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Update FHIR R5 structures to 4.2.0 version (#1665) 

* Work on upgrading core

* Work on R5 updates

* Work on core updates

* Test fix

* Update model version properties file for R5

* Bump core version

* Test fixes

* Add 4.2.0-SNAPSHOT version to versions page in docs
This commit is contained in:
James Agnew 2020-01-14 10:27:01 +08:00 committed by GitHub
parent 62b50f06ad
commit 1390ea3c06
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44 changed files with 287423 additions and 288526 deletions
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10
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
View File

@ -233,13 +233,21 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
// check for the common case first - String value types
if (value.getValue() instanceof String) {
Object valueObj = value.getValue();
if (valueObj instanceof String) {
if (theChildName != null) {
theEventWriter.write(theChildName, valueStr);
} else {
theEventWriter.write(valueStr);
}
break;
} else if (valueObj instanceof Long) {
if (theChildName != null) {
theEventWriter.write(theChildName, (long)valueObj);
} else {
theEventWriter.write((long)valueObj);
}
break;
}
if (value instanceof IBaseIntegerDatatype) {

6
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/XmlParser.java
View File

@ -707,6 +707,12 @@ public class XmlParser extends BaseParser {
theEventWriter.writeStartElement(prefix, se.getName().getLocalPart(), namespaceURI);
theEventWriter.writeNamespace(prefix, namespaceURI);
}
for (Iterator<Attribute> iter= se.getAttributes(); iter.hasNext(); ) {
Attribute next = iter.next();
if ("lang".equals(next.getName().getLocalPart())) {
theEventWriter.writeAttribute("", "", next.getName().getLocalPart(), next.getValue());
}
}
firstElement = false;
} else {
if (isBlank(se.getName().getPrefix())) {

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/AttachmentUtil.java
View File

@ -85,6 +85,8 @@ public class AttachmentUtil {
BaseRuntimeChildDefinition entryChild = getChild(theContext, theAttachment, "size");
if (theLength == null) {
entryChild.getMutator().setValue(theAttachment, null);
} else if (theContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.R5)){
entryChild.getMutator().setValue(theAttachment, newPrimitive(theContext, "integer64", (long)theLength));
} else {
entryChild.getMutator().setValue(theAttachment, newPrimitive(theContext, "unsignedInt", theLength));
}

26
hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IBaseLongDatatype.java Normal file
View File

@ -0,0 +1,26 @@
package org.hl7.fhir.instance.model.api;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* 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.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
public interface IBaseLongDatatype extends IPrimitiveType<Integer> {
}

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/changes.yaml
View File

@ -64,6 +64,11 @@
issue: "1649"
type: "add"
title: "Support for LOINC 2.67 file format changes has been added to the JPA Server LOINC uploader. Thanks to Dan Vreeman for reporting!"
- item:
issue: "1658"
type: "fix"
title: "When parsing HTML Narratives, the `lang` attribute was stripped from the outer DIV tag if present. Thanks to
Sean McIlvenna for reporting!"
- item:
issue: "1655"
type: "fix"

10
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/introduction/versions.md
View File

@ -25,6 +25,16 @@ Note also that after the release of the FHIR DSTU2 specification, the FHIR
</tr>
</thead>
<tbody>
<tr>
<td>HAPI FHIR 4.2.0-SNAPSHOT</td>
<td>JDK8</td>
<td class="versions-table-cell-empty"></td>
<td class="versions-table-cell-draft">1.0.2</td>
<td class="versions-table-cell-release">1.4.0</td>
<td class="versions-table-cell-draft">3.0.2</td>
<td class="versions-table-cell-draft">4.0.1</td>
<td class="versions-table-cell-release">4.2.0<span class="download-version-hash"><br/>e0f3f5cc2c</span></td>
</tr>
<tr>
<td>HAPI FHIR 4.1.0</td>
<td>JDK8</td>

2
hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/client/GenericJaxRsClientDstu3Test.java
View File

@ -1356,7 +1356,7 @@ public class GenericJaxRsClientDstu3Test {
.execute();
fail();
} catch (InvalidResponseException e) {
assertThat(e.getMessage(), containsString("Unable to Parse HTML - node"));
assertThat(e.getMessage(), containsString("Unable to Parse HTML"));
}
//@formatter:on
}

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoSubscriptionR5.java
View File

@ -20,29 +20,20 @@ package ca.uhn.fhir.jpa.dao.r5;
* #L%
*/
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSubscription;
import ca.uhn.fhir.jpa.dao.data.ISubscriptionTableDao;
import ca.uhn.fhir.jpa.entity.SubscriptionTable;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.model.Subscription;
import org.hl7.fhir.r5.model.codesystems.SubscriptionChannelType;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nullable;
import java.util.Date;
import static org.apache.commons.lang3.StringUtils.isBlank;
public class FhirResourceDaoSubscriptionR5 extends BaseHapiFhirResourceDao<Subscription> implements IFhirResourceDaoSubscription<Subscription> {
@Autowired

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
View File

@ -38,15 +38,18 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r5.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.r5.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Enumerations;
import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r5.model.IntegerType;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetFilterComponent;
import org.hl7.fhir.r5.model.ValueSet.FilterOperator;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import java.util.Collections;
import java.util.Date;
@ -172,7 +175,7 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
ConceptSetComponent include = source.getCompose().addInclude();
ConceptSetFilterComponent filter = include.addFilter();
filter.setProperty("display");
filter.setOp(FilterOperator.EQUAL);
filter.setOp(Enumerations.FilterOperator.EQUAL);
filter.setValue(theFilter);
}
@ -207,7 +210,7 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
ConceptSetComponent include = source.getCompose().addInclude();
ConceptSetFilterComponent filter = include.addFilter();
filter.setProperty("display");
filter.setOp(FilterOperator.EQUAL);
filter.setOp(Enumerations.FilterOperator.EQUAL);
filter.setValue(theFilter);
}
@ -289,7 +292,7 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
private void addFilterIfPresent(String theFilter, ConceptSetComponent include) {
if (ElementUtil.isEmpty(include.getConcept())) {
if (isNotBlank(theFilter)) {
include.addFilter().setProperty("display").setOp(FilterOperator.EQUAL).setValue(theFilter);
include.addFilter().setProperty("display").setOp(Enumerations.FilterOperator.EQUAL).setValue(theFilter);
}
}
}

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java
View File

@ -127,7 +127,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
obs.getCode().getCodingFirstRep().setSystem("http://loinc.org").setCode("CODE3").setDisplay("Display 3");
obs.getCategoryFirstRep().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/observation-category").setCode("FOO");
oo = validateAndReturnOutcome(obs);
assertEquals(encode(oo), "Unknown code: http://terminology.hl7.org/CodeSystem/observation-category / FOO", oo.getIssueFirstRep().getDiagnostics());
assertEquals(encode(oo), "Unknown code[FOO] in system[http://terminology.hl7.org/CodeSystem/observation-category]", oo.getIssueFirstRep().getDiagnostics());
}
@ -208,7 +208,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
obs.getCode().getCodingFirstRep().setSystem("http://loinc.org").setCode("CODE3").setDisplay("Display 3");
obs.getCategoryFirstRep().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/observation-category").setCode("FOO");
oo = validateAndReturnOutcome(obs);
assertEquals(encode(oo), "Unknown code: http://terminology.hl7.org/CodeSystem/observation-category / FOO", oo.getIssueFirstRep().getDiagnostics());
assertEquals(encode(oo), "Unknown code[FOO] in system[http://terminology.hl7.org/CodeSystem/observation-category]", oo.getIssueFirstRep().getDiagnostics());
}

78
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5ValueSetTest.java
View File

@ -3,8 +3,13 @@ package ca.uhn.fhir.jpa.provider.r5;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
import ca.uhn.fhir.jpa.entity.TermValueSetConceptDesignation;
import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
@ -23,11 +28,10 @@ import org.apache.http.entity.ContentType;
import org.apache.http.entity.StringEntity;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.Bundle.HTTPVerb;
import org.hl7.fhir.r5.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.model.ValueSet.FilterOperator;
import org.hl7.fhir.r5.model.codesystems.HttpVerb;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Test;
@ -41,8 +45,16 @@ import java.util.Optional;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest.URL_MY_CODE_SYSTEM;
import static ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest.URL_MY_VALUE_SET;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.containsStringIgnoringCase;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertSame;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
@ -54,35 +66,35 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
private Long myExtensionalVsIdOnResourceTable;
private ValueSet myLocalVs;
private void loadAndPersistCodeSystemAndValueSet(HttpVerb theVerb) throws IOException {
private void loadAndPersistCodeSystemAndValueSet(HTTPVerb theVerb) throws IOException {
loadAndPersistCodeSystem(theVerb);
loadAndPersistValueSet(theVerb);
}
private void loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb theVerb) throws IOException {
private void loadAndPersistCodeSystemAndValueSetWithDesignations(HTTPVerb theVerb) throws IOException {
loadAndPersistCodeSystemWithDesignations(theVerb);
loadAndPersistValueSet(theVerb);
}
private void loadAndPersistCodeSystemAndValueSetWithDesignationsAndExclude(HttpVerb theVerb) throws IOException {
private void loadAndPersistCodeSystemAndValueSetWithDesignationsAndExclude(HTTPVerb theVerb) throws IOException {
loadAndPersistCodeSystemWithDesignations(theVerb);
loadAndPersistValueSetWithExclude(theVerb);
}
private void loadAndPersistCodeSystem(HttpVerb theVerb) throws IOException {
private void loadAndPersistCodeSystem(HTTPVerb theVerb) throws IOException {
CodeSystem codeSystem = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
codeSystem.setId("CodeSystem/cs");
persistCodeSystem(codeSystem, theVerb);
}
private void loadAndPersistCodeSystemWithDesignations(HttpVerb theVerb) throws IOException {
private void loadAndPersistCodeSystemWithDesignations(HTTPVerb theVerb) throws IOException {
CodeSystem codeSystem = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs-with-designations.xml");
codeSystem.setId("CodeSystem/cs");
persistCodeSystem(codeSystem, theVerb);
}
@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
private void persistCodeSystem(CodeSystem theCodeSystem, HttpVerb theVerb) {
private void persistCodeSystem(CodeSystem theCodeSystem, HTTPVerb theVerb) {
switch (theVerb) {
case POST:
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@ -106,20 +118,20 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
myExtensionalCsIdOnResourceTable = myCodeSystemDao.readEntity(myExtensionalCsId, null).getId();
}
private void loadAndPersistValueSet(HttpVerb theVerb) throws IOException {
private void loadAndPersistValueSet(HTTPVerb theVerb) throws IOException {
ValueSet valueSet = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
valueSet.setId("ValueSet/vs");
persistValueSet(valueSet, theVerb);
}
private void loadAndPersistValueSetWithExclude(HttpVerb theVerb) throws IOException {
private void loadAndPersistValueSetWithExclude(HTTPVerb theVerb) throws IOException {
ValueSet valueSet = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs-with-exclude.xml");
valueSet.setId("ValueSet/vs");
persistValueSet(valueSet, theVerb);
}
@SuppressWarnings("EnumSwitchStatementWhichMissesCases")
private void persistValueSet(ValueSet theValueSet, HttpVerb theVerb) {
private void persistValueSet(ValueSet theValueSet, HTTPVerb theVerb) {
switch (theVerb) {
case POST:
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@ -195,7 +207,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
myLocalVs.setUrl(URL_MY_VALUE_SET);
ConceptSetComponent include = myLocalVs.getCompose().addInclude();
include.setSystem(codeSystem.getUrl());
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("ParentA");
include.addFilter().setProperty("concept").setOp(Enumerations.FilterOperator.ISA).setValue("ParentA");
myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
}
@ -212,13 +224,13 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
myLocalVs.setUrl(URL_MY_VALUE_SET);
ConceptSetComponent include = myLocalVs.getCompose().addInclude();
include.setSystem(codeSystem.getUrl());
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("childFOOOOOOO");
include.addFilter().setProperty("concept").setOp(Enumerations.FilterOperator.ISA).setValue("childFOOOOOOO");
myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
}
@Test
public void testExpandById() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
Parameters respParam = ourClient
.operation()
@ -250,7 +262,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
public void testExpandByIdWithPreExpansion() throws Exception {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Parameters respParam = ourClient
@ -281,7 +293,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
@Test
public void testExpandByIdWithFilter() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
Parameters respParam = ourClient
.operation()
@ -302,7 +314,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
public void testExpandByIdWithFilterWithPreExpansion() throws Exception {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Parameters respParam = ourClient
@ -322,7 +334,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
@Test
public void testExpandByUrl() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
Parameters respParam = ourClient
.operation()
@ -342,7 +354,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
@Test
public void testExpandByUrlWithBogusUrl() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
try {
ourClient
@ -361,7 +373,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
public void testExpandByUrlWithPreExpansion() throws Exception {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Parameters respParam = ourClient
@ -384,7 +396,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
public void testExpandByUrlWithPreExpansionAndBogusUrl() throws Exception {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
try {
@ -402,7 +414,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
@Test
public void testExpandByValueSet() throws IOException {
loadAndPersistCodeSystem(HttpVerb.POST);
loadAndPersistCodeSystem(HTTPVerb.POST);
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
@ -426,7 +438,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
public void testExpandByValueSetWithPreExpansion() throws IOException {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystem(HttpVerb.POST);
loadAndPersistCodeSystem(HTTPVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
@ -491,7 +503,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
@Test
public void testExpandInvalidParams() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
try {
ourClient
@ -717,7 +729,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
public void testUpdateValueSetTriggersAnotherPreExpansion() throws Exception {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.POST);
loadAndPersistCodeSystemAndValueSetWithDesignations(HTTPVerb.POST);
CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
@ -732,7 +744,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
ValueSet updatedValueSet = valueSet;
updatedValueSet.setName(valueSet.getName().concat(" - MODIFIED"));
persistValueSet(updatedValueSet, HttpVerb.PUT);
persistValueSet(updatedValueSet, HTTPVerb.PUT);
updatedValueSet = myValueSetDao.read(myExtensionalVsId);
ourLog.info("Updated ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(updatedValueSet));
@ -746,7 +758,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
public void testUpdateValueSetTriggersAnotherPreExpansionUsingTransactionBundle() throws Exception {
myDaoConfig.setPreExpandValueSets(true);
loadAndPersistCodeSystemAndValueSetWithDesignations(HttpVerb.POST);
loadAndPersistCodeSystemAndValueSetWithDesignations(Bundle.HTTPVerb.POST);
CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
@ -877,7 +889,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
@Test
public void testValidateCodeOperationByCodeAndSystemInstance() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
Parameters respParam = ourClient
.operation()
@ -938,7 +950,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
@Test
public void testValidateCodeOperationByCodeAndSystemType() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
loadAndPersistCodeSystemAndValueSet(HTTPVerb.POST);
Parameters respParam = ourClient
.operation()
@ -996,7 +1008,7 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
.addInclude()
.setSystem("http://mycs")
.addFilter()
.setOp(FilterOperator.ISA)
.setOp(Enumerations.FilterOperator.ISA)
.setProperty("concept")
.setValue("ParentA");
IIdType vsId = myValueSetDao.create(vs).getId().toUnqualifiedVersionless();

23
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/BaseSubscriptionsR5Test.java
View File

@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.subscription;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.provider.r5.BaseResourceProviderR5Test;
import ca.uhn.fhir.jpa.subscription.module.CanonicalSubscriptionChannelType;
import ca.uhn.fhir.jpa.subscription.module.LinkedBlockingQueueSubscribableChannel;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.ResourceParam;
@ -21,9 +22,19 @@ import org.eclipse.jetty.servlet.ServletContextHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.codesystems.SubscriptionChannelType;
import org.junit.*;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Enumerations;
import org.hl7.fhir.r5.model.IdType;
import org.hl7.fhir.r5.model.Observation;
import org.hl7.fhir.r5.model.Subscription;
import org.hl7.fhir.r5.model.Topic;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Ignore;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.PostConstruct;
@ -131,8 +142,8 @@ public abstract class BaseSubscriptionsR5Test extends BaseResourceProviderR5Test
Subscription.SubscriptionChannelComponent channel = subscription.getChannel();
channel.getType().addCoding()
.setSystem(SubscriptionChannelType.RESTHOOK.getSystem())
.setCode(SubscriptionChannelType.RESTHOOK.toCode());
.setSystem(CanonicalSubscriptionChannelType.RESTHOOK.getSystem())
.setCode(CanonicalSubscriptionChannelType.RESTHOOK.toCode());
channel.getPayload().setContentType(thePayload);
channel.setEndpoint(ourListenerServerBase);
return subscription;
@ -158,7 +169,7 @@ public abstract class BaseSubscriptionsR5Test extends BaseResourceProviderR5Test
coding.setCode(code);
coding.setSystem(system);
observation.setStatus(Observation.ObservationStatus.FINAL);
observation.setStatus(Enumerations.ObservationStatus.FINAL);
IIdType id = myObservationDao.create(observation).getId();
observation.setId(id);

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/RestHookTestR5Test.java
View File

@ -131,7 +131,7 @@ public class RestHookTestR5Test extends BaseSubscriptionsR5Test {
Observation observation = new Observation();
observation.getIdentifierFirstRep().setSystem("foo").setValue("1");
observation.getCode().addCoding().setCode(code).setSystem("SNOMED-CT");
observation.setStatus(Observation.ObservationStatus.FINAL);
observation.setStatus(Enumerations.ObservationStatus.FINAL);
observation.getSubject().setReference(patient.getId());
bundle.addEntry().setResource(observation).getRequest().setMethod(Bundle.HTTPVerb.POST).setUrl("Observation");
@ -160,7 +160,7 @@ public class RestHookTestR5Test extends BaseSubscriptionsR5Test {
Observation observation = new Observation();
observation.getIdentifierFirstRep().setSystem("foo").setValue("1");
observation.getCode().addCoding().setCode(code).setSystem("SNOMED-CT");
observation.setStatus(Observation.ObservationStatus.FINAL);
observation.setStatus(Enumerations.ObservationStatus.FINAL);
Bundle bundle = new Bundle();
bundle.setType(Bundle.BundleType.TRANSACTION);
bundle.addEntry().setResource(observation).getRequest().setMethod(Bundle.HTTPVerb.POST).setUrl("Observation");
@ -187,7 +187,7 @@ public class RestHookTestR5Test extends BaseSubscriptionsR5Test {
observation.setId(obs.getId());
observation.getIdentifierFirstRep().setSystem("foo").setValue("2");
observation.getCode().addCoding().setCode(code).setSystem("SNOMED-CT");
observation.setStatus(Observation.ObservationStatus.FINAL);
observation.setStatus(Enumerations.ObservationStatus.FINAL);
bundle = new Bundle();
bundle.setType(Bundle.BundleType.TRANSACTION);
bundle.addEntry().setResource(observation).getRequest().setMethod(Bundle.HTTPVerb.PUT).setUrl(obs.getIdElement().toUnqualifiedVersionless().getValue());
@ -220,7 +220,7 @@ public class RestHookTestR5Test extends BaseSubscriptionsR5Test {
Observation observation = new Observation();
observation.getIdentifierFirstRep().setSystem("foo").setValue("ID" + i);
observation.getCode().addCoding().setCode(code).setSystem("SNOMED-CT");
observation.setStatus(Observation.ObservationStatus.FINAL);
observation.setStatus(Enumerations.ObservationStatus.FINAL);
myObservationDao.create(observation);
}
@ -669,7 +669,7 @@ public class RestHookTestR5Test extends BaseSubscriptionsR5Test {
CodeableConcept codeableConcept = new CodeableConcept()
.addCoding(new Coding().setCode(code).setSystem("SNOMED-CT"));
observation.setCode(codeableConcept);
observation.setStatus(Observation.ObservationStatus.FINAL);
observation.setStatus(Enumerations.ObservationStatus.FINAL);
Patient patient = new Patient();
patient.addIdentifier().setSystem("foo").setValue("bar2");
@ -848,7 +848,7 @@ public class RestHookTestR5Test extends BaseSubscriptionsR5Test {
@Test(expected = UnprocessableEntityException.class)
public void testInvalidProvenanceParam() {
String payload = "application/fhir+json";
String criteriabad = "Provenance?activity=http://hl7.org/fhir/v3/DocumentCompletion%7CAU";
String criteriabad = "Provenance?foo=http://hl7.org/fhir/v3/DocumentCompletion%7CAU";
Subscription subscription = newSubscription(criteriabad, payload);
ourClient.create().resource(subscription).execute();
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/validator/AttachmentUtilTest.java
View File

@ -49,7 +49,7 @@ public class AttachmentUtilTest {
AttachmentUtil.setSize(ctx, attachment, 123);
org.hl7.fhir.r5.model.Communication communication = new org.hl7.fhir.r5.model.Communication();
communication.addPayload().setContent((org.hl7.fhir.r5.model.Type) attachment);
communication.addPayload().setContent((org.hl7.fhir.r5.model.DataType) attachment);
String encoded = ctx.newJsonParser().encodeResourceToString(communication);
assertEquals("{\"resourceType\":\"Communication\",\"payload\":[{\"contentAttachment\":{\"contentType\":\"text/plain\",\"data\":\"AAECAw==\",\"url\":\"http://foo\",\"size\":123}}]}", encoded);
}

2
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/any/AnyListResource.java
View File

@ -298,7 +298,7 @@ public class AnyListResource {
private boolean removeItemR5(String theReferenceId) {
boolean removed = false;
for (org.hl7.fhir.r5.model.ListResource.ListEntryComponent entry : getR5().getEntry()) {
for (org.hl7.fhir.r5.model.ListResource.ListResourceEntryComponent entry : getR5().getEntry()) {
if (theReferenceId.equals(entry.getItem().getReference()) && !entry.getDeleted()) {
entry.setDeleted(true);
removed = true;

1
hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorMegaTest.java
View File

@ -163,6 +163,7 @@ public class SearchParamExtractorMegaTest {
case "instant":
leaf.setValueAsString("2019-10-10T11:11:11Z");
break;
case "integer64":
case "integer":
case "decimal":
leaf.setValueAsString("1");

19
hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2_1Test.java
View File

@ -1693,25 +1693,6 @@ public class JsonParserDstu2_1Test {
}
/**
* See #484
*/
@Test
public void testParseNarrativeWithEmptyDiv() {
String input = "{\"resourceType\":\"Basic\",\"id\":\"1\",\"text\":{\"status\":\"generated\",\"div\":\"<div/>\"}}";
Basic basic = ourCtx.newJsonParser().parseResource(Basic.class, input);
assertEquals(null, basic.getText().getDivAsString());
input = "{\"resourceType\":\"Basic\",\"id\":\"1\",\"text\":{\"status\":\"generated\",\"div\":\"<div></div>\"}}";
basic = ourCtx.newJsonParser().parseResource(Basic.class, input);
assertEquals(null, basic.getText().getDivAsString());
input = "{\"resourceType\":\"Basic\",\"id\":\"1\",\"text\":{\"status\":\"generated\",\"div\":\"<div> </div>\"}}";
basic = ourCtx.newJsonParser().parseResource(Basic.class, input);
assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"> </div>", basic.getText().getDivAsString());
}
/**
* See #163
*/

12
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/model/XhtmlNodeTest.java
View File

@ -30,7 +30,17 @@ public class XhtmlNodeTest {
assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">It’s January again</div>", new XhtmlNode().setValue(dt.getValue()).getValueAsString());
}
/**
* See #1658
*/
@Test
public void testLangAttributePreserved() {
XhtmlNode dt = new XhtmlNode();
dt.setValueAsString("<div xmlns=\"http://www.w3.org/1999/xhtml\" lang=\"en-US\">help i'm a bug</div>");
assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\" lang=\"en-US\">help i'm a bug</div>", dt.getValueAsString());
assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\" lang=\"en-US\">help i'm a bug</div>", new XhtmlNode().setValue(dt.getValue()).getValueAsString());
}
/**
* See #443
*/

16
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java
View File

@ -2187,11 +2187,11 @@ public class JsonParserDstu3Test {
public void testParseNarrativeWithEmptyDiv() {
String input = "{\"resourceType\":\"Basic\",\"id\":\"1\",\"text\":{\"status\":\"generated\",\"div\":\"<div/>\"}}";
Basic basic = ourCtx.newJsonParser().parseResource(Basic.class, input);
assertEquals(null, basic.getText().getDivAsString());
assertEquals("<div/>", basic.getText().getDivAsString());
input = "{\"resourceType\":\"Basic\",\"id\":\"1\",\"text\":{\"status\":\"generated\",\"div\":\"<div></div>\"}}";
basic = ourCtx.newJsonParser().parseResource(Basic.class, input);
assertEquals(null, basic.getText().getDivAsString());
assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"/>", basic.getText().getDivAsString());
input = "{\"resourceType\":\"Basic\",\"id\":\"1\",\"text\":{\"status\":\"generated\",\"div\":\"<div> </div>\"}}";
basic = ourCtx.newJsonParser().parseResource(Basic.class, input);
@ -2199,6 +2199,18 @@ public class JsonParserDstu3Test {
}
/**
* See #1658
*/
@Test
public void testParseNarrativeWithLang() {
String input = "{\"resourceType\":\"Basic\",\"id\":\"1\",\"text\":{\"status\":\"generated\",\"div\":\"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\" lang=\\\"en-US\\\">foo</div>\"}}";
Basic basic = ourCtx.newJsonParser().parseResource(Basic.class, input);
assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\" lang=\"en-US\">foo</div>", basic.getText().getDivAsString());
}
/**
* See #163
*/

19
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/XmlParserR4Test.java
View File

@ -1,21 +1,26 @@
package ca.uhn.fhir.parser;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertThat;
import ca.uhn.fhir.test.BaseTest;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Composition;
import org.hl7.fhir.r4.model.MessageHeader;
import org.hl7.fhir.r4.model.Narrative;
import org.hl7.fhir.r4.model.Observation;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import ca.uhn.fhir.context.FhirContext;
public class XmlParserR4Test {
import java.io.IOException;
public class XmlParserR4Test extends BaseTest {
private static final Logger ourLog = LoggerFactory.getLogger(XmlParserR4Test.class);
private static FhirContext ourCtx = FhirContext.forR4();
@ -74,5 +79,17 @@ public class XmlParserR4Test {
}
/**
* See #1658
*/
@Test
public void testNarrativeLangAttributePreserved() throws IOException {
Observation obs = loadResource(ourCtx, Observation.class, "/resource-with-lang-in-narrative.xml");
String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(obs);
assertThat(encoded, containsString("xmlns=\"http://www.w3.org/1999/xhtml\""));
assertThat(encoded, containsString("lang=\"en-US\""));
ourLog.info(encoded);
}
}

49
hapi-fhir-structures-r4/src/test/resources/resource-with-lang-in-narrative.xml Normal file
View File

@ -0,0 +1,49 @@
<?xml version="1.0" encoding="UTF-8"?><Observation xmlns="http://hl7.org/fhir">
<id value="f001"/><!-- urn:oid:2.16.840.1.113883.4.642.1.7 --><!-- 2.16.840.1.113883.4.642.1.118 -->
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml" lang="en-US"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: f001</p><p><b>identifier</b>: 6323 (OFFICIAL)</p><p><b>status</b>: final</p><p><b>code</b>: Glucose [Moles/volume] in Blood <span>(Details : {LOINC code &#39;15074-8&#39; = &#39;Glucose [Moles/volume] in Blood&#39;, given as &#39;Glucose [Moles/volume] in Blood&#39;})</span></p><p><b>subject</b>: <a>P. van de Heuvel</a></p><p><b>effective</b>: 02/04/2013 9:30:10 AM --&gt; (ongoing)</p><p><b>issued</b>: 03/04/2013 3:30:10 PM</p><p><b>performer</b>: <a>A. Langeveld</a></p><p><b>value</b>: 6.3 mmol/l<span> (Details: UCUM code mmol/L = &#39;mmol/L&#39;)</span></p><p><b>interpretation</b>: High <span>(Details : {http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation code &#39;H&#39; = &#39;High&#39;, given as &#39;High&#39;})</span></p><h3>ReferenceRanges</h3><table><tr><td>-</td><td><b>Low</b></td><td><b>High</b></td></tr><tr><td>*</td><td>3.1 mmol/l<span> (Details: UCUM code mmol/L = &#39;mmol/L&#39;)</span></td><td>6.2 mmol/l<span> (Details: UCUM code mmol/L = &#39;mmol/L&#39;)</span></td></tr></table></div></text><identifier>
<use value="official"/>
<system value="http://www.bmc.nl/zorgportal/identifiers/observations"/>
<value value="6323"/>
</identifier>
<status value="final"/>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="15074-8"/>
<display value="Glucose [Moles/volume] in Blood"/>
</coding>
</code>
<effectivePeriod>
<start value="2013-04-02T09:30:10+01:00"/>
</effectivePeriod>
<issued value="2013-04-03T15:30:10+01:00"/>
<valueQuantity>
<value value="6.3"/>
<unit value="mmol/l"/>
<system value="http://unitsofmeasure.org"/>
<code value="mmol/L"/>
</valueQuantity>
<interpretation>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation"/>
<code value="H"/>
<display value="High"/>
</coding>
</interpretation>
<referenceRange>
<low>
<value value="3.1"/>
<unit value="mmol/l"/>
<system value="http://unitsofmeasure.org"/>
<code value="mmol/L"/>
</low>
<high>
<value value="6.2"/>
<unit value="mmol/l"/>
<system value="http://unitsofmeasure.org"/>
<code value="mmol/L"/>
</high>
</referenceRange>
</Observation>

2
hapi-fhir-structures-r5/src/main/java/org/hl7/fhir/r5/hapi/ctx/DefaultProfileValidationSupport.java
View File

@ -314,7 +314,7 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
.filter(t -> (Constants.codeSystemNotNeeded(theCodeSystem) || t.getSystem().equals(theCodeSystem)) && t.getCode().equals(theCode))
.findFirst();
if (haveMatch.isPresent()) {
return new CodeValidationResult(new ConceptDefinitionComponent(new CodeType(theCode)));
return new CodeValidationResult(new ConceptDefinitionComponent(theCode));
}
}
} catch (Exception e) {

41
hapi-fhir-structures-r5/src/main/java/org/hl7/fhir/r5/hapi/ctx/HapiWorkerContext.java
View File

@ -24,11 +24,15 @@ import org.hl7.fhir.r5.terminologies.ValueSetExpander;
import org.hl7.fhir.r5.terminologies.ValueSetExpanderFactory;
import org.hl7.fhir.r5.terminologies.ValueSetExpanderSimple;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.hl7.fhir.utilities.TerminologyServiceOptions;
import org.hl7.fhir.utilities.TranslationServices;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import java.util.*;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.TimeUnit;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -144,15 +148,9 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
}
}
@Override
public Set<String> typeTails() {
return new HashSet<>(Arrays.asList("Integer", "UnsignedInt", "PositiveInt", "Decimal", "DateTime", "Date", "Time", "Instant", "String", "Uri", "Oid", "Uuid", "Id", "Boolean", "Code",
"Markdown", "Base64Binary", "Coding", "CodeableConcept", "Attachment", "Identifier", "Quantity", "SampledData", "Range", "Period", "Ratio", "HumanName", "Address", "ContactPoint",
"Timing", "Reference", "Annotation", "Signature", "Meta"));
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, CodeableConcept theCode, ValueSet theVs) {
public ValidationResult validateCode(ValidationOptions theOptions, CodeableConcept theCode, ValueSet theVs) {
for (Coding next : theCode.getCoding()) {
ValidationResult retVal = validateCode(theOptions, next, theVs);
if (retVal.isOk()) {
@ -164,7 +162,7 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, Coding theCode, ValueSet theVs) {
public ValidationResult validateCode(ValidationOptions theOptions, Coding theCode, ValueSet theVs) {
String system = theCode.getSystem();
String code = theCode.getCode();
String display = theCode.getDisplay();
@ -172,7 +170,7 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String theSystem, String theCode, String theDisplay) {
public ValidationResult validateCode(ValidationOptions theOptions, String theSystem, String theCode, String theDisplay) {
IContextValidationSupport.CodeValidationResult result = myValidationSupport.validateCode(myCtx, theSystem, theCode, theDisplay, null);
if (result == null) {
return null;
@ -181,12 +179,7 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String theSystem, String theCode, String theDisplay, ConceptSetComponent theVsi) {
throw new UnsupportedOperationException();
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String theSystem, String theCode, String theDisplay, ValueSet theVs) {
public ValidationResult validateCode(ValidationOptions theOptions, String theSystem, String theCode, String theDisplay, ValueSet theVs) {
/*
* The following valueset is a special case, since the BCP codesystem is very difficult to expand
@ -227,13 +220,13 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String code, ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, String code, ValueSet vs) {
return validateCode(theOptions, null, code, null, vs);
}
@Override
@CoverageIgnore
public List<MetadataResource> allConformanceResources() {
public List<CanonicalResource> allConformanceResources() {
throw new UnsupportedOperationException();
}
@ -242,6 +235,11 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
}
@Override
public void generateSnapshot(StructureDefinition mr, boolean ifLogical) {
}
@Override
public Parameters getExpansionParameters() {
return myExpansionProfile;
@ -400,4 +398,9 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
throw new UnsupportedOperationException();
}
@Override
public Map<String, byte[]> getBinaries() {
return null;
}
}

53
hapi-fhir-structures-r5/src/main/java/org/hl7/fhir/r5/hapi/rest/server/ServerCapabilityStatementProvider.java
View File

@ -1,5 +1,6 @@
package org.hl7.fhir.r5.hapi.rest.server;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
@ -14,31 +15,51 @@ import ca.uhn.fhir.rest.server.IServerConformanceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.RestfulServerConfiguration;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.method.*;
import ca.uhn.fhir.rest.server.method.SearchParameter;
import ca.uhn.fhir.rest.server.method.BaseMethodBinding;
import ca.uhn.fhir.rest.server.method.IParameter;
import ca.uhn.fhir.rest.server.method.OperationMethodBinding;
import ca.uhn.fhir.rest.server.method.OperationMethodBinding.ReturnType;
import ca.uhn.fhir.rest.server.method.OperationParameter;
import ca.uhn.fhir.rest.server.method.SearchMethodBinding;
import ca.uhn.fhir.rest.server.method.SearchParameter;
import ca.uhn.fhir.rest.server.util.BaseServerCapabilityStatementProvider;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.CapabilityStatement.*;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestComponent;
import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceComponent;
import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceSearchParamComponent;
import org.hl7.fhir.r5.model.CapabilityStatement.ConditionalDeleteStatus;
import org.hl7.fhir.r5.model.CapabilityStatement.ResourceInteractionComponent;
import org.hl7.fhir.r5.model.CapabilityStatement.SystemRestfulInteraction;
import org.hl7.fhir.r5.model.CapabilityStatement.TypeRestfulInteraction;
import org.hl7.fhir.r5.model.DateTimeType;
import org.hl7.fhir.r5.model.Enumerations;
import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r5.model.IdType;
import org.hl7.fhir.r5.model.OperationDefinition;
import org.hl7.fhir.r5.model.OperationDefinition.OperationDefinitionParameterComponent;
import org.hl7.fhir.r5.model.OperationDefinition.OperationKind;
import org.hl7.fhir.r5.model.OperationDefinition.OperationParameterUse;
import org.hl7.fhir.r5.model.ResourceType;
import javax.servlet.ServletContext;
import javax.servlet.http.HttpServletRequest;
import java.util.*;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.TreeSet;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import ca.uhn.fhir.context.FhirContext;
/*
* #%L
* HAPI FHIR Structures - DSTU2 (FHIR v1.0.0)
@ -160,7 +181,7 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
.setUrl(serverBase)
.setDescription(configuration.getImplementationDescription());
retVal.setKind(CapabilityStatementKind.INSTANCE);
retVal.setKind(Enumerations.CapabilityStatementKind.INSTANCE);
retVal.getSoftware().setName(configuration.getServerName());
retVal.getSoftware().setVersion(configuration.getServerVersion());
retVal.addFormat(Constants.CT_FHIR_XML_NEW);
@ -168,7 +189,7 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
retVal.setStatus(PublicationStatus.ACTIVE);
CapabilityStatementRestComponent rest = retVal.addRest();
rest.setMode(RestfulCapabilityMode.SERVER);
rest.setMode(Enumerations.RestfulCapabilityMode.SERVER);
Set<SystemRestfulInteraction> systemOps = new HashSet<>();
Set<String> operationNames = new HashSet<>();
@ -442,8 +463,8 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
continue;
}
OperationDefinitionParameterComponent param = op.addParameter();
param.setUse(OperationParameterUse.IN);
param.setType("string");
param.setUse(Enumerations.OperationParameterUse.IN);
param.setType(Enumerations.FHIRAllTypes.STRING);
param.getSearchTypeElement().setValueAsString(nextParam.getParamType().getCode());
param.setMin(nextParam.isRequired() ? 1 : 0);
param.setMax("1");
@ -511,9 +532,9 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
if (!inParams.add(nextParam.getName())) {
continue;
}
param.setUse(OperationParameterUse.IN);
param.setUse(Enumerations.OperationParameterUse.IN);
if (nextParam.getParamType() != null) {
param.setType(nextParam.getParamType());
param.setType(Enumerations.FHIRAllTypes.fromCode(nextParam.getParamType()));
}
if (nextParam.getSearchParamType() != null) {
param.getSearchTypeElement().setValueAsString(nextParam.getSearchParamType());
@ -529,9 +550,9 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
continue;
}
OperationDefinitionParameterComponent param = op.addParameter();
param.setUse(OperationParameterUse.OUT);
param.setUse(Enumerations.OperationParameterUse.OUT);
if (nextParam.getType() != null) {
param.setType(nextParam.getType());
param.setType(Enumerations.FHIRAllTypes.fromCode(nextParam.getType()));
}
param.setMin(nextParam.getMin());
param.setMax(nextParam.getMax() == -1 ? "*" : Integer.toString(nextParam.getMax()));

8
hapi-fhir-structures-r5/src/main/resources/org/hl7/fhir/r5/model/fhirversion.properties
View File

@ -1,5 +1,5 @@
# This file contains version definitions
# Generated: 2019-10-26T18:45:40.876-04:00
# Generated: 2020-01-12T11:10:06.793+08:00
resource.Account=org.hl7.fhir.r5.model.Account
resource.ActivityDefinition=org.hl7.fhir.r5.model.ActivityDefinition
@ -148,14 +148,16 @@ datatype.Address=org.hl7.fhir.r5.model.Address
datatype.Age=org.hl7.fhir.r5.model.Age
datatype.Annotation=org.hl7.fhir.r5.model.Annotation
datatype.Attachment=org.hl7.fhir.r5.model.Attachment
datatype.BackboneElement=org.hl7.fhir.r5.model.BackboneType
datatype.BackboneType=org.hl7.fhir.r5.model.BackboneType
datatype.CodeableConcept=org.hl7.fhir.r5.model.CodeableConcept
datatype.CodeableReference=org.hl7.fhir.r5.model.CodeableReference
datatype.Coding=org.hl7.fhir.r5.model.Coding
datatype.ContactDetail=org.hl7.fhir.r5.model.ContactDetail
datatype.ContactPoint=org.hl7.fhir.r5.model.ContactPoint
datatype.Contributor=org.hl7.fhir.r5.model.Contributor
datatype.Count=org.hl7.fhir.r5.model.Count
datatype.DataRequirement=org.hl7.fhir.r5.model.DataRequirement
datatype.DataType=org.hl7.fhir.r5.model.DataType
datatype.Distance=org.hl7.fhir.r5.model.Distance
datatype.Dosage=org.hl7.fhir.r5.model.Dosage
datatype.Duration=org.hl7.fhir.r5.model.Duration
@ -199,6 +201,7 @@ datatype.decimal=org.hl7.fhir.r5.model.DecimalType
datatype.id=org.hl7.fhir.r5.model.IdType
datatype.instant=org.hl7.fhir.r5.model.InstantType
datatype.integer=org.hl7.fhir.r5.model.IntegerType
datatype.integer64=org.hl7.fhir.r5.model.Integer64Type
datatype.markdown=org.hl7.fhir.r5.model.MarkdownType
datatype.oid=org.hl7.fhir.r5.model.OidType
datatype.positiveInt=org.hl7.fhir.r5.model.PositiveIntType
@ -207,4 +210,5 @@ datatype.time=org.hl7.fhir.r5.model.TimeType
datatype.unsignedInt=org.hl7.fhir.r5.model.UnsignedIntType
datatype.uri=org.hl7.fhir.r5.model.UriType
datatype.url=org.hl7.fhir.r5.model.UrlType
datatype.uuid=org.hl7.fhir.r5.model.UuidType
datatype.xhtml=org.hl7.fhir.utilities.xhtml.XhtmlNode

55
hapi-fhir-structures-r5/src/test/java/ca/uhn/fhir/rest/server/ServerCapabilityStatementProviderR5Test.java
View File

@ -3,13 +3,19 @@ package ca.uhn.fhir.rest.server;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.QuantityParam;
import ca.uhn.fhir.rest.param.ReferenceAndListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.method.BaseMethodBinding;
import ca.uhn.fhir.rest.server.method.IParameter;
import ca.uhn.fhir.rest.server.method.SearchMethodBinding;
@ -21,26 +27,41 @@ import com.google.common.collect.Lists;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r5.hapi.rest.server.ServerCapabilityStatementProvider;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.CapabilityStatement.*;
import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestComponent;
import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceComponent;
import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceOperationComponent;
import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceSearchParamComponent;
import org.hl7.fhir.r5.model.CapabilityStatement.ConditionalDeleteStatus;
import org.hl7.fhir.r5.model.CapabilityStatement.SystemRestfulInteraction;
import org.hl7.fhir.r5.model.CapabilityStatement.TypeRestfulInteraction;
import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r5.model.OperationDefinition.OperationDefinitionParameterComponent;
import org.hl7.fhir.r5.model.OperationDefinition.OperationKind;
import org.hl7.fhir.r5.model.OperationDefinition.OperationParameterUse;
import org.junit.AfterClass;
import org.junit.Ignore;
import org.junit.Test;
import javax.servlet.ServletConfig;
import javax.servlet.http.HttpServletRequest;
import java.util.*;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.nullValue;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
public class ServerCapabilityStatementProviderR5Test {
private static FhirContext ourCtx;
@ -265,9 +286,9 @@ public class ServerCapabilityStatementProviderR5Test {
assertThat(types, containsInAnyOrder("Patient"));
assertEquals(2, opDef.getParameter().size());
assertEquals("someOpParam1", opDef.getParameter().get(0).getName());
assertEquals("date", opDef.getParameter().get(0).getType());
assertEquals("date", opDef.getParameter().get(0).getType().toCode());
assertEquals("someOpParam2", opDef.getParameter().get(1).getName());
assertEquals("Patient", opDef.getParameter().get(1).getType());
assertEquals("Patient", opDef.getParameter().get(1).getType().toCode());
}
{
OperationDefinition opDef = sc.readOperationDefinition(new IdType("OperationDefinition/Encounter-i-someOp"), createRequestDetails(rs));
@ -280,9 +301,9 @@ public class ServerCapabilityStatementProviderR5Test {
assertThat(types, containsInAnyOrder("Encounter"));
assertEquals(2, opDef.getParameter().size());
assertEquals("someOpParam1", opDef.getParameter().get(0).getName());
assertEquals("date", opDef.getParameter().get(0).getType());
assertEquals("date", opDef.getParameter().get(0).getType().toCode());
assertEquals("someOpParam2", opDef.getParameter().get(1).getName());
assertEquals("Encounter", opDef.getParameter().get(1).getType());
assertEquals("Encounter", opDef.getParameter().get(1).getType().toCode());
}
{
OperationDefinition opDef = sc.readOperationDefinition(new IdType("OperationDefinition/Patient-i-validate"), createRequestDetails(rs));
@ -295,7 +316,7 @@ public class ServerCapabilityStatementProviderR5Test {
assertThat(types, containsInAnyOrder("Patient"));
assertEquals(1, opDef.getParameter().size());
assertEquals("resource", opDef.getParameter().get(0).getName());
assertEquals("Patient", opDef.getParameter().get(0).getType());
assertEquals("Patient", opDef.getParameter().get(0).getType().toCode());
}
}
@ -672,11 +693,11 @@ public class ServerCapabilityStatementProviderR5Test {
assertThat(parameters.size(), is(1));
OperationDefinitionParameterComponent param = parameters.get(0);
assertThat(param.getName(), is(NamedQueryPlainProvider.SP_QUANTITY));
assertThat(param.getType(), is("string"));
assertThat(param.getType().toCode(), is("string"));
assertThat(param.getSearchTypeElement().asStringValue(), is(RestSearchParameterTypeEnum.QUANTITY.getCode()));
assertThat(param.getMin(), is(1));
assertThat(param.getMax(), is("1"));
assertThat(param.getUse(), is(OperationParameterUse.IN));
assertThat(param.getUse(), is(Enumerations.OperationParameterUse.IN));
}
@Test
@ -710,11 +731,11 @@ public class ServerCapabilityStatementProviderR5Test {
assertThat(parameters.size(), is(1));
OperationDefinitionParameterComponent param = parameters.get(0);
assertThat(param.getName(), is(NamedQueryResourceProvider.SP_PARAM));
assertThat(param.getType(), is("string"));
assertThat(param.getType().toCode(), is("string"));
assertThat(param.getSearchTypeElement().asStringValue(), is(RestSearchParameterTypeEnum.STRING.getCode()));
assertThat(param.getMin(), is(0));
assertThat(param.getMax(), is("1"));
assertThat(param.getUse(), is(OperationParameterUse.IN));
assertThat(param.getUse(), is(Enumerations.OperationParameterUse.IN));
CapabilityStatementRestResourceComponent patientResource = restComponent.getResource().stream()
.filter(r -> patientResourceName.equals(r.getType()))

242530
hapi-fhir-validation-resources-r5/src/main/resources/org/hl7/fhir/r5/model/extension/extension-definitions.xml
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48
hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu2016may/hapi/validation/FhirInstanceValidator.java
View File

@ -18,11 +18,12 @@ import org.apache.commons.lang3.time.DateUtils;
import org.fhir.ucum.UcumService;
import org.hl7.fhir.common.hapi.validation.ValidatorWrapper;
import org.hl7.fhir.convertors.VersionConvertor_14_50;
import org.hl7.fhir.dstu2016may.terminologies.ValueSetExpander;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.ParserType;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.utils.INarrativeGenerator;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.hl7.fhir.r5.model.Resource;
@ -31,6 +32,7 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.TerminologyServiceOptions;
import org.hl7.fhir.utilities.TranslationServices;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.w3c.dom.*;
import org.w3c.dom.Element;
@ -326,17 +328,27 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
}
@Override
public List<org.hl7.fhir.r5.model.MetadataResource> allConformanceResources() {
public List<CanonicalResource> allConformanceResources() {
throw new UnsupportedOperationException();
}
@Override
public void generateSnapshot(org.hl7.fhir.r5.model.StructureDefinition theStructureDefinition) throws DefinitionException, FHIRException {
// nothing yet
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
@Override
public void generateSnapshot(org.hl7.fhir.r5.model.StructureDefinition p) throws FHIRException {
public Map<String, byte[]> getBinaries() {
throw new UnsupportedOperationException();
}
@Override
public void generateSnapshot(org.hl7.fhir.r5.model.StructureDefinition p, boolean theb) throws FHIRException {
// nothing yet
}
@ -469,7 +481,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions options, String system, String code, String display) {
public ValidationResult validateCode(ValidationOptions options, String system, String code, String display) {
return null;
}
@ -646,14 +658,9 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
return myWrap.supportsSystem(system);
}
@Override
public Set<String> typeTails() {
return myWrap.typeTails();
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String system, String code, String display, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, String system, String code, String display, org.hl7.fhir.r5.model.ValueSet vs) {
ValueSet convertedVs = null;
try {
@ -669,7 +676,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String code, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, String code, org.hl7.fhir.r5.model.ValueSet vs) {
ValueSet convertedVs = null;
try {
if (vs != null) {
@ -684,7 +691,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, org.hl7.fhir.r5.model.Coding code, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, org.hl7.fhir.r5.model.Coding code, org.hl7.fhir.r5.model.ValueSet vs) {
Coding convertedCode = null;
ValueSet convertedVs = null;
@ -704,7 +711,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, org.hl7.fhir.r5.model.CodeableConcept code, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, org.hl7.fhir.r5.model.CodeableConcept code, org.hl7.fhir.r5.model.ValueSet vs) {
CodeableConcept convertedCode = null;
ValueSet convertedVs = null;
@ -723,21 +730,6 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
return convertValidationResult(result);
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String system, String code, String display, org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent vsi) {
ValueSet.ConceptSetComponent conceptSetComponent = null;
if (vsi != null) {
try {
conceptSetComponent = VersionConvertor_14_50.convertConceptSetComponent(vsi);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
}
org.hl7.fhir.dstu2016may.utils.IWorkerContext.ValidationResult result = myWrap.validateCode(system, code, display, conceptSetComponent);
return convertValidationResult(result);
}
}
private static class ResourceKey {

63
hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidator.java
View File

@ -5,7 +5,6 @@ import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.validation.IInstanceValidatorModule;
import ca.uhn.fhir.validation.IValidationContext;
import ca.uhn.fhir.validation.IValidatorModule;
import com.github.benmanes.caffeine.cache.Caffeine;
import com.github.benmanes.caffeine.cache.LoadingCache;
import org.apache.commons.lang3.Validate;
@ -18,20 +17,28 @@ import org.hl7.fhir.convertors.VersionConvertor_30_50;
import org.hl7.fhir.dstu3.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.ImplementationGuide;
import org.hl7.fhir.dstu3.model.Questionnaire;
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.dstu3.model.StructureDefinition;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.ParserType;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.terminologies.ValueSetExpander;
import org.hl7.fhir.r5.utils.INarrativeGenerator;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.hl7.fhir.r5.utils.IResourceValidator.BestPracticeWarningLevel;
import org.hl7.fhir.utilities.TerminologyServiceOptions;
import org.hl7.fhir.utilities.TranslationServices;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;
@ -40,7 +47,13 @@ import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.TimeUnit;
@SuppressWarnings({"PackageAccessibility", "Duplicates"})
@ -331,7 +344,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
}
@Override
public List<org.hl7.fhir.r5.model.MetadataResource> allConformanceResources() {
public List<CanonicalResource> allConformanceResources() {
throw new UnsupportedOperationException();
}
@ -340,11 +353,21 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
throw new UnsupportedOperationException();
}
@Override
public Map<String, byte[]> getBinaries() {
return null;
}
@Override
public void generateSnapshot(org.hl7.fhir.r5.model.StructureDefinition p) throws FHIRException {
// nothing yet
}
@Override
public void generateSnapshot(org.hl7.fhir.r5.model.StructureDefinition theStructureDefinition, boolean theB) {
// nothing yet
}
@Override
public org.hl7.fhir.r5.model.Parameters getExpansionParameters() {
return myExpansionProfile;
@ -642,18 +665,13 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
}
@Override
public Set<String> typeTails() {
return myWrap.typeTails();
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String system, String code, String display) {
public ValidationResult validateCode(ValidationOptions theOptions, String system, String code, String display) {
org.hl7.fhir.dstu3.context.IWorkerContext.ValidationResult result = myWrap.validateCode(system, code, display);
return convertValidationResult(result);
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String system, String code, String display, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, String system, String code, String display, org.hl7.fhir.r5.model.ValueSet vs) {
ValueSet convertedVs = null;
try {
@ -669,7 +687,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String code, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, String code, org.hl7.fhir.r5.model.ValueSet vs) {
ValueSet convertedVs = null;
try {
if (vs != null) {
@ -684,7 +702,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, org.hl7.fhir.r5.model.Coding code, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, org.hl7.fhir.r5.model.Coding code, org.hl7.fhir.r5.model.ValueSet vs) {
Coding convertedCode = null;
ValueSet convertedVs = null;
@ -704,7 +722,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, org.hl7.fhir.r5.model.CodeableConcept code, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, org.hl7.fhir.r5.model.CodeableConcept code, org.hl7.fhir.r5.model.ValueSet vs) {
CodeableConcept convertedCode = null;
ValueSet convertedVs = null;
@ -723,21 +741,6 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
return convertValidationResult(result);
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String system, String code, String display, org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent vsi) {
ValueSet.ConceptSetComponent conceptSetComponent = null;
if (vsi != null) {
try {
conceptSetComponent = VersionConvertor_30_50.convertConceptSetComponent(vsi);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
}
org.hl7.fhir.dstu3.context.IWorkerContext.ValidationResult result = myWrap.validateCode(system, code, display, conceptSetComponent);
return convertValidationResult(result);
}
}
private static class ResourceKey {

71
hapi-fhir-validation/src/main/java/org/hl7/fhir/instance/hapi/validation/FhirInstanceValidator.java
View File

@ -1,17 +1,24 @@
package org.hl7.fhir.instance.hapi.validation;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimePrimitiveDatatypeDefinition;
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.util.XmlUtil;
import ca.uhn.fhir.validation.IInstanceValidatorModule;
import ca.uhn.fhir.validation.IValidationContext;
import ca.uhn.fhir.validation.IValidatorModule;
import com.github.benmanes.caffeine.cache.CacheLoader;
import com.github.benmanes.caffeine.cache.Caffeine;
import com.github.benmanes.caffeine.cache.LoadingCache;
import com.google.gson.*;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.EqualsBuilder;
@ -20,13 +27,18 @@ import org.fhir.ucum.UcumService;
import org.hl7.fhir.converter.NullVersionConverterAdvisor50;
import org.hl7.fhir.convertors.VersionConvertorAdvisor50;
import org.hl7.fhir.convertors.VersionConvertor_10_50;
import org.hl7.fhir.dstu2.model.*;
import org.hl7.fhir.dstu2.model.CodeableConcept;
import org.hl7.fhir.dstu2.model.Coding;
import org.hl7.fhir.dstu2.model.Questionnaire;
import org.hl7.fhir.dstu2.model.StructureDefinition;
import org.hl7.fhir.dstu2.model.ValueSet;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.ParserType;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.terminologies.ValueSetExpander;
@ -36,10 +48,10 @@ import org.hl7.fhir.r5.utils.IResourceValidator;
import org.hl7.fhir.r5.utils.IResourceValidator.BestPracticeWarningLevel;
import org.hl7.fhir.r5.utils.IResourceValidator.IdStatus;
import org.hl7.fhir.r5.validation.InstanceValidator;
import org.hl7.fhir.utilities.TerminologyServiceOptions;
import org.hl7.fhir.utilities.TranslationServices;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;
@ -48,7 +60,12 @@ import java.io.IOException;
import java.io.InputStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.*;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.TimeUnit;
import static org.apache.commons.lang3.StringUtils.isBlank;
@ -488,7 +505,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
}
@Override
public List<org.hl7.fhir.r5.model.MetadataResource> allConformanceResources() {
public List<CanonicalResource> allConformanceResources() {
throw new UnsupportedOperationException();
}
@ -497,11 +514,21 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
}
@Override
public void generateSnapshot(org.hl7.fhir.r5.model.StructureDefinition theStructureDefinition, boolean theB) {
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
@Override
public Map<String, byte[]> getBinaries() {
return null;
}
@Override
public Parameters getExpansionParameters() {
return myExpansionProfile;
@ -787,18 +814,13 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
}
@Override
public Set<String> typeTails() {
throw new UnsupportedOperationException();
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String system, String code, String display) {
public ValidationResult validateCode(ValidationOptions theOptions, String system, String code, String display) {
org.hl7.fhir.dstu2.utils.IWorkerContext.ValidationResult result = myWrap.validateCode(system, code, display);
return convertValidationResult(result);
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String system, String code, String display, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, String system, String code, String display, org.hl7.fhir.r5.model.ValueSet vs) {
ValueSet convertedVs = null;
try {
@ -814,7 +836,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String code, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, String code, org.hl7.fhir.r5.model.ValueSet vs) {
ValueSet convertedVs = null;
try {
if (vs != null) {
@ -830,7 +852,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, org.hl7.fhir.r5.model.Coding code, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, org.hl7.fhir.r5.model.Coding code, org.hl7.fhir.r5.model.ValueSet vs) {
Coding convertedCode = null;
ValueSet convertedVs = null;
@ -850,7 +872,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, org.hl7.fhir.r5.model.CodeableConcept code, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, org.hl7.fhir.r5.model.CodeableConcept code, org.hl7.fhir.r5.model.ValueSet vs) {
CodeableConcept convertedCode = null;
ValueSet convertedVs = null;
@ -869,21 +891,6 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
return convertValidationResult(result);
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String system, String code, String display, org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent vsi) {
ValueSet.ConceptSetComponent conceptSetComponent = null;
if (vsi != null) {
try {
conceptSetComponent = new VersionConvertor_10_50(myAdvisor).convertConceptSetComponent(vsi);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
}
org.hl7.fhir.dstu2.utils.IWorkerContext.ValidationResult result = myWrap.validateCode(system, code, display, conceptSetComponent);
return convertValidationResult(result);
}
}

74
hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/FhirInstanceValidator.java
View File

@ -18,10 +18,18 @@ import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ImplementationGuide;
import org.hl7.fhir.r4.model.Questionnaire;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.ParserType;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.terminologies.ValueSetExpander;
import org.hl7.fhir.r5.utils.INarrativeGenerator;
import org.hl7.fhir.r5.utils.IResourceValidator;
@ -30,10 +38,17 @@ import org.hl7.fhir.utilities.TerminologyServiceOptions;
import org.hl7.fhir.utilities.TranslationServices;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.util.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.TimeUnit;
@SuppressWarnings({"PackageAccessibility", "Duplicates"})
@ -270,7 +285,7 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
}
@Override
public List<org.hl7.fhir.r5.model.MetadataResource> allConformanceResources() {
public List<CanonicalResource> allConformanceResources() {
throw new UnsupportedOperationException();
}
@ -279,6 +294,11 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
// nothing yet
}
@Override
public void generateSnapshot(org.hl7.fhir.r5.model.StructureDefinition theStructureDefinition, boolean theB) {
}
@Override
public org.hl7.fhir.r5.model.Parameters getExpansionParameters() {
return myExpansionProfile;
@ -570,18 +590,17 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
}
@Override
public Set<String> typeTails() {
return myWrap.typeTails();
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String system, String code, String display) {
org.hl7.fhir.r4.context.IWorkerContext.ValidationResult result = myWrap.validateCode(theOptions, system, code, display);
public ValidationResult validateCode(ValidationOptions theOptions, String system, String code, String display) {
org.hl7.fhir.r4.context.IWorkerContext.ValidationResult result = myWrap.validateCode(toValidationOptions(theOptions), system, code, display);
return convertValidationResult(result);
}
private TerminologyServiceOptions toValidationOptions(ValidationOptions theOptions) {
return new TerminologyServiceOptions();
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String system, String code, String display, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, String system, String code, String display, org.hl7.fhir.r5.model.ValueSet vs) {
ValueSet convertedVs = null;
try {
@ -592,12 +611,12 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
throw new InternalErrorException(e);
}
org.hl7.fhir.r4.context.IWorkerContext.ValidationResult result = myWrap.validateCode(theOptions, system, code, display, convertedVs);
org.hl7.fhir.r4.context.IWorkerContext.ValidationResult result = myWrap.validateCode(toValidationOptions(theOptions), system, code, display, convertedVs);
return convertValidationResult(result);
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String code, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, String code, org.hl7.fhir.r5.model.ValueSet vs) {
ValueSet convertedVs = null;
try {
if (vs != null) {
@ -607,12 +626,12 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
throw new InternalErrorException(e);
}
org.hl7.fhir.r4.context.IWorkerContext.ValidationResult result = myWrap.validateCode(theOptions, Constants.CODESYSTEM_VALIDATE_NOT_NEEDED, code, null, convertedVs);
org.hl7.fhir.r4.context.IWorkerContext.ValidationResult result = myWrap.validateCode(toValidationOptions(theOptions), Constants.CODESYSTEM_VALIDATE_NOT_NEEDED, code, null, convertedVs);
return convertValidationResult(result);
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, org.hl7.fhir.r5.model.Coding code, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, org.hl7.fhir.r5.model.Coding code, org.hl7.fhir.r5.model.ValueSet vs) {
Coding convertedCode = null;
ValueSet convertedVs = null;
@ -627,12 +646,12 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
throw new InternalErrorException(e);
}
org.hl7.fhir.r4.context.IWorkerContext.ValidationResult result = myWrap.validateCode(theOptions, convertedCode, convertedVs);
org.hl7.fhir.r4.context.IWorkerContext.ValidationResult result = myWrap.validateCode(toValidationOptions(theOptions), convertedCode, convertedVs);
return convertValidationResult(result);
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, org.hl7.fhir.r5.model.CodeableConcept code, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, org.hl7.fhir.r5.model.CodeableConcept code, org.hl7.fhir.r5.model.ValueSet vs) {
CodeableConcept convertedCode = null;
ValueSet convertedVs = null;
@ -647,30 +666,21 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
throw new InternalErrorException(e);
}
org.hl7.fhir.r4.context.IWorkerContext.ValidationResult result = myWrap.validateCode(theOptions, convertedCode, convertedVs);
org.hl7.fhir.r4.context.IWorkerContext.ValidationResult result = myWrap.validateCode(toValidationOptions(theOptions), convertedCode, convertedVs);
return convertValidationResult(result);
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String system, String code, String display, org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent vsi) {
ValueSet.ConceptSetComponent conceptSetComponent = null;
if (vsi != null) {
try {
conceptSetComponent = org.hl7.fhir.convertors.conv40_50.ValueSet.convertConceptSetComponent(vsi);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
}
org.hl7.fhir.r4.context.IWorkerContext.ValidationResult result = myWrap.validateCode(theOptions, system, code, display, conceptSetComponent);
return convertValidationResult(result);
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
@Override
public Map<String, byte[]> getBinaries() {
return null;
}
}
private static class ResourceKey {

51
hapi-fhir-validation/src/main/java/org/hl7/fhir/r5/hapi/validation/FhirInstanceValidator.java
View File

@ -29,14 +29,20 @@ import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.INarrativeGenerator;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.hl7.fhir.r5.utils.IResourceValidator.BestPracticeWarningLevel;
import org.hl7.fhir.utilities.TerminologyServiceOptions;
import org.hl7.fhir.utilities.TranslationServices;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.util.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.TimeUnit;
@SuppressWarnings({"PackageAccessibility", "Duplicates"})
@ -273,7 +279,7 @@ public class FhirInstanceValidator extends org.hl7.fhir.r5.hapi.validation.BaseV
}
@Override
public List<org.hl7.fhir.r5.model.MetadataResource> allConformanceResources() {
public List<CanonicalResource> allConformanceResources() {
throw new UnsupportedOperationException();
}
@ -282,11 +288,21 @@ public class FhirInstanceValidator extends org.hl7.fhir.r5.hapi.validation.BaseV
// nothing yet
}
@Override
public void generateSnapshot(StructureDefinition theStructureDefinition, boolean theB) {
}
@Override
public String getLinkForUrl(String corePath, String url) {
throw new UnsupportedOperationException();
}
@Override
public Map<String, byte[]> getBinaries() {
return null;
}
@Override
public org.hl7.fhir.r5.model.Parameters getExpansionParameters() {
return myExpansionProfile;
@ -579,18 +595,13 @@ public class FhirInstanceValidator extends org.hl7.fhir.r5.hapi.validation.BaseV
}
@Override
public Set<String> typeTails() {
return myWrap.typeTails();
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String system, String code, String display) {
public ValidationResult validateCode(ValidationOptions theOptions, String system, String code, String display) {
org.hl7.fhir.r5.context.IWorkerContext.ValidationResult result = myWrap.validateCode(theOptions, system, code, display);
return convertValidationResult(result);
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String system, String code, String display, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, String system, String code, String display, org.hl7.fhir.r5.model.ValueSet vs) {
ValueSet convertedVs = null;
try {
@ -606,7 +617,7 @@ public class FhirInstanceValidator extends org.hl7.fhir.r5.hapi.validation.BaseV
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String code, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, String code, org.hl7.fhir.r5.model.ValueSet vs) {
ValueSet convertedVs = null;
try {
if (vs != null) {
@ -621,7 +632,7 @@ public class FhirInstanceValidator extends org.hl7.fhir.r5.hapi.validation.BaseV
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, org.hl7.fhir.r5.model.Coding code, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, org.hl7.fhir.r5.model.Coding code, org.hl7.fhir.r5.model.ValueSet vs) {
Coding convertedCode = null;
ValueSet convertedVs = null;
@ -641,7 +652,7 @@ public class FhirInstanceValidator extends org.hl7.fhir.r5.hapi.validation.BaseV
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, org.hl7.fhir.r5.model.CodeableConcept code, org.hl7.fhir.r5.model.ValueSet vs) {
public ValidationResult validateCode(ValidationOptions theOptions, org.hl7.fhir.r5.model.CodeableConcept code, org.hl7.fhir.r5.model.ValueSet vs) {
CodeableConcept convertedCode = null;
ValueSet convertedVs = null;
@ -660,20 +671,6 @@ public class FhirInstanceValidator extends org.hl7.fhir.r5.hapi.validation.BaseV
return convertValidationResult(result);
}
@Override
public ValidationResult validateCode(TerminologyServiceOptions theOptions, String system, String code, String display, org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent vsi) {
ValueSet.ConceptSetComponent conceptSetComponent = null;
if (vsi != null) {
try {
conceptSetComponent = vsi;
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
}
org.hl7.fhir.r5.context.IWorkerContext.ValidationResult result = myWrap.validateCode(theOptions, system, code, display, conceptSetComponent);
return convertValidationResult(result);
}
}

2
hapi-fhir-validation/src/main/java/org/hl7/fhir/r5/hapi/validation/PrePopulatedValidationSupport.java
View File

@ -92,7 +92,7 @@ public class PrePopulatedValidationSupport implements IValidationSupport {
addToMap(theStructureDefinition, myStructureDefinitions, theStructureDefinition.getUrl());
}
private <T extends MetadataResource> void addToMap(T theStructureDefinition, Map<String, T> map, String theUrl) {
private <T extends IBaseResource> void addToMap(T theStructureDefinition, Map<String, T> map, String theUrl) {
if (isNotBlank(theUrl)) {
map.put(theUrl, theStructureDefinition);

4
hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/ResourceValidatorDstu3Test.java
View File

@ -333,7 +333,7 @@ public class ResourceValidatorDstu3Test {
TestPatientFor327 patient = new TestPatientFor327();
patient.setBirthDate(new Date());
patient.setId("123");
patient.getText().setDivAsString("<div>FOO</div>");
patient.getText().setDivAsString("<div lang=\"en\">FOO</div>");
patient.getText().setStatus(NarrativeStatus.GENERATED);
patient.getLanguageElement().setValue("en");
patient.addExtension().setUrl("http://foo").setValue(new StringType("MOD"));
@ -478,7 +478,7 @@ public class ResourceValidatorDstu3Test {
private static final long serialVersionUID = 1L;
@Child(name = "testCondition")
@ca.uhn.fhir.model.api.annotation.Extension(url = "testCondition", definedLocally = true, isModifier = false)
@ca.uhn.fhir.model.api.annotation.Extension(url = "http://testCondition", definedLocally = true, isModifier = false)
private List<Reference> testConditions = null;
public List<Reference> getConditions() {

27
hapi-fhir-validation/src/test/java/org/hl7/fhir/r5/validation/FhirInstanceValidatorR5Test.java
View File

@ -18,7 +18,6 @@ import org.hl7.fhir.r5.hapi.validation.FhirInstanceValidator;
import org.hl7.fhir.r5.hapi.validation.ValidationSupportChain;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.Observation.ObservationStatus;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.r5.terminologies.ValueSetExpander;
@ -160,7 +159,7 @@ public class FhirInstanceValidatorR5Test {
String valueSetUrl = theInvocation.getArgument(4, String.class);
IContextValidationSupport.CodeValidationResult retVal;
if (myValidConcepts.contains(system + "___" + code)) {
retVal = new IContextValidationSupport.CodeValidationResult(new ConceptDefinitionComponent(new CodeType(code)));
retVal = new IContextValidationSupport.CodeValidationResult(new ConceptDefinitionComponent((code)));
} else {
retVal = myDefaultValidationSupport.validateCode(ctx, system, code, display, valueSetUrl);
}
@ -261,7 +260,7 @@ public class FhirInstanceValidatorR5Test {
public void testValidateDoesntEnforceBestPracticesByDefault() {
Observation input = new Observation();
input.getText().setDiv(new XhtmlNode().setValue("<div>AA</div>")).setStatus(Narrative.NarrativeStatus.GENERATED);
input.setStatus(ObservationStatus.AMENDED);
input.setStatus(Enumerations.ObservationStatus.AMENDED);
input.getCode().addCoding().setSystem("http://loinc.org").setCode("1234").setDisplay("FOO");
FhirInstanceValidator instanceModule;
@ -369,7 +368,7 @@ public class FhirInstanceValidatorR5Test {
@Ignore
public void testCompareTimesWithDifferentTimezones() {
Procedure procedure = new Procedure();
procedure.setStatus(Procedure.ProcedureStatus.COMPLETED);
procedure.setStatus(Enumerations.EventStatus.COMPLETED);
procedure.getSubject().setReference("Patient/1");
procedure.getCode().setText("Some proc");
@ -729,7 +728,7 @@ public class FhirInstanceValidatorR5Test {
input.addIdentifier().setSystem("http://acme").setValue("12345");
input.getEncounter().setReference("http://foo.com/Encounter/9");
input.setStatus(ObservationStatus.FINAL);
input.setStatus(Enumerations.ObservationStatus.FINAL);
input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
myInstanceVal.setValidationSupport(myMockSupport);
@ -750,7 +749,7 @@ public class FhirInstanceValidatorR5Test {
input.addIdentifier().setSystem("http://acme").setValue("12345");
input.getEncounter().setReference("http://foo.com/Encounter/9");
input.setStatus(ObservationStatus.FINAL);
input.setStatus(Enumerations.ObservationStatus.FINAL);
input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
myInstanceVal.setValidationSupport(myMockSupport);
@ -772,7 +771,7 @@ public class FhirInstanceValidatorR5Test {
input.getMeta().addProfile("http://foo/structuredefinition/myprofile");
input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
input.setStatus(ObservationStatus.FINAL);
input.setStatus(Enumerations.ObservationStatus.FINAL);
myInstanceVal.setValidationSupport(myMockSupport);
ValidationResult output = myVal.validateWithResult(input);
@ -800,7 +799,7 @@ public class FhirInstanceValidatorR5Test {
Observation input = new Observation();
input.getText().setDiv(new XhtmlNode().setValue("<div>AA</div>")).setStatus(Narrative.NarrativeStatus.GENERATED);
input.setStatus(ObservationStatus.FINAL);
input.setStatus(Enumerations.ObservationStatus.FINAL);
input.getCode().setText("No code here!");
ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(input));
@ -825,7 +824,7 @@ public class FhirInstanceValidatorR5Test {
ValidationResult output = myVal.validateWithResult(input);
logResultsAndReturnAll(output);
assertEquals(
"The value provided ('notvalidcode') is not in the value set http://hl7.org/fhir/ValueSet/observation-status|4.1.0 (http://hl7.org/fhir/ValueSet/observation-status, and a code is required from this value set) (error message = Unknown code[notvalidcode] in system[(none)])",
"The value provided ('notvalidcode') is not in the value set http://hl7.org/fhir/ValueSet/observation-status|4.2.0 (http://hl7.org/fhir/ValueSet/observation-status, and a code is required from this value set) (error message = Unknown code[notvalidcode] in system[(none)])",
output.getMessages().get(0).getMessage());
}
@ -836,7 +835,7 @@ public class FhirInstanceValidatorR5Test {
myInstanceVal.setValidationSupport(myMockSupport);
input.setStatus(ObservationStatus.FINAL);
input.setStatus(Enumerations.ObservationStatus.FINAL);
input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
ValidationResult output = myVal.validateWithResult(input);
@ -853,7 +852,7 @@ public class FhirInstanceValidatorR5Test {
myInstanceVal.setValidationSupport(myMockSupport);
addValidConcept("http://acme.org", "12345");
input.setStatus(ObservationStatus.FINAL);
input.setStatus(Enumerations.ObservationStatus.FINAL);
input.getCode().addCoding().setSystem("http://acme.org").setCode("9988877");
ValidationResult output = myVal.validateWithResult(input);
@ -871,7 +870,7 @@ public class FhirInstanceValidatorR5Test {
myInstanceVal.setValidationSupport(myMockSupport);
addValidConcept("http://loinc.org", "12345");
input.setStatus(ObservationStatus.FINAL);
input.setStatus(Enumerations.ObservationStatus.FINAL);
input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
ValidationResult output = myVal.validateWithResult(input);
@ -891,7 +890,7 @@ public class FhirInstanceValidatorR5Test {
myInstanceVal.setValidationSupport(myMockSupport);
addValidConcept("http://loinc.org", "12345");
input.setStatus(ObservationStatus.FINAL);
input.setStatus(Enumerations.ObservationStatus.FINAL);
input.getCode().addCoding().setSystem("http://loinc.org").setCode("1234");
ValidationResult output = myVal.validateWithResult(input);
@ -908,7 +907,7 @@ public class FhirInstanceValidatorR5Test {
myInstanceVal.setValidationSupport(myMockSupport);
addValidConcept("http://acme.org", "12345");
input.setStatus(ObservationStatus.FINAL);
input.setStatus(Enumerations.ObservationStatus.FINAL);
input.getCode().addCoding().setSystem("http://acme.org").setCode("12345");
ValidationResult output = myVal.validateWithResult(input);

8
hapi-fhir-validation/src/test/java/org/hl7/fhir/r5/validation/QuestionnaireResponseValidatorR5Test.java
View File

@ -121,7 +121,7 @@ public class QuestionnaireResponseValidatorR5Test {
questionnaireItemTypes[14] = QuestionnaireItemType.REFERENCE;
questionnaireItemTypes[15] = QuestionnaireItemType.QUANTITY;
Type[] answerValues = new Type[itemCnt];
DataType[] answerValues = new DataType[itemCnt];
answerValues[0] = new BooleanType(true);
answerValues[1] = new DecimalType(42.0);
answerValues[2] = new IntegerType(42);
@ -359,7 +359,7 @@ public class QuestionnaireResponseValidatorR5Test {
when(myValSupport.fetchResource(any(FhirContext.class), eq(ValueSet.class), eq(valueSetRef)))
.thenReturn(options);
when(myValSupport.validateCode(any(FhirContext.class), eq(codeSystemUrl), eq(codeValue), any(String.class), anyString()))
.thenReturn(new IContextValidationSupport.CodeValidationResult(new ConceptDefinitionComponent(new CodeType(codeValue))));
.thenReturn(new IContextValidationSupport.CodeValidationResult(new ConceptDefinitionComponent(codeValue)));
IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
String qXml = xmlParser.encodeResourceToString(q);
@ -416,7 +416,7 @@ public class QuestionnaireResponseValidatorR5Test {
when(myValSupport.fetchResource(any(FhirContext.class), eq(ValueSet.class), eq(valueSetRef)))
.thenReturn(options);
when(myValSupport.validateCode(any(FhirContext.class), eq(codeSystemUrl), eq(codeValue), any(String.class), anyString()))
.thenReturn(new IContextValidationSupport.CodeValidationResult(new ConceptDefinitionComponent(new CodeType(codeValue))));
.thenReturn(new IContextValidationSupport.CodeValidationResult(new ConceptDefinitionComponent((codeValue))));
IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
String qXml = xmlParser.encodeResourceToString(q);
@ -679,7 +679,7 @@ public class QuestionnaireResponseValidatorR5Test {
when(myValSupport.fetchResource(any(FhirContext.class), eq(Questionnaire.class), eq(qa.getQuestionnaire()))).thenReturn(questionnaire);
when(myValSupport.fetchResource(any(FhirContext.class), eq(ValueSet.class), eq(ID_VS_SCHOOLTYPE))).thenReturn(iccSchoolTypeVs);
when(myValSupport.validateCodeInValueSet(any(), any(), any(), any(), any(ValueSet.class) )).thenReturn(new IContextValidationSupport.CodeValidationResult(new ConceptDefinitionComponent(new CodeType(CODE_ICC_SCHOOLTYPE_PT))));
when(myValSupport.validateCodeInValueSet(any(), any(), any(), any(), any(ValueSet.class) )).thenReturn(new IContextValidationSupport.CodeValidationResult(new ConceptDefinitionComponent(CODE_ICC_SCHOOLTYPE_PT)));
ValidationResult errors = myVal.validateWithResult(qa);
ourLog.info(errors.toString());

8
hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/ResourceMinimizerMojo.java
View File

@ -261,6 +261,14 @@ public class ResourceMinimizerMojo extends AbstractMojo {
byteCount += m.getByteCount();
fileCount += m.getFileCount();
m = new ResourceMinimizerMojo();
m.myCtx = ctxR5;
m.targetDirectory = new File("./hapi-fhir-validation-resources-r5/src/main/resources/org/hl7/fhir/r5/model/extension");
m.fhirVersion = "R5";
m.execute();
byteCount += m.getByteCount();
fileCount += m.getFileCount();
ourLog.info("Trimmed {} files", fileCount);
ourLog.info("Trimmed {} bytes", FileUtils.byteCountToDisplaySize(byteCount));
}

2
pom.xml
View File

@ -598,7 +598,7 @@
<properties>
<fhir_core_version>4.1.7-SNAPSHOT</fhir_core_version>
<fhir_core_version>4.1.42-SNAPSHOT</fhir_core_version>
<ucum_version>1.0.2</ucum_version>
<surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx2048m</surefire_jvm_args>