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Builds the hapi fhir base. Requires Common lang, commons-text, and guava be built first.
/*-
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2024 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
package ca.uhn.fhir.parser;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeDeclaredChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeChildContainedResources;
import ca.uhn.fhir.context.RuntimeChildDirectResource;
import ca.uhn.fhir.context.RuntimeChildExtension;
import ca.uhn.fhir.context.RuntimeChildNarrativeDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.narrative.INarrativeGenerator;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.util.rdf.RDFUtil;
import org.apache.commons.lang3.StringUtils;
import org.apache.jena.datatypes.xsd.XSDDatatype;
import org.apache.jena.irix.IRIs;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.Statement;
import org.apache.jena.rdf.model.StmtIterator;
import org.apache.jena.riot.Lang;
import org.apache.jena.vocabulary.RDF;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
import org.hl7.fhir.instance.model.api.IBaseDatatypeElement;
import org.hl7.fhir.instance.model.api.IBaseElement;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IBaseXhtml;
import org.hl7.fhir.instance.model.api.IDomainResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.INarrative;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import java.io.Reader;
import java.io.Writer;
import java.util.Arrays;
import java.util.Comparator;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.ID_DATATYPE;
import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.PRIMITIVE_DATATYPE;
import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.PRIMITIVE_XHTML;
import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.PRIMITIVE_XHTML_HL7ORG;
/**
* This class is the FHIR RDF parser/encoder. Users should not interact with this class directly, but should use
* {@link FhirContext#newRDFParser()} to get an instance.
*/
public class RDFParser extends BaseParser {
private static final String VALUE = "value";
private static final String FHIR_INDEX = "index";
private static final String FHIR_PREFIX = "fhir";
private static final String FHIR_NS = "http://hl7.org/fhir/";
private static final String RDF_PREFIX = "rdf";
private static final String RDF_NS = "http://www.w3.org/1999/02/22-rdf-syntax-ns#";
private static final String RDFS_PREFIX = "rdfs";
private static final String RDFS_NS = "http://www.w3.org/2000/01/rdf-schema#";
private static final String XSD_PREFIX = "xsd";
private static final String XSD_NS = "http://www.w3.org/2001/XMLSchema#";
private static final String SCT_PREFIX = "sct";
private static final String SCT_NS = "http://snomed.info/id#";
private static final String EXTENSION_URL = "Extension.url";
private static final String ELEMENT_EXTENSION = "Element.extension";
private static final org.slf4j.Logger logger = org.slf4j.LoggerFactory.getLogger(RDFParser.class);
public static final String NODE_ROLE = "nodeRole";
private static final List ignoredPredicates =
Arrays.asList(RDF.type.getURI(), FHIR_NS + FHIR_INDEX, FHIR_NS + NODE_ROLE);
public static final String TREE_ROOT = "treeRoot";
public static final String RESOURCE_ID = "Resource.id";
public static final String ID = "id";
public static final String ELEMENT_ID = "Element.id";
public static final String DOMAIN_RESOURCE_CONTAINED = "DomainResource.contained";
public static final String EXTENSION = "extension";
public static final String CONTAINED = "contained";
public static final String MODIFIER_EXTENSION = "modifierExtension";
private final Map classToFhirTypeMap = new HashMap<>();
private final Lang lang;
/**
* Do not use this constructor, the recommended way to obtain a new instance of the RDF parser is to invoke
* {@link FhirContext#newRDFParser()}.
*
* @param parserErrorHandler the Parser Error Handler
*/
public RDFParser(final FhirContext context, final IParserErrorHandler parserErrorHandler, final Lang lang) {
super(context, parserErrorHandler);
this.lang = lang;
}
@Override
public EncodingEnum getEncoding() {
return EncodingEnum.RDF;
}
@Override
public IParser setPrettyPrint(final boolean prettyPrint) {
return this;
}
/**
* Writes the provided resource to the writer. This should only be called for the top-level resource being encoded.
* @param resource FHIR resource for writing
* @param writer The writer to write to -- Note: Jena prefers streams over writers
* @param encodeContext encoding content from parent
*/
@Override
protected void doEncodeResourceToWriter(
final IBaseResource resource, final Writer writer, final EncodeContext encodeContext) {
Model rdfModel = RDFUtil.initializeRDFModel();
// Establish the namespaces and prefixes needed
HashMap prefixes = new HashMap<>();
prefixes.put(RDF_PREFIX, RDF_NS);
prefixes.put(RDFS_PREFIX, RDFS_NS);
prefixes.put(XSD_PREFIX, XSD_NS);
prefixes.put(FHIR_PREFIX, FHIR_NS);
prefixes.put(SCT_PREFIX, SCT_NS);
for (String key : prefixes.keySet()) {
rdfModel.setNsPrefix(key, prefixes.get(key));
}
IIdType resourceId = processResourceID(resource, encodeContext);
encodeResourceToRDFStreamWriter(resource, rdfModel, false, resourceId, encodeContext, true, null);
RDFUtil.writeRDFModel(writer, rdfModel, lang);
}
/**
* Parses RDF content to a FHIR resource using Apache Jena
* @param resourceType Class of FHIR resource being deserialized
* @param reader Reader containing RDF (turtle) content
* @param Type parameter denoting which resource is being parsed
* @return Populated FHIR resource
* @throws DataFormatException Exception that can be thrown from parser
*/
@Override
protected T doParseResource(final Class resourceType, final Reader reader)
throws DataFormatException {
Model model = RDFUtil.readRDFToModel(reader, this.lang);
return parseResource(resourceType, model);
}
private Resource encodeResourceToRDFStreamWriter(
final IBaseResource resource,
final Model rdfModel,
final boolean containedResource,
final IIdType resourceId,
final EncodeContext encodeContext,
final boolean rootResource,
Resource parentResource) {
RuntimeResourceDefinition resDef = getContext().getResourceDefinition(resource);
if (resDef == null) {
throw new ConfigurationException(Msg.code(1845) + "Unknown resource type: " + resource.getClass());
}
if (!containedResource) {
containResourcesInReferences(resource);
}
if (!(resource instanceof IAnyResource)) {
throw new IllegalStateException(Msg.code(1846) + "Unsupported resource found: "
+ resource.getClass().getName());
}
// Create absolute IRI for the resource
String uriBase = resource.getIdElement().getBaseUrl();
if (uriBase == null) {
uriBase = getServerBaseUrl();
}
if (uriBase == null) {
uriBase = FHIR_NS;
}
if (!uriBase.endsWith("/")) {
uriBase = uriBase + "/";
}
if (parentResource == null) {
if (!resource.getIdElement().toUnqualified().hasIdPart()) {
parentResource = rdfModel.getResource(null);
} else {
String resourceUri = IRIs.resolve(
uriBase, resource.getIdElement().toUnqualified().toString())
.toString();
parentResource = rdfModel.getResource(resourceUri);
}
// If the resource already exists and has statements, return that existing resource.
if (parentResource != null
&& parentResource.listProperties().toList().size() > 0) {
return parentResource;
} else if (parentResource == null) {
return null;
}
}
parentResource.addProperty(RDF.type, rdfModel.createProperty(FHIR_NS + resDef.getName()));
// Only the top-level resource should have the nodeRole set to treeRoot
if (rootResource) {
parentResource.addProperty(
rdfModel.createProperty(FHIR_NS + NODE_ROLE), rdfModel.createProperty(FHIR_NS + TREE_ROOT));
}
if (resourceId != null
&& resourceId.getIdPart() != null
&& !resourceId.getValue().startsWith("urn:")) {
parentResource.addProperty(
rdfModel.createProperty(FHIR_NS + RESOURCE_ID),
createFhirValueBlankNode(rdfModel, resourceId.getIdPart()));
}
encodeCompositeElementToStreamWriter(
resource,
resource,
rdfModel,
parentResource,
containedResource,
new CompositeChildElement(resDef, encodeContext),
encodeContext);
return parentResource;
}
/**
* Utility method to create a blank node with a fhir:value predicate
* @param rdfModel Model to create node within
* @param value value object - assumed to be xsd:string
* @return Blank node resource containing fhir:value
*/
private Resource createFhirValueBlankNode(Model rdfModel, String value) {
return createFhirValueBlankNode(rdfModel, value, XSDDatatype.XSDstring, null);
}
/**
* Utility method to create a blank node with a fhir:value predicate accepting a specific data type and index
* @param rdfModel Model to create node within
* @param value value object
* @param xsdDataType data type for value
* @param cardinalityIndex if a collection, this value is written as a fhir:index predicate
* @return Blank node resource containing fhir:value (and possibly fhir:index)
*/
private Resource createFhirValueBlankNode(
Model rdfModel, String value, XSDDatatype xsdDataType, Integer cardinalityIndex) {
Resource fhirValueBlankNodeResource = rdfModel.createResource()
.addProperty(rdfModel.createProperty(FHIR_NS + VALUE), rdfModel.createTypedLiteral(value, xsdDataType));
if (cardinalityIndex != null && cardinalityIndex > -1) {
fhirValueBlankNodeResource.addProperty(
rdfModel.createProperty(FHIR_NS + FHIR_INDEX),
rdfModel.createTypedLiteral(cardinalityIndex, XSDDatatype.XSDinteger));
}
return fhirValueBlankNodeResource;
}
/**
* Builds the predicate name based on field definition
* @param resource Resource being interrogated
* @param definition field definition
* @param childName childName which been massaged for different data types
* @return String of predicate name
*/
private String constructPredicateName(
IBaseResource resource, BaseRuntimeChildDefinition definition, String childName, IBase parentElement) {
String basePropertyName = FHIR_NS + resource.fhirType() + "." + childName;
String classBasedPropertyName;
if (definition instanceof BaseRuntimeDeclaredChildDefinition) {
BaseRuntimeDeclaredChildDefinition declaredDef = (BaseRuntimeDeclaredChildDefinition) definition;
Class declaringClass = declaredDef.getField().getDeclaringClass();
if (declaringClass != resource.getClass()) {
String property = null;
if (IBaseBackboneElement.class.isAssignableFrom(declaringClass)
|| IBaseDatatypeElement.class.isAssignableFrom(declaringClass)) {
if (classToFhirTypeMap.containsKey(declaringClass)) {
property = classToFhirTypeMap.get(declaringClass);
} else {
try {
IBase elem = (IBase)
declaringClass.getDeclaredConstructor().newInstance();
property = elem.fhirType();
classToFhirTypeMap.put(declaringClass, property);
} catch (Exception ex) {
logger.debug("Error instantiating an " + declaringClass.getSimpleName()
+ " to retrieve its FhirType");
}
}
} else {
if ("MetadataResource".equals(declaringClass.getSimpleName())) {
property = resource.getClass().getSimpleName();
} else {
property = declaredDef.getField().getDeclaringClass().getSimpleName();
}
}
classBasedPropertyName = FHIR_NS + property + "." + childName;
return classBasedPropertyName;
}
}
return basePropertyName;
}
private Model encodeChildElementToStreamWriter(
final IBaseResource resource,
IBase parentElement,
Model rdfModel,
Resource rdfResource,
final BaseRuntimeChildDefinition childDefinition,
final IBase element,
final String childName,
final BaseRuntimeElementDefinition childDef,
final boolean includedResource,
final CompositeChildElement parent,
final EncodeContext encodeContext,
final Integer cardinalityIndex) {
String childGenericName = childDefinition.getElementName();
encodeContext.pushPath(childGenericName, false);
try {
if (element == null || element.isEmpty()) {
if (!isChildContained(childDef, includedResource)) {
return rdfModel;
}
}
switch (childDef.getChildType()) {
case ID_DATATYPE: {
IIdType value = (IIdType) element;
assert value != null;
String encodedValue = ID.equals(childName) ? value.getIdPart() : value.getValue();
if (StringUtils.isNotBlank(encodedValue) || !hasNoExtensions(value)) {
if (StringUtils.isNotBlank(encodedValue)) {
String propertyName =
constructPredicateName(resource, childDefinition, childName, parentElement);
if (element != null) {
XSDDatatype dataType = getXSDDataTypeForFhirType(element.fhirType(), encodedValue);
rdfResource.addProperty(
rdfModel.createProperty(propertyName),
this.createFhirValueBlankNode(
rdfModel, encodedValue, dataType, cardinalityIndex));
}
}
}
break;
}
case PRIMITIVE_DATATYPE: {
IPrimitiveType pd = (IPrimitiveType) element;
assert pd != null;
String value = pd.getValueAsString();
if (value != null || !hasNoExtensions(pd)) {
if (value != null) {
String propertyName =
constructPredicateName(resource, childDefinition, childName, parentElement);
XSDDatatype dataType = getXSDDataTypeForFhirType(pd.fhirType(), value);
Resource valueResource =
this.createFhirValueBlankNode(rdfModel, value, dataType, cardinalityIndex);
if (!hasNoExtensions(pd)) {
IBaseHasExtensions hasExtension = (IBaseHasExtensions) pd;
if (hasExtension.getExtension() != null
&& hasExtension.getExtension().size() > 0) {
int i = 0;
for (IBaseExtension extension : hasExtension.getExtension()) {
RuntimeResourceDefinition resDef =
getContext().getResourceDefinition(resource);
Resource extensionResource = rdfModel.createResource();
extensionResource.addProperty(
rdfModel.createProperty(FHIR_NS + FHIR_INDEX),
rdfModel.createTypedLiteral(i, XSDDatatype.XSDinteger));
valueResource.addProperty(
rdfModel.createProperty(FHIR_NS + ELEMENT_EXTENSION),
extensionResource);
encodeCompositeElementToStreamWriter(
resource,
extension,
rdfModel,
extensionResource,
false,
new CompositeChildElement(resDef, encodeContext),
encodeContext);
}
}
}
rdfResource.addProperty(rdfModel.createProperty(propertyName), valueResource);
}
}
break;
}
case RESOURCE_BLOCK:
case COMPOSITE_DATATYPE: {
String idString = null;
String idPredicate = null;
if (element instanceof IBaseResource) {
idPredicate = FHIR_NS + RESOURCE_ID;
IIdType resourceId = processResourceID((IBaseResource) element, encodeContext);
if (resourceId != null) {
idString = resourceId.getIdPart();
}
} else if (element instanceof IBaseElement) {
idPredicate = FHIR_NS + ELEMENT_ID;
if (((IBaseElement) element).getId() != null) {
idString = ((IBaseElement) element).getId();
}
}
if (idString != null) {
rdfResource.addProperty(
rdfModel.createProperty(idPredicate), createFhirValueBlankNode(rdfModel, idString));
}
rdfModel = encodeCompositeElementToStreamWriter(
resource, element, rdfModel, rdfResource, includedResource, parent, encodeContext);
break;
}
case CONTAINED_RESOURCE_LIST:
case CONTAINED_RESOURCES: {
if (element != null) {
IIdType resourceId = ((IBaseResource) element).getIdElement();
Resource containedResource = rdfModel.createResource();
rdfResource.addProperty(
rdfModel.createProperty(FHIR_NS + DOMAIN_RESOURCE_CONTAINED), containedResource);
if (cardinalityIndex != null) {
containedResource.addProperty(
rdfModel.createProperty(FHIR_NS + FHIR_INDEX),
cardinalityIndex.toString(),
XSDDatatype.XSDinteger);
}
encodeResourceToRDFStreamWriter(
(IBaseResource) element,
rdfModel,
true,
super.fixContainedResourceId(resourceId.getValue()),
encodeContext,
false,
containedResource);
}
break;
}
case RESOURCE: {
IBaseResource baseResource = (IBaseResource) element;
String resourceName = getContext().getResourceType(baseResource);
if (!super.shouldEncodeResource(resourceName)) {
break;
}
encodeContext.pushPath(resourceName, true);
IIdType resourceId = processResourceID(resource, encodeContext);
encodeResourceToRDFStreamWriter(resource, rdfModel, false, resourceId, encodeContext, false, null);
encodeContext.popPath();
break;
}
case PRIMITIVE_XHTML:
case PRIMITIVE_XHTML_HL7ORG: {
IBaseXhtml xHtmlNode = (IBaseXhtml) element;
if (xHtmlNode != null) {
String value = xHtmlNode.getValueAsString();
String propertyName =
constructPredicateName(resource, childDefinition, childName, parentElement);
rdfResource.addProperty(rdfModel.createProperty(propertyName), value);
}
break;
}
case EXTENSION_DECLARED:
case UNDECL_EXT:
default: {
throw new IllegalStateException(
Msg.code(1847) + "Unexpected node - should not happen: " + childDef.getName());
}
}
} finally {
encodeContext.popPath();
}
return rdfModel;
}
/**
* Maps hapi internal fhirType attribute to XSDDatatype enumeration
* @param fhirType hapi field type
* @return XSDDatatype value
*/
private XSDDatatype getXSDDataTypeForFhirType(String fhirType, String value) {
switch (fhirType) {
case "boolean":
return XSDDatatype.XSDboolean;
case "uri":
return XSDDatatype.XSDanyURI;
case "decimal":
return XSDDatatype.XSDdecimal;
case "date":
return XSDDatatype.XSDdate;
case "dateTime":
case "instant":
switch (value.length()) { // assumes valid lexical value
case 4:
return XSDDatatype.XSDgYear;
case 7:
return XSDDatatype.XSDgYearMonth;
case 10:
return XSDDatatype.XSDdate;
default:
return XSDDatatype.XSDdateTime;
}
case "code":
case "string":
default:
return XSDDatatype.XSDstring;
}
}
private IIdType processResourceID(final IBaseResource resource, final EncodeContext encodeContext) {
IIdType resourceId = null;
if (StringUtils.isNotBlank(resource.getIdElement().getIdPart())) {
resourceId = resource.getIdElement();
if (resource.getIdElement().getValue().startsWith("urn:")) {
resourceId = null;
}
}
if (!super.shouldEncodeResourceId(resource, encodeContext)) {
resourceId = null;
} else if (encodeContext.getResourcePath().size() == 1 && super.getEncodeForceResourceId() != null) {
resourceId = super.getEncodeForceResourceId();
}
return resourceId;
}
private Model encodeExtension(
final IBaseResource resource,
Model rdfModel,
Resource rdfResource,
final boolean containedResource,
final CompositeChildElement nextChildElem,
final BaseRuntimeChildDefinition nextChild,
final IBase nextValue,
final String childName,
final BaseRuntimeElementDefinition childDef,
final EncodeContext encodeContext,
Integer cardinalityIndex) {
BaseRuntimeDeclaredChildDefinition extDef = (BaseRuntimeDeclaredChildDefinition) nextChild;
Resource childResource = rdfModel.createResource();
String extensionPredicateName = constructPredicateName(resource, extDef, extDef.getElementName(), null);
rdfResource.addProperty(rdfModel.createProperty(extensionPredicateName), childResource);
if (cardinalityIndex != null && cardinalityIndex > -1) {
childResource.addProperty(
rdfModel.createProperty(FHIR_NS + FHIR_INDEX), cardinalityIndex.toString(), XSDDatatype.XSDinteger);
}
rdfModel = encodeChildElementToStreamWriter(
resource,
null,
rdfModel,
childResource,
nextChild,
nextValue,
childName,
childDef,
containedResource,
nextChildElem,
encodeContext,
cardinalityIndex);
return rdfModel;
}
private Model encodeCompositeElementToStreamWriter(
final IBaseResource resource,
final IBase element,
Model rdfModel,
Resource rdfResource,
final boolean containedResource,
final CompositeChildElement parent,
final EncodeContext encodeContext) {
for (CompositeChildElement nextChildElem :
super.compositeChildIterator(element, containedResource, parent, encodeContext)) {
BaseRuntimeChildDefinition nextChild = nextChildElem.getDef();
if (nextChild instanceof RuntimeChildNarrativeDefinition) {
INarrativeGenerator gen = getContext().getNarrativeGenerator();
if (gen != null) {
INarrative narrative;
if (resource instanceof IResource) {
narrative = ((IResource) resource).getText();
} else if (resource instanceof IDomainResource) {
narrative = ((IDomainResource) resource).getText();
} else {
narrative = null;
}
assert narrative != null;
if (narrative.isEmpty()) {
gen.populateResourceNarrative(getContext(), resource);
} else {
RuntimeChildNarrativeDefinition child = (RuntimeChildNarrativeDefinition) nextChild;
// This is where we populate the parent of the narrative
Resource childResource = rdfModel.createResource();
String propertyName = constructPredicateName(resource, child, child.getElementName(), element);
rdfResource.addProperty(rdfModel.createProperty(propertyName), childResource);
String childName = nextChild.getChildNameByDatatype(child.getDatatype());
BaseRuntimeElementDefinition type = child.getChildByName(childName);
rdfModel = encodeChildElementToStreamWriter(
resource,
element,
rdfModel,
childResource,
nextChild,
narrative,
childName,
type,
containedResource,
nextChildElem,
encodeContext,
null);
continue;
}
}
}
if (nextChild instanceof RuntimeChildDirectResource) {
List values = nextChild.getAccessor().getValues(element);
if (values == null || values.isEmpty()) {
continue;
}
IBaseResource directChildResource = (IBaseResource) values.get(0);
// If it is a direct resource, we need to create a new subject for it.
Resource childResource = encodeResourceToRDFStreamWriter(
directChildResource,
rdfModel,
false,
directChildResource.getIdElement(),
encodeContext,
false,
null);
String propertyName = constructPredicateName(resource, nextChild, nextChild.getElementName(), element);
rdfResource.addProperty(rdfModel.createProperty(propertyName), childResource);
continue;
}
if (nextChild instanceof RuntimeChildContainedResources) {
List values = nextChild.getAccessor().getValues(element);
int i = 0;
for (IBase containedResourceEntity : values) {
rdfModel = encodeChildElementToStreamWriter(
resource,
element,
rdfModel,
rdfResource,
nextChild,
containedResourceEntity,
nextChild.getChildNameByDatatype(null),
nextChild.getChildElementDefinitionByDatatype(null),
containedResource,
nextChildElem,
encodeContext,
i);
i++;
}
} else {
List values = nextChild.getAccessor().getValues(element);
values = super.preProcessValues(nextChild, resource, values, nextChildElem, encodeContext);
if (values == null || values.isEmpty()) {
continue;
}
Integer cardinalityIndex = null;
int indexCounter = 0;
for (IBase nextValue : values) {
if (nextChild.getMax() != 1) {
cardinalityIndex = indexCounter;
indexCounter++;
}
if ((nextValue == null || nextValue.isEmpty())) {
continue;
}
ChildNameAndDef childNameAndDef = super.getChildNameAndDef(nextChild, nextValue);
if (childNameAndDef == null) {
continue;
}
String childName = childNameAndDef.getChildName();
BaseRuntimeElementDefinition childDef = childNameAndDef.getChildDef();
String extensionUrl = getExtensionUrl(nextChild.getExtensionUrl());
if (extensionUrl != null && !childName.equals(EXTENSION)) {
rdfModel = encodeExtension(
resource,
rdfModel,
rdfResource,
containedResource,
nextChildElem,
nextChild,
nextValue,
childName,
childDef,
encodeContext,
cardinalityIndex);
} else if (nextChild instanceof RuntimeChildExtension) {
IBaseExtension extension = (IBaseExtension) nextValue;
if ((extension.getValue() == null
|| extension.getValue().isEmpty())) {
if (extension.getExtension().isEmpty()) {
continue;
}
}
rdfModel = encodeExtension(
resource,
rdfModel,
rdfResource,
containedResource,
nextChildElem,
nextChild,
nextValue,
childName,
childDef,
encodeContext,
cardinalityIndex);
} else if (!(nextChild instanceof RuntimeChildNarrativeDefinition) || !containedResource) {
// If the child is not a value type, create a child object (blank node) for subordinate
// predicates to be attached to
if (childDef.getChildType() != PRIMITIVE_DATATYPE
&& childDef.getChildType() != PRIMITIVE_XHTML_HL7ORG
&& childDef.getChildType() != PRIMITIVE_XHTML
&& childDef.getChildType() != ID_DATATYPE) {
Resource childResource = rdfModel.createResource();
String propertyName = constructPredicateName(resource, nextChild, childName, nextValue);
rdfResource.addProperty(rdfModel.createProperty(propertyName), childResource);
if (cardinalityIndex != null && cardinalityIndex > -1) {
childResource.addProperty(
rdfModel.createProperty(FHIR_NS + FHIR_INDEX),
cardinalityIndex.toString(),
XSDDatatype.XSDinteger);
}
rdfModel = encodeChildElementToStreamWriter(
resource,
element,
rdfModel,
childResource,
nextChild,
nextValue,
childName,
childDef,
containedResource,
nextChildElem,
encodeContext,
cardinalityIndex);
} else {
rdfModel = encodeChildElementToStreamWriter(
resource,
element,
rdfModel,
rdfResource,
nextChild,
nextValue,
childName,
childDef,
containedResource,
nextChildElem,
encodeContext,
cardinalityIndex);
}
}
}
}
}
return rdfModel;
}
private T parseResource(Class resourceType, Model rdfModel) {
// jsonMode of true is passed in so that the xhtml parser state behaves as expected
// Push PreResourceState
ParserState parserState =
ParserState.getPreResourceInstance(this, resourceType, getContext(), true, getErrorHandler());
return parseRootResource(rdfModel, parserState, resourceType);
}
private T parseRootResource(Model rdfModel, ParserState parserState, Class resourceType) {
logger.trace("Entering parseRootResource with state: {}", parserState);
StmtIterator rootStatementIterator = rdfModel.listStatements(
null, rdfModel.getProperty(FHIR_NS + NODE_ROLE), rdfModel.getProperty(FHIR_NS + TREE_ROOT));
Resource rootResource;
String fhirResourceType, fhirTypeString;
while (rootStatementIterator.hasNext()) {
Statement rootStatement = rootStatementIterator.next();
rootResource = rootStatement.getSubject();
// If a resourceType is not provided via the server framework, discern it based on the rdf:type Arc
if (resourceType == null) {
Statement resourceTypeStatement = rootResource.getProperty(RDF.type);
fhirTypeString = resourceTypeStatement.getObject().toString();
if (fhirTypeString.startsWith(FHIR_NS)) {
fhirTypeString = fhirTypeString.replace(FHIR_NS, "");
}
} else {
fhirTypeString = resourceType.getSimpleName();
}
RuntimeResourceDefinition definition = getContext().getResourceDefinition(fhirTypeString);
fhirResourceType = definition.getName();
parseResource(parserState, fhirResourceType, rootResource);
// Pop PreResourceState
parserState.endingElement();
}
return parserState.getObject();
}
private void parseResource(ParserState parserState, String resourceType, RDFNode rootNode) {
// Push top-level entity
parserState.enteringNewElement(FHIR_NS, resourceType);
if (rootNode instanceof Resource) {
Resource rootResource = rootNode.asResource();
List statements = rootResource.listProperties().toList();
statements.sort(new FhirIndexStatementComparator());
for (Statement statement : statements) {
String predicateAttributeName = extractAttributeNameFromPredicate(statement);
if (predicateAttributeName != null) {
if (predicateAttributeName.equals(MODIFIER_EXTENSION)) {
processExtension(parserState, statement.getObject(), true);
} else if (predicateAttributeName.equals(EXTENSION)) {
processExtension(parserState, statement.getObject(), false);
} else {
processStatementObject(parserState, predicateAttributeName, statement.getObject());
}
}
}
} else if (rootNode instanceof Literal) {
parserState.attributeValue(VALUE, rootNode.asLiteral().getString());
}
// Pop top-level entity
parserState.endingElement();
}
private String extractAttributeNameFromPredicate(Statement statement) {
String predicateUri = statement.getPredicate().getURI();
// If the predicateURI is one we're ignoring, return null
// This minimizes 'Unknown Element' warnings in the parsing process
if (ignoredPredicates.contains(predicateUri)) {
return null;
}
String predicateObjectAttribute = predicateUri.substring(predicateUri.lastIndexOf("/") + 1);
String predicateAttributeName;
if (predicateObjectAttribute.contains(".")) {
predicateAttributeName = predicateObjectAttribute.substring(predicateObjectAttribute.lastIndexOf(".") + 1);
} else {
predicateAttributeName = predicateObjectAttribute;
}
return predicateAttributeName;
}
private void processStatementObject(
ParserState parserState, String predicateAttributeName, RDFNode statementObject) {
logger.trace(
"Entering processStatementObject with state: {}, for attribute {}",
parserState,
predicateAttributeName);
// Push attribute element
parserState.enteringNewElement(FHIR_NS, predicateAttributeName);
if (statementObject != null) {
if (statementObject.isLiteral()) {
// If the object is a literal, apply the value directly
parserState.attributeValue(VALUE, statementObject.asLiteral().getLexicalForm());
} else if (statementObject.isAnon()) {
// If the object is a blank node,
Resource resourceObject = statementObject.asResource();
boolean containedResource = false;
if (predicateAttributeName.equals(CONTAINED)) {
containedResource = true;
parserState.enteringNewElement(
FHIR_NS,
resourceObject
.getProperty(resourceObject.getModel().createProperty(RDF.type.getURI()))
.getObject()
.toString()
.replace(FHIR_NS, ""));
}
List objectStatements =
resourceObject.listProperties().toList();
objectStatements.sort(new FhirIndexStatementComparator());
for (Statement objectProperty : objectStatements) {
if (objectProperty.getPredicate().hasURI(FHIR_NS + VALUE)) {
predicateAttributeName = VALUE;
parserState.attributeValue(
predicateAttributeName,
objectProperty.getObject().asLiteral().getLexicalForm());
} else {
// Otherwise, process it as a net-new node
predicateAttributeName = extractAttributeNameFromPredicate(objectProperty);
if (predicateAttributeName != null) {
if (predicateAttributeName.equals(EXTENSION)) {
processExtension(parserState, objectProperty.getObject(), false);
} else if (predicateAttributeName.equals(MODIFIER_EXTENSION)) {
processExtension(parserState, objectProperty.getObject(), true);
} else {
processStatementObject(parserState, predicateAttributeName, objectProperty.getObject());
}
}
}
}
if (containedResource) {
// Leave the contained resource element we created
parserState.endingElement();
}
} else if (statementObject.isResource()) {
Resource innerResource = statementObject.asResource();
Statement resourceTypeStatement = innerResource.getProperty(RDF.type);
String fhirTypeString = resourceTypeStatement.getObject().toString();
if (fhirTypeString.startsWith(FHIR_NS)) {
fhirTypeString = fhirTypeString.replace(FHIR_NS, "");
}
parseResource(parserState, fhirTypeString, innerResource);
}
}
// Pop attribute element
parserState.endingElement();
}
private void processExtension(ParserState parserState, RDFNode statementObject, boolean isModifier) {
logger.trace("Entering processExtension with state: {}", parserState);
Resource resource = statementObject.asResource();
Statement urlProperty = resource.getProperty(resource.getModel().createProperty(FHIR_NS + EXTENSION_URL));
Resource urlPropertyResource = urlProperty.getObject().asResource();
String extensionUrl = urlPropertyResource
.getProperty(resource.getModel().createProperty(FHIR_NS + VALUE))
.getObject()
.asLiteral()
.getString();
List extensionStatements = resource.listProperties().toList();
String extensionValueType = null;
RDFNode extensionValueResource = null;
for (Statement statement : extensionStatements) {
String propertyUri = statement.getPredicate().getURI();
if (propertyUri.contains("Extension.value")) {
extensionValueType = propertyUri.replace(FHIR_NS + "Extension.", "");
BaseRuntimeElementDefinition target = getContext()
.getRuntimeChildUndeclaredExtensionDefinition()
.getChildByName(extensionValueType);
if (target.getChildType().equals(ID_DATATYPE)
|| target.getChildType().equals(PRIMITIVE_DATATYPE)) {
extensionValueResource = statement
.getObject()
.asResource()
.getProperty(resource.getModel().createProperty(FHIR_NS + VALUE))
.getObject()
.asLiteral();
} else {
extensionValueResource = statement.getObject().asResource();
}
break;
}
}
parserState.enteringNewElementExtension(null, extensionUrl, isModifier, null);
// Some extensions don't have their own values - they then have more extensions inside of them
if (extensionValueType != null) {
parseResource(parserState, extensionValueType, extensionValueResource);
}
for (Statement statement : extensionStatements) {
String propertyUri = statement.getPredicate().getURI();
if (propertyUri.equals(FHIR_NS + ELEMENT_EXTENSION)) {
processExtension(parserState, statement.getObject(), false);
}
}
parserState.endingElement();
}
static class FhirIndexStatementComparator implements Comparator {
@Override
public int compare(Statement arg0, Statement arg1) {
int result =
arg0.getPredicate().getURI().compareTo(arg1.getPredicate().getURI());
if (result == 0) {
if (arg0.getObject().isResource() && arg1.getObject().isResource()) {
Resource resource0 = arg0.getObject().asResource();
Resource resource1 = arg1.getObject().asResource();
result = Integer.compare(getFhirIndex(resource0), getFhirIndex(resource1));
}
}
return result;
}
private int getFhirIndex(Resource resource) {
if (resource.hasProperty(resource.getModel().createProperty(FHIR_NS + FHIR_INDEX))) {
return resource.getProperty(resource.getModel().createProperty(FHIR_NS + FHIR_INDEX))
.getInt();
}
return -1;
}
}
}
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