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hapi-fhir
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Add support for Binary X-Security-Context header in server

This commit is contained in:
James Agnew 2017-11-02 11:38:43 -04:00
parent 256d541dda
commit 75bfb6af1b
16 changed files with 1058 additions and 843 deletions
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1
hapi-deployable-pom/pom.xml
View File

@ -118,6 +118,7 @@
</ignoredDependencies>
<ignoredResources>
<ignoredResource>changelog.txt</ignoredResource>
<ignoredResource>javac.bat</ignoredResource>
</ignoredResources>
</configuration>
</plugin>

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirVersionEnum.java
View File

@ -78,6 +78,10 @@ public enum FhirVersionEnum {
return myVersionImplementation;
}
public boolean isEqualOrNewerThan(FhirVersionEnum theVersion) {
return ordinal() >= theVersion.ordinal();
}
public boolean isEquivalentTo(FhirVersionEnum theVersion) {
if (this.equals(theVersion)) {
return true;

529
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
View File

@ -19,19 +19,6 @@ package ca.uhn.fhir.parser;
* limitations under the License.
* #L%
*/
import static org.apache.commons.lang3.StringUtils.*;
import java.io.*;
import java.math.BigDecimal;
import java.util.*;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.text.WordUtils;
import org.hl7.fhir.instance.model.api.*;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum;
@ -46,10 +33,27 @@ import ca.uhn.fhir.parser.json.*;
import ca.uhn.fhir.parser.json.JsonLikeValue.ScalarType;
import ca.uhn.fhir.parser.json.JsonLikeValue.ValueType;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.util.BinaryUtil;
import ca.uhn.fhir.util.ElementUtil;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.text.WordUtils;
import org.hl7.fhir.instance.model.api.*;
import java.io.IOException;
import java.io.Reader;
import java.io.Writer;
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Set;
import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.ID_DATATYPE;
import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.PRIMITIVE_DATATYPE;
import java.lang.reflect.Method;
import static org.apache.commons.lang3.StringUtils.*;
/**
* This class is the FHIR JSON parser/encoder. Users should not interact with this class directly, but should use
@ -89,7 +93,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
private boolean addToHeldExtensions(int valueIdx, List<? extends IBaseExtension<?, ?>> ext, ArrayList<ArrayList<HeldExtension>> list, boolean theIsModifier, CompositeChildElement theChildElem,
CompositeChildElement theParent) {
CompositeChildElement theParent) {
if (ext.size() > 0) {
list.ensureCapacity(valueIdx);
while (list.size() <= valueIdx) {
@ -140,12 +144,6 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
return retVal;
}
@Override
protected void doEncodeResourceToWriter(IBaseResource theResource, Writer theWriter) throws IOException {
JsonLikeWriter eventWriter = createJsonWriter(theWriter);
doEncodeResourceToJsonLikeWriter(theResource, eventWriter);
}
public void doEncodeResourceToJsonLikeWriter(IBaseResource theResource, JsonLikeWriter theEventWriter) throws IOException {
if (myPrettyPrint) {
theEventWriter.setPrettyPrint(myPrettyPrint);
@ -157,6 +155,12 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
theEventWriter.flush();
}
@Override
protected void doEncodeResourceToWriter(IBaseResource theResource, Writer theWriter) throws IOException {
JsonLikeWriter eventWriter = createJsonWriter(theWriter);
doEncodeResourceToJsonLikeWriter(theResource, eventWriter);
}
@Override
public <T extends IBaseResource> T doParseResource(Class<T> theResourceType, Reader theReader) {
JsonLikeStructure jsonStructure = new GsonStructure();
@ -192,136 +196,136 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
private void encodeChildElementToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, IBase theNextValue,
BaseRuntimeElementDefinition<?> theChildDef, String theChildName, boolean theContainedResource, boolean theSubResource, CompositeChildElement theChildElem,
boolean theForceEmpty) throws IOException {
BaseRuntimeElementDefinition<?> theChildDef, String theChildName, boolean theContainedResource, boolean theSubResource, CompositeChildElement theChildElem,
boolean theForceEmpty) throws IOException {
switch (theChildDef.getChildType()) {
case ID_DATATYPE: {
IIdType value = (IIdType) theNextValue;
String encodedValue = "id".equals(theChildName) ? value.getIdPart() : value.getValue();
if (isBlank(encodedValue)) {
break;
}
if (theChildName != null) {
write(theEventWriter, theChildName, encodedValue);
} else {
theEventWriter.write(encodedValue);
}
break;
}
case PRIMITIVE_DATATYPE: {
final IPrimitiveType<?> value = (IPrimitiveType<?>) theNextValue;
if (isBlank(value.getValueAsString())) {
if (theForceEmpty) {
theEventWriter.writeNull();
case ID_DATATYPE: {
IIdType value = (IIdType) theNextValue;
String encodedValue = "id".equals(theChildName) ? value.getIdPart() : value.getValue();
if (isBlank(encodedValue)) {
break;
}
if (theChildName != null) {
write(theEventWriter, theChildName, encodedValue);
} else {
theEventWriter.write(encodedValue);
}
break;
}
if (value instanceof IBaseIntegerDatatype) {
if (theChildName != null) {
write(theEventWriter, theChildName, ((IBaseIntegerDatatype) value).getValue());
} else {
theEventWriter.write(((IBaseIntegerDatatype) value).getValue());
}
} else if (value instanceof IBaseDecimalDatatype) {
BigDecimal decimalValue = ((IBaseDecimalDatatype) value).getValue();
decimalValue = new BigDecimal(decimalValue.toString()) {
private static final long serialVersionUID = 1L;
@Override
public String toString() {
return value.getValueAsString();
case PRIMITIVE_DATATYPE: {
final IPrimitiveType<?> value = (IPrimitiveType<?>) theNextValue;
if (isBlank(value.getValueAsString())) {
if (theForceEmpty) {
theEventWriter.writeNull();
}
};
if (theChildName != null) {
write(theEventWriter, theChildName, decimalValue);
} else {
theEventWriter.write(decimalValue);
break;
}
} else if (value instanceof IBaseBooleanDatatype) {
if (theChildName != null) {
write(theEventWriter, theChildName, ((IBaseBooleanDatatype) value).getValue());
if (value instanceof IBaseIntegerDatatype) {
if (theChildName != null) {
write(theEventWriter, theChildName, ((IBaseIntegerDatatype) value).getValue());
} else {
theEventWriter.write(((IBaseIntegerDatatype) value).getValue());
}
} else if (value instanceof IBaseDecimalDatatype) {
BigDecimal decimalValue = ((IBaseDecimalDatatype) value).getValue();
decimalValue = new BigDecimal(decimalValue.toString()) {
private static final long serialVersionUID = 1L;
@Override
public String toString() {
return value.getValueAsString();
}
};
if (theChildName != null) {
write(theEventWriter, theChildName, decimalValue);
} else {
theEventWriter.write(decimalValue);
}
} else if (value instanceof IBaseBooleanDatatype) {
if (theChildName != null) {
write(theEventWriter, theChildName, ((IBaseBooleanDatatype) value).getValue());
} else {
Boolean booleanValue = ((IBaseBooleanDatatype) value).getValue();
if (booleanValue != null) {
theEventWriter.write(booleanValue.booleanValue());
}
}
} else {
Boolean booleanValue = ((IBaseBooleanDatatype) value).getValue();
if (booleanValue != null) {
theEventWriter.write(booleanValue.booleanValue());
String valueStr = value.getValueAsString();
if (theChildName != null) {
write(theEventWriter, theChildName, valueStr);
} else {
theEventWriter.write(valueStr);
}
}
} else {
String valueStr = value.getValueAsString();
break;
}
case RESOURCE_BLOCK:
case COMPOSITE_DATATYPE: {
if (theChildName != null) {
write(theEventWriter, theChildName, valueStr);
theEventWriter.beginObject(theChildName);
} else {
theEventWriter.write(valueStr);
theEventWriter.beginObject();
}
encodeCompositeElementToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, theContainedResource, theSubResource, theChildElem);
theEventWriter.endObject();
break;
}
break;
}
case RESOURCE_BLOCK:
case COMPOSITE_DATATYPE: {
if (theChildName != null) {
theEventWriter.beginObject(theChildName);
} else {
theEventWriter.beginObject();
}
encodeCompositeElementToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, theContainedResource, theSubResource, theChildElem);
theEventWriter.endObject();
break;
}
case CONTAINED_RESOURCE_LIST:
case CONTAINED_RESOURCES: {
case CONTAINED_RESOURCE_LIST:
case CONTAINED_RESOURCES: {
/*
* Disabled per #103 ContainedDt value = (ContainedDt) theNextValue; for (IResource next :
* value.getContainedResources()) { if (getContainedResources().getResourceId(next) != null) { continue; }
* encodeResourceToJsonStreamWriter(theResDef, next, theWriter, null, true,
* fixContainedResourceId(next.getId().getValue())); }
*/
List<IBaseResource> containedResources = getContainedResources().getContainedResources();
if (containedResources.size() > 0) {
beginArray(theEventWriter, theChildName);
List<IBaseResource> containedResources = getContainedResources().getContainedResources();
if (containedResources.size() > 0) {
beginArray(theEventWriter, theChildName);
for (IBaseResource next : containedResources) {
IIdType resourceId = getContainedResources().getResourceId(next);
encodeResourceToJsonStreamWriter(theResDef, next, theEventWriter, null, true, false, fixContainedResourceId(resourceId.getValue()));
}
for (IBaseResource next : containedResources) {
IIdType resourceId = getContainedResources().getResourceId(next);
encodeResourceToJsonStreamWriter(theResDef, next, theEventWriter, null, true, false, fixContainedResourceId(resourceId.getValue()));
}
theEventWriter.endArray();
}
break;
}
case PRIMITIVE_XHTML_HL7ORG:
case PRIMITIVE_XHTML: {
if (!isSuppressNarratives()) {
IPrimitiveType<?> dt = (IPrimitiveType<?>) theNextValue;
if (theChildName != null) {
write(theEventWriter, theChildName, dt.getValueAsString());
} else {
theEventWriter.write(dt.getValueAsString());
}
} else {
if (theChildName != null) {
// do nothing
} else {
theEventWriter.writeNull();
theEventWriter.endArray();
}
break;
}
break;
}
case RESOURCE:
IBaseResource resource = (IBaseResource) theNextValue;
RuntimeResourceDefinition def = myContext.getResourceDefinition(resource);
encodeResourceToJsonStreamWriter(def, resource, theEventWriter, theChildName, false, true);
break;
case UNDECL_EXT:
default:
throw new IllegalStateException("Should not have this state here: " + theChildDef.getChildType().name());
case PRIMITIVE_XHTML_HL7ORG:
case PRIMITIVE_XHTML: {
if (!isSuppressNarratives()) {
IPrimitiveType<?> dt = (IPrimitiveType<?>) theNextValue;
if (theChildName != null) {
write(theEventWriter, theChildName, dt.getValueAsString());
} else {
theEventWriter.write(dt.getValueAsString());
}
} else {
if (theChildName != null) {
// do nothing
} else {
theEventWriter.writeNull();
}
}
break;
}
case RESOURCE:
IBaseResource resource = (IBaseResource) theNextValue;
RuntimeResourceDefinition def = myContext.getResourceDefinition(resource);
encodeResourceToJsonStreamWriter(def, resource, theEventWriter, theChildName, false, true);
break;
case UNDECL_EXT:
default:
throw new IllegalStateException("Should not have this state here: " + theChildDef.getChildType().name());
}
}
private void encodeCompositeElementChildrenToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, IBase theElement, JsonLikeWriter theEventWriter,
boolean theContainedResource, boolean theSubResource, CompositeChildElement theParent) throws IOException {
boolean theContainedResource, boolean theSubResource, CompositeChildElement theParent) throws IOException {
{
String elementId = getCompositeElementId(theElement);
@ -336,7 +340,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
BaseRuntimeChildDefinition nextChild = nextChildElem.getDef();
if (nextChildElem.getDef().getElementName().equals("extension") || nextChildElem.getDef().getElementName().equals("modifierExtension")
|| nextChild instanceof RuntimeChildDeclaredExtensionDefinition) {
|| nextChild instanceof RuntimeChildDeclaredExtensionDefinition) {
if (!haveWrittenExtensions) {
extractAndWriteExtensionsAsDirectChild(theElement, theEventWriter, myContext.getElementDefinition(theElement.getClass()), theResDef, theResource, nextChildElem, theParent);
haveWrittenExtensions = true;
@ -452,15 +456,15 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
if (nextChild.getMax() > 1 || nextChild.getMax() == Child.MAX_UNLIMITED) {
beginArray(theEventWriter, childName);
inArray = true;
encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource, theSubResource,nextChildElem, force);
encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource, theSubResource, nextChildElem, force);
} else if (nextChild instanceof RuntimeChildNarrativeDefinition && theContainedResource) {
// suppress narratives from contained resources
} else {
encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, childName, theContainedResource, theSubResource,nextChildElem, false);
encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, childName, theContainedResource, theSubResource, nextChildElem, false);
}
currentChildName = childName;
} else {
encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource,theSubResource, nextChildElem, force);
encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource, theSubResource, nextChildElem, force);
}
valueIdx++;
@ -542,7 +546,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
private void encodeCompositeElementToStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, IBase theNextValue, JsonLikeWriter theEventWriter, boolean theContainedResource, boolean theSubResource,
CompositeChildElement theParent) throws IOException, DataFormatException {
CompositeChildElement theParent) throws IOException, DataFormatException {
writeCommentsPreAndPost(theNextValue, theEventWriter);
encodeCompositeElementChildrenToStreamWriter(theResDef, theResource, theNextValue, theEventWriter, theContainedResource, theSubResource, theParent);
@ -555,14 +559,14 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
if (theResource.getStructureFhirVersionEnum() != myContext.getVersion().getVersion()) {
throw new IllegalArgumentException(
"This parser is for FHIR version " + myContext.getVersion().getVersion() + " - Can not encode a structure for version " + theResource.getStructureFhirVersionEnum());
"This parser is for FHIR version " + myContext.getVersion().getVersion() + " - Can not encode a structure for version " + theResource.getStructureFhirVersionEnum());
}
doEncodeResourceToJsonLikeWriter(theResource, theJsonLikeWriter);
}
private void encodeResourceToJsonStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, String theObjectNameOrNull,
boolean theContainedResource, boolean theSubResource) throws IOException {
boolean theContainedResource, boolean theSubResource) throws IOException {
IIdType resourceId = null;
// if (theResource instanceof IResource) {
// IResource res = (IResource) theResource;
@ -599,7 +603,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
private void encodeResourceToJsonStreamWriter(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter, String theObjectNameOrNull,
boolean theContainedResource, boolean theSubResource, IIdType theResourceId) throws IOException {
boolean theContainedResource, boolean theSubResource, IIdType theResourceId) throws IOException {
if (!theContainedResource) {
super.containResourcesForEncoding(theResource);
}
@ -613,28 +617,28 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
write(theEventWriter, "resourceType", resDef.getName());
if (theResourceId != null && theResourceId.hasIdPart()) {
write(theEventWriter, "id", theResourceId.getIdPart());
final List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
final List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
// Undeclared extensions
extractUndeclaredExtensions(theResourceId, extensions, modifierExtensions, null, null);
boolean haveExtension = false;
if (!extensions.isEmpty()) {
haveExtension = true;
}
if (theResourceId != null && theResourceId.hasIdPart()) {
write(theEventWriter, "id", theResourceId.getIdPart());
final List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
final List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
// Undeclared extensions
extractUndeclaredExtensions(theResourceId, extensions, modifierExtensions, null, null);
boolean haveExtension = false;
if (!extensions.isEmpty()) {
haveExtension = true;
}
if (theResourceId.hasFormatComment() || haveExtension) {
beginObject(theEventWriter, "_id");
if (theResourceId.hasFormatComment()) {
writeCommentsPreAndPost(theResourceId, theEventWriter);
}
if (haveExtension) {
writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions);
}
theEventWriter.endObject();
}
}
if (theResourceId.hasFormatComment() || haveExtension) {
beginObject(theEventWriter, "_id");
if (theResourceId.hasFormatComment()) {
writeCommentsPreAndPost(theResourceId, theEventWriter);
}
if (haveExtension) {
writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions);
}
theEventWriter.endObject();
}
}
if (theResource instanceof IResource) {
IResource resource = (IResource) theResource;
@ -696,34 +700,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
}
if (theResource instanceof IBaseBinary) {
IBaseBinary bin = (IBaseBinary) theResource;
String contentType = bin.getContentType();
if (isNotBlank(contentType)) {
write(theEventWriter, "contentType", contentType);
}
String contentAsBase64 = bin.getContentAsBase64();
if (isNotBlank(contentAsBase64)) {
write(theEventWriter, "content", contentAsBase64);
}
try {
Method getSC = bin.getClass().getMethod("getSecurityContext");
Object securityContext = getSC.invoke(bin);
if (securityContext != null) {
Method getRef = securityContext.getClass().getMethod("getReference");
String securityContextRef = (String) getRef.invoke(securityContext);
if (securityContextRef != null) {
beginObject(theEventWriter, "securityContext");
writeOptionalTagWithTextNode(theEventWriter, "reference", securityContextRef);
theEventWriter.endObject();
}
}
} catch (Exception e) {
e.printStackTrace();
}
} else {
encodeCompositeElementToStreamWriter(theResDef, theResource, theResource, theEventWriter, theContainedResource, theSubResource, new CompositeChildElement(resDef, theSubResource));
}
encodeCompositeElementToStreamWriter(theResDef, theResource, theResource, theEventWriter, theContainedResource, theSubResource, new CompositeChildElement(resDef, theSubResource));
theEventWriter.endObject();
}
@ -731,12 +708,12 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
/**
* This is useful only for the two cases where extensions are encoded as direct children (e.g. not in some object
* called _name): resource extensions, and extension extensions
*
*
* @param theChildElem
* @param theParent
*/
private void extractAndWriteExtensionsAsDirectChild(IBase theElement, JsonLikeWriter theEventWriter, BaseRuntimeElementDefinition<?> theElementDef, RuntimeResourceDefinition theResDef,
IBaseResource theResource, CompositeChildElement theChildElem, CompositeChildElement theParent) throws IOException {
IBaseResource theResource, CompositeChildElement theChildElem, CompositeChildElement theParent) throws IOException {
List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
@ -753,7 +730,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
private void extractDeclaredExtensions(IBase theResource, BaseRuntimeElementDefinition<?> resDef, List<HeldExtension> extensions, List<HeldExtension> modifierExtensions,
CompositeChildElement theChildElem) {
CompositeChildElement theChildElem) {
for (RuntimeChildDeclaredExtensionDefinition nextDef : resDef.getExtensionsNonModifier()) {
for (IBase nextValue : nextDef.getAccessor().getValues(theResource)) {
if (nextValue != null) {
@ -777,7 +754,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
private void extractUndeclaredExtensions(IBase theElement, List<HeldExtension> extensions, List<HeldExtension> modifierExtensions, CompositeChildElement theChildElem,
CompositeChildElement theParent) {
CompositeChildElement theParent) {
if (theElement instanceof ISupportsUndeclaredExtensions) {
ISupportsUndeclaredExtensions element = (ISupportsUndeclaredExtensions) theElement;
List<ExtensionDt> ext = element.getUndeclaredExtensions();
@ -1045,78 +1022,78 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
}
private void parseExtension(ParserState<?> theState, JsonLikeArray theValues, boolean theIsModifier) {
int allUnderscoreNames = 0;
int handledUnderscoreNames = 0;
private void parseExtension(ParserState<?> theState, JsonLikeArray theValues, boolean theIsModifier) {
int allUnderscoreNames = 0;
int handledUnderscoreNames = 0;
for (int i = 0; i < theValues.size(); i++) {
JsonLikeObject nextExtObj = JsonLikeValue.asObject(theValues.get(i));
JsonLikeValue jsonElement = nextExtObj.get("url");
String url;
if (null == jsonElement || !(jsonElement.isScalar())) {
String parentElementName;
if (theIsModifier) {
parentElementName = "modifierExtension";
} else {
parentElementName = "extension";
}
getErrorHandler().missingRequiredElement(new ParseLocation(parentElementName), "url");
url = null;
} else {
url = getExtensionUrl(jsonElement.getAsString());
}
theState.enteringNewElementExtension(null, url, theIsModifier, getServerBaseUrl());
for (String next : nextExtObj.keySet()) {
if ("url".equals(next)) {
continue;
} else if ("extension".equals(next)) {
JsonLikeArray jsonVal = JsonLikeValue.asArray(nextExtObj.get(next));
parseExtension(theState, jsonVal, false);
} else if ("modifierExtension".equals(next)) {
JsonLikeArray jsonVal = JsonLikeValue.asArray(nextExtObj.get(next));
parseExtension(theState, jsonVal, true);
} else if (next.charAt(0) == '_') {
allUnderscoreNames++;
continue;
} else {
JsonLikeValue jsonVal = nextExtObj.get(next);
String alternateName = '_' + next;
JsonLikeValue alternateVal = nextExtObj.get(alternateName);
if (alternateVal != null) {
handledUnderscoreNames++;
}
parseChildren(theState, next, jsonVal, alternateVal, alternateName, false);
}
}
for (int i = 0; i < theValues.size(); i++) {
JsonLikeObject nextExtObj = JsonLikeValue.asObject(theValues.get(i));
JsonLikeValue jsonElement = nextExtObj.get("url");
String url;
if (null == jsonElement || !(jsonElement.isScalar())) {
String parentElementName;
if (theIsModifier) {
parentElementName = "modifierExtension";
} else {
parentElementName = "extension";
}
getErrorHandler().missingRequiredElement(new ParseLocation(parentElementName), "url");
url = null;
} else {
url = getExtensionUrl(jsonElement.getAsString());
}
theState.enteringNewElementExtension(null, url, theIsModifier, getServerBaseUrl());
for (String next : nextExtObj.keySet()) {
if ("url".equals(next)) {
continue;
} else if ("extension".equals(next)) {
JsonLikeArray jsonVal = JsonLikeValue.asArray(nextExtObj.get(next));
parseExtension(theState, jsonVal, false);
} else if ("modifierExtension".equals(next)) {
JsonLikeArray jsonVal = JsonLikeValue.asArray(nextExtObj.get(next));
parseExtension(theState, jsonVal, true);
} else if (next.charAt(0) == '_') {
allUnderscoreNames++;
continue;
} else {
JsonLikeValue jsonVal = nextExtObj.get(next);
String alternateName = '_' + next;
JsonLikeValue alternateVal = nextExtObj.get(alternateName);
if (alternateVal != null) {
handledUnderscoreNames++;
}
parseChildren(theState, next, jsonVal, alternateVal, alternateName, false);
}
}
/*
* This happens if an element has an extension but no actual value. I.e.
* This happens if an element has an extension but no actual value. I.e.
* if a resource has a "_status" element but no corresponding "status"
* element. This could be used to handle a null value with an extension
* for example.
*/
if (allUnderscoreNames > handledUnderscoreNames) {
for (String alternateName : nextExtObj.keySet()) {
if (alternateName.startsWith("_") && alternateName.length() > 1) {
JsonLikeValue nextValue = nextExtObj.get(alternateName);
if (nextValue != null) {
if (nextValue.isObject()) {
String nextName = alternateName.substring(1);
if (nextExtObj.get(nextName) == null) {
theState.enteringNewElement(null, nextName);
parseAlternates(nextValue, theState, alternateName, alternateName);
theState.endingElement();
}
} else {
getErrorHandler().incorrectJsonType(null, alternateName, ValueType.OBJECT, null, nextValue.getJsonType(), null);
}
}
}
}
}
theState.endingElement();
}
}
if (allUnderscoreNames > handledUnderscoreNames) {
for (String alternateName : nextExtObj.keySet()) {
if (alternateName.startsWith("_") && alternateName.length() > 1) {
JsonLikeValue nextValue = nextExtObj.get(alternateName);
if (nextValue != null) {
if (nextValue.isObject()) {
String nextName = alternateName.substring(1);
if (nextExtObj.get(nextName) == null) {
theState.enteringNewElement(null, nextName);
parseAlternates(nextValue, theState, alternateName, alternateName);
theState.endingElement();
}
} else {
getErrorHandler().incorrectJsonType(null, alternateName, ValueType.OBJECT, null, nextValue.getJsonType(), null);
}
}
}
}
}
theState.endingElement();
}
}
private void parseFhirComments(JsonLikeValue theObject, ParserState<?> theState) {
if (theObject.isArray()) {
@ -1270,7 +1247,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
private void writeExtensionsAsDirectChild(IBaseResource theResource, JsonLikeWriter theEventWriter, RuntimeResourceDefinition resDef, List<HeldExtension> extensions,
List<HeldExtension> modifierExtensions) throws IOException {
List<HeldExtension> modifierExtensions) throws IOException {
if (extensions.isEmpty() == false) {
beginArray(theEventWriter, "extension");
for (HeldExtension next : extensions) {
@ -1344,6 +1321,28 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
return url1.compareTo(url2);
}
private void managePrimitiveExtension(final IBase theValue, final RuntimeResourceDefinition theResDef, final IBaseResource theResource, final JsonLikeWriter theEventWriter, final BaseRuntimeElementDefinition<?> def, final String childName) throws IOException {
if (def.getChildType().equals(ID_DATATYPE) || def.getChildType().equals(PRIMITIVE_DATATYPE)) {
final List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
final List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
// Undeclared extensions
extractUndeclaredExtensions(theValue, extensions, modifierExtensions, myParent, null);
// Declared extensions
if (def != null) {
extractDeclaredExtensions(theValue, def, extensions, modifierExtensions, myParent);
}
boolean haveContent = false;
if (!extensions.isEmpty() || !modifierExtensions.isEmpty()) {
haveContent = true;
}
if (haveContent) {
beginObject(theEventWriter, '_' + childName);
writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions);
theEventWriter.endObject();
}
}
}
public void write(RuntimeResourceDefinition theResDef, IBaseResource theResource, JsonLikeWriter theEventWriter) throws IOException {
if (myUndeclaredExtension != null) {
writeUndeclaredExtension(theResDef, theResource, theEventWriter, myUndeclaredExtension);
@ -1357,7 +1356,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
/*
* This makes sure that even if the extension contains a reference to a contained
* resource which has a HAPI-assigned ID we'll still encode that ID.
*
*
* See #327
*/
List<? extends IBase> preProcessedValue = preProcessValues(myDef, theResource, Collections.singletonList(myValue), myChildElem);
@ -1383,7 +1382,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
} else {
String childName = myDef.getChildNameByDatatype(myValue.getClass());
encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, myValue, def, childName, false, false, myParent, false);
managePrimitiveExtension(myValue, theResDef, theResource, theEventWriter, def, childName);
managePrimitiveExtension(myValue, theResDef, theResource, theEventWriter, def, childName);
}
theEventWriter.endObject();
@ -1438,34 +1437,12 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
throw new ConfigurationException("Unable to encode extension, unregognized child element type: " + value.getClass().getCanonicalName());
}
encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, value, childDef, childName, true, false, myParent, false);
managePrimitiveExtension(value, theResDef, theResource, theEventWriter, childDef, childName);
managePrimitiveExtension(value, theResDef, theResource, theEventWriter, childDef, childName);
}
// theEventWriter.name(myUndeclaredExtension.get);
theEventWriter.endObject();
}
private void managePrimitiveExtension(final IBase theValue, final RuntimeResourceDefinition theResDef, final IBaseResource theResource, final JsonLikeWriter theEventWriter, final BaseRuntimeElementDefinition<?> def, final String childName) throws IOException {
if (def.getChildType().equals(ID_DATATYPE) || def.getChildType().equals(PRIMITIVE_DATATYPE)) {
final List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
final List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
// Undeclared extensions
extractUndeclaredExtensions(theValue, extensions, modifierExtensions, myParent, null);
// Declared extensions
if (def != null) {
extractDeclaredExtensions(theValue, def, extensions, modifierExtensions, myParent);
}
boolean haveContent = false;
if (!extensions.isEmpty() || !modifierExtensions.isEmpty()) {
haveContent = true;
}
if (haveContent) {
beginObject(theEventWriter, '_' + childName);
writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions);
theEventWriter.endObject();
}
}
}
}
}
}

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java
View File

@ -187,6 +187,7 @@ public class Constants {
public static final String OO_INFOSTATUS_PROCESSING = "processing";
public static final String PARAM_GRAPHQL_QUERY = "query";
public static final String HEADER_X_CACHE = "X-Cache";
public static final String HEADER_X_SECURITY_CONTEXT = "X-Security-Context";
static {
CHARSET_UTF8 = Charset.forName(CHARSET_NAME_UTF8);

46
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/BinaryUtil.java Normal file
View File

@ -0,0 +1,46 @@
package ca.uhn.fhir.util;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBinary;
import org.hl7.fhir.instance.model.api.IBaseReference;
import java.util.List;
public class BinaryUtil {
private BinaryUtil() {
// non instantiable
}
public static IBaseReference getSecurityContext(FhirContext theCtx, IBaseBinary theBinary) {
RuntimeResourceDefinition def = theCtx.getResourceDefinition("Binary");
BaseRuntimeChildDefinition child = def.getChildByName("securityContext");
List<IBase> values = child.getAccessor().getValues(theBinary);
IBaseReference retVal = null;
if (values.size() > 0) {
retVal = (IBaseReference) values.get(0);
}
return retVal;
}
public static IBaseBinary newBinary(FhirContext theCtx) {
return (IBaseBinary) theCtx.getResourceDefinition("Binary").newInstance();
}
public static void setSecurityContext(FhirContext theCtx, IBaseBinary theBinary, String theSecurityContext) {
RuntimeResourceDefinition def = theCtx.getResourceDefinition("Binary");
BaseRuntimeChildDefinition child = def.getChildByName("securityContext");
BaseRuntimeElementDefinition<?> referenceDef = theCtx.getElementDefinition("reference");
IBaseReference reference = (IBaseReference) referenceDef.newInstance();
child.getMutator().addValue(theBinary, reference);
reference.setReference(theSecurityContext);
}
}

38
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/StaleSearchDeletingSvcImpl.java
View File

@ -20,8 +20,12 @@ package ca.uhn.fhir.jpa.search;
* #L%
*/
import java.util.Date;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
import ca.uhn.fhir.jpa.dao.data.ISearchIncludeDao;
import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
import ca.uhn.fhir.jpa.entity.Search;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.time.DateUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.PageRequest;
@ -34,11 +38,7 @@ import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionCallback;
import org.springframework.transaction.support.TransactionTemplate;
import com.google.common.annotations.VisibleForTesting;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.*;
import ca.uhn.fhir.jpa.entity.Search;
import java.util.Date;
/**
* Deletes old searches
@ -46,26 +46,21 @@ import ca.uhn.fhir.jpa.entity.Search;
public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
public static final long DEFAULT_CUTOFF_SLACK = 10 * DateUtils.MILLIS_PER_SECOND;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(StaleSearchDeletingSvcImpl.class);
private static Long ourNowForUnitTests;
/*
* We give a bit of extra leeway just to avoid race conditions where a query result
* is being reused (because a new client request came in with the same params) right before
* the result is to be deleted
*/
private long myCutoffSlack = DEFAULT_CUTOFF_SLACK;
@Autowired
private DaoConfig myDaoConfig;
@Autowired
private ISearchDao mySearchDao;
@Autowired
private ISearchIncludeDao mySearchIncludeDao;
@Autowired
private ISearchResultDao mySearchResultDao;
@Autowired
private PlatformTransactionManager myTransactionManager;
@ -87,7 +82,7 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
if (myDaoConfig.getReuseCachedSearchResultsForMillis() != null) {
cutoffMillis = Math.max(cutoffMillis, myDaoConfig.getReuseCachedSearchResultsForMillis());
}
final Date cutoff = new Date((System.currentTimeMillis() - cutoffMillis) - myCutoffSlack);
final Date cutoff = new Date((now() - cutoffMillis) - myCutoffSlack);
ourLog.debug("Searching for searches which are before {}", cutoff);
@ -131,4 +126,19 @@ public class StaleSearchDeletingSvcImpl implements IStaleSearchDeletingSvc {
myCutoffSlack = theCutoffSlack;
}
private static long now() {
if (ourNowForUnitTests != null) {
return ourNowForUnitTests;
}
return System.currentTimeMillis();
}
/**
* This is for unit tests only, do not call otherwise
*/
@VisibleForTesting
public static void setNowForUnitTests(Long theNowForUnitTests) {
ourNowForUnitTests = theNowForUnitTests;
}
}

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/TestUtil.java
View File

@ -130,4 +130,19 @@ public class TestUtil {
}
}
public static void sleepAtLeast(int theMillis) {
long start = System.currentTimeMillis();
while (System.currentTimeMillis() <= start + theMillis) {
try {
long timeSinceStarted = System.currentTimeMillis() - start;
long timeToSleep = Math.max(0, theMillis - timeSinceStarted);
ourLog.info("Sleeping for {}ms", timeToSleep);
Thread.sleep(timeToSleep);
} catch (InterruptedException theE) {
theE.printStackTrace();
}
}
}
}

138
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchPageExpiryTest.java
View File

@ -1,12 +1,16 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import static ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.Assert.*;
import ca.uhn.fhir.jpa.util.StopWatch;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.test.util.AopTestUtils;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
@ -18,15 +22,13 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.StringParam;
public class FhirResourceDaoDstu3SearchPageExpiryTest extends BaseJpaDstu3Test {
@Before
public void beforeDisableResultReuse() {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
}
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoDstu3SearchPageExpiryTest.class);
@After()
public void after() {
StaleSearchDeletingSvcImpl staleSearchDeletingSvc = AopTestUtils.getTargetObject(myStaleSearchDeletingSvc);
staleSearchDeletingSvc.setCutoffSlackForUnitTest(StaleSearchDeletingSvcImpl.DEFAULT_CUTOFF_SLACK);
StaleSearchDeletingSvcImpl.setNowForUnitTests(null);
}
@Before
@ -35,48 +37,9 @@ public class FhirResourceDaoDstu3SearchPageExpiryTest extends BaseJpaDstu3Test {
staleSearchDeletingSvc.setCutoffSlackForUnitTest(0);
}
@Test
public void testExpirePagesAfterSingleUse() throws Exception {
IIdType pid1;
IIdType pid2;
{
Patient patient = new Patient();
patient.addName().setFamily("EXPIRE");
pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
Thread.sleep(10);
{
Patient patient = new Patient();
patient.addName().setFamily("EXPIRE");
pid2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
Thread.sleep(10);
SearchParameterMap params;
params = new SearchParameterMap();
params.add(Patient.SP_FAMILY, new StringParam("EXPIRE"));
final IBundleProvider bundleProvider = myPatientDao.search(params);
assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
myDaoConfig.setExpireSearchResultsAfterMillis(500);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNotNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
}
});
Thread.sleep(750);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
}
});
@Before
public void beforeDisableResultReuse() {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
}
@Test
@ -98,6 +61,7 @@ public class FhirResourceDaoDstu3SearchPageExpiryTest extends BaseJpaDstu3Test {
myDaoConfig.setExpireSearchResultsAfterMillis(1000L);
myDaoConfig.setReuseCachedSearchResultsForMillis(500L);
long start = System.currentTimeMillis();
final String searchUuid1;
{
@ -109,7 +73,7 @@ public class FhirResourceDaoDstu3SearchPageExpiryTest extends BaseJpaDstu3Test {
Validate.notBlank(searchUuid1);
}
Thread.sleep(250);
sleepAtLeast(250);
String searchUuid2;
{
@ -122,7 +86,7 @@ public class FhirResourceDaoDstu3SearchPageExpiryTest extends BaseJpaDstu3Test {
}
assertEquals(searchUuid1, searchUuid2);
Thread.sleep(500);
sleepAtLeast(500);
// We're now past 500ms so we shouldn't reuse the search
@ -139,18 +103,31 @@ public class FhirResourceDaoDstu3SearchPageExpiryTest extends BaseJpaDstu3Test {
// Search just got used so it shouldn't be deleted
Thread.sleep(750);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNotNull(mySearchEntityDao.findByUuid(searchUuid3));
}
});
StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 1400);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNull(mySearchEntityDao.findByUuid(searchUuid1));
assertNotNull(mySearchEntityDao.findByUuid(searchUuid3));
}
});
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNull(mySearchEntityDao.findByUuid(searchUuid1));
}
});
Thread.sleep(300);
StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 2200);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@ -162,4 +139,63 @@ public class FhirResourceDaoDstu3SearchPageExpiryTest extends BaseJpaDstu3Test {
});
}
@Test
public void testExpirePagesAfterSingleUse() throws Exception {
IIdType pid1;
IIdType pid2;
{
Patient patient = new Patient();
patient.addName().setFamily("EXPIRE");
pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
Thread.sleep(10);
{
Patient patient = new Patient();
patient.addName().setFamily("EXPIRE");
pid2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
Thread.sleep(10);
final StopWatch sw = new StopWatch();
long start = System.currentTimeMillis();
SearchParameterMap params;
params = new SearchParameterMap();
params.add(Patient.SP_FAMILY, new StringParam("EXPIRE"));
final IBundleProvider bundleProvider = myPatientDao.search(params);
assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
myDaoConfig.setExpireSearchResultsAfterMillis(500);
StaleSearchDeletingSvcImpl.setNowForUnitTests(start);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNotNull("Failed after " + sw.toString(), mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
}
});
StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 499);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNotNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
}
});
StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 600);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
}
});
}
}

143
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchPageExpiryTest.java
View File

@ -1,33 +1,35 @@
package ca.uhn.fhir.jpa.dao.r4;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.Assert.*;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
import ca.uhn.fhir.jpa.util.StopWatch;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.StringParam;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.*;
import org.hl7.fhir.r4.model.Patient;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.test.util.AopTestUtils;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.StringParam;
import static ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.Assert.*;
public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
@Before
public void beforeDisableResultReuse() {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
}
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4SearchPageExpiryTest.class);
@After()
public void after() {
StaleSearchDeletingSvcImpl staleSearchDeletingSvc = AopTestUtils.getTargetObject(myStaleSearchDeletingSvc);
staleSearchDeletingSvc.setCutoffSlackForUnitTest(StaleSearchDeletingSvcImpl.DEFAULT_CUTOFF_SLACK);
StaleSearchDeletingSvcImpl.setNowForUnitTests(null);
}
@Before
@ -36,50 +38,9 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
staleSearchDeletingSvc.setCutoffSlackForUnitTest(0);
}
@Test
public void testExpirePagesAfterSingleUse() throws Exception {
IIdType pid1;
IIdType pid2;
{
Patient patient = new Patient();
patient.addName().setFamily("EXPIRE");
pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
Thread.sleep(10);
{
Patient patient = new Patient();
patient.addName().setFamily("EXPIRE");
pid2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
Thread.sleep(10);
final StopWatch sw = new StopWatch();
SearchParameterMap params;
params = new SearchParameterMap();
params.add(Patient.SP_FAMILY, new StringParam("EXPIRE"));
final IBundleProvider bundleProvider = myPatientDao.search(params);
assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
myDaoConfig.setExpireSearchResultsAfterMillis(500);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNotNull("Failed after " + sw.toString(), mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
}
});
Thread.sleep(750);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
}
});
@Before
public void beforeDisableResultReuse() {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
}
@Test
@ -101,6 +62,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
myDaoConfig.setExpireSearchResultsAfterMillis(1000L);
myDaoConfig.setReuseCachedSearchResultsForMillis(500L);
long start = System.currentTimeMillis();
final String searchUuid1;
{
@ -112,7 +74,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
Validate.notBlank(searchUuid1);
}
Thread.sleep(250);
sleepAtLeast(250);
String searchUuid2;
{
@ -125,7 +87,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
}
assertEquals(searchUuid1, searchUuid2);
Thread.sleep(500);
sleepAtLeast(500);
// We're now past 500ms so we shouldn't reuse the search
@ -150,7 +112,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
}
});
Thread.sleep(750);
StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 1400);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@ -166,7 +128,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
}
});
Thread.sleep(300);
StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 2200);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@ -178,4 +140,63 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
});
}
@Test
public void testExpirePagesAfterSingleUse() throws Exception {
IIdType pid1;
IIdType pid2;
{
Patient patient = new Patient();
patient.addName().setFamily("EXPIRE");
pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
Thread.sleep(10);
{
Patient patient = new Patient();
patient.addName().setFamily("EXPIRE");
pid2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
Thread.sleep(10);
final StopWatch sw = new StopWatch();
long start = System.currentTimeMillis();
SearchParameterMap params;
params = new SearchParameterMap();
params.add(Patient.SP_FAMILY, new StringParam("EXPIRE"));
final IBundleProvider bundleProvider = myPatientDao.search(params);
assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
assertThat(toUnqualifiedVersionlessIds(bundleProvider), containsInAnyOrder(pid1, pid2));
myDaoConfig.setExpireSearchResultsAfterMillis(500);
StaleSearchDeletingSvcImpl.setNowForUnitTests(start);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNotNull("Failed after " + sw.toString(), mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
}
});
StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 499);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNotNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
}
});
StaleSearchDeletingSvcImpl.setNowForUnitTests(start + 600);
myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
txTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
assertNull(mySearchEntityDao.findByUuid(bundleProvider.getUuid()));
}
});
}
}

8
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/RestfulServerUtils.java
View File

@ -29,6 +29,7 @@ import java.util.regex.Pattern;
import javax.servlet.http.HttpServletRequest;
import ca.uhn.fhir.util.BinaryUtil;
import org.hl7.fhir.instance.model.api.*;
import ca.uhn.fhir.context.FhirContext;
@ -580,10 +581,17 @@ public class RestfulServerUtils {
} else {
contentType = Constants.CT_OCTET_STREAM;
}
// Force binary resources to download - This is a security measure to prevent
// malicious images or HTML blocks being served up as content.
response.addHeader(Constants.HEADER_CONTENT_DISPOSITION, "Attachment;");
IBaseReference securityContext = BinaryUtil.getSecurityContext(theServer.getFhirContext(), bin);
String securityContextRef = securityContext.getReferenceElement().getValue();
if (isNotBlank(securityContextRef)) {
response.addHeader(Constants.HEADER_X_SECURITY_CONTEXT, securityContextRef);
}
return response.sendAttachmentResponse(bin, theStausCode, contentType);
}

18
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/BaseResourceReturningMethodBinding.java
View File

@ -149,24 +149,6 @@ public abstract class BaseResourceReturningMethodBinding extends BaseMethodBindi
return theRequest.getResponse().streamResponseAsResource(response, prettyPrint, summaryMode, Constants.STATUS_HTTP_200_OK, null, theRequest.isRespondGzip(), isAddContentLocationHeader());
// DSTU1 Bundle
// // Is this request coming from a browser
// String uaHeader = theRequest.getHeader("user-agent");
// boolean requestIsBrowser = false;
// if (uaHeader != null && uaHeader.contains("Mozilla")) {
// requestIsBrowser = true;
// }
//
// for (int i = theServer.getInterceptors().size() - 1; i >= 0; i--) {
// IServerInterceptor next = theServer.getInterceptors().get(i);
// boolean continueProcessing = next.outgoingResponse(theRequest, responseObject.getDstu1Bundle());
// if (!continueProcessing) {
// ourLog.debug("Interceptor {} returned false, not continuing processing");
// return null;
// }
// }
//
// return theRequest.getResponse().streamResponseAsBundle(responseObject.getDstu1Bundle(), summaryMode, theRequest.isRespondGzip(), requestIsBrowser);
}
public IBaseResource doInvokeServer(IRestfulServer<?> theServer, RequestDetails theRequest) {

55
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/ResourceParameter.java
View File

@ -19,7 +19,24 @@ package ca.uhn.fhir.rest.server.method;
* limitations under the License.
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServerUtils;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.BinaryUtil;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseBinary;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.io.ByteArrayInputStream;
import java.io.IOException;
@ -30,27 +47,8 @@ import java.lang.reflect.Modifier;
import java.nio.charset.Charset;
import java.util.Collection;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseBinary;
import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServerUtils;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class ResourceParameter implements IParameter {
@ -193,11 +191,22 @@ public class ResourceParameter implements IParameter {
String ct = theRequest.getHeader(Constants.HEADER_CONTENT_TYPE);
if (EncodingEnum.forContentTypeStrict(ct) == null) {
FhirContext ctx = theRequest.getServer().getFhirContext();
IBaseBinary binary = (IBaseBinary) ctx.getResourceDefinition("Binary").newInstance();
IBaseBinary binary = BinaryUtil.newBinary(ctx);
binary.setId(theRequest.getId());
binary.setContentType(ct);
binary.setContent(theRequest.loadRequestContents());
retVal = binary;
/*
* Security context header, which is only in
* DSTU3+
*/
if (ctx.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
String securityContext = theRequest.getHeader(Constants.HEADER_X_SECURITY_CONTEXT);
if (isNotBlank(securityContext)) {
BinaryUtil.setSecurityContext(ctx, binary, securityContext);
}
}
}
}

742
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java
View File

@ -51,14 +51,14 @@ import static org.mockito.Matchers.isNull;
import static org.mockito.Mockito.*;
public class JsonParserDstu3Test {
private static FhirContext ourCtx = FhirContext.forDstu3();
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParserDstu3Test.class);
private static FhirContext ourCtx = FhirContext.forDstu3();
@After
public void after() {
ourCtx.setNarrativeGenerator(null);
}
/**
* See #563
@ -77,22 +77,6 @@ public class JsonParserDstu3Test {
}
}
/**
* See #720
*/
@Test
public void testParseCustomResourceType() {
String input = "{\"resourceType\":\"Bug720ResourceType\",\"meta\":{\"profile\":[\"http://example.com/StructureDefinition/dontuse#Bug720ResourceType\"]},\"supportedVersion\":\"2.5.x\",\"templatesConsentTemplate\":[{\"domainName\":\"name\",\"Name\":\"template_01\",\"version\":\"1.0\",\"title\":\"title\",\"comment\":\"comment\",\"contact\":{\"resourceType\":\"Person\",\"name\":[{\"family\":\"Mustermann\",\"given\":[\"Max\"]}],\"telecom\":[{\"system\":\"email\",\"value\":\"max.mustermann@mail.de\"},{\"system\":\"phone\",\"value\":\"+49 1234 23232\"}],\"address\":[{\"text\":\"street 1-2\",\"city\":\"city\",\"postalCode\":\"12345\",\"country\":\"Germany\"}]}}]}";
Bug720ResourceType parsed = ourCtx.newJsonParser().parseResource(Bug720ResourceType.class, input);
assertEquals(1, parsed.getTemplates().size());
assertEquals(Bug720Datatype.class, parsed.getTemplates().get(0).getClass());
assertEquals("Mustermann", ((Bug720Datatype)parsed.getTemplates().get(0)).getContact().getNameFirstRep().getFamily());
ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(parsed));
}
/**
* See #563
*/
@ -110,6 +94,26 @@ public class JsonParserDstu3Test {
}
}
@Test
public void testBaseUrlFooResourceCorrectlySerializedInExtensionValueReference() {
String refVal = "http://my.org/FooBar";
Patient fhirPat = new Patient();
fhirPat.addExtension().setUrl("x1").setValue(new Reference(refVal));
IParser parser = ourCtx.newJsonParser();
String output = parser.encodeResourceToString(fhirPat);
System.out.println("output: " + output);
// Deserialize then check that valueReference value is still correct
fhirPat = parser.parseResource(Patient.class, output);
List<Extension> extlst = fhirPat.getExtensionsByUrl("x1");
Assert.assertEquals(1, extlst.size());
Assert.assertEquals(refVal, ((Reference) extlst.get(0).getValue()).getReference());
}
/**
* See #544
*/
@ -271,12 +275,12 @@ public class JsonParserDstu3Test {
String enc = ourCtx.newJsonParser().encodeResourceToString(patient);
assertThat(enc, Matchers.stringContainsInOrder("{\"resourceType\":\"Patient\",", "\"extension\":[{\"url\":\"http://example.com/extensions#someext\",\"valueDateTime\":\"2011-01-02T11:13:15\"}",
"{\"url\":\"http://example.com#parent\",\"extension\":[{\"url\":\"http://example.com#child\",\"valueString\":\"value1\"},{\"url\":\"http://example.com#child\",\"valueString\":\"value2\"}]}"));
"{\"url\":\"http://example.com#parent\",\"extension\":[{\"url\":\"http://example.com#child\",\"valueString\":\"value1\"},{\"url\":\"http://example.com#child\",\"valueString\":\"value2\"}]}"));
assertThat(enc, Matchers.stringContainsInOrder("\"modifierExtension\":[" + "{" + "\"url\":\"http://example.com/extensions#modext\"," + "\"valueDate\":\"1995-01-02\"" + "}" + "],"));
assertThat(enc,
containsString("\"_given\":[" + "{" + "\"extension\":[" + "{" + "\"url\":\"http://examples.com#givenext\"," + "\"valueString\":\"given\"" + "}" + "]" + "}," + "{" + "\"extension\":[" + "{"
+ "\"url\":\"http://examples.com#givenext_parent\"," + "\"extension\":[" + "{" + "\"url\":\"http://examples.com#givenext_child\"," + "\"valueString\":\"CHILD\"" + "}" + "]" + "}"
+ "]" + "}"));
containsString("\"_given\":[" + "{" + "\"extension\":[" + "{" + "\"url\":\"http://examples.com#givenext\"," + "\"valueString\":\"given\"" + "}" + "]" + "}," + "{" + "\"extension\":[" + "{"
+ "\"url\":\"http://examples.com#givenext_parent\"," + "\"extension\":[" + "{" + "\"url\":\"http://examples.com#givenext_child\"," + "\"valueString\":\"CHILD\"" + "}" + "]" + "}"
+ "]" + "}"));
/*
* Now parse this back
@ -334,36 +338,36 @@ public class JsonParserDstu3Test {
ourLog.info(enc);
//@formatter:off
assertThat(enc, stringContainsInOrder("\"meta\": {",
"\"profile\": [",
"\"http://foo/Profile1\",",
"\"http://foo/Profile2\"",
"],",
"\"security\": [",
"{",
"\"system\": \"sec_scheme1\",",
"\"code\": \"sec_term1\",",
"\"display\": \"sec_label1\"",
"},",
"{",
"\"system\": \"sec_scheme2\",",
"\"code\": \"sec_term2\",",
"\"display\": \"sec_label2\"",
"}",
"],",
"\"tag\": [",
"{",
"\"system\": \"scheme1\",",
"\"code\": \"term1\",",
"\"display\": \"label1\"",
"},",
"{",
"\"system\": \"scheme2\",",
"\"code\": \"term2\",",
"\"display\": \"label2\"",
"}",
"]",
"},"));
assertThat(enc, stringContainsInOrder("\"meta\": {",
"\"profile\": [",
"\"http://foo/Profile1\",",
"\"http://foo/Profile2\"",
"],",
"\"security\": [",
"{",
"\"system\": \"sec_scheme1\",",
"\"code\": \"sec_term1\",",
"\"display\": \"sec_label1\"",
"},",
"{",
"\"system\": \"sec_scheme2\",",
"\"code\": \"sec_term2\",",
"\"display\": \"sec_label2\"",
"}",
"],",
"\"tag\": [",
"{",
"\"system\": \"scheme1\",",
"\"code\": \"term1\",",
"\"display\": \"label1\"",
"},",
"{",
"\"system\": \"scheme2\",",
"\"code\": \"term2\",",
"\"display\": \"label2\"",
"}",
"]",
"},"));
//@formatter:on
Patient parsed = ourCtx.newJsonParser().parseResource(Patient.class, enc);
@ -462,29 +466,29 @@ public class JsonParserDstu3Test {
ourLog.info(enc);
//@formatter:off
assertEquals("{\n" +
" \"resourceType\": \"Patient\",\n" +
" \"meta\": {\n" +
" \"security\": [\n" +
" {\n" +
" \"system\": \"SYSTEM1\",\n" +
" \"version\": \"VERSION1\",\n" +
" \"code\": \"CODE1\",\n" +
" \"display\": \"DISPLAY1\"\n" +
" },\n" +
" {\n" +
" \"system\": \"SYSTEM2\",\n" +
" \"version\": \"VERSION2\",\n" +
" \"code\": \"CODE2\",\n" +
" \"display\": \"DISPLAY2\"\n" +
" }\n" +
" ]\n" +
" },\n" +
" \"name\": [\n" +
" {\n" +
" \"family\": \"FAMILY\"\n" +
" }\n" +
" ]\n" +
assertEquals("{\n" +
" \"resourceType\": \"Patient\",\n" +
" \"meta\": {\n" +
" \"security\": [\n" +
" {\n" +
" \"system\": \"SYSTEM1\",\n" +
" \"version\": \"VERSION1\",\n" +
" \"code\": \"CODE1\",\n" +
" \"display\": \"DISPLAY1\"\n" +
" },\n" +
" {\n" +
" \"system\": \"SYSTEM2\",\n" +
" \"version\": \"VERSION2\",\n" +
" \"code\": \"CODE2\",\n" +
" \"display\": \"DISPLAY2\"\n" +
" }\n" +
" ]\n" +
" },\n" +
" \"name\": [\n" +
" {\n" +
" \"family\": \"FAMILY\"\n" +
" }\n" +
" ]\n" +
"}", enc.trim());
//@formatter:on
@ -506,6 +510,22 @@ public class JsonParserDstu3Test {
assertEquals("VERSION2", label.getVersion());
}
@Test
public void testEncodeBinaryWithSecurityContext() {
Binary bin = new Binary();
bin.setContentType("text/plain");
bin.setContent("Now is the time".getBytes());
Reference securityContext = new Reference();
securityContext.setReference("DiagnosticReport/1");
bin.setSecurityContext(securityContext);
String encoded = ourCtx.newJsonParser().encodeResourceToString(bin);
ourLog.info(encoded);
assertThat(encoded, containsString("Binary"));
assertThat(encoded, containsString("\"contentType\":\"text/plain\""));
assertThat(encoded, containsString("\"content\":\"Tm93IGlzIHRoZSB0aW1l\""));
assertThat(encoded, containsString("\"securityContext\":{\"reference\":\"DiagnosticReport/1\"}"));
}
@Test
public void testEncodeBundleNewBundleNoText() {
@ -539,22 +559,22 @@ public class JsonParserDstu3Test {
//@formatter:off
assertThat(encoded, stringContainsInOrder(
"{",
"\"resourceType\": \"Patient\",",
"\"contained\": [",
"{",
"\"resourceType\": \"Condition\",",
"\"id\": \"1\"",
"}",
"],",
"\"extension\": [",
"{",
"\"url\": \"test\",",
"\"valueReference\": {",
"\"reference\": \"#1\"",
"}",
"}",
"],",
"\"birthDate\": \"2016-04-05\"",
"\"resourceType\": \"Patient\",",
"\"contained\": [",
"{",
"\"resourceType\": \"Condition\",",
"\"id\": \"1\"",
"}",
"],",
"\"extension\": [",
"{",
"\"url\": \"test\",",
"\"valueReference\": {",
"\"reference\": \"#1\"",
"}",
"}",
"],",
"\"birthDate\": \"2016-04-05\"",
"}"
));
//@formatter:on
@ -575,23 +595,6 @@ public class JsonParserDstu3Test {
String output = ourCtx.newJsonParser().encodeResourceToString(new Binary());
assertEquals("{\"resourceType\":\"Binary\"}", output);
}
@Test
public void testEncodeBinaryWithSecurityContext() {
Binary bin = new Binary();
bin.setContentType("text/plain");
bin.setContent("Now is the time".getBytes());
Reference securityContext = new Reference();
securityContext.setReference("DiagnosticReport/1");
bin.setSecurityContext(securityContext);
String encoded = ourCtx.newJsonParser().encodeResourceToString(bin);
assertThat(encoded, containsString("Binary"));
assertThat(encoded, containsString("contentType"));
assertThat(encoded, containsString("text/plain"));
assertThat(encoded, containsString("Tm93IGlzIHRoZSB0aW1l"));
assertThat(encoded, containsString("securityContext"));
assertThat(encoded, containsString("{\"reference\":\"DiagnosticReport/1\"}"));
}
/**
* #158
@ -663,8 +666,8 @@ public class JsonParserDstu3Test {
ourLog.info(val);
assertEquals(
"{\"resourceType\":\"Patient\",\"id\":\"123\",\"contact\":[{\"extension\":[{\"url\":\"http://foo.com/contact-eyecolour\",\"valueIdentifier\":{\"value\":\"EYE\"}}],\"name\":{\"family\":\"FAMILY\"}}]}",
val);
"{\"resourceType\":\"Patient\",\"id\":\"123\",\"contact\":[{\"extension\":[{\"url\":\"http://foo.com/contact-eyecolour\",\"valueIdentifier\":{\"value\":\"EYE\"}}],\"name\":{\"family\":\"FAMILY\"}}]}",
val);
FhirContext newCtx = FhirContext.forDstu3();
PatientWithExtendedContactDstu3 actual = newCtx.newJsonParser().parseResource(PatientWithExtendedContactDstu3.class, val);
@ -706,9 +709,9 @@ public class JsonParserDstu3Test {
Patient p = new Patient();
p.setId("Patient/B");
p
.addExtension()
.setUrl("http://foo")
.setValue(new Reference("Practitioner/A"));
.addExtension()
.setUrl("http://foo")
.setValue(new Reference("Practitioner/A"));
IParser parser = ourCtx.newJsonParser().setPrettyPrint(true);
parser.setDontEncodeElements(new HashSet<String>(Arrays.asList("*.id", "*.meta")));
@ -777,20 +780,20 @@ public class JsonParserDstu3Test {
//@formatter:off
assertThat(output, stringContainsInOrder(
"\"id\": \"1\"",
"\"meta\"",
"\"extension\"",
"\"url\": \"http://exturl\"",
"\"extension\"",
"\"url\": \"http://subext\"",
"\"valueString\": \"sub_ext_value\"",
"\"code\":"
));
assertThat(output, not(stringContainsInOrder(
"\"url\": \"http://exturl\"",
",",
"\"url\": \"http://exturl\""
)));
"\"id\": \"1\"",
"\"meta\"",
"\"extension\"",
"\"url\": \"http://exturl\"",
"\"extension\"",
"\"url\": \"http://subext\"",
"\"valueString\": \"sub_ext_value\"",
"\"code\":"
));
assertThat(output, not(stringContainsInOrder(
"\"url\": \"http://exturl\"",
",",
"\"url\": \"http://exturl\""
)));
//@formatter:on
obs = parser.parseResource(Observation.class, output);
@ -821,17 +824,17 @@ public class JsonParserDstu3Test {
//@formatter:off
assertThat(encoded, stringContainsInOrder(
"\"resourceType\": \"Patient\"",
"\"resourceType\": \"Patient\"",
"\"contained\": [",
"\"resourceType\": \"Condition\"",
"\"id\": \"1\"",
"\"bodySite\": [",
"\"text\": \"BODY SITE\"",
"\"extension\": [",
"\"url\": \"testCondition\",",
"\"valueReference\": {",
"\"reference\": \"#1\"",
"\"birthDate\": \"2016-04-14\"",
"\"resourceType\": \"Condition\"",
"\"id\": \"1\"",
"\"bodySite\": [",
"\"text\": \"BODY SITE\"",
"\"extension\": [",
"\"url\": \"testCondition\",",
"\"valueReference\": {",
"\"reference\": \"#1\"",
"\"birthDate\": \"2016-04-14\"",
"}"
));
//@formatter:on
@ -1071,7 +1074,7 @@ public class JsonParserDstu3Test {
assertThat(encoded, containsString("Patient"));
assertThat(encoded, stringContainsInOrder("\"tag\"", "\"system\": \"foo\",", "\"code\": \"bar\"", "\"system\": \"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_SYSTEM + "\"",
"\"code\": \"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_CODE + "\""));
"\"code\": \"" + ca.uhn.fhir.rest.api.Constants.TAG_SUBSETTED_CODE + "\""));
assertThat(encoded, not(containsString("THE DIV")));
assertThat(encoded, containsString("family"));
assertThat(encoded, not(containsString("maritalStatus")));
@ -1091,7 +1094,7 @@ public class JsonParserDstu3Test {
ourLog.info(enc);
assertEquals("{\"resourceType\":\"Patient\",\"meta\":{\"tag\":[{\"system\":\"scheme\",\"code\":\"term\",\"display\":\"display\"}]},\"identifier\":[{\"system\":\"sys\",\"value\":\"val\"}]}",
enc);
enc);
}
@ -1268,19 +1271,19 @@ public class JsonParserDstu3Test {
@Test
public void testExplanationOfBenefit() {
//@formatter:off
String input = "{" +
" \"resourceType\": \"ExplanationOfBenefit\"," +
" \"insurance\": {\n" +
" \"coverage\": {\n" +
" \"reference\": \"Coverage/123\"\n" +
" }\n" +
" },\n" +
" \"relationship\": {\n" +
" \"system\": \"http://hl7.org/fhir/relationship\",\n" +
" \"code\": \"1\",\n" +
" \"display\": \"self\"\n" +
" }\n" +
"}";
String input = "{" +
" \"resourceType\": \"ExplanationOfBenefit\"," +
" \"insurance\": {\n" +
" \"coverage\": {\n" +
" \"reference\": \"Coverage/123\"\n" +
" }\n" +
" },\n" +
" \"relationship\": {\n" +
" \"system\": \"http://hl7.org/fhir/relationship\",\n" +
" \"code\": \"1\",\n" +
" \"display\": \"self\"\n" +
" }\n" +
"}";
//@formatter:on
ExplanationOfBenefit eob = ourCtx.newJsonParser().parseResource(ExplanationOfBenefit.class, input);
@ -1334,14 +1337,14 @@ public class JsonParserDstu3Test {
// ID should be a String and communication should be an Array
String input = "{\"resourceType\": \"Patient\",\n" +
" \"id\": 123,\n" +
" \"communication\": {\n" +
" \"language\": {\n" +
" \"text\": \"Hindi\"\n" +
" },\n" +
" \"preferred\": true\n" +
" }\n" +
"}";
" \"id\": 123,\n" +
" \"communication\": {\n" +
" \"language\": {\n" +
" \"text\": \"Hindi\"\n" +
" },\n" +
" \"preferred\": true\n" +
" }\n" +
"}";
IParser p = ourCtx.newJsonParser();
@ -1375,14 +1378,14 @@ public class JsonParserDstu3Test {
// ID should be a String and communication should be an Array
String input = "{\"resourceType\": \"Patient\",\n" +
" \"id\": \"123\",\n" +
" \"communication\": [{\n" +
" \"language\": {\n" +
" \"text\": \"Hindi\"\n" +
" },\n" +
" \"preferred\": true\n" +
" }]\n" +
"}";
" \"id\": \"123\",\n" +
" \"communication\": [{\n" +
" \"language\": {\n" +
" \"text\": \"Hindi\"\n" +
" },\n" +
" \"preferred\": true\n" +
" }]\n" +
"}";
IParser p = ourCtx.newJsonParser();
@ -1503,14 +1506,14 @@ public class JsonParserDstu3Test {
@Ignore
public void testNamespacePreservationEncode() throws Exception {
//@formatter:off
String input = "<Patient xmlns=\"http://hl7.org/fhir\" xmlns:xhtml=\"http://www.w3.org/1999/xhtml\">" +
"<text>" +
"<xhtml:div>" +
"<xhtml:img src=\"foo\"/>" +
"@fhirabend" +
"</xhtml:div>" +
"</text>" +
"</Patient>";
String input = "<Patient xmlns=\"http://hl7.org/fhir\" xmlns:xhtml=\"http://www.w3.org/1999/xhtml\">" +
"<text>" +
"<xhtml:div>" +
"<xhtml:img src=\"foo\"/>" +
"@fhirabend" +
"</xhtml:div>" +
"</text>" +
"</Patient>";
//@formatter:on
Patient parsed = ourCtx.newXmlParser().parseResource(Patient.class, input);
@ -1712,69 +1715,69 @@ public class JsonParserDstu3Test {
@Test
public void testParseAndEncodeBundleWithUuidBase() {
//@formatter:off
String input =
"{\n" +
" \"resourceType\":\"Bundle\",\n" +
" \"type\":\"document\",\n" +
" \"entry\":[\n" +
" {\n" +
" \"fullUrl\":\"urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57\",\n" +
" \"resource\":{\n" +
" \"resourceType\":\"Composition\",\n" +
" \"id\":\"180f219f-97a8-486d-99d9-ed631fe4fc57\",\n" +
" \"meta\":{\n" +
" \"lastUpdated\":\"2013-05-28T22:12:21Z\"\n" +
" },\n" +
" \"text\":{\n" +
" \"status\":\"generated\",\n" +
" \"div\":\"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: 180f219f-97a8-486d-99d9-ed631fe4fc57</p><p><b>meta</b>: </p><p><b>date</b>: Feb 1, 2013 12:30:02 PM</p><p><b>type</b>: Discharge Summary from Responsible Clinician <span>(Details : {LOINC code '28655-9' = 'Physician attending Discharge summary)</span></p><p><b>status</b>: final</p><p><b>confidentiality</b>: N</p><p><b>author</b>: <a>Doctor Dave. Generated Summary: 23; Adam Careful </a></p><p><b>encounter</b>: <a>http://fhir.healthintersections.com.au/open/Encounter/doc-example</a></p></div>\"\n" +
" },\n" +
" \"date\":\"2013-02-01T12:30:02Z\",\n" +
" \"type\":{\n" +
" \"coding\":[\n" +
" {\n" +
" \"system\":\"http://loinc.org\",\n" +
" \"code\":\"28655-9\"\n" +
" }\n" +
" ],\n" +
" \"text\":\"Discharge Summary from Responsible Clinician\"\n" +
" },\n" +
" \"status\":\"final\",\n" +
" \"confidentiality\":\"N\",\n" +
" \"subject\":{\n" +
" \"reference\":\"http://fhir.healthintersections.com.au/open/Patient/d1\",\n" +
" \"display\":\"Eve Everywoman\"\n" +
" },\n" +
" \"author\":[\n" +
" {\n" +
" \"reference\":\"Practitioner/example\",\n" +
" \"display\":\"Doctor Dave\"\n" +
" }\n" +
" ],\n" +
" \"encounter\":{\n" +
" \"reference\":\"http://fhir.healthintersections.com.au/open/Encounter/doc-example\"\n" +
" },\n" +
" \"section\":[\n" +
" {\n" +
" \"title\":\"Reason for admission\",\n" +
" \"content\":{\n" +
" \"reference\":\"urn:uuid:d0dd51d3-3ab2-4c84-b697-a630c3e40e7a\"\n" +
" }\n" +
" },\n" +
" {\n" +
" \"title\":\"Medications on Discharge\",\n" +
" \"content\":{\n" +
" \"reference\":\"urn:uuid:673f8db5-0ffd-4395-9657-6da00420bbc1\"\n" +
" }\n" +
" },\n" +
" {\n" +
" \"title\":\"Known allergies\",\n" +
" \"content\":{\n" +
" \"reference\":\"urn:uuid:68f86194-e6e1-4f65-b64a-5314256f8d7b\"\n" +
" }\n" +
" }\n" +
" ]\n" +
" }\n" +
String input =
"{\n" +
" \"resourceType\":\"Bundle\",\n" +
" \"type\":\"document\",\n" +
" \"entry\":[\n" +
" {\n" +
" \"fullUrl\":\"urn:uuid:180f219f-97a8-486d-99d9-ed631fe4fc57\",\n" +
" \"resource\":{\n" +
" \"resourceType\":\"Composition\",\n" +
" \"id\":\"180f219f-97a8-486d-99d9-ed631fe4fc57\",\n" +
" \"meta\":{\n" +
" \"lastUpdated\":\"2013-05-28T22:12:21Z\"\n" +
" },\n" +
" \"text\":{\n" +
" \"status\":\"generated\",\n" +
" \"div\":\"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: 180f219f-97a8-486d-99d9-ed631fe4fc57</p><p><b>meta</b>: </p><p><b>date</b>: Feb 1, 2013 12:30:02 PM</p><p><b>type</b>: Discharge Summary from Responsible Clinician <span>(Details : {LOINC code '28655-9' = 'Physician attending Discharge summary)</span></p><p><b>status</b>: final</p><p><b>confidentiality</b>: N</p><p><b>author</b>: <a>Doctor Dave. Generated Summary: 23; Adam Careful </a></p><p><b>encounter</b>: <a>http://fhir.healthintersections.com.au/open/Encounter/doc-example</a></p></div>\"\n" +
" },\n" +
" \"date\":\"2013-02-01T12:30:02Z\",\n" +
" \"type\":{\n" +
" \"coding\":[\n" +
" {\n" +
" \"system\":\"http://loinc.org\",\n" +
" \"code\":\"28655-9\"\n" +
" }\n" +
" ],\n" +
" \"text\":\"Discharge Summary from Responsible Clinician\"\n" +
" },\n" +
" \"status\":\"final\",\n" +
" \"confidentiality\":\"N\",\n" +
" \"subject\":{\n" +
" \"reference\":\"http://fhir.healthintersections.com.au/open/Patient/d1\",\n" +
" \"display\":\"Eve Everywoman\"\n" +
" },\n" +
" \"author\":[\n" +
" {\n" +
" \"reference\":\"Practitioner/example\",\n" +
" \"display\":\"Doctor Dave\"\n" +
" }\n" +
" ],\n" +
" \"encounter\":{\n" +
" \"reference\":\"http://fhir.healthintersections.com.au/open/Encounter/doc-example\"\n" +
" },\n" +
" \"section\":[\n" +
" {\n" +
" \"title\":\"Reason for admission\",\n" +
" \"content\":{\n" +
" \"reference\":\"urn:uuid:d0dd51d3-3ab2-4c84-b697-a630c3e40e7a\"\n" +
" }\n" +
" },\n" +
" {\n" +
" \"title\":\"Medications on Discharge\",\n" +
" \"content\":{\n" +
" \"reference\":\"urn:uuid:673f8db5-0ffd-4395-9657-6da00420bbc1\"\n" +
" }\n" +
" },\n" +
" {\n" +
" \"title\":\"Known allergies\",\n" +
" \"content\":{\n" +
" \"reference\":\"urn:uuid:68f86194-e6e1-4f65-b64a-5314256f8d7b\"\n" +
" }\n" +
" }\n" +
" ]\n" +
" }\n" +
" }" +
" ]" +
"}";
@ -1794,34 +1797,34 @@ public class JsonParserDstu3Test {
@Test
public void testParseAndEncodeComments() {
//@formatter:off
String input = "{\n" +
" \"resourceType\": \"Patient\",\n" +
" \"id\": \"pat1\",\n" +
" \"text\": {\n" +
" \"status\": \"generated\",\n" +
" \"div\": \"<div>\\n \\n <p>Patient Donald DUCK @ Acme Healthcare, Inc. MR = 654321</p>\\n \\n </div>\"\n" +
" },\n" +
" \"identifier\": [\n" +
" {\n" +
" \"fhir_comments\":[\"identifier comment 1\",\"identifier comment 2\"],\n" +
" \"use\": \"usual\",\n" +
" \"_use\": {\n" +
" \"fhir_comments\":[\"use comment 1\",\"use comment 2\"]\n" +
" },\n" +
" \"type\": {\n" +
" \"coding\": [\n" +
" {\n" +
" \"system\": \"http://hl7.org/fhir/v2/0203\",\n" +
" \"code\": \"MR\"\n" +
" }\n" +
" ]\n" +
" },\n" +
" \"system\": \"urn:oid:0.1.2.3.4.5.6.7\",\n" +
" \"value\": \"654321\"\n" +
" }\n" +
" ],\n" +
" \"active\": true" +
"}";
String input = "{\n" +
" \"resourceType\": \"Patient\",\n" +
" \"id\": \"pat1\",\n" +
" \"text\": {\n" +
" \"status\": \"generated\",\n" +
" \"div\": \"<div>\\n \\n <p>Patient Donald DUCK @ Acme Healthcare, Inc. MR = 654321</p>\\n \\n </div>\"\n" +
" },\n" +
" \"identifier\": [\n" +
" {\n" +
" \"fhir_comments\":[\"identifier comment 1\",\"identifier comment 2\"],\n" +
" \"use\": \"usual\",\n" +
" \"_use\": {\n" +
" \"fhir_comments\":[\"use comment 1\",\"use comment 2\"]\n" +
" },\n" +
" \"type\": {\n" +
" \"coding\": [\n" +
" {\n" +
" \"system\": \"http://hl7.org/fhir/v2/0203\",\n" +
" \"code\": \"MR\"\n" +
" }\n" +
" ]\n" +
" },\n" +
" \"system\": \"urn:oid:0.1.2.3.4.5.6.7\",\n" +
" \"value\": \"654321\"\n" +
" }\n" +
" ],\n" +
" \"active\": true" +
"}";
//@formatter:off
Patient res = ourCtx.newJsonParser().parseResource(Patient.class, input);
@ -1829,33 +1832,33 @@ public class JsonParserDstu3Test {
assertEquals("Patient/pat1", res.getId());
assertEquals("654321", res.getIdentifier().get(0).getValue());
assertEquals(true, res.getActive());
assertThat(res.getIdentifier().get(0).getFormatCommentsPre(), contains("identifier comment 1", "identifier comment 2"));
assertThat(res.getIdentifier().get(0).getUseElement().getFormatCommentsPre(), contains("use comment 1", "use comment 2"));
String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(res);
ourLog.info(encoded);
//@formatter:off
assertThat(encoded, stringContainsInOrder(
"\"identifier\": [",
"{",
"\"fhir_comments\":",
"[",
"\"identifier comment 1\"",
",",
"\"identifier comment 2\"",
"]",
"\"use\": \"usual\",",
"\"_use\": {",
"\"fhir_comments\":",
"[",
"\"use comment 1\"",
",",
"\"use comment 2\"",
"]",
"},",
"\"type\""
"\"identifier\": [",
"{",
"\"fhir_comments\":",
"[",
"\"identifier comment 1\"",
",",
"\"identifier comment 2\"",
"]",
"\"use\": \"usual\",",
"\"_use\": {",
"\"fhir_comments\":",
"[",
"\"use comment 1\"",
",",
"\"use comment 2\"",
"]",
"},",
"\"type\""
));
//@formatter:off
}
@ -1865,7 +1868,7 @@ public class JsonParserDstu3Test {
Binary patient = new Binary();
patient.setId(new IdType("http://base/Binary/11/_history/22"));
patient.setContentType("foo");
patient.setContent(new byte[] { 1, 2, 3, 4 });
patient.setContent(new byte[]{1, 2, 3, 4});
String val = ourCtx.newJsonParser().encodeResourceToString(patient);
@ -1916,7 +1919,7 @@ public class JsonParserDstu3Test {
"\"resourceType\":\"Patient\",",
"\"id\":\"1\"",
"\"reference\":\"#1\""
));
));
//@formatter:on
o = parser.parseResource(Observation.class, enc);
@ -1927,6 +1930,21 @@ public class JsonParserDstu3Test {
assertEquals("patient family", p.getName().get(0).getFamilyElement().getValue());
}
/**
* See #720
*/
@Test
public void testParseCustomResourceType() {
String input = "{\"resourceType\":\"Bug720ResourceType\",\"meta\":{\"profile\":[\"http://example.com/StructureDefinition/dontuse#Bug720ResourceType\"]},\"supportedVersion\":\"2.5.x\",\"templatesConsentTemplate\":[{\"domainName\":\"name\",\"Name\":\"template_01\",\"version\":\"1.0\",\"title\":\"title\",\"comment\":\"comment\",\"contact\":{\"resourceType\":\"Person\",\"name\":[{\"family\":\"Mustermann\",\"given\":[\"Max\"]}],\"telecom\":[{\"system\":\"email\",\"value\":\"max.mustermann@mail.de\"},{\"system\":\"phone\",\"value\":\"+49 1234 23232\"}],\"address\":[{\"text\":\"street 1-2\",\"city\":\"city\",\"postalCode\":\"12345\",\"country\":\"Germany\"}]}}]}";
Bug720ResourceType parsed = ourCtx.newJsonParser().parseResource(Bug720ResourceType.class, input);
assertEquals(1, parsed.getTemplates().size());
assertEquals(Bug720Datatype.class, parsed.getTemplates().get(0).getClass());
assertEquals("Mustermann", ((Bug720Datatype) parsed.getTemplates().get(0)).getContact().getNameFirstRep().getFamily());
ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(parsed));
}
/**
* #480
*/
@ -1987,10 +2005,10 @@ public class JsonParserDstu3Test {
@Test
public void testParseJsonExtensionWithoutUrl() {
//@formatter:off
String input =
String input =
"{\"resourceType\":\"Patient\"," +
"\"extension\":[ {\"valueDateTime\":\"2011-01-02T11:13:15\"} ]" +
"}";
"\"extension\":[ {\"valueDateTime\":\"2011-01-02T11:13:15\"} ]" +
"}";
//@formatter:on
IParser parser = ourCtx.newJsonParser();
@ -2017,10 +2035,10 @@ public class JsonParserDstu3Test {
@Test
public void testParseJsonModifierExtensionWithoutUrl() {
//@formatter:off
String input =
String input =
"{\"resourceType\":\"Patient\"," +
"\"modifierExtension\":[ {\"valueDateTime\":\"2011-01-02T11:13:15\"} ]" +
"}";
"\"modifierExtension\":[ {\"valueDateTime\":\"2011-01-02T11:13:15\"} ]" +
"}";
//@formatter:on
IParser parser = ourCtx.newJsonParser();
@ -2044,24 +2062,24 @@ public class JsonParserDstu3Test {
@Test
public void testParseMetadata() throws Exception {
//@formatter:off
String bundle = "{\n" +
" \"resourceType\" : \"Bundle\",\n" +
" \"total\" : 1,\n" +
" \"link\": [{\n" +
" \"relation\" : \"self\",\n" +
" \"url\" : \"http://localhost:52788/Binary?_pretty=true\"\n" +
" }],\n" +
" \"entry\" : [{\n" +
String bundle = "{\n" +
" \"resourceType\" : \"Bundle\",\n" +
" \"total\" : 1,\n" +
" \"link\": [{\n" +
" \"relation\" : \"self\",\n" +
" \"url\" : \"http://localhost:52788/Binary?_pretty=true\"\n" +
" }],\n" +
" \"entry\" : [{\n" +
" \"fullUrl\" : \"http://foo/fhirBase2/Patient/1/_history/2\",\n" +
" \"resource\" : {\n" +
" \"resourceType\" : \"Patient\",\n" +
" \"id\" : \"1\",\n" +
" \"resource\" : {\n" +
" \"resourceType\" : \"Patient\",\n" +
" \"id\" : \"1\",\n" +
" \"meta\" : {\n" +
" \"versionId\" : \"2\",\n" +
" \"lastUpdated\" : \"2001-02-22T11:22:33-05:00\"\n" +
" },\n" +
" \"birthDate\" : \"2012-01-02\"\n" +
" },\n" +
" },\n" +
" \"birthDate\" : \"2012-01-02\"\n" +
" },\n" +
" \"search\" : {\n" +
" \"mode\" : \"match\",\n" +
" \"score\" : 0.123\n" +
@ -2070,7 +2088,7 @@ public class JsonParserDstu3Test {
" \"method\" : \"POST\",\n" +
" \"url\" : \"http://foo/Patient?identifier=value\"\n" +
" }\n" +
" }]\n" +
" }]\n" +
"}";
//@formatter:on
@ -2182,6 +2200,43 @@ public class JsonParserDstu3Test {
}
}
@Test
public void testParseWithPrecision() {
String input = "{\"resourceType\":\"Observation\",\"valueQuantity\":{\"value\":0.000000000000000100}}";
Observation obs = ourCtx.newJsonParser().parseResource(Observation.class, input);
DecimalType valueElement = ((Quantity) obs.getValue()).getValueElement();
assertEquals("0.000000000000000100", valueElement.getValueAsString());
String str = ourCtx.newJsonParser().encodeResourceToString(obs);
ourLog.info(str);
assertEquals("{\"resourceType\":\"Observation\",\"valueQuantity\":{\"value\":0.000000000000000100}}", str);
}
@Test(expected = DataFormatException.class)
public void testParseWithTrailingContent() throws Exception {
//@formatter:off
String bundle = "{\n" +
" \"resourceType\" : \"Bundle\",\n" +
" \"total\" : 1\n" +
"}}";
//@formatter:on
Bundle b = ourCtx.newJsonParser().parseResource(Bundle.class, bundle);
}
@Test
@Ignore
public void testParseWithWrongTypeObjectShouldBeArray() throws Exception {
String input = IOUtils.toString(getClass().getResourceAsStream("/invalid_metadata.json"));
try {
ourCtx.newJsonParser().parseResource(CapabilityStatement.class, input);
fail();
} catch (DataFormatException e) {
assertEquals("Syntax error parsing JSON FHIR structure: Expected ARRAY at element 'modifierExtension', found 'OBJECT'", e.getMessage());
}
}
/**
* See #344
*/
@ -2215,43 +2270,6 @@ public class JsonParserDstu3Test {
}
}
@Test
public void testParseWithPrecision() {
String input = "{\"resourceType\":\"Observation\",\"valueQuantity\":{\"value\":0.000000000000000100}}";
Observation obs = ourCtx.newJsonParser().parseResource(Observation.class, input);
DecimalType valueElement = ((Quantity) obs.getValue()).getValueElement();
assertEquals("0.000000000000000100", valueElement.getValueAsString());
String str = ourCtx.newJsonParser().encodeResourceToString(obs);
ourLog.info(str);
assertEquals("{\"resourceType\":\"Observation\",\"valueQuantity\":{\"value\":0.000000000000000100}}", str);
}
@Test(expected = DataFormatException.class)
public void testParseWithTrailingContent() throws Exception {
//@formatter:off
String bundle = "{\n" +
" \"resourceType\" : \"Bundle\",\n" +
" \"total\" : 1\n" +
"}}";
//@formatter:on
Bundle b = ourCtx.newJsonParser().parseResource(Bundle.class, bundle);
}
@Test
@Ignore
public void testParseWithWrongTypeObjectShouldBeArray() throws Exception {
String input = IOUtils.toString(getClass().getResourceAsStream("/invalid_metadata.json"));
try {
ourCtx.newJsonParser().parseResource(CapabilityStatement.class, input);
fail();
} catch (DataFormatException e) {
assertEquals("Syntax error parsing JSON FHIR structure: Expected ARRAY at element 'modifierExtension', found 'OBJECT'", e.getMessage());
}
}
/**
* See #144 and #146
*/
@ -2323,13 +2341,13 @@ public class JsonParserDstu3Test {
ArgumentCaptor<ScalarType> expectedScalar = ArgumentCaptor.forClass(ScalarType.class);
ArgumentCaptor<ScalarType> actualScalar = ArgumentCaptor.forClass(ScalarType.class);
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), elementName.capture(), expected.capture(), expectedScalar.capture(), actual.capture(),
actualScalar.capture());
actualScalar.capture());
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), Mockito.eq("_id"), Mockito.eq(ValueType.OBJECT), expectedScalar.capture(), Mockito.eq(ValueType.SCALAR),
actualScalar.capture());
actualScalar.capture());
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), Mockito.eq("__v"), Mockito.eq(ValueType.OBJECT), expectedScalar.capture(), Mockito.eq(ValueType.SCALAR),
actualScalar.capture());
actualScalar.capture());
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), Mockito.eq("_status"), Mockito.eq(ValueType.OBJECT), expectedScalar.capture(),
Mockito.eq(ValueType.SCALAR), actualScalar.capture());
Mockito.eq(ValueType.SCALAR), actualScalar.capture());
assertEquals("_id", elementName.getAllValues().get(0));
assertEquals(ValueType.OBJECT, expected.getAllValues().get(0));
@ -2361,26 +2379,6 @@ public class JsonParserDstu3Test {
assertTrue(result.isSuccessful());
}
@Test
public void testBaseUrlFooResourceCorrectlySerializedInExtensionValueReference() {
String refVal = "http://my.org/FooBar";
Patient fhirPat = new Patient();
fhirPat.addExtension().setUrl("x1").setValue(new Reference(refVal));
IParser parser = ourCtx.newJsonParser();
String output = parser.encodeResourceToString(fhirPat);
System.out.println("output: " + output);
// Deserialize then check that valueReference value is still correct
fhirPat = parser.parseResource(Patient.class, output);
List<Extension> extlst = fhirPat.getExtensionsByUrl("x1");
Assert.assertEquals(1, extlst.size());
Assert.assertEquals(refVal, ((Reference) extlst.get(0).getValue()).getReference());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

17
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java
View File

@ -82,6 +82,23 @@ public class XmlParserDstu3Test {
ourCtx.setNarrativeGenerator(null);
}
@Test
public void testEncodeBinaryWithSecurityContext() {
Binary bin = new Binary();
bin.setContentType("text/plain");
bin.setContent("Now is the time".getBytes());
Reference securityContext = new Reference();
securityContext.setReference("DiagnosticReport/1");
bin.setSecurityContext(securityContext);
String encoded = ourCtx.newXmlParser().encodeResourceToString(bin);
ourLog.info(encoded);
assertThat(encoded, containsString("Binary"));
assertThat(encoded, containsString("<contentType value=\"text/plain\"/>"));
assertThat(encoded, containsString("<securityContext><reference value=\"DiagnosticReport/1\"/></securityContext>"));
assertThat(encoded, containsString("<content value=\"Tm93IGlzIHRoZSB0aW1l\"/>"));
}
/**
* See #544
*/

141
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/CreateBinaryR4Test.java → hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/BinaryServerR4Test.java
View File

@ -1,14 +1,16 @@
package ca.uhn.fhir.rest.server;
import static org.junit.Assert.assertArrayEquals;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;
import java.util.concurrent.TimeUnit;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.util.PortUtil;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.client.methods.HttpPut;
import org.apache.http.entity.ByteArrayEntity;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.CloseableHttpClient;
@ -18,18 +20,20 @@ import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.*;
import org.junit.*;
import org.hl7.fhir.r4.model.Binary;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Reference;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.util.PortUtil;
import ca.uhn.fhir.util.TestUtil;
import java.util.concurrent.TimeUnit;
public class CreateBinaryR4Test {
import static org.junit.Assert.*;
public class BinaryServerR4Test {
private static CloseableHttpClient ourClient;
private static FhirContext ourCtx = FhirContext.forR4();
private static Binary ourLastBinary;
@ -37,24 +41,73 @@ public class CreateBinaryR4Test {
private static String ourLastBinaryString;
private static int ourPort;
private static Server ourServer;
private static IdType ourLastId;
private static Binary ourNextBinary;
@Before
public void before() {
ourLastBinary = null;
ourLastBinaryBytes = null;
ourLastBinaryString = null;
ourLastId = null;
ourNextBinary = null;
}
@Test
public void testRawBytesBinaryContentType() throws Exception {
public void testGetWithNoAccept() throws Exception {
ourNextBinary = new Binary();
ourNextBinary.setId("Binary/A/_history/222");
ourNextBinary.setContent(new byte[]{0, 1, 2, 3, 4});
ourNextBinary.setSecurityContext(new Reference("Patient/1"));
ourNextBinary.setContentType("application/foo");
HttpGet get = new HttpGet("http://localhost:" + ourPort + "/Binary/A");
get.addHeader("Content-Type", "application/foo");
CloseableHttpResponse status = ourClient.execute(get);
try {
assertEquals(200, status.getStatusLine().getStatusCode());
assertEquals("application/foo", status.getEntity().getContentType().getValue());
assertEquals("Patient/1", status.getFirstHeader(Constants.HEADER_X_SECURITY_CONTEXT).getValue());
assertEquals("W/\"222\"", status.getFirstHeader(Constants.HEADER_ETAG).getValue());
assertEquals("http://localhost:" + ourPort + "/Binary/A/_history/222", status.getFirstHeader(Constants.HEADER_LOCATION).getValue());
byte[] content = IOUtils.toByteArray(status.getEntity().getContent());
assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, content);
} finally {
IOUtils.closeQuietly(status);
}
}
@Test
public void testPostBinaryWithSecurityContext() throws Exception {
HttpPost post = new HttpPost("http://localhost:" + ourPort + "/Binary");
post.setEntity(new ByteArrayEntity(new byte[] { 0, 1, 2, 3, 4 }));
post.setEntity(new ByteArrayEntity(new byte[]{0, 1, 2, 3, 4}));
post.addHeader("Content-Type", "application/foo");
post.addHeader(Constants.HEADER_X_SECURITY_CONTEXT, "Encounter/2");
CloseableHttpResponse status = ourClient.execute(post);
try {
assertNull(ourLastId);
assertEquals("application/foo", ourLastBinary.getContentType());
assertEquals("Encounter/2", ourLastBinary.getSecurityContext().getReference());
assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, ourLastBinary.getContent());
assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, ourLastBinaryBytes);
} finally {
IOUtils.closeQuietly(status);
}
}
@Test
public void testPostRawBytesBinaryContentType() throws Exception {
HttpPost post = new HttpPost("http://localhost:" + ourPort + "/Binary");
post.setEntity(new ByteArrayEntity(new byte[]{0, 1, 2, 3, 4}));
post.addHeader("Content-Type", "application/foo");
CloseableHttpResponse status = ourClient.execute(post);
try {
assertNull(ourLastId);
assertEquals("application/foo", ourLastBinary.getContentType());
assertArrayEquals(new byte[] { 0, 1, 2, 3, 4 }, ourLastBinary.getContent());
assertArrayEquals(new byte[] { 0, 1, 2, 3, 4 }, ourLastBinaryBytes);
assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, ourLastBinary.getContent());
assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, ourLastBinaryBytes);
} finally {
IOUtils.closeQuietly(status);
}
@ -64,11 +117,11 @@ public class CreateBinaryR4Test {
* Technically the client shouldn't be doing it this way, but we'll be accepting
*/
@Test
public void testRawBytesFhirContentType() throws Exception {
public void testPostRawBytesFhirContentType() throws Exception {
Binary b = new Binary();
b.setContentType("application/foo");
b.setContent(new byte[] { 0, 1, 2, 3, 4 });
b.setContent(new byte[]{0, 1, 2, 3, 4});
String encoded = ourCtx.newJsonParser().encodeResourceToString(b);
HttpPost post = new HttpPost("http://localhost:" + ourPort + "/Binary");
@ -77,14 +130,14 @@ public class CreateBinaryR4Test {
CloseableHttpResponse status = ourClient.execute(post);
try {
assertEquals("application/foo", ourLastBinary.getContentType());
assertArrayEquals(new byte[] { 0, 1, 2, 3, 4 }, ourLastBinary.getContent());
assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, ourLastBinary.getContent());
} finally {
IOUtils.closeQuietly(status);
}
}
@Test
public void testRawBytesFhirContentTypeContainingFhir() throws Exception {
public void testPostRawBytesFhirContentTypeContainingFhir() throws Exception {
Patient p = new Patient();
p.getText().setDivAsString("A PATIENT");
@ -109,13 +162,32 @@ public class CreateBinaryR4Test {
}
@Test
public void testRawBytesNoContentType() throws Exception {
public void testPostRawBytesNoContentType() throws Exception {
HttpPost post = new HttpPost("http://localhost:" + ourPort + "/Binary");
post.setEntity(new ByteArrayEntity(new byte[] { 0, 1, 2, 3, 4 }));
post.setEntity(new ByteArrayEntity(new byte[]{0, 1, 2, 3, 4}));
CloseableHttpResponse status = ourClient.execute(post);
try {
assertNull(ourLastBinary.getContentType());
assertArrayEquals(new byte[] { 0, 1, 2, 3, 4 }, ourLastBinary.getContent());
assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, ourLastBinary.getContent());
} finally {
IOUtils.closeQuietly(status);
}
}
@Test
public void testPutBinaryWithSecurityContext() throws Exception {
HttpPut post = new HttpPut("http://localhost:" + ourPort + "/Binary/A");
post.setEntity(new ByteArrayEntity(new byte[]{0, 1, 2, 3, 4}));
post.addHeader("Content-Type", "application/foo");
post.addHeader(Constants.HEADER_X_SECURITY_CONTEXT, "Encounter/2");
CloseableHttpResponse status = ourClient.execute(post);
try {
assertEquals("Binary/A", ourLastId.getValue());
assertEquals("Binary/A", ourLastBinary.getId());
assertEquals("application/foo", ourLastBinary.getContentType());
assertEquals("Encounter/2", ourLastBinary.getSecurityContext().getReference());
assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, ourLastBinary.getContent());
assertArrayEquals(new byte[]{0, 1, 2, 3, 4}, ourLastBinaryBytes);
} finally {
IOUtils.closeQuietly(status);
}
@ -149,7 +221,6 @@ public class CreateBinaryR4Test {
}
public static class BinaryProvider implements IResourceProvider {
@Create()
public MethodOutcome createBinary(@ResourceParam Binary theBinary, @ResourceParam String theBinaryString, @ResourceParam byte[] theBinaryBytes) {
ourLastBinary = theBinary;
@ -163,6 +234,20 @@ public class CreateBinaryR4Test {
return Binary.class;
}
@Read
public Binary read(@IdParam IdType theId) {
return ourNextBinary;
}
@Update()
public MethodOutcome updateBinary(@IdParam IdType theId, @ResourceParam Binary theBinary, @ResourceParam String theBinaryString, @ResourceParam byte[] theBinaryBytes) {
ourLastId = theId;
ourLastBinary = theBinary;
ourLastBinaryString = theBinaryString;
ourLastBinaryBytes = theBinaryBytes;
return new MethodOutcome(new IdType("Binary/001/_history/002"));
}
}
}

5
src/changes/changes.xml
View File

@ -175,6 +175,11 @@
was not encoded correctly. Thanks to Malcolm McRoberts for the pull
request with fix and test case!
</action>
<action type="add">
The Binary resource endpoint now supports the `X-Security-Context` header when
reading or writing Binary contents using their native Content-Type (i.e exchanging
the raw binary with the server, as opposed to exchanging a FHIR resource).
</action>
</release>
<release version="3.0.0" date="2017-09-27">
<action type="add">