    }.run();
}

Example 10 with ConceptAnswer

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

the class QuickVisitFragmentController method getConceptAnswers.

public SimpleObject getConceptAnswers(@RequestParam("conceptId") Concept concept) {
    SimpleObject results = new SimpleObject();
    List<SimpleObject> values = new LinkedList<SimpleObject>();
    for (ConceptAnswer conceptAnswer : concept.getAnswers()) {
        SimpleObject conceptAnswerMap = new SimpleObject();
        conceptAnswerMap.put("uuid", conceptAnswer.getUuid());
        conceptAnswerMap.put("name", conceptAnswer.getAnswerConcept().getName().getName());
        values.add(conceptAnswerMap);
    }
    results.put("results", values);
    return results;
}