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Merge branch 'master' of github.com:jamesagnew/hapi-fhir

This commit is contained in:
James Agnew 2015-04-15 10:57:43 -04:00
parent ddd68b8d57 7f7ff5c936
commit 41c215efe2
9 changed files with 133 additions and 76 deletions
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6
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java
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@ -2001,7 +2001,7 @@ class ParserState<T> {
terser.visit(myInstance, new IModelVisitor() {
@Override
public void acceptElement(IBase theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
public void acceptElement(IBase theElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
if (theElement instanceof BaseResourceReferenceDt) {
BaseResourceReferenceDt nextRef = (BaseResourceReferenceDt) theElement;
String ref = nextRef.getReference().getValue();
@ -2019,8 +2019,8 @@ class ParserState<T> {
}
@Override
public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, ExtensionDt theNextExt) {
acceptElement(theNextExt.getValue(), null, null);
public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, ExtensionDt theNextExt) {
acceptElement(theNextExt.getValue(), null, null, null);
}
});

18
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ParameterUtil.java
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@ -20,6 +20,8 @@ package ca.uhn.fhir.rest.param;
* #L%
*/
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Collections;
@ -217,6 +219,22 @@ public class ParameterUtil {
return b.toString();
}
/**
* Escapes a string according to the rules for parameter escaping specified in the <a href="http://www.hl7.org/implement/standards/fhir/search.html#escaping">FHIR Specification Escaping
* Section</a>
*/
public static String escapeAndUrlEncode(String theValue) {
if (theValue == null) {
return null;
}
try {
return URLEncoder.encode(escape(theValue), "UTF-8");
} catch (UnsupportedEncodingException e) {
throw new Error("UTF-8 not supported on this platform");
}
}
/**
* Unescapes a string according to the rules for parameter escaping specified in the <a href="http://www.hl7.org/implement/standards/fhir/search.html#escaping">FHIR Specification Escaping
* Section</a>

57
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/FhirTerser.java
View File

@ -39,7 +39,6 @@ import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
import ca.uhn.fhir.context.RuntimeChildDirectResource;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.model.api.IElement;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
import ca.uhn.fhir.model.base.composite.BaseContainedDt;
@ -61,7 +60,7 @@ public class FhirTerser {
if (theElement instanceof ISupportsUndeclaredExtensions) {
ISupportsUndeclaredExtensions containingElement = (ISupportsUndeclaredExtensions) theElement;
for (ExtensionDt nextExt : containingElement.getUndeclaredExtensions()) {
theCallback.acceptUndeclaredExtension(containingElement, theChildDefinition, theDefinition, nextExt);
theCallback.acceptUndeclaredExtension(containingElement, null, theChildDefinition, theDefinition, nextExt);
addUndeclaredExtensions(nextExt, theDefinition, theChildDefinition, theCallback);
}
}
@ -87,10 +86,10 @@ public class FhirTerser {
public <T extends IBase> List<T> getAllPopulatedChildElementsOfType(IBaseResource theResource, final Class<T> theType) {
final ArrayList<T> retVal = new ArrayList<T>();
BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
visit(theResource, null, def, new IModelVisitor() {
visit(theResource, null, null, def, new IModelVisitor() {
@SuppressWarnings("unchecked")
@Override
public void acceptElement(IBase theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
public void acceptElement(IBase theElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
if (theElement == null || theElement.isEmpty()) {
return;
}
@ -102,7 +101,7 @@ public class FhirTerser {
@SuppressWarnings("unchecked")
@Override
public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition,
public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition,
ExtensionDt theNextExt) {
if (theType.isAssignableFrom(theNextExt.getClass())) {
retVal.add((T) theNextExt);
@ -118,36 +117,31 @@ public class FhirTerser {
public <T extends IBase> List<ResourceReferenceInfo> getAllResourceReferences(final IBaseResource theResource) {
final ArrayList<ResourceReferenceInfo> retVal = new ArrayList<ResourceReferenceInfo>();
BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
visit(theResource, null, def, new IModelVisitor() {
visit(theResource, null, null, def, new IModelVisitor() {
@SuppressWarnings("unchecked")
@Override
public void acceptElement(IBase theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
public void acceptElement(IBase theElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition) {
if (theElement == null || theElement.isEmpty()) {
return;
}
String name = null;
if (theChildDefinition != null) {
name = theChildDefinition.getElementName();
}
if (BaseResourceReferenceDt.class.isAssignableFrom(theElement.getClass())) {
retVal.add(new ResourceReferenceInfo(theResource, name, (BaseResourceReferenceDt)theElement));
retVal.add(new ResourceReferenceInfo(theResource, thePathToElement, (BaseResourceReferenceDt)theElement));
}
}
@SuppressWarnings("unchecked")
@Override
public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition,
public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition,
ExtensionDt theNextExt) {
String name = null;
if (theChildDefinition != null) {
name = theChildDefinition.getElementName();
}
if (theNextExt.getValue() != null && BaseResourceReferenceDt.class.isAssignableFrom(theNextExt.getValue().getClass())) {
retVal.add(new ResourceReferenceInfo(theResource, name, (BaseResourceReferenceDt)theNextExt.getValue()));
retVal.add(new ResourceReferenceInfo(theResource, thePathToElement, (BaseResourceReferenceDt)theNextExt.getValue()));
}
}
});
return retVal; } private BaseRuntimeChildDefinition getDefinition(BaseRuntimeElementCompositeDefinition<?> theCurrentDef, List<String> theSubList) {
return retVal;
}
private BaseRuntimeChildDefinition getDefinition(BaseRuntimeElementCompositeDefinition<?> theCurrentDef, List<String> theSubList) {
BaseRuntimeChildDefinition nextDef = theCurrentDef.getChildByNameOrThrowDataFormatException(theSubList.get(0));
if (theSubList.size() == 1) {
@ -220,8 +214,19 @@ public class FhirTerser {
}
private void visit(IBase theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, IModelVisitor theCallback) {
theCallback.acceptElement(theElement, theChildDefinition, theDefinition);
private List<String> addNameToList(List<String> theCurrentList, BaseRuntimeChildDefinition theChildDefinition) {
if (theChildDefinition == null)
return null;
if (theCurrentList== null || theCurrentList.isEmpty())
return new ArrayList<String>(Arrays.asList(theChildDefinition.getElementName()));
List<String> newList = new ArrayList<String>(theCurrentList);
newList.add(theChildDefinition.getElementName());
return newList;
}
private void visit(IBase theElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, IModelVisitor theCallback) {
List<String> pathToElement = addNameToList(thePathToElement, theChildDefinition);
theCallback.acceptElement(theElement, pathToElement, theChildDefinition, theDefinition);
addUndeclaredExtensions(theElement, theDefinition, theChildDefinition, theCallback);
// if (theElement.isEmpty()) {
@ -242,7 +247,7 @@ public class FhirTerser {
IResource theResource = resRefDt.getResource();
if (theResource.getId() == null || theResource.getId().isEmpty() || theResource.getId().isLocal()) {
BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
visit(theResource, null, def, theCallback);
visit(theResource, pathToElement, null, def, theCallback);
}
}
break;
@ -284,9 +289,9 @@ public class FhirTerser {
if (nextChild instanceof RuntimeChildDirectResource) {
// Don't descend into embedded resources
theCallback.acceptElement(nextValue, nextChild, childElementDef);
theCallback.acceptElement(nextValue, null, nextChild, childElementDef);
} else {
visit(nextValue, nextChild, childElementDef, theCallback);
visit(nextValue, pathToElement, nextChild, childElementDef, theCallback);
}
}
}
@ -297,7 +302,7 @@ public class FhirTerser {
BaseContainedDt value = (BaseContainedDt) theElement;
for (IResource next : value.getContainedResources()) {
BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(next);
visit(next, null, def, theCallback);
visit(next, pathToElement, null, def, theCallback);
}
break;
}
@ -322,7 +327,7 @@ public class FhirTerser {
*/
public void visit(IBaseResource theResource, IModelVisitor theVisitor) {
BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
visit(theResource, null, def, theVisitor);
visit(theResource, null, null, def, theVisitor);
}
public Object getSingleValueOrNull(IBase theTarget, String thePath) {

6
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/IModelVisitor.java
View File

@ -28,6 +28,8 @@ import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
import java.util.List;
/**
* @see FhirTerser#visit(IBaseResource, IModelVisitor)
*/
@ -39,7 +41,7 @@ public interface IModelVisitor {
* @param theChildDefinition May be null if this is a root element
* @param theDefinition
*/
void acceptElement(IBase theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition);
void acceptElement(IBase theElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition);
/**
*
@ -48,7 +50,7 @@ public interface IModelVisitor {
* @param theDefinition
* @param theNextExt
*/
void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, ExtensionDt theNextExt);
void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, ExtensionDt theNextExt);

17
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ResourceReferenceInfo.java
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@ -28,6 +28,8 @@ import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.hl7.fhir.instance.model.IBaseResource;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
/**
@ -38,10 +40,21 @@ public class ResourceReferenceInfo {
private String myName;
private BaseResourceReferenceDt myResource;
public ResourceReferenceInfo(IBaseResource theOwningResource, String theName, BaseResourceReferenceDt theResource) {
public ResourceReferenceInfo(IBaseResource theOwningResource, List<String> thePathToElement, BaseResourceReferenceDt theResource) {
myOwningResource = theOwningResource.getClass().getAnnotation(ResourceDef.class).name();
myName = theName;
myResource = theResource;
if (thePathToElement != null && !thePathToElement.isEmpty()) {
StringBuilder sb = new StringBuilder();
thePathToElement.iterator();
for (Iterator<String> iterator = thePathToElement.iterator(); iterator.hasNext(); ) {
sb.append(iterator.next());
if (iterator.hasNext())
sb.append(".");
}
myName = sb.toString();
} else {
myName = null;
}
}
@Override

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseFhirDao.java
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@ -123,7 +123,8 @@ public abstract class BaseFhirDao implements IDao {
private FhirContext myContext;
@PersistenceContext(name = "FHIR_UT", type = PersistenceContextType.TRANSACTION, unitName = "FHIR_UT")
// @PersistenceContext(name = "FHIR_UT", type = PersistenceContextType.TRANSACTION, unitName = "FHIR_UT")
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
private EntityManager myEntityManager;
private List<IDaoListener> myListeners = new ArrayList<IDaoListener>();

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseFhirResourceDao.java
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@ -39,6 +39,7 @@ import java.util.Set;
import javax.annotation.PostConstruct;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import javax.persistence.TemporalType;
import javax.persistence.Tuple;
import javax.persistence.TypedQuery;
@ -129,7 +130,7 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseFhirResourceDao.class);
@PersistenceContext()
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
private EntityManager myEntityManager;
@Autowired

17
hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/server/Dstu1BundleFactoryTest.java
View File

@ -76,6 +76,23 @@ public class Dstu1BundleFactoryTest {
myBundleFactory = new Dstu1BundleFactory(ourCtx);
}
@Test
public void whenMedicationHasIngredients_include_shouldIncludeThem() throws Exception {
Medication medication = new Medication();
medication.setName("Main Medication");
medication.setId("Medication/1");
Medication ingredientMedication = new Medication();
ingredientMedication.setName("Ingredient");
ingredientMedication.setId("Medication/2");
Medication.ProductIngredient ingredient = new Medication.ProductIngredient();
ingredient.setItem(new ResourceReferenceDt(ingredientMedication));
medication.getProduct().getIngredient().add(ingredient);
myResourceList = Arrays.asList(new IResource[]{medication});
Bundle bundle = makeBundle(BundleInclusionRule.BASED_ON_INCLUDES, includes("Medication.product.ingredient.item"));
assertEquals(2, bundle.getEntries().size());
}
@Test
public void whenIncludeIsAsterisk_bundle_shouldContainAllReferencedResources() throws Exception {
Bundle bundle = makeBundle(BundleInclusionRule.BASED_ON_INCLUDES, includes("*"));

2
pom.xml
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@ -202,7 +202,7 @@
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<servlet_api_version>3.1.0</servlet_api_version>
<slf4j_version>1.7.10</slf4j_version>
<spring_version>4.1.5.RELEASE</spring_version>
<spring_version>4.1.6.RELEASE</spring_version>
<spring_security_version>3.2.4.RELEASE</spring_security_version>
<thymeleaf-version>2.1.4.RELEASE</thymeleaf-version>
<ebay_cors_filter_version>1.0.1</ebay_cors_filter_version>