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https://github.com/hapifhir/hapi-fhir.git
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Fix #113 - Handle contained resources with non-local IDs
This commit is contained in:
James Agnew
parent
c3877c1da9
commit
95d5503a9a
@ -20,7 +20,7 @@ package ca.uhn.fhir.parser;
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* #L%
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*/
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import static org.apache.commons.lang3.StringUtils.*;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import java.io.IOException;
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import java.io.Reader;
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@ -47,7 +47,6 @@ import org.hl7.fhir.instance.model.api.IReference;
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import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
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import ca.uhn.fhir.context.BaseRuntimeDeclaredChildDefinition;
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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.ConfigurationException;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
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@ -62,6 +61,7 @@ import ca.uhn.fhir.model.primitive.IdDt;
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public abstract class BaseParser implements IParser {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseParser.class);
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private ContainedResources myContainedResources;
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private FhirContext myContext;
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private boolean mySuppressNarratives;
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@ -80,6 +80,9 @@ public abstract class BaseParser implements IParser {
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for (IResource next : containedResources) {
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String nextId = next.getId().getValue();
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if (StringUtils.isNotBlank(nextId)) {
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if (!nextId.startsWith("#")) {
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nextId = '#' + nextId;
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}
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allIds.add(nextId);
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if (existingIdToContainedResource == null) {
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existingIdToContainedResource = new HashMap<String, IBaseResource>();
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@ -119,7 +122,7 @@ public abstract class BaseParser implements IParser {
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if (existingIdToContainedResource != null) {
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IBaseResource potentialTarget = existingIdToContainedResource.remove(next.getReference().getValue());
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if (potentialTarget != null) {
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theContained.addContained(potentialTarget);
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theContained.addContained(next.getReference(), potentialTarget);
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containResourcesForEncoding(theContained, potentialTarget, theTarget);
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}
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}
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@ -387,6 +390,11 @@ public abstract class BaseParser implements IParser {
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myResources.add(theResource);
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}
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public void addContained(IdDt theId, IBaseResource theResource) {
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myResourceToId.put(theResource, theId);
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myResources.add(theResource);
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}
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public List<IBaseResource> getContainedResources() {
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return myResources;
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}
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@ -104,6 +104,10 @@ import ca.uhn.fhir.narrative.INarrativeGenerator;
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import ca.uhn.fhir.util.ElementUtil;
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import ca.uhn.fhir.util.UrlUtil;
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/**
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* This class is the FHIR JSON parser/encoder. Users should not interact with this
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* class directly, but should use {@link FhirContext#newJsonParser()} to get an instance.
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*/
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public class JsonParser extends BaseParser implements IParser {
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private static final Set<String> BUNDLE_TEXTNODE_CHILDREN_DSTU1;
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@ -20,14 +20,15 @@ package ca.uhn.fhir.parser;
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* #L%
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*/
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import static org.apache.commons.lang3.StringUtils.*;
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import static org.apache.commons.lang3.StringUtils.defaultString;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import java.io.IOException;
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import java.io.Reader;
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import java.io.StringWriter;
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import java.io.Writer;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.Iterator;
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import java.util.List;
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@ -49,8 +50,8 @@ import org.apache.commons.lang3.StringUtils;
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import org.hl7.fhir.instance.model.IBase;
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import org.hl7.fhir.instance.model.IBaseResource;
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import org.hl7.fhir.instance.model.IPrimitiveType;
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import org.hl7.fhir.instance.model.api.IBaseBinary;
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import org.hl7.fhir.instance.model.api.IAnyResource;
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import org.hl7.fhir.instance.model.api.IBaseBinary;
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import org.hl7.fhir.instance.model.api.IBaseDatatype;
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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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@ -91,7 +92,12 @@ import ca.uhn.fhir.util.NonPrettyPrintWriterWrapper;
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import ca.uhn.fhir.util.PrettyPrintWriterWrapper;
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import ca.uhn.fhir.util.XmlUtil;
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/**
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* This class is the FHIR XML parser/encoder. Users should not interact with this
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* class directly, but should use {@link FhirContext#newXmlParser()} to get an instance.
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*/
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public class XmlParser extends BaseParser implements IParser {
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static final String ATOM_NS = "http://www.w3.org/2005/Atom";
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static final String FHIR_NS = "http://hl7.org/fhir";
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static final String OPENSEARCH_NS = "http://a9.com/-/spec/opensearch/1.1/";
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@ -20,11 +20,14 @@ import org.junit.Test;
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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.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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import ca.uhn.fhir.model.api.Tag;
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import ca.uhn.fhir.model.api.TagList;
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import ca.uhn.fhir.model.base.composite.BaseCodingDt;
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import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
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import ca.uhn.fhir.model.dstu2.composite.CodingDt;
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import ca.uhn.fhir.model.dstu2.composite.ContainedDt;
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import ca.uhn.fhir.model.dstu2.composite.DurationDt;
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import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
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import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
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@ -32,6 +35,7 @@ import ca.uhn.fhir.model.dstu2.resource.AllergyIntolerance;
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import ca.uhn.fhir.model.dstu2.resource.Binary;
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import ca.uhn.fhir.model.dstu2.resource.Composition;
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import ca.uhn.fhir.model.dstu2.resource.Encounter;
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import ca.uhn.fhir.model.dstu2.resource.Medication;
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import ca.uhn.fhir.model.dstu2.resource.MedicationPrescription;
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import ca.uhn.fhir.model.dstu2.resource.Organization;
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import ca.uhn.fhir.model.dstu2.resource.Patient;
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@ -53,6 +57,160 @@ public class XmlParserTest {
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XMLUnit.setIgnoreWhitespace(true);
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}
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/**
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* See #113
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*/
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@Test
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public void testEncodeContainedResources() {
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MedicationPrescription medicationPrescript = new MedicationPrescription();
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String medId = "123";
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CodeableConceptDt codeDt = new CodeableConceptDt("urn:sys", "code1");
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// Adding medication to Contained.
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Medication medResource = new Medication();
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medResource.setCode(codeDt);
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medResource.setId("#" + String.valueOf(medId));
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ArrayList<IResource> medResList = new ArrayList<IResource>();
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medResList.add(medResource);
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ContainedDt medContainedDt = new ContainedDt();
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medContainedDt.setContainedResources(medResList);
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medicationPrescript.setContained(medContainedDt);
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// Medication reference. This should point to the contained resource.
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ResourceReferenceDt medRefDt = new ResourceReferenceDt("#" + medId);
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medRefDt.setDisplay("MedRef");
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medicationPrescript.setMedication(medRefDt);
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IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
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String encoded = p.encodeResourceToString(medicationPrescript);
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ourLog.info(encoded);
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//@formatter:on
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assertThat(encoded, stringContainsInOrder(
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"<MedicationPrescription xmlns=\"http://hl7.org/fhir\">",
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"<contained>",
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"<Medication xmlns=\"http://hl7.org/fhir\">",
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"<id value=\"123\"/>",
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"<code>",
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"<coding>",
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"<system value=\"urn:sys\"/>",
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"<code value=\"code1\"/>",
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"</coding>",
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"</code>",
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"</Medication>",
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"</contained>",
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"<medication>",
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"<reference value=\"#123\"/>",
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"<display value=\"MedRef\"/>",
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"</medication>",
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"</MedicationPrescription>"));
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//@formatter:off
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}
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/**
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* See #113
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*/
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@Test
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public void testEncodeContainedResourcesManualContainUsingNonLocalId() {
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MedicationPrescription medicationPrescript = new MedicationPrescription();
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String medId = "123";
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CodeableConceptDt codeDt = new CodeableConceptDt("urn:sys", "code1");
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// Adding medication to Contained.
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Medication medResource = new Medication();
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medResource.setCode(codeDt);
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medResource.setId(String.valueOf(medId)); // ID does not start with '#'
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ArrayList<IResource> medResList = new ArrayList<IResource>();
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medResList.add(medResource);
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ContainedDt medContainedDt = new ContainedDt();
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medContainedDt.setContainedResources(medResList);
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medicationPrescript.setContained(medContainedDt);
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// Medication reference. This should point to the contained resource.
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ResourceReferenceDt medRefDt = new ResourceReferenceDt("#" + medId);
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medRefDt.setDisplay("MedRef");
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medicationPrescript.setMedication(medRefDt);
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IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
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String encoded = p.encodeResourceToString(medicationPrescript);
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ourLog.info(encoded);
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//@formatter:on
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assertThat(encoded, stringContainsInOrder(
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"<MedicationPrescription xmlns=\"http://hl7.org/fhir\">",
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"<contained>",
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"<Medication xmlns=\"http://hl7.org/fhir\">",
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"<id value=\"123\"/>",
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"<code>",
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"<coding>",
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"<system value=\"urn:sys\"/>",
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"<code value=\"code1\"/>",
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"</coding>",
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"</code>",
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"</Medication>",
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"</contained>",
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"<medication>",
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"<reference value=\"#123\"/>",
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"<display value=\"MedRef\"/>",
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"</medication>",
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"</MedicationPrescription>"));
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//@formatter:off
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}
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/**
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* See #113
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*/
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@Test
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public void testEncodeContainedResourcesAutomatic() {
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MedicationPrescription medicationPrescript = new MedicationPrescription();
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String nameDisp = "MedRef";
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CodeableConceptDt codeDt = new CodeableConceptDt("urn:sys", "code1");
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// Adding medication to Contained.
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Medication medResource = new Medication();
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// No ID set
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medResource.setCode(codeDt);
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// Medication reference. This should point to the contained resource.
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ResourceReferenceDt medRefDt = new ResourceReferenceDt();
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medRefDt.setDisplay(nameDisp);
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// Resource reference set, but no ID
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medRefDt.setResource(medResource);
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medicationPrescript.setMedication(medRefDt);
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IParser p = ourCtx.newXmlParser().setPrettyPrint(true);
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String encoded = p.encodeResourceToString(medicationPrescript);
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ourLog.info(encoded);
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//@formatter:on
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assertThat(encoded, stringContainsInOrder(
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"<MedicationPrescription xmlns=\"http://hl7.org/fhir\">",
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"<contained>",
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"<Medication xmlns=\"http://hl7.org/fhir\">",
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"<id value=\"1\"/>",
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"<code>",
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"<coding>",
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"<system value=\"urn:sys\"/>",
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"<code value=\"code1\"/>",
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"</coding>",
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"</code>",
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"</Medication>",
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"</contained>",
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"<medication>",
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"<reference value=\"#1\"/>",
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"<display value=\"MedRef\"/>",
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"</medication>",
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"</MedicationPrescription>"));
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//@formatter:off
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}
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@Test
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public void testEncodeAndParseSecurityLabels() {
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Patient p = new Patient();
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