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Merge branch 'master' of github.com:jamesagnew/hapi-fhir

This commit is contained in:
jamesagnew 2018-03-01 06:20:46 -05:00
parent a6e59a0f76 790aaeb4ea
commit 7e4877c524
7 changed files with 203 additions and 116 deletions
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24
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
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@ -25,6 +25,9 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.ValidationResult;
import com.google.common.base.Charsets;
import com.google.common.collect.Lists;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
@ -131,6 +134,27 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
return retVal;
}
/**
* See #872
*/
@Test
public void testExtensionUrlWithHl7Url() throws IOException {
String input = IOUtils.toString(ResourceProviderR4Test.class.getResourceAsStream("/bug872-ext-with-hl7-url.json"), Charsets.UTF_8);
HttpPost post = new HttpPost(ourServerBase + "/Patient/$validate");
post.setEntity(new StringEntity(input, ContentType.APPLICATION_JSON));
CloseableHttpResponse resp = ourHttpClient.execute(post);
try {
String respString = IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8);
ourLog.info(respString);
assertEquals(200, resp.getStatusLine().getStatusCode());
} finally {
IOUtils.closeQuietly(resp);
}
}
/**
* See #484
*/

9
hapi-fhir-jpaserver-base/src/test/resources/bug872-ext-with-hl7-url.json Normal file
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@ -0,0 +1,9 @@
{
"resourceType": "Patient",
"extension": [
{
"url": "http://hl7.org/fhir/ValueSet/v3-ActInvoiceGroupCode",
"valueString": "test"
}
]
}

2
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/provider/HashMapResourceProvider.java
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@ -111,7 +111,7 @@ public class HashMapResourceProvider<T extends IBaseResource> implements IResour
return myResourceType;
}
private TreeMap<Long, T> getVersionToResource(String theIdPart) {
private synchronized TreeMap<Long, T> getVersionToResource(String theIdPart) {
if (!myIdToVersionToResourceMap.containsKey(theIdPart)) {
myIdToVersionToResourceMap.put(theIdPart, new TreeMap<Long, T>());
}

29
hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidatorDstu3Test.java
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@ -89,7 +89,7 @@ public class FhirInstanceValidatorDstu3Test {
if (retVal == null) {
retVal = myDefaultValidationSupport.expandValueSet(any(FhirContext.class), arg);
}
ourLog.debug("expandValueSet({}) : {}", new Object[]{theInvocation.getArguments()[0], retVal});
ourLog.debug("expandValueSet({}) : {}", new Object[] {theInvocation.getArguments()[0], retVal});
return retVal;
}
});
@ -97,7 +97,7 @@ public class FhirInstanceValidatorDstu3Test {
@Override
public Boolean answer(InvocationOnMock theInvocation) {
boolean retVal = myValidSystems.contains(theInvocation.getArguments()[1]);
ourLog.debug("isCodeSystemSupported({}) : {}", new Object[]{theInvocation.getArguments()[1], retVal});
ourLog.debug("isCodeSystemSupported({}) : {}", new Object[] {theInvocation.getArguments()[1], retVal});
return retVal;
}
});
@ -126,7 +126,7 @@ public class FhirInstanceValidatorDstu3Test {
}
}
if (retVal == null) {
ourLog.info("fetchResource({}, {}) : {}", new Object[]{type, id, retVal});
ourLog.info("fetchResource({}, {}) : {}", new Object[] {type, id, retVal});
}
return retVal;
}
@ -143,7 +143,7 @@ public class FhirInstanceValidatorDstu3Test {
} else {
retVal = myDefaultValidationSupport.validateCode(ctx, system, code, (String) theInvocation.getArguments()[2]);
}
ourLog.debug("validateCode({}, {}, {}) : {}", new Object[]{system, code, theInvocation.getArguments()[2], retVal});
ourLog.debug("validateCode({}, {}, {}) : {}", new Object[] {system, code, theInvocation.getArguments()[2], retVal});
return retVal;
}
});
@ -151,7 +151,7 @@ public class FhirInstanceValidatorDstu3Test {
@Override
public CodeSystem answer(InvocationOnMock theInvocation) {
CodeSystem retVal = myDefaultValidationSupport.fetchCodeSystem((FhirContext) theInvocation.getArguments()[0], (String) theInvocation.getArguments()[1]);
ourLog.debug("fetchCodeSystem({}) : {}", new Object[]{theInvocation.getArguments()[1], retVal});
ourLog.debug("fetchCodeSystem({}) : {}", new Object[] {theInvocation.getArguments()[1], retVal});
return retVal;
}
});
@ -166,7 +166,7 @@ public class FhirInstanceValidatorDstu3Test {
if (retVal == null) {
retVal = myDefaultValidationSupport.fetchStructureDefinition((FhirContext) theInvocation.getArguments()[0], url);
}
ourLog.info("fetchStructureDefinition({}) : {}", new Object[]{url, retVal});
ourLog.info("fetchStructureDefinition({}) : {}", new Object[] {url, retVal});
return retVal;
}
});
@ -174,7 +174,7 @@ public class FhirInstanceValidatorDstu3Test {
@Override
public List<StructureDefinition> answer(InvocationOnMock theInvocation) {
List<StructureDefinition> retVal = myDefaultValidationSupport.fetchAllStructureDefinitions((FhirContext) theInvocation.getArguments()[0]);
ourLog.debug("fetchAllStructureDefinitions()", new Object[]{});
ourLog.debug("fetchAllStructureDefinitions()", new Object[] {});
return retVal;
}
});
@ -195,7 +195,7 @@ public class FhirInstanceValidatorDstu3Test {
int index = 0;
for (SingleValidationMessage next : theOutput.getMessages()) {
ourLog.info("Result {}: {} - {}:{} {} - {}",
new Object[]{index, next.getSeverity(), defaultString(next.getLocationLine()), defaultString(next.getLocationCol()), next.getLocationString(), next.getMessage()});
new Object[] {index, next.getSeverity(), defaultString(next.getLocationLine()), defaultString(next.getLocationCol()), next.getLocationString(), next.getMessage()});
index++;
retVal.add(next);
@ -209,7 +209,7 @@ public class FhirInstanceValidatorDstu3Test {
int index = 0;
for (SingleValidationMessage next : theOutput.getMessages()) {
ourLog.info("Result {}: {} - {} - {}", new Object[]{index, next.getSeverity(), next.getLocationString(), next.getMessage()});
ourLog.info("Result {}: {} - {} - {}", new Object[] {index, next.getSeverity(), next.getLocationString(), next.getMessage()});
index++;
if (next.getSeverity() != ResultSeverityEnum.INFORMATION) {
@ -249,6 +249,17 @@ public class FhirInstanceValidatorDstu3Test {
}
/**
* See #872
*/
@Test
public void testExtensionUrlWithHl7Url() throws IOException {
String input = IOUtils.toString(FhirInstanceValidatorDstu3Test.class.getResourceAsStream("/bug872-ext-with-hl7-url.json"), Charsets.UTF_8);
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> nonInfo = logResultsAndReturnNonInformationalOnes(output);
assertThat(nonInfo, empty());
}
@Test
public void testGoal() {
Goal goal = new Goal();

234
hapi-fhir-validation/src/test/java/org/hl7/fhir/instance/hapi/validation/FhirInstanceValidatorTest.java
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@ -1,14 +1,5 @@
package org.hl7.fhir.instance.hapi.validation;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.*;
import org.hl7.fhir.instance.model.*;
import org.hl7.fhir.instance.model.Observation.ObservationStatus;
import org.hl7.fhir.instance.model.QuestionnaireResponse.QuestionnaireResponseStatus;
import org.junit.*;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.dstu2.resource.Parameters;
import ca.uhn.fhir.model.dstu2.resource.Patient;
@ -17,69 +8,46 @@ import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.ValidationResult;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.instance.model.DateType;
import org.hl7.fhir.instance.model.Observation;
import org.hl7.fhir.instance.model.Observation.ObservationStatus;
import org.hl7.fhir.instance.model.QuestionnaireResponse;
import org.hl7.fhir.instance.model.QuestionnaireResponse.QuestionnaireResponseStatus;
import org.hl7.fhir.instance.model.StringType;
import org.junit.AfterClass;
import org.junit.Ignore;
import org.junit.Test;
import java.io.IOException;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.*;
public class FhirInstanceValidatorTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirInstanceValidatorTest.class);
private static FhirInstanceValidator ourValidator = new FhirInstanceValidator(new DefaultProfileValidationSupport());
private static FhirContext ourCtxDstu2 = FhirContext.forDstu2();
private static FhirContext ourCtxHl7OrgDstu2 = FhirContext.forDstu2Hl7Org();
/**
* See #872
*/
@Test
public void testParametersOkDstu2() {
Patient patient = new Patient();
patient.addName().addGiven("James");
patient.setBirthDate(new DateDt("2011-02-02"));
Parameters input = new Parameters();
input.addParameter().setName("resource").setResource(patient);
public void testExtensionUrlWithHl7Url() throws IOException {
String input = IOUtils.toString(FhirInstanceValidatorTest.class.getResourceAsStream("/bug872-ext-with-hl7-url.json"), Charsets.UTF_8);
FhirValidator val = ourCtxDstu2.newValidator();
val.registerValidatorModule(ourValidator);
ValidationResult result = val.validateWithResult(input);
ourLog.info(ourCtxDstu2.newJsonParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome()));
assertTrue(result.isSuccessful());
}
@Test
@Ignore
public void testParametersWithParameterNoValue() {
Parameters input = new Parameters();
input.addParameter().setName("resource");
FhirValidator val = ourCtxDstu2.newValidator();
val.registerValidatorModule(ourValidator);
ValidationResult result = val.validateWithResult(input);
String encoded = ourCtxDstu2.newJsonParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome());
ourLog.info(encoded);
assertFalse(result.isSuccessful());
assertThat(encoded, containsString("A parameter must have a value or a resource, but not both"));
}
@Test
public void testQuestionnaireResponse() {
QuestionnaireResponse qr = new QuestionnaireResponse();
qr.setStatus(QuestionnaireResponseStatus.COMPLETED);
qr.getGroup().addGroup().addQuestion().setLinkId("foo");
qr.getGroup().addQuestion().setLinkId("bar");
FhirValidator val = ourCtxHl7OrgDstu2.newValidator();
val.registerValidatorModule(ourValidator);
ValidationResult result = val.validateWithResult(qr);
String encoded = ourCtxHl7OrgDstu2.newJsonParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome());
ourLog.info(encoded);
assertTrue(result.isSuccessful());
}
/*
* {
@ -116,19 +84,99 @@ public class FhirInstanceValidatorTest {
o.setStatus(ObservationStatus.FINAL);
o.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
o.getEncounter().setReference("Encounter/1234");
FhirValidator val = ourCtxHl7OrgDstu2.newValidator();
val.registerValidatorModule(ourValidator);
ValidationResult result = val.validateWithResult(o);
String encoded = ourCtxHl7OrgDstu2.newJsonParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome());
ourLog.info(encoded);
assertTrue(result.isSuccessful());
}
@Test
public void testParametersHl7OrgDstu2() {
org.hl7.fhir.instance.model.Patient patient = new org.hl7.fhir.instance.model.Patient();
patient.addName().addGiven("James");
patient.setBirthDateElement(new DateType("2011-02-02"));
org.hl7.fhir.instance.model.Parameters input = new org.hl7.fhir.instance.model.Parameters();
input.addParameter().setName("resource").setResource(patient);
FhirValidator val = ourCtxHl7OrgDstu2.newValidator();
val.registerValidatorModule(ourValidator);
ValidationResult result = val.validateWithResult(input);
ourLog.info(ourCtxHl7OrgDstu2.newJsonParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome()));
assertTrue(result.isSuccessful());
}
@Test
public void testParametersOkDstu2() {
Patient patient = new Patient();
patient.addName().addGiven("James");
patient.setBirthDate(new DateDt("2011-02-02"));
Parameters input = new Parameters();
input.addParameter().setName("resource").setResource(patient);
FhirValidator val = ourCtxDstu2.newValidator();
val.registerValidatorModule(ourValidator);
ValidationResult result = val.validateWithResult(input);
ourLog.info(ourCtxDstu2.newJsonParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome()));
assertTrue(result.isSuccessful());
}
@Test
@Ignore
public void testParametersWithParameterNoValue() {
Parameters input = new Parameters();
input.addParameter().setName("resource");
FhirValidator val = ourCtxDstu2.newValidator();
val.registerValidatorModule(ourValidator);
ValidationResult result = val.validateWithResult(input);
String encoded = ourCtxDstu2.newJsonParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome());
ourLog.info(encoded);
assertFalse(result.isSuccessful());
assertThat(encoded, containsString("A parameter must have a value or a resource, but not both"));
}
@Test
@Ignore
public void testParametersWithParameterTwoValues() {
Patient patient = new Patient();
patient.addName().addGiven("James");
patient.setBirthDate(new DateDt("2011-02-02"));
Parameters input = new Parameters();
input.addParameter().setName("resource").setResource(patient).setValue(new StringDt("AAA"));
FhirValidator val = ourCtxDstu2.newValidator();
val.registerValidatorModule(ourValidator);
ValidationResult result = val.validateWithResult(input);
String encoded = ourCtxDstu2.newJsonParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome());
ourLog.info(encoded);
assertFalse(result.isSuccessful());
assertThat(encoded, containsString("A parameter must have a value or a resource, but not both"));
}
@Test
public void testParametersWithTwoParameters() {
org.hl7.fhir.instance.model.Patient patient = new org.hl7.fhir.instance.model.Patient();
@ -140,63 +188,37 @@ public class FhirInstanceValidatorTest {
input.addParameter().setName("resource").setResource(patient);
FhirValidator val = ourCtxHl7OrgDstu2.newValidator();
val.registerValidatorModule(ourValidator);
ValidationResult result = val.validateWithResult(input);
String encoded = ourCtxHl7OrgDstu2.newJsonParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome());
ourLog.info(encoded);
assertTrue(result.isSuccessful());
assertThat(encoded, not(containsString("A parameter must have a value or a resource, but not both")));
}
@Test
@Ignore
public void testParametersWithParameterTwoValues() {
Patient patient = new Patient();
patient.addName().addGiven("James");
patient.setBirthDate(new DateDt("2011-02-02"));
Parameters input = new Parameters();
input.addParameter().setName("resource").setResource(patient).setValue(new StringDt("AAA"));
FhirValidator val = ourCtxDstu2.newValidator();
val.registerValidatorModule(ourValidator);
ValidationResult result = val.validateWithResult(input);
String encoded = ourCtxDstu2.newJsonParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome());
ourLog.info(encoded);
assertFalse(result.isSuccessful());
assertThat(encoded, containsString("A parameter must have a value or a resource, but not both"));
}
@Test
public void testParametersHl7OrgDstu2() {
org.hl7.fhir.instance.model.Patient patient = new org.hl7.fhir.instance.model.Patient();
patient.addName().addGiven("James");
patient.setBirthDateElement(new DateType("2011-02-02"));
org.hl7.fhir.instance.model.Parameters input = new org.hl7.fhir.instance.model.Parameters();
input.addParameter().setName("resource").setResource(patient);
public void testQuestionnaireResponse() {
QuestionnaireResponse qr = new QuestionnaireResponse();
qr.setStatus(QuestionnaireResponseStatus.COMPLETED);
qr.getGroup().addGroup().addQuestion().setLinkId("foo");
qr.getGroup().addQuestion().setLinkId("bar");
FhirValidator val = ourCtxHl7OrgDstu2.newValidator();
val.registerValidatorModule(ourValidator);
ValidationResult result = val.validateWithResult(input);
ourLog.info(ourCtxHl7OrgDstu2.newJsonParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome()));
ValidationResult result = val.validateWithResult(qr);
String encoded = ourCtxHl7OrgDstu2.newJsonParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome());
ourLog.info(encoded);
assertTrue(result.isSuccessful());
}
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirInstanceValidatorTest.class);
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

12
hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java
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@ -22,6 +22,7 @@ import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import ca.uhn.fhir.validation.SingleValidationMessage;
import ca.uhn.fhir.validation.ValidationResult;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidatorDstu3Test;
@ -293,6 +294,17 @@ public class FhirInstanceValidatorR4Test {
assertThat(nonInfo, empty());
}
/**
* See #872
*/
@Test
public void testExtensionUrlWithHl7Url() throws IOException {
String input = IOUtils.toString(FhirInstanceValidator.class.getResourceAsStream("/bug872-ext-with-hl7-url.json"), Charsets.UTF_8);
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> nonInfo = logResultsAndReturnNonInformationalOnes(output);
assertThat(nonInfo, empty());
}
@SuppressWarnings("unchecked")
@Before
public void before() {

9
hapi-fhir-validation/src/test/resources/bug872-ext-with-hl7-url.json Normal file
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@ -0,0 +1,9 @@
{
"resourceType": "Patient",
"extension": [
{
"url": "http://hl7.org/fhir/ValueSet/v3-ActInvoiceGroupCode",
"valueString": "test"
}
]
}