Parser enhancements when parsing bundles
This commit is contained in:
jamesagnew
parent
891dddff1e
commit
079f966086
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@ -35,10 +35,12 @@ import javax.xml.stream.events.XMLEvent;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.Validate;
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import org.apache.commons.lang3.tuple.Pair;
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import org.hl7.fhir.instance.model.api.IAnyResource;
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import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
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import org.hl7.fhir.instance.model.api.IBaseBinary;
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import org.hl7.fhir.instance.model.api.IBaseBundle;
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import org.hl7.fhir.instance.model.api.IBaseElement;
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import org.hl7.fhir.instance.model.api.IBaseExtension;
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import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
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@ -49,6 +51,7 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IBaseXhtml;
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import org.hl7.fhir.instance.model.api.ICompositeType;
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import org.hl7.fhir.instance.model.api.IDomainResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.instance.model.api.IPrimitiveType;
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import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
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@ -84,6 +87,7 @@ import ca.uhn.fhir.model.primitive.InstantDt;
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import ca.uhn.fhir.model.primitive.StringDt;
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import ca.uhn.fhir.model.primitive.XhtmlDt;
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import ca.uhn.fhir.rest.server.Constants;
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import ca.uhn.fhir.util.BundleUtil;
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import ca.uhn.fhir.util.FhirTerser;
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import ca.uhn.fhir.util.IModelVisitor;
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@ -2073,8 +2077,6 @@ class ParserState<T> {
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@Override
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public void wereBack() {
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final boolean bundle = "Bundle".equals(myContext.getResourceDefinition(myInstance).getName());
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if (myContext.hasDefaultTypeForProfile()) {
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IBaseMetaType meta = myInstance.getMeta();
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Class<? extends IBaseResource> wantedProfileType = null;
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@ -2149,26 +2151,27 @@ class ParserState<T> {
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}
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});
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final boolean bundle = "Bundle".equals(myContext.getResourceDefinition(myInstance).getName());
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if (bundle) {
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/*
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* Stitch together resource references
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*/
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Map<IdDt, IResource> idToResource = new HashMap<IdDt, IResource>();
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Map<IIdType, IBaseResource> idToResource = new HashMap<IIdType, IBaseResource>();
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FhirTerser t = myContext.newTerser();
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List<IResource> resources = t.getAllPopulatedChildElementsOfType(myInstance, IResource.class);
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for (IResource next : resources) {
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IdDt id = next.getId();
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List<IBaseResource> resources = t.getAllPopulatedChildElementsOfType(myInstance, IBaseResource.class);
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for (IBaseResource next : resources) {
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IIdType id = next.getIdElement();
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if (id != null && id.isEmpty() == false) {
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String resName = myContext.getResourceDefinition(next).getName();
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idToResource.put(id.withResourceType(resName).toUnqualifiedVersionless(), next);
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}
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}
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for (IResource next : resources) {
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List<BaseResourceReferenceDt> refs = myContext.newTerser().getAllPopulatedChildElementsOfType(next, BaseResourceReferenceDt.class);
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for (BaseResourceReferenceDt nextRef : refs) {
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if (nextRef.isEmpty() == false && nextRef.getReference() != null) {
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IResource target = idToResource.get(nextRef.getReference().toUnqualifiedVersionless());
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for (IBaseResource next : resources) {
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List<IBaseReference> refs = myContext.newTerser().getAllPopulatedChildElementsOfType(next, IBaseReference.class);
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for (IBaseReference nextRef : refs) {
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if (nextRef.isEmpty() == false && nextRef.getReferenceElement() != null) {
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IBaseResource target = idToResource.get(nextRef.getReferenceElement().toUnqualifiedVersionless());
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if (target != null) {
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nextRef.setResource(target);
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}
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@ -2176,6 +2179,18 @@ class ParserState<T> {
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}
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}
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/*
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* Set resource IDs based on Bundle.entry.request.url
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*/
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List<Pair<String, IBaseResource>> urlsAndResources = BundleUtil.getBundleEntryUrlsAndResources(myContext, (IBaseBundle) myInstance);
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for (Pair<String, IBaseResource> pair : urlsAndResources) {
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if (pair.getRight() != null && isNotBlank(pair.getLeft()) && pair.getRight().getIdElement().isEmpty()) {
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if (pair.getLeft().startsWith("urn:")) {
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pair.getRight().setId(pair.getLeft());
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}
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}
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}
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}
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populateTarget();
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@ -23,12 +23,15 @@ package ca.uhn.fhir.util;
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import java.util.ArrayList;
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import java.util.List;
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import org.apache.commons.lang3.tuple.Pair;
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import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseBundle;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IPrimitiveType;
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import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
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import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
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import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.RuntimeResourceDefinition;
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@ -57,5 +60,42 @@ public class BundleUtil {
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return retVal;
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}
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@SuppressWarnings("unchecked")
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public static List<Pair<String, IBaseResource>> getBundleEntryUrlsAndResources(FhirContext theContext, IBaseBundle theBundle) {
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RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
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BaseRuntimeChildDefinition entryChild = def.getChildByName("entry");
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List<IBase> entries = entryChild.getAccessor().getValues(theBundle);
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BaseRuntimeElementCompositeDefinition<?> entryChildElem = (BaseRuntimeElementCompositeDefinition<?>) entryChild.getChildByName("entry");
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BaseRuntimeChildDefinition resourceChild = entryChildElem.getChildByName("resource");
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BaseRuntimeChildDefinition requestChild = entryChildElem.getChildByName("request");
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BaseRuntimeElementCompositeDefinition<?> requestDef = (BaseRuntimeElementCompositeDefinition<?>) requestChild.getChildByName("request");
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BaseRuntimeChildDefinition urlChild = requestDef.getChildByName("url");
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List<Pair<String, IBaseResource>> retVal = new ArrayList<Pair<String,IBaseResource>>(entries.size());
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for (IBase nextEntry : entries) {
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String url = null;
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IBaseResource resource = null;
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for (IBase nextEntryValue : requestChild.getAccessor().getValues(nextEntry)) {
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for (IBase nextUrlValue : urlChild.getAccessor().getValues(nextEntryValue)) {
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url = ((IPrimitiveType<String>)nextUrlValue).getValue();
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}
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}
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// Should return 0..1 only
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for (IBase nextValue : resourceChild.getAccessor().getValues(nextEntry)) {
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resource = (IBaseResource) nextValue;
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}
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retVal.add(Pair.of(url, resource));
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}
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return retVal;
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}
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}
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@ -42,6 +42,7 @@ import com.google.common.collect.Sets;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.model.api.Bundle;
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import ca.uhn.fhir.model.api.BundleEntry;
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import ca.uhn.fhir.model.api.ExtensionDt;
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import ca.uhn.fhir.model.api.IResource;
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import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
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@ -100,25 +101,6 @@ public class XmlParserDstu2Test {
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private static final FhirContext ourCtx = FhirContext.forDstu2();
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserDstu2Test.class);
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/**
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* See #312
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*/
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@Test
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public void testEncodeNullExtension() {
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Patient patient = new Patient();
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patient.getUndeclaredExtensions().add(null); // Purposely add null
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patient.getUndeclaredModifierExtensions().add(null); // Purposely add null
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patient.getUndeclaredExtensions().add(new ExtensionDt(false, "http://hello.world", new StringDt("Hello World")));
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patient.getName().add(null);
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patient.addName().getFamily().add(null);
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IParser parser = ourCtx.newXmlParser();
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String xml = parser.encodeResourceToString(patient);
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ourLog.info(xml);
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assertEquals("<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://hello.world\"><valueString value=\"Hello World\"/></extension></Patient>", xml);
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}
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@Test
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public void testBundleWithBinary() {
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//@formatter:off
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@ -150,7 +132,7 @@ public class XmlParserDstu2Test {
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assertArrayEquals(new byte[] { 1, 2, 3, 4 }, bin.getContent());
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}
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@Test
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public void testChoiceTypeWithProfiledType() {
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//@formatter:off
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@ -170,7 +152,7 @@ public class XmlParserDstu2Test {
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String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(parsed);
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assertThat(encoded, containsString("<valueMarkdown value=\"THIS IS MARKDOWN\"/>"));
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}
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@Test
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public void testChoiceTypeWithProfiledType2() {
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Parameters par = new Parameters();
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@ -256,6 +238,43 @@ public class XmlParserDstu2Test {
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assertTrue(parsed.getEntries().get(0).getResource().getId().isEmpty());
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}
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@Test
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public void testEncodeAndParseBundleWithResourceRefs() {
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Patient pt = new Patient();
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pt.setId("patid");
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pt.addName().addFamily("PATIENT");
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Organization org = new Organization();
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org.setId("orgid");
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org.setName("ORG");
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pt.getManagingOrganization().setResource(org);
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ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
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bundle.addEntry().setResource(pt);
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bundle.addEntry().setResource(org);
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String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(bundle);
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ourLog.info(encoded);
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//@formatter:off
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assertThat(encoded, stringContainsInOrder(
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"<Patient xmlns=\"http://hl7.org/fhir\">",
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"<managingOrganization>",
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"<reference value=\"Organization/orgid\"/>",
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"</managingOrganization>"
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));
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//@formatter:on
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bundle = ourCtx.newXmlParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, encoded);
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pt = (Patient) bundle.getEntry().get(0).getResource();
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org = (Organization) bundle.getEntry().get(1).getResource();
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assertEquals("Organization/orgid", org.getId().getValue());
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assertEquals("Organization/orgid", pt.getManagingOrganization().getReference().getValue());
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assertSame(org, pt.getManagingOrganization().getResource());
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}
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@Test
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public void testEncodeAndParseContained() {
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IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
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@ -664,6 +683,31 @@ public class XmlParserDstu2Test {
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assertEquals("VERSION2", label.getVersion());
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}
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/**
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* https://chat.fhir.org/#narrow/stream/implementers/topic/fullUrl.20and.20MessageHeader.2Eid
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*/
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@Test
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public void testEncodeAndParseUuid() {
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Patient p = new Patient();
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p.addName().addFamily("FAMILY");
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p.setId("urn:uuid:4f08cf3d-9f41-41bb-9e10-6e34c5b8f602");
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ca.uhn.fhir.model.dstu2.resource.Bundle b = new ca.uhn.fhir.model.dstu2.resource.Bundle();
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Entry be = b.addEntry();
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be.setResource(p);
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be.getRequest().setUrl(p.getId().getValue());
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String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(b);
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ourLog.info(output);
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ca.uhn.fhir.model.dstu2.resource.Bundle parsedBundle = ourCtx.newXmlParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, output);
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Entry parsedEntry = parsedBundle.getEntry().get(0);
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assertEquals("urn:uuid:4f08cf3d-9f41-41bb-9e10-6e34c5b8f602", parsedEntry.getRequest().getUrl());
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assertEquals("urn:uuid:4f08cf3d-9f41-41bb-9e10-6e34c5b8f602", parsedEntry.getResource().getId().getValue());
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}
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/**
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* See #103
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*/
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@ -1052,6 +1096,25 @@ public class XmlParserDstu2Test {
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}
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/**
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* See #312
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*/
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@Test
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public void testEncodeNullExtension() {
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Patient patient = new Patient();
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patient.getUndeclaredExtensions().add(null); // Purposely add null
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patient.getUndeclaredModifierExtensions().add(null); // Purposely add null
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patient.getUndeclaredExtensions().add(new ExtensionDt(false, "http://hello.world", new StringDt("Hello World")));
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patient.getName().add(null);
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patient.addName().getFamily().add(null);
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IParser parser = ourCtx.newXmlParser();
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String xml = parser.encodeResourceToString(patient);
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ourLog.info(xml);
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assertEquals("<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://hello.world\"><valueString value=\"Hello World\"/></extension></Patient>", xml);
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}
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@Test
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public void testEncodeReferenceUsingUnqualifiedResourceWorksCorrectly() {
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@ -1089,6 +1152,7 @@ public class XmlParserDstu2Test {
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assertThat(str, containsString("<reference value=\"Observation/phitcc_obs_bp_dia\"/>"));
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}
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@Test
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public void testEncodeSummary() {
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Patient patient = new Patient();
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@ -1107,7 +1171,6 @@ public class XmlParserDstu2Test {
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assertThat(encoded, not(containsString("maritalStatus")));
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}
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@Test
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public void testEncodeSummary2() {
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Patient patient = new Patient();
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@ -1131,54 +1194,6 @@ public class XmlParserDstu2Test {
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assertThat(encoded, not(containsString("maritalStatus")));
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}
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@Test
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public void testEncodeWithEncodeElements() throws Exception {
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Patient patient = new Patient();
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patient.addName().addFamily("FAMILY");
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patient.addAddress().addLine("LINE1");
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ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
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bundle.setTotal(100);
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bundle.addEntry().setResource(patient);
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{
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IParser p = ourCtx.newXmlParser();
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p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name", "Bundle.entry")));
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p.setPrettyPrint(true);
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String out = p.encodeResourceToString(bundle);
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ourLog.info(out);
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assertThat(out, not(containsString("total")));
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assertThat(out, (containsString("Patient")));
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assertThat(out, (containsString("name")));
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assertThat(out, not(containsString("address")));
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}
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{
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IParser p = ourCtx.newXmlParser();
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p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
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p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
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p.setPrettyPrint(true);
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String out = p.encodeResourceToString(bundle);
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ourLog.info(out);
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assertThat(out, (containsString("total")));
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assertThat(out, (containsString("Patient")));
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assertThat(out, (containsString("name")));
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assertThat(out, not(containsString("address")));
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}
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{
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IParser p = ourCtx.newXmlParser();
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p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient")));
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p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
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p.setPrettyPrint(true);
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String out = p.encodeResourceToString(bundle);
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ourLog.info(out);
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assertThat(out, (containsString("total")));
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assertThat(out, (containsString("Patient")));
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assertThat(out, (containsString("name")));
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assertThat(out, (containsString("address")));
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}
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}
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@Test
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public void testEncodeWithDontEncodeElements() throws Exception {
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@ -1252,6 +1267,54 @@ public class XmlParserDstu2Test {
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}
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@Test
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public void testEncodeWithEncodeElements() throws Exception {
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Patient patient = new Patient();
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patient.addName().addFamily("FAMILY");
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patient.addAddress().addLine("LINE1");
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ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
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bundle.setTotal(100);
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bundle.addEntry().setResource(patient);
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{
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IParser p = ourCtx.newXmlParser();
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p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name", "Bundle.entry")));
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p.setPrettyPrint(true);
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String out = p.encodeResourceToString(bundle);
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ourLog.info(out);
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assertThat(out, not(containsString("total")));
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assertThat(out, (containsString("Patient")));
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assertThat(out, (containsString("name")));
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assertThat(out, not(containsString("address")));
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}
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{
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IParser p = ourCtx.newXmlParser();
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p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
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p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
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p.setPrettyPrint(true);
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String out = p.encodeResourceToString(bundle);
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ourLog.info(out);
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assertThat(out, (containsString("total")));
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assertThat(out, (containsString("Patient")));
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assertThat(out, (containsString("name")));
|
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assertThat(out, not(containsString("address")));
|
||||
}
|
||||
{
|
||||
IParser p = ourCtx.newXmlParser();
|
||||
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient")));
|
||||
p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
|
||||
p.setPrettyPrint(true);
|
||||
String out = p.encodeResourceToString(bundle);
|
||||
ourLog.info(out);
|
||||
assertThat(out, (containsString("total")));
|
||||
assertThat(out, (containsString("Patient")));
|
||||
assertThat(out, (containsString("name")));
|
||||
assertThat(out, (containsString("address")));
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testMoreExtensions() throws Exception {
|
||||
|
||||
|
|
@ -1351,7 +1414,8 @@ public class XmlParserDstu2Test {
|
|||
assertTrue(d.toString(), d.identical());
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
@Test
|
||||
public void testParseAndEncodeBundleNewStyle() throws Exception {
|
||||
|
|
|
|||
|
|
@ -199,6 +199,39 @@ public class GenericClientDstu2Test {
|
|||
|
||||
}
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* See #322
|
||||
*/
|
||||
@Test
|
||||
public void testFetchConformanceWithSmartExtensionsAltCase() throws Exception {
|
||||
final String respString = IOUtils.toString(GenericClientDstu2Test.class.getResourceAsStream("/conformance_322.json")).replace("valueuri", "valueUri");
|
||||
ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
|
||||
when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
|
||||
when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
|
||||
when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
|
||||
when(myHttpResponse.getEntity().getContent()).thenAnswer(new Answer<ReaderInputStream>() {
|
||||
@Override
|
||||
public ReaderInputStream answer(InvocationOnMock theInvocation) throws Throwable {
|
||||
return new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8"));
|
||||
}
|
||||
});
|
||||
|
||||
IGenericClient client = ourCtx.newRestfulGenericClient("http://localhost:8080/fhir");
|
||||
Conformance conf = client.fetchConformance().ofType(Conformance.class).execute();
|
||||
|
||||
Rest rest = conf.getRest().get(0);
|
||||
RestSecurity security = rest.getSecurity();
|
||||
|
||||
List<ExtensionDt> ext = security.getUndeclaredExtensionsByUrl("http://fhir-registry.smarthealthit.org/StructureDefinition/oauth-uris");
|
||||
List<ExtensionDt> tokenExts = ext.get(0).getUndeclaredExtensionsByUrl("token");
|
||||
ExtensionDt tokenExt = tokenExts.get(0);
|
||||
UriDt value = (UriDt) tokenExt.getValue();
|
||||
assertEquals("https://my-server.org/token", value.getValueAsString());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testAcceptHeaderPreflightConformance() throws Exception {
|
||||
String methodName = "testAcceptHeaderPreflightConformance";
|
||||
|
|
|
|||
|
|
@ -102,6 +102,45 @@ public class XmlParserDstu3Test {
|
|||
ourCtx.setNarrativeGenerator(null);
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testEncodeAndParseBundleWithResourceRefs() {
|
||||
|
||||
Patient pt = new Patient();
|
||||
pt.setId("patid");
|
||||
pt.addName().addFamily("PATIENT");
|
||||
|
||||
Organization org = new Organization();
|
||||
org.setId("orgid");
|
||||
org.setName("ORG");
|
||||
pt.getManagingOrganization().setResource(org);
|
||||
|
||||
Bundle bundle = new Bundle();
|
||||
bundle.addEntry().setResource(pt);
|
||||
bundle.addEntry().setResource(org);
|
||||
|
||||
String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(bundle);
|
||||
ourLog.info(encoded);
|
||||
|
||||
//@formatter:off
|
||||
assertThat(encoded, stringContainsInOrder(
|
||||
"<Patient xmlns=\"http://hl7.org/fhir\">",
|
||||
"<managingOrganization>",
|
||||
"<reference value=\"Organization/orgid\"/>",
|
||||
"</managingOrganization>"
|
||||
));
|
||||
//@formatter:on
|
||||
|
||||
bundle = ourCtx.newXmlParser().parseResource(Bundle.class, encoded);
|
||||
pt = (Patient) bundle.getEntry().get(0).getResource();
|
||||
org = (Organization) bundle.getEntry().get(1).getResource();
|
||||
|
||||
assertEquals("Organization/orgid", org.getIdElement().getValue());
|
||||
assertEquals("Organization/orgid", pt.getManagingOrganization().getReferenceElement().getValue());
|
||||
assertSame(org, pt.getManagingOrganization().getResource());
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testBundleWithBinary() {
|
||||
//@formatter:off
|
||||
|
|
|
|||
|
|
@ -371,6 +371,17 @@
|
|||
DateTimeType should fail to parse 1974-12-25+10:00 as this is not
|
||||
a valid time in FHIR. Thanks to Grahame Grieve for reporting!
|
||||
</action>
|
||||
<action type="fix">
|
||||
When parsing a Bundle resource, if the Bundle.entry.request.url contains a UUID
|
||||
but the resource body has no ID, the Resource.id will be populated with the ID from the
|
||||
Bundle.entry.request.url. This is helpful when round tripping Bundles containing
|
||||
UUIDs.
|
||||
</action>
|
||||
<action type="fix">
|
||||
When parsing a DSTU3 bundle, references between resources did not have
|
||||
the actual resource instance populated into the reference if the
|
||||
IDs matched as they did in DSTU1/2.
|
||||
</action>
|
||||
</release>
|
||||
<release version="1.4" date="2016-02-04">
|
||||
<action type="add">
|
||||
|
|
|
|||
Loading…
Reference in New Issue