mirror of
https://github.com/hapifhir/hapi-fhir.git
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Fix Xml parse issue: do not override the references with global contained resources if they have already been resolved
This commit is contained in:
August Langhout
James Agnew
parent
300c4e66ba
commit
2b23a6f2f0
@ -1054,6 +1054,8 @@ class ParserState<T> {
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private void stitchBundleCrossReferences() {
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final boolean bundle = "Bundle".equals(myContext.getResourceDefinition(myInstance).getName());
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if (bundle) {
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//if (myGlobalReferences.stream().map(x -> x.))
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//throw new DataFormatException("resourceType does not appear to be 'TagList', found: " + theLocalPart);
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FhirTerser t = myContext.newTerser();
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@ -1074,7 +1076,7 @@ class ParserState<T> {
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*/
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for (IBaseResource next : myGlobalResources) {
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IIdType id = next.getIdElement();
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if (id != null && id.isEmpty() == false) {
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if (id != null && !id.isEmpty()) {
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String resName = myContext.getResourceDefinition(next).getName();
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IIdType idType = id.withResourceType(resName).toUnqualifiedVersionless();
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idToResource.put(idType.getValueAsString(), next);
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@ -1082,10 +1084,11 @@ class ParserState<T> {
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}
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for (IBaseReference nextRef : myGlobalReferences) {
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if (nextRef.isEmpty() == false && nextRef.getReferenceElement() != null) {
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if (!nextRef.isEmpty() && nextRef.getReferenceElement() != null) {
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IIdType unqualifiedVersionless = nextRef.getReferenceElement().toUnqualifiedVersionless();
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IBaseResource target = idToResource.get(unqualifiedVersionless.getValueAsString());
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if (target != null) {
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// resource can already be filled with local contained resource by populateTarget()
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if (target != null && nextRef.getResource() == null) {
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nextRef.setResource(target);
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}
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}
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@ -7,18 +7,25 @@ import static org.junit.Assert.assertNotEquals;
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import static org.junit.Assert.assertThat;
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import ca.uhn.fhir.test.BaseTest;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.r4.model.Bundle;
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import org.hl7.fhir.r4.model.Composition;
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import org.hl7.fhir.r4.model.DocumentReference;
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import org.hl7.fhir.r4.model.MessageHeader;
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import org.hl7.fhir.r4.model.Narrative;
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import org.hl7.fhir.r4.model.Observation;
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import org.hl7.fhir.r4.model.Patient;
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import org.junit.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import ca.uhn.fhir.context.FhirContext;
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import com.google.common.base.Charsets;
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import com.google.common.io.Resources;
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import java.io.IOException;
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import java.net.URL;
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public class XmlParserR4Test extends BaseTest {
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private static final Logger ourLog = LoggerFactory.getLogger(XmlParserR4Test.class);
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@ -79,6 +86,21 @@ public class XmlParserR4Test extends BaseTest {
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}
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@Test
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public void testParseBundleWithMultipleNestedContainedResources() throws Exception {
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URL url = Resources.getResource("bundle-with-two-patient-resources.xml");
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String text = Resources.toString(url, Charsets.UTF_8);
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Bundle input = ourCtx.newXmlParser().parseResource(Bundle.class, text);
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assertEquals("12346", getPatientIdValue(input, 0));
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assertEquals("12345", getPatientIdValue(input, 1));
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}
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private String getPatientIdValue(Bundle input, int entry) {
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final DocumentReference documentReference = (DocumentReference)input.getEntry().get(entry).getResource();
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final Patient patient = (Patient) documentReference.getSubject().getResource();
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return patient.getIdentifier().get(0).getValue();
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}
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/**
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* See #1658
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*/
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@ -0,0 +1,197 @@
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<Bundle xmlns="http://hl7.org/fhir">
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<meta>
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<profile value="http://forcare.com/fhir/createCda" />
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</meta>
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<type value="transaction" />
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<entry>
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<resource>
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<DocumentReference>
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<id value="doc1" />
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<contained>
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<Patient>
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<id value="patient" />
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<identifier>
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<system value="urn:oid:1.3.6.1.4.1.21367.2005.3.7" />
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<value value="12346" />
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</identifier>
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<name>
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<use value="official" />
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<family value="Beugels" />
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<given value="Kees" />
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</name>
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<gender value="male" />
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<birthDate value="1986-11-28" />
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</Patient>
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</contained>
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<subject>
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<reference value="#patient" />
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</subject>
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<type>
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<coding>
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<system value="2.16.840.1.113883.6.1" />
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<code value="57016-8" />
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<display value="Privacy Policy Acknowledgment" />
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</coding>
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</type>
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<category>
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<coding>
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<system value="2.16.840.1.113883.6.1" />
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<code value="57016-8" />
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<display value="Privacy Policy Acknowledgment" />
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</coding>
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</category>
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<author>
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<reference value="#patient" />
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</author>
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<date value="2016-05-04T08:18:03.203Z" />
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<status value="current" />
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<description value="Hospital Privacy Consent" />
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<securityLabel>
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<coding>
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<system value="2.16.840.1.113883.5.25" />
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<code value="N" />
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<display value="Normal" />
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</coding>
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</securityLabel>
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<content>
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<attachment>
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<contentType value="text/xml" />
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<language value="en-US" />
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<url value="urn:uuid:d7d8ffca-e364-484b-bbf9-6a730854aea5" />
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</attachment>
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<format>
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<system value="1.3.6.1.4.1.19376.1.2.3" />
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<code value="urn:ihe:iti:bppc-sd:2007" />
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<display value="Basic Patient Privacy Consent (scanned part)" />
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</format>
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</content>
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<context>
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<event>
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<coding>
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<system value="1.2.826.0.1.3680043.2.1611.2.10" />
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<code value="allowMedicalDoctorsFromHospitalAToSeeDocuments" />
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<display value="I allow Medical Doctors in Hospital A to access my medical record" />
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</coding>
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</event>
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<event>
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<coding>
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<system value="1.2.826.0.1.3680043.2.1611.2.10" />
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<code value="denyMedicalDoctorsFromHospitalBToSeeDocuments" />
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<display value="I deny Medical Doctors in Hospital B to access my medical record" />
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</coding>
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</event>
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<period>
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<start value="2016-05-04T08:18:03.203Z" />
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<end value="2016-09-04T08:18:03.203Z" />
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</period>
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<facilityType>
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<coding>
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<system value="2.16.840.1.113883.5.10588" />
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<code value="HOSP" />
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<display value="Hospital" />
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</coding>
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</facilityType>
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<practiceSetting>
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<coding>
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<system value="2.16.840.1.113883.2.1.6.8" />
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<code value="300" />
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<display value="General Medicine" />
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</coding>
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</practiceSetting>
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</context>
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</DocumentReference>
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</resource>
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</entry>
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<entry>
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<resource>
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<DocumentReference xmlns="http://hl7.org/fhir">
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<id value="doc2" />
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<contained>
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<Patient xmlns="http://hl7.org/fhir">
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<id value="patient" />
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<identifier>
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<system value="urn:oid:1.3.6.1.4.1.21367.2005.3.7" />
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<value value="12345" />
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</identifier>
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<name>
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<use value="official" />
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<family value="Bakker" />
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<given value="Eddy" />
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</name>
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<gender value="male" />
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<birthDate value="1986-11-28" />
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</Patient>
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</contained>
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<subject>
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<reference value="#patient" />
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</subject>
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<type>
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<coding>
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<system value="2.16.840.1.113883.6.1" />
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<code value="57016-8" />
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<display value="Privacy Policy Acknowledgment" />
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</coding>
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</type>
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<category>
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<coding>
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<system value="2.16.840.1.113883.6.1" />
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<code value="57016-8" />
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<display value="Privacy Policy Acknowledgment" />
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</coding>
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</category>
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<author>
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<reference value="#patient" />
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</author>
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<date value="2016-05-04T08:18:03.203Z" />
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<status value="current" />
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<description value="GPs Privacy Consent" />
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<securityLabel>
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<coding>
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<system value="2.16.840.1.113883.5.25" />
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<code value="N" />
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<display value="Normal" />
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</coding>
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</securityLabel>
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<content>
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<attachment>
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<contentType value="text/xml" />
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<language value="en-US" />
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<url value="urn:uuid:d7d8ffca-e364-484b-bbf9-6a730854aea5" />
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</attachment>
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<format>
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<system value="1.3.6.1.4.1.19376.1.2.3" />
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<code value="urn:ihe:iti:bppc-sd:2007" />
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<display value="Basic Patient Privacy Consent (scanned part)" />
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</format>
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</content>
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<context>
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<event>
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<coding>
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<system value="1.2.826.0.1.3680043.2.1611.2.10" />
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<code value="denyGeneralPractitionersFromHestiaToSeeDocuments" />
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<display value="I deny Medical Doctors in Hestia General Practitioners to access my medical record" />
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</coding>
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</event>
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<period>
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<start value="2016-05-04T08:18:03.203Z" />
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<end value="2016-09-04T08:18:03.203Z" />
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</period>
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<facilityType>
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<coding>
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<system value="2.16.840.1.113883.5.10588" />
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<code value="HOSP" />
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<display value="Hospital" />
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</coding>
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</facilityType>
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<practiceSetting>
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<coding>
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<system value="2.16.840.1.113883.2.1.6.8" />
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<code value="300" />
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<display value="General Medicine" />
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</coding>
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</practiceSetting>
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</context>
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</DocumentReference>
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</resource>
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</entry>
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</Bundle>
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