Changes working now
This commit is contained in:
James Agnew
parent
5c752cdace
commit
1ab9b58e9f
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@ -67,6 +67,34 @@ public class JsonParserDstu2Test {
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private static FhirContext ourCtx = FhirContext.forDstu2();
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParserDstu2Test.class);
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/**
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* See #544
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*/
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@Test
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public void testBundleStitchReferencesByUuid() throws Exception {
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ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
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DocumentManifest dm = new DocumentManifest();
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dm.getSubject().setReference("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
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bundle.addEntry().setResource(dm);
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Patient patient = new Patient();
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patient.addName().addFamily("FAMILY");
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bundle.addEntry().setResource(patient).setFullUrl("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
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String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle);
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ourLog.info(encoded);
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bundle = ourCtx.newJsonParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, encoded);
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dm = (DocumentManifest) bundle.getEntry().get(0).getResource();
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assertEquals("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3", dm.getSubject().getReference());
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Patient subject = (Patient) dm.getSubject().getResource();
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assertNotNull(subject);
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assertEquals("FAMILY", subject.getNameFirstRep().getFamilyAsSingleString());
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}
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@Test
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public void testContainedResourceInExtensionUndeclared() {
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Patient p = new Patient();
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@ -34,52 +34,16 @@ import java.util.UUID;
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import org.apache.commons.io.IOUtils;
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import org.hamcrest.Matchers;
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import org.hamcrest.core.StringContains;
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import org.hl7.fhir.dstu3.model.*;
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import org.hl7.fhir.dstu3.model.Address.AddressUse;
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import org.hl7.fhir.dstu3.model.Address.AddressUseEnumFactory;
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import org.hl7.fhir.dstu3.model.Attachment;
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import org.hl7.fhir.dstu3.model.AuditEvent;
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import org.hl7.fhir.dstu3.model.Basic;
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import org.hl7.fhir.dstu3.model.Binary;
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import org.hl7.fhir.dstu3.model.Bundle;
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import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
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import org.hl7.fhir.dstu3.model.Bundle.BundleType;
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import org.hl7.fhir.dstu3.model.Claim;
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import org.hl7.fhir.dstu3.model.Coding;
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import org.hl7.fhir.dstu3.model.Communication;
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import org.hl7.fhir.dstu3.model.Condition;
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import org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus;
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import org.hl7.fhir.dstu3.model.Conformance;
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import org.hl7.fhir.dstu3.model.Conformance.UnknownContentCode;
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import org.hl7.fhir.dstu3.model.Coverage;
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import org.hl7.fhir.dstu3.model.DateTimeType;
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import org.hl7.fhir.dstu3.model.DateType;
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import org.hl7.fhir.dstu3.model.DecimalType;
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import org.hl7.fhir.dstu3.model.DiagnosticReport;
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import org.hl7.fhir.dstu3.model.EnumFactory;
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import org.hl7.fhir.dstu3.model.Enumeration;
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import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
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import org.hl7.fhir.dstu3.model.ExplanationOfBenefit;
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import org.hl7.fhir.dstu3.model.Extension;
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import org.hl7.fhir.dstu3.model.HumanName;
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import org.hl7.fhir.dstu3.model.IdType;
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import org.hl7.fhir.dstu3.model.Identifier.IdentifierUse;
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import org.hl7.fhir.dstu3.model.Linkage;
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import org.hl7.fhir.dstu3.model.Medication;
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import org.hl7.fhir.dstu3.model.MedicationRequest;
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import org.hl7.fhir.dstu3.model.Observation;
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import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
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import org.hl7.fhir.dstu3.model.Parameters;
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import org.hl7.fhir.dstu3.model.Patient;
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import org.hl7.fhir.dstu3.model.PrimitiveType;
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import org.hl7.fhir.dstu3.model.Quantity;
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import org.hl7.fhir.dstu3.model.QuestionnaireResponse;
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import org.hl7.fhir.dstu3.model.Reference;
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import org.hl7.fhir.dstu3.model.RelatedPerson;
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import org.hl7.fhir.dstu3.model.SampledData;
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import org.hl7.fhir.dstu3.model.SimpleQuantity;
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import org.hl7.fhir.dstu3.model.StringType;
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import org.hl7.fhir.dstu3.model.UriType;
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import org.hl7.fhir.dstu3.model.ValueSet;
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import org.hl7.fhir.utilities.xhtml.XhtmlNode;
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import org.junit.After;
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import org.junit.AfterClass;
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@ -115,6 +79,35 @@ public class JsonParserDstu3Test {
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ourCtx.setNarrativeGenerator(null);
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}
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/**
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* See #544
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*/
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@Test
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public void testBundleStitchReferencesByUuid() throws Exception {
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Bundle bundle = new Bundle();
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DocumentManifest dm = new DocumentManifest();
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dm.getSubject().setReference("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
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bundle.addEntry().setResource(dm);
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Patient patient = new Patient();
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patient.addName().setFamily("FAMILY");
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bundle.addEntry().setResource(patient).setFullUrl("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
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String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle);
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ourLog.info(encoded);
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bundle = ourCtx.newJsonParser().parseResource(Bundle.class, encoded);
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dm = (DocumentManifest) bundle.getEntry().get(0).getResource();
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assertEquals("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3", dm.getSubject().getReference());
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Patient subject = (Patient) dm.getSubject().getResource();
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assertNotNull(subject);
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assertEquals("FAMILY", subject.getNameFirstRep().getFamily());
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}
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@Test
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public void testIncorrectJsonTypesIdAndArray() {
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@ -81,165 +81,27 @@ public class XmlParserDstu3Test {
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*/
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@Test
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public void testBundleStitchReferencesByUuid() throws Exception {
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String body = IOUtils.toString(XmlParserDstu3Test.class.getResourceAsStream("/bundle_ref_by_uuid_544.xml"), StandardCharsets.UTF_8);
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Bundle bundle = ourCtx.newXmlParser().parseResource(Bundle.class, body);
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Bundle bundle = new Bundle();
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DocumentManifest dm = (DocumentManifest) bundle.getEntry().get(0).getResource();
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DocumentManifest dm = new DocumentManifest();
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dm.getSubject().setReference("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
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bundle.addEntry().setResource(dm);
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Patient patient = new Patient();
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patient.addName().setFamily("FAMILY");
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bundle.addEntry().setResource(patient).setFullUrl("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3");
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String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(bundle);
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ourLog.info(encoded);
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bundle = ourCtx.newXmlParser().parseResource(Bundle.class, encoded);
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dm = (DocumentManifest) bundle.getEntry().get(0).getResource();
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assertEquals("urn:uuid:96e85cca-9797-45d6-834a-c4eb27f331d3", dm.getSubject().getReference());
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Patient subject = (Patient) dm.getSubject().getResource();
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assertNotNull(subject);
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}
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/**
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* See #414
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*/
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@Test
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public void testParseXmlExtensionWithoutUrl() {
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//@formatter:off
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String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
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" <extension>\n" +
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" <valueDateTime value=\"2011-01-02T11:13:15\"/>\n" +
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" </extension>\n" +
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"</Patient>";
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//@formatter:on
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IParser parser = ourCtx.newXmlParser();
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parser.setParserErrorHandler(new LenientErrorHandler());
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Patient parsed = (Patient) parser.parseResource(input);
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assertEquals(1, parsed.getExtension().size());
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assertEquals(null, parsed.getExtension().get(0).getUrl());
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assertEquals("2011-01-02T11:13:15", parsed.getExtension().get(0).getValueAsPrimitive().getValueAsString());
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try {
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parser = ourCtx.newXmlParser();
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parser.setParserErrorHandler(new StrictErrorHandler());
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parser.parseResource(input);
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fail();
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} catch (DataFormatException e) {
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assertEquals("Resource is missing required element 'url' in parent element 'extension'", e.getCause().getMessage());
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}
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}
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/**
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* See #414
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*/
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@Test
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public void testParseXmlModifierExtensionWithoutUrl() {
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//@formatter:off
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String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
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" <modifierExtension>\n" +
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" <valueDateTime value=\"2011-01-02T11:13:15\"/>\n" +
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" </modifierExtension>\n" +
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"</Patient>";
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//@formatter:on
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IParser parser = ourCtx.newXmlParser();
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parser.setParserErrorHandler(new LenientErrorHandler());
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Patient parsed = (Patient) parser.parseResource(input);
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assertEquals(1, parsed.getModifierExtension().size());
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assertEquals(null, parsed.getModifierExtension().get(0).getUrl());
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assertEquals("2011-01-02T11:13:15", parsed.getModifierExtension().get(0).getValueAsPrimitive().getValueAsString());
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try {
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parser = ourCtx.newXmlParser();
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parser.setParserErrorHandler(new StrictErrorHandler());
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parser.parseResource(input);
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fail();
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} catch (DataFormatException e) {
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assertEquals("Resource is missing required element 'url' in parent element 'modifierExtension'", e.getCause().getMessage());
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}
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}
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@Test
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public void testEncodeChainedContainedResourcer() {
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Organization gp = new Organization();
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gp.setName("grandparent");
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Organization parent = new Organization();
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parent.setName("parent");
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parent.getPartOf().setResource(gp);
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Organization child = new Organization();
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child.setName("child");
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child.getPartOf().setResource(parent);
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Patient patient = new Patient();
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patient.getManagingOrganization().setResource(child);
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String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
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ourLog.info(encoded);
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patient = ourCtx.newXmlParser().parseResource(Patient.class, encoded);
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child = (Organization) patient.getManagingOrganization().getResource();
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assertEquals("child", child.getName());
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parent = (Organization) child.getPartOf().getResource();
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assertEquals("parent", parent.getName());
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gp = (Organization) parent.getPartOf().getResource();
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assertEquals("grandparent", gp.getName());
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}
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/**
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* If a contained resource refers to a contained resource that comes after it, it should still be successfully
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* woven together.
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*/
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@Test
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public void testParseWovenContainedResources() throws IOException {
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String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_woven_obs.xml"), StandardCharsets.UTF_8);
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IParser parser = ourCtx.newXmlParser();
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parser.setParserErrorHandler(new StrictErrorHandler());
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org.hl7.fhir.dstu3.model.Bundle bundle = parser.parseResource(Bundle.class, string);
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DiagnosticReport resource = (DiagnosticReport) bundle.getEntry().get(0).getResource();
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Observation obs = (Observation) resource.getResult().get(1).getResource();
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assertEquals("#2", obs.getId());
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Reference performerFirstRep = obs.getPerformerFirstRep();
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Practitioner performer = (Practitioner) performerFirstRep.getResource();
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assertEquals("#3", performer.getId());
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}
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@Test(expected = DataFormatException.class)
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public void testContainedResourceWithNoId() throws IOException {
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String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_contained_with_no_id.xml"), StandardCharsets.UTF_8);
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IParser parser = ourCtx.newXmlParser();
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parser.setParserErrorHandler(new StrictErrorHandler());
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parser.parseResource(Bundle.class, string);
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}
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@Test()
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public void testContainedResourceWithNoIdLenient() throws IOException {
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String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_contained_with_no_id.xml"), StandardCharsets.UTF_8);
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IParser parser = ourCtx.newXmlParser();
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parser.setParserErrorHandler(new LenientErrorHandler());
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parser.parseResource(Bundle.class, string);
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}
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@Test(expected = DataFormatException.class)
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public void testParseWithInvalidLocalRef() throws IOException {
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String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
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IParser parser = ourCtx.newXmlParser();
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parser.setParserErrorHandler(new StrictErrorHandler());
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parser.parseResource(Bundle.class, string);
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}
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@Test()
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public void testParseWithInvalidLocalRefLenient() throws IOException {
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String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
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IParser parser = ourCtx.newXmlParser();
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parser.setParserErrorHandler(new LenientErrorHandler());
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parser.parseResource(Bundle.class, string);
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assertEquals("FAMILY", subject.getNameFirstRep().getFamily());
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}
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@Test
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@ -273,6 +135,7 @@ public class XmlParserDstu3Test {
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}
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@Test
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public void testContainedResourceInExtensionUndeclared() {
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Patient p = new Patient();
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@ -295,6 +158,24 @@ public class XmlParserDstu3Test {
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assertEquals("ORG", o.getName());
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}
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@Test(expected = DataFormatException.class)
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public void testContainedResourceWithNoId() throws IOException {
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String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_contained_with_no_id.xml"), StandardCharsets.UTF_8);
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IParser parser = ourCtx.newXmlParser();
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parser.setParserErrorHandler(new StrictErrorHandler());
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parser.parseResource(Bundle.class, string);
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}
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@Test()
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public void testContainedResourceWithNoIdLenient() throws IOException {
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String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_contained_with_no_id.xml"), StandardCharsets.UTF_8);
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IParser parser = ourCtx.newXmlParser();
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parser.setParserErrorHandler(new LenientErrorHandler());
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parser.parseResource(Bundle.class, string);
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}
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@Test
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public void testDuration() {
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Encounter enc = new Encounter();
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@ -1039,6 +920,37 @@ public class XmlParserDstu3Test {
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assertThat(encoded, not(stringContainsInOrder("<DiagnosticReport", "<contained", "<Observation", "<contained", "<Observation", "</DiagnosticReport")));
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}
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@Test
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public void testEncodeChainedContainedResourcer() {
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Organization gp = new Organization();
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gp.setName("grandparent");
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Organization parent = new Organization();
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parent.setName("parent");
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parent.getPartOf().setResource(gp);
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Organization child = new Organization();
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child.setName("child");
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child.getPartOf().setResource(parent);
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Patient patient = new Patient();
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patient.getManagingOrganization().setResource(child);
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String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient);
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ourLog.info(encoded);
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patient = ourCtx.newXmlParser().parseResource(Patient.class, encoded);
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child = (Organization) patient.getManagingOrganization().getResource();
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assertEquals("child", child.getName());
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parent = (Organization) child.getPartOf().getResource();
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assertEquals("parent", parent.getName());
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gp = (Organization) parent.getPartOf().getResource();
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assertEquals("grandparent", gp.getName());
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}
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/**
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* See #326
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*/
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@ -1945,8 +1857,6 @@ public class XmlParserDstu3Test {
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assertThat(output, containsString("<text><status value=\"generated\"/><div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\">John <b>SMITH </b>"));
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}
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@Test
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public void testMoreExtensions() throws Exception {
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@ -2192,6 +2102,8 @@ public class XmlParserDstu3Test {
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}
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@Test
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public void testParseAndEncodeCommentsOnExtensions() {
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//@formatter:off
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@ -3121,6 +3033,106 @@ public class XmlParserDstu3Test {
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}
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}
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@Test(expected = DataFormatException.class)
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public void testParseWithInvalidLocalRef() throws IOException {
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String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
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IParser parser = ourCtx.newXmlParser();
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parser.setParserErrorHandler(new StrictErrorHandler());
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parser.parseResource(Bundle.class, string);
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}
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@Test()
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public void testParseWithInvalidLocalRefLenient() throws IOException {
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String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
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IParser parser = ourCtx.newXmlParser();
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parser.setParserErrorHandler(new LenientErrorHandler());
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parser.parseResource(Bundle.class, string);
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}
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/**
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* If a contained resource refers to a contained resource that comes after it, it should still be successfully
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* woven together.
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*/
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@Test
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||||
public void testParseWovenContainedResources() throws IOException {
|
||||
String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_woven_obs.xml"), StandardCharsets.UTF_8);
|
||||
|
||||
IParser parser = ourCtx.newXmlParser();
|
||||
parser.setParserErrorHandler(new StrictErrorHandler());
|
||||
org.hl7.fhir.dstu3.model.Bundle bundle = parser.parseResource(Bundle.class, string);
|
||||
|
||||
DiagnosticReport resource = (DiagnosticReport) bundle.getEntry().get(0).getResource();
|
||||
Observation obs = (Observation) resource.getResult().get(1).getResource();
|
||||
assertEquals("#2", obs.getId());
|
||||
Reference performerFirstRep = obs.getPerformerFirstRep();
|
||||
Practitioner performer = (Practitioner) performerFirstRep.getResource();
|
||||
assertEquals("#3", performer.getId());
|
||||
}
|
||||
|
||||
/**
|
||||
* See #414
|
||||
*/
|
||||
@Test
|
||||
public void testParseXmlExtensionWithoutUrl() {
|
||||
//@formatter:off
|
||||
String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
|
||||
" <extension>\n" +
|
||||
" <valueDateTime value=\"2011-01-02T11:13:15\"/>\n" +
|
||||
" </extension>\n" +
|
||||
"</Patient>";
|
||||
//@formatter:on
|
||||
|
||||
IParser parser = ourCtx.newXmlParser();
|
||||
parser.setParserErrorHandler(new LenientErrorHandler());
|
||||
Patient parsed = (Patient) parser.parseResource(input);
|
||||
assertEquals(1, parsed.getExtension().size());
|
||||
assertEquals(null, parsed.getExtension().get(0).getUrl());
|
||||
assertEquals("2011-01-02T11:13:15", parsed.getExtension().get(0).getValueAsPrimitive().getValueAsString());
|
||||
|
||||
try {
|
||||
parser = ourCtx.newXmlParser();
|
||||
parser.setParserErrorHandler(new StrictErrorHandler());
|
||||
parser.parseResource(input);
|
||||
fail();
|
||||
} catch (DataFormatException e) {
|
||||
assertEquals("Resource is missing required element 'url' in parent element 'extension'", e.getCause().getMessage());
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* See #414
|
||||
*/
|
||||
@Test
|
||||
public void testParseXmlModifierExtensionWithoutUrl() {
|
||||
//@formatter:off
|
||||
String input = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
|
||||
" <modifierExtension>\n" +
|
||||
" <valueDateTime value=\"2011-01-02T11:13:15\"/>\n" +
|
||||
" </modifierExtension>\n" +
|
||||
"</Patient>";
|
||||
//@formatter:on
|
||||
|
||||
IParser parser = ourCtx.newXmlParser();
|
||||
parser.setParserErrorHandler(new LenientErrorHandler());
|
||||
Patient parsed = (Patient) parser.parseResource(input);
|
||||
assertEquals(1, parsed.getModifierExtension().size());
|
||||
assertEquals(null, parsed.getModifierExtension().get(0).getUrl());
|
||||
assertEquals("2011-01-02T11:13:15", parsed.getModifierExtension().get(0).getValueAsPrimitive().getValueAsString());
|
||||
|
||||
try {
|
||||
parser = ourCtx.newXmlParser();
|
||||
parser.setParserErrorHandler(new StrictErrorHandler());
|
||||
parser.parseResource(input);
|
||||
fail();
|
||||
} catch (DataFormatException e) {
|
||||
assertEquals("Resource is missing required element 'url' in parent element 'modifierExtension'", e.getCause().getMessage());
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* See #339
|
||||
*
|
||||
|
|
|
|||
|
|
@ -222,6 +222,17 @@
|
|||
return an HTTP 404 and not a 400, per the HTTP spec. Thanks to
|
||||
GitHub user @CarthageKing for the pull request!
|
||||
</action>
|
||||
<action type="fix" issue="544">
|
||||
When parsing a Bundle containing placeholder fullUrls and references
|
||||
(e.g. "urn:uuid:0000-0000") the resource reference targets did not get
|
||||
populated with the given resources. Note that as a part of this
|
||||
change, <![CDATA[<code>IdType</code> and <code>IdDt</code>]]> have been modified
|
||||
so that when parsing a placeholder ID, the complete placeholder including the
|
||||
"urn:uuid:" or "urn:oid:" prefix will be placed into the ID part. Previously,
|
||||
the prefix was treated as the base URL, which led to strange behaviour
|
||||
like the placeholder being treated as a real IDs. Thanks to GitHub
|
||||
user @jodue for reporting!
|
||||
</action>
|
||||
</release>
|
||||
<release version="2.1" date="2016-11-11">
|
||||
<action type="add">
|
||||
|
|
|
|||
Loading…
Reference in New Issue