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hapi-fhir
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Syncing master into working branch.

This commit is contained in:
Diederik Muylwyk 2019-08-01 13:51:26 -04:00
parent 78842164fd 46c8c61932
commit d67de13708
43 changed files with 2481 additions and 248 deletions
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6
hapi-fhir-base/pom.xml
View File

@ -69,6 +69,12 @@
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>apache-jena-libs</artifactId>
<optional>true</optional>
<type>pom</type>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>

90
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java
View File

@ -20,6 +20,7 @@ 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.apache.jena.riot.Lang;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -111,7 +112,7 @@ public class FhirContext {
* of this method, e.g. {@link #forDstu2()} or {@link #forDstu3()} or {@link #forR4()}
*/
@Deprecated
public FhirContext(Class<? extends IBaseResource> theResourceType) {
public FhirContext(final Class<? extends IBaseResource> theResourceType) {
this(toCollection(theResourceType));
}
@ -120,7 +121,7 @@ public class FhirContext {
* of this method, e.g. {@link #forDstu2()} or {@link #forDstu3()} or {@link #forR4()}
*/
@Deprecated
public FhirContext(Class<?>... theResourceTypes) {
public FhirContext(final Class<?>... theResourceTypes) {
this(toCollection(theResourceTypes));
}
@ -129,7 +130,7 @@ public class FhirContext {
* of this method, e.g. {@link #forDstu2()} or {@link #forDstu3()} or {@link #forR4()}
*/
@Deprecated
public FhirContext(Collection<Class<? extends IBaseResource>> theResourceTypes) {
public FhirContext(final Collection<Class<? extends IBaseResource>> theResourceTypes) {
this(null, theResourceTypes);
}
@ -138,11 +139,11 @@ public class FhirContext {
* 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) {
public FhirContext(final FhirVersionEnum theVersion) {
this(theVersion, null);
}
private FhirContext(FhirVersionEnum theVersion, Collection<Class<? extends IBaseResource>> theResourceTypes) {
private FhirContext(final FhirVersionEnum theVersion, final Collection<Class<? extends IBaseResource>> theResourceTypes) {
VersionUtil.getVersion();
if (theVersion != null) {
@ -191,7 +192,7 @@ public class FhirContext {
}
private String createUnknownResourceNameError(String theResourceName, FhirVersionEnum theVersion) {
private String createUnknownResourceNameError(final String theResourceName, final FhirVersionEnum theVersion) {
return getLocalizer().getMessage(FhirContext.class, "unknownResourceName", theResourceName, theVersion);
}
@ -232,7 +233,7 @@ public class FhirContext {
*
* @param theAddProfileTagWhenEncoding The add profile mode (must not be <code>null</code>)
*/
public void setAddProfileTagWhenEncoding(AddProfileTagEnum theAddProfileTagWhenEncoding) {
public void setAddProfileTagWhenEncoding(final AddProfileTagEnum theAddProfileTagWhenEncoding) {
Validate.notNull(theAddProfileTagWhenEncoding, "theAddProfileTagWhenEncoding must not be null");
myAddProfileTagWhenEncoding = theAddProfileTagWhenEncoding;
}
@ -247,7 +248,7 @@ public class FhirContext {
*
* @see #setDefaultTypeForProfile(String, Class)
*/
public Class<? extends IBaseResource> getDefaultTypeForProfile(String theProfile) {
public Class<? extends IBaseResource> getDefaultTypeForProfile(final String theProfile) {
validateInitialized();
return myDefaultTypeForProfile.get(theProfile);
}
@ -257,7 +258,7 @@ public class FhirContext {
* for extending the core library.
*/
@SuppressWarnings("unchecked")
public BaseRuntimeElementDefinition<?> getElementDefinition(Class<? extends IBase> theElementType) {
public BaseRuntimeElementDefinition<?> getElementDefinition(final Class<? extends IBase> theElementType) {
validateInitialized();
BaseRuntimeElementDefinition<?> retVal = myClassToElementDefinition.get(theElementType);
if (retVal == null) {
@ -273,7 +274,7 @@ public class FhirContext {
* Note that this method is case insensitive!
* </p>
*/
public BaseRuntimeElementDefinition<?> getElementDefinition(String theElementName) {
public BaseRuntimeElementDefinition<?> getElementDefinition(final String theElementName) {
validateInitialized();
return myNameToElementDefinition.get(theElementName.toLowerCase());
}
@ -301,7 +302,7 @@ 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) {
public void setLocalizer(final HapiLocalizer theMessages) {
myLocalizer = theMessages;
}
@ -309,7 +310,7 @@ public class FhirContext {
return myNarrativeGenerator;
}
public void setNarrativeGenerator(INarrativeGenerator theNarrativeGenerator) {
public void setNarrativeGenerator(final INarrativeGenerator theNarrativeGenerator) {
myNarrativeGenerator = theNarrativeGenerator;
}
@ -329,7 +330,7 @@ public class FhirContext {
*
* @param theParserOptions The parser options object - Must not be <code>null</code>
*/
public void setParserOptions(ParserOptions theParserOptions) {
public void setParserOptions(final ParserOptions theParserOptions) {
Validate.notNull(theParserOptions, "theParserOptions must not be null");
myParserOptions = theParserOptions;
}
@ -360,7 +361,7 @@ public class FhirContext {
*
* @see PerformanceOptionsEnum for a list of available options
*/
public void setPerformanceOptions(Collection<PerformanceOptionsEnum> theOptions) {
public void setPerformanceOptions(final Collection<PerformanceOptionsEnum> theOptions) {
myPerformanceOptions.clear();
if (theOptions != null) {
myPerformanceOptions.addAll(theOptions);
@ -371,7 +372,7 @@ public class FhirContext {
* 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) {
public RuntimeResourceDefinition getResourceDefinition(final Class<? extends IBaseResource> theResourceType) {
validateInitialized();
if (theResourceType == null) {
throw new NullPointerException("theResourceType can not be null");
@ -387,7 +388,7 @@ public class FhirContext {
return retVal;
}
public RuntimeResourceDefinition getResourceDefinition(FhirVersionEnum theVersion, String theResourceName) {
public RuntimeResourceDefinition getResourceDefinition(final FhirVersionEnum theVersion, final String theResourceName) {
Validate.notNull(theVersion, "theVersion can not be null");
validateInitialized();
@ -419,7 +420,7 @@ public class FhirContext {
* 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) {
public RuntimeResourceDefinition getResourceDefinition(final IBaseResource theResource) {
validateInitialized();
Validate.notNull(theResource, "theResource must not be null");
return getResourceDefinition(theResource.getClass());
@ -434,7 +435,7 @@ public class FhirContext {
*
* @throws DataFormatException If the resource name is not known
*/
public RuntimeResourceDefinition getResourceDefinition(String theResourceName) throws DataFormatException {
public RuntimeResourceDefinition getResourceDefinition(final String theResourceName) throws DataFormatException {
validateInitialized();
Validate.notBlank(theResourceName, "theResourceName must not be blank");
@ -462,7 +463,7 @@ public class FhirContext {
* 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) {
public RuntimeResourceDefinition getResourceDefinitionById(final String theId) {
validateInitialized();
return myIdToResourceDefinition.get(theId);
}
@ -528,7 +529,7 @@ public class FhirContext {
*
* @param theRestfulClientFactory
*/
public void setRestfulClientFactory(IRestfulClientFactory theRestfulClientFactory) {
public void setRestfulClientFactory(final IRestfulClientFactory theRestfulClientFactory) {
Validate.notNull(theRestfulClientFactory, "theRestfulClientFactory must not be null");
this.myRestfulClientFactory = theRestfulClientFactory;
}
@ -619,6 +620,23 @@ public class FhirContext {
return new JsonParser(this, myParserErrorHandler);
}
/**
* Create and return a new RDF 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 newRDFParser() {
return new RDFParser(this, myParserErrorHandler, Lang.TURTLE);
}
/**
* Instantiates a new client instance. This method requires an interface which is defined specifically for your use
* cases to contain methods for each of the RESTful operations you wish to implement (e.g. "read ImagingStudy",
@ -637,7 +655,7 @@ public class FhirContext {
* @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) {
public <T extends IRestfulClient> T newRestfulClient(final Class<T> theClientType, final String theServerBase) {
return getRestfulClientFactory().newClient(theClientType, theServerBase);
}
@ -653,7 +671,7 @@ public class FhirContext {
*
* @param theServerBase The URL of the base for the restful FHIR server to connect to
*/
public IGenericClient newRestfulGenericClient(String theServerBase) {
public IGenericClient newRestfulGenericClient(final String theServerBase) {
return getRestfulClientFactory().newGenericClient(theServerBase);
}
@ -704,7 +722,7 @@ public class FhirContext {
*
* @param theType The custom type to add (must not be <code>null</code>)
*/
public void registerCustomType(Class<? extends IBase> theType) {
public void registerCustomType(final Class<? extends IBase> theType) {
Validate.notNull(theType, "theType must not be null");
ensureCustomTypeList();
@ -723,7 +741,7 @@ public class FhirContext {
*
* @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) {
public void registerCustomTypes(final Collection<Class<? extends IBase>> theTypes) {
Validate.notNull(theTypes, "theTypes must not be null");
Validate.noNullElements(theTypes.toArray(), "theTypes must not contain any null elements");
@ -732,22 +750,22 @@ public class FhirContext {
myCustomTypes.addAll(theTypes);
}
private BaseRuntimeElementDefinition<?> scanDatatype(Class<? extends IElement> theResourceType) {
ArrayList<Class<? extends IElement>> resourceTypes = new ArrayList<>();
private BaseRuntimeElementDefinition<?> scanDatatype(final 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<>();
private RuntimeResourceDefinition scanResourceType(final 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<>();
private synchronized Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> scanResourceTypes(final Collection<Class<? extends IElement>> theResourceTypes) {
List<Class<? extends IBase>> typesToScan = new ArrayList<Class<? extends IBase>>();
if (theResourceTypes != null) {
typesToScan.addAll(theResourceTypes);
}
@ -819,7 +837,7 @@ public class FhirContext {
* <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) {
public void setDefaultTypeForProfile(final String theProfile, final Class<? extends IBaseResource> theClass) {
Validate.notBlank(theProfile, "theProfile must not be null or empty");
if (theClass == null) {
myDefaultTypeForProfile.remove(theProfile);
@ -833,7 +851,7 @@ public class FhirContext {
*
* @param theParserErrorHandler The error handler
*/
public void setParserErrorHandler(IParserErrorHandler theParserErrorHandler) {
public void setParserErrorHandler(final IParserErrorHandler theParserErrorHandler) {
Validate.notNull(theParserErrorHandler, "theParserErrorHandler must not be null");
myParserErrorHandler = theParserErrorHandler;
}
@ -843,7 +861,7 @@ public class FhirContext {
*
* @see PerformanceOptionsEnum for a list of available options
*/
public void setPerformanceOptions(PerformanceOptionsEnum... thePerformanceOptions) {
public void setPerformanceOptions(final PerformanceOptionsEnum... thePerformanceOptions) {
Collection<PerformanceOptionsEnum> asList = null;
if (thePerformanceOptions != null) {
asList = Arrays.asList(thePerformanceOptions);
@ -852,7 +870,7 @@ public class FhirContext {
}
@SuppressWarnings({"cast"})
private List<Class<? extends IElement>> toElementList(Collection<Class<? extends IBaseResource>> theResourceTypes) {
private List<Class<? extends IElement>> toElementList(final Collection<Class<? extends IBaseResource>> theResourceTypes) {
if (theResourceTypes == null) {
return null;
}
@ -922,8 +940,8 @@ public class FhirContext {
}
@SuppressWarnings("unchecked")
private static List<Class<? extends IBaseResource>> toCollection(Class<?>[] theResourceTypes) {
ArrayList<Class<? extends IBaseResource>> retVal = new ArrayList<>(1);
private static List<Class<? extends IBaseResource>> toCollection(final 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());

542
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/RDFParser.java Normal file
View File

@ -0,0 +1,542 @@
package ca.uhn.fhir.parser;
/*-
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2019 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 ca.uhn.fhir.context.*;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
import ca.uhn.fhir.narrative.INarrativeGenerator;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.util.ElementUtil;
import ca.uhn.fhir.util.rdf.RDFUtil;
import org.apache.commons.lang3.StringUtils;
import org.apache.jena.riot.Lang;
import org.apache.jena.riot.system.StreamRDF;
import org.hl7.fhir.instance.model.api.*;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/**
* This class is the FHIR RDF parser/encoder. Users should not interact with this class directly, but should use
* {@link FhirContext#newRDFParser()} to get an instance.
*/
public class RDFParser extends BaseParser {
private static final String FHIR_NS = "http://hl7.org/fhir";
private static final org.slf4j.Logger logger = org.slf4j.LoggerFactory.getLogger(RDFParser.class);
private FhirContext context;
private Lang lang;
/**
* Do not use this constructor, the recommended way to obtain a new instance of the RDF parser is to invoke
* {@link FhirContext#newRDFParser()}.
*
* @param parserErrorHandler the Parser Error Handler
*/
public RDFParser(final FhirContext context, final IParserErrorHandler parserErrorHandler, final Lang lang) {
super(context, parserErrorHandler);
this.context = context;
this.lang = lang;
}
@Override
protected void doEncodeResourceToWriter(final IBaseResource resource,
final Writer writer,
final EncodeContext encodeContext) {
StreamRDF eventWriter = RDFUtil.createRDFWriter(writer, this.lang);
eventWriter.base(FHIR_NS);
encodeResourceToRDFStreamWriter(resource, eventWriter, encodeContext);
}
@Override
protected <T extends IBaseResource> T doParseResource(final Class<T> resourceType,
final Reader reader) throws DataFormatException {
StreamRDF streamReader = RDFUtil.createRDFReader(reader, this.lang);
streamReader.base(FHIR_NS);
return parseResource(resourceType, streamReader);
}
@Override
public EncodingEnum getEncoding() {
return EncodingEnum.RDF;
}
@Override
public IParser setPrettyPrint(final boolean prettyPrint) {
return this;
}
private void encodeResourceToRDFStreamWriter(final IBaseResource resource,
final StreamRDF streamWriter,
final boolean containedResource,
final IIdType resourceId,
final EncodeContext encodeContext) {
RuntimeResourceDefinition resDef = this.context.getResourceDefinition(resource);
if (resDef == null) {
throw new ConfigurationException("Unknown resource type: " + resource.getClass());
}
if (!containedResource) {
super.containResourcesForEncoding(resource);
}
if (resource instanceof IAnyResource) {
// HL7.org Structures
if (resourceId != null) {
writeCommentsPre(streamWriter, resourceId);
streamWriter.start();
streamWriter.triple(RDFUtil.triple("<value> " + resourceId.getIdPart() + " </value>"));
streamWriter.finish();
writeCommentsPost(streamWriter, resourceId);
}
encodeCompositeElementToStreamWriter(resource, resource, streamWriter, containedResource, new CompositeChildElement(resDef, encodeContext), encodeContext);
} else {
// DSTU2+
if (resourceId != null) {
streamWriter.start();
streamWriter.triple(RDFUtil.triple("<value> " + resourceId.getIdPart() + " </value>"));
encodeExtensionsIfPresent(resource, streamWriter, resourceId, false, encodeContext);
streamWriter.finish();
writeCommentsPost(streamWriter, resourceId);
}
/*
InstantDt updated = (InstantDt) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED);
IdDt idDt = resource.getId();
String versionIdPart = idDt.getVersionIdPart();
if (isBlank(versionIdPart)) {
versionIdPart = ResourceMetadataKeyEnum.VERSION.get(resource);
}
List<BaseCodingDt> securityLabels = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.SECURITY_LABELS);
List<? extends IIdType> profiles = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
profiles = super.getProfileTagsForEncoding(resource, profiles);
TagList tags = getMetaTagsForEncoding((resource), encodeContext);
if (!ElementUtil.isEmpty(versionIdPart, updated, securityLabels, tags, profiles)) {
streamWriter.start();
for (IIdType profile : profiles) {
streamWriter.start();
streamWriter.triple(RDFUtil.triple("<value> " + profile.getValue() + " </value>"));
streamWriter.finish();
}
for (BaseCodingDt securityLabel : securityLabels) {
streamWriter.start();
encodeCompositeElementToStreamWriter(resource, securityLabel, streamWriter, containedResource, null, encodeContext);
streamWriter.finish();
}
if (tags != null) {
for (Tag tag : tags) {
if (tag.isEmpty()) {
continue;
}
streamWriter.start();
streamWriter.triple(RDFUtil.triple("<system> " + tag.getScheme() + " </system>"));
streamWriter.triple(RDFUtil.triple("<code> " + tag.getTerm() + " </code>"));
streamWriter.triple(RDFUtil.triple("<display> " + tag.getLabel() + " </display>"));
streamWriter.finish();
}
}
streamWriter.finish();
}
*/
if (resource instanceof IBaseBinary) {
IBaseBinary bin = (IBaseBinary) resource;
streamWriter.triple(RDFUtil.triple("<contentType> " + bin.getContentType() + " </contentType>"));
streamWriter.triple(RDFUtil.triple("<content> " + bin.getContentAsBase64() + " </content>"));
} else {
encodeCompositeElementToStreamWriter(resource, resource, streamWriter, containedResource, new CompositeChildElement(resDef, encodeContext), encodeContext);
}
}
streamWriter.finish();
}
private void writeCommentsPre(final StreamRDF eventWriter, final IBase element) {
if (element != null && element.hasFormatComment()) {
for (String next : element.getFormatCommentsPre()) {
if (isNotBlank(next)) {
eventWriter.base(next);
}
}
}
}
private void writeCommentsPost(final StreamRDF eventWriter, final IBase element) {
if (element != null && element.hasFormatComment()) {
for (String next : element.getFormatCommentsPost()) {
if (isNotBlank(next)) {
eventWriter.base(next);
}
}
}
}
private void encodeChildElementToStreamWriter(final IBaseResource resource,
final StreamRDF eventWriter,
final BaseRuntimeChildDefinition childDefinition,
final IBase element,
final String childName,
final BaseRuntimeElementDefinition<?> childDef,
final String extensionUrl,
final boolean includedResource,
final CompositeChildElement parent,
final EncodeContext encodeContext) {
String childGenericName = childDefinition.getElementName();
encodeContext.pushPath(childGenericName, false);
try {
if (element == null || element.isEmpty()) {
if (!isChildContained(childDef, includedResource)) {
return;
}
}
writeCommentsPre(eventWriter, element);
switch (childDef.getChildType()) {
case ID_DATATYPE: {
IIdType value = (IIdType) element;
assert value != null;
String encodedValue = "id".equals(childName) ? value.getIdPart() : value.getValue();
if (StringUtils.isNotBlank(encodedValue) || !hasNoExtensions(value)) {
eventWriter.start();
if (StringUtils.isNotBlank(encodedValue)) {
eventWriter.triple(RDFUtil.triple("<value> " + encodedValue + " </value>"));
}
encodeExtensionsIfPresent(resource, eventWriter, element, includedResource, encodeContext);
eventWriter.finish();
}
break;
}
case PRIMITIVE_DATATYPE: {
IPrimitiveType<?> pd = (IPrimitiveType) element;
assert pd != null;
String value = pd.getValueAsString();
if (value != null || !hasNoExtensions(pd)) {
eventWriter.start();
String elementId = getCompositeElementId(element);
if (isNotBlank(elementId)) {
eventWriter.triple(RDFUtil.triple("<id> " + elementId + " </id>"));
}
if (value != null) {
eventWriter.triple(RDFUtil.triple("<value> " + value + " </value>"));
}
encodeExtensionsIfPresent(resource, eventWriter, element, includedResource, encodeContext);
eventWriter.finish();
}
break;
}
case RESOURCE_BLOCK:
case COMPOSITE_DATATYPE: {
eventWriter.start();
String elementId = getCompositeElementId(element);
if (isNotBlank(elementId)) {
eventWriter.triple(RDFUtil.triple("<id> " + elementId + " </id>"));
}
if (isNotBlank(extensionUrl)) {
eventWriter.triple(RDFUtil.triple("<url> " + extensionUrl + " </url>"));
}
encodeCompositeElementToStreamWriter(resource, element, eventWriter, includedResource, parent, encodeContext);
eventWriter.finish();
break;
}
case CONTAINED_RESOURCE_LIST:
case CONTAINED_RESOURCES: {
/*
* Disable per #103 for (IResource next : value.getContainedResources()) { if (getContainedResources().getResourceId(next) != null) { continue; }
* theEventWriter.writeStartElement("contained"); encodeResourceToRDFStreamWriter(next, theEventWriter, true, fixContainedResourceId(next.getId().getValue()));
* theEventWriter.writeEndElement(); }
*/
for (IBaseResource next : getContainedResources().getContainedResources()) {
IIdType resourceId = getContainedResources().getResourceId(next);
eventWriter.start();
encodeResourceToRDFStreamWriter(next, eventWriter, true, fixContainedResourceId(resourceId.getValue()), encodeContext);
eventWriter.finish();
}
break;
}
case RESOURCE: {
IBaseResource baseResource = (IBaseResource) element;
String resourceName = this.context.getResourceDefinition(baseResource).getName();
if (!super.shouldEncodeResource(resourceName)) {
break;
}
eventWriter.start();
encodeContext.pushPath(resourceName, true);
encodeResourceToRDFStreamWriter(resource, eventWriter, encodeContext);
encodeContext.popPath();
eventWriter.finish();
break;
}
case EXTENSION_DECLARED:
case UNDECL_EXT: {
throw new IllegalStateException("state should not happen: " + childDef.getName());
}
}
writeCommentsPost(eventWriter, element);
} finally {
encodeContext.popPath();
}
}
private void encodeResourceToRDFStreamWriter(final IBaseResource resource,
final StreamRDF eventWriter,
final EncodeContext encodeContext) {
IIdType resourceId = null;
if (StringUtils.isNotBlank(resource.getIdElement().getIdPart())) {
resourceId = resource.getIdElement();
if (resource.getIdElement().getValue().startsWith("urn:")) {
resourceId = null;
}
}
if (!super.shouldEncodeResourceId(resource, encodeContext)) {
resourceId = null;
} else if (encodeContext.getResourcePath().size() == 1 && getEncodeForceResourceId() != null) {
resourceId = getEncodeForceResourceId();
}
encodeResourceToRDFStreamWriter(resource, eventWriter, false, resourceId, encodeContext);
}
private void encodeUndeclaredExtensions(final IBaseResource resource,
final StreamRDF eventWriter,
final List<? extends IBaseExtension<?, ?>> extensions,
final boolean includedResource,
final EncodeContext encodeContext) {
for (IBaseExtension<?, ?> next : extensions) {
if (next == null || (ElementUtil.isEmpty(next.getValue()) && next.getExtension().isEmpty())) {
continue;
}
writeCommentsPre(eventWriter, next);
eventWriter.start();
String elementId = getCompositeElementId(next);
if (isNotBlank(elementId)) {
eventWriter.triple(RDFUtil.triple("<id> " + elementId + " </id>"));
}
String url = getExtensionUrl(next.getUrl());
eventWriter.triple(RDFUtil.triple("<url> " + url + " </url>"));
if (next.getValue() != null) {
IBaseDatatype value = next.getValue();
RuntimeChildUndeclaredExtensionDefinition extDef = this.context.getRuntimeChildUndeclaredExtensionDefinition();
String childName = extDef.getChildNameByDatatype(value.getClass());
BaseRuntimeElementDefinition<?> childDef;
if (childName == null) {
childDef = this.context.getElementDefinition(value.getClass());
if (childDef == null) {
throw new ConfigurationException("Unable to encode extension, unrecognized child element type: " + value.getClass().getCanonicalName());
}
childName = RuntimeChildUndeclaredExtensionDefinition.createExtensionChildName(childDef);
} else {
childDef = extDef.getChildElementDefinitionByDatatype(value.getClass());
if (childDef == null) {
throw new ConfigurationException("Unable to encode extension, unrecognized child element type: " + value.getClass().getCanonicalName());
}
}
encodeChildElementToStreamWriter(resource, eventWriter, extDef, value, childName,
childDef, null, includedResource, null, encodeContext);
}
// child extensions
encodeExtensionsIfPresent(resource, eventWriter, next, includedResource, encodeContext);
eventWriter.finish();
writeCommentsPost(eventWriter, next);
}
}
private void encodeExtensionsIfPresent(final IBaseResource resource,
final StreamRDF writer,
final IBase element,
final boolean includedResource,
final EncodeContext encodeContext) {
if (element instanceof ISupportsUndeclaredExtensions) {
ISupportsUndeclaredExtensions res = (ISupportsUndeclaredExtensions) element;
encodeUndeclaredExtensions(resource, writer, toBaseExtensionList(res.getUndeclaredExtensions()), includedResource, encodeContext);
encodeUndeclaredExtensions(resource, writer, toBaseExtensionList(res.getUndeclaredModifierExtensions()), includedResource, encodeContext);
}
if (element instanceof IBaseHasExtensions) {
IBaseHasExtensions res = (IBaseHasExtensions) element;
encodeUndeclaredExtensions(resource, writer, res.getExtension(), includedResource, encodeContext);
}
if (element instanceof IBaseHasModifierExtensions) {
IBaseHasModifierExtensions res = (IBaseHasModifierExtensions) element;
encodeUndeclaredExtensions(resource, writer, res.getModifierExtension(), includedResource, encodeContext);
}
}
private void encodeExtension(final IBaseResource resource,
final StreamRDF eventWriter,
final boolean containedResource,
final CompositeChildElement nextChildElem,
final BaseRuntimeChildDefinition nextChild,
final IBase nextValue,
final String childName,
final String extensionUrl,
final BaseRuntimeElementDefinition<?> childDef,
final EncodeContext encodeContext) {
BaseRuntimeDeclaredChildDefinition extDef = (BaseRuntimeDeclaredChildDefinition) nextChild;
eventWriter.start();
String elementId = getCompositeElementId(nextValue);
if (isNotBlank(elementId)) {
eventWriter.triple(RDFUtil.triple("<id> " + elementId + " </id>"));
}
eventWriter.triple(RDFUtil.triple("<url> " + extensionUrl + " </url>"));
encodeChildElementToStreamWriter(resource, eventWriter, nextChild, nextValue, childName,
childDef, null, containedResource, nextChildElem, encodeContext);
eventWriter.finish();
}
private void encodeCompositeElementToStreamWriter(final IBaseResource resource,
final IBase element,
final StreamRDF streamRDF,
final boolean containedResource,
final CompositeChildElement parent,
final EncodeContext encodeContext) {
for (CompositeChildElement nextChildElem : super.compositeChildIterator(element, containedResource, parent, encodeContext)) {
BaseRuntimeChildDefinition nextChild = nextChildElem.getDef();
if (nextChild.getElementName().equals("url") && element instanceof IBaseExtension) {
/*
* RDF encoding is a one-off for extensions. The URL element goes in an attribute
* instead of being encoded as a normal element, only for RDF encoding
*/
continue;
}
if (nextChild instanceof RuntimeChildNarrativeDefinition) {
INarrativeGenerator gen = this.context.getNarrativeGenerator();
INarrative narr;
if (resource instanceof IResource) {
narr = ((IResource) resource).getText();
} else if (resource instanceof IDomainResource) {
narr = ((IDomainResource) resource).getText();
} else {
narr = null;
}
assert narr != null;
if (gen != null && narr.isEmpty()) {
gen.populateResourceNarrative(this.context, resource);
}
if (!narr.isEmpty()) {
RuntimeChildNarrativeDefinition child = (RuntimeChildNarrativeDefinition) nextChild;
String childName = nextChild.getChildNameByDatatype(child.getDatatype());
BaseRuntimeElementDefinition<?> type = child.getChildByName(childName);
encodeChildElementToStreamWriter(resource,
streamRDF, nextChild, narr, childName, type, null,
containedResource, nextChildElem, encodeContext);
continue;
}
}
if (nextChild instanceof RuntimeChildContainedResources) {
encodeChildElementToStreamWriter(resource, streamRDF, nextChild, null,
nextChild.getChildNameByDatatype(null),
nextChild.getChildElementDefinitionByDatatype(null), null,
containedResource, nextChildElem, encodeContext);
} else {
List<? extends IBase> values = nextChild.getAccessor().getValues(element);
values = super.preProcessValues(nextChild, resource, values, nextChildElem, encodeContext);
if (values == null || values.isEmpty()) {
continue;
}
for (IBase nextValue : values) {
if ((nextValue == null || nextValue.isEmpty())) {
continue;
}
ChildNameAndDef childNameAndDef = super.getChildNameAndDef(nextChild, nextValue);
if (childNameAndDef == null) {
continue;
}
String childName = childNameAndDef.getChildName();
BaseRuntimeElementDefinition<?> childDef = childNameAndDef.getChildDef();
String extensionUrl = getExtensionUrl(nextChild.getExtensionUrl());
if (extensionUrl != null && !childName.equals("extension")) {
encodeExtension(resource, streamRDF, containedResource, nextChildElem, nextChild,
nextValue, childName, extensionUrl, childDef, encodeContext);
} else if (nextChild instanceof RuntimeChildExtension) {
IBaseExtension<?, ?> extension = (IBaseExtension<?, ?>) nextValue;
if ((extension.getValue() == null || extension.getValue().isEmpty())) {
if (extension.getExtension().isEmpty()) {
continue;
}
}
encodeChildElementToStreamWriter(resource, streamRDF, nextChild, nextValue,
childName, childDef, getExtensionUrl(extension.getUrl()),
containedResource, nextChildElem, encodeContext);
} else if (!(nextChild instanceof RuntimeChildNarrativeDefinition) || !containedResource) {
encodeChildElementToStreamWriter(resource, streamRDF, nextChild, nextValue,
childName, childDef, extensionUrl, containedResource, nextChildElem, encodeContext);
}
}
}
}
}
private <Q extends IBaseExtension<?, ?>> List<IBaseExtension<?, ?>> toBaseExtensionList(final List<Q> theList) {
List<IBaseExtension<?, ?>> retVal = new ArrayList<>(theList.size());
retVal.addAll(theList);
return retVal;
}
private <T extends IBaseResource> T parseResource(Class<T> resourceType, StreamRDF streamReader) {
ParserState<T> parserState = ParserState.getPreResourceInstance(this, resourceType, context, false, getErrorHandler());
return doRDFLoop(streamReader, parserState);
}
private <T> T doRDFLoop(StreamRDF streamReader, ParserState<T> parserState) {
logger.trace("Entering RDF parsing loop with state: {}", parserState);
return parserState.getObject();
}
}

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java
View File

@ -43,6 +43,7 @@ public class Constants {
*/
public static final Set<String> CORS_ALLWED_METHODS;
public static final String CT_FHIR_JSON = "application/json+fhir";
public static final String CT_RDF_TURTLE = "application/x-turtle";
/**
* The FHIR MimeType for JSON encoding in FHIR DSTU3+
*/
@ -71,6 +72,9 @@ public class Constants {
public static final String FORMAT_HTML = "html";
public static final String FORMAT_JSON = "json";
public static final String FORMAT_XML = "xml";
public static final String FORMAT_TURTLE = "text/turtle";
/**
* "text/html" and "html"
*/

21
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/EncodingEnum.java
View File

@ -42,16 +42,25 @@ public enum EncodingEnum {
public IParser newParser(FhirContext theContext) {
return theContext.newXmlParser();
}
},
RDF(Constants.CT_RDF_TURTLE, Constants.CT_RDF_TURTLE, Constants.FORMAT_TURTLE) {
@Override
public IParser newParser(FhirContext theContext) {
return theContext.newRDFParser();
}
};
/**
* "json"
*/
public static final String JSON_PLAIN_STRING = "json";
/**
* "xml"
*/
public static final String XML_PLAIN_STRING = "xml";
private static Map<String, EncodingEnum> ourContentTypeToEncoding;
private static Map<String, EncodingEnum> ourContentTypeToEncodingLegacy;
private static Map<String, EncodingEnum> ourContentTypeToEncodingStrict;
@ -127,9 +136,9 @@ public enum EncodingEnum {
return myResourceContentTypeNonLegacy;
}
public abstract IParser newParser(FhirContext theContext);
public abstract IParser newParser(final FhirContext theContext);
public static EncodingEnum detectEncoding(String theBody) {
public static EncodingEnum detectEncoding(final String theBody) {
EncodingEnum retVal = detectEncodingNoDefault(theBody);
retVal = ObjectUtils.defaultIfNull(retVal, EncodingEnum.XML);
return retVal;
@ -158,7 +167,7 @@ public enum EncodingEnum {
* even if the "+fhir" part is missing from the expected content type.
* </p>
*/
public static EncodingEnum forContentType(String theContentType) {
public static EncodingEnum forContentType(final String theContentType) {
String contentTypeSplitted = getTypeWithoutCharset(theContentType);
if (contentTypeSplitted == null) {
return null;
@ -177,7 +186,7 @@ public enum EncodingEnum {
*
* @see #forContentType(String)
*/
public static EncodingEnum forContentTypeStrict(String theContentType) {
public static EncodingEnum forContentTypeStrict(final String theContentType) {
String contentTypeSplitted = getTypeWithoutCharset(theContentType);
if (contentTypeSplitted == null) {
return null;
@ -186,7 +195,7 @@ public enum EncodingEnum {
}
}
private static String getTypeWithoutCharset(String theContentType) {
private static String getTypeWithoutCharset(final String theContentType) {
if (theContentType == null) {
return null;
} else {
@ -198,7 +207,7 @@ public enum EncodingEnum {
/**
* Is the given type a FHIR legacy (pre-DSTU3) content type?
*/
public static boolean isLegacy(String theContentType) {
public static boolean isLegacy(final String theContentType) {
String contentTypeSplitted = getTypeWithoutCharset(theContentType);
if (contentTypeSplitted == null) {
return false;

14
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ParametersUtil.java
View File

@ -165,6 +165,13 @@ public class ParametersUtil {
}
@SuppressWarnings("unchecked")
public static void addParameterToParametersCode(FhirContext theCtx, IBaseParameters theParameters, String theName, String theValue) {
IPrimitiveType<String> value = (IPrimitiveType<String>) theCtx.getElementDefinition("code").newInstance();
value.setValue(theValue);
addParameterToParameters(theCtx, theParameters, theName, value);
}
@SuppressWarnings("unchecked")
public static void addParameterToParametersInteger(FhirContext theCtx, IBaseParameters theParameters, String theName, int theValue) {
IPrimitiveType<Integer> count = (IPrimitiveType<Integer>) theCtx.getElementDefinition("integer").newInstance();
@ -184,6 +191,13 @@ public class ParametersUtil {
IPrimitiveType<String> value = (IPrimitiveType<String>) theCtx.getElementDefinition("string").newInstance();
value.setValue(theValue);
addParameterToParameters(theCtx, theParameters, theName, value);
}
@SuppressWarnings("unchecked")
public static void addParameterToParametersUri(FhirContext theCtx, IBaseParameters theParameters, String theName, String theValue) {
IPrimitiveType<String> value = (IPrimitiveType<String>) theCtx.getElementDefinition("uri").newInstance();
value.setValue(theValue);
addParameterToParameters(theCtx, theParameters, theName, value);
}

5
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/StopWatch.java
View File

@ -221,7 +221,7 @@ public class StopWatch {
*
* @see #formatThroughput(int, TimeUnit)
*/
public double getThroughput(int theNumOperations, TimeUnit theUnit) {
public double getThroughput(long theNumOperations, TimeUnit theUnit) {
if (theNumOperations <= 0) {
return 0.0f;
}
@ -229,10 +229,9 @@ public class StopWatch {
long millisElapsed = Math.max(1, getMillis());
long periodMillis = theUnit.toMillis(1);
double numerator = theNumOperations;
double denominator = ((double) millisElapsed) / ((double) periodMillis);
return numerator / denominator;
return (double) theNumOperations / denominator;
}
public void restart() {

10
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ValidateUtil.java
View File

@ -63,15 +63,21 @@ public class ValidateUtil {
}
}
public static void isNotNullOrThrowUnprocessableEntity(Object theObject, String theMessage, Object... theValues) {
if (theObject == null) {
throw new UnprocessableEntityException(String.format(theMessage, theValues));
}
}
public static void isNotTooLongOrThrowIllegalArgument(String theString, int theMaxLength, String theMessage) {
if (length(theString) > theMaxLength) {
throw new IllegalArgumentException(theMessage);
}
}
public static void isTrueOrThrowInvalidRequest(boolean theSuccess, String theMessage) {
public static void isTrueOrThrowInvalidRequest(boolean theSuccess, String theMessage, Object... theValues) {
if (theSuccess == false) {
throw new InvalidRequestException(theMessage);
throw new InvalidRequestException(String.format(theMessage, theValues));
}
}

61
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/rdf/RDFUtil.java Normal file
View File

@ -0,0 +1,61 @@
package ca.uhn.fhir.util.rdf;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2019 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 org.apache.commons.io.input.ReaderInputStream;
import org.apache.commons.io.output.WriterOutputStream;
import org.apache.jena.graph.Triple;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.riot.Lang;
import org.apache.jena.riot.system.StreamRDF;
import org.apache.jena.riot.system.StreamRDFWriter;
import java.io.*;
import java.nio.charset.Charset;
import java.util.*;
public class RDFUtil {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RDFUtil.class);
private static final Map<String, Integer> VALID_ENTITY_NAMES;
static {
HashMap<String, Integer> validEntityNames = new HashMap<>(1448);
VALID_ENTITY_NAMES = Collections.unmodifiableMap(validEntityNames);
}
public static StreamRDF createRDFWriter(final Writer writer, final Lang lang) {
WriterOutputStream wos = new WriterOutputStream(writer, Charset.defaultCharset());
return StreamRDFWriter.getWriterStream(wos, lang);
}
public static StreamRDF createRDFReader(final Reader reader, final Lang lang) {
ReaderInputStream ris = new ReaderInputStream(reader, Charset.defaultCharset());
return StreamRDFWriter.getWriterStream(null, lang);
}
public static Triple triple(String tripleAsTurtle) {
Model m = ModelFactory.createDefaultModel();
m.read(new StringReader(tripleAsTurtle), "urn:x-base:", "TURTLE");
return m.listStatements().next().asTriple();
}
}

82
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/rdf/StreamRDFDedup.java Normal file
View File

@ -0,0 +1,82 @@
package ca.uhn.fhir.util.rdf;
import java.util.HashSet;
import java.util.LinkedList;
import org.apache.jena.graph.Triple;
import org.apache.jena.riot.system.StreamRDF;
import org.apache.jena.sparql.core.Quad;
/**
* Wraps another {@link StreamRDF} and attempts to remove duplicate
* triples and quads. To maintain streaming, duplicates are only
* removed within a sliding window of configurable size. Default
* size is 10000 triples and quads.
*/
public class StreamRDFDedup implements StreamRDF {
private final StreamRDF wrapped;
private final int windowSize;
private final HashSet<Object> tripleAndQuadCache;
private final LinkedList<Object> tripleAndQuadList = new LinkedList<Object>();
public StreamRDFDedup(StreamRDF wrapped) {
this(wrapped, 10000);
}
public StreamRDFDedup(StreamRDF wrapped, int windowSize) {
this.wrapped = wrapped;
this.windowSize = windowSize;
// Initial capacity big enough to avoid rehashing
this.tripleAndQuadCache = new HashSet<Object>(windowSize * 3 / 2);
}
@Override
public void start() {
wrapped.start();
}
@Override
public void triple(Triple triple) {
if (!seen(triple)) {
wrapped.triple(triple);
}
}
@Override
public void quad(Quad quad) {
if (!seen(quad)) {
wrapped.quad(quad);
}
}
@Override
public void base(String base) {
wrapped.base(base);
}
@Override
public void prefix(String prefix, String iri) {
wrapped.prefix(prefix, iri);
}
@Override
public void finish() {
wrapped.finish();
}
private boolean seen(Object tuple) {
if (tripleAndQuadCache.contains(tuple)) {
return true;
}
tripleAndQuadCache.add(tuple);
tripleAndQuadList.add(tuple);
if (tripleAndQuadList.size() > windowSize) {
forgetOldest();
}
return false;
}
private void forgetOldest() {
tripleAndQuadCache.remove(tripleAndQuadList.removeFirst());
}
}

90
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/rdf/StreamingRDFWriter.java Normal file
View File

@ -0,0 +1,90 @@
package ca.uhn.fhir.util.rdf;
import java.io.OutputStream;
import java.util.Iterator;
import java.util.Map.Entry;
import org.apache.jena.atlas.io.IndentedWriter;
import org.apache.jena.graph.Triple;
import org.apache.jena.riot.system.RiotLib;
import org.apache.jena.riot.system.StreamOps;
import org.apache.jena.riot.system.StreamRDF;
import org.apache.jena.riot.writer.WriterStreamRDFBlocks;
import org.apache.jena.riot.writer.WriterStreamRDFPlain;
import org.apache.jena.shared.PrefixMapping;
import org.apache.jena.shared.impl.PrefixMappingImpl;
import org.apache.jena.vocabulary.RDF;
/**
* Writes an iterator over triples to N-Triples or Turtle
* in a streaming fashion, that is, without needing to hold
* the entire thing in memory.
* <p>
* Instances are single-use.
* <p>
* There doesn't seem to be a pre-packaged version of this
* functionality in Jena/ARQ that doesn't require a Graph or Model.
*/
public class StreamingRDFWriter {
private final OutputStream out;
private final Iterator<Triple> triples;
private int dedupWindowSize = 10000;
public StreamingRDFWriter(OutputStream out, Iterator<Triple> triples) {
this.out = out;
this.triples = triples;
}
public void setDedupWindowSize(int newSize) {
this.dedupWindowSize = newSize;
}
public void writeNTriples() {
StreamRDF writer = new WriterStreamRDFPlain(new IndentedWriter(out));
if (dedupWindowSize > 0) {
writer = new StreamRDFDedup(writer, dedupWindowSize);
}
writer.start();
StreamOps.sendTriplesToStream(triples, writer);
writer.finish();
}
public void writeTurtle(String baseIRI, PrefixMapping prefixes, boolean writeBase) {
// Auto-register RDF prefix so that rdf:type is displayed well
// All other prefixes come from the query and should be as author intended
prefixes = ensureRDFPrefix(prefixes);
if (writeBase) {
// Jena's streaming Turtle writers don't output base even if it is provided,
// so we write it directly.
IndentedWriter w = new IndentedWriter(out);
RiotLib.writeBase(w, baseIRI);
w.flush();
}
StreamRDF writer = new WriterStreamRDFBlocks(out);
if (dedupWindowSize > 0) {
writer = new StreamRDFDedup(writer, dedupWindowSize);
}
writer.start();
writer.base(baseIRI);
for (Entry<String, String> e : prefixes.getNsPrefixMap().entrySet()) {
writer.prefix(e.getKey(), e.getValue());
}
StreamOps.sendTriplesToStream(triples, writer);
writer.finish();
}
private PrefixMapping ensureRDFPrefix(PrefixMapping prefixes) {
// Some prefix already registered for the RDF namespace -- good enough
if (prefixes.getNsURIPrefix(RDF.getURI()) != null) return prefixes;
// rdf: is registered to something else -- give up
if (prefixes.getNsPrefixURI("rdf") != null) return prefixes;
// Register rdf:
PrefixMapping newPrefixes = new PrefixMappingImpl();
newPrefixes.setNsPrefixes(prefixes);
newPrefixes.setNsPrefix("rdf", RDF.getURI());
return newPrefixes;
}
}

15
hapi-fhir-base/src/test/java/ca/uhn/fhir/util/ValidateUtilTest.java
View File

@ -3,6 +3,7 @@ package ca.uhn.fhir.util;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.fail;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import org.junit.Test;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -69,4 +70,18 @@ public class ValidateUtilTest {
}
}
@Test
public void testIsNotNull() {
ValidateUtil.isNotNullOrThrowUnprocessableEntity("aa", "");
try {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(null, "The message %s", "123");
fail();
} catch (UnprocessableEntityException e) {
assertEquals("The message 123", e.getMessage());
}
}
}

22
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java
View File

@ -25,6 +25,7 @@ import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.util.ParametersUtil;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
@ -56,6 +57,7 @@ public class UploadTerminologyCommand extends BaseCommand {
addBaseUrlOption(options);
addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + IHapiTerminologyLoaderSvc.SCT_URI + ")");
addOptionalOption(options, "d", "data", true, "Local file to use to upload (can be a raw file or a ZIP containing the raw file)");
addOptionalOption(options, null, "custom", false, "Indicates that this upload uses the HAPI FHIR custom external terminology format");
addBasicAuthOption(options);
addVerboseLoggingOption(options);
@ -78,23 +80,13 @@ public class UploadTerminologyCommand extends BaseCommand {
}
IGenericClient client = super.newClient(theCommandLine);
IBaseParameters inputParameters;
if (ctx.getVersion().getVersion() == FhirVersionEnum.DSTU3) {
org.hl7.fhir.dstu3.model.Parameters p = new org.hl7.fhir.dstu3.model.Parameters();
p.addParameter().setName("url").setValue(new org.hl7.fhir.dstu3.model.UriType(termUrl));
IBaseParameters inputParameters = ParametersUtil.newInstance(myFhirCtx);
ParametersUtil.addParameterToParametersUri(myFhirCtx, inputParameters, "url", termUrl);
for (String next : datafile) {
p.addParameter().setName("localfile").setValue(new org.hl7.fhir.dstu3.model.StringType(next));
ParametersUtil.addParameterToParametersString(myFhirCtx, inputParameters, "localfile", next);
}
inputParameters = p;
} else if (ctx.getVersion().getVersion() == FhirVersionEnum.R4) {
org.hl7.fhir.r4.model.Parameters p = new org.hl7.fhir.r4.model.Parameters();
p.addParameter().setName("url").setValue(new org.hl7.fhir.r4.model.UriType(termUrl));
for (String next : datafile) {
p.addParameter().setName("localfile").setValue(new org.hl7.fhir.r4.model.StringType(next));
}
inputParameters = p;
} else {
throw new ParseException("This command does not support FHIR version " + ctx.getVersion().getVersion());
if (theCommandLine.hasOption("custom")) {
ParametersUtil.addParameterToParametersCode(myFhirCtx, inputParameters, "contentMode", "custom");
}
if (theCommandLine.hasOption(VERBOSE_LOGGING_PARAM)) {

37
hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsResourceProvider.java
View File

@ -220,7 +220,7 @@ implements IRestfulServer<JaxRsRequest>, IResourceProvider {
* @see <a href="https://www.hl7.org/fhir/http.html#read">https://www.hl7.org/fhir/http.html#read</a>
*/
@GET
@Path("/{id}")
@Path("/{id : ((?!_history).)*}")
public Response find(@PathParam("id") final String id)
throws IOException {
return execute(getResourceRequest(RequestTypeEnum.GET, RestOperationTypeEnum.READ).id(id));
@ -245,7 +245,7 @@ implements IRestfulServer<JaxRsRequest>, IResourceProvider {
}
/**
* Retrieve the update history for a particular resource
* Retrieve a version of a resource
*
* @param id the id of the resource
* @param version the version of the resource
@ -254,12 +254,41 @@ implements IRestfulServer<JaxRsRequest>, IResourceProvider {
*/
@GET
@Path("/{id}/_history/{version}")
public Response findHistory(@PathParam("id") final String id, @PathParam("version") final String version)
public Response findVersion(@PathParam("id") final String id, @PathParam("version") final String version)
throws IOException {
final Builder theRequest = getResourceRequest(RequestTypeEnum.GET, RestOperationTypeEnum.VREAD).id(id).version(version);
return execute(theRequest);
}
/**
* Retrieve the update history for a particular resource
*
* @param id the id of the resource
* @return the response
* @see <a href="https://www.hl7.org/fhir/http.html#history">https://www.hl7.org/fhir/http.html#history</a>
*/
@GET
@Path("/{id}/_history")
public Response historyForInstance(@PathParam("id") final String id)
throws IOException {
final Builder theRequest = getResourceRequest(RequestTypeEnum.GET, RestOperationTypeEnum.HISTORY_INSTANCE).id(id);
return execute(theRequest);
}
/**
* Retrieve the update history for a particular type
*
* @return the response
* @see <a href="https://www.hl7.org/fhir/http.html#history">https://www.hl7.org/fhir/http.html#history</a>
*/
@GET
@Path("/_history")
public Response historyForType()
throws IOException {
final Builder theRequest = getResourceRequest(RequestTypeEnum.GET, RestOperationTypeEnum.HISTORY_TYPE);
return execute(theRequest);
}
/**
* Compartment Based Access
*
@ -270,7 +299,7 @@ implements IRestfulServer<JaxRsRequest>, IResourceProvider {
* @see <a href="https://www.hl7.org/fhir/compartments.html#compartment">https://www.hl7.org/fhir/compartments.html#compartment</a>
*/
@GET
@Path("/{id}/{compartment}")
@Path("/{id}/{compartment : ((?!_history).)*}")
public Response findCompartment(@PathParam("id") final String id, @PathParam("compartment") final String compartment)
throws IOException {
final Builder theRequest = getResourceRequest(RequestTypeEnum.GET, RestOperationTypeEnum.SEARCH_TYPE).id(id).compartment(

30
hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsResourceProviderTest.java
View File

@ -22,6 +22,7 @@ import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.SimpleBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.lang3.StringUtils;
@ -36,6 +37,7 @@ import org.mockito.Matchers;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import static org.junit.Assert.*;
@ -83,6 +85,12 @@ public class AbstractJaxRsResourceProviderTest {
return theResource;
}
private Patient createPatient(long id, String version) {
Patient theResource = new Patient();
theResource.setId(new IdDt(id).withVersion(version));
return theResource;
}
private List<Patient> createPatients(int firstId, int lastId) {
List<Patient> result = new ArrayList<Patient>(lastId - firstId);
for (long i = firstId; i <= lastId; i++) {
@ -341,7 +349,7 @@ public class AbstractJaxRsResourceProviderTest {
@Test
public void testVRead() {
when(mock.findHistory(idCaptor.capture())).thenReturn(createPatient(1));
when(mock.findVersion(idCaptor.capture())).thenReturn(createPatient(1));
final Patient patient = client.vread(Patient.class, "1", "2");
compareResultId(1, patient);
compareResultUrl("/Patient/1", patient);
@ -349,6 +357,26 @@ public class AbstractJaxRsResourceProviderTest {
assertEquals("2", idCaptor.getValue().getVersionIdPart());
}
@Test
public void testInstanceHistory() {
when(mock.getHistoryForInstance(idCaptor.capture())).thenReturn(new SimpleBundleProvider(Collections.singletonList(createPatient(1, "1"))));
final Bundle bundle = client.history().onInstance(new IdDt("Patient", 1L)).returnBundle(Bundle.class).execute();
Patient patient = (Patient) bundle.getEntryFirstRep().getResource();
compareResultId(1, patient);
compareResultUrl("/Patient/1/_history/1", patient);
assertEquals("1", idCaptor.getValue().getIdPart());
assertNull(idCaptor.getValue().getVersionIdPart());
}
@Test
public void testTypeHistory() {
when(mock.getHistoryForType()).thenReturn(new SimpleBundleProvider(Collections.singletonList(createPatient(1, "1"))));
final Bundle bundle = client.history().onType(Patient.class).returnBundle(Bundle.class).execute();
Patient patient = (Patient) bundle.getEntryFirstRep().getResource();
compareResultId(1, patient);
compareResultUrl("/Patient/1/_history/1", patient);
}
@Test
public void testXFindUnknownPatient() {
try {

21
hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/server/test/TestJaxRsMockPatientRestProvider.java
View File

@ -1,5 +1,7 @@
package ca.uhn.fhir.jaxrs.server.test;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import javax.ejb.Stateless;
@ -8,6 +10,11 @@ import javax.ws.rs.*;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.SimpleBundleProvider;
import org.hl7.fhir.instance.model.api.IIdType;
import org.mockito.Mockito;
import ca.uhn.fhir.jaxrs.server.AbstractJaxRsResourceProvider;
@ -68,8 +75,18 @@ public class TestJaxRsMockPatientRestProvider extends AbstractJaxRsResourceProvi
}
@Read(version = true)
public Patient findHistory(@IdParam final IdDt theId) {
return mock.findHistory(theId);
public Patient findVersion(@IdParam final IdDt theId) {
return mock.findVersion(theId);
}
@History
public IBundleProvider getHistoryForInstance(@IdParam IIdType theId) {
return mock.getHistoryForInstance(theId);
}
@History
public IBundleProvider getHistoryForType() {
return mock.getHistoryForType();
}
@Create

16
hapi-fhir-jaxrsserver-example/src/main/java/ca/uhn/fhir/jaxrs/server/example/JaxRsPatientRestProvider.java
View File

@ -19,6 +19,9 @@ import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.*;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@ -89,7 +92,7 @@ public class JaxRsPatientRestProvider extends AbstractJaxRsResourceProvider<Pati
}
@Read(version = true)
public Patient findHistory(@IdParam final IdDt theId) {
public Patient findVersion(@IdParam final IdDt theId) {
if (patients.containsKey(theId.getIdPart())) {
final List<Patient> list = patients.get(theId.getIdPart());
for (final Patient patient : list) {
@ -101,6 +104,17 @@ public class JaxRsPatientRestProvider extends AbstractJaxRsResourceProvider<Pati
throw new ResourceNotFoundException(theId);
}
// from BaseJpaResourceProvider
@History
public IBundleProvider getHistoryForInstance(@IdParam IdDt theId, @Since Date theSince, @At DateRangeParam theAt, RequestDetails theRequestDetails) {
return new SimpleBundleProvider(Collections.emptyList(), "myTestId");
}
@History
public IBundleProvider getHistoryForType(@Since Date theSince, @At DateRangeParam theAt, RequestDetails theRequestDetails) {
return new SimpleBundleProvider(Collections.emptyList(), "myTestId");
}
@Operation(name = "firstVersion", idempotent = true, returnParameters = { @OperationParam(name = "return", type = StringDt.class) })
public Parameters firstVersion(@IdParam final IdDt theId, @OperationParam(name = "dummy") StringDt dummyInput) {
Parameters parameters = new Parameters();

15
hapi-fhir-jaxrsserver-example/src/main/java/ca/uhn/fhir/jaxrs/server/example/JaxRsPatientRestProviderDstu3.java
View File

@ -10,6 +10,9 @@ import javax.ws.rs.*;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateRangeParam;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -90,7 +93,7 @@ public class JaxRsPatientRestProviderDstu3 extends AbstractJaxRsResourceProvider
}
@Read(version = true)
public Patient findHistory(@IdParam final IdType theId) {
public Patient findVersion(@IdParam final IdType theId) {
if (patients.containsKey(theId.getIdPart())) {
final List<Patient> list = patients.get(theId.getIdPart());
for (final Patient patient : list) {
@ -102,6 +105,16 @@ public class JaxRsPatientRestProviderDstu3 extends AbstractJaxRsResourceProvider
throw new ResourceNotFoundException(theId);
}
@History
public IBundleProvider getHistoryForInstance(@IdParam IdType theId, @Since Date theSince, @At DateRangeParam theAt, RequestDetails theRequestDetails) {
return new SimpleBundleProvider(Collections.emptyList(), "myTestId");
}
@History
public IBundleProvider getHistoryForType(@Since Date theSince, @At DateRangeParam theAt, RequestDetails theRequestDetails) {
return new SimpleBundleProvider(Collections.emptyList(), "myTestId");
}
@Operation(name = "firstVersion", idempotent = true, returnParameters = { @OperationParam(name = "return", type = StringType.class) })
public Parameters firstVersion(@IdParam final IdType theId, @OperationParam(name = "dummy") StringType dummyInput) {
Parameters parameters = new Parameters();

241
hapi-fhir-jaxrsserver-example/src/main/java/ca/uhn/fhir/jaxrs/server/example/JaxRsPatientRestProviderR4.java Normal file
View File

@ -0,0 +1,241 @@
package ca.uhn.fhir.jaxrs.server.example;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.api.AddProfileTagEnum;
import ca.uhn.fhir.context.api.BundleInclusionRule;
import ca.uhn.fhir.jaxrs.server.AbstractJaxRsResourceProvider;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.ETagSupportEnum;
import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
import ca.uhn.fhir.rest.server.IPagingProvider;
import ca.uhn.fhir.rest.server.SimpleBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.*;
import javax.ejb.Local;
import javax.ejb.Stateless;
import javax.ws.rs.*;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
import java.io.IOException;
import java.util.*;
import java.util.concurrent.ConcurrentHashMap;
/**
* A demo JaxRs Patient Rest Provider
*/
@Local
@Path(JaxRsPatientRestProviderR4.PATH)
@Stateless
@Produces({ MediaType.APPLICATION_JSON, Constants.CT_FHIR_JSON, Constants.CT_FHIR_XML })
public class JaxRsPatientRestProviderR4 extends AbstractJaxRsResourceProvider<Patient> {
private static Long counter = 1L;
/**
* The HAPI paging provider for this server
*/
public static final IPagingProvider PAGE_PROVIDER;
static final String PATH = "/Patient";
private static final ConcurrentHashMap<String, List<Patient>> patients = new ConcurrentHashMap<String, List<Patient>>();
static {
PAGE_PROVIDER = new FifoMemoryPagingProvider(10);
}
static {
patients.put(String.valueOf(counter), createPatient("Van Houte"));
patients.put(String.valueOf(counter), createPatient("Agnew"));
for (int i = 0; i < 20; i++) {
patients.put(String.valueOf(counter), createPatient("Random Patient " + counter));
}
}
public JaxRsPatientRestProviderR4() {
super(FhirContext.forDstu3(), JaxRsPatientRestProviderR4.class);
}
@Create
public MethodOutcome create(@ResourceParam final Patient patient, @ConditionalUrlParam String theConditional) throws Exception {
patients.put("" + counter, createPatient(patient));
final MethodOutcome result = new MethodOutcome().setCreated(true);
result.setResource(patient);
result.setId(new IdType(patient.getId()));
return result;
}
@Delete
public MethodOutcome delete(@IdParam final IdType theId) {
final Patient deletedPatient = find(theId);
patients.remove(deletedPatient.getIdElement().getIdPart());
final MethodOutcome result = new MethodOutcome().setCreated(true);
result.setResource(deletedPatient);
return result;
}
@Read
public Patient find(@IdParam final IdType theId) {
if (patients.containsKey(theId.getIdPart())) {
return getLast(patients.get(theId.getIdPart()));
} else {
throw new ResourceNotFoundException(theId);
}
}
@Read(version = true)
public Patient findVersion(@IdParam final IdType theId) {
if (patients.containsKey(theId.getIdPart())) {
final List<Patient> list = patients.get(theId.getIdPart());
for (final Patient patient : list) {
if (patient.getIdElement().getVersionIdPartAsLong().equals(theId.getVersionIdPartAsLong())) {
return patient;
}
}
}
throw new ResourceNotFoundException(theId);
}
@History
public IBundleProvider getHistoryForInstance(@IdParam IdType theId, @Since Date theSince, @At DateRangeParam theAt, RequestDetails theRequestDetails) {
return new SimpleBundleProvider(Collections.emptyList(), "myTestId");
}
@History
public IBundleProvider getHistoryForType(@Since Date theSince, @At DateRangeParam theAt, RequestDetails theRequestDetails) {
return new SimpleBundleProvider(Collections.emptyList(), "myTestId");
}
@Operation(name = "firstVersion", idempotent = true, returnParameters = { @OperationParam(name = "return", type = StringType.class) })
public Parameters firstVersion(@IdParam final IdType theId, @OperationParam(name = "dummy") StringType dummyInput) {
Parameters parameters = new Parameters();
Patient patient = find(new IdType(theId.getResourceType(), theId.getIdPart(), "0"));
parameters.addParameter().setName("return").setResource(patient).setValue(new StringType((counter - 1) + "" + "inputVariable [ " + dummyInput.getValue() + "]"));
return parameters;
}
@Override
public AddProfileTagEnum getAddProfileTag() {
return AddProfileTagEnum.NEVER;
}
@Override
public BundleInclusionRule getBundleInclusionRule() {
return BundleInclusionRule.BASED_ON_INCLUDES;
}
@Override
public ETagSupportEnum getETagSupport() {
return ETagSupportEnum.DISABLED;
}
/** THE DEFAULTS */
@Override
public List<IServerInterceptor> getInterceptors_() {
return Collections.emptyList();
}
private Patient getLast(final List<Patient> list) {
return list.get(list.size() - 1);
}
@Override
public IPagingProvider getPagingProvider() {
return PAGE_PROVIDER;
}
@Override
public Class<Patient> getResourceType() {
return Patient.class;
}
@Override
public boolean isDefaultPrettyPrint() {
return true;
}
@GET
@Path("/{id}/$firstVersion")
public Response operationFirstVersionUsingGet(@PathParam("id") String id) throws IOException {
return customOperation(null, RequestTypeEnum.GET, id, "$firstVersion", RestOperationTypeEnum.EXTENDED_OPERATION_INSTANCE);
}
@POST
@Path("/{id}/$firstVersion")
public Response operationFirstVersionUsingGet(@PathParam("id") String id, final String resource) throws Exception {
return customOperation(resource, RequestTypeEnum.POST, id, "$firstVersion", RestOperationTypeEnum.EXTENDED_OPERATION_INSTANCE);
}
@Search
public List<Patient> search(@RequiredParam(name = Patient.SP_NAME) final StringParam name) {
final List<Patient> result = new LinkedList<Patient>();
for (final List<Patient> patientIterator : patients.values()) {
Patient single = null;
for (Patient patient : patientIterator) {
if (name == null || patient.getName().get(0).getFamilyElement().getValueNotNull().equals(name.getValueNotNull())) {
single = patient;
}
}
if (single != null) {
result.add(single);
}
}
return result;
}
@Search(compartmentName = "Condition")
public List<IBaseResource> searchCompartment(@IdParam IdType thePatientId) {
List<IBaseResource> retVal = new ArrayList<IBaseResource>();
Condition condition = new Condition();
condition.setId(new IdType("665577"));
retVal.add(condition);
return retVal;
}
@Update
public MethodOutcome update(@IdParam final IdType theId, @ResourceParam final Patient patient) {
final String idPart = theId.getIdPart();
if (patients.containsKey(idPart)) {
final List<Patient> patientList = patients.get(idPart);
final Patient lastPatient = getLast(patientList);
patient.setId(createId(theId.getIdPartAsLong(), lastPatient.getIdElement().getVersionIdPartAsLong() + 1));
patientList.add(patient);
final MethodOutcome result = new MethodOutcome().setCreated(false);
result.setResource(patient);
result.setId(new IdType(patient.getId()));
return result;
} else {
throw new ResourceNotFoundException(theId);
}
}
private static IdType createId(final Long id, final Long theVersionId) {
return new IdType("Patient", "" + id, "" + theVersionId);
}
private static List<Patient> createPatient(final Patient patient) {
patient.setId(createId(counter, 1L));
final LinkedList<Patient> list = new LinkedList<Patient>();
list.add(patient);
counter++;
return list;
}
private static List<Patient> createPatient(final String name) {
final Patient patient = new Patient();
patient.getName().add(new HumanName().setFamily(name));
return createPatient(patient);
}
}

13
hapi-fhir-jaxrsserver-example/src/test/java/ca/uhn/fhir/jaxrs/server/example/JaxRsPatientProviderDstu3Test.java
View File

@ -5,6 +5,7 @@ import static org.junit.Assert.*;
import java.util.Arrays;
import java.util.List;
import ca.uhn.fhir.model.primitive.IdDt;
import org.apache.commons.lang3.StringUtils;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletContextHandler;
@ -285,4 +286,16 @@ public class JaxRsPatientProviderDstu3Test {
System.out.println(patient);
}
@Test
public void testInstanceHistory() {
final Bundle history = client.history().onInstance(new IdDt("Patient", 1L)).returnBundle(Bundle.class).execute();
assertEquals("myTestId", history.getIdElement().getIdPart());
}
@Test
public void testTypeHistory() {
final Bundle history = client.history().onType(Patient.class).returnBundle(Bundle.class).execute();
assertEquals("myTestId", history.getIdElement().getIdPart());
}
}

308
hapi-fhir-jaxrsserver-example/src/test/java/ca/uhn/fhir/jaxrs/server/example/JaxRsPatientProviderR4Test.java Normal file
View File

@ -0,0 +1,308 @@
package ca.uhn.fhir.jaxrs.server.example;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jaxrs.client.JaxRsRestfulClientFactory;
import ca.uhn.fhir.model.primitive.BoundCodeDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.PreferReturnEnum;
import ca.uhn.fhir.rest.api.SearchStyleEnum;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.lang3.StringUtils;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletContextHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.hl7.fhir.r4.model.*;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Ignore;
import org.junit.Test;
import java.util.Arrays;
import java.util.List;
import static org.junit.Assert.*;
public class JaxRsPatientProviderR4Test {
private static IGenericClient client;
private static FhirContext ourCtx = FhirContext.forR4();
private static final String PATIENT_NAME = "Van Houte";
private static int ourPort;
private static Server jettyServer;
@AfterClass
public static void afterClassClearContext() throws Exception {
JettyUtil.closeServer(jettyServer);
TestUtil.clearAllStaticFieldsForUnitTest();
}
@BeforeClass
public static void setUpClass()
throws Exception {
ServletContextHandler context = new ServletContextHandler(ServletContextHandler.SESSIONS);
context.setContextPath("/");
jettyServer = new Server(0);
jettyServer.setHandler(context);
ServletHolder jerseyServlet = context.addServlet(org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.class, "/*");
jerseyServlet.setInitOrder(0);
//@formatter:off
jerseyServlet.setInitParameter("resteasy.resources",
StringUtils.join(Arrays.asList(
JaxRsConformanceProvider.class.getCanonicalName(),
JaxRsPatientRestProvider.class.getCanonicalName(),
JaxRsPageProvider.class.getCanonicalName()
), ","));
//@formatter:on
JettyUtil.startServer(jettyServer);
ourPort = JettyUtil.getPortForStartedServer(jettyServer);
ourCtx.setRestfulClientFactory(new JaxRsRestfulClientFactory(ourCtx));
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
client = ourCtx.newRestfulGenericClient("http://localhost:" + ourPort + "/");
client.setEncoding(EncodingEnum.JSON);
client.registerInterceptor(new LoggingInterceptor(true));
}
/** Search/Query - Type */
@Test
public void findUsingGenericClientBySearch() {
// Perform a search
final Bundle results = client
.search()
.forResource(Patient.class)
.where(Patient.NAME.matchesExactly().value(PATIENT_NAME))
.returnBundle(Bundle.class)
.execute();
System.out.println(results.getEntry().get(0));
assertEquals(results.getEntry().size(), 1);
}
/** Search - Multi-valued Parameters (ANY/OR) */
@Test
public void findUsingGenericClientBySearchWithMultiValues() {
final Bundle response = client
.search()
.forResource(Patient.class)
.where(Patient.ADDRESS.matches().values("Toronto")).and(Patient.ADDRESS.matches().values("Ontario"))
.and(Patient.ADDRESS.matches().values("Canada"))
.where(Patient.IDENTIFIER.exactly().systemAndIdentifier("SHORTNAME", "TOYS"))
.returnBundle(Bundle.class)
.execute();
System.out.println(response.getEntry().get(0));
}
/** Search - Paging */
@Test
public void findWithPaging() {
// Perform a search
final Bundle results = client.search().forResource(Patient.class).limitTo(8).returnBundle(Bundle.class).execute();
System.out.println(results.getEntry().size());
if (results.getLink(Bundle.LINK_NEXT) != null) {
// load next page
final Bundle nextPage = client.loadPage().next(results).execute();
System.out.println(nextPage.getEntry().size());
}
}
/** */
@Test
public void testSearchPost() {
Bundle response = client.search()
.forResource("Patient")
.usingStyle(SearchStyleEnum.POST)
.returnBundle(Bundle.class)
.execute();
assertTrue(response.getEntry().size() > 0);
}
/** Search - Compartments */
@Test
public void testSearchCompartements() {
Bundle response = client.search()
.forResource(Patient.class)
.withIdAndCompartment("1", "Condition")
.returnBundle(Bundle.class)
.execute();
assertTrue(response.getEntry().size() > 0);
}
/** Search - Subsetting (_summary and _elements) */
@Test
@Ignore
public void testSummary() {
client.search()
.forResource(Patient.class)
.returnBundle(Bundle.class)
.execute();
}
@Test
public void testCreatePatient() {
final Patient existing = new Patient();
existing.setId((IdDt) null);
existing.getNameFirstRep().setFamily("Created Patient 54");
client.setEncoding(EncodingEnum.JSON);
final MethodOutcome results = client.create().resource(existing).prefer(PreferReturnEnum.REPRESENTATION).execute();
System.out.println(results.getId());
final Patient patient = (Patient) results.getResource();
System.out.println(patient);
assertNotNull(client.read().resource(Patient.class).withId(patient.getId()));
client.setEncoding(EncodingEnum.JSON);
}
/** Conditional Creates */
@Test
public void testConditionalCreate() {
final Patient existing = new Patient();
existing.setId((IdDt) null);
existing.getNameFirstRep().setFamily("Created Patient 54");
client.setEncoding(EncodingEnum.XML);
final MethodOutcome results = client.create().resource(existing).prefer(PreferReturnEnum.REPRESENTATION).execute();
System.out.println(results.getId());
final Patient patient = (Patient) results.getResource();
client.create()
.resource(patient)
.conditional()
.where(Patient.IDENTIFIER.exactly().identifier(patient.getIdentifierFirstRep().toString()))
.execute();
}
/** Find By Id */
@Test
public void findUsingGenericClientById() {
final Patient results = client.read().resource(Patient.class).withId("1").execute();
assertEquals(results.getIdElement().getIdPartAsLong().longValue(), 1L);
}
@Test
public void testUpdateById() {
final Patient existing = client.read().resource(Patient.class).withId("1").execute();
final List<HumanName> name = existing.getName();
name.get(0).addSuffix("The Second");
existing.setName(name);
client.setEncoding(EncodingEnum.XML);
final MethodOutcome results = client.update().resource(existing).withId("1").execute();
}
@Test
public void testDeletePatient() {
final Patient existing = new Patient();
existing.getNameFirstRep().setFamily("Created Patient XYZ");
final MethodOutcome results = client.create().resource(existing).prefer(PreferReturnEnum.REPRESENTATION).execute();
System.out.println(results.getId());
final Patient patient = (Patient) results.getResource();
client.delete().resource(patient).execute();
try {
client.read().resource(Patient.class).withId(patient.getId()).execute();
fail();
} catch (final Exception e) {
// assertEquals(e.getStatusCode(), Constants.STATUS_HTTP_404_NOT_FOUND);
}
}
/** Transaction - Server */
@Ignore
@Test
public void testTransaction() {
Bundle bundle = new Bundle();
Bundle.BundleEntryComponent entry = bundle.addEntry();
final Patient existing = new Patient();
existing.getNameFirstRep().setFamily("Created with bundle");
entry.setResource(existing);
BoundCodeDt<BundleEntryTransactionMethodEnum> theTransactionOperation = new BoundCodeDt(
BundleEntryTransactionMethodEnum.VALUESET_BINDER,
BundleEntryTransactionMethodEnum.POST);
Bundle response = client.transaction().withBundle(bundle).execute();
}
/** Conformance - Server */
@Test
@Ignore
public void testConformance() {
final CapabilityStatement caps = client.capabilities().ofType(CapabilityStatement.class).execute();
System.out.println(caps.getRest().get(0).getResource().get(0).getType());
assertEquals(caps.getRest().get(0).getResource().get(0).getType().toString(), "Patient");
}
/** Extended Operations */
// Create a client to talk to the HeathIntersections server
@Test
public void testExtendedOperations() {
client.registerInterceptor(new LoggingInterceptor(true));
// Create the input parameters to pass to the server
Parameters inParams = new Parameters();
inParams.addParameter().setName("start").setValue(new DateTimeType("2001-01-01"));
inParams.addParameter().setName("end").setValue(new DateTimeType("2015-03-01"));
inParams.addParameter().setName("dummy").setValue(new StringType("myAwesomeDummyValue"));
// Invoke $everything on "Patient/1"
Parameters outParams = client
.operation()
.onInstance(new IdDt("Patient", "1"))
.named("$firstVersion")
.withParameters(inParams)
// .useHttpGet() // Use HTTP GET instead of POST
.execute();
String resultValue = outParams.getParameter().get(0).getValue().toString();
System.out.println(resultValue);
assertEquals("expected but found : " + resultValue, resultValue.contains("myAwesomeDummyValue"), true);
}
@Test
public void testExtendedOperationsUsingGet() {
// Create the input parameters to pass to the server
Parameters inParams = new Parameters();
inParams.addParameter().setName("start").setValue(new DateTimeType("2001-01-01"));
inParams.addParameter().setName("end").setValue(new DateTimeType("2015-03-01"));
inParams.addParameter().setName("dummy").setValue(new StringType("myAwesomeDummyValue"));
// Invoke $everything on "Patient/1"
Parameters outParams = client
.operation()
.onInstance(new IdDt("Patient", "1"))
.named("$firstVersion")
.withParameters(inParams)
.useHttpGet() // Use HTTP GET instead of POST
.execute();
String resultValue = outParams.getParameter().get(0).getValue().toString();
System.out.println(resultValue);
assertEquals("expected but found : " + resultValue, resultValue.contains("myAwesomeDummyValue"), true);
}
@Test
public void testVRead() {
final Patient patient = client.read().resource(Patient.class).withIdAndVersion("1", "1").execute();
System.out.println(patient);
}
@Test
public void testRead() {
final Patient patient = client.read().resource(Patient.class).withId("1").execute();
System.out.println(patient);
}
@Test
public void testInstanceHistory() {
final Bundle history = client.history().onInstance(new IdDt("Patient", 1L)).returnBundle(Bundle.class).execute();
assertEquals("myTestId", history.getIdElement().getIdPart());
}
@Test
public void testTypeHistory() {
final Bundle history = client.history().onType(Patient.class).returnBundle(Bundle.class).execute();
assertEquals("myTestId", history.getIdElement().getIdPart());
}
}

11
hapi-fhir-jaxrsserver-example/src/test/java/ca/uhn/fhir/jaxrs/server/example/JaxRsPatientProviderTest.java
View File

@ -291,4 +291,15 @@ public class JaxRsPatientProviderTest {
System.out.println(patient);
}
@Test
public void testInstanceHistory() {
final Bundle history = client.history().onInstance(new IdDt("Patient", 1L)).returnBundle(Bundle.class).execute();
assertEquals("myTestId", history.getId().getIdPart());
}
@Test
public void testTypeHistory() {
final Bundle history = client.history().onType(Patient.class).returnBundle(Bundle.class).execute();
assertEquals("myTestId", history.getId().getIdPart());
}
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
View File

@ -50,15 +50,12 @@ import static org.apache.commons.lang3.StringUtils.length;
@Index(name = "IDX_CONCEPT_UPDATED", columnList = "CONCEPT_UPDATED")
})
public class TermConcept implements Serializable {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermConcept.class);
private static final long serialVersionUID = 1L;
public static final int MAX_CODE_LENGTH = 500;
public static final int MAX_DESC_LENGTH = 400;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermConcept.class);
private static final long serialVersionUID = 1L;
@OneToMany(fetch = FetchType.LAZY, mappedBy = "myParent", cascade = {})
private Collection<TermConceptParentChildLink> myChildren;
private List<TermConceptParentChildLink> myChildren;
@Column(name = "CODEVAL", nullable = false, length = MAX_CODE_LENGTH)
@Fields({@Field(name = "myCode", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "exactAnalyzer")),})
@ -178,7 +175,7 @@ public class TermConcept implements Serializable {
return b.isEquals();
}
public Collection<TermConceptParentChildLink> getChildren() {
public List<TermConceptParentChildLink> getChildren() {
if (myChildren == null) {
myChildren = new ArrayList<>();
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/TerminologyUploaderProvider.java
View File

@ -177,6 +177,7 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
public IBaseParameters uploadExternalCodeSystem(
HttpServletRequest theServletRequest,
@OperationParam(name = "url", min = 1, typeName = "uri") IPrimitiveType<String> theCodeSystemUrl,
@OperationParam(name = "contentMode", min = 0, typeName = "code") IPrimitiveType<String> theContentMode,
@OperationParam(name = "localfile", min = 1, max = OperationParam.MAX_UNLIMITED, typeName = "string") List<IPrimitiveType<String>> theLocalFile,
@OperationParam(name = "package", min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "attachment") List<ICompositeType> thePackage,
RequestDetails theRequestDetails
@ -245,11 +246,15 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
}
}
String url = theCodeSystemUrl != null ? theCodeSystemUrl.getValue() : null;
url = defaultString(url);
String codeSystemUrl = theCodeSystemUrl != null ? theCodeSystemUrl.getValue() : null;
codeSystemUrl = defaultString(codeSystemUrl);
String contentMode = theContentMode != null ? theContentMode.getValue() : null;
UploadStatistics stats;
switch (url) {
if ("custom".equals(contentMode)) {
stats = myTerminologyLoaderSvc.loadCustom(codeSystemUrl, localFiles, theRequestDetails);
} else {
switch (codeSystemUrl) {
case IHapiTerminologyLoaderSvc.SCT_URI:
stats = myTerminologyLoaderSvc.loadSnomedCt(localFiles, theRequestDetails);
break;
@ -260,7 +265,8 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
stats = myTerminologyLoaderSvc.loadImgthla(localFiles, theRequestDetails);
break;
default:
throw new InvalidRequestException("Unknown URL: " + url);
throw new InvalidRequestException("Unknown URL: " + codeSystemUrl);
}
}
IBaseParameters retVal = ParametersUtil.newInstance(myCtx);

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologyLoaderSvc.java
View File

@ -39,6 +39,9 @@ public interface IHapiTerminologyLoaderSvc {
UploadStatistics loadSnomedCt(List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
// FIXME: remove the default implementation before 4.0.0
default UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) { return null; };
interface FileDescriptor {
String getFilename();

153
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java
View File

@ -4,15 +4,19 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.term.custom.ConceptHandler;
import ca.uhn.fhir.jpa.term.custom.HierarchyHandler;
import ca.uhn.fhir.jpa.term.loinc.*;
import ca.uhn.fhir.jpa.term.snomedct.SctHandlerConcept;
import ca.uhn.fhir.jpa.term.snomedct.SctHandlerDescription;
import ca.uhn.fhir.jpa.term.snomedct.SctHandlerRelationship;
import ca.uhn.fhir.jpa.util.Counter;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.ValidateUtil;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Charsets;
import org.apache.commons.csv.CSVFormat;
@ -83,15 +87,19 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
public static final String LOINC_GROUP_FILE = "Group.csv";
public static final String LOINC_GROUP_TERMS_FILE = "GroupLoincTerms.csv";
public static final String LOINC_PARENT_GROUP_FILE = "ParentGroup.csv";
public static final String CUSTOM_CONCEPTS_FILE = "concepts.csv";
public static final String CUSTOM_HIERARCHY_FILE = "hierarchy.csv";
public static final String CUSTOM_CODESYSTEM_JSON = "codesystem.json";
public static final String CUSTOM_CODESYSTEM_XML = "codesystem.xml";
private static final int LOG_INCREMENT = 1000;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcImpl.class);
@Autowired
private IHapiTerminologySvc myTermSvc;
@Autowired(required = false)
private IHapiTerminologySvcDstu3 myTermSvcDstu3;
@Autowired(required = false)
private IHapiTerminologySvcR4 myTermSvcR4;
// FYI: Hardcoded to R4 because that's what the term svc uses internally
private final FhirContext myCtx = FhirContext.forR4();
private void dropCircularRefs(TermConcept theConcept, ArrayList<String> theChain, Map<String, TermConcept> theCode2concept, Counter theCircularCounter) {
@ -203,8 +211,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
ourLog.info("Beginning IMGTHLA processing");
return processImgthlaFiles(descriptors, theRequestDetails);
}
finally {
} finally {
IOUtils.closeQuietly(descriptors);
}
}
@ -257,6 +264,67 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
}
}
@Override
public UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
final Map<String, TermConcept> code2concept = new HashMap<>();
IRecordHandler handler;
Optional<String> codeSystemContent = loadFile(descriptors, CUSTOM_CODESYSTEM_JSON, CUSTOM_CODESYSTEM_XML);
CodeSystem codeSystem;
if (codeSystemContent.isPresent()) {
codeSystem = EncodingEnum
.detectEncoding(codeSystemContent.get())
.newParser(myCtx)
.parseResource(CodeSystem.class, codeSystemContent.get());
ValidateUtil.isTrueOrThrowInvalidRequest(theSystem.equalsIgnoreCase(codeSystem.getUrl()), "CodeSystem.url does not match the supplied system: %s", theSystem);
ValidateUtil.isTrueOrThrowInvalidRequest(CodeSystem.CodeSystemContentMode.NOTPRESENT.equals(codeSystem.getContent()), "CodeSystem.content does not match the expected value: %s", CodeSystem.CodeSystemContentMode.NOTPRESENT.toCode());
} else {
codeSystem = new CodeSystem();
codeSystem.setUrl(theSystem);
codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
}
TermCodeSystemVersion csv = new TermCodeSystemVersion();
// Concept File
handler = new ConceptHandler(code2concept, csv);
iterateOverZipFile(descriptors, CUSTOM_CONCEPTS_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
// Hierarchy
if (descriptors.hasFile(CUSTOM_HIERARCHY_FILE)) {
handler = new HierarchyHandler(code2concept);
iterateOverZipFile(descriptors, CUSTOM_HIERARCHY_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
}
// Add root concepts to CodeSystemVersion
for (TermConcept nextConcept : code2concept.values()) {
if (nextConcept.getParents().isEmpty()) {
csv.getConcepts().add(nextConcept);
}
}
IIdType target = storeCodeSystem(theRequestDetails, csv, codeSystem, null, null);
return new UploadStatistics(code2concept.size(), target);
}
}
private Optional<String> loadFile(LoadedFileDescriptors theDescriptors, String... theFilenames) {
for (FileDescriptor next : theDescriptors.getUncompressedFileDescriptors()) {
for (String nextFilename : theFilenames) {
if (next.getFilename().endsWith(nextFilename)) {
try {
String contents = IOUtils.toString(next.getInputStream(), Charsets.UTF_8);
return Optional.of(contents);
} catch (IOException e) {
throw new InternalErrorException(e);
}
}
}
}
return Optional.empty();
}
UploadStatistics processImgthlaFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) {
final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
final Map<String, TermConcept> code2concept = new HashMap<>();
@ -309,13 +377,13 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
}
LineNumberReader lnr = new LineNumberReader(reader);
while(lnr.readLine() != null) {}
while (lnr.readLine() != null) {
}
ourLog.warn("Lines read from {}: {}", nextFilename, lnr.getLineNumber());
} catch (IOException e) {
throw new InternalErrorException(e);
}
finally {
} finally {
IOUtils.closeQuietly(reader);
}
@ -340,13 +408,13 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
}
LineNumberReader lnr = new LineNumberReader(reader);
while(lnr.readLine() != null) {}
while (lnr.readLine() != null) {
}
ourLog.warn("Lines read from {}: {}", nextFilename, lnr.getLineNumber());
} catch (IOException e) {
throw new InternalErrorException(e);
}
finally {
} finally {
IOUtils.closeQuietly(reader);
}
@ -553,11 +621,6 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
return new UploadStatistics(code2concept.size(), target);
}
@VisibleForTesting
void setTermSvcDstu3ForUnitTest(IHapiTerminologySvcDstu3 theTermSvcDstu3) {
myTermSvcDstu3 = theTermSvcDstu3;
}
@VisibleForTesting
void setTermSvcForUnitTests(IHapiTerminologySvc theTermSvc) {
myTermSvc = theTermSvc;
@ -571,38 +634,12 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
IIdType retVal;
myTermSvc.setProcessDeferred(false);
if (myTermSvcDstu3 != null) {
retVal = myTermSvcDstu3.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
} else {
retVal = myTermSvcR4.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
}
retVal = myTermSvc.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
myTermSvc.setProcessDeferred(true);
return retVal;
}
public static String firstNonBlank(String... theStrings) {
String retVal = "";
for (String nextString : theStrings) {
if (isNotBlank(nextString)) {
retVal = nextString;
break;
}
}
return retVal;
}
public static TermConcept getOrCreateConcept(TermCodeSystemVersion codeSystemVersion, Map<String, TermConcept> id2concept, String id) {
TermConcept concept = id2concept.get(id);
if (concept == null) {
concept = new TermConcept();
id2concept.put(id, concept);
concept.setCodeSystemVersion(codeSystemVersion);
}
return concept;
}
static class LoadedFileDescriptors implements Closeable {
private List<File> myTemporaryFiles = new ArrayList<>();
@ -651,6 +688,13 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
}
}
boolean hasFile(String theFilename) {
return myUncompressedFileDescriptors
.stream()
.map(t -> t.getFilename().replaceAll(".*[\\\\/]", "")) // Strip the path from the filename
.anyMatch(t -> t.equals(theFilename));
}
@Override
public void close() {
for (File next : myTemporaryFiles) {
@ -694,4 +738,25 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
}
public static String firstNonBlank(String... theStrings) {
String retVal = "";
for (String nextString : theStrings) {
if (isNotBlank(nextString)) {
retVal = nextString;
break;
}
}
return retVal;
}
public static TermConcept getOrCreateConcept(TermCodeSystemVersion codeSystemVersion, Map<String, TermConcept> id2concept, String id) {
TermConcept concept = id2concept.get(id);
if (concept == null) {
concept = new TermConcept();
id2concept.put(id, concept);
concept.setCodeSystemVersion(codeSystemVersion);
}
return concept;
}
}

63
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/custom/ConceptHandler.java Normal file
View File

@ -0,0 +1,63 @@
package ca.uhn.fhir.jpa.term.custom;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 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 ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
import org.apache.commons.csv.CSVRecord;
import org.apache.commons.lang3.Validate;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.Map;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
public class ConceptHandler implements IRecordHandler {
private static final Logger ourLog = LoggerFactory.getLogger(ConceptHandler.class);
private final Map<String, TermConcept> myCode2Concept;
private final TermCodeSystemVersion myCodeSystemVersion;
public ConceptHandler(Map<String, TermConcept> theCode2concept, TermCodeSystemVersion theCodeSystemVersion) {
myCode2Concept = theCode2concept;
myCodeSystemVersion = theCodeSystemVersion;
}
@Override
public void accept(CSVRecord theRecord) {
String code = trim(theRecord.get("CODE"));
if (isNotBlank(code)) {
String display = trim(theRecord.get("DISPLAY"));
Validate.isTrue(!myCode2Concept.containsKey(code), "The code %s has appeared more than once", code);
TermConcept concept = TerminologyLoaderSvcImpl.getOrCreateConcept(myCodeSystemVersion, myCode2Concept, code);
concept.setCode(code);
concept.setDisplay(display);
myCode2Concept.put(code, concept);
}
}
}

58
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/custom/HierarchyHandler.java Normal file
View File

@ -0,0 +1,58 @@
package ca.uhn.fhir.jpa.term.custom;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 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 ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.csv.CSVRecord;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.Map;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
public class HierarchyHandler implements IRecordHandler {
private final Map<String, TermConcept> myCode2Concept;
public HierarchyHandler(Map<String, TermConcept> theCode2concept) {
myCode2Concept = theCode2concept;
}
@Override
public void accept(CSVRecord theRecord) {
String parent = trim(theRecord.get("PARENT"));
String child = trim(theRecord.get("CHILD"));
if (isNotBlank(parent) && isNotBlank(child)) {
TermConcept parentConcept = myCode2Concept.get(parent);
ValidateUtil.isNotNullOrThrowUnprocessableEntity(parentConcept, "Parent code %s not found", parent);
TermConcept childConcept = myCode2Concept.get(child);
ValidateUtil.isNotNullOrThrowUnprocessableEntity(childConcept, "Child code %s not found", child);
parentConcept.addChild(childConcept, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
}
}
}

58
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/BaseLoaderTest.java Normal file
View File

@ -0,0 +1,58 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.runner.RunWith;
import org.mockito.ArgumentCaptor;
import org.mockito.Captor;
import org.mockito.Mock;
import org.mockito.junit.MockitoJUnitRunner;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@RunWith(MockitoJUnitRunner.class)
abstract class BaseLoaderTest {
@Mock
protected RequestDetails mySrd;
@Captor
protected ArgumentCaptor<List<ConceptMap>> myConceptMapCaptor;
@Captor
protected ArgumentCaptor<TermCodeSystemVersion> myCsvCaptor;
@Captor
protected ArgumentCaptor<List<ValueSet>> myValueSetsCaptor;
@Captor
protected ArgumentCaptor<CodeSystem> mySystemCaptor;
Map<String, ConceptMap> extractConceptMaps() {
Map<String, ConceptMap> conceptMaps = new HashMap<>();
for (ConceptMap next : myConceptMapCaptor.getAllValues().get(0)) {
conceptMaps.put(next.getId(), next);
}
return conceptMaps;
}
Map<String, TermConcept> extractConcepts() {
Map<String, TermConcept> concepts = new HashMap<>();
for (TermConcept next : myCsvCaptor.getValue().getConcepts()) {
concepts.put(next.getCode(), next);
}
return concepts;
}
Map<String, ValueSet> extractValueSets() {
Map<String, ValueSet> valueSets = new HashMap<>();
for (ValueSet next : myValueSetsCaptor.getValue()) {
valueSets.put(next.getId(), next);
}
return valueSets;
}
}

115
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcCustomTest.java Normal file
View File

@ -0,0 +1,115 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.r4.model.CodeSystem;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.Mock;
import org.mockito.junit.MockitoJUnitRunner;
import java.util.Map;
import static org.junit.Assert.assertEquals;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
@RunWith(MockitoJUnitRunner.class)
public class TerminologyLoaderSvcCustomTest extends BaseLoaderTest {
private TerminologyLoaderSvcImpl mySvc;
@Mock
private IHapiTerminologySvc myTermSvc;
private ZipCollectionBuilder myFiles;
@Before
public void before() {
mySvc = new TerminologyLoaderSvcImpl();
mySvc.setTermSvcForUnitTests(myTermSvc);
myFiles = new ZipCollectionBuilder();
}
@Test
public void testLoadComplete() throws Exception {
myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_CODESYSTEM_JSON);
myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_CONCEPTS_FILE);
myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_HIERARCHY_FILE);
// Actually do the load
mySvc.loadCustom("http://example.com/labCodes", myFiles.getFiles(), mySrd);
verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
Map<String, TermConcept> concepts = extractConcepts();
// Verify codesystem
assertEquals("http://example.com/labCodes", mySystemCaptor.getValue().getUrl());
assertEquals(CodeSystem.CodeSystemContentMode.NOTPRESENT, mySystemCaptor.getValue().getContent());
assertEquals("Example Lab Codes", mySystemCaptor.getValue().getName());
// Root code
TermConcept code;
assertEquals(2, concepts.size());
code = concepts.get("CHEM");
assertEquals("CHEM", code.getCode());
assertEquals("Chemistry", code.getDisplay());
assertEquals(2, code.getChildren().size());
assertEquals("HB", code.getChildren().get(0).getChild().getCode());
assertEquals("Hemoglobin", code.getChildren().get(0).getChild().getDisplay());
assertEquals("NEUT", code.getChildren().get(1).getChild().getCode());
assertEquals("Neutrophils", code.getChildren().get(1).getChild().getDisplay());
}
@Test
public void testLoadWithNoCodeSystem() throws Exception {
myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_CONCEPTS_FILE);
// Actually do the load
mySvc.loadCustom("http://example.com/labCodes", myFiles.getFiles(), mySrd);
verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
Map<String, TermConcept> concepts = extractConcepts();
// Verify codesystem
assertEquals("http://example.com/labCodes", mySystemCaptor.getValue().getUrl());
assertEquals(CodeSystem.CodeSystemContentMode.NOTPRESENT, mySystemCaptor.getValue().getContent());
}
/**
* No hierarchy file supplied
*/
@Test
public void testLoadCodesOnly() throws Exception {
myFiles.addFileZip("/custom_term/", TerminologyLoaderSvcImpl.CUSTOM_CONCEPTS_FILE);
// Actually do the load
mySvc.loadCustom("http://example.com/labCodes", myFiles.getFiles(), mySrd);
verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
Map<String, TermConcept> concepts = extractConcepts();
TermConcept code;
// Root code
assertEquals(5, concepts.size());
code = concepts.get("CHEM");
assertEquals("CHEM", code.getCode());
assertEquals("Chemistry", code.getDisplay());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

19
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImgthlaTest.java
View File

@ -1,6 +1,5 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil;
@ -8,9 +7,7 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.Mock;
import org.mockito.junit.MockitoJUnitRunner;
import java.io.IOException;
@ -18,19 +15,12 @@ import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
@RunWith(MockitoJUnitRunner.class)
public class TerminologyLoaderSvcImgthlaTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcImgthlaTest.class);
public class TerminologyLoaderSvcImgthlaTest extends BaseLoaderTest {
private TerminologyLoaderSvcImpl mySvc;
@Mock
private IHapiTerminologySvc myTermSvc;
@Mock
private IHapiTerminologySvcDstu3 myTermSvcDstu3;
@Mock
private RequestDetails details;
private ZipCollectionBuilder myFiles;
@ -38,7 +28,6 @@ public class TerminologyLoaderSvcImgthlaTest {
public void before() {
mySvc = new TerminologyLoaderSvcImpl();
mySvc.setTermSvcForUnitTests(myTermSvc);
mySvc.setTermSvcDstu3ForUnitTest(myTermSvcDstu3);
myFiles = new ZipCollectionBuilder();
}
@ -49,7 +38,7 @@ public class TerminologyLoaderSvcImgthlaTest {
// Actually do the load
try {
mySvc.loadImgthla(myFiles.getFiles(), details);
mySvc.loadImgthla(myFiles.getFiles(), mySrd);
fail("Expected \"not yet fully implemented\" InternalErrorException");
} catch(InternalErrorException e) {
// for now, expect "not yet fully implemented" exception
@ -65,7 +54,7 @@ public class TerminologyLoaderSvcImgthlaTest {
addImgthlaMandatoryFilesToZip(myFiles);
// Actually do the load
mySvc.loadImgthla(myFiles.getFiles(), details);
mySvc.loadImgthla(myFiles.getFiles(), mySrd);
// TODO: verify the code system was loaded correctly (similarly to TerminologyLoaderSvcLoincTest.testLoadLoincMandatoryFilesOnly)
}
@ -76,7 +65,7 @@ public class TerminologyLoaderSvcImgthlaTest {
// Actually do the load
try {
mySvc.loadImgthla(myFiles.getFiles(), details);
mySvc.loadImgthla(myFiles.getFiles(), mySrd);
fail("Expected UnprocessableEntityException");
} catch (UnprocessableEntityException e) {
assertThat(e.getMessage(), containsString("Could not find the following mandatory files in input:"));

60
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
View File

@ -1,7 +1,6 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.loinc.*;
import ca.uhn.fhir.rest.api.server.RequestDetails;
@ -15,46 +14,28 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.ArgumentCaptor;
import org.mockito.Captor;
import org.mockito.Mock;
import org.mockito.junit.MockitoJUnitRunner;
import java.io.IOException;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
@RunWith(MockitoJUnitRunner.class)
public class TerminologyLoaderSvcLoincTest {
public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcLoincTest.class);
private TerminologyLoaderSvcImpl mySvc;
@Mock
private IHapiTerminologySvc myTermSvc;
@Mock
private IHapiTerminologySvcDstu3 myTermSvcDstu3;
@Captor
private ArgumentCaptor<TermCodeSystemVersion> myCsvCaptor;
@Captor
private ArgumentCaptor<CodeSystem> mySystemCaptor;
@Mock
private RequestDetails details;
@Captor
private ArgumentCaptor<List<ValueSet>> myValueSetsCaptor;
@Captor
private ArgumentCaptor<List<ConceptMap>> myConceptMapCaptor;
private ZipCollectionBuilder myFiles;
@ -62,43 +43,18 @@ public class TerminologyLoaderSvcLoincTest {
public void before() {
mySvc = new TerminologyLoaderSvcImpl();
mySvc.setTermSvcForUnitTests(myTermSvc);
mySvc.setTermSvcDstu3ForUnitTest(myTermSvcDstu3);
myFiles = new ZipCollectionBuilder();
}
private Map<String, ConceptMap> extractConceptMaps() {
Map<String, ConceptMap> conceptMaps = new HashMap<>();
for (ConceptMap next : myConceptMapCaptor.getAllValues().get(0)) {
conceptMaps.put(next.getId(), next);
}
return conceptMaps;
}
private Map<String, TermConcept> extractConcepts() {
Map<String, TermConcept> concepts = new HashMap<>();
for (TermConcept next : myCsvCaptor.getValue().getConcepts()) {
concepts.put(next.getCode(), next);
}
return concepts;
}
private Map<String, ValueSet> extractValueSets() {
Map<String, ValueSet> valueSets = new HashMap<>();
for (ValueSet next : myValueSetsCaptor.getValue()) {
valueSets.put(next.getId(), next);
}
return valueSets;
}
@Test
public void testLoadLoinc() throws Exception {
addLoincMandatoryFilesToZip(myFiles);
// Actually do the load
mySvc.loadLoinc(myFiles.getFiles(), details);
mySvc.loadLoinc(myFiles.getFiles(), mySrd);
verify(myTermSvcDstu3, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
Map<String, TermConcept> concepts = extractConcepts();
Map<String, ValueSet> valueSets = extractValueSets();
Map<String, ConceptMap> conceptMaps = extractConceptMaps();
@ -347,9 +303,9 @@ public class TerminologyLoaderSvcLoincTest {
addLoincMandatoryFilesToZip(myFiles);
// Actually do the load
mySvc.loadLoinc(myFiles.getFiles(), details);
mySvc.loadLoinc(myFiles.getFiles(), mySrd);
verify(myTermSvcDstu3, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
Map<String, TermConcept> concepts = extractConcepts();
Map<String, ValueSet> valueSets = extractValueSets();
Map<String, ConceptMap> conceptMaps = extractConceptMaps();
@ -371,7 +327,7 @@ public class TerminologyLoaderSvcLoincTest {
// Actually do the load
try {
mySvc.loadLoinc(myFiles.getFiles(), details);
mySvc.loadLoinc(myFiles.getFiles(), mySrd);
fail();
} catch (UnprocessableEntityException e) {
assertThat(e.getMessage(), containsString("Could not find the following mandatory files in input:"));

39
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcSnomedCtTest.java
View File

@ -4,39 +4,36 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.ArgumentCaptor;
import org.mockito.Captor;
import org.mockito.Mock;
import org.mockito.runners.MockitoJUnitRunner;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.FileInputStream;
import java.io.InputStream;
import java.util.*;
import java.util.ArrayList;
import java.util.TreeSet;
import java.util.zip.ZipOutputStream;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.mockito.Matchers.any;
import static org.mockito.Matchers.anyListOf;
import static org.mockito.Mockito.mock;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.Matchers.hasItem;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import static org.mockito.ArgumentMatchers.*;
import static org.mockito.Mockito.verify;
@RunWith(MockitoJUnitRunner.class)
public class TerminologyLoaderSvcSnomedCtTest {
public class TerminologyLoaderSvcSnomedCtTest extends BaseLoaderTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcSnomedCtTest.class);
private TerminologyLoaderSvcImpl mySvc;
@ -44,15 +41,12 @@ public class TerminologyLoaderSvcSnomedCtTest {
private IHapiTerminologySvc myTermSvc;
@Captor
private ArgumentCaptor<TermCodeSystemVersion> myCsvCaptor;
@Mock
private IHapiTerminologySvcDstu3 myTermSvcDstu3;
private ZipCollectionBuilder myFiles;
@Before
public void before() {
mySvc = new TerminologyLoaderSvcImpl();
mySvc.setTermSvcForUnitTests(myTermSvc);
mySvc.setTermSvcDstu3ForUnitTest(myTermSvcDstu3);
myFiles = new ZipCollectionBuilder();
}
@ -84,17 +78,16 @@ public class TerminologyLoaderSvcSnomedCtTest {
myFiles.addFileZip("/sct/", "sct2_StatedRelationship_Full_INT_20160131.txt");
myFiles.addFileZip("/sct/", "sct2_TextDefinition_Full-en_INT_20160131.txt");
RequestDetails details = mock(RequestDetails.class);
mySvc.loadSnomedCt(myFiles.getFiles(), details);
mySvc.loadSnomedCt(myFiles.getFiles(), mySrd);
verify(myTermSvcDstu3).storeNewCodeSystemVersion(any(CodeSystem.class), myCsvCaptor.capture(), any(RequestDetails.class), anyListOf(ValueSet.class), anyListOf(ConceptMap.class));
verify(myTermSvc).storeNewCodeSystemVersion(any(CodeSystem.class), myCsvCaptor.capture(), any(RequestDetails.class), anyList(), anyListOf(ConceptMap.class));
TermCodeSystemVersion csv = myCsvCaptor.getValue();
TreeSet<String> allCodes = toCodes(csv, true);
ourLog.info(allCodes.toString());
assertThat(allCodes, containsInRelativeOrder("116680003"));
assertThat(allCodes, not(containsInRelativeOrder("207527008")));
assertThat(allCodes, hasItem("116680003"));
assertThat(allCodes, not(hasItem("207527008")));
allCodes = toCodes(csv, false);
ourLog.info(allCodes.toString());
@ -110,8 +103,7 @@ public class TerminologyLoaderSvcSnomedCtTest {
public void testLoadSnomedCtAgainstRealFile() throws Exception {
byte[] bytes = IOUtils.toByteArray(new FileInputStream("/Users/james/Downloads/SnomedCT_Release_INT_20160131_Full.zip"));
RequestDetails details = mock(RequestDetails.class);
mySvc.loadSnomedCt(list(bytes), details);
mySvc.loadSnomedCt(list(bytes), mySrd);
}
@Test
@ -123,9 +115,8 @@ public class TerminologyLoaderSvcSnomedCtTest {
ourLog.info("ZIP file has {} bytes", bos.toByteArray().length);
RequestDetails details = mock(RequestDetails.class);
try {
mySvc.loadSnomedCt(list(bos.toByteArray()), details);
mySvc.loadSnomedCt(list(bos.toByteArray()), mySrd);
fail();
} catch (UnprocessableEntityException e) {
assertThat(e.getMessage(), containsString("Could not find the following mandatory files in input: "));

10
hapi-fhir-jpaserver-base/src/test/resources/custom_term/codesystem.json Normal file
View File

@ -0,0 +1,10 @@
{
"resourceType": "CodeSystem",
"url": "http://example.com/labCodes",
"name": "Example Lab Codes",
"description": "A set of lab codes",
"status": "active",
"publisher": "Example Organization Corporation Worldwide",
"date": "2019-07-30",
"content": "not-present"
}

8
hapi-fhir-jpaserver-base/src/test/resources/custom_term/concepts.csv Normal file
View File

@ -0,0 +1,8 @@
CODE,DISPLAY
CHEM,Chemistry
HB,Hemoglobin
NEUT,Neutrophils
MICRO,Microbiology
C&S,Culture and Sensitivity
1 CODE DISPLAY
2 CHEM Chemistry
3 HB Hemoglobin
4 NEUT Neutrophils
5 MICRO Microbiology
6 C&S Culture and Sensitivity

6
hapi-fhir-jpaserver-base/src/test/resources/custom_term/hierarchy.csv Normal file
View File

@ -0,0 +1,6 @@
PARENT,CHILD
CHEM,HB
CHEM,NEUT
MICRO,C&S
1 PARENT CHILD
2 CHEM HB
3 CHEM NEUT
4 MICRO C&S

4
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/any/AnyListResource.java
View File

@ -94,6 +94,10 @@ public class AnyListResource {
return (org.hl7.fhir.r4.model.ListResource) get();
}
public FhirVersionEnum getFhirVersion() {
return myFhirVersion;
}
public void addCode(String theSystem, String theCode) {
switch (myFhirVersion) {
case DSTU3:

6
hapi-fhir-structures-r4/pom.xml
View File

@ -186,6 +186,12 @@
</dependency>
<!-- UNIT TEST DEPENDENCIES -->
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>apache-jena-libs</artifactId>
<type>pom</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>net.sf.json-lib</groupId>
<artifactId>json-lib</artifactId>

281
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/RDFParserR4Test.java Normal file
View File

@ -0,0 +1,281 @@
package ca.uhn.fhir.parser;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.util.TestUtil;
import com.google.common.collect.Sets;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.r4.model.*;
import org.junit.AfterClass;
import org.junit.Ignore;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.*;
@Ignore
public class RDFParserR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(RDFParserR4Test.class);
private static FhirContext ourCtx = FhirContext.forR4();
/*
private Bundle createBundleWithPatient() {
Bundle b = new Bundle();
b.setId("BUNDLEID");
b.getMeta().addProfile("http://FOO");
Patient p = new Patient();
p.setId("PATIENTID");
p.getMeta().addProfile("http://BAR");
p.addName().addGiven("GIVEN");
b.addEntry().setResource(p);
return b;
}
*/
@Test
public void testDontStripVersions() {
FhirContext ctx = FhirContext.forR4();
ctx.getParserOptions().setDontStripVersionsFromReferencesAtPaths("QuestionnaireResponse.questionnaire");
QuestionnaireResponse qr = new QuestionnaireResponse();
qr.getQuestionnaireElement().setValueAsString("Questionnaire/123/_history/456");
String output = ctx.newRDFParser().setPrettyPrint(true).encodeResourceToString(qr);
ourLog.info(output);
assertThat(output, containsString("\"Questionnaire/123/_history/456\""));
}
@Test
public void testDuplicateContainedResourcesNotOutputtedTwice() {
MedicationDispense md = new MedicationDispense();
MedicationRequest mr = new MedicationRequest();
md.addAuthorizingPrescription().setResource(mr);
Medication med = new Medication();
md.setMedication(new Reference(med));
mr.setMedication(new Reference(med));
String encoded = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(md);
ourLog.info(encoded);
int idx = encoded.indexOf("\"Medication\"");
assertNotEquals(-1, idx);
idx = encoded.indexOf("\"Medication\"", idx + 1);
assertEquals(-1, idx);
}
/**
* See #814
*/
@Test
public void testDuplicateContainedResourcesNotOutputtedTwiceWithManualIds() {
MedicationDispense md = new MedicationDispense();
MedicationRequest mr = new MedicationRequest();
mr.setId("#MR");
md.addAuthorizingPrescription().setResource(mr);
Medication med = new Medication();
med.setId("#MED");
md.setMedication(new Reference(med));
mr.setMedication(new Reference(med));
String encoded = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(md);
ourLog.info(encoded);
int idx = encoded.indexOf("\"Medication\"");
assertNotEquals(-1, idx);
idx = encoded.indexOf("\"Medication\"", idx + 1);
assertEquals(-1, idx);
}
/*
* See #814
*/
@Test
public void testDuplicateContainedResourcesNotOutputtedTwiceWithManualIdsAndManualAddition() {
MedicationDispense md = new MedicationDispense();
MedicationRequest mr = new MedicationRequest();
mr.setId("#MR");
md.addAuthorizingPrescription().setResource(mr);
Medication med = new Medication();
med.setId("#MED");
Reference medRef = new Reference();
medRef.setReference("#MED");
md.setMedication(medRef);
mr.setMedication(medRef);
md.getContained().add(mr);
md.getContained().add(med);
String encoded = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(md);
ourLog.info(encoded);
int idx = encoded.indexOf("\"Medication\"");
assertNotEquals(-1, idx);
idx = encoded.indexOf("\"Medication\"", idx + 1);
assertEquals(-1, idx);
}
@Test
public void testEncodeAndParseUnicodeCharacterInNarrative() {
Patient p = new Patient();
p.getText().getDiv().setValueAsString("<div>Copy © 1999</div>");
String encoded = ourCtx.newRDFParser().encodeResourceToString(p);
ourLog.info(encoded);
p = (Patient) ourCtx.newRDFParser().parseResource(encoded);
assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">Copy &copy; 1999</div>", p.getText().getDivAsString());
}
@Test
public void testEncodeResourceWithMixedManualAndAutomaticContainedResourcesLocalFirst() {
Observation obs = new Observation();
Patient pt = new Patient();
pt.setId("#1");
pt.addName().setFamily("FAM");
obs.getSubject().setReference("#1");
obs.getContained().add(pt);
Encounter enc = new Encounter();
enc.setStatus(Encounter.EncounterStatus.ARRIVED);
obs.getEncounter().setResource(enc);
String encoded = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(obs);
ourLog.info(encoded);
obs = ourCtx.newRDFParser().parseResource(Observation.class, encoded);
assertEquals("#1", obs.getContained().get(0).getId());
assertEquals("#2", obs.getContained().get(1).getId());
pt = (Patient) obs.getSubject().getResource();
assertEquals("FAM", pt.getNameFirstRep().getFamily());
enc = (Encounter) obs.getEncounter().getResource();
assertEquals(Encounter.EncounterStatus.ARRIVED, enc.getStatus());
}
@Test
public void testEncodeResourceWithMixedManualAndAutomaticContainedResourcesLocalLast() {
Observation obs = new Observation();
Patient pt = new Patient();
pt.addName().setFamily("FAM");
obs.getSubject().setResource(pt);
Encounter enc = new Encounter();
enc.setId("#1");
enc.setStatus(Encounter.EncounterStatus.ARRIVED);
obs.getEncounter().setReference("#1");
obs.getContained().add(enc);
String encoded = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(obs);
ourLog.info(encoded);
obs = ourCtx.newRDFParser().parseResource(Observation.class, encoded);
assertEquals("#1", obs.getContained().get(0).getId());
assertEquals("#2", obs.getContained().get(1).getId());
pt = (Patient) obs.getSubject().getResource();
assertEquals("FAM", pt.getNameFirstRep().getFamily());
enc = (Encounter) obs.getEncounter().getResource();
assertEquals(Encounter.EncounterStatus.ARRIVED, enc.getStatus());
}
@Test
public void testEncodeResourceWithMixedManualAndAutomaticContainedResourcesLocalLast2() {
MedicationRequest mr = new MedicationRequest();
Practitioner pract = new Practitioner().setActive(true);
mr.getRequester().setResource(pract);
String encoded = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(mr);
ourLog.info(encoded);
mr = ourCtx.newRDFParser().parseResource(MedicationRequest.class, encoded);
mr.setMedication(new Reference(new Medication().setStatus(Medication.MedicationStatus.ACTIVE)));
encoded = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(mr);
ourLog.info(encoded);
mr = ourCtx.newRDFParser().parseResource(MedicationRequest.class, encoded);
assertEquals("#2", mr.getContained().get(0).getId());
assertEquals("#1", mr.getContained().get(1).getId());
}
/**
* Test that long JSON strings don't get broken up
*/
@Test
public void testNoBreakInLongString() {
String longString = StringUtils.leftPad("", 100000, 'A');
Patient p = new Patient();
p.addName().setFamily(longString);
String encoded = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(p);
assertThat(encoded, containsString(longString));
}
@Test
public void testParseAndEncodeExtensionWithValueWithExtension() {
String input = "{\n" +
" \"resourceType\": \"Patient\",\n" +
" \"extension\": [\n" +
" {\n" +
" \"url\": \"https://purl.org/elab/fhir/network/StructureDefinition/1/BirthWeight\",\n" +
" \"_valueDecimal\": {\n" +
" \"extension\": [\n" +
" {\n" +
" \"url\": \"http://www.hl7.org/fhir/extension-data-absent-reason.html\",\n" +
" \"valueCoding\": {\n" +
" \"system\": \"http://hl7.org/fhir/ValueSet/birthweight\",\n" +
" \"code\": \"Underweight\",\n" +
" \"userSelected\": false\n" +
" }\n" +
" }\n" +
" ]\n" +
" }\n" +
" }\n" +
" ],\n" +
" \"identifier\": [\n" +
" {\n" +
" \"system\": \"https://purl.org/elab/fhir/network/StructureDefinition/1/EuroPrevallStudySubjects\",\n" +
" \"value\": \"1\"\n" +
" }\n" +
" ],\n" +
" \"gender\": \"female\"\n" +
"}";
IParser jsonParser = ourCtx.newRDFParser();
IParser xmlParser = ourCtx.newXmlParser();
jsonParser.setDontEncodeElements(Sets.newHashSet("id", "meta"));
xmlParser.setDontEncodeElements(Sets.newHashSet("id", "meta"));
Patient parsed = jsonParser.parseResource(Patient.class, input);
ourLog.info(jsonParser.setPrettyPrint(true).encodeResourceToString(parsed));
assertThat(xmlParser.encodeResourceToString(parsed), containsString("Underweight"));
assertThat(jsonParser.encodeResourceToString(parsed), containsString("Underweight"));
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

61
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/RDFParserTest.java Normal file
View File

@ -0,0 +1,61 @@
package ca.uhn.fhir.parser;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.json.*;
import org.junit.Ignore;
import org.junit.Test;
import org.hl7.fhir.r4.model.*;
import java.io.StringReader;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
@Ignore
public class RDFParserTest {
private static FhirContext ourCtx = FhirContext.forR4();
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RDFParserTest.class);
private static final String TEST_STRUCTURELOADING_DATA =
"{" +
" \"resourceType\":\"Organization\"," +
" \"id\":\"11111\"," +
" \"meta\":{" +
" \"lastUpdated\":\"3900-09-20T10:10:10.000-07:00\"" +
" }," +
" \"identifier\":[" +
" {" +
" \"value\":\"15250\"" +
" }" +
" ]," +
" \"type\":{" +
" \"coding\":[" +
" {" +
" \"system\":\"http://test\"," +
" \"code\":\"ins\"," +
" \"display\":\"General Ledger System\"," +
" \"userSelected\":false" +
" }" +
" ]" +
" }," +
" \"name\":\"Acme Investments\"" +
"}";
@Test
public void testDontStripVersions() {
FhirContext ctx = FhirContext.forR4();
ctx.getParserOptions().setDontStripVersionsFromReferencesAtPaths("QuestionnaireResponse.questionnaire");
QuestionnaireResponse qr = new QuestionnaireResponse();
qr.getQuestionnaireElement().setValueAsString("Questionnaire/123/_history/456");
String output = ctx.newRDFParser().setPrettyPrint(true).encodeResourceToString(qr);
ourLog.info(output);
assertThat(output, containsString("\"Questionnaire/123/_history/456\""));
}
}

32
hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/CachingValidationSupport.java
View File

@ -3,15 +3,17 @@ package org.hl7.fhir.r4.hapi.validation;
import ca.uhn.fhir.context.FhirContext;
import com.github.benmanes.caffeine.cache.Cache;
import com.github.benmanes.caffeine.cache.Caffeine;
import org.checkerframework.checker.nullness.qual.Nullable;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.terminologies.ValueSetExpander;
import java.util.List;
import java.util.concurrent.TimeUnit;
import java.util.function.Function;
@SuppressWarnings("unchecked")
public class CachingValidationSupport implements IValidationSupport {
@ -21,7 +23,11 @@ public class CachingValidationSupport implements IValidationSupport {
public CachingValidationSupport(IValidationSupport theWrap) {
myWrap = theWrap;
myCache = Caffeine.newBuilder().expireAfterWrite(60, TimeUnit.SECONDS).build();
myCache = Caffeine
.newBuilder()
.expireAfterWrite(60, TimeUnit.SECONDS)
.maximumSize(5000)
.build();
}
@Override
@ -31,14 +37,14 @@ public class CachingValidationSupport implements IValidationSupport {
@Override
public List<IBaseResource> fetchAllConformanceResources(FhirContext theContext) {
return (List<IBaseResource>) myCache.get("fetchAllConformanceResources",
t -> myWrap.fetchAllConformanceResources(theContext));
String key = "fetchAllConformanceResources";
return loadFromCache(key, t -> myWrap.fetchAllConformanceResources(theContext));
}
@Override
public List<StructureDefinition> fetchAllStructureDefinitions(FhirContext theContext) {
return (List<StructureDefinition>) myCache.get("fetchAllStructureDefinitions",
t -> myWrap.fetchAllStructureDefinitions(theContext));
String key = "fetchAllStructureDefinitions";
return loadFromCache(key, t -> myWrap.fetchAllStructureDefinitions(theContext));
}
@Override
@ -63,7 +69,8 @@ public class CachingValidationSupport implements IValidationSupport {
@Override
public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
return myWrap.isCodeSystemSupported(theContext, theSystem);
String key = "isCodeSystemSupported " + theSystem;
return loadFromCache(key, t -> myWrap.isCodeSystemSupported(theContext, theSystem));
}
@Override
@ -73,11 +80,18 @@ public class CachingValidationSupport implements IValidationSupport {
@Override
public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
return myWrap.validateCode(theContext, theCodeSystem, theCode, theDisplay);
String key = "validateCode " + theCodeSystem + " " + theCode;
return loadFromCache(key, t -> myWrap.validateCode(theContext, theCodeSystem, theCode, theDisplay));
}
@Override
public LookupCodeResult lookupCode(FhirContext theContext, String theSystem, String theCode) {
return myWrap.lookupCode(theContext, theSystem, theCode);
String key = "lookupCode " + theSystem + " " + theCode;
return loadFromCache(key, t -> myWrap.lookupCode(theContext, theSystem, theCode));
}
@Nullable
private <T> T loadFromCache(String theKey, Function<String, T> theLoader) {
return (T) myCache.get(theKey, theLoader);
}
}

15
pom.xml
View File

@ -530,6 +530,15 @@
<id>gteichrow</id>
<name>Gary Teichrow</name>
</developer>
<developer>
<id>sethrylan</id>
<name>Seth Rylan Gainey</name>
<url>http://sethrylan.org/</url>
</developer>
<developer>
<id>uurl</id>
<name>Raul Estrada</name>
</developer>
</developers>
<licenses>
@ -971,6 +980,12 @@
<artifactId>httpcore</artifactId>
<version>${httpcore_version}</version>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>apache-jena-libs</artifactId>
<version>3.12.0</version>
<type>pom</type>
</dependency>
<dependency>
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-highlighter</artifactId>

15
src/changes/changes.xml
View File

@ -79,6 +79,11 @@
</li>The rule list is now cached on a per-request basis, which should improve performance</ul>
]]>
</action>
<action type="add" issue="1321">
Support has been added for RDF encoding and parsing in the
<![CDATA[<a href="https://www.hl7.org/fhir/rdf.html#instance">Turtle</a>]]>
format. Thanks to Raul Estrada for the pull request!
</action>
<action type="add">
The $expunge global everything operation has been refactored to do deletes
in small batches. This change will likely reduce performance, but does allow
@ -354,6 +359,16 @@
type for an operation declared on a plain provider without needing to use
a specific version of the FHIR structures.
</action>
<action type="add">
The $upload-external-code-system operation and the corresponding HAPI FHIR CLI command
can now be used to upload custom vocabulary that has been converted into a standard file format
defined by HAPI FHIR. This is useful for uploading large organizational code systems.
</action>
<action type="fix" issue="1404">
In the JAX-RS server, the resource type history and instance vread
operations had ambiguous paths that could lead to the wrong method
being called. Thanks to Seth Rylan Gainey for the pull request!
</action>
</release>
<release version="3.8.0" date="2019-05-30" description="Hippo">
<action type="fix">