Performance tweaks to the validator and get the DSTU2.1 endpoint working
with validation
This commit is contained in:
James Agnew
parent
685bd9345b
commit
7005cd52d9
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@ -107,7 +107,11 @@ public class RuntimeResourceDefinition extends BaseRuntimeElementCompositeDefini
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}
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if (!UrlUtil.isValid(profile)) {
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String profileWithUrl = theServerBase + "/Profile/" + profile;
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String resourceName = "/StructureDefinition/";
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if (myContext.getVersion().getVersion() == FhirVersionEnum.DSTU1) {
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resourceName = "/Profile/";
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}
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String profileWithUrl = theServerBase + resourceName + profile;
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if (UrlUtil.isValid(profileWithUrl)) {
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return profileWithUrl;
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}
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@ -1,49 +1,21 @@
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package ca.uhn.fhir.rest.server.interceptor;
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import java.nio.charset.Charset;
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/*
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* #%L
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* HAPI FHIR - Core Library
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* %%
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* Copyright (C) 2014 - 2015 University Health Network
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* %%
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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* #L%
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*/
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import javax.servlet.http.HttpServletRequest;
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import javax.servlet.http.HttpServletResponse;
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import java.util.HashSet;
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import java.util.Set;
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import org.apache.commons.lang3.Validate;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import ca.uhn.fhir.model.api.Bundle;
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import ca.uhn.fhir.model.api.TagList;
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import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
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import ca.uhn.fhir.rest.method.RequestDetails;
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import ca.uhn.fhir.rest.param.ResourceParameter;
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import ca.uhn.fhir.rest.server.EncodingEnum;
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import ca.uhn.fhir.rest.server.RestfulServerUtils;
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import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
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import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
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import ca.uhn.fhir.validation.FhirValidator;
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import ca.uhn.fhir.validation.ResultSeverityEnum;
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import ca.uhn.fhir.validation.ValidationResult;
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/**
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* This interceptor intercepts each outgoing response and if it contains a FHIR resource, validates that resource. The
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* interceptor may be configured to run any validator modules, and will then add headers to the response or fail the
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* request with an {@link UnprocessableEntityException HTTP 422 Unprocessable Entity}.
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* This interceptor intercepts each outgoing response and if it contains a FHIR resource, validates that resource. The interceptor may be configured to run any validator modules, and will then add
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* headers to the response or fail the request with an {@link UnprocessableEntityException HTTP 422 Unprocessable Entity}.
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*/
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public class ResponseValidatingInterceptor extends BaseValidatingInterceptor<IBaseResource> {
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@ -54,12 +26,42 @@ public class ResponseValidatingInterceptor extends BaseValidatingInterceptor<IBa
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResponseValidatingInterceptor.class);
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private Set<RestOperationTypeEnum> myExcludeOperationTypes;
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/**
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* Do not validate the following operations. A common use for this is to exclude {@link RestOperationTypeEnum#METADATA} so that this operation will execute as quickly as possible.
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*/
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public void addExcludeOperationType(RestOperationTypeEnum theOperationType) {
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Validate.notNull(theOperationType, "theOperationType must not be null");
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if (myExcludeOperationTypes == null) {
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myExcludeOperationTypes = new HashSet<RestOperationTypeEnum>();
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}
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myExcludeOperationTypes.add(theOperationType);
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}
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@Override
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ValidationResult doValidate(FhirValidator theValidator, IBaseResource theRequest) {
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return theValidator.validateWithResult(theRequest);
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}
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@Override
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public boolean outgoingResponse(RequestDetails theRequestDetails, IBaseResource theResponseObject) {
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RestOperationTypeEnum operationType = theRequestDetails.getRestOperationType();
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if (operationType != null && myExcludeOperationTypes != null && myExcludeOperationTypes.contains(operationType)) {
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ourLog.trace("Operation type {} is excluded from validation", operationType);
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return true;
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}
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validate(theResponseObject, theRequestDetails);
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return true;
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}
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@Override
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String provideDefaultResponseHeaderName() {
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return DEFAULT_RESPONSE_HEADER_NAME;
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}
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/**
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* Sets the name of the response header to add validation failures to
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*
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@ -71,14 +73,4 @@ public class ResponseValidatingInterceptor extends BaseValidatingInterceptor<IBa
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super.setResponseHeaderName(theResponseHeaderName);
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}
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@Override
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String provideDefaultResponseHeaderName() {
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return DEFAULT_RESPONSE_HEADER_NAME;
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}
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@Override
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ValidationResult doValidate(FhirValidator theValidator, IBaseResource theRequest) {
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return theValidator.validateWithResult(theRequest);
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}
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}
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@ -1,3 +1,4 @@
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ca.uhn.fhir.jpa.entity.ResourceTable/
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target/
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/bin
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nohup.out
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@ -206,6 +206,13 @@ public class TestRestfulServer extends RestfulServer {
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}
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@Override
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public void destroy() {
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super.destroy();
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ourLog.info("Server is shutting down");
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myAppCtx.destroy();
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}
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/**
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* The public server is deployed to http://fhirtest.uhn.ca and the JEE webserver
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* where this FHIR server is deployed is actually fronted by an Apache HTTPd instance,
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@ -24,6 +24,7 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
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import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu21;
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu21;
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import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
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import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
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import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
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import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
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@ -120,6 +121,7 @@ public class TestDstu21Config extends BaseJavaConfigDstu21 {
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responseValidator.addValidatorModule(myQuestionnaireResponseValidatorDstu21);
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responseValidator.setResponseHeaderValueNoIssues("Validation did not detect any issues");
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responseValidator.setFailOnSeverity(null);
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responseValidator.addExcludeOperationType(RestOperationTypeEnum.METADATA);
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return responseValidator;
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}
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@ -12,14 +12,14 @@
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<bean class="ca.uhn.fhir.to.TesterConfig">
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<property name="servers">
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<list>
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<value>home_dev , DSTU2 , UHN/HAPI Server (DSTU2 FHIR) , http://fhirtest.uhn.ca/baseDstu2</value>
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<value>home_21 , DSTU2 , UHN/HAPI Server (DSTU2.1 FHIR) , http://fhirtest.uhn.ca/baseDstu2.1</value>
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<value>home , DSTU1 , UHN/HAPI Server (DSTU1 FHIR) , http://fhirtest.uhn.ca/baseDstu1</value>
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<value>hidev , DSTU2 , Health Intersections (DSTU2 FHIR) , http://fhir-dev.healthintersections.com.au/open</value>
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<value>hi , DSTU1 , Health Intersections (DSTU1 FHIR) , http://fhir.healthintersections.com.au/open</value>
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<value>furored2 , DSTU2 , Spark - Furore (DSTU2 FHIR) , http://spark-dstu2.furore.com/fhir</value>
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<value>furore , DSTU1 , Spark - Furore (DSTU1 FHIR) , http://spark.furore.com/fhir</value>
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<value>sof , DSTU2 , SQL on FHIR - HealthConnex (DSTU2 FHIR) , http://sqlonfhir.azurewebsites.net/fhir</value>
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<value>home_dev , DSTU2 , UHN/HAPI Server (DSTU2 FHIR) , http://fhirtest.uhn.ca/baseDstu2</value>
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<value>home_21 , DSTU2_1 , UHN/HAPI Server (DSTU2.1 FHIR) , http://fhirtest.uhn.ca/baseDstu2.1</value>
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<value>home , DSTU1 , UHN/HAPI Server (DSTU1 FHIR) , http://fhirtest.uhn.ca/baseDstu1</value>
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<value>hidev , DSTU2 , Health Intersections (DSTU2 FHIR) , http://fhir-dev.healthintersections.com.au/open</value>
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<value>hi , DSTU1 , Health Intersections (DSTU1 FHIR) , http://fhir.healthintersections.com.au/open</value>
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<value>furored2 , DSTU2 , Spark - Furore (DSTU2 FHIR) , http://spark-dstu2.furore.com/fhir</value>
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<value>furore , DSTU1 , Spark - Furore (DSTU1 FHIR) , http://spark.furore.com/fhir</value>
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<value>sof , DSTU2 , SQL on FHIR - HealthConnex (DSTU2 FHIR) , http://sqlonfhir.azurewebsites.net/fhir</value>
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<!--
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<value>blaze , DSTU1 , Blaze (Orion Health) , https://fhir.orionhealth.com/blaze/fhir</value>
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<value>oridashi , DSTU1 , Oridashi , http://demo.oridashi.com.au:8190</value>
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@ -2,7 +2,9 @@ package org.hl7.fhir.dstu21.hapi.validation;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import org.apache.commons.lang3.StringUtils;
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import org.hl7.fhir.dstu21.formats.IParser;
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@ -33,6 +35,7 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander, ValueSetExpanderFactory {
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private final FhirContext myCtx;
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private IValidationSupport myValidationSupport;
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private Map<String, Resource> myFetchedResourceCache = new HashMap<String, Resource>();
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public HapiWorkerContext(FhirContext theCtx, IValidationSupport theValidationSupport) {
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myCtx = theCtx;
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@ -58,7 +61,15 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
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if (myValidationSupport == null) {
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return null;
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} else {
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return myValidationSupport.fetchResource(myCtx, theClass, theUri);
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@SuppressWarnings("unchecked")
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T retVal = (T) myFetchedResourceCache.get(theUri);
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if (retVal == null) {
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retVal = myValidationSupport.fetchResource(myCtx, theClass, theUri);
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if (retVal != null) {
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myFetchedResourceCache.put(theUri, retVal);
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}
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}
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return retVal;
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}
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}
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@ -132,7 +143,7 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
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}
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for (ConceptSetComponent nextComposeConceptSet : theVs.getCompose().getInclude()) {
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if (StringUtils.equals(theSystem, nextComposeConceptSet.getSystem())) {
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if (theSystem == null || StringUtils.equals(theSystem, nextComposeConceptSet.getSystem())) {
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for (ConceptReferenceComponent nextComposeCode : nextComposeConceptSet.getConcept()) {
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ConceptDefinitionComponent conceptDef = new ConceptDefinitionComponent();
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conceptDef.setCode(nextComposeCode.getCode());
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@ -21,6 +21,7 @@ import org.hl7.fhir.dstu21.model.ElementDefinition.TypeRefComponent;
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import org.hl7.fhir.dstu21.model.Enumerations.BindingStrength;
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import org.hl7.fhir.dstu21.model.Extension;
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import org.hl7.fhir.dstu21.model.HumanName;
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import org.hl7.fhir.dstu21.model.IdType;
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import org.hl7.fhir.dstu21.model.Identifier;
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import org.hl7.fhir.dstu21.model.OperationOutcome.IssueSeverity;
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import org.hl7.fhir.dstu21.model.OperationOutcome.IssueType;
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@ -946,11 +947,15 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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WrapperElement we = resolve(ref, stack);
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String ft;
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if (we != null)
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boolean hint;
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if (we != null) {
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ft = we.getResourceType();
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else
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hint = hint(errors, IssueType.STRUCTURE, element.line(), element.col(), path, ft != null, "Unable to determine type of target resource");
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} else {
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ft = tryParse(ref);
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if (hint(errors, IssueType.STRUCTURE, element.line(), element.col(), path, ft != null, "Unable to determine type of target resource")) {
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hint = hint(errors, IssueType.STRUCTURE, element.line(), element.col(), path, ft != null, "Unable to determine type of target resource in: {0}", ref);
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}
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if (hint) {
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boolean ok = false;
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CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
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for (TypeRefComponent type : container.getType()) {
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@ -1493,18 +1498,11 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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}
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private String tryParse(String ref) {
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String[] parts = ref.split("\\/");
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switch (parts.length) {
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case 1:
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IdType id = new IdType(ref);
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if (!id.hasResourceType()) {
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return null;
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case 2:
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return checkResourceType(parts[0]);
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default:
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if (parts[parts.length - 2].equals("_history"))
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return checkResourceType(parts[parts.length - 4]);
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else
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return checkResourceType(parts[parts.length - 2]);
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}
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return checkResourceType(id.getResourceType());
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}
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private boolean typesAreAllReference(List<TypeRefComponent> theType) {
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@ -30,6 +30,7 @@ import org.junit.Test;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.rest.annotation.OptionalParam;
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import ca.uhn.fhir.rest.annotation.Search;
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import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
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import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
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import ca.uhn.fhir.util.PortUtil;
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@ -111,6 +112,7 @@ public class ResponseValidatingInterceptorTest {
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assertThat(status.toString(), not(containsString("X-HAPI-Response-Validation")));
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}
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@Test
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public void testSearchJsonValidNoValidatorsSpecifiedDefaultMessage() throws Exception {
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myInterceptor.setResponseHeaderValueNoIssues("NO ISSUES");
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@ -185,6 +187,45 @@ public class ResponseValidatingInterceptorTest {
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assertThat(status.toString(), containsString("X-HAPI-Response-Validation"));
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}
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@Test
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public void testSkipEnabled() throws Exception {
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IValidatorModule module = new FhirInstanceValidator();
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myInterceptor.addValidatorModule(module);
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myInterceptor.addExcludeOperationType(RestOperationTypeEnum.METADATA);
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myInterceptor.setResponseHeaderValueNoIssues("No issues");
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HttpGet httpPost = new HttpGet("http://localhost:" + ourPort + "/metadata");
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HttpResponse status = ourClient.execute(httpPost);
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String responseContent = IOUtils.toString(status.getEntity().getContent());
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IOUtils.closeQuietly(status.getEntity().getContent());
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ourLog.info("Response was:\n{}", status);
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ourLog.info("Response was:\n{}", responseContent);
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assertEquals(200, status.getStatusLine().getStatusCode());
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assertThat(status.toString(), not(containsString("X-HAPI-Response-Validation")));
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}
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@Test
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public void testSkipNotEnabled() throws Exception {
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IValidatorModule module = new FhirInstanceValidator();
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myInterceptor.addValidatorModule(module);
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myInterceptor.setResponseHeaderValueNoIssues("No issues");
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HttpGet httpPost = new HttpGet("http://localhost:" + ourPort + "/metadata");
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HttpResponse status = ourClient.execute(httpPost);
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String responseContent = IOUtils.toString(status.getEntity().getContent());
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IOUtils.closeQuietly(status.getEntity().getContent());
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ourLog.info("Response was:\n{}", status);
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ourLog.info("Response was:\n{}", responseContent);
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assertEquals(200, status.getStatusLine().getStatusCode());
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assertThat(status.toString(), (containsString("X-HAPI-Response-Validation")));
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}
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@Test
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public void testSearchXmlValidNoValidatorsSpecified() throws Exception {
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Patient patient = new Patient();
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@ -9,10 +9,13 @@ import static org.mockito.Matchers.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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import java.io.IOException;
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import java.io.InputStream;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.zip.GZIPInputStream;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.dstu21.hapi.validation.DefaultProfileValidationSupport;
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@ -95,7 +98,8 @@ public class FhirInstanceValidatorTest {
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when(myMockSupport.fetchResource(any(FhirContext.class), any(Class.class), any(String.class))).thenAnswer(new Answer<IBaseResource>() {
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@Override
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public IBaseResource answer(InvocationOnMock theInvocation) throws Throwable {
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IBaseResource retVal = myDefaultValidationSupport.fetchResource((FhirContext) theInvocation.getArguments()[0], (Class<IBaseResource>) theInvocation.getArguments()[1], (String) theInvocation.getArguments()[2]);
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IBaseResource retVal = myDefaultValidationSupport.fetchResource((FhirContext) theInvocation.getArguments()[0], (Class<IBaseResource>) theInvocation.getArguments()[1],
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(String) theInvocation.getArguments()[2]);
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ourLog.info("fetchResource({}, {}) : {}", new Object[] { theInvocation.getArguments()[1], theInvocation.getArguments()[2], retVal });
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return retVal;
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}
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@ -166,9 +170,9 @@ public class FhirInstanceValidatorTest {
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@Test
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public void testValidateRawJsonResource() {
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// @formatter:off
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String input = "{" + "\"resourceType\":\"Patient\"," + "\"id\":\"123\"" + "}";
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// @formatter:on
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//@formatter:off
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String input = "{" + "\"resourceType\":\"Patient\"," + "\"id\":\"123\"" + "}";
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//@formatter:on
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|
||||
ValidationResult output = myVal.validateWithResult(input);
|
||||
assertEquals(output.toString(), 0, output.getMessages().size());
|
||||
|
|
@ -177,8 +181,8 @@ public class FhirInstanceValidatorTest {
|
|||
@Test
|
||||
public void testValidateRawJsonResourceBadAttributes() {
|
||||
// @formatter:off
|
||||
String input = "{" + "\"resourceType\":\"Patient\"," + "\"id\":\"123\"," + "\"foo\":\"123\"" + "}";
|
||||
// @formatter:on
|
||||
String input = "{" + "\"resourceType\":\"Patient\"," + "\"id\":\"123\"," + "\"foo\":\"123\"" + "}";
|
||||
// @formatter:on
|
||||
|
||||
ValidationResult output = myVal.validateWithResult(input);
|
||||
assertEquals(output.toString(), 1, output.getMessages().size());
|
||||
|
|
@ -191,13 +195,35 @@ public class FhirInstanceValidatorTest {
|
|||
@Test
|
||||
public void testValidateRawXmlResource() {
|
||||
// @formatter:off
|
||||
String input = "<Patient xmlns=\"http://hl7.org/fhir\">" + "<id value=\"123\"/>" + "</Patient>";
|
||||
// @formatter:on
|
||||
String input = "<Patient xmlns=\"http://hl7.org/fhir\">" + "<id value=\"123\"/>" + "</Patient>";
|
||||
// @formatter:on
|
||||
|
||||
ValidationResult output = myVal.validateWithResult(input);
|
||||
assertEquals(output.toString(), 0, output.getMessages().size());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateBigRawJsonResource() throws Exception {
|
||||
InputStream stream = FhirInstanceValidatorTest.class.getResourceAsStream("/conformance.json.gz");
|
||||
stream = new GZIPInputStream(stream);
|
||||
String input = IOUtils.toString(stream);
|
||||
|
||||
long start = System.currentTimeMillis();
|
||||
ValidationResult output = null;
|
||||
int passes = 1;
|
||||
for (int i = 0; i < passes; i++) {
|
||||
ourLog.info("Pass {}", i+1);
|
||||
output = myVal.validateWithResult(input);
|
||||
}
|
||||
|
||||
long delay = System.currentTimeMillis() - start;
|
||||
long per = delay / passes;
|
||||
|
||||
logResultsAndReturnAll(output);
|
||||
|
||||
ourLog.info("Took {} ms -- {}ms / pass", delay, per);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateRawXmlResourceBadAttributes() {
|
||||
// @formatter:off
|
||||
|
|
@ -304,9 +330,12 @@ public class FhirInstanceValidatorTest {
|
|||
|
||||
@Test
|
||||
public void testValidateResourceWithDefaultValuesetBadCode() {
|
||||
String input = "<Observation xmlns=\"http://hl7.org/fhir\">\n" + " <status value=\"notvalidcode\"/>\n" + " <code>\n" + " <text value=\"No code here!\"/>\n" + " </code>\n" + "</Observation>";
|
||||
String input = "<Observation xmlns=\"http://hl7.org/fhir\">\n" + " <status value=\"notvalidcode\"/>\n" + " <code>\n" + " <text value=\"No code here!\"/>\n" + " </code>\n"
|
||||
+ "</Observation>";
|
||||
ValidationResult output = myVal.validateWithResult(input);
|
||||
assertEquals("The value provided is not in the value set http://hl7.org/fhir/ValueSet/observation-status (http://hl7.org/fhir/ValueSet/observation-status, and a code is required from this value set", output.getMessages().get(0).getMessage());
|
||||
assertEquals(
|
||||
"The value provided is not in the value set http://hl7.org/fhir/ValueSet/observation-status (http://hl7.org/fhir/ValueSet/observation-status, and a code is required from this value set",
|
||||
output.getMessages().get(0).getMessage());
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -319,7 +348,9 @@ public class FhirInstanceValidatorTest {
|
|||
List<SingleValidationMessage> all = logResultsAndReturnAll(output);
|
||||
assertEquals(1, all.size());
|
||||
assertEquals("/f:Patient/f:identifier/f:type", all.get(0).getLocationString());
|
||||
assertEquals("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type, and a code should come from this value set unless it has no suitable code", all.get(0).getMessage());
|
||||
assertEquals(
|
||||
"None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type, and a code should come from this value set unless it has no suitable code",
|
||||
all.get(0).getMessage());
|
||||
assertEquals(ResultSeverityEnum.WARNING, all.get(0).getSeverity());
|
||||
|
||||
}
|
||||
|
|
|
|||
Binary file not shown.
|
|
@ -99,7 +99,7 @@ public class TesterConfig {
|
|||
Validate.notBlank(nextSplit[3], "theServerBase can not be blank");
|
||||
myIdToServerName.put(nextSplit[0].trim(), nextSplit[2].trim());
|
||||
myIdToServerBase.put(nextSplit[0].trim(), nextSplit[3].trim());
|
||||
myIdToFhirVersion.put(nextSplit[0].trim(), FhirVersionEnum.valueOf(nextSplit[1].trim().toUpperCase()));
|
||||
myIdToFhirVersion.put(nextSplit[0].trim(), FhirVersionEnum.valueOf(nextSplit[1].trim().toUpperCase().replace('.', '_')));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -106,6 +106,10 @@
|
|||
Introduce custom @CoverageIgnore annotation to hapi-fhir-base in order to
|
||||
remove dependency on cobertura during build and in runtime.
|
||||
</action>
|
||||
<action type="fix">
|
||||
Server-generated conformance statements incorrectly used /Profile/ instead
|
||||
of /StructureDefinition/ in URL links to structures.
|
||||
</action>
|
||||
</release>
|
||||
<release version="1.3" date="2015-11-14">
|
||||
<action type="add">
|
||||
|
|
|
|||
Loading…
Reference in New Issue