Clean up terminology uploading
This commit is contained in:
parent
36b4ed28e4
commit
43ac912033
|
@ -1,7 +1,34 @@
|
|||
package ca.uhn.fhir.context;
|
||||
|
||||
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.IElement;
|
||||
import ca.uhn.fhir.model.api.IFhirVersion;
|
||||
import ca.uhn.fhir.model.api.IResource;
|
||||
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.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.util.FhirTerser;
|
||||
import ca.uhn.fhir.util.ReflectionUtil;
|
||||
import ca.uhn.fhir.util.VersionUtil;
|
||||
import ca.uhn.fhir.validation.FhirValidator;
|
||||
import org.apache.commons.lang3.Validate;
|
||||
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 java.io.IOException;
|
||||
import java.lang.reflect.Method;
|
||||
import java.lang.reflect.Modifier;
|
||||
import java.util.*;
|
||||
import java.util.Map.Entry;
|
||||
|
||||
/*
|
||||
* #%L
|
||||
|
@ -12,9 +39,9 @@ import java.lang.reflect.Method;
|
|||
* 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.
|
||||
|
@ -23,30 +50,10 @@ import java.lang.reflect.Method;
|
|||
* #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>
|
||||
|
@ -68,6 +75,7 @@ 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 final IFhirVersion myVersion;
|
||||
private AddProfileTagEnum myAddProfileTagWhenEncoding = AddProfileTagEnum.ONLY_FOR_CUSTOM;
|
||||
private volatile Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> myClassToElementDefinition = Collections.emptyMap();
|
||||
private ArrayList<Class<? extends IBase>> myCustomTypes;
|
||||
|
@ -87,14 +95,11 @@ public class FhirContext {
|
|||
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()}
|
||||
* of this method, e.g. {@link #forDstu2()} or {@link #forDstu3()} or {@link #forR4()}
|
||||
*/
|
||||
@Deprecated
|
||||
public FhirContext() {
|
||||
|
@ -103,7 +108,7 @@ public class FhirContext {
|
|||
|
||||
/**
|
||||
* @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()}
|
||||
* of this method, e.g. {@link #forDstu2()} or {@link #forDstu3()} or {@link #forR4()}
|
||||
*/
|
||||
@Deprecated
|
||||
public FhirContext(Class<? extends IBaseResource> theResourceType) {
|
||||
|
@ -112,7 +117,7 @@ public class FhirContext {
|
|||
|
||||
/**
|
||||
* @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()}
|
||||
* of this method, e.g. {@link #forDstu2()} or {@link #forDstu3()} or {@link #forR4()}
|
||||
*/
|
||||
@Deprecated
|
||||
public FhirContext(Class<?>... theResourceTypes) {
|
||||
|
@ -121,7 +126,7 @@ public class FhirContext {
|
|||
|
||||
/**
|
||||
* @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()}
|
||||
* of this method, e.g. {@link #forDstu2()} or {@link #forDstu3()} or {@link #forR4()}
|
||||
*/
|
||||
@Deprecated
|
||||
public FhirContext(Collection<Class<? extends IBaseResource>> theResourceTypes) {
|
||||
|
@ -161,7 +166,7 @@ public class FhirContext {
|
|||
|
||||
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());
|
||||
myVersion.getVersion().name());
|
||||
} else {
|
||||
ourLog.info("Creating new FHIR context for FHIR version [{}]", myVersion.getVersion().name());
|
||||
}
|
||||
|
@ -201,13 +206,37 @@ public class FhirContext {
|
|||
* 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}.
|
||||
* <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;
|
||||
}
|
||||
|
||||
Collection<RuntimeResourceDefinition> getAllResourceDefinitions() {
|
||||
validateInitialized();
|
||||
return myNameToResourceDefinition.values();
|
||||
|
@ -215,7 +244,7 @@ public class FhirContext {
|
|||
|
||||
/**
|
||||
* Returns the default resource type for the given profile
|
||||
*
|
||||
*
|
||||
* @see #setDefaultTypeForProfile(String, Class)
|
||||
*/
|
||||
public Class<? extends IBaseResource> getDefaultTypeForProfile(String theProfile) {
|
||||
|
@ -249,7 +278,9 @@ public class FhirContext {
|
|||
return myNameToElementDefinition.get(theElementName.toLowerCase());
|
||||
}
|
||||
|
||||
/** For unit tests only */
|
||||
/**
|
||||
* For unit tests only
|
||||
*/
|
||||
int getElementDefinitionCount() {
|
||||
validateInitialized();
|
||||
return myClassToElementDefinition.size();
|
||||
|
@ -274,20 +305,43 @@ public class FhirContext {
|
|||
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(HapiLocalizer theMessages) {
|
||||
myLocalizer = theMessages;
|
||||
}
|
||||
|
||||
public INarrativeGenerator getNarrativeGenerator() {
|
||||
return myNarrativeGenerator;
|
||||
}
|
||||
|
||||
public void setNarrativeGenerator(INarrativeGenerator theNarrativeGenerator) {
|
||||
myNarrativeGenerator = theNarrativeGenerator;
|
||||
}
|
||||
|
||||
/**
|
||||
* 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;
|
||||
}
|
||||
|
||||
/**
|
||||
* 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;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the configured performance options
|
||||
*/
|
||||
|
@ -295,6 +349,32 @@ public class FhirContext {
|
|||
return myPerformanceOptions;
|
||||
}
|
||||
|
||||
// /**
|
||||
// * 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());
|
||||
// }
|
||||
|
||||
/**
|
||||
* 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);
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the scanned runtime model for the given type. This is an advanced feature which is generally only needed
|
||||
* for extending the core library.
|
||||
|
@ -359,8 +439,12 @@ public class FhirContext {
|
|||
* <p>
|
||||
* Note that this method is case insensitive!
|
||||
* </p>
|
||||
*
|
||||
* @throws DataFormatException If the resource name is not known
|
||||
*/
|
||||
public RuntimeResourceDefinition getResourceDefinition(String theResourceName) {
|
||||
// Multiple spots in HAPI FHIR and Smile CDR depend on DataFormatException being
|
||||
// thrown by this method, don't change that.
|
||||
public RuntimeResourceDefinition getResourceDefinition(String theResourceName) throws DataFormatException {
|
||||
validateInitialized();
|
||||
Validate.notBlank(theResourceName, "theResourceName must not be blank");
|
||||
|
||||
|
@ -380,20 +464,6 @@ public class FhirContext {
|
|||
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.
|
||||
|
@ -412,10 +482,40 @@ public class FhirContext {
|
|||
return myIdToResourceDefinition.values();
|
||||
}
|
||||
|
||||
/**
|
||||
* 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);
|
||||
}
|
||||
|
||||
/**
|
||||
* 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() {
|
||||
|
@ -429,6 +529,16 @@ public class FhirContext {
|
|||
return myRestfulClientFactory;
|
||||
}
|
||||
|
||||
/**
|
||||
* Set the restful client factory
|
||||
*
|
||||
* @param theRestfulClientFactory
|
||||
*/
|
||||
public void setRestfulClientFactory(IRestfulClientFactory theRestfulClientFactory) {
|
||||
Validate.notNull(theRestfulClientFactory, "theRestfulClientFactory must not be null");
|
||||
this.myRestfulClientFactory = theRestfulClientFactory;
|
||||
}
|
||||
|
||||
public RuntimeChildUndeclaredExtensionDefinition getRuntimeChildUndeclaredExtensionDefinition() {
|
||||
validateInitialized();
|
||||
return myRuntimeChildUndeclaredExtensionDefinition;
|
||||
|
@ -438,7 +548,7 @@ public class FhirContext {
|
|||
* 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() {
|
||||
|
@ -448,6 +558,15 @@ public class FhirContext {
|
|||
return myValidationSupport;
|
||||
}
|
||||
|
||||
/**
|
||||
* 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;
|
||||
}
|
||||
|
||||
public IFhirVersion getVersion() {
|
||||
return myVersion;
|
||||
}
|
||||
|
@ -455,7 +574,7 @@ public class FhirContext {
|
|||
/**
|
||||
* Returns <code>true</code> if any default types for specific profiles have been defined
|
||||
* within this context.
|
||||
*
|
||||
*
|
||||
* @see #setDefaultTypeForProfile(String, Class)
|
||||
* @see #getDefaultTypeForProfile(String)
|
||||
*/
|
||||
|
@ -483,7 +602,7 @@ public class FhirContext {
|
|||
* on a context for a previous version of fhir will result in an
|
||||
* {@link UnsupportedOperationException}
|
||||
* </p>
|
||||
*
|
||||
*
|
||||
* @since 2.2
|
||||
*/
|
||||
public IFluentPath newFluentPath() {
|
||||
|
@ -492,7 +611,7 @@ public class FhirContext {
|
|||
|
||||
/**
|
||||
* 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.
|
||||
|
@ -513,19 +632,16 @@ public class FhirContext {
|
|||
* 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
|
||||
*
|
||||
* @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
|
||||
* @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);
|
||||
|
@ -535,14 +651,13 @@ public class FhirContext {
|
|||
* 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
|
||||
*
|
||||
* @param theServerBase The URL of the base for the restful FHIR server to connect to
|
||||
*/
|
||||
public IGenericClient newRestfulGenericClient(String theServerBase) {
|
||||
return getRestfulClientFactory().newGenericClient(theServerBase);
|
||||
|
@ -569,7 +684,7 @@ public class FhirContext {
|
|||
|
||||
/**
|
||||
* 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.
|
||||
|
@ -592,9 +707,8 @@ public class FhirContext {
|
|||
* <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>)
|
||||
*
|
||||
* @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");
|
||||
|
@ -612,9 +726,8 @@ public class FhirContext {
|
|||
* <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)
|
||||
*
|
||||
* @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");
|
||||
|
@ -698,31 +811,6 @@ public class FhirContext {
|
|||
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.
|
||||
|
@ -732,12 +820,10 @@ public class FhirContext {
|
|||
* 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
|
||||
*
|
||||
* @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");
|
||||
|
@ -748,56 +834,19 @@ public class FhirContext {
|
|||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* 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
|
||||
*
|
||||
* @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) {
|
||||
|
@ -808,26 +857,7 @@ public class FhirContext {
|
|||
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" })
|
||||
@SuppressWarnings({"cast"})
|
||||
private List<Class<? extends IElement>> toElementList(Collection<Class<? extends IBaseResource>> theResourceTypes) {
|
||||
if (theResourceTypes == null) {
|
||||
return null;
|
||||
|
@ -858,13 +888,6 @@ public class FhirContext {
|
|||
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)
|
||||
|
@ -873,9 +896,16 @@ public class FhirContext {
|
|||
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() {
|
||||
|
@ -884,14 +914,13 @@ public class FhirContext {
|
|||
|
||||
/**
|
||||
* 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);
|
||||
|
@ -909,34 +938,4 @@ public class FhirContext {
|
|||
}
|
||||
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);
|
||||
}
|
||||
}
|
||||
|
|
|
@ -31,6 +31,13 @@
|
|||
<appender-ref ref="STDOUT" />
|
||||
</logger>
|
||||
|
||||
<!--
|
||||
It's useful to have this log when uploading big terminologies
|
||||
-->
|
||||
<logger name="ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl" additivity="false" level="info">
|
||||
<appender-ref ref="STDOUT" />
|
||||
</logger>
|
||||
|
||||
|
||||
<root level="warn">
|
||||
<appender-ref ref="STDOUT" />
|
||||
|
|
|
@ -2060,10 +2060,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
|
|||
*/
|
||||
if (theCreateNewHistoryEntry) {
|
||||
final ResourceHistoryTable historyEntry = theEntity.toHistory();
|
||||
// if (theEntity.getVersion() > 1) {
|
||||
// existing = myResourceHistoryTableDao.findForIdAndVersion(theEntity.getId(), theEntity.getVersion());
|
||||
// ourLog.warn("Reusing existing history entry entity {}", theEntity.getIdDt().getValue());
|
||||
// }
|
||||
historyEntry.setEncoding(changed.getEncoding());
|
||||
historyEntry.setResource(changed.getResource());
|
||||
|
||||
|
|
|
@ -21,9 +21,9 @@ import java.util.List;
|
|||
* 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.
|
||||
|
@ -43,6 +43,9 @@ public interface ITermConceptDao extends JpaRepository<TermConcept, Long> {
|
|||
@Query("SELECT t FROM TermConcept t WHERE t.myCodeSystem.myId = :cs_pid")
|
||||
Slice<TermConcept> findByCodeSystemVersion(Pageable thePage, @Param("cs_pid") Long thePid);
|
||||
|
||||
@Query("SELECT COUNT(t) FROM TermConcept t WHERE t.myCodeSystem.myId = :cs_pid")
|
||||
Integer countByCodeSystemVersion(@Param("cs_pid") Long thePid);
|
||||
|
||||
@Query("SELECT t FROM TermConcept t WHERE t.myIndexStatus = null")
|
||||
Page<TermConcept> findResourcesRequiringReindexing(Pageable thePageRequest);
|
||||
|
||||
|
|
|
@ -32,4 +32,7 @@ public interface ITermConceptDesignationDao extends JpaRepository<TermConceptDes
|
|||
@Query("SELECT t FROM TermConceptDesignation t WHERE t.myCodeSystemVersion.myId = :csv_pid")
|
||||
Slice<TermConceptDesignation> findByCodeSystemVersion(Pageable thePage, @Param("csv_pid") Long thePid);
|
||||
|
||||
@Query("SELECT COUNT(t) FROM TermConceptDesignation t WHERE t.myCodeSystemVersion.myId = :csv_pid")
|
||||
Integer countByCodeSystemVersion(@Param("csv_pid") Long thePid);
|
||||
|
||||
}
|
||||
|
|
|
@ -18,9 +18,9 @@ import java.util.Collection;
|
|||
* 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.
|
||||
|
@ -31,6 +31,9 @@ import java.util.Collection;
|
|||
|
||||
public interface ITermConceptParentChildLinkDao extends JpaRepository<TermConceptParentChildLink, Long> {
|
||||
|
||||
@Query("SELECT COUNT(t) FROM TermConceptParentChildLink t WHERE t.myCodeSystem.myId = :cs_pid")
|
||||
Integer countByCodeSystemVersion(@Param("cs_pid") Long thePid);
|
||||
|
||||
@Query("SELECT t.myParentPid FROM TermConceptParentChildLink t WHERE t.myChildPid = :child_pid")
|
||||
Collection<Long> findAllWithChild(@Param("child_pid") Long theConceptPid);
|
||||
|
||||
|
|
|
@ -32,4 +32,6 @@ public interface ITermConceptPropertyDao extends JpaRepository<TermConceptProper
|
|||
@Query("SELECT t FROM TermConceptProperty t WHERE t.myCodeSystemVersion.myId = :cs_pid")
|
||||
Slice<TermConceptProperty> findByCodeSystemVersion(Pageable thePage, @Param("cs_pid") Long thePid);
|
||||
|
||||
@Query("SELECT COUNT(t) FROM TermConceptProperty t WHERE t.myCodeSystemVersion.myId = :cs_pid")
|
||||
Integer countByCodeSystemVersion(@Param("cs_pid") Long thePid);
|
||||
}
|
||||
|
|
|
@ -25,6 +25,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
|||
|
||||
import java.util.Collections;
|
||||
import java.util.List;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.codec.binary.StringUtils;
|
||||
import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
|
||||
|
@ -35,6 +36,8 @@ import org.hl7.fhir.dstu3.model.ValueSet.*;
|
|||
import org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.instance.model.api.IPrimitiveType;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.beans.factory.annotation.Qualifier;
|
||||
|
||||
|
@ -223,6 +226,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
|
|||
if (vs != null) {
|
||||
ValueSet expansion = doExpand(vs);
|
||||
List<ValueSetExpansionContainsComponent> contains = expansion.getExpansion().getContains();
|
||||
|
||||
ValidateCodeResult result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
|
||||
if (result != null) {
|
||||
if (theDisplay != null && isNotBlank(theDisplay.getValue()) && isNotBlank(result.getDisplay())) {
|
||||
|
@ -238,6 +242,9 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
|
|||
|
||||
}
|
||||
|
||||
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoValueSetDstu3.class);
|
||||
|
||||
private String toStringOrNull(IPrimitiveType<String> thePrimitive) {
|
||||
return thePrimitive != null ? thePrimitive.getValue() : null;
|
||||
}
|
||||
|
|
|
@ -66,6 +66,7 @@ import org.springframework.context.ApplicationContextAware;
|
|||
import org.springframework.data.domain.Page;
|
||||
import org.springframework.data.domain.PageRequest;
|
||||
import org.springframework.data.domain.Slice;
|
||||
import org.springframework.data.jpa.repository.JpaRepository;
|
||||
import org.springframework.scheduling.annotation.Scheduled;
|
||||
import org.springframework.transaction.PlatformTransactionManager;
|
||||
import org.springframework.transaction.TransactionStatus;
|
||||
|
@ -82,6 +83,7 @@ import javax.persistence.TypedQuery;
|
|||
import javax.persistence.criteria.*;
|
||||
import java.util.*;
|
||||
import java.util.concurrent.TimeUnit;
|
||||
import java.util.function.Supplier;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.isBlank;
|
||||
|
@ -273,74 +275,43 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
myEntityManager.flush();
|
||||
}
|
||||
|
||||
public void deleteCodeSystemVersion(Long theCodeSystemVersionPid) {
|
||||
public void deleteCodeSystemVersion(final Long theCodeSystemVersionPid) {
|
||||
ourLog.info(" * Deleting code system version {}", theCodeSystemVersionPid);
|
||||
|
||||
PageRequest page = PageRequest.of(0, 1000);
|
||||
int count;
|
||||
PageRequest page1000 = PageRequest.of(0, 1000);
|
||||
|
||||
// Parent/Child links
|
||||
ourLog.info(" * Deleting parent/child links");
|
||||
count = 0;
|
||||
while (true) {
|
||||
Slice<TermConceptParentChildLink> link = myConceptParentChildLinkDao.findByCodeSystemVersion(page, theCodeSystemVersionPid);
|
||||
if (link.hasContent() == false) {
|
||||
break;
|
||||
}
|
||||
|
||||
myConceptParentChildLinkDao.deleteInBatch(link);
|
||||
|
||||
count += link.getNumberOfElements();
|
||||
ourLog.info(" * {} parent/child links deleted", count);
|
||||
{
|
||||
String descriptor = "parent/child links";
|
||||
Supplier<Slice<TermConceptParentChildLink>> loader = () -> myConceptParentChildLinkDao.findByCodeSystemVersion(page1000, theCodeSystemVersionPid);
|
||||
Supplier<Integer> counter = () -> myConceptParentChildLinkDao.countByCodeSystemVersion(theCodeSystemVersionPid);
|
||||
doDelete(descriptor, loader, counter, myConceptParentChildLinkDao);
|
||||
}
|
||||
myConceptParentChildLinkDao.flush();
|
||||
|
||||
// Properties
|
||||
ourLog.info(" * Deleting properties");
|
||||
count = 0;
|
||||
while (true) {
|
||||
Slice<TermConceptProperty> link = myConceptPropertyDao.findByCodeSystemVersion(page, theCodeSystemVersionPid);
|
||||
if (link.hasContent() == false) {
|
||||
break;
|
||||
}
|
||||
|
||||
myConceptPropertyDao.deleteInBatch(link);
|
||||
|
||||
count += link.getNumberOfElements();
|
||||
ourLog.info(" * {} concept properties deleted", count);
|
||||
{
|
||||
String descriptor = "concept properties";
|
||||
Supplier<Slice<TermConceptProperty>> loader = () -> myConceptPropertyDao.findByCodeSystemVersion(page1000, theCodeSystemVersionPid);
|
||||
Supplier<Integer> counter = () -> myConceptPropertyDao.countByCodeSystemVersion(theCodeSystemVersionPid);
|
||||
doDelete(descriptor, loader, counter, myConceptPropertyDao);
|
||||
}
|
||||
myConceptPropertyDao.flush();
|
||||
|
||||
// Properties
|
||||
ourLog.info(" * Deleting designations");
|
||||
count = 0;
|
||||
while (true) {
|
||||
Slice<TermConceptDesignation> link = myConceptDesignationDao.findByCodeSystemVersion(page, theCodeSystemVersionPid);
|
||||
if (link.hasContent() == false) {
|
||||
break;
|
||||
}
|
||||
|
||||
myConceptDesignationDao.deleteInBatch(link);
|
||||
|
||||
count += link.getNumberOfElements();
|
||||
ourLog.info(" * {} concept designations deleted", count);
|
||||
// Designations
|
||||
{
|
||||
String descriptor = "concept designations";
|
||||
Supplier<Slice<TermConceptDesignation>> loader = () -> myConceptDesignationDao.findByCodeSystemVersion(page1000, theCodeSystemVersionPid);
|
||||
Supplier<Integer> counter = () -> myConceptDesignationDao.countByCodeSystemVersion(theCodeSystemVersionPid);
|
||||
doDelete(descriptor, loader, counter, myConceptDesignationDao);
|
||||
}
|
||||
myConceptDesignationDao.flush();
|
||||
|
||||
// Concepts
|
||||
ourLog.info(" * Deleting concepts");
|
||||
count = 0;
|
||||
while (true) {
|
||||
Slice<TermConcept> link = myConceptDao.findByCodeSystemVersion(page, theCodeSystemVersionPid);
|
||||
if (link.hasContent() == false) {
|
||||
break;
|
||||
}
|
||||
|
||||
myConceptDao.deleteInBatch(link);
|
||||
myConceptDao.flush();
|
||||
|
||||
count += link.getNumberOfElements();
|
||||
ourLog.info(" * {} concepts deleted", count);
|
||||
{
|
||||
String descriptor = "concepts";
|
||||
// For some reason, concepts are much slower to delete, so use a smaller batch size
|
||||
PageRequest page100 = PageRequest.of(0, 100);
|
||||
Supplier<Slice<TermConcept>> loader = () -> myConceptDao.findByCodeSystemVersion(page100, theCodeSystemVersionPid);
|
||||
Supplier<Integer> counter = () -> myConceptDao.countByCodeSystemVersion(theCodeSystemVersionPid);
|
||||
doDelete(descriptor, loader, counter, myConceptDao);
|
||||
}
|
||||
|
||||
Optional<TermCodeSystem> codeSystemOpt = myCodeSystemDao.findWithCodeSystemVersionAsCurrentVersion(theCodeSystemVersionPid);
|
||||
|
@ -356,6 +327,26 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
|
||||
}
|
||||
|
||||
private <T> void doDelete(String theDescriptor, Supplier<Slice<T>> theLoader, Supplier<Integer> theCounter, JpaRepository<T, ?> theDao) {
|
||||
int count;
|
||||
ourLog.info(" * Deleting {}", theDescriptor);
|
||||
int totalCount = theCounter.get();
|
||||
StopWatch sw = new StopWatch();
|
||||
count = 0;
|
||||
while (true) {
|
||||
Slice<T> link = theLoader.get();
|
||||
if (link.hasContent() == false) {
|
||||
break;
|
||||
}
|
||||
|
||||
theDao.deleteInBatch(link);
|
||||
|
||||
count += link.getNumberOfElements();
|
||||
ourLog.info(" * {} {} deleted - {}/sec - ETA: {}", count, theDescriptor, sw.formatThroughput(count, TimeUnit.SECONDS), sw.getEstimatedTimeRemaining(count, totalCount));
|
||||
}
|
||||
theDao.flush();
|
||||
}
|
||||
|
||||
public void deleteConceptMap(ResourceTable theResourceTable) {
|
||||
// Get existing entity so it can be deleted.
|
||||
Optional<TermConceptMap> optionalExistingTermConceptMapById = myConceptMapDao.findTermConceptMapByResourcePid(theResourceTable.getId());
|
||||
|
|
|
@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.provider.dstu3;
|
|||
|
||||
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
|
||||
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
|
||||
import ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest;
|
||||
import ca.uhn.fhir.jpa.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
|
@ -10,8 +11,11 @@ import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
|
|||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import ca.uhn.fhir.util.UrlUtil;
|
||||
import com.google.common.base.Charsets;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.http.client.methods.CloseableHttpResponse;
|
||||
import org.apache.http.client.methods.HttpGet;
|
||||
import org.apache.http.client.methods.HttpPost;
|
||||
import org.apache.http.entity.ContentType;
|
||||
import org.apache.http.entity.StringEntity;
|
||||
|
@ -109,6 +113,16 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
|
||||
private void createLocalVsWithIncludeConcept() {
|
||||
myLocalVs = new ValueSet();
|
||||
myLocalVs.setUrl(URL_MY_VALUE_SET);
|
||||
ConceptSetComponent include = myLocalVs.getCompose().addInclude();
|
||||
include.setSystem(URL_MY_CODE_SYSTEM);
|
||||
include.addConcept().setCode("A");
|
||||
include.addConcept().setCode("AA");
|
||||
myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
|
||||
private void createLocalVsWithUnknownCode(CodeSystem codeSystem) {
|
||||
myLocalVs = new ValueSet();
|
||||
myLocalVs.setUrl(URL_MY_VALUE_SET);
|
||||
|
@ -172,7 +186,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
* $expand?identifier=foo is legacy.. It's actually not valid in FHIR as of STU3
|
||||
* but we supported it for longer than we should have so I don't want to delete
|
||||
* it right now.
|
||||
*
|
||||
* <p>
|
||||
* https://groups.google.com/d/msgid/hapi-fhir/CAN2Cfy8kW%2BAOkgC6VjPsU3gRCpExCNZBmJdi-k5R_TWeyWH4tA%40mail.gmail.com?utm_medium=email&utm_source=footer
|
||||
*/
|
||||
@Test
|
||||
|
@ -462,6 +476,29 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemInstanceOnInstance() throws IOException {
|
||||
createLocalCsAndVs();
|
||||
createLocalVsWithIncludeConcept();
|
||||
|
||||
String url = ourServerBase +
|
||||
"/ValueSet/" + myLocalValueSetId.getIdPart() + "/$validate-code?system=" +
|
||||
UrlUtil.escapeUrlParam(FhirResourceDaoR4TerminologyTest.URL_MY_CODE_SYSTEM) +
|
||||
"&code=AA";
|
||||
|
||||
ourLog.info("* Requesting: {}", url);
|
||||
|
||||
HttpGet request = new HttpGet(url);
|
||||
request.addHeader("Accept", "application/fhir+json");
|
||||
try (CloseableHttpResponse response = ourHttpClient.execute(request)) {
|
||||
String respString = IOUtils.toString(response.getEntity().getContent(), Charsets.UTF_8);
|
||||
ourLog.info(respString);
|
||||
|
||||
Parameters respParam = myFhirCtx.newJsonParser().parseResource(Parameters.class, respString);
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemType() {
|
||||
//@formatter:off
|
||||
|
|
|
@ -10,8 +10,11 @@ import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
|
|||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import ca.uhn.fhir.util.UrlUtil;
|
||||
import com.google.common.base.Charsets;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.http.client.methods.CloseableHttpResponse;
|
||||
import org.apache.http.client.methods.HttpGet;
|
||||
import org.apache.http.client.methods.HttpPost;
|
||||
import org.apache.http.entity.ContentType;
|
||||
import org.apache.http.entity.StringEntity;
|
||||
|
@ -72,7 +75,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
}
|
||||
|
||||
private void createLocalCsAndVs() {
|
||||
//@formatter:off
|
||||
CodeSystem codeSystem = new CodeSystem();
|
||||
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
|
||||
codeSystem.setContent(CodeSystemContentMode.COMPLETE);
|
||||
|
@ -86,10 +88,17 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
.addConcept().setCode("B").setDisplay("Code B")
|
||||
.addConcept(new ConceptDefinitionComponent().setCode("BA").setDisplay("Code BA"))
|
||||
.addConcept(new ConceptDefinitionComponent().setCode("BB").setDisplay("Code BB"));
|
||||
//@formatter:on
|
||||
myCodeSystemDao.create(codeSystem, mySrd);
|
||||
}
|
||||
|
||||
createLocalVs(codeSystem);
|
||||
private void createLocalVsWithIncludeConcept() {
|
||||
myLocalVs = new ValueSet();
|
||||
myLocalVs.setUrl(URL_MY_VALUE_SET);
|
||||
ConceptSetComponent include = myLocalVs.getCompose().addInclude();
|
||||
include.setSystem(URL_MY_CODE_SYSTEM);
|
||||
include.addConcept().setCode("A");
|
||||
include.addConcept().setCode("AA");
|
||||
myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
|
||||
private void createLocalVs(CodeSystem codeSystem) {
|
||||
|
@ -97,7 +106,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
myLocalVs.setUrl(URL_MY_VALUE_SET);
|
||||
ConceptSetComponent include = myLocalVs.getCompose().addInclude();
|
||||
include.setSystem(codeSystem.getUrl());
|
||||
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("childAA");
|
||||
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
|
||||
myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
|
||||
}
|
||||
|
||||
|
@ -119,7 +128,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testExpandById() throws IOException {
|
||||
public void testExpandById() {
|
||||
//@formatter:off
|
||||
Parameters respParam = myClient
|
||||
.operation()
|
||||
|
@ -149,7 +158,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testExpandByIdWithFilter() throws IOException {
|
||||
public void testExpandByIdWithFilter() {
|
||||
|
||||
//@formatter:off
|
||||
Parameters respParam = myClient
|
||||
|
@ -208,7 +217,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
|
||||
|
||||
@Test
|
||||
public void testExpandInlineVsAgainstBuiltInCs() throws IOException {
|
||||
public void testExpandInlineVsAgainstBuiltInCs() {
|
||||
createLocalVsPointingAtBuiltInCodeSystem();
|
||||
assertNotNull(myLocalValueSetId);
|
||||
|
||||
|
@ -229,7 +238,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testExpandInlineVsAgainstExternalCs() throws IOException {
|
||||
public void testExpandInlineVsAgainstExternalCs() {
|
||||
createExternalCsAndLocalVs();
|
||||
assertNotNull(myLocalVs);
|
||||
myLocalVs.setId("");
|
||||
|
@ -304,7 +313,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testExpandLocalVsAgainstBuiltInCs() throws IOException {
|
||||
public void testExpandLocalVsAgainstBuiltInCs() {
|
||||
createLocalVsPointingAtBuiltInCodeSystem();
|
||||
assertNotNull(myLocalValueSetId);
|
||||
|
||||
|
@ -325,7 +334,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testExpandLocalVsAgainstExternalCs() throws IOException {
|
||||
public void testExpandLocalVsAgainstExternalCs() {
|
||||
createExternalCsAndLocalVs();
|
||||
assertNotNull(myLocalValueSetId);
|
||||
|
||||
|
@ -349,7 +358,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testExpandLocalVsCanonicalAgainstExternalCs() throws IOException {
|
||||
public void testExpandLocalVsCanonicalAgainstExternalCs() {
|
||||
createExternalCsAndLocalVs();
|
||||
assertNotNull(myLocalValueSetId);
|
||||
|
||||
|
@ -373,7 +382,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testExpandLocalVsWithUnknownCode() throws IOException {
|
||||
public void testExpandLocalVsWithUnknownCode() {
|
||||
createExternalCsAndLocalVsWithUnknownCode();
|
||||
assertNotNull(myLocalValueSetId);
|
||||
|
||||
|
@ -400,8 +409,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
HttpPost post = new HttpPost(ourServerBase + "/ValueSet/%24expand");
|
||||
post.setEntity(new StringEntity(string, ContentType.parse(ca.uhn.fhir.rest.api.Constants.CT_FHIR_JSON_NEW)));
|
||||
|
||||
CloseableHttpResponse resp = ourHttpClient.execute(post);
|
||||
try {
|
||||
try (CloseableHttpResponse resp = ourHttpClient.execute(post)) {
|
||||
|
||||
String respString = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
|
||||
ourLog.info(respString);
|
||||
|
@ -411,14 +419,11 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
assertEquals(400, resp.getStatusLine().getStatusCode());
|
||||
assertThat(respString, containsString("Unknown FilterOperator code 'n'"));
|
||||
|
||||
} finally {
|
||||
IOUtils.closeQuietly(resp);
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemInstance() {
|
||||
//@formatter:off
|
||||
Parameters respParam = myClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId)
|
||||
|
@ -426,7 +431,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
.withParameter(Parameters.class, "code", new CodeType("8495-4"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.execute();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
@ -434,9 +438,51 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
assertEquals(true, ((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemInstanceOnType() throws IOException {
|
||||
createLocalCsAndVs();
|
||||
|
||||
String url = ourServerBase +
|
||||
"/ValueSet/$validate-code?system=" +
|
||||
UrlUtil.escapeUrlParam(URL_MY_CODE_SYSTEM) +
|
||||
"&code=AA";
|
||||
|
||||
HttpGet request = new HttpGet(url);
|
||||
request.addHeader("Accept", "application/fhir+json");
|
||||
try (CloseableHttpResponse response = ourHttpClient.execute(request)) {
|
||||
String respString = IOUtils.toString(response.getEntity().getContent(), Charsets.UTF_8);
|
||||
ourLog.info(respString);
|
||||
|
||||
Parameters respParam = myFhirCtx.newJsonParser().parseResource(Parameters.class, respString);
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemInstanceOnInstance() throws IOException {
|
||||
createLocalCsAndVs();
|
||||
createLocalVsWithIncludeConcept();
|
||||
|
||||
String url = ourServerBase +
|
||||
"/ValueSet/" + myLocalValueSetId.getIdPart() + "/$validate-code?system=" +
|
||||
UrlUtil.escapeUrlParam(URL_MY_CODE_SYSTEM) +
|
||||
"&code=AA";
|
||||
|
||||
ourLog.info("* Requesting: {}", url);
|
||||
|
||||
HttpGet request = new HttpGet(url);
|
||||
request.addHeader("Accept", "application/fhir+json");
|
||||
try (CloseableHttpResponse response = ourHttpClient.execute(request)) {
|
||||
String respString = IOUtils.toString(response.getEntity().getContent(), Charsets.UTF_8);
|
||||
ourLog.info(respString);
|
||||
|
||||
Parameters respParam = myFhirCtx.newJsonParser().parseResource(Parameters.class, respString);
|
||||
assertTrue(((BooleanType) respParam.getParameter().get(0).getValue()).booleanValue());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemType() {
|
||||
//@formatter:off
|
||||
Parameters respParam = myClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
|
@ -444,7 +490,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
.withParameter(Parameters.class, "code", new CodeType("8450-9"))
|
||||
.andParameter("system", new UriType("http://acme.org"))
|
||||
.execute();
|
||||
//@formatter:on
|
||||
|
||||
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
|
||||
ourLog.info(resp);
|
||||
|
|
|
@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.term;
|
|||
|
||||
import ca.uhn.fhir.jpa.dao.DaoConfig;
|
||||
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
|
||||
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
|
||||
import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import com.google.common.collect.Lists;
|
||||
|
@ -52,17 +53,6 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
|
|||
.findFirst();
|
||||
}
|
||||
|
||||
private <T extends Type> Optional<T> getPropertyPart(Parameters theParameters, String thePropName, String thePart) {
|
||||
return theParameters
|
||||
.getParameter()
|
||||
.stream()
|
||||
.filter(t -> t.getName().equals(thePropName))
|
||||
.flatMap(t -> t.getPart().stream())
|
||||
.filter(t -> t.getName().equals(thePart))
|
||||
.map(t -> (T) t.getValue())
|
||||
.findFirst();
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandWithPropertyCoding() throws Exception {
|
||||
ZipCollectionBuilder files = new ZipCollectionBuilder();
|
||||
|
@ -169,7 +159,6 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
|
|||
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testLookupWithProperties2() throws Exception {
|
||||
ZipCollectionBuilder files = new ZipCollectionBuilder();
|
||||
|
@ -189,7 +178,6 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
|
|||
assertEquals("Large unstained cells/100 leukocytes", propertyValue.get().getDisplay());
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testLookupWithPropertiesExplicit() throws Exception {
|
||||
ZipCollectionBuilder files = new ZipCollectionBuilder();
|
||||
|
@ -214,6 +202,30 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeFound() throws Exception {
|
||||
ZipCollectionBuilder files = new ZipCollectionBuilder();
|
||||
TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesToZip(files);
|
||||
myLoader.loadLoinc(files.getFiles(), mySrd);
|
||||
|
||||
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(null, null, new StringType("10013-1"), new StringType(IHapiTerminologyLoaderSvc.LOINC_URI), null, null, null, mySrd);
|
||||
|
||||
assertTrue(result.isResult());
|
||||
assertEquals("Found code", result.getMessage());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeNotFound() throws Exception {
|
||||
ZipCollectionBuilder files = new ZipCollectionBuilder();
|
||||
TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesToZip(files);
|
||||
myLoader.loadLoinc(files.getFiles(), mySrd);
|
||||
|
||||
IFhirResourceDaoValueSet.ValidateCodeResult result = myValueSetDao.validateCode(null, null, new StringType("10013-1-9999999999"), new StringType(IHapiTerminologyLoaderSvc.LOINC_URI), null, null, null, mySrd);
|
||||
|
||||
assertFalse(result.isResult());
|
||||
assertEquals("Code not found", result.getMessage());
|
||||
}
|
||||
|
||||
private Set<String> toExpandedCodes(ValueSet theExpanded) {
|
||||
return theExpanded
|
||||
.getExpansion()
|
||||
|
|
|
@ -26,11 +26,20 @@ import ca.uhn.fhir.jpa.dao.*;
|
|||
@Configuration
|
||||
public abstract class BaseJavaConfig${versionCapitalized} extends ca.uhn.fhir.jpa.config${package_suffix}.Base${versionCapitalized}Config {
|
||||
|
||||
/**
|
||||
* Subclasses may override
|
||||
*/
|
||||
protected boolean isSupported(String theResourceType) {
|
||||
return true;
|
||||
}
|
||||
|
||||
@Bean(name="myResourceProviders${versionCapitalized}")
|
||||
public List<IResourceProvider> resourceProviders${versionCapitalized}() {
|
||||
List<IResourceProvider> retVal = new ArrayList<IResourceProvider>();
|
||||
#foreach ( $res in $resources )
|
||||
retVal.add(rp${res.declaringClassNameComplete}${versionCapitalized}());
|
||||
if (isSupported("${res.name}")) {
|
||||
retVal.add(rp${res.declaringClassNameComplete}${versionCapitalized}());
|
||||
}
|
||||
#end
|
||||
return retVal;
|
||||
}
|
||||
|
@ -39,7 +48,9 @@ public abstract class BaseJavaConfig${versionCapitalized} extends ca.uhn.fhir.jp
|
|||
public List<IFhirResourceDao<?>> resourceDaos${versionCapitalized}() {
|
||||
List<IFhirResourceDao<?>> retVal = new ArrayList<IFhirResourceDao<?>>();
|
||||
#foreach ( $res in $resources )
|
||||
retVal.add(dao${res.declaringClassNameComplete}${versionCapitalized}());
|
||||
if (isSupported("${res.name}")) {
|
||||
retVal.add(dao${res.declaringClassNameComplete}${versionCapitalized}());
|
||||
}
|
||||
#end
|
||||
return retVal;
|
||||
}
|
||||
|
|
Loading…
Reference in New Issue