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

Example 11 with ConceptNumeric

use of org.openmrs.ConceptNumeric 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 12 with ConceptNumeric

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

the class ConceptServiceTest method saveConcept_shouldSaveNonConceptNumericObjectAsConceptNumeric.

/**
 * @see ConceptService#saveConcept(Concept)
 */
@Test
public void saveConcept_shouldSaveNonConceptNumericObjectAsConceptNumeric() {
    executeDataSet(INITIAL_CONCEPTS_XML);
    // this tests saving a current concept as a newly changed conceptnumeric
    // assumes there is already a concept in the database
    // with a concept id of #1
    ConceptNumeric cn = new ConceptNumeric(1);
    cn.setDatatype(new ConceptDatatype(1));
    cn.setConceptClass(new ConceptClass(1));
    cn.addName(new ConceptName("a new conceptnumeric", Locale.US));
    cn.addDescription(new ConceptDescription("some description", null));
    cn.setHiAbsolute(20.0);
    conceptService.saveConcept(cn);
    Concept firstConcept = conceptService.getConceptNumeric(1);
    firstConcept.addDescription(new ConceptDescription("some description", null));
    assertEquals("a new conceptnumeric", firstConcept.getName(Locale.US).getName());
    assertTrue(firstConcept instanceof ConceptNumeric);
    ConceptNumeric firstConceptNumeric = (ConceptNumeric) firstConcept;
    assertEquals(20.0, firstConceptNumeric.getHiAbsolute(), 0);
}

Example 13 with ConceptNumeric

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

the class AuditableInterceptorTest method onFlushDirty_shouldNotFailWhenTheDaemonUserModifiesSomething.

/**
 * @see AuditableInterceptor#onFlushDirty(Object,Serializable,null,null,null,null)
 */
@Test
public void onFlushDirty_shouldNotFailWhenTheDaemonUserModifiesSomething() throws Throwable {
    new AsDaemonTask(new AbstractTask() {

        @Override
        public void execute() {
            ConceptNumeric weight = Context.getConceptService().getConceptNumeric(5089);
            Date dateChangedBefore = weight.getDateChanged();
            weight.setHiAbsolute(75d);
            Context.getConceptService().saveConcept(weight);
            Assert.assertNotSame(dateChangedBefore, weight.getDateChanged());
        }
    }).runTheTask();
}

Example 14 with ConceptNumeric

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

the class ObsValidator method validateHelper.

/**
 * Checks whether obs has all required values, and also checks to make sure that no obs group
 * contains any of its ancestors
 *
 * @param obs
 * @param errors
 * @param ancestors
 * @param atRootNode whether or not this is the obs that validate() was originally called on. If
 *            not then we shouldn't reject fields by name.
 */
private void validateHelper(Obs obs, Errors errors, List<Obs> ancestors, boolean atRootNode) {
    if (obs.getPersonId() == null) {
        errors.rejectValue("person", "error.null");
    }
    if (obs.getObsDatetime() == null) {
        errors.rejectValue("obsDatetime", "error.null");
    }
    // if this is an obs group (i.e., parent) make sure that it has no values (other than valueGroupId) set
    if (obs.hasGroupMembers()) {
        if (obs.getValueCoded() != null) {
            errors.rejectValue("valueCoded", "error.not.null");
        }
        if (obs.getValueDrug() != null) {
            errors.rejectValue("valueDrug", "error.not.null");
        }
        if (obs.getValueDatetime() != null) {
            errors.rejectValue("valueDatetime", "error.not.null");
        }
        if (obs.getValueNumeric() != null) {
            errors.rejectValue("valueNumeric", "error.not.null");
        }
        if (obs.getValueModifier() != null) {
            errors.rejectValue("valueModifier", "error.not.null");
        }
        if (obs.getValueText() != null) {
            errors.rejectValue("valueText", "error.not.null");
        }
        if (obs.getValueBoolean() != null) {
            errors.rejectValue("valueBoolean", "error.not.null");
        }
        if (obs.getValueComplex() != null) {
            errors.rejectValue("valueComplex", "error.not.null");
        }
    } else // if this is NOT an obs group, make sure that it has at least one value set (not counting obsGroupId)
    if (obs.getValueBoolean() == null && obs.getValueCoded() == null && obs.getValueCodedName() == null && obs.getValueComplex() == null && obs.getValueDatetime() == null && obs.getValueDrug() == null && obs.getValueModifier() == null && obs.getValueNumeric() == null && obs.getValueText() == null && obs.getComplexData() == null) {
        errors.reject("error.noValue");
    }
    // make sure there is a concept associated with the obs
    Concept c = obs.getConcept();
    if (c == null) {
        errors.rejectValue("concept", "error.null");
    } else // if there is a concept, and this isn't a group, perform validation tests specific to the concept datatype
    if (!obs.hasGroupMembers()) {
        ConceptDatatype dt = c.getDatatype();
        if (dt != null) {
            if (dt.isBoolean() && obs.getValueBoolean() == null) {
                if (atRootNode) {
                    errors.rejectValue("valueBoolean", "error.null");
                } else {
                    errors.rejectValue("groupMembers", "Obs.error.inGroupMember");
                }
            } else if (dt.isCoded() && obs.getValueCoded() == null) {
                if (atRootNode) {
                    errors.rejectValue("valueCoded", "error.null");
                } else {
                    errors.rejectValue("groupMembers", "Obs.error.inGroupMember");
                }
            } else if ((dt.isDateTime() || dt.isDate() || dt.isTime()) && obs.getValueDatetime() == null) {
                if (atRootNode) {
                    errors.rejectValue("valueDatetime", "error.null");
                } else {
                    errors.rejectValue("groupMembers", "Obs.error.inGroupMember");
                }
            } else if (dt.isNumeric() && obs.getValueNumeric() == null) {
                if (atRootNode) {
                    errors.rejectValue("valueNumeric", "error.null");
                } else {
                    errors.rejectValue("groupMembers", "Obs.error.inGroupMember");
                }
            } else if (dt.isNumeric()) {
                ConceptNumeric cn = Context.getConceptService().getConceptNumeric(c.getConceptId());
                // If the concept numeric is not precise, the value cannot be a float, so raise an error
                if (!cn.getAllowDecimal() && Math.ceil(obs.getValueNumeric()) != obs.getValueNumeric()) {
                    if (atRootNode) {
                        errors.rejectValue("valueNumeric", "Obs.error.precision");
                    } else {
                        errors.rejectValue("groupMembers", "Obs.error.inGroupMember");
                    }
                }
                // If the number is higher than the absolute range, raise an error
                if (cn.getHiAbsolute() != null && cn.getHiAbsolute() < obs.getValueNumeric()) {
                    if (atRootNode) {
                        errors.rejectValue("valueNumeric", "error.outOfRange.high");
                    } else {
                        errors.rejectValue("groupMembers", "Obs.error.inGroupMember");
                    }
                }
                // If the number is lower than the absolute range, raise an error as well
                if (cn.getLowAbsolute() != null && cn.getLowAbsolute() > obs.getValueNumeric()) {
                    if (atRootNode) {
                        errors.rejectValue("valueNumeric", "error.outOfRange.low");
                    } else {
                        errors.rejectValue("groupMembers", "Obs.error.inGroupMember");
                    }
                }
            } else if (dt.isText() && obs.getValueText() == null) {
                if (atRootNode) {
                    errors.rejectValue("valueText", "error.null");
                } else {
                    errors.rejectValue("groupMembers", "Obs.error.inGroupMember");
                }
            }
            // If valueText is longer than the maxlength, raise an error as well.
            if (dt.isText() && obs.getValueText() != null && obs.getValueText().length() > VALUE_TEXT_MAX_LENGTH) {
                if (atRootNode) {
                    errors.rejectValue("valueText", "error.exceededMaxLengthOfField");
                } else {
                    errors.rejectValue("groupMembers", "Obs.error.inGroupMember");
                }
            }
        } else {
            // dt is null
            errors.rejectValue("concept", "must have a datatype");
        }
    }
    // If an obs fails validation, don't bother checking its children
    if (errors.hasErrors()) {
        return;
    }
    if (ancestors.contains(obs)) {
        errors.rejectValue("groupMembers", "Obs.error.groupContainsItself");
    }
    if (obs.isObsGrouping()) {
        ancestors.add(obs);
        for (Obs child : obs.getGroupMembers()) {
            validateHelper(child, errors, ancestors, false);
        }
        ancestors.remove(ancestors.size() - 1);
    }
    if (obs.getValueCoded() != null && obs.getValueDrug() != null && obs.getValueDrug().getConcept() != null) {
        Concept trueConcept = Context.getConceptService().getTrueConcept();
        Concept falseConcept = Context.getConceptService().getFalseConcept();
        // Ignore if this is not a true or false response since they are stored as coded too
        if (!obs.getValueCoded().equals(trueConcept) && !obs.getValueCoded().equals(falseConcept) && !obs.getValueDrug().getConcept().equals(obs.getValueCoded())) {
            errors.rejectValue("valueDrug", "Obs.error.invalidDrug");
        }
    }
}

Example 15 with ConceptNumeric

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

the class OpenmrsUtilUnitTest method isValidNumericValue_shouldReturnTrueIfValueIsEqualToHiRangeLimit.

@Test
public void isValidNumericValue_shouldReturnTrueIfValueIsEqualToHiRangeLimit() {
    ConceptNumeric concept = new ConceptNumeric();
    concept.setHiCritical(4.34d);
    concept.setLowCritical(3.67d);
    assertFalse(OpenmrsUtil.isInAbsoluteNumericRange(4.34f, concept));
}