fixed validation issue (#6041)
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-mbp.home>
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TipzCM
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7b68c4d91d
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@ -0,0 +1,8 @@
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---
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type: fix
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issue: 6040
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title: "The `meta.profile` element on resources was not being respected as
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canonical (ie, allowing for a version to be appended, `http://example.com/StructureDefinition/abc|1.0.0`),
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and was thus being ignored during validation.
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This has been fixed.
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"
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@ -1,7 +1,5 @@
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package ca.uhn.fhir.jpa.dao.r4;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import static org.junit.jupiter.api.Assertions.assertFalse;
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import ca.uhn.fhir.context.support.IValidationSupport;
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import ca.uhn.fhir.context.support.ValidationSupportContext;
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import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
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@ -20,6 +18,7 @@ import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
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import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
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import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
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import ca.uhn.fhir.jpa.validation.ValidationSettings;
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import ca.uhn.fhir.parser.IParser;
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import ca.uhn.fhir.parser.LenientErrorHandler;
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import ca.uhn.fhir.parser.StrictErrorHandler;
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import ca.uhn.fhir.rest.api.EncodingEnum;
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@ -33,6 +32,8 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
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import ca.uhn.fhir.util.OperationOutcomeUtil;
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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 ch.qos.logback.classic.Level;
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import ch.qos.logback.classic.spi.ILoggingEvent;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
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import org.hl7.fhir.common.hapi.validation.support.UnknownCodeSystemWarningValidationSupport;
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@ -40,13 +41,46 @@ import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
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import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
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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.*;
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import org.hl7.fhir.r4.model.AllergyIntolerance;
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import org.hl7.fhir.r4.model.Binary;
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import org.hl7.fhir.r4.model.Bundle;
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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.CapabilityStatement;
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import org.hl7.fhir.r4.model.CodeSystem;
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import org.hl7.fhir.r4.model.CodeType;
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import org.hl7.fhir.r4.model.CodeableConcept;
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import org.hl7.fhir.r4.model.Coding;
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import org.hl7.fhir.r4.model.Condition;
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import org.hl7.fhir.r4.model.DateTimeType;
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import org.hl7.fhir.r4.model.ElementDefinition;
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import org.hl7.fhir.r4.model.Enumerations;
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import org.hl7.fhir.r4.model.Group;
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import org.hl7.fhir.r4.model.IdType;
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import org.hl7.fhir.r4.model.IntegerType;
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import org.hl7.fhir.r4.model.Location;
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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.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.Parameters;
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import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.Practitioner;
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import org.hl7.fhir.r4.model.Quantity;
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import org.hl7.fhir.r4.model.Questionnaire;
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import org.hl7.fhir.r4.model.QuestionnaireResponse;
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import org.hl7.fhir.r4.model.Reference;
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import org.hl7.fhir.r4.model.SearchParameter;
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import org.hl7.fhir.r4.model.StringType;
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import org.hl7.fhir.r4.model.StructureDefinition;
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import org.hl7.fhir.r4.model.UriType;
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import org.hl7.fhir.r4.model.ValueSet;
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import org.hl7.fhir.r5.utils.validation.constants.BestPracticeWarningLevel;
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import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
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import org.hl7.fhir.utilities.i18n.I18nConstants;
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import org.hl7.fhir.utilities.xhtml.XhtmlNode;
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import org.intellij.lang.annotations.Language;
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import org.junit.jupiter.api.AfterEach;
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import org.junit.jupiter.api.Disabled;
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import org.junit.jupiter.api.Nested;
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@ -59,16 +93,19 @@ 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 java.util.Collections;
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import java.util.List;
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import java.util.stream.Collectors;
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import static ca.uhn.fhir.rest.api.Constants.JAVA_VALIDATOR_DETAILS_SYSTEM;
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import static org.assertj.core.api.Assertions.assertThat;
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import static org.junit.jupiter.api.Assertions.fail;
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import static org.awaitility.Awaitility.await;
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import static org.hl7.fhir.common.hapi.validation.support.CommonCodeSystemsTerminologyService.CURRENCIES_CODESYSTEM_URL;
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import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertFalse;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import static org.junit.jupiter.api.Assertions.fail;
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import static org.mockito.ArgumentMatchers.any;
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import static org.mockito.Mockito.mock;
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import static org.mockito.Mockito.when;
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@ -1452,6 +1489,181 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
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throw new IllegalStateException(); // shouldn't get here
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}
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@Test
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public void validateResource_withUnknownMetaProfileurl_validatesButLogsWarning() {
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// setup
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IParser parser = myFhirContext.newJsonParser();
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myLogbackTestExtension.setUp(Level.WARN);
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String obsStr ="""
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{
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"resourceType": "Observation",
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"meta": {
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"profile": [
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"http://example.com/StructureDefinition|a|b|c"
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]
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}
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}
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""";
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Observation observation = parser.parseResource(Observation.class, obsStr);
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// test
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ValidationModeEnum mode = ValidationModeEnum.CREATE;
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MethodOutcome outcome = myObservationDao.validate(observation, null, obsStr, EncodingEnum.JSON, mode, null, mySrd);
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// validator
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assertNotNull(outcome);
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assertTrue(outcome.getOperationOutcome() instanceof OperationOutcome);
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List<OperationOutcome.OperationOutcomeIssueComponent> issues = ((OperationOutcome) outcome.getOperationOutcome()).getIssue();
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assertFalse(issues.isEmpty());
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List<OperationOutcome.OperationOutcomeIssueComponent> errors = issues.stream()
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.filter(i -> i.getSeverity() == OperationOutcome.IssueSeverity.ERROR)
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.toList();
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// we have errors
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assertFalse(errors.isEmpty());
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List<ILoggingEvent> events = myLogbackTestExtension.filterLoggingEventsWithPredicate(e -> {
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return e.getLevel() == Level.WARN;
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});
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// and we have warning logs
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assertFalse(events.isEmpty());
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assertTrue(events.stream().anyMatch(e -> e.getFormattedMessage().contains("Unrecognized profile uri")));
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}
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@Test
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public void validateResource_withMetaProfileWithVersion_validatesAsExpected() {
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// setup
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IParser parser = myFhirContext.newJsonParser();
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// create our structure definition
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@Language("JSON")
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String strDefStr =
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"""
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{
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"resourceType": "StructureDefinition",
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"id": "example-profile",
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"url": "http://example.com/StructureDefinition",
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"version": "1.0.0",
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"name": "observation-example",
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"title": "Example Profile",
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"status": "active",
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"experimental": false,
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"date": "2016-03-25",
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"description": "Example Profile",
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"fhirVersion": "4.0.1",
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"kind": "resource",
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"abstract": false,
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"type": "Observation",
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"baseDefinition": "http://hl7.org/fhir/StructureDefinition/Observation",
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"derivation": "constraint",
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"differential": {
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"element": [
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{
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"id": "Observation",
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"path": "Observation",
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"short": "Example Profile",
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"alias": [
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"Example"
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],
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"min": 0,
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"max": "*"
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},
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{
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"id": "Observation.code",
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"path": "Observation.code",
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"short": "Coded Responses from C-CDA Vital Sign Results",
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"definition": "Coded Responses from C-CDA Vital Sign Results.",
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"requirements": "5. SHALL contain exactly one [1..1] code, where the @code SHOULD be selected from ValueSet Example",
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"min": 1,
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"max": "1",
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"type": [
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{
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"code": "CodeableConcept"
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}
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],
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"mustSupport": true,
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"binding": {
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"strength": "required",
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"description": "This identifies the vital sign result type.",
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"valueSet": "http://example.com/valueset"
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}
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}
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]
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}
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}
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""";
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StructureDefinition sd = parser.parseResource(StructureDefinition.class, strDefStr);
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myStructureDefinitionDao.create(sd, mySrd);
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@Language("JSON")
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String obsStr ="""
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{
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"resourceType": "Observation",
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"meta": {
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"profile": [
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"http://example.com/StructureDefinition|1.0.0"
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]
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},
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"identifier": [
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{
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"use": "official",
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"system": "http://www.bmc.nl/zorgportal/identifiers/observations",
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"value": "6323"
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}
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],
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"status": "final",
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"code": {
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"coding": [
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{
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"system": "http://example.com/codesystem",
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"code": "some-code",
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"display": "Some Code"
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}
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]
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},
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"subject": {
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"reference": "Patient/1452"
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},
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"effectiveDateTime": "2013-05-02T09:30:10+01:00",
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"issued": "2013-04-03T15:30:10+01:00",
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"valueQuantity": {
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"value": 6.3,
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"unit": "mmol/l",
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"system": "http://unitsofmeasure.org",
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"code": "mmol/L"
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},
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"interpretation": [
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{
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"coding": [
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{
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"system": "http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation",
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"code": "H",
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"display": "High"
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}
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]
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}
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]
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}
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""";
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Observation observation = parser.parseResource(Observation.class, obsStr);
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// test
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ValidationModeEnum mode = ValidationModeEnum.CREATE;
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MethodOutcome outcome = myObservationDao.validate(observation, null, obsStr, EncodingEnum.JSON, mode, null, mySrd);
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// verify
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assertNotNull(outcome);
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assertTrue(outcome.getOperationOutcome() instanceof OperationOutcome);
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List<OperationOutcome.OperationOutcomeIssueComponent> issues = ((OperationOutcome) outcome.getOperationOutcome()).getIssue();
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assertFalse(issues.isEmpty());
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List<OperationOutcome.OperationOutcomeIssueComponent> errors = issues.stream()
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.filter(i -> i.getSeverity() == OperationOutcome.IssueSeverity.ERROR)
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.toList();
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// no errors - just warnings
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assertTrue(errors.isEmpty(), errors.stream().map(OperationOutcome.OperationOutcomeIssueComponent::getDiagnostics).collect(Collectors.joining(",")));
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}
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@Test
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public void testValidateResourceContainingProfileDeclarationInvalid() {
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String methodName = "testValidateResourceContainingProfileDeclarationInvalid";
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@ -116,6 +116,7 @@ import ca.uhn.fhir.test.utilities.ITestDataBuilder;
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import ca.uhn.fhir.util.UrlUtil;
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import ca.uhn.fhir.validation.FhirValidator;
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import ca.uhn.fhir.validation.ValidationResult;
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import ca.uhn.test.util.LogbackTestExtension;
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import jakarta.persistence.EntityManager;
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import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
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import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
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@ -566,6 +567,9 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
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@RegisterExtension
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private final PreventDanglingInterceptorsExtension myPreventDanglingInterceptorsExtension = new PreventDanglingInterceptorsExtension(()-> myInterceptorRegistry);
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@RegisterExtension
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public LogbackTestExtension myLogbackTestExtension = new LogbackTestExtension();
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@AfterEach()
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@Order(0)
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public void afterCleanupDao() {
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@ -51,7 +51,11 @@ import org.slf4j.LoggerFactory;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.util.*;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Locale;
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import java.util.Map;
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import java.util.Set;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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@ -486,12 +490,22 @@ public class VersionSpecificWorkerContextWrapper extends I18nBase implements IWo
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}
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@Override
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public <T extends Resource> T fetchResource(Class<T> class_, String uri) {
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if (isBlank(uri)) {
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public <T extends Resource> T fetchResource(Class<T> class_, String theUri) {
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if (isBlank(theUri)) {
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return null;
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}
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String uri = theUri;
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// handle profile version, if present
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if (theUri.contains("|")) {
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String[] parts = theUri.split("\\|");
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if (parts.length == 2) {
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uri = parts[0];
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} else {
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ourLog.warn("Unrecognized profile uri: {}", theUri);
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}
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}
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ResourceKey key = new ResourceKey(class_.getSimpleName(), uri);
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@SuppressWarnings("unchecked")
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T retVal = (T) myFetchResourceCache.get(key);
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