Examples with CanonicalType org.hl7.fhir.r4.model.CanonicalType used on opensource projects

Example 51 with CanonicalType

use of org.hl7.fhir.r4.model.CanonicalType in project pathling by aehrc.

the class ConformanceProvider method buildResources.

@Nonnull
private List<CapabilityStatementRestResourceComponent> buildResources() {
    final List<CapabilityStatementRestResourceComponent> resources = new ArrayList<>();
    final Set<ResourceType> supported = FhirServer.supportedResourceTypes();
    final Set<ResourceType> supportedResourceTypes = supported.isEmpty() ? EnumSet.noneOf(ResourceType.class) : EnumSet.copyOf(supported);
    for (final ResourceType resourceType : supportedResourceTypes) {
        final CapabilityStatementRestResourceComponent resource = new CapabilityStatementRestResourceComponent(new CodeType(resourceType.toCode()));
        resource.setProfile(FHIR_RESOURCE_BASE + resourceType.toCode());
        // Add the search operation to all resources.
        final ResourceInteractionComponent search = new ResourceInteractionComponent();
        search.setCode(TypeRestfulInteraction.SEARCHTYPE);
        resource.getInteraction().add(search);
        // Add the create and update operations to all resources.
        final ResourceInteractionComponent create = new ResourceInteractionComponent();
        final ResourceInteractionComponent update = new ResourceInteractionComponent();
        create.setCode(TypeRestfulInteraction.CREATE);
        update.setCode(TypeRestfulInteraction.UPDATE);
        resource.getInteraction().add(create);
        resource.getInteraction().add(update);
        // Add the `aggregate` operation to all resources.
        final CanonicalType aggregateOperationUri = new CanonicalType(getOperationUri("aggregate"));
        final CapabilityStatementRestResourceOperationComponent aggregateOperation = new CapabilityStatementRestResourceOperationComponent(new StringType("aggregate"), aggregateOperationUri);
        resource.addOperation(aggregateOperation);
        // Add the `fhirPath` search parameter to all resources.
        final CapabilityStatementRestResourceOperationComponent searchOperation = new CapabilityStatementRestResourceOperationComponent();
        searchOperation.setName("fhirPath");
        searchOperation.setDefinition(getOperationUri("search"));
        resource.addOperation(searchOperation);
        resources.add(resource);
    }
    // Add the read operation to the OperationDefinition resource.
    final String opDefCode = ResourceType.OPERATIONDEFINITION.toCode();
    final CapabilityStatementRestResourceComponent opDefResource = new CapabilityStatementRestResourceComponent(new CodeType(opDefCode));
    opDefResource.setProfile(FHIR_RESOURCE_BASE + opDefCode);
    final ResourceInteractionComponent readInteraction = new ResourceInteractionComponent();
    readInteraction.setCode(TypeRestfulInteraction.READ);
    opDefResource.addInteraction(readInteraction);
    resources.add(opDefResource);
    return resources;
}

Example 52 with CanonicalType

use of org.hl7.fhir.r4.model.CanonicalType in project eCRNow by drajer-health.

the class ApplicationUtils method getCovidValueSetByIds.

public static Set<ValueSet> getCovidValueSetByIds(List<CanonicalType> valueSetIdList) {
    Set<ValueSet> valueSets = new HashSet<>();
    if (Optional.ofNullable(valueSetIdList).isPresent()) {
        for (CanonicalType canonicalType : valueSetIdList) {
            logger.debug("Checking Value set {}", canonicalType.getValueAsString());
            for (ValueSet valueSet : ValueSetSingleton.getInstance().getValueSets()) {
                if (valueSet.getId().equalsIgnoreCase(canonicalType.getValueAsString()) && isACovidValueSet(valueSet)) {
                    logger.debug("Found a Covid Value Set for Grouper using Id {}", valueSet.getId());
                    valueSets.add(valueSet);
                    break;
                } else if ((valueSet.getUrl() != null) && (valueSet.getUrl().equalsIgnoreCase(canonicalType.getValueAsString())) && isACovidValueSet(valueSet)) {
                    logger.debug("Urls Matched for a Covid Value Set {}", valueSet.getId());
                    valueSets.add(valueSet);
                    break;
                }
            }
            for (ValueSet valueSet : ValueSetSingleton.getInstance().getCovidValueSets()) {
                if (valueSet.getId().equalsIgnoreCase(canonicalType.getValueAsString()) && isACovidValueSet(valueSet)) {
                    logger.debug("Found a Covid Value Set for Grouper using Id {}", valueSet.getId());
                    valueSets.add(valueSet);
                    break;
                } else if ((valueSet.getUrl() != null) && (valueSet.getUrl().equalsIgnoreCase(canonicalType.getValueAsString())) && isACovidValueSet(valueSet)) {
                    logger.debug("Urls Matched for a Covid Value Set {}", valueSet.getId());
                    valueSets.add(valueSet);
                    break;
                }
            }
        }
    }
    return valueSets;
}

Example 53 with CanonicalType

use of org.hl7.fhir.r4.model.CanonicalType in project eCRNow by drajer-health.

the class ValueSetServiceImpl method createValueSetGrouper.

@Override
public void createValueSetGrouper(ValueSet valueSet) {
    List<CanonicalType> valuesetList = null;
    ValueSetGrouperModel valueSetGrouperModel = null;
    ValueSetComposeComponent valueSetComposeComponent = valueSet.getCompose();
    List<ConceptSetComponent> conceptSetComponentList = valueSetComposeComponent.getInclude();
    for (ConceptSetComponent conceptSetComponent : conceptSetComponentList) {
        valuesetList = conceptSetComponent.getValueSet();
        for (CanonicalType canonicalType : valuesetList) {
            valueSetGrouperModel = new ValueSetGrouperModel();
            valueSetGrouperModel.setValueSetGrouper(valueSet.getUrl());
            valueSetGrouperModel.setValueSetId(canonicalType.getValueAsString());
            valueSetDao.createValuesetGrouper(valueSetGrouperModel);
        }
    }
}

Example 54 with CanonicalType

use of org.hl7.fhir.r4.model.CanonicalType in project eCRNow by drajer-health.

the class ActionData method print.

public void print() {
    if (logger.isInfoEnabled()) {
        logger.info(" *** Printing Action Data *** ");
        if (fhirDataType != null)
            logger.info(" Fhir Data Type = {}", fhirDataType.toString());
        if (triggerType != null)
            logger.info(" Trigger Type = {}", triggerType.toString());
        logger.info(" Path  = {}", path);
        if (valueSet != null)
            logger.info(" ValueSet Canonical URL = {}", valueSet.getValue());
        if (profiles != null) {
            for (CanonicalType ct : profiles) {
                logger.info(" Profile Name = {}", ct.getValue());
            }
        }
        logger.info(" *** End Printing Action Data *** ");
    }
}

Example 55 with CanonicalType

use of org.hl7.fhir.r4.model.CanonicalType in project redmatch by aehrc.

the class FhirExporter method getValue.

/**
 * Resolves a value.
 *
 * @param value The value specified in the transformation rules.
 * @param fhirType The type of the FHIR attribute where this value will be set.
 * @param vertex A vertex with patient data.
 * @param recordId The id of this record. Used to create the references to FHIR ids.
 * @param enumFactory If the type is an enumeration, this is the factory to create an instance.
 * @param fhirPackage The target FHIR package.
 * @return The value or null if the value cannot be determined. This can also be a list.
 */
private Base getValue(Value value, Class<?> fhirType, JsonObject vertex, String recordId, Class<?> enumFactory, VersionedFhirPackage fhirPackage) throws IOException {
    // If this is a field-based value then make sure that there is a value and if not return null
    if (value instanceof FieldBasedValue) {
        FieldBasedValue fbv = (FieldBasedValue) value;
        // Account for field ids of the form xx___y
        String fieldId = fbv.getFieldId();
        String shortFieldId = null;
        String regex = "(?<fieldId>.*)___\\d+$";
        Pattern pattern = Pattern.compile(regex);
        Matcher matcher = pattern.matcher(fieldId);
        if (matcher.find()) {
            shortFieldId = matcher.group("fieldId");
            log.debug("Transformed fieldId into '" + fieldId + "'");
        }
        boolean hasValue = false;
        JsonElement jsonElement = vertex.get(fieldId);
        if (jsonElement != null) {
            String rawValue = jsonElement.getAsString();
            if (!rawValue.isEmpty()) {
                hasValue = true;
            }
        }
        if (!hasValue && shortFieldId != null) {
            jsonElement = vertex.get(shortFieldId);
            if (jsonElement != null) {
                String rawValue = jsonElement.getAsString();
                if (!rawValue.isEmpty()) {
                    hasValue = true;
                }
            }
        }
        if (!hasValue) {
            return null;
        }
    }
    if (value instanceof BooleanValue) {
        return new BooleanType(((BooleanValue) value).getValue());
    } else if (value instanceof CodeLiteralValue) {
        String code = ((CodeLiteralValue) value).getCode();
        return getCode(code, enumFactory);
    } else if (value instanceof ConceptLiteralValue) {
        ConceptLiteralValue clv = (ConceptLiteralValue) value;
        String system = clv.getSystem();
        String code = clv.getCode();
        String display = clv.getDisplay() != null ? clv.getDisplay() : "";
        return getConcept(system, code, display, fhirType);
    } else if (value instanceof DoubleValue) {
        return new DecimalType(((DoubleValue) value).getValue());
    } else if (value instanceof IntegerValue) {
        return new IntegerType(((IntegerValue) value).getValue());
    } else if (value instanceof ReferenceValue) {
        ReferenceValue rv = (ReferenceValue) value;
        Reference ref = new Reference();
        String resourceType = rv.getResourceType();
        String resourceId = rv.getResourceId();
        boolean unique = uniqueIds.contains(resourceType + "<" + resourceId + ">");
        CodeInfo codeInfo = terminologyService.lookup(fhirPackage, resourceType);
        if (codeInfo.isProfile()) {
            resourceType = StringUtils.getLastPath(codeInfo.getBaseResource());
        }
        if (unique) {
            // This is a reference to a unique resource - no need to append row id
            if (fhirResourceMap.containsKey(resourceId)) {
                ref.setReference("/" + resourceType + "/" + resourceId);
            } else {
                log.debug("Did not find resource " + resourceType + "/" + resourceId);
            }
        } else {
            if (fhirResourceMap.containsKey(resourceId + "-" + recordId)) {
                ref.setReference("/" + resourceType + "/" + resourceId + "-" + recordId);
            } else {
                log.debug("Did not find resource " + resourceType + "/" + resourceId + "-" + recordId);
            }
        }
        return ref;
    } else if (value instanceof StringValue) {
        if (fhirType.equals(StringType.class)) {
            return new StringType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(MarkdownType.class)) {
            return new MarkdownType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(IdType.class)) {
            return new IdType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(UriType.class)) {
            return new UriType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(OidType.class)) {
            return new OidType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(UuidType.class)) {
            return new UuidType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(CanonicalType.class)) {
            return new CanonicalType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(UrlType.class)) {
            return new UrlType(((StringValue) value).getStringValue());
        } else {
            throw new TransformationException("Got StringValue for FHIR type " + fhirType.getName() + ". This should not happen!");
        }
    } else if (value instanceof CodeSelectedValue) {
        CodeSelectedValue csv = (CodeSelectedValue) value;
        String fieldId = csv.getFieldId();
        Mapping m = getSelectedMapping(fieldId, vertex);
        if (m == null) {
            throw new TransformationException("Mapping for field " + fieldId + " is required but was not found.");
        }
        return getTarget(m).getCodeElement();
    } else if (value instanceof ConceptSelectedValue) {
        ConceptSelectedValue csv = (ConceptSelectedValue) value;
        String fieldId = csv.getFieldId();
        Mapping m = getSelectedMapping(fieldId, vertex);
        if (m == null) {
            throw new TransformationException("Mapping for field " + fieldId + " is required but was not found.");
        }
        if (fhirType.isAssignableFrom(Coding.class)) {
            return getTarget(m);
        } else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
            return new CodeableConcept().addCoding(getTarget(m));
        } else {
            throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT_SELECTED.");
        }
    } else if (value instanceof ConceptValue) {
        // Ontoserver REDCap plugin format: 74400008|Appendicitis|http://snomed.info/sct
        ConceptValue cv = (ConceptValue) value;
        String fieldId = cv.getFieldId();
        Mapping m = getMapping(fieldId);
        if (m != null) {
            if (fhirType.isAssignableFrom(Coding.class)) {
                return getTarget(m);
            } else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
                return new CodeableConcept().addCoding(getTarget(m));
            } else {
                throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT.");
            }
        } else {
            au.csiro.redmatch.model.Field field = doc.getSchema().getField(fieldId);
            Coding c = field.getCoding(vertex);
            if (c != null) {
                if (fhirType.isAssignableFrom(Coding.class)) {
                    return c;
                } else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
                    return new CodeableConcept().addCoding(c);
                } else {
                    throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT.");
                }
            }
        }
        throw new TransformationException("Could not get concept for field " + fieldId + ".");
    } else if (value instanceof FieldValue) {
        FieldValue fv = (FieldValue) value;
        String fieldId = fv.getFieldId();
        FieldValue.DatePrecision pr = fv.getDatePrecision();
        au.csiro.redmatch.model.Field field = doc.getSchema().getField(fieldId);
        return field.getValue(vertex, fhirType, pr);
    } else {
        throw new TransformationException("Unable to get VALUE for " + value);
    }
}