Tweak to validator
This commit is contained in:
James Agnew
parent
64f57b9736
commit
61902da527
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@ -1,9 +1,5 @@
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package ca.uhn.fhir.jpa.dao.dstu3;
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import static org.hamcrest.Matchers.containsString;
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import static org.junit.Assert.assertThat;
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import static org.junit.Assert.fail;
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import ca.uhn.fhir.jpa.util.TestUtil;
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import ca.uhn.fhir.rest.api.EncodingEnum;
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import ca.uhn.fhir.rest.api.MethodOutcome;
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@ -12,21 +8,33 @@ import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
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import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
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import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
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import ca.uhn.fhir.util.StopWatch;
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import ca.uhn.fhir.validation.IValidatorModule;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
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import org.hl7.fhir.dstu3.model.*;
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import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
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import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.utils.IResourceValidator;
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import org.junit.After;
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import org.junit.AfterClass;
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import org.junit.Ignore;
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import org.junit.Test;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.test.util.AopTestUtils;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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import static org.hamcrest.Matchers.containsString;
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import static org.junit.Assert.assertThat;
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import static org.junit.Assert.fail;
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public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3ValidateTest.class);
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@Autowired
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private IValidatorModule myValidatorModule;
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@Test
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public void testValidateChangedQuestionnaire() {
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@ -73,6 +81,77 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
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}
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@After
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public void after() {
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FhirInstanceValidator val = AopTestUtils.getTargetObject(myValidatorModule);
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val.setBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel.Warning);
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}
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@Test
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public void testValidateWithCanonicalReference() {
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FhirInstanceValidator val = AopTestUtils.getTargetObject(myValidatorModule);
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IResourceValidator.BestPracticeWarningLevel a = IResourceValidator.BestPracticeWarningLevel.Ignore;
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val.setBestPracticeWarningLevel(a);
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ValueSet vs = new ValueSet();
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vs.setId("MYVS");
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vs.setUrl("http://myvs");
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vs.getCompose()
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.addInclude()
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.setSystem("http://hl7.org/fhir/administrative-gender")
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.addConcept(new ValueSet.ConceptReferenceComponent().setCode("male"))
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.addConcept(new ValueSet.ConceptReferenceComponent().setCode("female"));
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myValueSetDao.update(vs);
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Questionnaire q = new Questionnaire();
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q.setId("MYQ");
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q.setUrl("http://hl7.org/fhir/Questionnaire/myq");
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q.addItem()
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.setLinkId("LINKID")
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.setType(Questionnaire.QuestionnaireItemType.CHOICE)
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.setOptions(new Reference().setReference("ValueSet/MYVS"));
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myQuestionnaireDao.update(q);
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// Validate with matching code
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QuestionnaireResponse qr = new QuestionnaireResponse();
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qr.setStatus(QuestionnaireResponse.QuestionnaireResponseStatus.COMPLETED);
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qr.setQuestionnaire(new Reference("Questionnaire/MYQ"));
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qr.addItem()
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.setLinkId("LINKID")
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.addAnswer()
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.setValue(new Coding().setSystem("http://hl7.org/fhir/administrative-gender").setCode("aaa").setDisplay("AAAA"));
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// Validate as resource
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try {
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MethodOutcome outcome = myQuestionnaireResponseDao.validate(qr, null, null, null, ValidationModeEnum.CREATE, null, mySrd);
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OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
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ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
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fail();
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} catch (PreconditionFailedException e) {
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OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
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String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
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ourLog.info(encoded);
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assertThat(encoded, containsString("is not in the options value set"));
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}
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// Validate as string
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try {
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String raw = myFhirCtx.newJsonParser().encodeResourceToString(qr);
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MethodOutcome outcome = myQuestionnaireResponseDao.validate(qr, null, raw, EncodingEnum.JSON, ValidationModeEnum.CREATE, null, mySrd);
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OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
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ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
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fail();
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} catch (PreconditionFailedException e) {
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OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
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String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
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ourLog.info(encoded);
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assertThat(encoded, containsString("is not in the options value set"));
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}
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}
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@Test
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public void testValidateStructureDefinition() throws Exception {
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String input = IOUtils.toString(getClass().getResourceAsStream("/sd-david-dhtest7.json"), StandardCharsets.UTF_8);
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@ -1,9 +1,5 @@
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package ca.uhn.fhir.jpa.dao.r4;
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import static org.hamcrest.Matchers.containsString;
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import static org.junit.Assert.assertThat;
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import static org.junit.Assert.fail;
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import ca.uhn.fhir.rest.api.EncodingEnum;
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import ca.uhn.fhir.rest.api.MethodOutcome;
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import ca.uhn.fhir.rest.api.ValidationModeEnum;
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@ -13,41 +9,40 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
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import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
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import ca.uhn.fhir.util.StopWatch;
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import ca.uhn.fhir.util.TestUtil;
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import ca.uhn.fhir.validation.IValidatorModule;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.Bundle;
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import org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator;
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import org.hl7.fhir.r4.model.*;
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import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
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import org.hl7.fhir.r4.model.CanonicalType;
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import org.hl7.fhir.r4.model.IdType;
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import org.hl7.fhir.r4.model.Observation;
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import org.hl7.fhir.r4.model.Observation.ObservationStatus;
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import org.hl7.fhir.r4.model.OperationOutcome;
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import org.hl7.fhir.r4.model.Organization;
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import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.StructureDefinition;
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import org.hl7.fhir.r4.model.ValueSet;
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import org.hl7.fhir.r4.utils.IResourceValidator;
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import org.junit.After;
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import org.junit.AfterClass;
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import org.junit.Ignore;
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import org.junit.Test;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.test.util.AopTestUtils;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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import static org.hamcrest.Matchers.containsString;
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import static org.junit.Assert.assertThat;
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import static org.junit.Assert.fail;
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public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4ValidateTest.class);
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@AfterClass
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public static void afterClassClearContext() {
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TestUtil.clearAllStaticFieldsForUnitTest();
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}
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@Autowired
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private IValidatorModule myValidatorModule;
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@Test
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public void testValidateStructureDefinition() throws Exception {
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String input = IOUtils.toString(getClass().getResourceAsStream("/r4/sd-david-dhtest7.json"), StandardCharsets.UTF_8);
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StructureDefinition sd = myFhirCtx.newJsonParser().parseResource(StructureDefinition.class, input);
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ourLog.info("Starting validation");
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try {
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myStructureDefinitionDao.validate(sd, null, null, null, ValidationModeEnum.UPDATE, null, mySrd);
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@ -55,7 +50,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
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ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
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}
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ourLog.info("Done validation");
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StopWatch sw = new StopWatch();
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ourLog.info("Starting validation");
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try {
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@ -66,13 +61,13 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
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ourLog.info("Done validation in {}ms", sw.getMillis());
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}
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@Test
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public void testValidateDocument() throws Exception {
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String input = IOUtils.toString(getClass().getResourceAsStream("/r4/document-bundle.json"), StandardCharsets.UTF_8);
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Bundle document = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
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ourLog.info("Starting validation");
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try {
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MethodOutcome outcome = myBundleDao.validate(document, null, null, null, ValidationModeEnum.CREATE, null, mySrd);
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@ -80,7 +75,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
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ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
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}
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ourLog.info("Done validation");
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// ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome.getOperationOutcome()));
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}
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@ -139,24 +134,24 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
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MethodOutcome outcome = null;
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ValidationModeEnum mode = ValidationModeEnum.CREATE;
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switch (enc) {
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case JSON:
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encoded = myFhirCtx.newJsonParser().encodeResourceToString(input);
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try {
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myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
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fail();
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} catch (PreconditionFailedException e) {
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return (OperationOutcome) e.getOperationOutcome();
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}
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break;
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case XML:
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encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
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try {
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myObservationDao.validate(input, null, encoded, EncodingEnum.XML, mode, null, mySrd);
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fail();
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} catch (PreconditionFailedException e) {
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return (OperationOutcome) e.getOperationOutcome();
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}
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break;
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case JSON:
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encoded = myFhirCtx.newJsonParser().encodeResourceToString(input);
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try {
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myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
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fail();
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} catch (PreconditionFailedException e) {
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return (OperationOutcome) e.getOperationOutcome();
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}
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break;
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case XML:
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encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
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try {
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myObservationDao.validate(input, null, encoded, EncodingEnum.XML, mode, null, mySrd);
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fail();
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} catch (PreconditionFailedException e) {
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return (OperationOutcome) e.getOperationOutcome();
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}
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break;
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}
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throw new IllegalStateException(); // shouldn't get here
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@ -185,6 +180,57 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
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}
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@Test
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public void testValidateWithCanonicalReference() {
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FhirInstanceValidator val = AopTestUtils.getTargetObject(myValidatorModule);
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val.setBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel.Ignore);
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ValueSet vs = new ValueSet();
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vs.setId("MYVS");
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vs.setUrl("http://myvs");
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vs.getCompose()
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.addInclude()
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.setSystem("http://hl7.org/fhir/administrative-gender")
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.addConcept(new ValueSet.ConceptReferenceComponent().setCode("male"))
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.addConcept(new ValueSet.ConceptReferenceComponent().setCode("female"));
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myValueSetDao.update(vs);
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Questionnaire q = new Questionnaire();
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q.setId("MYQ");
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q.setUrl("http://myquestionnaire");
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q.addItem()
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.setLinkId("LINKID")
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.setType(Questionnaire.QuestionnaireItemType.CHOICE)
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.setAnswerValueSet("ValueSet/MYVS");
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myQuestionnaireDao.update(q);
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// Validate with matching code
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QuestionnaireResponse qr = new QuestionnaireResponse();
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qr.setStatus(QuestionnaireResponse.QuestionnaireResponseStatus.COMPLETED);
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qr.setQuestionnaire("Questionnaire/MYQ");
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qr.addItem()
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.setLinkId("LINKID")
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.addAnswer()
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.setValue(new Coding().setSystem("http://hl7.org/fhir/administrative-gender").setCode("aaa"));
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try {
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MethodOutcome outcome = myQuestionnaireResponseDao.validate(qr, null, null, null, ValidationModeEnum.CREATE, null, mySrd);
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OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
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ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
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fail();
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} catch (PreconditionFailedException e) {
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OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
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String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
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ourLog.info(encoded);
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assertThat(encoded, containsString("is not in the options value set"));
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}
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}
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@After
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public void after() {
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FhirInstanceValidator val = AopTestUtils.getTargetObject(myValidatorModule);
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val.setBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel.Warning);
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}
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@Test
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public void testValidateForCreate() {
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String methodName = "testValidateForCreate";
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@ -337,18 +383,18 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
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}
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return retVal;
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}
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/**
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* Format has changed, this is out of date
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*/
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@Test
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@Ignore
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public void testValidateNewQuestionnaireFormat() throws Exception {
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String input =IOUtils.toString(FhirResourceDaoR4ValidateTest.class.getResourceAsStream("/questionnaire_r4.xml"));
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String input = IOUtils.toString(FhirResourceDaoR4ValidateTest.class.getResourceAsStream("/questionnaire_r4.xml"));
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try {
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MethodOutcome results = myQuestionnaireDao.validate(null, null, input, EncodingEnum.XML, ValidationModeEnum.UPDATE, null, mySrd);
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OperationOutcome oo = (OperationOutcome) results.getOperationOutcome();
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ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
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MethodOutcome results = myQuestionnaireDao.validate(null, null, input, EncodingEnum.XML, ValidationModeEnum.UPDATE, null, mySrd);
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OperationOutcome oo = (OperationOutcome) results.getOperationOutcome();
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ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
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} catch (PreconditionFailedException e) {
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// this is a failure of the test
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ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
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@ -356,4 +402,9 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
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}
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}
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@AfterClass
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public static void afterClassClearContext() {
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TestUtil.clearAllStaticFieldsForUnitTest();
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}
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}
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@ -391,6 +391,26 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
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}
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@Test
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public void testCreateWithClientAssignedId() throws IOException {
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Patient p = new Patient();
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p.setActive(true);
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p.setId("AAA");
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String encoded = myFhirCtx.newJsonParser().encodeResourceToString(p);
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HttpPut httpPut = new HttpPut(ourServerBase + "/Patient/AAA");
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httpPut.setEntity(new StringEntity(encoded, ContentType.parse("application/json+fhir")));
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try (CloseableHttpResponse status = ourHttpClient.execute(httpPut)) {
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String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
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ourLog.info(status.getStatusLine().toString());
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ourLog.info(responseContent);
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assertEquals(201, status.getStatusLine().getStatusCode());
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assertThat(responseContent, containsString("true"));
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}
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}
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@Before
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@ -2371,13 +2371,17 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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return null;
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} else {
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long t = System.nanoTime();
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if (!Utilities.isAbsoluteUrl(reference))
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reference = resolve(uri, reference);
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ValueSet fr = context.fetchResource(ValueSet.class, reference);
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txTime = txTime + (System.nanoTime() - t);
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ValueSet fr = context.fetchResource(ValueSet.class, reference);
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if (fr == null) {
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if (!Utilities.isAbsoluteUrl(reference)) {
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reference = resolve(uri, reference);
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fr = context.fetchResource(ValueSet.class, reference);
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}
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}
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txTime = txTime + (System.nanoTime() - t);
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return fr;
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}
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} else
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} else
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return null;
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}
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