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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.context;
import ca.uhn.fhir.context.api.AddProfileTagEnum;
import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.fhirpath.IFhirPath;
import ca.uhn.fhir.i18n.HapiLocalizer;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.api.IElement;
import ca.uhn.fhir.model.api.IFhirVersion;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
import ca.uhn.fhir.model.view.ViewGenerator;
import ca.uhn.fhir.narrative.INarrativeGenerator;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.parser.IParserErrorHandler;
import ca.uhn.fhir.parser.JsonParser;
import ca.uhn.fhir.parser.LenientErrorHandler;
import ca.uhn.fhir.parser.NDJsonParser;
import ca.uhn.fhir.parser.RDFParser;
import ca.uhn.fhir.parser.XmlParser;
import ca.uhn.fhir.rest.api.IVersionSpecificBundleFactory;
import ca.uhn.fhir.rest.client.api.IBasicClient;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.IRestfulClient;
import ca.uhn.fhir.rest.client.api.IRestfulClientFactory;
import ca.uhn.fhir.system.HapiSystemProperties;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.ReflectionUtil;
import ca.uhn.fhir.util.VersionUtil;
import ca.uhn.fhir.validation.FhirValidator;
import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.exception.ExceptionUtils;
import org.apache.jena.riot.Lang;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import java.io.IOException;
import java.io.InputStream;
import java.lang.reflect.Method;
import java.lang.reflect.Modifier;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.EnumMap;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Objects;
import java.util.Optional;
import java.util.Properties;
import java.util.Set;
import java.util.stream.Collectors;
/**
* The FHIR context is the central starting point for the use of the HAPI FHIR API. It should be created once, and then
* used as a factory for various other types of objects (parsers, clients, etc.).
*
*
* Important usage notes:
*
*
* -
* Thread safety: This class is thread safe and may be shared between multiple processing
* threads, except for the {@link #registerCustomType} and {@link #registerCustomTypes} methods.
*
* -
* Performance: This class is expensive to create, as it scans every resource class it needs to parse or encode
* to build up an internal model of those classes. For that reason, you should try to create one FhirContext instance
* which remains for the life of your application and reuse that instance. Note that it will not cause problems to
* create multiple instances (ie. resources originating from one FhirContext may be passed to parsers originating from
* another) but you will incur a performance penalty if a new FhirContext is created for every message you parse/encode.
*
*
*/
public class FhirContext {
private static final List> EMPTY_LIST = Collections.emptyList();
private static final Map ourStaticContexts =
Collections.synchronizedMap(new EnumMap<>(FhirVersionEnum.class));
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirContext.class);
private final IFhirVersion myVersion;
private final Map> myDefaultTypeForProfile = new HashMap<>();
private final Set myPerformanceOptions = new HashSet<>();
private final Collection> myResourceTypesToScan;
private AddProfileTagEnum myAddProfileTagWhenEncoding = AddProfileTagEnum.ONLY_FOR_CUSTOM;
private volatile Map, BaseRuntimeElementDefinition> myClassToElementDefinition =
Collections.emptyMap();
private ArrayList> myCustomTypes;
private final Set myCustomResourceNames = new HashSet<>();
private volatile Map myIdToResourceDefinition = Collections.emptyMap();
private volatile boolean myInitialized;
private volatile boolean myInitializing = false;
private HapiLocalizer myLocalizer = new HapiLocalizer();
private volatile Map> myNameToElementDefinition = Collections.emptyMap();
private volatile Map myNameToResourceDefinition = Collections.emptyMap();
private volatile Map> myNameToResourceType;
private volatile INarrativeGenerator myNarrativeGenerator;
private volatile IParserErrorHandler myParserErrorHandler = new LenientErrorHandler();
private ParserOptions myParserOptions = new ParserOptions();
private volatile IRestfulClientFactory myRestfulClientFactory;
private volatile RuntimeChildUndeclaredExtensionDefinition myRuntimeChildUndeclaredExtensionDefinition;
private IValidationSupport myValidationSupport;
private Map>> myVersionToNameToResourceType =
Collections.emptyMap();
private volatile Set myResourceNames;
private volatile Boolean myFormatXmlSupported;
private volatile Boolean myFormatJsonSupported;
private volatile Boolean myFormatNDJsonSupported;
private volatile Boolean myFormatRdfSupported;
private IFhirValidatorFactory myFhirValidatorFactory = FhirValidator::new;
/**
* @deprecated It is recommended that you use one of the static initializer methods instead
* of this method, e.g. {@link #forDstu2()} or {@link #forDstu3()} or {@link #forR4()}
*/
@Deprecated
public FhirContext() {
this(EMPTY_LIST);
}
/**
* @deprecated It is recommended that you use one of the static initializer methods instead
* of this method, e.g. {@link #forDstu2()} or {@link #forDstu3()} or {@link #forR4()}
*/
@Deprecated
public FhirContext(final Class theResourceType) {
this(toCollection(theResourceType));
}
/**
* @deprecated It is recommended that you use one of the static initializer methods instead
* of this method, e.g. {@link #forDstu2()} or {@link #forDstu3()} or {@link #forR4()}
*/
@Deprecated
public FhirContext(final Class... theResourceTypes) {
this(toCollection(theResourceTypes));
}
/**
* @deprecated It is recommended that you use one of the static initializer methods instead
* of this method, e.g. {@link #forDstu2()} or {@link #forDstu3()} or {@link #forR4()}
*/
@Deprecated
public FhirContext(final Collection> theResourceTypes) {
this(null, theResourceTypes);
}
/**
* In most cases it is recommended that you use one of the static initializer methods instead
* of this method, e.g. {@link #forDstu2()} or {@link #forDstu3()} or {@link #forR4()}, but
* this method can also be used if you wish to supply the version programmatically.
*/
public FhirContext(final FhirVersionEnum theVersion) {
this(theVersion, null);
}
private FhirContext(
final FhirVersionEnum theVersion, final Collection> theResourceTypes) {
VersionUtil.getVersion();
if (theVersion != null) {
if (!theVersion.isPresentOnClasspath()) {
throw new IllegalStateException(Msg.code(1680)
+ getLocalizer()
.getMessage(FhirContext.class, "noStructuresForSpecifiedVersion", theVersion.name()));
}
myVersion = theVersion.getVersionImplementation();
} else if (FhirVersionEnum.DSTU2.isPresentOnClasspath()) {
myVersion = FhirVersionEnum.DSTU2.getVersionImplementation();
} else if (FhirVersionEnum.DSTU2_HL7ORG.isPresentOnClasspath()) {
myVersion = FhirVersionEnum.DSTU2_HL7ORG.getVersionImplementation();
} else if (FhirVersionEnum.DSTU2_1.isPresentOnClasspath()) {
myVersion = FhirVersionEnum.DSTU2_1.getVersionImplementation();
} else if (FhirVersionEnum.DSTU3.isPresentOnClasspath()) {
myVersion = FhirVersionEnum.DSTU3.getVersionImplementation();
} else if (FhirVersionEnum.R4.isPresentOnClasspath()) {
myVersion = FhirVersionEnum.R4.getVersionImplementation();
} else if (FhirVersionEnum.R4B.isPresentOnClasspath()) {
myVersion = FhirVersionEnum.R4B.getVersionImplementation();
} else {
throw new IllegalStateException(
Msg.code(1681) + getLocalizer().getMessage(FhirContext.class, "noStructures"));
}
if (theVersion == null) {
ourLog.info(
"Creating new FhirContext with auto-detected version [{}]. It is recommended to explicitly select a version for future compatibility by invoking FhirContext.forDstuX()",
myVersion.getVersion().name());
} else {
if (HapiSystemProperties.isUnitTestModeEnabled()) {
String calledAt = ExceptionUtils.getStackFrames(new Throwable())[4];
ourLog.info(
"Creating new FHIR context for FHIR version [{}]{}",
myVersion.getVersion().name(),
calledAt);
} else {
ourLog.info(
"Creating new FHIR context for FHIR version [{}]",
myVersion.getVersion().name());
}
}
myResourceTypesToScan = theResourceTypes;
/*
* Check if we're running in Android mode and configure the context appropriately if so
*/
try {
Class clazz = Class.forName("ca.uhn.fhir.android.AndroidMarker");
ourLog.info("Android mode detected, configuring FhirContext for Android operation");
try {
Method method = clazz.getMethod("configureContext", FhirContext.class);
method.invoke(null, this);
} catch (Throwable e) {
ourLog.warn("Failed to configure context for Android operation", e);
}
} catch (ClassNotFoundException e) {
ourLog.trace("Android mode not detected");
}
}
/**
* @since 5.6.0
*/
public static FhirContext forDstu2Cached() {
return forCached(FhirVersionEnum.DSTU2);
}
/**
* @since 6.2.0
*/
public static FhirContext forDstu2Hl7OrgCached() {
return forCached(FhirVersionEnum.DSTU2_HL7ORG);
}
/**
* @since 5.5.0
*/
public static FhirContext forDstu3Cached() {
return forCached(FhirVersionEnum.DSTU3);
}
/**
* @since 5.5.0
*/
public static FhirContext forR4Cached() {
return forCached(FhirVersionEnum.R4);
}
/**
* @since 6.1.0
*/
public static FhirContext forR4BCached() {
return forCached(FhirVersionEnum.R4B);
}
/**
* @since 5.5.0
*/
public static FhirContext forR5Cached() {
return forCached(FhirVersionEnum.R5);
}
private String createUnknownResourceNameError(final String theResourceName, final FhirVersionEnum theVersion) {
return getLocalizer().getMessage(FhirContext.class, "unknownResourceName", theResourceName, theVersion);
}
private void ensureCustomTypeList() {
myClassToElementDefinition.clear();
if (myCustomTypes == null) {
myCustomTypes = new ArrayList<>();
}
}
/**
* When encoding resources, this setting configures the parser to include
* an entry in the resource's metadata section which indicates which profile(s) the
* resource claims to conform to. The default is {@link AddProfileTagEnum#ONLY_FOR_CUSTOM}.
*
* @see #setAddProfileTagWhenEncoding(AddProfileTagEnum) for more information
*/
public AddProfileTagEnum getAddProfileTagWhenEncoding() {
return myAddProfileTagWhenEncoding;
}
/**
* When encoding resources, this setting configures the parser to include
* an entry in the resource's metadata section which indicates which profile(s) the
* resource claims to conform to. The default is {@link AddProfileTagEnum#ONLY_FOR_CUSTOM}.
*
* This feature is intended for situations where custom resource types are being used,
* avoiding the need to manually add profile declarations for these custom types.
*
*
* See Profiling and Extensions
* for more information on using custom types.
*
*
* Note that this feature automatically adds the profile, but leaves any profile tags
* which have been manually added in place as well.
*
*
* @param theAddProfileTagWhenEncoding The add profile mode (must not be null)
*/
public void setAddProfileTagWhenEncoding(final AddProfileTagEnum theAddProfileTagWhenEncoding) {
Validate.notNull(theAddProfileTagWhenEncoding, "theAddProfileTagWhenEncoding must not be null");
myAddProfileTagWhenEncoding = theAddProfileTagWhenEncoding;
}
Collection getAllResourceDefinitions() {
validateInitialized();
return myNameToResourceDefinition.values();
}
/**
* Returns the default resource type for the given profile
*
* @see #setDefaultTypeForProfile(String, Class)
*/
public Class getDefaultTypeForProfile(final String theProfile) {
validateInitialized();
return myDefaultTypeForProfile.get(theProfile);
}
/**
* Returns the scanned runtime model for the given type. This is an advanced feature which is generally only needed
* for extending the core library.
*/
@SuppressWarnings("unchecked")
public BaseRuntimeElementDefinition getElementDefinition(final Class theElementType) {
validateInitialized();
BaseRuntimeElementDefinition retVal = myClassToElementDefinition.get(theElementType);
if (retVal == null) {
retVal = scanDatatype((Class) theElementType);
}
return retVal;
}
/**
* Returns the scanned runtime model for the given type. This is an advanced feature which is generally only needed
* for extending the core library.
*
* Note that this method is case insensitive!
*
*/
@Nullable
public BaseRuntimeElementDefinition getElementDefinition(final String theElementName) {
validateInitialized();
return myNameToElementDefinition.get(theElementName.toLowerCase());
}
/**
* Returns all element definitions (resources, datatypes, etc.)
*/
public Collection> getElementDefinitions() {
validateInitialized();
return Collections.unmodifiableCollection(myClassToElementDefinition.values());
}
/**
* This feature is not yet in its final state and should be considered an internal part of HAPI for now - use with
* caution
*/
public HapiLocalizer getLocalizer() {
if (myLocalizer == null) {
myLocalizer = new HapiLocalizer();
}
return myLocalizer;
}
/**
* This feature is not yet in its final state and should be considered an internal part of HAPI for now - use with
* caution
*/
public void setLocalizer(final HapiLocalizer theMessages) {
myLocalizer = theMessages;
}
public INarrativeGenerator getNarrativeGenerator() {
return myNarrativeGenerator;
}
public FhirContext setNarrativeGenerator(final INarrativeGenerator theNarrativeGenerator) {
myNarrativeGenerator = theNarrativeGenerator;
return this;
}
/**
* Returns the parser options object which will be used to supply default
* options to newly created parsers
*
* @return The parser options - Will not return null
*/
public ParserOptions getParserOptions() {
return myParserOptions;
}
/**
* Sets the parser options object which will be used to supply default
* options to newly created parsers
*
* @param theParserOptions The parser options object - Must not be null
*/
public void setParserOptions(final ParserOptions theParserOptions) {
Validate.notNull(theParserOptions, "theParserOptions must not be null");
myParserOptions = theParserOptions;
}
/**
* Get the configured performance options
*/
public Set getPerformanceOptions() {
return myPerformanceOptions;
}
// /**
// * Return an unmodifiable collection containing all known resource definitions
// */
// public Collection getResourceDefinitions() {
//
// Set> datatypes = Collections.emptySet();
// Map, BaseRuntimeElementDefinition> existing = Collections.emptyMap();
// HashMap> types = new HashMap>();
// ModelScanner.scanVersionPropertyFile(datatypes, types, myVersion.getVersion(), existing);
// for (int next : types.)
//
// return Collections.unmodifiableCollection(myIdToResourceDefinition.values());
// }
/**
* Sets the configured performance options
*
* @see PerformanceOptionsEnum for a list of available options
*/
public void setPerformanceOptions(final Collection theOptions) {
myPerformanceOptions.clear();
if (theOptions != null) {
myPerformanceOptions.addAll(theOptions);
}
}
/**
* Sets the configured performance options
*
* @see PerformanceOptionsEnum for a list of available options
*/
public void setPerformanceOptions(final PerformanceOptionsEnum... thePerformanceOptions) {
Collection asList = null;
if (thePerformanceOptions != null) {
asList = Arrays.asList(thePerformanceOptions);
}
setPerformanceOptions(asList);
}
/**
* Returns the scanned runtime model for the given type. This is an advanced feature which is generally only needed
* for extending the core library.
*/
public RuntimeResourceDefinition getResourceDefinition(final Class theResourceType) {
validateInitialized();
Validate.notNull(theResourceType, "theResourceType can not be null");
if (Modifier.isAbstract(theResourceType.getModifiers())) {
throw new IllegalArgumentException(Msg.code(1682)
+ "Can not scan abstract or interface class (resource definitions must be concrete classes): "
+ theResourceType.getName());
}
RuntimeResourceDefinition retVal = (RuntimeResourceDefinition) myClassToElementDefinition.get(theResourceType);
if (retVal == null) {
retVal = scanResourceType(theResourceType);
}
return retVal;
}
public RuntimeResourceDefinition getResourceDefinition(
final FhirVersionEnum theVersion, final String theResourceName) {
Validate.notNull(theVersion, "theVersion can not be null");
validateInitialized();
if (theVersion.equals(myVersion.getVersion())) {
return getResourceDefinition(theResourceName);
}
Map> nameToType = myVersionToNameToResourceType.get(theVersion);
if (nameToType == null) {
nameToType = new HashMap<>();
Map, BaseRuntimeElementDefinition> existing = new HashMap<>();
ModelScanner.scanVersionPropertyFile(null, nameToType, theVersion, existing);
Map>> newVersionToNameToResourceType =
new HashMap<>();
newVersionToNameToResourceType.putAll(myVersionToNameToResourceType);
newVersionToNameToResourceType.put(theVersion, nameToType);
myVersionToNameToResourceType = newVersionToNameToResourceType;
}
Class resourceType = nameToType.get(theResourceName.toLowerCase());
if (resourceType == null) {
throw new DataFormatException(Msg.code(1683) + createUnknownResourceNameError(theResourceName, theVersion));
}
return getResourceDefinition(resourceType);
}
/**
* Returns the scanned runtime model for the given type. This is an advanced feature which is generally only needed
* for extending the core library.
*/
public RuntimeResourceDefinition getResourceDefinition(final IBaseResource theResource) {
validateInitialized();
Validate.notNull(theResource, "theResource must not be null");
return getResourceDefinition(theResource.getClass());
}
/**
* Returns the name of a given resource class.
*/
public String getResourceType(final Class theResourceType) {
return getResourceDefinition(theResourceType).getName();
}
/**
* Returns the name of the scanned runtime model for the given type. This is an advanced feature which is generally only needed
* for extending the core library.
*/
public String getResourceType(final IBaseResource theResource) {
return getResourceDefinition(theResource).getName();
}
/*
* Returns the type of the scanned runtime model for the given type. This is an advanced feature which is generally only needed
* for extending the core library.
*
* Note that this method is case insensitive!
*
*
* @throws DataFormatException If the resource name is not known
*/
public String getResourceType(final String theResourceName) throws DataFormatException {
return getResourceDefinition(theResourceName).getName();
}
/*
* Returns the scanned runtime model for the given type. This is an advanced feature which is generally only needed
* for extending the core library.
*
* Note that this method is case insensitive!
*
*
* @throws DataFormatException If the resource name is not known
*/
public RuntimeResourceDefinition getResourceDefinition(final String theResourceName) throws DataFormatException {
validateInitialized();
Validate.notBlank(theResourceName, "theResourceName must not be blank");
String resourceName = theResourceName.toLowerCase();
RuntimeResourceDefinition retVal = myNameToResourceDefinition.get(resourceName);
if (retVal == null) {
Class clazz = myNameToResourceType.get(resourceName.toLowerCase());
if (clazz == null) {
// ***********************************************************************
// Multiple spots in HAPI FHIR and Smile CDR depend on DataFormatException
// being thrown by this method, don't change that.
// ***********************************************************************
throw new DataFormatException(
Msg.code(1684) + createUnknownResourceNameError(theResourceName, myVersion.getVersion()));
}
if (IBaseResource.class.isAssignableFrom(clazz)) {
retVal = scanResourceType(clazz);
}
}
return retVal;
}
/**
* Returns the scanned runtime model for the given type. This is an advanced feature which is generally only needed
* for extending the core library.
*/
public RuntimeResourceDefinition getResourceDefinitionById(final String theId) {
validateInitialized();
return myIdToResourceDefinition.get(theId);
}
/**
* Returns the scanned runtime models. This is an advanced feature which is generally only needed for extending the
* core library.
*/
public Collection getResourceDefinitionsWithExplicitId() {
validateInitialized();
return myIdToResourceDefinition.values();
}
/**
* Returns an unmodifiable set containing all resource names known to this
* context
*
* @since 5.1.0
*/
public Set getResourceTypes() {
Set resourceNames = myResourceNames;
if (resourceNames == null) {
resourceNames = buildResourceNames();
myResourceNames = resourceNames;
}
return resourceNames;
}
@Nonnull
private Set buildResourceNames() {
Set retVal = new HashSet<>();
Properties props = new Properties();
try (InputStream propFile = myVersion.getFhirVersionPropertiesFile()) {
props.load(propFile);
} catch (IOException e) {
throw new ConfigurationException(Msg.code(1685) + "Failed to load version properties file", e);
}
Enumeration propNames = props.propertyNames();
while (propNames.hasMoreElements()) {
String next = (String) propNames.nextElement();
if (next.startsWith("resource.")) {
retVal.add(next.substring("resource.".length()).trim());
}
}
retVal.addAll(myCustomResourceNames);
return retVal;
}
/**
* Get the restful client factory. If no factory has been set, this will be initialized with
* a new ApacheRestfulClientFactory.
*
* @return the factory used to create the restful clients
*/
public IRestfulClientFactory getRestfulClientFactory() {
if (myRestfulClientFactory == null) {
try {
myRestfulClientFactory = (IRestfulClientFactory) ReflectionUtil.newInstance(
Class.forName("ca.uhn.fhir.rest.client.apache.ApacheRestfulClientFactory"),
FhirContext.class,
this);
} catch (ClassNotFoundException e) {
throw new ConfigurationException(
Msg.code(1686) + "hapi-fhir-client does not appear to be on the classpath");
}
}
return myRestfulClientFactory;
}
/**
* Set the restful client factory
*
* @param theRestfulClientFactory The new client factory (must not be null)
*/
public void setRestfulClientFactory(final IRestfulClientFactory theRestfulClientFactory) {
Validate.notNull(theRestfulClientFactory, "theRestfulClientFactory must not be null");
this.myRestfulClientFactory = theRestfulClientFactory;
}
public RuntimeChildUndeclaredExtensionDefinition getRuntimeChildUndeclaredExtensionDefinition() {
validateInitialized();
return myRuntimeChildUndeclaredExtensionDefinition;
}
/**
* Returns the validation support module configured for this context, creating a default
* implementation if no module has been passed in via the {@link #setValidationSupport(IValidationSupport)}
* method
*
* @see #setValidationSupport(IValidationSupport)
*/
public IValidationSupport getValidationSupport() {
IValidationSupport retVal = myValidationSupport;
if (retVal == null) {
retVal = new DefaultProfileValidationSupport(this);
/*
* If hapi-fhir-validation is on the classpath, we can create a much more robust
* validation chain using the classes found in that package
*/
String inMemoryTermSvcType =
"org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport";
String commonCodeSystemsSupportType =
"org.hl7.fhir.common.hapi.validation.support.CommonCodeSystemsTerminologyService";
if (ReflectionUtil.typeExists(inMemoryTermSvcType)) {
IValidationSupport inMemoryTermSvc = ReflectionUtil.newInstanceOrReturnNull(
inMemoryTermSvcType,
IValidationSupport.class,
new Class[] {FhirContext.class},
new Object[] {this});
IValidationSupport commonCodeSystemsSupport = ReflectionUtil.newInstanceOrReturnNull(
commonCodeSystemsSupportType,
IValidationSupport.class,
new Class[] {FhirContext.class},
new Object[] {this});
retVal = ReflectionUtil.newInstanceOrReturnNull(
"org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain",
IValidationSupport.class,
new Class[] {IValidationSupport[].class},
new Object[] {new IValidationSupport[] {retVal, inMemoryTermSvc, commonCodeSystemsSupport}});
assert retVal != null
: "Failed to instantiate "
+ "org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain";
}
myValidationSupport = retVal;
}
return retVal;
}
/**
* Sets the validation support module to use for this context. The validation support module
* is used to supply underlying infrastructure such as conformance resources (StructureDefinition, ValueSet, etc)
* as well as to provide terminology services to modules such as the validator and FluentPath executor
*/
public void setValidationSupport(IValidationSupport theValidationSupport) {
myValidationSupport = theValidationSupport;
}
public IFhirVersion getVersion() {
return myVersion;
}
/**
* Returns true if any default types for specific profiles have been defined
* within this context.
*
* @see #setDefaultTypeForProfile(String, Class)
* @see #getDefaultTypeForProfile(String)
*/
public boolean hasDefaultTypeForProfile() {
validateInitialized();
return !myDefaultTypeForProfile.isEmpty();
}
/**
* @return Returns true if the XML serialization format is supported, based on the
* available libraries on the classpath.
*
* @since 5.4.0
*/
public boolean isFormatXmlSupported() {
Boolean retVal = myFormatXmlSupported;
if (retVal == null) {
retVal = tryToInitParser(() -> newXmlParser());
myFormatXmlSupported = retVal;
}
return retVal;
}
/**
* @return Returns true if the JSON serialization format is supported, based on the
* available libraries on the classpath.
*
* @since 5.4.0
*/
public boolean isFormatJsonSupported() {
Boolean retVal = myFormatJsonSupported;
if (retVal == null) {
retVal = tryToInitParser(() -> newJsonParser());
myFormatJsonSupported = retVal;
}
return retVal;
}
/**
* @return Returns true if the NDJSON serialization format is supported, based on the
* available libraries on the classpath.
*
* @since 5.6.0
*/
public boolean isFormatNDJsonSupported() {
Boolean retVal = myFormatNDJsonSupported;
if (retVal == null) {
retVal = tryToInitParser(() -> newNDJsonParser());
myFormatNDJsonSupported = retVal;
}
return retVal;
}
/**
* @return Returns true if the RDF serialization format is supported, based on the
* available libraries on the classpath.
*
* @since 5.4.0
*/
public boolean isFormatRdfSupported() {
Boolean retVal = myFormatRdfSupported;
if (retVal == null) {
retVal = tryToInitParser(() -> newRDFParser());
myFormatRdfSupported = retVal;
}
return retVal;
}
public IVersionSpecificBundleFactory newBundleFactory() {
return myVersion.newBundleFactory(this);
}
/**
* @since 2.2
* @deprecated Deprecated in HAPI FHIR 5.0.0. Use {@link #newFhirPath()} instead.
*/
@Deprecated
public IFhirPath newFluentPath() {
return newFhirPath();
}
/**
* Creates a new FhirPath engine which can be used to evaluate
* path expressions over FHIR resources. Note that this engine will use the
* {@link IValidationSupport context validation support} module which is
* configured on the context at the time this method is called.
*
* In other words, you may wish to call {@link #setValidationSupport(IValidationSupport)} before
* calling {@link #newFluentPath()}
*
*
* Note that this feature was added for FHIR DSTU3 and is not available
* for contexts configured to use an older version of FHIR. Calling this method
* on a context for a previous version of fhir will result in an
* {@link UnsupportedOperationException}
*
*
* @since 5.0.0
*/
public IFhirPath newFhirPath() {
return myVersion.createFhirPathExecutor(this);
}
/**
* Create and return a new JSON parser.
*
*
* Thread safety: Parsers are not guaranteed to be thread safe. Create a new parser instance for every thread
* or every message being parsed/encoded.
*
*
* Performance Note: This method is cheap to call, and may be called once for every message being processed
* without incurring any performance penalty
*
*/
public IParser newJsonParser() {
return new JsonParser(this, myParserErrorHandler);
}
/**
* Create and return a new NDJSON parser.
*
*
* Thread safety: Parsers are not guaranteed to be thread safe. Create a new parser instance for every thread
* or every message being parsed/encoded.
*
*
* Performance Note: This method is cheap to call, and may be called once for every message being processed
* without incurring any performance penalty
*
*
* The NDJsonParser provided here is expected to translate between legal NDJson and FHIR Bundles.
* In particular, it is able to encode the resources in a FHIR Bundle to NDJson, as well as decode
* NDJson into a FHIR "collection"-type Bundle populated with the resources described in the NDJson.
* It will throw an exception in the event where it is asked to encode to anything other than a FHIR Bundle
* or where it is asked to decode into anything other than a FHIR Bundle.
*
*/
public IParser newNDJsonParser() {
return new NDJsonParser(this, myParserErrorHandler);
}
/**
* Create and return a new RDF parser.
*
*
* Thread safety: Parsers are not guaranteed to be thread safe. Create a new parser instance for every thread
* or every message being parsed/encoded.
*
*
* Performance Note: This method is cheap to call, and may be called once for every message being processed
* without incurring any performance penalty
*
*/
public IParser newRDFParser() {
return new RDFParser(this, myParserErrorHandler, Lang.TURTLE);
}
/**
* Instantiates a new client instance. This method requires an interface which is defined specifically for your use
* cases to contain methods for each of the RESTful operations you wish to implement (e.g. "read ImagingStudy",
* "search Patient by identifier", etc.). This interface must extend {@link IRestfulClient} (or commonly its
* sub-interface {@link IBasicClient}). See the RESTful Client documentation for more
* information on how to define this interface.
*
*
* Performance Note: This method is cheap to call, and may be called once for every operation invocation
* without incurring any performance penalty
*
*
* @param theClientType The client type, which is an interface type to be instantiated
* @param theServerBase The URL of the base for the restful FHIR server to connect to
* @return A newly created client
* @throws ConfigurationException If the interface type is not an interface
*/
public T newRestfulClient(final Class theClientType, final String theServerBase) {
return getRestfulClientFactory().newClient(theClientType, theServerBase);
}
/**
* Instantiates a new generic client. A generic client is able to perform any of the FHIR RESTful operations against
* a compliant server, but does not have methods defining the specific functionality required (as is the case with
* {@link #newRestfulClient(Class, String) non-generic clients}).
*
*
* Performance Note: This method performs an additional GET request to /metadata before
* the desired request is performed.
*
*
* @param theServerBase The URL of the base for the restful FHIR server to connect to
*/
public IGenericClient newRestfulGenericClient(final String theServerBase) {
return getRestfulClientFactory().newGenericClient(theServerBase);
}
public FhirTerser newTerser() {
return new FhirTerser(this);
}
/**
* Create a new validator instance.
*
* Note on thread safety: Validators are thread safe, you may use a single validator
* in multiple threads. (This is in contrast to parsers)
*
*/
public FhirValidator newValidator() {
return myFhirValidatorFactory.newFhirValidator(this);
}
public ViewGenerator newViewGenerator() {
return new ViewGenerator(this);
}
/**
* Create and return a new XML parser.
*
*
* Thread safety: Parsers are not guaranteed to be thread safe. Create a new parser instance for every thread
* or every message being parsed/encoded.
*
*
* Performance Note: This method is cheap to call, and may be called once for every message being processed
* without incurring any performance penalty
*
*/
public IParser newXmlParser() {
return new XmlParser(this, myParserErrorHandler);
}
/**
* This method may be used to register a custom resource or datatype. Note that by using
* custom types, you are creating a system that will not interoperate with other systems that
* do not know about your custom type. There are valid reasons however for wanting to create
* custom types and this method can be used to enable them.
*
* THREAD SAFETY WARNING: This method is not thread safe. It should be called before any
* threads are able to call any methods on this context.
*
*
* @param theType The custom type to add (must not be null)
*/
public void registerCustomType(final Class theType) {
Validate.notNull(theType, "theType must not be null");
ensureCustomTypeList();
myCustomTypes.add(theType);
myResourceNames = null;
}
/**
* This method may be used to register a custom resource or datatype. Note that by using
* custom types, you are creating a system that will not interoperate with other systems that
* do not know about your custom type. There are valid reasons however for wanting to create
* custom types and this method can be used to enable them.
*
* THREAD SAFETY WARNING: This method is not thread safe. It should be called before any
* threads are able to call any methods on this context.
*
*
* @param theTypes The custom types to add (must not be null or contain null elements in the collection)
*/
public void registerCustomTypes(final Collection> theTypes) {
Validate.notNull(theTypes, "theTypes must not be null");
Validate.noNullElements(theTypes.toArray(), "theTypes must not contain any null elements");
ensureCustomTypeList();
myCustomTypes.addAll(theTypes);
myResourceNames = null;
}
private BaseRuntimeElementDefinition scanDatatype(final Class theResourceType) {
ArrayList> resourceTypes = new ArrayList<>();
resourceTypes.add(theResourceType);
Map, BaseRuntimeElementDefinition> defs = scanResourceTypes(resourceTypes);
return defs.get(theResourceType);
}
private RuntimeResourceDefinition scanResourceType(final Class theResourceType) {
ArrayList> resourceTypes = new ArrayList<>();
resourceTypes.add(theResourceType);
Map, BaseRuntimeElementDefinition> defs = scanResourceTypes(resourceTypes);
return (RuntimeResourceDefinition) defs.get(theResourceType);
}
private synchronized Map, BaseRuntimeElementDefinition> scanResourceTypes(
final Collection> theResourceTypes) {
List> typesToScan = new ArrayList<>();
if (theResourceTypes != null) {
typesToScan.addAll(theResourceTypes);
}
if (myCustomTypes != null) {
typesToScan.addAll(myCustomTypes);
myCustomResourceNames.addAll(myCustomTypes.stream()
.map(customType -> Optional.ofNullable(customType.getAnnotation(ResourceDef.class))
.map(ResourceDef::name)
.orElse(null)) // This will be caught by the call to ModelScanner
.filter(Objects::nonNull)
.collect(Collectors.toSet()));
myCustomTypes = null;
}
ModelScanner scanner = new ModelScanner(this, myVersion.getVersion(), myClassToElementDefinition, typesToScan);
if (myRuntimeChildUndeclaredExtensionDefinition == null) {
myRuntimeChildUndeclaredExtensionDefinition = scanner.getRuntimeChildUndeclaredExtensionDefinition();
}
Map> nameToElementDefinition = new HashMap<>();
nameToElementDefinition.putAll(myNameToElementDefinition);
for (Entry> next :
scanner.getNameToElementDefinitions().entrySet()) {
if (!nameToElementDefinition.containsKey(next.getKey())) {
nameToElementDefinition.put(next.getKey().toLowerCase(), next.getValue());
}
}
Map nameToResourceDefinition = new HashMap<>();
nameToResourceDefinition.putAll(myNameToResourceDefinition);
for (Entry next :
scanner.getNameToResourceDefinition().entrySet()) {
if (!nameToResourceDefinition.containsKey(next.getKey())) {
nameToResourceDefinition.put(next.getKey(), next.getValue());
}
}
Map, BaseRuntimeElementDefinition> classToElementDefinition = new HashMap<>();
classToElementDefinition.putAll(myClassToElementDefinition);
classToElementDefinition.putAll(scanner.getClassToElementDefinitions());
for (BaseRuntimeElementDefinition next : classToElementDefinition.values()) {
if (next instanceof RuntimeResourceDefinition) {
if ("Bundle".equals(next.getName())) {
if (!IBaseBundle.class.isAssignableFrom(next.getImplementingClass())) {
throw new ConfigurationException(Msg.code(1687)
+ "Resource type declares resource name Bundle but does not implement IBaseBundle");
}
}
}
}
Map idToElementDefinition = new HashMap<>();
idToElementDefinition.putAll(myIdToResourceDefinition);
idToElementDefinition.putAll(scanner.getIdToResourceDefinition());
myNameToElementDefinition = nameToElementDefinition;
myClassToElementDefinition = classToElementDefinition;
myIdToResourceDefinition = idToElementDefinition;
myNameToResourceDefinition = nameToResourceDefinition;
myNameToResourceType = scanner.getNameToResourceType();
myInitialized = true;
return classToElementDefinition;
}
/**
* Sets the default type which will be used when parsing a resource that is found to be
* of the given profile.
*
* For example, this method is invoked with the profile string of
* "http://example.com/some_patient_profile" and the type of MyPatient.class,
* if the parser is parsing a resource and finds that it declares that it conforms to that profile,
* the MyPatient type will be used unless otherwise specified.
*
*
* @param theProfile The profile string, e.g. "http://example.com/some_patient_profile". Must not be
* null or empty.
* @param theClass The resource type, or null to clear any existing type
*/
public void setDefaultTypeForProfile(final String theProfile, final Class theClass) {
Validate.notBlank(theProfile, "theProfile must not be null or empty");
if (theClass == null) {
myDefaultTypeForProfile.remove(theProfile);
} else {
myDefaultTypeForProfile.put(theProfile, theClass);
}
}
/**
* Sets a parser error handler to use by default on all parsers
*
* @param theParserErrorHandler The error handler
*/
public FhirContext setParserErrorHandler(final IParserErrorHandler theParserErrorHandler) {
Validate.notNull(theParserErrorHandler, "theParserErrorHandler must not be null");
myParserErrorHandler = theParserErrorHandler;
return this;
}
/**
* Set the factory method used to create FhirValidator instances
*
* @param theFhirValidatorFactory
* @return this
* @since 5.6.0
*/
public FhirContext setFhirValidatorFactory(IFhirValidatorFactory theFhirValidatorFactory) {
myFhirValidatorFactory = theFhirValidatorFactory;
return this;
}
@SuppressWarnings({"cast"})
private List> toElementList(
final Collection> theResourceTypes) {
if (theResourceTypes == null) {
return null;
}
List> resTypes = new ArrayList<>();
for (Class next : theResourceTypes) {
resTypes.add(next);
}
return resTypes;
}
private void validateInitialized() {
// See #610
if (!myInitialized) {
synchronized (this) {
if (!myInitialized && !myInitializing) {
myInitializing = true;
try {
scanResourceTypes(toElementList(myResourceTypesToScan));
} catch (Exception e) {
ourLog.error("Failed to initialize FhirContext", e);
throw e;
} finally {
myInitializing = false;
}
}
}
}
}
@Override
public String toString() {
return "FhirContext[" + myVersion.getVersion().name() + "]";
}
// TODO KHS add the other primitive types
@Deprecated(since = "6.6.0", forRemoval = true)
public IPrimitiveType getPrimitiveBoolean(Boolean theValue) {
return newPrimitiveBoolean(theValue);
}
public IPrimitiveType newPrimitiveBoolean(Boolean theValue) {
IPrimitiveType retval =
(IPrimitiveType) getElementDefinition("boolean").newInstance();
retval.setValue(theValue);
return retval;
}
public IPrimitiveType newPrimitiveString(String theValue) {
IPrimitiveType retval =
(IPrimitiveType) getElementDefinition("string").newInstance();
retval.setValue(theValue);
return retval;
}
private static boolean tryToInitParser(Runnable run) {
boolean retVal;
try {
run.run();
retVal = true;
} catch (UnsupportedClassVersionError | Exception | NoClassDefFoundError e) {
retVal = false;
}
return retVal;
}
/**
* Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU2 DSTU2}
*/
public static FhirContext forDstu2() {
return new FhirContext(FhirVersionEnum.DSTU2);
}
/**
* Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU2_HL7ORG DSTU2} (using the Reference
* Implementation Structures)
*/
public static FhirContext forDstu2Hl7Org() {
return new FhirContext(FhirVersionEnum.DSTU2_HL7ORG);
}
/**
* Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU2 DSTU2} (2016 May DSTU3 Snapshot)
*/
public static FhirContext forDstu2_1() {
return new FhirContext(FhirVersionEnum.DSTU2_1);
}
/**
* Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU3 DSTU3}
*
* @since 1.4
*/
public static FhirContext forDstu3() {
return new FhirContext(FhirVersionEnum.DSTU3);
}
/**
* Creates and returns a new FhirContext with version {@link FhirVersionEnum#R4 R4}
*
* @since 3.0.0
*/
public static FhirContext forR4() {
return new FhirContext(FhirVersionEnum.R4);
}
/**
* Creates and returns a new FhirContext with version {@link FhirVersionEnum#R4B R4B}
*
* @since 6.2.0
*/
public static FhirContext forR4B() {
return new FhirContext(FhirVersionEnum.R4B);
}
/**
* Creates and returns a new FhirContext with version {@link FhirVersionEnum#R5 R5}
*
* @since 4.0.0
*/
public static FhirContext forR5() {
return new FhirContext(FhirVersionEnum.R5);
}
/**
* Returns a statically cached {@literal FhirContext} instance for the given version, creating one if none exists in the
* cache. One FhirContext will be kept in the cache for each FHIR version that is requested (by calling
* this method for that version), and the cache will never be expired.
*
* @since 5.1.0
*/
public static FhirContext forCached(FhirVersionEnum theFhirVersionEnum) {
return ourStaticContexts.computeIfAbsent(theFhirVersionEnum, v -> new FhirContext(v));
}
private static Collection> toCollection(
Class theResourceType) {
ArrayList> retVal = new ArrayList<>(1);
retVal.add(theResourceType);
return retVal;
}
@SuppressWarnings("unchecked")
private static List> toCollection(final Class[] theResourceTypes) {
ArrayList> retVal = new ArrayList>(1);
for (Class clazz : theResourceTypes) {
if (!IResource.class.isAssignableFrom(clazz)) {
throw new IllegalArgumentException(Msg.code(1688) + clazz.getCanonicalName() + " is not an instance of "
+ IResource.class.getSimpleName());
}
retVal.add((Class) clazz);
}
return retVal;
}
}
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