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Fix this issue

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This commit is contained in:
James Agnew 2018-09-01 14:38:52 +08:00
parent fee0166800
commit f4a21eadda
7 changed files with 113 additions and 76 deletions
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15
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.rest.api;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -21,12 +21,7 @@ package ca.uhn.fhir.rest.api;
*/
import java.nio.charset.Charset;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.*;
public class Constants {
@ -197,6 +192,10 @@ public class Constants {
public static final String POWERED_BY_HEADER = "X-Powered-By";
public static final Charset CHARSET_US_ASCII;
public static final String PARAM_PAGEID = "_pageId";
/**
* This is provided for testing only! Use with caution as this property may change.
*/
public static final String TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS = "TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS";
static {
CHARSET_UTF8 = Charset.forName(CHARSET_NAME_UTF8);

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java
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@ -12,6 +12,7 @@ import ca.uhn.fhir.jpa.util.JpaConstants;
import ca.uhn.fhir.jpa.util.LoggingRule;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.IRequestOperationCallback;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
@ -58,6 +59,10 @@ import static org.mockito.Mockito.when;
public abstract class BaseJpaTest {
static {
System.setProperty(Constants.TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS, "1000");
}
protected static final String CM_URL = "http://example.com/my_concept_map";
protected static final String CS_URL = "http://example.com/my_code_system";
protected static final String CS_URL_2 = "http://example.com/my_code_system2";

117
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValidateTest.java
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@ -1,33 +1,34 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.*;
import org.junit.AfterClass;
import org.junit.Ignore;
import org.junit.Test;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.util.TestUtil;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import static ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast;
import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3ValidateTest.class);
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
@Test
public void testValidateChangedQuestionnaire() {
Questionnaire q = new Questionnaire();
@ -54,14 +55,17 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
q.addItem().setLinkId("B").setType(Questionnaire.QuestionnaireItemType.STRING).setRequired(true);
myQuestionnaireDao.update(q);
try {
QuestionnaireResponse qr = new QuestionnaireResponse();
qr.setStatus(QuestionnaireResponse.QuestionnaireResponseStatus.COMPLETED);
qr.getQuestionnaire().setReference("Questionnaire/QUEST");
qr.addItem().setLinkId("A").addAnswer().setValue(new StringType("AAA"));
QuestionnaireResponse qr = new QuestionnaireResponse();
qr.setStatus(QuestionnaireResponse.QuestionnaireResponseStatus.COMPLETED);
qr.getQuestionnaire().setReference("Questionnaire/QUEST");
qr.addItem().setLinkId("A").addAnswer().setValue(new StringType("AAA"));
MethodOutcome results = myQuestionnaireResponseDao.validate(qr, null, null, null, null, null, null);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(results.getOperationOutcome()));
MethodOutcome results = myQuestionnaireResponseDao.validate(qr, null, null, null, null, null, null);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(results.getOperationOutcome()));
sleepAtLeast(2500);
try {
myQuestionnaireResponseDao.validate(qr, null, null, null, null, null, null);
fail();
} catch (PreconditionFailedException e) {
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
@ -74,8 +78,8 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
public void testValidateStructureDefinition() throws Exception {
String input = IOUtils.toString(getClass().getResourceAsStream("/sd-david-dhtest7.json"), StandardCharsets.UTF_8);
StructureDefinition sd = myFhirCtx.newJsonParser().parseResource(StructureDefinition.class, input);
ourLog.info("Starting validation");
try {
myStructureDefinitionDao.validate(sd, null, null, null, ValidationModeEnum.UPDATE, null, mySrd);
@ -83,7 +87,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
}
ourLog.info("Done validation");
StopWatch sw = new StopWatch();
ourLog.info("Starting validation");
try {
@ -94,13 +98,13 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
ourLog.info("Done validation in {}ms", sw.getMillis());
}
@Test
public void testValidateDocument() throws Exception {
String input = IOUtils.toString(getClass().getResourceAsStream("/document-bundle-dstu3.json"), StandardCharsets.UTF_8);
Bundle document = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
ourLog.info("Starting validation");
try {
MethodOutcome outcome = myBundleDao.validate(document, null, null, null, ValidationModeEnum.CREATE, null, mySrd);
@ -108,7 +112,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
}
ourLog.info("Done validation");
// ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome.getOperationOutcome()));
}
@ -167,24 +171,24 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
MethodOutcome outcome = null;
ValidationModeEnum mode = ValidationModeEnum.CREATE;
switch (enc) {
case JSON:
encoded = myFhirCtx.newJsonParser().encodeResourceToString(input);
try {
myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
fail();
} catch (PreconditionFailedException e) {
return (OperationOutcome) e.getOperationOutcome();
}
break;
case XML:
encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
try {
myObservationDao.validate(input, null, encoded, EncodingEnum.XML, mode, null, mySrd);
fail();
} catch (PreconditionFailedException e) {
return (OperationOutcome) e.getOperationOutcome();
}
break;
case JSON:
encoded = myFhirCtx.newJsonParser().encodeResourceToString(input);
try {
myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
fail();
} catch (PreconditionFailedException e) {
return (OperationOutcome) e.getOperationOutcome();
}
break;
case XML:
encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
try {
myObservationDao.validate(input, null, encoded, EncodingEnum.XML, mode, null, mySrd);
fail();
} catch (PreconditionFailedException e) {
return (OperationOutcome) e.getOperationOutcome();
}
break;
}
throw new IllegalStateException(); // shouldn't get here
@ -325,18 +329,18 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
}
return retVal;
}
/**
* Format has changed, this is out of date
*/
@Test
@Ignore
public void testValidateNewQuestionnaireFormat() throws Exception {
String input =IOUtils.toString(FhirResourceDaoDstu3ValidateTest.class.getResourceAsStream("/questionnaire_dstu3.xml"));
String input = IOUtils.toString(FhirResourceDaoDstu3ValidateTest.class.getResourceAsStream("/questionnaire_dstu3.xml"));
try {
MethodOutcome results = myQuestionnaireDao.validate(null, null, input, EncodingEnum.XML, ValidationModeEnum.UPDATE, null, mySrd);
OperationOutcome oo = (OperationOutcome) results.getOperationOutcome();
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
MethodOutcome results = myQuestionnaireDao.validate(null, null, input, EncodingEnum.XML, ValidationModeEnum.UPDATE, null, mySrd);
OperationOutcome oo = (OperationOutcome) results.getOperationOutcome();
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
} catch (PreconditionFailedException e) {
// this is a failure of the test
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
@ -344,4 +348,9 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
}
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

9
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/ctx/HapiWorkerContext.java
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@ -1,12 +1,14 @@
package org.hl7.fhir.dstu3.hapi.ctx;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.CoverageIgnore;
import com.github.benmanes.caffeine.cache.Cache;
import com.github.benmanes.caffeine.cache.Caffeine;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.dstu3.context.IWorkerContext;
import org.hl7.fhir.dstu3.formats.IParser;
import org.hl7.fhir.dstu3.formats.ParserType;
@ -41,7 +43,12 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
Validate.notNull(theValidationSupport, "theValidationSupport must not be null");
myCtx = theCtx;
myValidationSupport = theValidationSupport;
myFetchedResourceCache = Caffeine.newBuilder().expireAfterWrite(10, TimeUnit.SECONDS).build();
long timeoutMillis = 10 * DateUtils.MILLIS_PER_SECOND;
if (System.getProperties().containsKey(Constants.TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS)) {
timeoutMillis = Long.parseLong(System.getProperty(Constants.TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS));
}
myFetchedResourceCache = Caffeine.newBuilder().expireAfterWrite(timeoutMillis, TimeUnit.MILLISECONDS).build();
}
@Override

10
hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/ctx/HapiWorkerContext.java
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@ -1,12 +1,14 @@
package org.hl7.fhir.r4.hapi.ctx;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.CoverageIgnore;
import com.github.benmanes.caffeine.cache.Cache;
import com.github.benmanes.caffeine.cache.Caffeine;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import org.fhir.ucum.UcumService;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.TerminologyServiceException;
@ -45,7 +47,13 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
Validate.notNull(theValidationSupport, "theValidationSupport must not be null");
myCtx = theCtx;
myValidationSupport = theValidationSupport;
myFetchedResourceCache = Caffeine.newBuilder().expireAfterWrite(10, TimeUnit.SECONDS).build();
long timeoutMillis = 10 * DateUtils.MILLIS_PER_SECOND;
if (System.getProperties().containsKey(ca.uhn.fhir.rest.api.Constants.TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS)) {
timeoutMillis = Long.parseLong(System.getProperty(Constants.TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS));
}
myFetchedResourceCache = Caffeine.newBuilder().expireAfterWrite(timeoutMillis, TimeUnit.MILLISECONDS).build();
}
@Override

26
hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidator.java
View File

@ -2,6 +2,7 @@ package org.hl7.fhir.dstu3.hapi.validation;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.validation.IValidationContext;
@ -15,6 +16,7 @@ import com.google.gson.JsonObject;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.time.DateUtils;
import org.fhir.ucum.UcumService;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
@ -272,14 +274,24 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
private final HapiWorkerContext myWrap;
private final VersionConvertor_30_40 myConverter;
private volatile List<org.hl7.fhir.r4.model.StructureDefinition> myAllStructures;
private LoadingCache<ResourceKey, org.hl7.fhir.r4.model.Resource> myFetchResourceCache
= Caffeine.newBuilder()
.expireAfterWrite(10, TimeUnit.SECONDS)
private LoadingCache<ResourceKey, org.hl7.fhir.r4.model.Resource> myFetchResourceCache;
public WorkerContextWrapper(HapiWorkerContext theWorkerContext) {
myWrap = theWorkerContext;
myConverter = new VersionConvertor_30_40();
long timeoutMillis = 10 * DateUtils.MILLIS_PER_SECOND;
if (System.getProperties().containsKey(ca.uhn.fhir.rest.api.Constants.TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS)) {
timeoutMillis = Long.parseLong(System.getProperty(Constants.TEST_SYSTEM_PROP_VALIDATION_RESOURCE_CACHES_MS));
}
myFetchResourceCache = Caffeine.newBuilder()
.expireAfterWrite(timeoutMillis, TimeUnit.MILLISECONDS)
.maximumSize(10000)
.build(new CacheLoader<ResourceKey, org.hl7.fhir.r4.model.Resource>() {
@Override
public org.hl7.fhir.r4.model.Resource load(FhirInstanceValidator.ResourceKey key) throws Exception {
org.hl7.fhir.dstu3.model.Resource fetched;
public org.hl7.fhir.r4.model.Resource load(ResourceKey key) throws Exception {
Resource fetched;
switch (key.getResourceName()) {
case "StructureDefinition":
fetched = myWrap.fetchResource(StructureDefinition.class, key.getUri());
@ -308,10 +320,6 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
}
}
});
public WorkerContextWrapper(HapiWorkerContext theWorkerContext) {
myWrap = theWorkerContext;
myConverter = new VersionConvertor_30_40();
}
@Override

7
pom.xml
View File

@ -465,12 +465,13 @@
<name>Ana Maria Radu</name>
<organization>Cerner Corporation</organization>
</developer>
<developer>
<id>jbalbien</id>
</developer>
<developer>
<id>alinleonard</id>
<name>Alin Leonard</name>
<organization>Cerner Corporation</organization>
</developer>
<developer>
<id>jbalbien</id>
</developer>
</developers>