package ca.uhn.fhir.context;

import java.io.IOException;
import java.lang.reflect.Method;

/*
 * #%L
 * HAPI FHIR - Core Library
 * %%
 * Copyright (C) 2014 - 2017 University Health Network
 * %%
 * 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%
 */

import java.lang.reflect.Modifier;
import java.util.*;
import java.util.Map.Entry;

import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.*;

import ca.uhn.fhir.context.api.AddProfileTagEnum;
import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.fluentpath.IFluentPath;
import ca.uhn.fhir.i18n.HapiLocalizer;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.view.ViewGenerator;
import ca.uhn.fhir.narrative.INarrativeGenerator;
import ca.uhn.fhir.parser.*;
import ca.uhn.fhir.rest.api.IVersionSpecificBundleFactory;
import ca.uhn.fhir.rest.client.api.*;
import ca.uhn.fhir.util.*;
import ca.uhn.fhir.validation.FhirValidator;

/**
 * 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.).
 * 
 * <p>
 * Important usage notes:
 * </p>
 * <ul>
 * <li>
 * Thread safety: <b>This class is thread safe</b> and may be shared between multiple processing
 * threads, except for the {@link #registerCustomType} and {@link #registerCustomTypes} methods.
 * </li>
 * <li>
 * Performance: <b>This class is expensive</b> 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.
 * </li>
 * </ul>
 */
public class FhirContext {

        private static final List<Class<? extends IBaseResource>> EMPTY_LIST = Collections.emptyList();
        private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirContext.class);
        private AddProfileTagEnum myAddProfileTagWhenEncoding = AddProfileTagEnum.ONLY_FOR_CUSTOM;
        private volatile Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> myClassToElementDefinition = Collections.emptyMap();
        private ArrayList<Class<? extends IBase>> myCustomTypes;
        private Map<String, Class<? extends IBaseResource>> myDefaultTypeForProfile = new HashMap<String, Class<? extends IBaseResource>>();
        private volatile Map<String, RuntimeResourceDefinition> myIdToResourceDefinition = Collections.emptyMap();
        private volatile boolean myInitialized;
        private volatile boolean myInitializing = false;
        private HapiLocalizer myLocalizer = new HapiLocalizer();
        private volatile Map<String, BaseRuntimeElementDefinition<?>> myNameToElementDefinition = Collections.emptyMap();
        private volatile Map<String, RuntimeResourceDefinition> myNameToResourceDefinition = Collections.emptyMap();
        private volatile Map<String, Class<? extends IBaseResource>> myNameToResourceType;
        private volatile INarrativeGenerator myNarrativeGenerator;
        private volatile IParserErrorHandler myParserErrorHandler = new LenientErrorHandler();
        private ParserOptions myParserOptions = new ParserOptions();
        private Set<PerformanceOptionsEnum> myPerformanceOptions = new HashSet<PerformanceOptionsEnum>();
        private Collection<Class<? extends IBaseResource>> myResourceTypesToScan;
        private volatile IRestfulClientFactory myRestfulClientFactory;
        private volatile RuntimeChildUndeclaredExtensionDefinition myRuntimeChildUndeclaredExtensionDefinition;
        private IContextValidationSupport<?, ?, ?, ?, ?, ?> myValidationSupport;

        private final IFhirVersion myVersion;

        private Map<FhirVersionEnum, Map<String, Class<? extends IBaseResource>>> myVersionToNameToResourceType = Collections.emptyMap();

        /**
         * @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(Class<? extends IBaseResource> 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(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(Collection<Class<? extends IBaseResource>> 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(FhirVersionEnum theVersion) {
                this(theVersion, null);
        }

        private FhirContext(FhirVersionEnum theVersion, Collection<Class<? extends IBaseResource>> theResourceTypes) {
                VersionUtil.getVersion();

                if (theVersion != null) {
                        if (!theVersion.isPresentOnClasspath()) {
                                throw new IllegalStateException(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.DSTU3.isPresentOnClasspath()) {
                        myVersion = FhirVersionEnum.DSTU3.getVersionImplementation();
                } else {
                        throw new IllegalStateException(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 {
                        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");
                }

        }

        private String createUnknownResourceNameError(String theResourceName, FhirVersionEnum theVersion) {
                return getLocalizer().getMessage(FhirContext.class, "unknownResourceName", theResourceName, theVersion);
        }

        private void ensureCustomTypeList() {
                myClassToElementDefinition.clear();
                if (myCustomTypes == null) {
                        myCustomTypes = new ArrayList<Class<? extends IBase>>();
                }
        }

        /**
         * 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;
        }

        Collection<RuntimeResourceDefinition> getAllResourceDefinitions() {
                validateInitialized();
                return myNameToResourceDefinition.values();
        }

        /**
         * Returns the default resource type for the given profile
         * 
         * @see #setDefaultTypeForProfile(String, Class)
         */
        public Class<? extends IBaseResource> getDefaultTypeForProfile(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(Class<? extends IBase> theElementType) {
                validateInitialized();
                BaseRuntimeElementDefinition<?> retVal = myClassToElementDefinition.get(theElementType);
                if (retVal == null) {
                        retVal = scanDatatype((Class<? extends IElement>) 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.
         * <p>
         * Note that this method is case insensitive!
         * </p>
         */
        public BaseRuntimeElementDefinition<?> getElementDefinition(String theElementName) {
                validateInitialized();
                return myNameToElementDefinition.get(theElementName.toLowerCase());
        }

        /** For unit tests only */
        int getElementDefinitionCount() {
                validateInitialized();
                return myClassToElementDefinition.size();
        }

        /**
         * Returns all element definitions (resources, datatypes, etc.)
         */
        public Collection<BaseRuntimeElementDefinition<?>> 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;
        }

        public INarrativeGenerator getNarrativeGenerator() {
                return myNarrativeGenerator;
        }

        /**
         * Returns the parser options object which will be used to supply default
         * options to newly created parsers
         * 
         * @return The parser options - Will not return <code>null</code>
         */
        public ParserOptions getParserOptions() {
                return myParserOptions;
        }

        /**
         * Get the configured performance options
         */
        public Set<PerformanceOptionsEnum> getPerformanceOptions() {
                return myPerformanceOptions;
        }

        /**
         * 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(Class<? extends IBaseResource> theResourceType) {
                validateInitialized();
                if (theResourceType == null) {
                        throw new NullPointerException("theResourceType can not be null");
                }
                if (Modifier.isAbstract(theResourceType.getModifiers())) {
                        throw new IllegalArgumentException("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(FhirVersionEnum theVersion, String theResourceName) {
                Validate.notNull(theVersion, "theVersion can not be null");
                validateInitialized();

                if (theVersion.equals(myVersion.getVersion())) {
                        return getResourceDefinition(theResourceName);
                }

                Map<String, Class<? extends IBaseResource>> nameToType = myVersionToNameToResourceType.get(theVersion);
                if (nameToType == null) {
                        nameToType = new HashMap<>();
                        Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> existing = new HashMap<>();
                        ModelScanner.scanVersionPropertyFile(null, nameToType, theVersion, existing);

                        Map<FhirVersionEnum, Map<String, Class<? extends IBaseResource>>> newVersionToNameToResourceType = new HashMap<>();
                        newVersionToNameToResourceType.putAll(myVersionToNameToResourceType);
                        newVersionToNameToResourceType.put(theVersion, nameToType);
                        myVersionToNameToResourceType = newVersionToNameToResourceType;
                }

                Class<? extends IBaseResource> resourceType = nameToType.get(theResourceName.toLowerCase());
                if (resourceType == null) {
                        throw new DataFormatException(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(IBaseResource theResource) {
                validateInitialized();
                Validate.notNull(theResource, "theResource must not be null");
                return getResourceDefinition(theResource.getClass());
        }

        /**
         * Returns the scanned runtime model for the given type. This is an advanced feature which is generally only needed
         * for extending the core library.
         * <p>
         * Note that this method is case insensitive!
         * </p>
         */
        public RuntimeResourceDefinition getResourceDefinition(String theResourceName) {
                validateInitialized();
                Validate.notBlank(theResourceName, "theResourceName must not be blank");

                String resourceName = theResourceName.toLowerCase();
                RuntimeResourceDefinition retVal = myNameToResourceDefinition.get(resourceName);

                if (retVal == null) {
                        Class<? extends IBaseResource> clazz = myNameToResourceType.get(resourceName.toLowerCase());
                        if (clazz == null) {
                                throw new DataFormatException(createUnknownResourceNameError(theResourceName, myVersion.getVersion()));
                        }
                        if (IBaseResource.class.isAssignableFrom(clazz)) {
                                retVal = scanResourceType(clazz);
                        }
                }

                return retVal;
        }

        // /**
        // * Return an unmodifiable collection containing all known resource definitions
        // */
        // public Collection<RuntimeResourceDefinition> getResourceDefinitions() {
        //
        // Set<Class<? extends IBase>> datatypes = Collections.emptySet();
        // Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> existing = Collections.emptyMap();
        // HashMap<String, Class<? extends IBaseResource>> types = new HashMap<String, Class<? extends IBaseResource>>();
        // ModelScanner.scanVersionPropertyFile(datatypes, types, myVersion.getVersion(), existing);
        // for (int next : types.)
        //
        // return Collections.unmodifiableCollection(myIdToResourceDefinition.values());
        // }

        /**
         * 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(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<RuntimeResourceDefinition> getResourceDefinitionsWithExplicitId() {
                validateInitialized();
                return myIdToResourceDefinition.values();
        }

        /**
         * 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("hapi-fhir-client does not appear to be on the classpath");
                        }
                }
                return myRestfulClientFactory;
        }

        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(IContextValidationSupport)}
         * method
         * 
         * @see #setValidationSupport(IContextValidationSupport)
         */
        public IContextValidationSupport<?, ?, ?, ?, ?, ?> getValidationSupport() {
                if (myValidationSupport == null) {
                        myValidationSupport = myVersion.createValidationSupport();
                }
                return myValidationSupport;
        }

        public IFhirVersion getVersion() {
                return myVersion;
        }

        /**
         * Returns <code>true</code> 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();
        }

        public IVersionSpecificBundleFactory newBundleFactory() {
                return myVersion.newBundleFactory(this);
        }

        /**
         * Creates a new FluentPath engine which can be used to exvaluate
         * path expressions over FHIR resources. Note that this engine will use the
         * {@link IContextValidationSupport context validation support} module which is
         * configured on the context at the time this method is called.
         * <p>
         * In other words, call {@link #setValidationSupport(IContextValidationSupport)} before
         * calling {@link #newFluentPath()}
         * </p>
         * <p>
         * 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}
         * </p>
         * 
         * @since 2.2
         */
        public IFluentPath newFluentPath() {
                return myVersion.createFluentPathExecutor(this);
        }

        /**
         * Create and return a new JSON parser.
         * 
         * <p>
         * Thread safety: <b>Parsers are not guaranteed to be thread safe</b>. Create a new parser instance for every thread
         * or every message being parsed/encoded.
         * </p>
         * <p>
         * Performance Note: <b>This method is cheap</b> to call, and may be called once for every message being processed
         * without incurring any performance penalty
         * </p>
         */
        public IParser newJsonParser() {
                return new JsonParser(this, myParserErrorHandler);
        }

        /**
         * 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 <a
         * href="http://jamesagnew.github.io/hapi-fhir/doc_rest_client.html">RESTful Client</a> documentation for more
         * information on how to define this interface.
         * 
         * <p>
         * Performance Note: <b>This method is cheap</b> to call, and may be called once for every operation invocation
         * without incurring any performance penalty
         * </p>
         * 
         * @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 extends IRestfulClient> T newRestfulClient(Class<T> theClientType, 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}).
         * 
         * <p>
         * Performance Note: <b>This method is cheap</b> to call, and may be called once for every operation invocation
         * without incurring any performance penalty
         * </p>
         * 
         * @param theServerBase
         *          The URL of the base for the restful FHIR server to connect to
         */
        public IGenericClient newRestfulGenericClient(String theServerBase) {
                return getRestfulClientFactory().newGenericClient(theServerBase);
        }

        public FhirTerser newTerser() {
                return new FhirTerser(this);
        }

        /**
         * Create a new validator instance.
         * <p>
         * Note on thread safety: Validators are thread safe, you may use a single validator
         * in multiple threads. (This is in contrast to parsers)
         * </p>
         */
        public FhirValidator newValidator() {
                return new FhirValidator(this);
        }

        public ViewGenerator newViewGenerator() {
                return new ViewGenerator(this);
        }

        /**
         * Create and return a new XML parser.
         * 
         * <p>
         * Thread safety: <b>Parsers are not guaranteed to be thread safe</b>. Create a new parser instance for every thread
         * or every message being parsed/encoded.
         * </p>
         * <p>
         * Performance Note: <b>This method is cheap</b> to call, and may be called once for every message being processed
         * without incurring any performance penalty
         * </p>
         */
        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.
         * <p>
         * <b>THREAD SAFETY WARNING:</b> This method is not thread safe. It should be called before any
         * threads are able to call any methods on this context.
         * </p>
         * 
         * @param theType
         *          The custom type to add (must not be <code>null</code>)
         */
        public void registerCustomType(Class<? extends IBase> theType) {
                Validate.notNull(theType, "theType must not be null");

                ensureCustomTypeList();
                myCustomTypes.add(theType);
        }

        /**
         * 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.
         * <p>
         * <b>THREAD SAFETY WARNING:</b> This method is not thread safe. It should be called before any
         * threads are able to call any methods on this context.
         * </p>
         * 
         * @param theTypes
         *          The custom types to add (must not be <code>null</code> or contain null elements in the collection)
         */
        public void registerCustomTypes(Collection<Class<? extends IBase>> theTypes) {
                Validate.notNull(theTypes, "theTypes must not be null");
                Validate.noNullElements(theTypes.toArray(), "theTypes must not contain any null elements");

                ensureCustomTypeList();

                myCustomTypes.addAll(theTypes);
        }

        private BaseRuntimeElementDefinition<?> scanDatatype(Class<? extends IElement> theResourceType) {
                ArrayList<Class<? extends IElement>> resourceTypes = new ArrayList<Class<? extends IElement>>();
                resourceTypes.add(theResourceType);
                Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> defs = scanResourceTypes(resourceTypes);
                return defs.get(theResourceType);
        }

        private RuntimeResourceDefinition scanResourceType(Class<? extends IBaseResource> theResourceType) {
                ArrayList<Class<? extends IElement>> resourceTypes = new ArrayList<Class<? extends IElement>>();
                resourceTypes.add(theResourceType);
                Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> defs = scanResourceTypes(resourceTypes);
                return (RuntimeResourceDefinition) defs.get(theResourceType);
        }

        private synchronized Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> scanResourceTypes(Collection<Class<? extends IElement>> theResourceTypes) {
                List<Class<? extends IBase>> typesToScan = new ArrayList<Class<? extends IBase>>();
                if (theResourceTypes != null) {
                        typesToScan.addAll(theResourceTypes);
                }
                if (myCustomTypes != null) {
                        typesToScan.addAll(myCustomTypes);
                        myCustomTypes = null;
                }

                ModelScanner scanner = new ModelScanner(this, myVersion.getVersion(), myClassToElementDefinition, typesToScan);
                if (myRuntimeChildUndeclaredExtensionDefinition == null) {
                        myRuntimeChildUndeclaredExtensionDefinition = scanner.getRuntimeChildUndeclaredExtensionDefinition();
                }

                Map<String, BaseRuntimeElementDefinition<?>> nameToElementDefinition = new HashMap<String, BaseRuntimeElementDefinition<?>>();
                nameToElementDefinition.putAll(myNameToElementDefinition);
                for (Entry<String, BaseRuntimeElementDefinition<?>> next : scanner.getNameToElementDefinitions().entrySet()) {
                        if (!nameToElementDefinition.containsKey(next.getKey())) {
                                nameToElementDefinition.put(next.getKey(), next.getValue());
                        }
                }

                Map<String, RuntimeResourceDefinition> nameToResourceDefinition = new HashMap<String, RuntimeResourceDefinition>();
                nameToResourceDefinition.putAll(myNameToResourceDefinition);
                for (Entry<String, RuntimeResourceDefinition> next : scanner.getNameToResourceDefinition().entrySet()) {
                        if (!nameToResourceDefinition.containsKey(next.getKey())) {
                                nameToResourceDefinition.put(next.getKey(), next.getValue());
                        }
                }

                Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> classToElementDefinition = new HashMap<Class<? extends IBase>, BaseRuntimeElementDefinition<?>>();
                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("Resource type declares resource name Bundle but does not implement IBaseBundle");
                                        }
                                }
                        }
                }

                Map<String, RuntimeResourceDefinition> idToElementDefinition = new HashMap<String, RuntimeResourceDefinition>();
                idToElementDefinition.putAll(myIdToResourceDefinition);
                idToElementDefinition.putAll(scanner.getIdToResourceDefinition());

                myNameToElementDefinition = nameToElementDefinition;
                myClassToElementDefinition = classToElementDefinition;
                myIdToResourceDefinition = idToElementDefinition;
                myNameToResourceDefinition = nameToResourceDefinition;

                myNameToResourceType = scanner.getNameToResourceType();

                myInitialized = true;
                return classToElementDefinition;
        }

        /**
         * 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}.
         * <p>
         * 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.
         * </p>
         * <p>
         * See <a href="http://jamesagnew.gihhub.io/hapi-fhir/doc_extensions.html">Profiling and Extensions</a>
         * for more information on using custom types.
         * </p>
         * <p>
         * Note that this feature automatically adds the profile, but leaves any profile tags
         * which have been manually added in place as well.
         * </p>
         * 
         * @param theAddProfileTagWhenEncoding
         *          The add profile mode (must not be <code>null</code>)
         */
        public void setAddProfileTagWhenEncoding(AddProfileTagEnum theAddProfileTagWhenEncoding) {
                Validate.notNull(theAddProfileTagWhenEncoding, "theAddProfileTagWhenEncoding must not be null");
                myAddProfileTagWhenEncoding = theAddProfileTagWhenEncoding;
        }

        /**
         * Sets the default type which will be used when parsing a resource that is found to be
         * of the given profile.
         * <p>
         * For example, this method is invoked with the profile string of
         * <code>"http://example.com/some_patient_profile"</code> and the type of <code>MyPatient.class</code>,
         * if the parser is parsing a resource and finds that it declares that it conforms to that profile,
         * the <code>MyPatient</code> type will be used unless otherwise specified.
         * </p>
         * 
         * @param theProfile
         *          The profile string, e.g. <code>"http://example.com/some_patient_profile"</code>. Must not be
         *          <code>null</code> or empty.
         * @param theClass
         *          The resource type, or <code>null</code> to clear any existing type
         */
        public void setDefaultTypeForProfile(String theProfile, Class<? extends IBaseResource> theClass) {
                Validate.notBlank(theProfile, "theProfile must not be null or empty");
                if (theClass == null) {
                        myDefaultTypeForProfile.remove(theProfile);
                } else {
                        myDefaultTypeForProfile.put(theProfile, theClass);
                }
        }

        /**
         * 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(HapiLocalizer theMessages) {
                myLocalizer = theMessages;
        }

        public void setNarrativeGenerator(INarrativeGenerator theNarrativeGenerator) {
                myNarrativeGenerator = theNarrativeGenerator;
        }

        /**
         * Sets a parser error handler to use by default on all parsers
         * 
         * @param theParserErrorHandler
         *          The error handler
         */
        public void setParserErrorHandler(IParserErrorHandler theParserErrorHandler) {
                Validate.notNull(theParserErrorHandler, "theParserErrorHandler must not be null");
                myParserErrorHandler = theParserErrorHandler;
        }

        /**
         * 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 <code>null</code>
         */
        public void setParserOptions(ParserOptions theParserOptions) {
                Validate.notNull(theParserOptions, "theParserOptions must not be null");
                myParserOptions = theParserOptions;
        }

        /**
         * Sets the configured performance options
         * 
         * @see PerformanceOptionsEnum for a list of available options
         */
        public void setPerformanceOptions(Collection<PerformanceOptionsEnum> 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(PerformanceOptionsEnum... thePerformanceOptions) {
                Collection<PerformanceOptionsEnum> asList = null;
                if (thePerformanceOptions != null) {
                        asList = Arrays.asList(thePerformanceOptions);
                }
                setPerformanceOptions(asList);
        }

        /**
         * Set the restful client factory
         * 
         * @param theRestfulClientFactory
         */
        public void setRestfulClientFactory(IRestfulClientFactory theRestfulClientFactory) {
                Validate.notNull(theRestfulClientFactory, "theRestfulClientFactory must not be null");
                this.myRestfulClientFactory = theRestfulClientFactory;
        }

        /**
         * 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(IContextValidationSupport<?, ?, ?, ?, ?, ?> theValidationSupport) {
                myValidationSupport = theValidationSupport;
        }
        
        @SuppressWarnings({ "cast" })
        private List<Class<? extends IElement>> toElementList(Collection<Class<? extends IBaseResource>> theResourceTypes) {
                if (theResourceTypes == null) {
                        return null;
                }
                List<Class<? extends IElement>> resTypes = new ArrayList<Class<? extends IElement>>();
                for (Class<? extends IBaseResource> next : theResourceTypes) {
                        resTypes.add((Class<? extends IElement>) next);
                }
                return resTypes;
        }

        private void validateInitialized() {
                // See #610
                if (!myInitialized) {
                        synchronized (this) {
                                if (!myInitialized && !myInitializing) {
                                        myInitializing = true;
                                        scanResourceTypes(toElementList(myResourceTypesToScan));
                                }
                        }
                }
        }

        /**
         * 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 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#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#DSTU3 DSTU3}
         * 
         * @since 1.4
         */
        public static FhirContext forDstu3() {
                return new FhirContext(FhirVersionEnum.DSTU3);
        }

        /**
         * Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU3 DSTU3}
         * 
         * @since 3.0.0
         */
        public static FhirContext forR4() {
                return new FhirContext(FhirVersionEnum.R4);
        }


        private static Collection<Class<? extends IBaseResource>> toCollection(Class<? extends IBaseResource> theResourceType) {
                ArrayList<Class<? extends IBaseResource>> retVal = new ArrayList<Class<? extends IBaseResource>>(1);
                retVal.add(theResourceType);
                return retVal;
        }

        @SuppressWarnings("unchecked")
        private static List<Class<? extends IBaseResource>> toCollection(Class<?>[] theResourceTypes) {
                ArrayList<Class<? extends IBaseResource>> retVal = new ArrayList<Class<? extends IBaseResource>>(1);
                for (Class<?> clazz : theResourceTypes) {
                        if (!IResource.class.isAssignableFrom(clazz)) {
                                throw new IllegalArgumentException(clazz.getCanonicalName() + " is not an instance of " + IResource.class.getSimpleName());
                        }
                        retVal.add((Class<? extends IResource>) clazz);
                }
                return retVal;
        }

        /**
         * Returns an unmodifiable set containing all resource names known to this
         * context
         */
        public Set<String> getResourceNames() {
                Set<String> resourceNames= new HashSet<>();

                if (myNameToResourceDefinition.isEmpty()) {
                        Properties props = new Properties();
                        try {
                                props.load(myVersion.getFhirVersionPropertiesFile());
                        } catch (IOException theE) {
                                throw new ConfigurationException("Failed to load version properties file");
                        }
                        Enumeration<?> propNames = props.propertyNames();
                        while (propNames.hasMoreElements()){
                                String next = (String) propNames.nextElement();
                                if (next.startsWith("resource.")) {
                                        resourceNames.add(next.substring("resource.".length()).trim());
                                }
                        }
                }

                for (RuntimeResourceDefinition next : myNameToResourceDefinition.values()) {
                        resourceNames.add(next.getName());
                }

                return Collections.unmodifiableSet(resourceNames);
        }
}