Add line numbers to validation failures
This commit is contained in:
James Agnew
parent
13b80a294a
commit
a71d969ba1
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@ -19,22 +19,17 @@ package ca.uhn.fhir.util;
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* limitations under the License.
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* #L%
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*/
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import java.util.List;
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import ca.uhn.fhir.context.*;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import org.hl7.fhir.instance.model.api.IBase;
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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.IPrimitiveType;
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import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
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import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
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import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.FhirVersionEnum;
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import ca.uhn.fhir.context.RuntimeResourceDefinition;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import java.util.List;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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/**
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* Utilities for dealing with OperationOutcome resources across various model versions
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@ -43,20 +38,17 @@ public class OperationOutcomeUtil {
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/**
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* Add an issue to an OperationOutcome
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*
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* @param theCtx
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* The fhir context
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* @param theOperationOutcome
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* The OO resource to add to
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* @param theSeverity
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* The severity (fatal | error | warning | information)
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* @param theDetails
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* The details string
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* @param theCtx The fhir context
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* @param theOperationOutcome The OO resource to add to
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* @param theSeverity The severity (fatal | error | warning | information)
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* @param theDetails The details string
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* @param theCode
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* @return Returns the newly added issue
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*/
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public static void addIssue(FhirContext theCtx, IBaseOperationOutcome theOperationOutcome, String theSeverity, String theDetails, String theLocation, String theCode) {
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public static IBase addIssue(FhirContext theCtx, IBaseOperationOutcome theOperationOutcome, String theSeverity, String theDetails, String theLocation, String theCode) {
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IBase issue = createIssue(theCtx, theOperationOutcome);
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populateDetails(theCtx, issue, theSeverity, theDetails, theLocation, theCode);
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return issue;
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}
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private static IBase createIssue(FhirContext theCtx, IBaseResource theOutcome) {
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@ -140,7 +132,6 @@ public class OperationOutcomeUtil {
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BaseRuntimeElementDefinition<?> stringDef = detailsChild.getChildByName(detailsChild.getElementName());
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BaseRuntimeChildDefinition severityChild = issueElement.getChildByName("severity");
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BaseRuntimeChildDefinition locationChild = issueElement.getChildByName("location");
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IPrimitiveType<?> severityElem = (IPrimitiveType<?>) severityChild.getChildByName("severity").newInstance(severityChild.getInstanceConstructorArguments());
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severityElem.setValueAsString(theSeverity);
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@ -150,7 +141,13 @@ public class OperationOutcomeUtil {
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string.setValueAsString(theDetails);
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detailsChild.getMutator().setValue(theIssue, string);
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addLocationToIssue(theCtx, theIssue, theLocation);
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}
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public static void addLocationToIssue(FhirContext theContext, IBase theIssue, String theLocation) {
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if (isNotBlank(theLocation)) {
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BaseRuntimeElementCompositeDefinition<?> issueElement = (BaseRuntimeElementCompositeDefinition<?>) theContext.getElementDefinition(theIssue.getClass());
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BaseRuntimeChildDefinition locationChild = issueElement.getChildByName("location");
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IPrimitiveType<?> locationElem = (IPrimitiveType<?>) locationChild.getChildByName("location").newInstance(locationChild.getInstanceConstructorArguments());
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locationElem.setValueAsString(theLocation);
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locationChild.getMutator().addValue(theIssue, locationElem);
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@ -0,0 +1,12 @@
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package ca.uhn.fhir.validation;
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/**
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* This interface marks a {@link IValidatorModule validator module} that uses the FHIR
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* FhirInstanceValidator as the underlying engine (i.e. it performs
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* profile validation)
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*/
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public interface IInstanceValidatorModule extends IValidatorModule {
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// nothing extra yet
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}
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@ -25,6 +25,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import java.util.Collections;
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import java.util.List;
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import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
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import ca.uhn.fhir.context.FhirContext;
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@ -120,7 +121,19 @@ public class ValidationResult {
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location = null;
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}
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String severity = next.getSeverity() != null ? next.getSeverity().getCode() : null;
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OperationOutcomeUtil.addIssue(myCtx, theOperationOutcome, severity, next.getMessage(), location, Constants.OO_INFOSTATUS_PROCESSING);
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IBase issue = OperationOutcomeUtil.addIssue(myCtx, theOperationOutcome, severity, next.getMessage(), location, Constants.OO_INFOSTATUS_PROCESSING);
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if (next.getLocationLine() != null || next.getLocationCol() != null) {
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String line = "(unknown)";
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if (next.getLocationLine() != null) {
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line = next.getLocationLine().toString();
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}
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String col = "(unknown)";
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if (next.getLocationCol() != null) {
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col = next.getLocationCol().toString();
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}
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OperationOutcomeUtil.addLocationToIssue(myCtx, issue, "Line " + line + ", Col " + col);
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}
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}
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if (myMessages.isEmpty()) {
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@ -0,0 +1,9 @@
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package ca.uhn.fhir.jpa.dao;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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public class JpaResourceDao<T extends IBaseResource> extends BaseHapiFhirResourceDao<T> {
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// nothing yet
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}
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@ -0,0 +1,37 @@
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package ca.uhn.fhir.util;
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import ca.uhn.fhir.context.FhirContext;
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import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.r4.model.OperationOutcome;
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import org.junit.Test;
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import static org.junit.Assert.*;
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public class OperationOutcomeUtilTest {
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private FhirContext myCtx = FhirContext.forR4();
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@Test
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public void testHasIssueTrue() {
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OperationOutcome oo =new OperationOutcome();
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oo.addIssue().setDiagnostics("foo");
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assertTrue(OperationOutcomeUtil.hasIssues(myCtx, oo));
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}
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@Test
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public void testHasIssueFalse() {
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OperationOutcome oo =new OperationOutcome();
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assertFalse(OperationOutcomeUtil.hasIssues(myCtx, oo));
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}
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@Test
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public void testAddIssue() {
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OperationOutcome oo = (OperationOutcome) OperationOutcomeUtil.newInstance(myCtx);
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IBase issue = OperationOutcomeUtil.addIssue(myCtx, oo, "error", "Help i'm a bug", "/Patient", "throttled");
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OperationOutcomeUtil.addLocationToIssue(myCtx, issue, null);
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OperationOutcomeUtil.addLocationToIssue(myCtx, issue, "");
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OperationOutcomeUtil.addLocationToIssue(myCtx, issue, "line 3");
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assertEquals("{\"resourceType\":\"OperationOutcome\",\"issue\":[{\"severity\":\"error\",\"code\":\"throttled\",\"diagnostics\":\"Help i'm a bug\",\"location\":[\"/Patient\",\"line 3\"]}]}", myCtx.newJsonParser().encodeResourceToString(oo));
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}
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}
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@ -1,19 +1,49 @@
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package ca.uhn.fhir.test;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.rest.api.EncodingEnum;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import com.google.common.base.Charsets;
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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 java.io.IOException;
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import java.io.InputStream;
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import java.util.function.Function;
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import java.util.zip.GZIPInputStream;
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public class BaseTest {
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protected String loadResource(String theClasspath) throws IOException {
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InputStream stream = BaseTest.class.getResourceAsStream(theClasspath);
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if (stream==null) {
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throw new IllegalArgumentException("Unable to find resource: " + theClasspath);
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}
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return IOUtils.toString(stream, Charsets.UTF_8);
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Function<InputStream, InputStream> streamTransform = t->t;
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return loadResource(theClasspath, streamTransform);
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}
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private String loadResource(String theClasspath, Function<InputStream, InputStream> theStreamTransform) throws IOException {
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try (InputStream stream = BaseTest.class.getResourceAsStream(theClasspath)) {
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if (stream == null) {
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throw new IllegalArgumentException("Unable to find resource: " + theClasspath);
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}
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InputStream newStream = theStreamTransform.apply(stream);
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return IOUtils.toString(newStream, Charsets.UTF_8);
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}
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}
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protected String loadCompressedResource(String theClasspath) throws IOException {
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Function<InputStream, InputStream> streamTransform = t-> {
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try {
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return new GZIPInputStream(t);
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} catch (IOException e) {
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throw new InternalErrorException(e);
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}
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};
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return loadResource(theClasspath, streamTransform);
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}
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protected <T extends IBaseResource> T loadResource(FhirContext theCtx, Class<T> theType, String theClasspath) throws IOException {
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String raw = loadResource(theClasspath);
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EncodingEnum.detectEncodingNoDefault(raw).newParser(theCtx).parseResource(theType, raw);
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}
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}
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@ -2,6 +2,7 @@ package org.hl7.fhir.r4.validation;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.rest.api.Constants;
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import ca.uhn.fhir.test.BaseTest;
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import ca.uhn.fhir.util.TestUtil;
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import ca.uhn.fhir.validation.FhirValidator;
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import ca.uhn.fhir.validation.ResultSeverityEnum;
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@ -54,7 +55,7 @@ import static org.mockito.ArgumentMatchers.nullable;
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import static org.mockito.Mockito.mock;
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import static org.mockito.Mockito.when;
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public class FhirInstanceValidatorR4Test {
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public class FhirInstanceValidatorR4Test extends BaseTest {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirInstanceValidatorR4Test.class);
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private static DefaultProfileValidationSupport myDefaultValidationSupport = new DefaultProfileValidationSupport();
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@ -71,7 +72,7 @@ public class FhirInstanceValidatorR4Test {
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private Map<String, ValueSetExpansionComponent> mySupportedCodeSystemsForExpansion;
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private FhirValidator myVal;
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private ArrayList<String> myValidConcepts;
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private Set<String> myValidSystems = new HashSet<String>();
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private Set<String> myValidSystems = new HashSet<>();
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private void addValidConcept(String theSystem, String theCode) {
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myValidSystems.add(theSystem);
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@ -111,21 +112,18 @@ public class FhirInstanceValidatorR4Test {
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myValidConcepts = new ArrayList<>();
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when(myMockSupport.expandValueSet(nullable(FhirContext.class), nullable(ConceptSetComponent.class))).thenAnswer(new Answer<ValueSetExpander.ValueSetExpansionOutcome>() {
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@Override
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public ValueSetExpander.ValueSetExpansionOutcome answer(InvocationOnMock theInvocation) throws Throwable {
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ConceptSetComponent arg = (ConceptSetComponent) theInvocation.getArguments()[1];
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when(myMockSupport.expandValueSet(nullable(FhirContext.class), nullable(ConceptSetComponent.class))).thenAnswer(t -> {
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ConceptSetComponent arg = (ConceptSetComponent) t.getArguments()[1];
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ValueSetExpansionComponent retVal = mySupportedCodeSystemsForExpansion.get(arg.getSystem());
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if (retVal == null) {
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ValueSetExpander.ValueSetExpansionOutcome outcome = myDefaultValidationSupport.expandValueSet(ourCtx, arg);
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return outcome;
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}
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ourLog.debug("expandValueSet({}) : {}", new Object[]{theInvocation.getArguments()[0], retVal});
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ourLog.debug("expandValueSet({}) : {}", new Object[]{t.getArguments()[0], retVal});
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ValueSet valueset = new ValueSet();
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valueset.setExpansion(retVal);
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return new ValueSetExpander.ValueSetExpansionOutcome(valueset);
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}
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});
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when(myMockSupport.isCodeSystemSupported(nullable(FhirContext.class), nullable(String.class))).thenAnswer(new Answer<Boolean>() {
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@Override
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@ -217,7 +215,7 @@ public class FhirInstanceValidatorR4Test {
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int index = 0;
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for (SingleValidationMessage next : theOutput.getMessages()) {
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ourLog.info("Result {}: {} - {}:{} {} - {}",
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new Object[]{index, next.getSeverity(), defaultString(next.getLocationLine()), defaultString(next.getLocationCol()), next.getLocationString(), next.getMessage()});
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index, next.getSeverity(), defaultString(next.getLocationLine()), defaultString(next.getLocationCol()), next.getLocationString(), next.getMessage());
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index++;
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retVal.add(next);
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@ -304,11 +302,11 @@ public class FhirInstanceValidatorR4Test {
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private List<SingleValidationMessage> logResultsAndReturnNonInformationalOnes(ValidationResult theOutput) {
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List<SingleValidationMessage> retVal = new ArrayList<SingleValidationMessage>();
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List<SingleValidationMessage> retVal = new ArrayList<>();
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int index = 0;
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for (SingleValidationMessage next : theOutput.getMessages()) {
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ourLog.info("Result {}: {} - {} - {}", new Object[]{index, next.getSeverity(), next.getLocationString(), next.getMessage()});
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ourLog.info("Result {}: {} - {} - {}", index, next.getSeverity(), next.getLocationString(), next.getMessage());
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index++;
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if (next.getSeverity() != ResultSeverityEnum.INFORMATION) {
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@ -320,11 +318,11 @@ public class FhirInstanceValidatorR4Test {
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}
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private List<SingleValidationMessage> logResultsAndReturnErrorOnes(ValidationResult theOutput) {
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List<SingleValidationMessage> retVal = new ArrayList<SingleValidationMessage>();
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List<SingleValidationMessage> retVal = new ArrayList<>();
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int index = 0;
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for (SingleValidationMessage next : theOutput.getMessages()) {
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ourLog.info("Result {}: {} - {} - {}", new Object[]{index, next.getSeverity(), next.getLocationString(), next.getMessage()});
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ourLog.info("Result {}: {} - {} - {}", index, next.getSeverity(), next.getLocationString(), next.getMessage());
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index++;
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if (next.getSeverity().ordinal() > ResultSeverityEnum.WARNING.ordinal()) {
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@ -359,7 +357,7 @@ public class FhirInstanceValidatorR4Test {
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@Test
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public void testValidateBundleWithNoFullUrl() throws IOException {
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String encoded = IOUtils.toString(FhirInstanceValidatorR4Test.class.getResourceAsStream("/r4/r4-caredove-bundle.json"));
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String encoded = loadResource("/r4/r4-caredove-bundle.json");
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ValidationResult output = myVal.validateWithResult(encoded);
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List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
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@ -459,9 +457,7 @@ public class FhirInstanceValidatorR4Test {
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@Test
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@Ignore
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public void testValidateBigRawJsonResource() throws Exception {
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InputStream stream = FhirInstanceValidatorR4Test.class.getResourceAsStream("/conformance.json.gz");
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stream = new GZIPInputStream(stream);
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String input = IOUtils.toString(stream);
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String input = super.loadCompressedResource("/conformance.json.gz");
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long start = System.currentTimeMillis();
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ValidationResult output = null;
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@ -485,8 +481,7 @@ public class FhirInstanceValidatorR4Test {
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org.hl7.fhir.r4.model.Bundle bundle;
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String name = "profiles-resources";
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ourLog.info("Uploading " + name);
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String vsContents;
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vsContents = IOUtils.toString(FhirInstanceValidatorR4Test.class.getResourceAsStream("/org/hl7/fhir/r4/model/profile/" + name + ".xml"), "UTF-8");
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String vsContents = loadResource("/org/hl7/fhir/r4/model/profile/" + name + ".xml");
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TreeSet<String> ids = new TreeSet<>();
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@ -532,7 +527,7 @@ public class FhirInstanceValidatorR4Test {
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@Test
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public void testValidateBundleWithNoType() throws Exception {
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String vsContents = IOUtils.toString(FhirInstanceValidatorR4Test.class.getResourceAsStream("/r4/bundle-with-no-type.json"), "UTF-8");
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String vsContents = loadResource("/r4/bundle-with-no-type.json");
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ValidationResult output = myVal.validateWithResult(vsContents);
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logResultsAndReturnNonInformationalOnes(output);
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@ -562,7 +557,7 @@ public class FhirInstanceValidatorR4Test {
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String name = "profiles-resources";
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ourLog.info("Uploading " + name);
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String inputString;
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inputString = IOUtils.toString(FhirInstanceValidatorR4Test.class.getResourceAsStream("/brian_reinhold_bundle.json"), "UTF-8");
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inputString = loadResource("/brian_reinhold_bundle.json");
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Bundle bundle = ourCtx.newJsonParser().parseResource(Bundle.class, inputString);
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FHIRPathEngine fp = new FHIRPathEngine(new HapiWorkerContext(ourCtx, myDefaultValidationSupport));
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@ -588,7 +583,7 @@ public class FhirInstanceValidatorR4Test {
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@Test
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@Ignore
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public void testValidateDocument() throws Exception {
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String vsContents = IOUtils.toString(FhirInstanceValidatorR4Test.class.getResourceAsStream("/sample-document.xml"), "UTF-8");
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String vsContents = loadResource("/sample-document.xml");
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ValidationResult output = myVal.validateWithResult(vsContents);
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logResultsAndReturnNonInformationalOnes(output);
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@ -608,7 +603,7 @@ public class FhirInstanceValidatorR4Test {
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FhirValidator val = ourCtx.newValidator();
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val.registerValidatorModule(new FhirInstanceValidator(support));
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Consent input = ourCtx.newJsonParser().parseResource(Consent.class, IOUtils.toString(ResourceValidatorDstu3Test.class.getResourceAsStream("/r4/myconsent-resource.json")));
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Consent input = super.loadResource(ourCtx, Consent.class, "/r4/myconsent-resource.json");
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input.getPolicyFirstRep().setAuthority("http://foo");
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//input.setScope(Consent.ConsentScope.ADR);
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@ -639,7 +634,7 @@ public class FhirInstanceValidatorR4Test {
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@Test
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@Ignore
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public void testValidateQuestionnaireResponse() throws IOException {
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String input = IOUtils.toString(FhirInstanceValidatorR4Test.class.getResourceAsStream("/qr_jon.xml"));
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String input = loadResource("/qr_jon.xml");
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ValidationResult output = myVal.validateWithResult(input);
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logResultsAndReturnAll(output);
|
||||
|
|
@ -681,14 +676,18 @@ public class FhirInstanceValidatorR4Test {
|
|||
ourLog.info(output.getMessages().get(0).getMessage());
|
||||
assertEquals("/Patient", output.getMessages().get(0).getLocationString());
|
||||
assertEquals("Unrecognised property '@foo'", output.getMessages().get(0).getMessage());
|
||||
|
||||
OperationOutcome operationOutcome = (OperationOutcome) output.toOperationOutcome();
|
||||
ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(operationOutcome));
|
||||
assertEquals("Unrecognised property '@foo'", operationOutcome.getIssue().get(0).getDiagnostics());
|
||||
assertEquals("/Patient", operationOutcome.getIssue().get(0).getLocation().get(0).getValue());
|
||||
assertEquals("Line 5, Col 24", operationOutcome.getIssue().get(0).getLocation().get(1).getValue());
|
||||
}
|
||||
|
||||
@Test
|
||||
@Ignore
|
||||
public void testValidateRawJsonResourceFromExamples() throws Exception {
|
||||
// @formatter:off
|
||||
String input = IOUtils.toString(FhirInstanceValidator.class.getResourceAsStream("/testscript-search.json"));
|
||||
// @formatter:on
|
||||
String input = loadResource("/testscript-search.json");
|
||||
|
||||
ValidationResult output = myVal.validateWithResult(input);
|
||||
logResultsAndReturnNonInformationalOnes(output);
|
||||
|
|
@ -884,7 +883,7 @@ public class FhirInstanceValidatorR4Test {
|
|||
* A reference with only an identifier should be valid
|
||||
*/
|
||||
@Test
|
||||
public void testValidateReferenceWithDisplayValid() throws Exception {
|
||||
public void testValidateReferenceWithDisplayValid() {
|
||||
Patient p = new Patient();
|
||||
p.getText().setDiv(new XhtmlNode().setValue("<div>AA</div>")).setStatus(Narrative.NarrativeStatus.GENERATED);
|
||||
p.getManagingOrganization().setDisplay("HELLO");
|
||||
|
|
@ -898,7 +897,7 @@ public class FhirInstanceValidatorR4Test {
|
|||
* A reference with only an identifier should be valid
|
||||
*/
|
||||
@Test
|
||||
public void testValidateReferenceWithIdentifierValid() throws Exception {
|
||||
public void testValidateReferenceWithIdentifierValid() {
|
||||
Patient p = new Patient();
|
||||
p.getText().setDiv(new XhtmlNode().setValue("<div>AA</div>")).setStatus(Narrative.NarrativeStatus.GENERATED);
|
||||
p.getManagingOrganization().getIdentifier().setSystem("http://acme.org");
|
||||
|
|
@ -1166,11 +1165,9 @@ public class FhirInstanceValidatorR4Test {
|
|||
|
||||
ValidationResult output = myVal.validateWithResult(o);
|
||||
List<SingleValidationMessage> valMessages = logResultsAndReturnAll(output);
|
||||
List<String> messages = new ArrayList<>();
|
||||
for (String msg : messages) {
|
||||
messages.add(msg);
|
||||
for (SingleValidationMessage msg : valMessages) {
|
||||
assertThat(msg.getMessage(), not(containsString("have a performer")));
|
||||
}
|
||||
assertThat(messages, not(hasItem("All observations should have a performer")));
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -1194,7 +1191,7 @@ public class FhirInstanceValidatorR4Test {
|
|||
@Test
|
||||
@Ignore
|
||||
public void testValidateStructureDefinition() throws IOException {
|
||||
String input = IOUtils.toString(FhirInstanceValidatorR4Test.class.getResourceAsStream("/sdc-questionnaire.profile.xml"));
|
||||
String input = loadResource("/sdc-questionnaire.profile.xml");
|
||||
|
||||
ValidationResult output = myVal.validateWithResult(input);
|
||||
logResultsAndReturnAll(output);
|
||||
|
|
|
|||
Loading…
Reference in New Issue