Examples with Range org.molgenis.api.metadata.v3.model.Range used on opensource projects

Example 11 with Range

use of org.molgenis.api.metadata.v3.model.Range in project molgenis by molgenis.

the class AttributeResponseMapperImpl method mapInternal.

private AttributeResponseData mapInternal(Attribute attr, boolean i18n) {
    Builder builder = AttributeResponseData.builder();
    builder.setId(attr.getIdentifier());
    builder.setName(attr.getName());
    builder.setSequenceNr(attr.getSequenceNumber());
    builder.setType(getValueString(attr.getDataType()));
    Optional.ofNullable(attr.getMaxLength()).ifPresent(builder::setMaxLength);
    builder.setIdAttribute(attr.isIdAttribute());
    builder.setLabelAttribute(attr.isLabelAttribute());
    builder.setLookupAttributeIndex(attr.getLookupAttributeIndex());
    if (EntityTypeUtils.isReferenceType(attr)) {
        builder.setRefEntityType(LinksResponse.create(null, createEntityTypeResponseUri(attr.getRefEntity()), null));
    }
    builder.setCascadeDelete(attr.getCascadeDelete());
    builder.setMappedBy(attr.getMappedBy() != null ? toAttributeResponse(attr.getMappedBy(), i18n) : null);
    if (attr.getDataType() == ONE_TO_MANY && attr.isMappedBy()) {
        builder.setOrderBy(map(attr));
    }
    builder.setLabel(attr.getLabel(LocaleContextHolder.getLocale().getLanguage()));
    builder.setDescription(attr.getDescription(LocaleContextHolder.getLocale().getLanguage()));
    if (i18n) {
        builder.setLabelI18n(getI18nAttrLabel(attr));
        getI18nAttrDesc(attr).ifPresent(builder::setDescriptionI18n);
    }
    builder.setNullable(attr.isNillable());
    builder.setAuto(attr.isAuto());
    builder.setVisible(attr.isVisible());
    builder.setUnique(attr.isUnique());
    builder.setReadOnly(attr.isReadOnly());
    builder.setAggregatable(attr.isAggregatable());
    builder.setExpression(attr.getExpression());
    if (attr.getDataType() == AttributeType.ENUM) {
        builder.setEnumOptions(attr.getEnumOptions());
    }
    if (attr.getDataType() == AttributeType.CATEGORICAL || attr.getDataType() == AttributeType.CATEGORICAL_MREF) {
        builder.setCategoricalOptions(getCategories(attr.getRefEntity()));
    }
    org.molgenis.data.Range range = attr.getRange();
    if (range != null) {
        builder.setRange(Range.create(range.getMin(), range.getMax()));
    }
    Attribute parent = attr.getParent();
    builder.setParentAttributeId(parent != null ? parent.getIdentifier() : null);
    builder.setNullableExpression(attr.getNullableExpression());
    builder.setVisibleExpression(attr.getVisibleExpression());
    builder.setValidationExpression(attr.getValidationExpression());
    builder.setDefaultValue(attr.getDefaultValue());
    return builder.build();
}

Example 12 with Range

use of org.molgenis.api.metadata.v3.model.Range in project FAAAST-Service by FraunhoferIOSB.

the class TypeExtractor method extractTypeInfo.

public static TypeInfo extractTypeInfo(Object obj) {
    if (obj == null) {
        return null;
    }
    Class<?> type = obj.getClass();
    if (SubmodelElement.class.isAssignableFrom(type)) {
        ElementValueTypeInfo.Builder builder = ElementValueTypeInfo.builder();
        SubmodelElement submodelElement = (SubmodelElement) obj;
        builder.type(ElementValueMapper.getValueClass(submodelElement.getClass()));
        if (AnnotatedRelationshipElement.class.isAssignableFrom(type)) {
            AnnotatedRelationshipElement annotatedRelationshipElement = (AnnotatedRelationshipElement) obj;
            annotatedRelationshipElement.getAnnotations().forEach(x -> builder.element(x.getIdShort(), extractTypeInfo(x)));
        } else if (SubmodelElementCollection.class.isAssignableFrom(type)) {
            SubmodelElementCollection submodelElementCollection = (SubmodelElementCollection) obj;
            submodelElementCollection.getValues().forEach(x -> builder.element(x.getIdShort(), extractTypeInfo(x)));
        } else if (Entity.class.isAssignableFrom(type)) {
            Entity entity = (Entity) obj;
            entity.getStatements().forEach(x -> builder.element(x.getIdShort(), extractTypeInfo(x)));
        } else if (Property.class.isAssignableFrom(obj.getClass())) {
            Property property = (Property) obj;
            builder.datatype(Datatype.fromName(property.getValueType()));
        } else if (Range.class.isAssignableFrom(obj.getClass())) {
            Range range = (Range) obj;
            builder.datatype(Datatype.fromName(range.getValueType()));
        }
        return builder.build();
    }
    if (Submodel.class.isAssignableFrom(type)) {
        Submodel submodel = (Submodel) obj;
        ContainerTypeInfo.Builder<Object> builder = ContainerTypeInfo.<Object>builder();
        builder.type(Submodel.class);
        submodel.getSubmodelElements().forEach(x -> builder.element(x.getIdShort(), extractTypeInfo(x)));
        return builder.build();
    }
    if (Collection.class.isAssignableFrom(type)) {
        Collection collection = (Collection) obj;
        ContainerTypeInfo.Builder<Integer> builder = ContainerTypeInfo.<Integer>builder();
        builder.type(Collection.class);
        builder.contentType(TypeToken.of(type).resolveType(COLLECTION_GENERIC_TOKEN).getRawType());
        Iterator iterator = collection.iterator();
        int i = 0;
        while (iterator.hasNext()) {
            builder.element(i, extractTypeInfo(iterator.next()));
            i++;
        }
        return builder.build();
    }
    if (Map.class.isAssignableFrom(type)) {
        Map map = (Map) obj;
        ContainerTypeInfo.Builder<String> builder = ContainerTypeInfo.<String>builder();
        builder.type(Map.class);
        builder.contentType(TypeToken.of(type).resolveType(MAP_GENERIC_TOKEN).getRawType());
        map.forEach((key, value) -> builder.element(key.toString(), extractTypeInfo(value)));
        return builder.build();
    }
    if (type.isArray()) {
        Object[] array = (Object[]) obj;
        ContainerTypeInfo.Builder<Integer> builder = ContainerTypeInfo.<Integer>builder();
        builder.type(Array.class);
        builder.contentType(type.getComponentType());
        for (int i = 0; i < array.length; i++) {
            builder.element(i, extractTypeInfo(array[i]));
        }
        return builder.build();
    }
    return ContainerTypeInfo.<Object>builder().build();
}

Example 13 with Range

use of org.molgenis.api.metadata.v3.model.Range in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7MedicationRequestFHIRConversionTest method dosageInstructionTestDoseRangeRXE.

@Test
void dosageInstructionTestDoseRangeRXE() {
    // Test dosageInstruction.DoseRange using RXE segment WITH a range
    String hl7message = "MSH|^~\\&||||||S1|RDE^O11||T|2.6|||||||||\n" + "PID|||1234^^^^MR||DOE^JANE^|||F||||||||||||||||||||||\n" + "ORC|NW|||||E|||||||||||||||||||||||I\n" + // RXE.6 through RXE.44 not used.
    "RXE||DUONEB3INH^3 ML PLAS CONT : IPRATROPIUM-ALBUTEROL 0.5-2.5 (3) MG/3ML IN SOLN^ADS|3|6|mL||||||||||||||||||||||||||||||||||\n";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    List<Resource> medicationRequestList = ResourceUtils.getResourceList(e, ResourceType.MedicationRequest);
    // Confirm that one medicationRequest was created.
    assertThat(medicationRequestList).hasSize(1);
    MedicationRequest medicationRequest = ResourceUtils.getResourceMedicationRequest(medicationRequestList.get(0), ResourceUtils.context);
    Range doseRange = medicationRequest.getDosageInstructionFirstRep().getDoseAndRateFirstRep().getDoseRange();
    // doseRange.low(RXE.3)
    // RXE.3
    assertThat(doseRange.getLow().getValue()).hasToString("3.0");
    // RXE.5
    assertThat(doseRange.getLow().getUnit()).isEqualTo("mL");
    // Defaulted
    assertThat(doseRange.getLow().getSystem()).isEqualTo("http://unitsofmeasure.org");
    // doseRange.high(RXE.4)
    assertThat(doseRange.getHigh().getValue()).hasToString("6.0");
    // RXE.5
    assertThat(doseRange.getHigh().getUnit()).isEqualTo("mL");
    assertThat(doseRange.getHigh().getSystem()).isEqualTo("http://unitsofmeasure.org");
    // Verify no extraneous resources
    // Expect MedicationRequest, Patient
    assertThat(e).hasSize(2);
}

Example 14 with Range

use of org.molgenis.api.metadata.v3.model.Range in project quality-measure-and-cohort-service by Alvearie.

the class R4ParameterDefinitionWithDefaultToCohortParameterConverter method toCohortParameter.

public static Parameter toCohortParameter(Extension extension) {
    Parameter parameter;
    Type extensionValue = extension.getValue();
    if (extensionValue instanceof Base64BinaryType) {
        parameter = new StringParameter(((Base64BinaryType) extensionValue).asStringValue());
    } else if (extensionValue instanceof BooleanType) {
        parameter = new BooleanParameter(((BooleanType) extensionValue).booleanValue());
    } else if (extensionValue instanceof DateType) {
        parameter = new DateParameter(((DateType) extensionValue).asStringValue());
    } else if (extensionValue instanceof DateTimeType) {
        parameter = convertDateTimeType((DateTimeType) extensionValue);
    } else if (extensionValue instanceof DecimalType) {
        parameter = new DecimalParameter(((DecimalType) extensionValue).getValueAsString());
    } else if (extensionValue instanceof InstantType) {
        parameter = new DatetimeParameter(((InstantType) extensionValue).getValueAsString());
    } else if (extensionValue instanceof IntegerType) {
        parameter = new IntegerParameter(((IntegerType) extensionValue).getValue());
    } else if (extensionValue instanceof StringType) {
        parameter = new StringParameter(((StringType) extensionValue).getValue());
    } else if (extensionValue instanceof TimeType) {
        parameter = new TimeParameter(((TimeType) extensionValue).asStringValue());
    } else if (extensionValue instanceof UriType) {
        parameter = new StringParameter(((UriType) extensionValue).getValue());
    } else if (extensionValue instanceof Coding) {
        parameter = convertCoding((Coding) extensionValue);
    } else if (extensionValue instanceof CodeableConcept) {
        parameter = convertCodeableConcept((CodeableConcept) extensionValue);
    } else if (extensionValue instanceof Period) {
        Period castValue = (Period) extensionValue;
        parameter = new IntervalParameter(convertDateTimeType(castValue.getStartElement()), true, convertDateTimeType(castValue.getEndElement()), true);
    } else if (extensionValue instanceof Quantity) {
        parameter = convertQuantity((Quantity) extensionValue);
    } else if (extensionValue instanceof Range) {
        Range castValue = (Range) extensionValue;
        parameter = new IntervalParameter(convertQuantity(castValue.getLow()), true, convertQuantity(castValue.getHigh()), true);
    } else if (extensionValue instanceof Ratio) {
        Ratio castValue = (Ratio) extensionValue;
        parameter = new RatioParameter().setDenominator(convertQuantity(castValue.getDenominator())).setNumerator(convertQuantity(castValue.getNumerator()));
    } else {
        throw new UnsupportedFhirTypeException(extensionValue);
    }
    return parameter;
}

Example 15 with Range

use of org.molgenis.api.metadata.v3.model.Range in project quality-measure-and-cohort-service by Alvearie.

the class FHIRRestUtils method complicatedTypeValueConstructor.

static String complicatedTypeValueConstructor(ParameterDefinition parameterDefinition) {
    FhirContext context = FhirContext.forCached(FhirVersionEnum.R4);
    IParser parser = context.newJsonParser();
    String valueKey;
    // In order to use the hapi parser, we cannot translate an extension by itself. The patient object wraps the extension
    Patient patient = new Patient();
    Extension extension = new Extension();
    switch(parameterDefinition.getType()) {
        case "Period":
            Period period = (Period) parameterDefinition.getExtension().get(0).getValue();
            extension.setValue(period);
            patient.addExtension(extension);
            valueKey = "valuePeriod";
            break;
        case "Range":
            Range range = (Range) parameterDefinition.getExtension().get(0).getValue();
            extension.setValue(range);
            patient.addExtension(extension);
            valueKey = "valueRange";
            break;
        case "Quantity":
            Quantity quantity = (Quantity) parameterDefinition.getExtension().get(0).getValue();
            extension.setValue(quantity);
            patient.addExtension(extension);
            valueKey = "valueQuantity";
            break;
        default:
            throw new RuntimeException("Complicated Type" + parameterDefinition.getType() + " not yet implemented");
    }
    String intermediateValue = parser.encodeResourceToString(patient);
    ObjectMapper mapper = new ObjectMapper();
    try {
        JsonNode root = mapper.readTree(intermediateValue);
        JsonNode nameNode = root.path("extension");
        return nameNode.get(0).path(valueKey).toString();
    } catch (JsonProcessingException e) {
        throw new RuntimeException("There was an issue with json translation", e);
    }
}