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hapi-fhir
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Update to 4.3.x core JAR (#1715) 

* Added optionality for adding resource fetcher

* Added coverage that proves invocations

* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences

* Added optionality for adding resource fetcher

* Added coverage that proves invocations

* Bumped version of fhir.core to latest version. Added wrapping of AssumeValidRestReferences

* Start working on converter

* Account for compile errors

* Test fix

* Work no validator

* Work on getting core working

* Add some test coverage

* Many test fixes

Co-authored-by: Jens Kristian Villadsen <46567685+jvitrifork@users.noreply.github.com>
This commit is contained in:
James Agnew 2020-02-17 14:28:29 -05:00 committed by GitHub
parent ddc7b601ee
commit 60f16dd91d
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52 changed files with 735 additions and 266 deletions
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12
examples/src/main/java/example/ConverterExamples.java
View File

@ -1,7 +1,7 @@
package example;
import org.hl7.fhir.converter.NullVersionConverterAdvisor30;
import org.hl7.fhir.convertors.*;
import org.hl7.fhir.convertors.conv10_30.Observation10_30;
import org.hl7.fhir.convertors.conv14_30.Questionnaire14_30;
import org.hl7.fhir.exceptions.FHIRException;
public class ConverterExamples {
@ -9,16 +9,12 @@ public class ConverterExamples {
@SuppressWarnings("unused")
public void c1020() throws FHIRException {
//START SNIPPET: 1020
// Create a converter
NullVersionConverterAdvisor30 advisor = new NullVersionConverterAdvisor30();
VersionConvertor_10_30 converter = new VersionConvertor_10_30(advisor);
// Create an input resource to convert
org.hl7.fhir.dstu2.model.Observation input = new org.hl7.fhir.dstu2.model.Observation();
input.setEncounter(new org.hl7.fhir.dstu2.model.Reference("Encounter/123"));
// Convert the resource
org.hl7.fhir.dstu3.model.Observation output = converter.convertObservation(input);
org.hl7.fhir.dstu3.model.Observation output = Observation10_30.convertObservation(input);
String context = output.getContext().getReference();
//END SNIPPET: 1020
}
@ -31,7 +27,7 @@ public class ConverterExamples {
input.setTitle("My title");
// Convert the resource
org.hl7.fhir.dstu3.model.Questionnaire output = VersionConvertor_14_30.convertQuestionnaire(input);
org.hl7.fhir.dstu3.model.Questionnaire output = Questionnaire14_30.convertQuestionnaire(input);
String context = output.getTitle();
//END SNIPPET: 1420
}

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/VersionEnum.java
View File

@ -58,7 +58,8 @@ public enum VersionEnum {
V4_0_0,
V4_0_3,
V4_1_0,
V4_2_0;
V4_2_0,
V4_3_0;
public static VersionEnum latestVersion() {
VersionEnum[] values = VersionEnum.values();

4
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ExportConceptMapToCsvCommand.java
View File

@ -26,7 +26,6 @@ import org.apache.commons.cli.Options;
import org.apache.commons.csv.CSVFormat;
import org.apache.commons.csv.CSVPrinter;
import org.apache.commons.csv.QuoteMode;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.ConceptMap;
@ -43,6 +42,7 @@ import java.util.List;
import java.util.concurrent.ExecutionException;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
public class ExportConceptMapToCsvCommand extends AbstractImportExportCsvConceptMapCommand {
// TODO: Don't use qualified names for loggers in HAPI CLI.
@ -114,7 +114,7 @@ public class ExportConceptMapToCsvCommand extends AbstractImportExportCsvConcept
private void convertConceptMapToCsv(org.hl7.fhir.dstu3.model.ConceptMap theConceptMap) throws ExecutionException {
try {
convertConceptMapToCsv(VersionConvertor_30_40.convertConceptMap(theConceptMap));
convertConceptMapToCsv(convertConceptMap(theConceptMap));
} catch (FHIRException fe) {
throw new ExecutionException(fe);
}

10
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ImportCsvToConceptMapCommand.java
View File

@ -28,7 +28,6 @@ import org.apache.commons.cli.Options;
import org.apache.commons.csv.CSVFormat;
import org.apache.commons.csv.CSVParser;
import org.apache.commons.csv.CSVRecord;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ConceptMap.ConceptMapGroupComponent;
@ -45,7 +44,10 @@ import java.util.Map;
import java.util.Set;
import java.util.concurrent.ExecutionException;
import static org.apache.commons.lang3.StringUtils.*;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConceptMapCommand {
// TODO: Don't use qualified names for loggers in HAPI CLI.
@ -154,7 +156,7 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
private org.hl7.fhir.dstu3.model.ConceptMap convertCsvToConceptMapDstu3() throws ExecutionException {
try {
return VersionConvertor_30_40.convertConceptMap(convertCsvToConceptMapR4());
return convertConceptMap(convertCsvToConceptMapR4());
} catch (FHIRException fe) {
throw new ExecutionException(fe);
}
@ -174,7 +176,7 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
.withFirstRecordAsHeader()
.withIgnoreHeaderCase()
.withIgnoreEmptyLines()
.withTrim());
.withTrim())
) {
retVal.setUrl(conceptMapUrl);

34
hapi-fhir-converter/src/main/java/ca/uhn/hapi/converters/server/VersionedApiConverterInterceptor.java
View File

@ -31,7 +31,11 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.interceptor.InterceptorAdapter;
import org.hl7.fhir.converter.NullVersionConverterAdvisor30;
import org.hl7.fhir.converter.NullVersionConverterAdvisor40;
import org.hl7.fhir.convertors.*;
import org.hl7.fhir.convertors.VersionConvertorAdvisor30;
import org.hl7.fhir.convertors.VersionConvertorAdvisor40;
import org.hl7.fhir.convertors.VersionConvertor_10_30;
import org.hl7.fhir.convertors.VersionConvertor_10_40;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -40,7 +44,9 @@ import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.util.StringTokenizer;
import static org.apache.commons.lang3.StringUtils.*;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/**
* <b>This is an experimental interceptor! Use with caution as
@ -54,16 +60,12 @@ import static org.apache.commons.lang3.StringUtils.*;
public class VersionedApiConverterInterceptor extends InterceptorAdapter {
private final FhirContext myCtxDstu2;
private final FhirContext myCtxDstu2Hl7Org;
private VersionConvertor_30_40 myVersionConvertor_30_40;
private VersionConvertor_10_40 myVersionConvertor_10_40;
private VersionConvertor_10_30 myVersionConvertor_10_30;
private final NullVersionConverterAdvisor40 advisor40;
private final NullVersionConverterAdvisor30 advisor30;
public VersionedApiConverterInterceptor() {
myVersionConvertor_30_40 = new VersionConvertor_30_40();
VersionConvertorAdvisor40 advisor40 = new NullVersionConverterAdvisor40();
myVersionConvertor_10_40 = new VersionConvertor_10_40(advisor40);
VersionConvertorAdvisor30 advisor30 = new NullVersionConverterAdvisor30();
myVersionConvertor_10_30 = new VersionConvertor_10_30(advisor30);
advisor40 = new NullVersionConverterAdvisor40();
advisor30 = new NullVersionConverterAdvisor30();
myCtxDstu2 = FhirContext.forDstu2();
myCtxDstu2Hl7Org = FhirContext.forDstu2Hl7Org();
@ -104,17 +106,17 @@ public class VersionedApiConverterInterceptor extends InterceptorAdapter {
IBaseResource converted = null;
try {
if (wantVersion == FhirVersionEnum.R4 && haveVersion == FhirVersionEnum.DSTU3) {
converted = myVersionConvertor_30_40.convertResource(toDstu3(responseResource), true);
converted = VersionConvertor_30_40.convertResource(toDstu3(responseResource), true);
} else if (wantVersion == FhirVersionEnum.DSTU3 && haveVersion == FhirVersionEnum.R4) {
converted = myVersionConvertor_30_40.convertResource(toR4(responseResource), true);
converted = VersionConvertor_30_40.convertResource(toR4(responseResource), true);
} else if (wantVersion == FhirVersionEnum.DSTU2 && haveVersion == FhirVersionEnum.R4) {
converted = myVersionConvertor_10_40.convertResource(toR4(responseResource));
converted = VersionConvertor_10_40.convertResource(toR4(responseResource), advisor40);
} else if (wantVersion == FhirVersionEnum.R4 && haveVersion == FhirVersionEnum.DSTU2) {
converted = myVersionConvertor_10_40.convertResource(toDstu2(responseResource));
converted = VersionConvertor_10_40.convertResource(toDstu2(responseResource), advisor40);
} else if (wantVersion == FhirVersionEnum.DSTU2 && haveVersion == FhirVersionEnum.DSTU3) {
converted = myVersionConvertor_10_30.convertResource(toDstu3(responseResource));
converted = VersionConvertor_10_30.convertResource(toDstu3(responseResource), advisor30);
} else if (wantVersion == FhirVersionEnum.DSTU3 && haveVersion == FhirVersionEnum.DSTU2) {
converted = myVersionConvertor_10_30.convertResource(toDstu2(responseResource));
converted = VersionConvertor_10_30.convertResource(toDstu2(responseResource), advisor30);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);

8
hapi-fhir-converter/src/main/java/org/hl7/fhir/converter/NullVersionConverterAdvisor50.java
View File

@ -27,8 +27,12 @@ import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.ValueSet;
import java.util.IdentityHashMap;
public class NullVersionConverterAdvisor50 implements VersionConvertorAdvisor50 {
private IdentityHashMap<ValueSet, CodeSystem> myCodeSystems = new IdentityHashMap<>();
@Override
public boolean ignoreEntry(Bundle.BundleEntryComponent src) {
return false;
@ -56,11 +60,11 @@ public class NullVersionConverterAdvisor50 implements VersionConvertorAdvisor50
@Override
public void handleCodeSystem(CodeSystem tgtcs, ValueSet source) throws FHIRException {
myCodeSystems.put(source, tgtcs);
}
@Override
public CodeSystem getCodeSystem(ValueSet src) throws FHIRException {
return null;
return myCodeSystems.get(src);
}
}

10
hapi-fhir-converter/src/test/java/org/hl7/fhir/converter/VersionConvertor_10_30Test.java
View File

@ -16,13 +16,10 @@ public class VersionConvertor_10_30Test {
@Test
public void testConvert() throws FHIRException {
NullVersionConverterAdvisor30 advisor = new NullVersionConverterAdvisor30();
VersionConvertor_10_30 converter = new VersionConvertor_10_30(advisor);
org.hl7.fhir.dstu2.model.Observation input = new org.hl7.fhir.dstu2.model.Observation();
input.setEncounter(new org.hl7.fhir.dstu2.model.Reference("Encounter/123"));
org.hl7.fhir.dstu3.model.Observation output = converter.convertObservation(input);
org.hl7.fhir.dstu3.model.Observation output = (Observation) VersionConvertor_10_30.convertResource(input);
String context = output.getContext().getReference();
assertEquals("Encounter/123", context);
@ -31,9 +28,6 @@ public class VersionConvertor_10_30Test {
@Test
public void testConvertSpecimen() throws FHIRException {
NullVersionConverterAdvisor30 advisor = new NullVersionConverterAdvisor30();
VersionConvertor_10_30 converter = new VersionConvertor_10_30(advisor);
Specimen spec = new Specimen();
CodeableConcept cc = new CodeableConcept();
Coding coding = new Coding();
@ -58,7 +52,7 @@ public class VersionConvertor_10_30Test {
Specimen.SpecimenContainerComponent specimenContainerComponent = new Specimen.SpecimenContainerComponent();
specimenContainerComponent.getExtension().add(new Extension().setUrl("some_url").setValue(new StringType("some_value")));
spec.setContainer(Collections.singletonList(specimenContainerComponent));
Resource resource = converter.convertResource(spec);
Resource resource = VersionConvertor_10_30.convertResource(spec);
}

3
hapi-fhir-converter/src/test/java/org/hl7/fhir/converter/VersionConvertor_14_30Test.java
View File

@ -3,6 +3,7 @@ package org.hl7.fhir.converter;
import static org.junit.Assert.assertEquals;
import org.hl7.fhir.convertors.VersionConvertor_14_30;
import org.hl7.fhir.dstu3.model.Questionnaire;
import org.hl7.fhir.exceptions.FHIRException;
import org.junit.Test;
@ -14,7 +15,7 @@ public class VersionConvertor_14_30Test {
org.hl7.fhir.dstu2016may.model.Questionnaire input = new org.hl7.fhir.dstu2016may.model.Questionnaire();
input.setTitle("My title");
org.hl7.fhir.dstu3.model.Questionnaire output = VersionConvertor_14_30.convertQuestionnaire(input);
org.hl7.fhir.dstu3.model.Questionnaire output = (Questionnaire) VersionConvertor_14_30.convertResource(input);
String context = output.getTitle();
assertEquals("My title", context);

13
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ConverterExamples.java
View File

@ -20,9 +20,8 @@ package ca.uhn.hapi.fhir.docs;
* #L%
*/
import org.hl7.fhir.converter.NullVersionConverterAdvisor30;
import org.hl7.fhir.convertors.VersionConvertor_10_30;
import org.hl7.fhir.convertors.VersionConvertor_14_30;
import org.hl7.fhir.convertors.conv10_30.Observation10_30;
import org.hl7.fhir.convertors.conv14_30.Questionnaire14_30;
import org.hl7.fhir.exceptions.FHIRException;
public class ConverterExamples {
@ -30,16 +29,12 @@ public class ConverterExamples {
@SuppressWarnings("unused")
public void c1020() throws FHIRException {
//START SNIPPET: 1020
// Create a converter
NullVersionConverterAdvisor30 advisor = new NullVersionConverterAdvisor30();
VersionConvertor_10_30 converter = new VersionConvertor_10_30(advisor);
// Create an input resource to convert
org.hl7.fhir.dstu2.model.Observation input = new org.hl7.fhir.dstu2.model.Observation();
input.setEncounter(new org.hl7.fhir.dstu2.model.Reference("Encounter/123"));
// Convert the resource
org.hl7.fhir.dstu3.model.Observation output = converter.convertObservation(input);
org.hl7.fhir.dstu3.model.Observation output = Observation10_30.convertObservation(input);
String context = output.getContext().getReference();
//END SNIPPET: 1020
}
@ -52,7 +47,7 @@ public class ConverterExamples {
input.setTitle("My title");
// Convert the resource
org.hl7.fhir.dstu3.model.Questionnaire output = VersionConvertor_14_30.convertQuestionnaire(input);
org.hl7.fhir.dstu3.model.Questionnaire output = Questionnaire14_30.convertQuestionnaire(input);
String context = output.getTitle();
//END SNIPPET: 1420
}

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1715-update-converters.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: change
issue: 1715
title: The version converters for all versions except R4/R5 have been reworked to be split into individual
classes per resource type (the R4/R5 converters were already organized this way). Thanks to Mark Iantorno
for a huge effort to write a Java source parser/serializer to acomplish this task.

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
View File

@ -24,10 +24,10 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
@ -35,7 +35,6 @@ import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.hapi.validation.ValidationSupportChain;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeableConcept;
@ -53,6 +52,7 @@ import java.util.List;
import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.hl7.fhir.convertors.conv30_40.CodeSystem30_40.convertCodeSystem;
@Transactional
public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<CodeSystem> implements IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> {
@ -147,7 +147,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
CodeSystem csDstu3 = (CodeSystem) theResource;
org.hl7.fhir.r4.model.CodeSystem cs = VersionConvertor_30_40.convertCodeSystem(csDstu3);
org.hl7.fhir.r4.model.CodeSystem cs = convertCodeSystem(csDstu3);
addPidToResource(theEntity, cs);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, (ResourceTable) theEntity);

17
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java
View File

@ -22,21 +22,24 @@ package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.TranslationMatch;
import ca.uhn.fhir.jpa.term.TranslationRequest;
import ca.uhn.fhir.jpa.term.TranslationResult;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.model.ConceptMap;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.Date;
@ -44,6 +47,8 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
public class FhirResourceDaoConceptMapDstu3 extends BaseHapiFhirResourceDao<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
@Autowired
private ITermReadSvc myHapiTerminologySvc;
@ -166,7 +171,7 @@ public class FhirResourceDaoConceptMapDstu3 extends BaseHapiFhirResourceDao<Conc
if (retVal.getDeleted() == null) {
try {
ConceptMap conceptMap = (ConceptMap) theResource;
org.hl7.fhir.r4.model.ConceptMap converted = VersionConvertor_30_40.convertConceptMap(conceptMap);
org.hl7.fhir.r4.model.ConceptMap converted = convertConceptMap(conceptMap);
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, converted);
} catch (FHIRException fe) {
throw new InternalErrorException(fe);

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
View File

@ -33,12 +33,15 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.ElementUtil;
import org.apache.commons.codec.binary.StringUtils;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
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.Enumerations.PublicationStatus;
import org.hl7.fhir.dstu3.model.IntegerType;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetFilterComponent;
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
@ -51,7 +54,6 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import java.util.Collections;
import java.util.Date;
@ -59,6 +61,7 @@ import java.util.List;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSet;
public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoValueSetDstu3.class);
@ -420,7 +423,7 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
if (retVal.getDeleted() == null) {
try {
ValueSet valueSet = (ValueSet) theResource;
org.hl7.fhir.r4.model.ValueSet converted = VersionConvertor_30_40.convertValueSet(valueSet);
org.hl7.fhir.r4.model.ValueSet converted = convertValueSet(valueSet);
myHapiTerminologySvc.storeTermValueSet(retVal, converted);
} catch (FHIRException fe) {
throw new InternalErrorException(fe);

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java
View File

@ -148,7 +148,7 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
CodeSystem cs = (CodeSystem) theResource;
addPidToResource(theEntity, theResource);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(cs), (ResourceTable) theEntity);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem(cs), (ResourceTable) theEntity);
}
return retVal;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoConceptMapR5.java
View File

@ -166,7 +166,7 @@ public class FhirResourceDaoConceptMapR5 extends BaseHapiFhirResourceDao<Concept
if (retVal.getDeleted() == null) {
ConceptMap conceptMap = (ConceptMap) theResource;
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, org.hl7.fhir.convertors.conv40_50.ConceptMap.convertConceptMap(conceptMap));
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, org.hl7.fhir.convertors.conv40_50.ConceptMap40_50.convertConceptMap(conceptMap));
} else {
myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
View File

@ -415,7 +415,7 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
if (myDaoConfig.isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
ValueSet valueSet = (ValueSet) theResource;
myHapiTerminologySvc.storeTermValueSet(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSet));
myHapiTerminologySvc.storeTermValueSet(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSet));
} else {
myHapiTerminologySvc.deleteValueSetAndChildren(retVal);
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/TerminologyUploaderProvider.java
View File

@ -39,7 +39,6 @@ import ca.uhn.fhir.util.ValidateUtil;
import com.google.common.base.Charsets;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.Multimap;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.ICompositeType;
@ -61,6 +60,7 @@ import java.util.Map;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
import static org.hl7.fhir.convertors.conv30_40.CodeSystem30_40.convertCodeSystem;
public class TerminologyUploaderProvider extends BaseJpaProvider {
@ -272,10 +272,10 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
CodeSystem nextCodeSystem;
switch (getContext().getVersion().getVersion()) {
case DSTU3:
nextCodeSystem = VersionConvertor_30_40.convertCodeSystem((org.hl7.fhir.dstu3.model.CodeSystem) theCodeSystem);
nextCodeSystem = convertCodeSystem((org.hl7.fhir.dstu3.model.CodeSystem) theCodeSystem);
break;
case R5:
nextCodeSystem = org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem((org.hl7.fhir.r5.model.CodeSystem) theCodeSystem);
nextCodeSystem = org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem((org.hl7.fhir.r5.model.CodeSystem) theCodeSystem);
break;
default:
nextCodeSystem = (CodeSystem) theCodeSystem;

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderConceptMapDstu3.java
View File

@ -21,9 +21,9 @@ package ca.uhn.fhir.jpa.provider.dstu3;
*/
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.term.TranslationRequest;
import ca.uhn.fhir.jpa.term.TranslationResult;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
@ -31,11 +31,21 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.CodeType;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.ConceptMap;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.UriType;
import org.hl7.fhir.exceptions.FHIRException;
import javax.servlet.http.HttpServletRequest;
import static org.hl7.fhir.convertors.conv30_40.Parameters30_40.convertParameters;
public class BaseJpaResourceProviderConceptMapDstu3 extends JpaResourceProviderDstu3<ConceptMap> {
@Operation(name = JpaConstants.OPERATION_TRANSLATE, idempotent = true, returnParameters = {
@OperationParam(name = "result", type = BooleanType.class, min = 1, max = 1),
@ -129,7 +139,7 @@ public class BaseJpaResourceProviderConceptMapDstu3 extends JpaResourceProviderD
TranslationResult result = dao.translate(translationRequest, theRequestDetails);
// Convert from R4 to DSTU3
return VersionConvertor_30_40.convertParameters(result.toParameters());
return convertParameters(result.toParameters());
} catch (FHIRException fe) {
throw new InternalErrorException(fe);
} finally {

24
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaResourceProviderDstu3.java
View File

@ -21,17 +21,28 @@ package ca.uhn.fhir.jpa.provider.dstu3;
*/
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.provider.BaseJpaResourceProvider;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.jpa.provider.BaseJpaResourceProvider;
import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.Delete;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.annotation.Update;
import ca.uhn.fhir.rest.annotation.Validate;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.IntegerType;
import org.hl7.fhir.dstu3.model.Meta;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IIdType;
@ -41,6 +52,7 @@ import javax.servlet.http.HttpServletRequest;
import static ca.uhn.fhir.jpa.model.util.JpaConstants.OPERATION_META;
import static ca.uhn.fhir.jpa.model.util.JpaConstants.OPERATION_META_ADD;
import static ca.uhn.fhir.jpa.model.util.JpaConstants.OPERATION_META_DELETE;
import static org.hl7.fhir.convertors.conv30_40.Parameters30_40.convertParameters;
public class JpaResourceProviderDstu3<T extends IAnyResource> extends BaseJpaResourceProvider<T> {
@ -91,7 +103,7 @@ public class JpaResourceProviderDstu3<T extends IAnyResource> extends BaseJpaRes
RequestDetails theRequest) {
org.hl7.fhir.r4.model.Parameters retVal = super.doExpunge(theIdParam, theLimit, theExpungeDeletedResources, theExpungeOldVersions, null, theRequest);
try {
return VersionConvertor_30_40.convertParameters(retVal);
return convertParameters(retVal);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -107,7 +119,7 @@ public class JpaResourceProviderDstu3<T extends IAnyResource> extends BaseJpaRes
RequestDetails theRequest) {
org.hl7.fhir.r4.model.Parameters retVal = super.doExpunge(null, theLimit, theExpungeDeletedResources, theExpungeOldVersions, null, theRequest);
try {
return VersionConvertor_30_40.convertParameters(retVal);
return convertParameters(retVal);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}

22
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaSystemProviderDstu3.java
View File

@ -3,17 +3,26 @@ package ca.uhn.fhir.jpa.provider.dstu3;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl.Suggestion;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.provider.BaseJpaSystemProviderDstu2Plus;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.BaseJpaSystemProviderDstu2Plus;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.annotation.Transaction;
import ca.uhn.fhir.rest.annotation.TransactionParam;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.DecimalType;
import org.hl7.fhir.dstu3.model.IntegerType;
import org.hl7.fhir.dstu3.model.Meta;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IIdType;
@ -29,6 +38,7 @@ import java.util.TreeMap;
import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.hl7.fhir.convertors.conv30_40.Parameters30_40.convertParameters;
/*
* #%L
@ -72,7 +82,7 @@ public class JpaSystemProviderDstu3 extends BaseJpaSystemProviderDstu2Plus<Bundl
) {
org.hl7.fhir.r4.model.Parameters retVal = super.doExpunge(theLimit, theExpungeDeletedResources, theExpungeOldVersions, theExpungeEverything, theRequestDetails);
try {
return VersionConvertor_30_40.convertParameters(retVal);
return convertParameters(retVal);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -90,7 +100,7 @@ public class JpaSystemProviderDstu3 extends BaseJpaSystemProviderDstu2Plus<Bundl
) {
org.hl7.fhir.r4.model.Parameters retVal = super.doExpunge(theLimit, theExpungeDeletedResources, theExpungeOldVersions, theExpungeEverything, theRequestDetails);
try {
return VersionConvertor_30_40.convertParameters(retVal);
return convertParameters(retVal);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderConceptMapR5.java
View File

@ -122,7 +122,7 @@ public class BaseJpaResourceProviderConceptMapR5 extends JpaResourceProviderR5<C
IFhirResourceDaoConceptMap<ConceptMap> dao = (IFhirResourceDaoConceptMap<ConceptMap>) getDao();
TranslationResult result = dao.translate(translationRequest, theRequestDetails);
org.hl7.fhir.r4.model.Parameters parameters = result.toParameters();
return org.hl7.fhir.convertors.conv40_50.Parameters.convertParameters(parameters);
return org.hl7.fhir.convertors.conv40_50.Parameters40_50.convertParameters(parameters);
} finally {
endRequest(theServletRequest);
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/JpaResourceProviderR5.java
View File

@ -86,7 +86,7 @@ public class JpaResourceProviderR5<T extends IAnyResource> extends BaseJpaResour
RequestDetails theRequest) {
org.hl7.fhir.r4.model.Parameters parameters = super.doExpunge(theIdParam, theLimit, theExpungeDeletedResources, theExpungeOldVersions, null, theRequest);
return org.hl7.fhir.convertors.conv40_50.Parameters.convertParameters(parameters);
return org.hl7.fhir.convertors.conv40_50.Parameters40_50.convertParameters(parameters);
}
@ -99,7 +99,7 @@ public class JpaResourceProviderR5<T extends IAnyResource> extends BaseJpaResour
@OperationParam(name = JpaConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_PREVIOUS_VERSIONS) BooleanType theExpungeOldVersions,
RequestDetails theRequest) {
org.hl7.fhir.r4.model.Parameters parameters = super.doExpunge(null, theLimit, theExpungeDeletedResources, theExpungeOldVersions, null, theRequest);
return org.hl7.fhir.convertors.conv40_50.Parameters.convertParameters(parameters);
return org.hl7.fhir.convertors.conv40_50.Parameters40_50.convertParameters(parameters);
}
@Operation(name = OPERATION_META, idempotent = true, returnParameters = {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/JpaSystemProviderR5.java
View File

@ -68,7 +68,7 @@ public class JpaSystemProviderR5 extends BaseJpaSystemProviderDstu2Plus<Bundle,
RequestDetails theRequestDetails
) {
org.hl7.fhir.r4.model.Parameters parameters = super.doExpunge(theLimit, theExpungeDeletedResources, theExpungeOldVersions, theExpungeEverything, theRequestDetails);
return org.hl7.fhir.convertors.conv40_50.Parameters.convertParameters(parameters);
return org.hl7.fhir.convertors.conv40_50.Parameters40_50.convertParameters(parameters);
}
@Operation(name = JpaConstants.OPERATION_EXPUNGE, idempotent = false, returnParameters = {
@ -82,7 +82,7 @@ public class JpaSystemProviderR5 extends BaseJpaSystemProviderDstu2Plus<Bundle,
RequestDetails theRequestDetails
) {
org.hl7.fhir.r4.model.Parameters parameters = super.doExpunge(theLimit, theExpungeDeletedResources, theExpungeOldVersions, theExpungeEverything, theRequestDetails);
return org.hl7.fhir.convertors.conv40_50.Parameters.convertParameters(parameters);
return org.hl7.fhir.convertors.conv40_50.Parameters40_50.convertParameters(parameters);
}
// This is generated by hand:

24
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcDstu3.java
View File

@ -9,10 +9,13 @@ import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.ValidateUtil;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
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.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.StructureDefinition;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.exceptions.FHIRException;
@ -31,6 +34,9 @@ import java.util.List;
import java.util.Optional;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.hl7.fhir.convertors.conv30_40.CodeSystem30_40.convertCodeSystem;
import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSet;
import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSetExpansionComponent;
/*
* #%L
@ -104,7 +110,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
valueSetToExpandR4 = toCanonicalValueSet(valueSetToExpand);
org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent expandedR4 = super.expandValueSetInMemory(valueSetToExpandR4, null).getExpansion();
return VersionConvertor_30_40.convertValueSetExpansionComponent(expandedR4);
return convertValueSetExpansionComponent(expandedR4);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -118,7 +124,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
valueSetToExpandR4 = toCanonicalValueSet(valueSetToExpand);
org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSetInMemory(valueSetToExpandR4, null);
return VersionConvertor_30_40.convertValueSet(expandedR4);
return convertValueSet(expandedR4);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -127,7 +133,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
@Override
protected org.hl7.fhir.r4.model.ValueSet toCanonicalValueSet(IBaseResource theValueSet) throws FHIRException {
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
valueSetToExpandR4 = VersionConvertor_30_40.convertValueSet((ValueSet) theValueSet);
valueSetToExpandR4 = convertValueSet((ValueSet) theValueSet);
return valueSetToExpandR4;
}
@ -139,7 +145,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
valueSetToExpandR4 = toCanonicalValueSet(valueSetToExpand);
org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSet(valueSetToExpandR4, theOffset, theCount);
return VersionConvertor_30_40.convertValueSet(expandedR4);
return convertValueSet(expandedR4);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -256,7 +262,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
public org.hl7.fhir.r4.model.CodeSystem getCodeSystemFromContext(String theSystem) {
CodeSystem codeSystem = myValidationSupport.fetchCodeSystem(myContext, theSystem);
try {
return VersionConvertor_30_40.convertCodeSystem(codeSystem);
return convertCodeSystem(codeSystem);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -323,7 +329,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet, "ValueSet must not be null");
ValueSet valueSet = (ValueSet) theValueSet;
org.hl7.fhir.r4.model.ValueSet valueSetR4 = VersionConvertor_30_40.convertValueSet(valueSet);
org.hl7.fhir.r4.model.ValueSet valueSetR4 = convertValueSet(valueSet);
Coding coding = (Coding) theCoding;
org.hl7.fhir.r4.model.Coding codingR4 = null;
@ -347,7 +353,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
public boolean isValueSetPreExpandedForCodeValidation(IBaseResource theValueSet) {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet, "ValueSet must not be null");
ValueSet valueSet = (ValueSet) theValueSet;
org.hl7.fhir.r4.model.ValueSet valueSetR4 = VersionConvertor_30_40.convertValueSet(valueSet);
org.hl7.fhir.r4.model.ValueSet valueSetR4 = convertValueSet(valueSet);
return super.isValueSetPreExpandedForCodeValidation(valueSetR4);
}
}

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcR5.java
View File

@ -90,21 +90,21 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
super.throwInvalidValueSet(theValueSet);
}
return expandValueSetAndReturnVersionIndependentConcepts(org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR5), null);
return expandValueSetAndReturnVersionIndependentConcepts(org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetR5), null);
}
@Override
public IBaseResource expandValueSet(IBaseResource theInput) {
org.hl7.fhir.r4.model.ValueSet valueSetToExpand = toCanonicalValueSet(theInput);
org.hl7.fhir.r4.model.ValueSet valueSetR4 = super.expandValueSetInMemory(valueSetToExpand, null);
return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR4);
return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetR4);
}
@Override
public IBaseResource expandValueSet(IBaseResource theInput, int theOffset, int theCount) {
org.hl7.fhir.r4.model.ValueSet valueSetToExpand = toCanonicalValueSet(theInput);
org.hl7.fhir.r4.model.ValueSet valueSetR4 = super.expandValueSet(valueSetToExpand, theOffset, theCount);
return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR4);
return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetR4);
}
@Override
@ -117,8 +117,8 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
public ValueSetExpander.ValueSetExpansionOutcome expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
ValueSet valueSetToExpand = new ValueSet();
valueSetToExpand.getCompose().addInclude(theInclude);
org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSetInMemory(org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetToExpand), null);
return new ValueSetExpander.ValueSetExpansionOutcome(org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(expandedR4));
org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSetInMemory(org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetToExpand), null);
return new ValueSetExpander.ValueSetExpansionOutcome(org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(expandedR4));
}
@Override
@ -199,13 +199,13 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
@Override
public org.hl7.fhir.r4.model.CodeSystem getCodeSystemFromContext(String theSystem) {
CodeSystem codeSystemR5 = myValidationSupport.fetchCodeSystem(myContext, theSystem);
return org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(codeSystemR5);
return org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem(codeSystemR5);
}
@Override
protected org.hl7.fhir.r4.model.ValueSet getValueSetFromResourceTable(ResourceTable theResourceTable) {
ValueSet valueSetR5 = myValueSetResourceDao.toResource(ValueSet.class, theResourceTable, null, false);
return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR5);
return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetR5);
}
@Override
@ -277,7 +277,7 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
@Override
protected org.hl7.fhir.r4.model.ValueSet toCanonicalValueSet(IBaseResource theValueSet) throws org.hl7.fhir.exceptions.FHIRException {
return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet((ValueSet) theValueSet);
return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet((ValueSet) theValueSet);
}
@Override

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcDstu3.java
View File

@ -37,6 +37,9 @@ import org.springframework.context.event.ContextStartedEvent;
import org.springframework.context.event.EventListener;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.hl7.fhir.convertors.conv30_40.CodeSystem30_40.convertCodeSystem;
import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSet;
public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl implements ITermVersionAdapterSvc {
@ -72,7 +75,7 @@ public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl im
public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
CodeSystem resourceToStore;
try {
resourceToStore = VersionConvertor_30_40.convertCodeSystem(theCodeSystemResource);
resourceToStore = convertCodeSystem(theCodeSystemResource);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -89,7 +92,7 @@ public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl im
public void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
ConceptMap resourceToStore;
try {
resourceToStore = VersionConvertor_30_40.convertConceptMap(theConceptMap);
resourceToStore = convertConceptMap(theConceptMap);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -105,7 +108,7 @@ public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl im
public void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
ValueSet valueSetDstu3;
try {
valueSetDstu3 = VersionConvertor_30_40.convertValueSet(theValueSet);
valueSetDstu3 = convertValueSet(theValueSet);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR5.java
View File

@ -62,7 +62,7 @@ public class TermVersionAdapterSvcR5 extends BaseTermVersionAdapterSvcImpl imple
public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
validateCodeSystemForStorage(theCodeSystemResource);
CodeSystem codeSystemR4 = org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(theCodeSystemResource);
CodeSystem codeSystemR4 = org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem(theCodeSystemResource);
if (isBlank(theCodeSystemResource.getIdElement().getIdPart())) {
String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
return myCodeSystemResourceDao.update(codeSystemR4, matchUrl).getId();
@ -74,7 +74,7 @@ public class TermVersionAdapterSvcR5 extends BaseTermVersionAdapterSvcImpl imple
@Override
public void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
ConceptMap conceptMapR4 = org.hl7.fhir.convertors.conv40_50.ConceptMap.convertConceptMap(theConceptMap);
ConceptMap conceptMapR4 = org.hl7.fhir.convertors.conv40_50.ConceptMap40_50.convertConceptMap(theConceptMap);
if (isBlank(theConceptMap.getIdElement().getIdPart())) {
String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
@ -87,7 +87,7 @@ public class TermVersionAdapterSvcR5 extends BaseTermVersionAdapterSvcImpl imple
@Override
public void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(theValueSet);
ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(theValueSet);
if (isBlank(theValueSet.getIdElement().getIdPart())) {
String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());

21
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2ValidateTest.java
View File

@ -1,9 +1,5 @@
package ca.uhn.fhir.jpa.dao.dstu2;
import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
@ -32,7 +28,11 @@ import org.junit.Before;
import org.junit.Test;
import java.io.IOException;
import java.util.Arrays;
import java.util.Collections;
import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu2ValidateTest.class);
@ -94,15 +94,14 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
myStructureDefinitionDao.create(sd, mySrd);
Observation input = new Observation();
ResourceMetadataKeyEnum.PROFILES.put(input, Arrays.asList(new IdDt(sd.getUrl())));
ResourceMetadataKeyEnum.PROFILES.put(input, Collections.singletonList(new IdDt(sd.getUrl())));
input.addIdentifier().setSystem("http://acme").setValue("12345");
input.getEncounter().setReference("http://foo.com/Encounter/9");
input.setStatus(ObservationStatusEnum.FINAL);
input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
String encoded = null;
MethodOutcome outcome = null;
String encoded;
ValidationModeEnum mode = ValidationModeEnum.CREATE;
switch (enc) {
case JSON:
@ -130,12 +129,12 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
}
@Test
public void testValidateResourceContainingProfileDeclarationInvalid() throws Exception {
public void testValidateResourceContainingProfileDeclarationInvalid() {
String methodName = "testValidateResourceContainingProfileDeclarationInvalid";
Observation input = new Observation();
String profileUri = "http://example.com/StructureDefinition/" + methodName;
ResourceMetadataKeyEnum.PROFILES.put(input, Arrays.asList(new IdDt(profileUri)));
ResourceMetadataKeyEnum.PROFILES.put(input, Collections.singletonList(new IdDt(profileUri)));
input.addIdentifier().setSystem("http://acme").setValue("12345");
input.getEncounter().setReference("http://foo.com/Encounter/9");
@ -148,7 +147,7 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome.getOperationOutcome());
ourLog.info(ooString);
assertThat(ooString, containsString("StructureDefinition reference \\\"" + profileUri + "\\\" could not be resolved"));
assertThat(ooString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' could not be resolved, so has not been checked"));
}

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
View File

@ -35,7 +35,6 @@ import ca.uhn.fhir.util.UrlUtil;
import org.apache.commons.io.IOUtils;
import org.hibernate.search.jpa.FullTextEntityManager;
import org.hibernate.search.jpa.Search;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.exceptions.FHIRException;
@ -60,6 +59,7 @@ import java.io.IOException;
import java.io.InputStream;
import java.util.Map;
import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
import static org.junit.Assert.fail;
@RunWith(SpringJUnit4ClassRunner.class)
@ -386,7 +386,7 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
*/
public static ConceptMap createConceptMap() {
try {
return VersionConvertor_30_40.convertConceptMap(BaseJpaR4Test.createConceptMap());
return convertConceptMap(BaseJpaR4Test.createConceptMap());
} catch (FHIRException fe) {
throw new InternalErrorException(fe);
}

17
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValidateTest.java
View File

@ -15,6 +15,7 @@ import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.utils.IResourceValidator;
@ -99,7 +100,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
myValueSetDao.create(vs);
ValueSet expansion = myValueSetDao.expandByIdentifier("http://ccim.on.ca/fhir/iar/ValueSet/iar-citizenship-status", null);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expansion));
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expansion));
// Questionnaire q = loadResourceFromClasspath(Questionnaire.class,"/dstu3/iar/Questionnaire-iar-test.xml" );
// myQuestionnaireDao.create(q);
@ -322,15 +323,11 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
ValidationModeEnum mode = ValidationModeEnum.CREATE;
String encoded = myFhirCtx.newJsonParser().encodeResourceToString(input);
try {
myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
fail();
} catch (PreconditionFailedException e) {
String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome());
ourLog.info(ooString);
assertThat(ooString, containsString("StructureDefinition reference \\\"" + profileUri + "\\\" could not be resolved"));
}
MethodOutcome output = myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
OperationOutcome oo = (OperationOutcome) output.getOperationOutcome();
String outputString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
ourLog.info(outputString);
assertThat(outputString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' could not be resolved, so has not been checked"));
}
@Test

14
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java
View File

@ -395,15 +395,11 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
ValidationModeEnum mode = ValidationModeEnum.CREATE;
String encoded = myFhirCtx.newJsonParser().encodeResourceToString(input);
try {
myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
fail();
} catch (PreconditionFailedException e) {
String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome());
ourLog.info(ooString);
assertThat(ooString, containsString("StructureDefinition reference \\\"" + profileUri + "\\\" could not be resolved"));
}
MethodOutcome output = myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
org.hl7.fhir.r4.model.OperationOutcome oo = (org.hl7.fhir.r4.model.OperationOutcome) output.getOperationOutcome();
String outputString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
ourLog.info(outputString);
assertThat(outputString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' could not be resolved, so has not been checked"));
}

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/validator/ValidatorAcrossVersionsTest.java
View File

@ -54,8 +54,8 @@ public class ValidatorAcrossVersionsTest {
ourLog.info(ctxDstu2.newJsonParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome()));
assertEquals(2, result.getMessages().size());
assertEquals("No questionnaire is identified, so no validation can be performed against the base questionnaire", result.getMessages().get(0).getMessage());
assertEquals("Profile http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse, Element 'QuestionnaireResponse.status': minimum required = 1, but only found 0", result.getMessages().get(1).getMessage());
assertEquals("Profile http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse, Element 'QuestionnaireResponse.status': minimum required = 1, but only found 0", result.getMessages().get(0).getMessage());
assertEquals("No questionnaire is identified, so no validation can be performed against the base questionnaire", result.getMessages().get(1).getMessage());
}
}

12
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR5.java
View File

@ -26,12 +26,16 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.hapi.ctx.HapiWorkerContext;
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.Base;
import org.hl7.fhir.r5.model.IdType;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.ResourceType;
import org.hl7.fhir.r5.model.TypeDetails;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.PostConstruct;
import java.util.Collections;
@ -115,7 +119,7 @@ public class SearchParamExtractorR5 extends BaseSearchParamExtractor implements
}
@Override
public Base resolveReference(Object theAppContext, String theUrl) throws FHIRException {
public Base resolveReference(Object appContext, String theUrl, Base refContext) throws FHIRException {
/*
* When we're doing resolution within the SearchParamExtractor, if we want

18
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/ctx/HapiWorkerContext.java
View File

@ -106,14 +106,22 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
@Override
public <T extends Resource> T fetchResource(Class<T> theClass, String theUri) {
Validate.notBlank(theUri, "theUri must not be null or blank");
if (myValidationSupport == null) {
return null;
} else {
@SuppressWarnings("unchecked")
T retVal = (T) myFetchedResourceCache.get(theUri, t->{
return myValidationSupport.fetchResource(myCtx, theClass, theUri);
});
return retVal;
try {
//noinspection unchecked
return (T) myFetchedResourceCache.get(theUri, t -> {
T resource = myValidationSupport.fetchResource(myCtx, theClass, theUri);
if (resource == null) {
throw new IllegalArgumentException();
}
return resource;
});
} catch (IllegalArgumentException e) {
return null;
}
}
}

5
hapi-fhir-structures-r5/src/main/java/org/hl7/fhir/r5/hapi/ctx/HapiWorkerContext.java
View File

@ -343,6 +343,11 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
return fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + typeName);
}
@Override
public StructureDefinition fetchRawProfile(String url) {
throw new UnsupportedOperationException();
}
@Override
public List<String> getTypeNames() {
throw new UnsupportedOperationException();

57
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/ValidatorWrapper.java
View File

@ -4,20 +4,24 @@ import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.util.XmlUtil;
import ca.uhn.fhir.validation.IValidationContext;
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.codec.Charsets;
import org.apache.commons.io.input.ReaderInputStream;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.hl7.fhir.r5.utils.ValidationProfileSet;
import org.hl7.fhir.r5.validation.InstanceValidator;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;
import java.io.InputStream;
@ -33,7 +37,9 @@ public class ValidatorWrapper {
private boolean myAnyExtensionsAllowed;
private boolean myErrorForUnknownProfiles;
private boolean myNoTerminologyChecks;
private boolean myAssumeValidRestReferences;
private Collection<? extends String> myExtensionDomains;
private IResourceValidator.IValidatorResourceFetcher myValidatorResourceFetcher;
/**
* Constructor
@ -42,6 +48,15 @@ public class ValidatorWrapper {
super();
}
public boolean isAssumeValidRestReferences() {
return myAssumeValidRestReferences;
}
public ValidatorWrapper setAssumeValidRestReferences(boolean assumeValidRestReferences) {
this.myAssumeValidRestReferences = assumeValidRestReferences;
return this;
}
public ValidatorWrapper setBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel theBestPracticeWarningLevel) {
myBestPracticeWarningLevel = theBestPracticeWarningLevel;
return this;
@ -67,6 +82,12 @@ public class ValidatorWrapper {
return this;
}
public ValidatorWrapper setValidatorResourceFetcher(IResourceValidator.IValidatorResourceFetcher validatorResourceFetcher) {
this.myValidatorResourceFetcher = validatorResourceFetcher;
return this;
}
public List<ValidationMessage> validate(IWorkerContext theWorkerContext, IValidationContext<?> theValidationContext) {
InstanceValidator v;
FHIRPathEngine.IEvaluationContext evaluationCtx = new org.hl7.fhir.r5.hapi.validation.FhirInstanceValidator.NullEvaluationContext();
@ -76,19 +97,21 @@ public class ValidatorWrapper {
throw new ConfigurationException(e);
}
v.setAssumeValidRestReferences(isAssumeValidRestReferences());
v.setBestPracticeWarningLevel(myBestPracticeWarningLevel);
v.setAnyExtensionsAllowed(myAnyExtensionsAllowed);
v.setResourceIdRule(IResourceValidator.IdStatus.OPTIONAL);
v.setNoTerminologyChecks(myNoTerminologyChecks);
v.setErrorForUnknownProfiles(myErrorForUnknownProfiles);
v.getExtensionDomains().addAll(myExtensionDomains);
v.setFetcher(myValidatorResourceFetcher);
v.setAllowXsiLocation(true);
List<ValidationMessage> messages = new ArrayList<>();
ValidationProfileSet profileSet = new ValidationProfileSet();
List<StructureDefinition> profileUrls = new ArrayList<>();
for (String next : theValidationContext.getOptions().getProfiles()) {
profileSet.getCanonical().add(new ValidationProfileSet.ProfileRegistration(next, true));
fetchAndAddProfile(theWorkerContext, profileUrls, next);
}
String input = theValidationContext.getResourceAsString();
@ -109,14 +132,14 @@ public class ValidatorWrapper {
// Determine if meta/profiles are present...
ArrayList<String> profiles = determineIfProfilesSpecified(document);
for (String nextProfile : profiles) {
profileSet.getCanonical().add(new ValidationProfileSet.ProfileRegistration(nextProfile, true));
fetchAndAddProfile(theWorkerContext, profileUrls, nextProfile);
}
String resourceAsString = theValidationContext.getResourceAsString();
InputStream inputStream = new ReaderInputStream(new StringReader(resourceAsString), Charsets.UTF_8);
Manager.FhirFormat format = Manager.FhirFormat.XML;
v.validate(null, messages, inputStream, format, profileSet);
v.validate(null, messages, inputStream, format, profileUrls);
} else if (encoding == EncodingEnum.JSON) {
@ -129,7 +152,8 @@ public class ValidatorWrapper {
if (profileElement != null && profileElement.isJsonArray()) {
JsonArray profiles = profileElement.getAsJsonArray();
for (JsonElement element : profiles) {
profileSet.getCanonical().add(new ValidationProfileSet.ProfileRegistration(element.getAsString(), true));
String nextProfile = element.getAsString();
fetchAndAddProfile(theWorkerContext, profileUrls, nextProfile);
}
}
}
@ -138,7 +162,7 @@ public class ValidatorWrapper {
InputStream inputStream = new ReaderInputStream(new StringReader(resourceAsString), Charsets.UTF_8);
Manager.FhirFormat format = Manager.FhirFormat.JSON;
v.validate(null, messages, inputStream, format, profileSet);
v.validate(null, messages, inputStream, format, profileUrls);
} else {
throw new IllegalArgumentException("Unknown encoding: " + encoding);
@ -157,17 +181,16 @@ public class ValidatorWrapper {
return messages;
}
private String determineResourceName(Document theDocument) {
NodeList list = theDocument.getChildNodes();
for (int i = 0; i < list.getLength(); i++) {
if (list.item(i) instanceof Element) {
return list.item(i).getLocalName();
}
private void fetchAndAddProfile(IWorkerContext theWorkerContext, List<StructureDefinition> theProfileStructureDefinitions, String theUrl) throws org.hl7.fhir.exceptions.FHIRException {
try {
StructureDefinition structureDefinition = theWorkerContext.fetchResourceWithException(StructureDefinition.class, theUrl);
theProfileStructureDefinitions.add(structureDefinition);
} catch (FHIRException e) {
ourLog.debug("Failed to load profile: {}", theUrl);
}
return theDocument.getDocumentElement().getLocalName();
}
private ArrayList<String> determineIfProfilesSpecified(Document theDocument) {
ArrayList<String> profileNames = new ArrayList<>();
NodeList list = theDocument.getChildNodes().item(0).getChildNodes();

74
hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu2016may/hapi/validation/FhirInstanceValidator.java
View File

@ -1,14 +1,10 @@
package org.hl7.fhir.dstu2016may.hapi.validation;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.*;
import java.util.concurrent.TimeUnit;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.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;
@ -18,28 +14,45 @@ 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.convertors.conv14_50.CodeSystem14_50;
import org.hl7.fhir.convertors.conv14_50.StructureDefinition14_50;
import org.hl7.fhir.convertors.conv14_50.ValueSet14_50;
import org.hl7.fhir.dstu2016may.model.CodeSystem;
import org.hl7.fhir.dstu2016may.model.CodeableConcept;
import org.hl7.fhir.dstu2016may.model.Coding;
import org.hl7.fhir.dstu2016may.model.ImplementationGuide;
import org.hl7.fhir.dstu2016may.model.Questionnaire;
import org.hl7.fhir.dstu2016may.model.StructureDefinition;
import org.hl7.fhir.dstu2016may.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.Resource;
import org.hl7.fhir.r5.utils.INarrativeGenerator;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.dstu2016may.model.*;
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.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.validation.IValidationContext;
import ca.uhn.fhir.validation.IValidatorModule;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.net.MalformedURLException;
import java.net.URL;
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;
public class FhirInstanceValidator extends BaseValidatorBridge implements IValidatorModule {
@ -382,7 +395,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
}
public org.hl7.fhir.r5.model.StructureDefinition convert(StructureDefinition next) {
org.hl7.fhir.r5.model.StructureDefinition structureDefinition = VersionConvertor_14_50.convertStructureDefinition(next);
org.hl7.fhir.r5.model.StructureDefinition structureDefinition = StructureDefinition14_50.convertStructureDefinition(next);
if (next.getDerivation() != org.hl7.fhir.dstu2016may.model.StructureDefinition.TypeDerivationRule.CONSTRAINT) {
structureDefinition.setType(next.getName());
}
@ -408,7 +421,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent conceptDefinition = null;
if (theResult.asConceptDefinition() != null) {
try {
conceptDefinition = VersionConvertor_14_50.convertConceptDefinitionComponent(theResult.asConceptDefinition());
conceptDefinition = CodeSystem14_50.convertConceptDefinitionComponent(theResult.asConceptDefinition());
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -428,7 +441,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
public org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome expandVS(org.hl7.fhir.r5.model.ValueSet source, boolean cacheOk, boolean heiarchical) {
ValueSet convertedSource;
try {
convertedSource = VersionConvertor_14_50.convertValueSet(source);
convertedSource = ValueSet14_50.convertValueSet(source);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -437,7 +450,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
org.hl7.fhir.r5.model.ValueSet convertedResult = null;
if (expanded.getValueset() != null) {
try {
convertedResult = VersionConvertor_14_50.convertValueSet(expanded.getValueset());
convertedResult = ValueSet14_50.convertValueSet(expanded.getValueset());
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -458,7 +471,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
ValueSet.ConceptSetComponent convertedInc = null;
if (inc != null) {
try {
convertedInc = VersionConvertor_14_50.convertConceptSetComponent(inc);
convertedInc = ValueSet14_50.convertConceptSetComponent(inc);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -468,7 +481,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionComponent valueSetExpansionComponent = null;
if (expansion != null) {
try {
valueSetExpansionComponent = VersionConvertor_14_50.convertValueSetExpansionComponent(expansion);
valueSetExpansionComponent = ValueSet14_50.convertValueSetExpansionComponent(expansion);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -492,7 +505,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
return null;
}
try {
return VersionConvertor_14_50.convertCodeSystem(fetched);
return CodeSystem14_50.convertCodeSystem(fetched);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -572,6 +585,11 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
return fetchResource(org.hl7.fhir.r5.model.StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + typeName);
}
@Override
public org.hl7.fhir.r5.model.StructureDefinition fetchRawProfile(String url) {
return fetchResource(org.hl7.fhir.r5.model.StructureDefinition.class, url);
}
@Override
public List<String> getTypeNames() {
@ -665,7 +683,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
try {
if (vs != null) {
convertedVs = VersionConvertor_14_50.convertValueSet(vs);
convertedVs = ValueSet14_50.convertValueSet(vs);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);
@ -680,7 +698,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
ValueSet convertedVs = null;
try {
if (vs != null) {
convertedVs = VersionConvertor_14_50.convertValueSet(vs);
convertedVs = ValueSet14_50.convertValueSet(vs);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);
@ -700,7 +718,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
convertedCode = VersionConvertor_14_50.convertCoding(code);
}
if (vs != null) {
convertedVs = VersionConvertor_14_50.convertValueSet(vs);
convertedVs = ValueSet14_50.convertValueSet(vs);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);
@ -720,7 +738,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
convertedCode = VersionConvertor_14_50.convertCodeableConcept(code);
}
if (vs != null) {
convertedVs = VersionConvertor_14_50.convertValueSet(vs);
convertedVs = ValueSet14_50.convertValueSet(vs);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);

58
hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidator.java
View File

@ -23,6 +23,7 @@ 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.SearchParameter;
import org.hl7.fhir.dstu3.model.StructureDefinition;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.exceptions.FHIRException;
@ -56,6 +57,13 @@ import java.util.Map;
import java.util.Set;
import java.util.concurrent.TimeUnit;
import static org.hl7.fhir.convertors.conv30_50.CodeSystem30_50.convertCodeSystem;
import static org.hl7.fhir.convertors.conv30_50.CodeSystem30_50.convertConceptDefinitionComponent;
import static org.hl7.fhir.convertors.conv30_50.StructureDefinition30_50.convertStructureDefinition;
import static org.hl7.fhir.convertors.conv30_50.ValueSet30_50.convertConceptSetComponent;
import static org.hl7.fhir.convertors.conv30_50.ValueSet30_50.convertValueSet;
import static org.hl7.fhir.convertors.conv30_50.ValueSet30_50.convertValueSetExpansionComponent;
@SuppressWarnings({"PackageAccessibility", "Duplicates"})
public class FhirInstanceValidator extends BaseValidatorBridge implements IInstanceValidatorModule {
@ -66,10 +74,12 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
private StructureDefinition myStructureDefintion;
private IValidationSupport myValidationSupport;
private boolean noTerminologyChecks = false;
private IResourceValidator.IValidatorResourceFetcher validatorResourceFetcher;
private volatile WorkerContextWrapper myWrappedWorkerContext;
private boolean errorForUnknownProfiles;
private List<String> myExtensionDomains = Collections.emptyList();
private boolean assumeValidRestReferences;
/**
* Constructor
@ -285,10 +295,28 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
.setErrorForUnknownProfiles(isErrorForUnknownProfiles())
.setExtensionDomains(getExtensionDomains())
.setNoTerminologyChecks(isNoTerminologyChecks())
.setValidatorResourceFetcher(getValidatorResourceFetcher())
.setAssumeValidRestReferences(isAssumeValidRestReferences())
.validate(wrappedWorkerContext, theValidationCtx);
}
public IResourceValidator.IValidatorResourceFetcher getValidatorResourceFetcher() {
return validatorResourceFetcher;
}
public void setValidatorResourceFetcher(IResourceValidator.IValidatorResourceFetcher validatorResourceFetcher) {
this.validatorResourceFetcher = validatorResourceFetcher;
}
public boolean isAssumeValidRestReferences() {
return assumeValidRestReferences;
}
public void setAssumeValidRestReferences(boolean assumeValidRestReferences) {
this.assumeValidRestReferences = assumeValidRestReferences;
}
private static class WorkerContextWrapper implements IWorkerContext {
private final HapiWorkerContext myWrap;
@ -327,6 +355,9 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
case "ImplementationGuide":
fetched = myWrap.fetchResource(ImplementationGuide.class, key.getUri());
break;
case "SearchParameter":
fetched = myWrap.fetchResource(SearchParameter.class, key.getUri());
break;
default:
throw new UnsupportedOperationException("Don't know how to fetch " + key.getResourceName());
}
@ -386,7 +417,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
retVal = new ArrayList<>();
for (StructureDefinition next : myWrap.allStructures()) {
try {
retVal.add(VersionConvertor_30_50.convertStructureDefinition(next));
retVal.add(convertStructureDefinition(next));
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -416,7 +447,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent conceptDefinition = null;
if (theResult.asConceptDefinition() != null) {
try {
conceptDefinition = VersionConvertor_30_50.convertConceptDefinitionComponent(theResult.asConceptDefinition());
conceptDefinition = convertConceptDefinitionComponent(theResult.asConceptDefinition());
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -436,7 +467,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
public ValueSetExpander.ValueSetExpansionOutcome expandVS(org.hl7.fhir.r5.model.ValueSet source, boolean cacheOk, boolean heiarchical) {
ValueSet convertedSource;
try {
convertedSource = VersionConvertor_30_50.convertValueSet(source);
convertedSource = convertValueSet(source);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -445,7 +476,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
org.hl7.fhir.r5.model.ValueSet convertedResult = null;
if (expanded.getValueset() != null) {
try {
convertedResult = VersionConvertor_30_50.convertValueSet(expanded.getValueset());
convertedResult = convertValueSet(expanded.getValueset());
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -467,7 +498,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
ValueSet.ConceptSetComponent convertedInc = null;
if (inc != null) {
try {
convertedInc = VersionConvertor_30_50.convertConceptSetComponent(inc);
convertedInc = convertConceptSetComponent(inc);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -477,7 +508,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionComponent valueSetExpansionComponent = null;
if (expansion != null) {
try {
valueSetExpansionComponent = VersionConvertor_30_50.convertValueSetExpansionComponent(expansion);
valueSetExpansionComponent = convertValueSetExpansionComponent(expansion);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -495,7 +526,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
return null;
}
try {
return VersionConvertor_30_50.convertCodeSystem(fetched);
return convertCodeSystem(fetched);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -584,6 +615,11 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
return fetchResource(org.hl7.fhir.r5.model.StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + typeName);
}
@Override
public org.hl7.fhir.r5.model.StructureDefinition fetchRawProfile(String url) {
return fetchResource(org.hl7.fhir.r5.model.StructureDefinition.class, url);
}
@Override
public List<String> getTypeNames() {
return myWrap.getTypeNames();
@ -676,7 +712,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
try {
if (vs != null) {
convertedVs = VersionConvertor_30_50.convertValueSet(vs);
convertedVs = convertValueSet(vs);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);
@ -691,7 +727,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
ValueSet convertedVs = null;
try {
if (vs != null) {
convertedVs = VersionConvertor_30_50.convertValueSet(vs);
convertedVs = convertValueSet(vs);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);
@ -711,7 +747,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
convertedCode = VersionConvertor_30_50.convertCoding(code);
}
if (vs != null) {
convertedVs = VersionConvertor_30_50.convertValueSet(vs);
convertedVs = convertValueSet(vs);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);
@ -731,7 +767,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
convertedCode = VersionConvertor_30_50.convertCodeableConcept(code);
}
if (vs != null) {
convertedVs = VersionConvertor_30_50.convertValueSet(vs);
convertedVs = convertValueSet(vs);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);

86
hapi-fhir-validation/src/main/java/org/hl7/fhir/instance/hapi/validation/FhirInstanceValidator.java
View File

@ -27,12 +27,13 @@ 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.convertors.conv10_50.ValueSet10_50;
import org.hl7.fhir.convertors.conv14_50.CodeSystem14_50;
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;
@ -60,6 +61,7 @@ import java.io.IOException;
import java.io.InputStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
@ -69,6 +71,11 @@ import java.util.Set;
import java.util.concurrent.TimeUnit;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.hl7.fhir.convertors.VersionConvertor_10_50.convertCoding;
import static org.hl7.fhir.convertors.conv10_50.StructureDefinition10_50.convertStructureDefinition;
import static org.hl7.fhir.convertors.conv10_50.ValueSet10_50.convertConceptSetComponent;
import static org.hl7.fhir.convertors.conv10_50.ValueSet10_50.convertValueSet;
import static org.hl7.fhir.convertors.conv10_50.ValueSet10_50.convertValueSetExpansionComponent;
public class FhirInstanceValidator extends BaseValidatorBridge implements IInstanceValidatorModule {
@ -81,8 +88,19 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
private StructureDefinition myStructureDefintion;
private IValidationSupport myValidationSupport;
private boolean noTerminologyChecks = false;
public boolean isAssumeValidRestReferences() {
return assumeValidRestReferences;
}
public void setAssumeValidRestReferences(boolean assumeValidRestReferences) {
this.assumeValidRestReferences = assumeValidRestReferences;
}
private boolean assumeValidRestReferences;
private volatile WorkerContextWrapper myWrappedWorkerContext;
private VersionConvertorAdvisor50 myAdvisor = new NullVersionConverterAdvisor50();
private IResourceValidator.IValidatorResourceFetcher validatorResourceFetcher;
/**
* Constructor
@ -287,6 +305,8 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
v.setAnyExtensionsAllowed(isAnyExtensionsAllowed());
v.setResourceIdRule(IdStatus.OPTIONAL);
v.setNoTerminologyChecks(isNoTerminologyChecks());
v.setFetcher(getValidatorResourceFetcher());
v.setAssumeValidRestReferences(isAssumeValidRestReferences());
List<ValidationMessage> messages = new ArrayList<>();
@ -388,6 +408,14 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
return messages;
}
public IResourceValidator.IValidatorResourceFetcher getValidatorResourceFetcher() {
return validatorResourceFetcher;
}
public void setValidatorResourceFetcher(IResourceValidator.IValidatorResourceFetcher validatorResourceFetcher) {
this.validatorResourceFetcher = validatorResourceFetcher;
}
@Override
protected List<ValidationMessage> validate(IValidationContext<?> theCtx) {
return validate(theCtx.getFhirContext(), theCtx.getResourceAsString(), theCtx.getResourceAsStringEncoding());
@ -428,7 +456,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
return null;
}
}
profileText = IOUtils.toString(inputStream, "UTF-8");
profileText = IOUtils.toString(inputStream, StandardCharsets.UTF_8);
} catch (IOException e1) {
if (theMessages != null) {
theMessages.add(new ValidationMessage().setLevel(IssueSeverity.FATAL)
@ -457,11 +485,17 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
case "StructureDefinition":
fetched = myWrap.fetchResource(StructureDefinition.class, key.getUri());
break;
case "CodeSystem":
case "ValueSet":
fetched = myWrap.fetchResource(ValueSet.class, key.getUri());
break;
case "CodeSystem":
fetched = myWrap.fetchResource(ValueSet.class, key.getUri());
ValueSet fetchedVs = (ValueSet) fetched;
if (!fetchedVs.hasCompose()) {
if (fetchedVs.hasCodeSystem()) {
fetchedVs.getCompose().addInclude().setSystem(fetchedVs.getCodeSystem().getSystem());
}
}
break;
case "Questionnaire":
fetched = myWrap.fetchResource(Questionnaire.class, key.getUri());
@ -477,7 +511,15 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
}
try {
org.hl7.fhir.r5.model.Resource converted = new VersionConvertor_10_50(myAdvisor).convertResource(fetched);
org.hl7.fhir.r5.model.Resource converted;
if ("CodeSystem".equals(key.getUri())) {
NullVersionConverterAdvisor50 advisor = new NullVersionConverterAdvisor50();
converted = ValueSet10_50.convertValueSet((ValueSet) fetched, advisor);
converted = advisor.getCodeSystem((org.hl7.fhir.r5.model.ValueSet) converted);
} else {
converted = VersionConvertor_10_50.convertResource(fetched);
}
if (fetched instanceof StructureDefinition) {
StructureDefinition fetchedSd = (StructureDefinition) fetched;
@ -501,7 +543,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
public WorkerContextWrapper(HapiWorkerContext theWorkerContext) {
myWrap = theWorkerContext;
myConverter = new VersionConvertor_10_50(myAdvisor);
myConverter = new VersionConvertor_10_50();
}
@Override
@ -510,7 +552,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
}
@Override
public void generateSnapshot(org.hl7.fhir.r5.model.StructureDefinition p) throws DefinitionException, FHIRException {
public void generateSnapshot(org.hl7.fhir.r5.model.StructureDefinition p) throws FHIRException {
}
@ -547,7 +589,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
retVal = new ArrayList<>();
for (StructureDefinition next : myWrap.allStructures()) {
try {
org.hl7.fhir.r5.model.StructureDefinition converted = new VersionConvertor_10_50(myAdvisor).convertStructureDefinition(next);
org.hl7.fhir.r5.model.StructureDefinition converted = convertStructureDefinition(next);
if (converted != null) {
retVal.add(converted);
}
@ -587,7 +629,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
public ValueSetExpander.ValueSetExpansionOutcome expandVS(org.hl7.fhir.r5.model.ValueSet source, boolean cacheOk, boolean heiarchical) {
ValueSet convertedSource = null;
try {
convertedSource = new VersionConvertor_10_50(myAdvisor).convertValueSet(source);
convertedSource = convertValueSet(source);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -596,7 +638,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
org.hl7.fhir.r5.model.ValueSet convertedResult = null;
if (expanded.getValueset() != null) {
try {
convertedResult = new VersionConvertor_10_50(myAdvisor).convertValueSet(expanded.getValueset());
convertedResult = convertValueSet(expanded.getValueset());
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -618,7 +660,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
ValueSet.ConceptSetComponent convertedInc = null;
if (inc != null) {
try {
convertedInc = new VersionConvertor_10_50(myAdvisor).convertConceptSetComponent(inc);
convertedInc = convertConceptSetComponent(inc);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -628,7 +670,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionComponent valueSetExpansionComponent = null;
if (expansion != null) {
try {
valueSetExpansionComponent = new VersionConvertor_10_50(myAdvisor).convertValueSetExpansionComponent(expansion);
valueSetExpansionComponent = convertValueSetExpansionComponent(expansion);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -733,6 +775,11 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
return fetchResource(org.hl7.fhir.r5.model.StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/"+typeName);
}
@Override
public org.hl7.fhir.r5.model.StructureDefinition fetchRawProfile(String url) {
return fetchResource(org.hl7.fhir.r5.model.StructureDefinition.class, url);
}
@Override
public void setUcumService(UcumService ucumService) {
throw new UnsupportedOperationException();
@ -825,7 +872,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
try {
if (vs != null) {
convertedVs = new VersionConvertor_10_50(myAdvisor).convertValueSet(vs);
convertedVs = convertValueSet(vs);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);
@ -840,8 +887,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
ValueSet convertedVs = null;
try {
if (vs != null) {
VersionConvertorAdvisor50 advisor50 = new NullVersionConverterAdvisor50();
convertedVs = new VersionConvertor_10_50(advisor50).convertValueSet(vs);
convertedVs = convertValueSet(vs);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);
@ -858,10 +904,10 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
try {
if (code != null) {
convertedCode = new VersionConvertor_10_50(myAdvisor).convertCoding(code);
convertedCode = convertCoding(code);
}
if (vs != null) {
convertedVs = new VersionConvertor_10_50(myAdvisor).convertValueSet(vs);
convertedVs = convertValueSet(vs);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);
@ -878,10 +924,10 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IInsta
try {
if (code != null) {
convertedCode = new VersionConvertor_10_50(myAdvisor).convertCodeableConcept(code);
convertedCode = VersionConvertor_10_50.convertCodeableConcept(code);
}
if (vs != null) {
convertedVs = new VersionConvertor_10_50(myAdvisor).convertValueSet(vs);
convertedVs = convertValueSet(vs);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);

10
hapi-fhir-validation/src/main/java/org/hl7/fhir/instance/hapi/validation/HapiWorkerContext.java
View File

@ -199,7 +199,7 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
nextSystem = nextComposeConceptSet.getSystem();
}
if (StringUtils.equals(nextSystem, nextComposeConceptSet.getSystem())) {
if (Constants.codeSystemNotNeeded(theSystem) || StringUtils.equals(nextSystem, nextComposeConceptSet.getSystem())) {
for (ConceptReferenceComponent nextComposeCode : nextComposeConceptSet.getConcept()) {
ConceptDefinitionComponent conceptDef = new ConceptDefinitionComponent();
conceptDef.setCode(nextComposeCode.getCode());
@ -211,7 +211,13 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
}
if (nextComposeConceptSet.getConcept().isEmpty()){
ValidationResult result = validateCode(nextSystem, theCode, null);
String validateSystem = nextSystem;
if (Constants.codeSystemNotNeeded(nextSystem)) {
validateSystem = nextComposeConceptSet.getSystem();
}
ValidationResult result = validateCode(validateSystem, theCode, null);
if (result.isOk()){
return result;
}

49
hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/FhirInstanceValidator.java
View File

@ -59,7 +59,8 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
private IValidationSupport myValidationSupport;
private boolean noTerminologyChecks = false;
private volatile WorkerContextWrapper myWrappedWorkerContext;
private IResourceValidator.IValidatorResourceFetcher validatorResourceFetcher;
private boolean assumeValidRestReferences;
private boolean errorForUnknownProfiles;
private List<String> extensionDomains = Collections.emptyList();
@ -225,13 +226,32 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
.setErrorForUnknownProfiles(isErrorForUnknownProfiles())
.setExtensionDomains(getExtensionDomains())
.setNoTerminologyChecks(isNoTerminologyChecks())
.setValidatorResourceFetcher(getValidatorResourceFetcher())
.setAssumeValidRestReferences(isAssumeValidRestReferences())
.validate(wrappedWorkerContext, theValidationCtx);
}
public IResourceValidator.IValidatorResourceFetcher getValidatorResourceFetcher() {
return validatorResourceFetcher;
}
public void setValidatorResourceFetcher(IResourceValidator.IValidatorResourceFetcher validatorResourceFetcher) {
this.validatorResourceFetcher = validatorResourceFetcher;
}
private List<String> getExtensionDomains() {
return extensionDomains;
}
public boolean isAssumeValidRestReferences() {
return assumeValidRestReferences;
}
public void setAssumeValidRestReferences(boolean assumeValidRestReferences) {
this.assumeValidRestReferences = assumeValidRestReferences;
}
private static class WorkerContextWrapper implements IWorkerContext {
private final HapiWorkerContext myWrap;
@ -317,7 +337,7 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
retVal = new ArrayList<>();
for (StructureDefinition next : myWrap.allStructures()) {
try {
retVal.add(org.hl7.fhir.convertors.conv40_50.StructureDefinition.convertStructureDefinition(next));
retVal.add(org.hl7.fhir.convertors.conv40_50.StructureDefinition40_50.convertStructureDefinition(next));
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -347,7 +367,7 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent conceptDefinition = null;
if (theResult.asConceptDefinition() != null) {
try {
conceptDefinition = org.hl7.fhir.convertors.conv40_50.CodeSystem.convertConceptDefinitionComponent(theResult.asConceptDefinition());
conceptDefinition = org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertConceptDefinitionComponent(theResult.asConceptDefinition());
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -367,7 +387,7 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
public ValueSetExpander.ValueSetExpansionOutcome expandVS(org.hl7.fhir.r5.model.ValueSet source, boolean cacheOk, boolean heiarchical) {
ValueSet convertedSource;
try {
convertedSource = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(source);
convertedSource = org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(source);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -376,7 +396,7 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
org.hl7.fhir.r5.model.ValueSet convertedResult = null;
if (expanded.getValueset() != null) {
try {
convertedResult = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(expanded.getValueset());
convertedResult = org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(expanded.getValueset());
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -398,7 +418,7 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
ValueSet.ConceptSetComponent convertedInc = null;
if (inc != null) {
try {
convertedInc = org.hl7.fhir.convertors.conv40_50.ValueSet.convertConceptSetComponent(inc);
convertedInc = org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertConceptSetComponent(inc);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -408,7 +428,7 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
org.hl7.fhir.r5.model.ValueSet valueSetExpansion = null;
if (expansion != null) {
try {
valueSetExpansion = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(expansion.getValueset());
valueSetExpansion = org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(expansion.getValueset());
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -424,7 +444,7 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
return null;
}
try {
return org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(fetched);
return org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem(fetched);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -509,6 +529,11 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
return fetchResource(org.hl7.fhir.r5.model.StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + typeName);
}
@Override
public org.hl7.fhir.r5.model.StructureDefinition fetchRawProfile(String url) {
return fetchResource(org.hl7.fhir.r5.model.StructureDefinition.class, url);
}
@Override
public List<String> getTypeNames() {
return myWrap.getTypeNames();
@ -605,7 +630,7 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
try {
if (vs != null) {
convertedVs = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(vs);
convertedVs = org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(vs);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);
@ -620,7 +645,7 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
ValueSet convertedVs = null;
try {
if (vs != null) {
convertedVs = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(vs);
convertedVs = org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(vs);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);
@ -640,7 +665,7 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
convertedCode = VersionConvertor_40_50.convertCoding(code);
}
if (vs != null) {
convertedVs = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(vs);
convertedVs = org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(vs);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);
@ -660,7 +685,7 @@ public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseV
convertedCode = VersionConvertor_40_50.convertCodeableConcept(code);
}
if (vs != null) {
convertedVs = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(vs);
convertedVs = org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(vs);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);

27
hapi-fhir-validation/src/main/java/org/hl7/fhir/r5/hapi/validation/FhirInstanceValidator.java
View File

@ -54,7 +54,9 @@ public class FhirInstanceValidator extends org.hl7.fhir.r5.hapi.validation.BaseV
private boolean noTerminologyChecks = false;
private volatile WorkerContextWrapper myWrappedWorkerContext;
private boolean errorForUnknownProfiles;
private boolean assumeValidRestReferences;
private List<String> myExtensionDomains = Collections.emptyList();
private IResourceValidator.IValidatorResourceFetcher validatorResourceFetcher;
/**
* Constructor
@ -220,9 +222,27 @@ public class FhirInstanceValidator extends org.hl7.fhir.r5.hapi.validation.BaseV
.setErrorForUnknownProfiles(isErrorForUnknownProfiles())
.setExtensionDomains(getExtensionDomains())
.setNoTerminologyChecks(isNoTerminologyChecks())
.setValidatorResourceFetcher(getValidatorResourceFetcher())
.setAssumeValidRestReferences(isAssumeValidRestReferences())
.validate(wrappedWorkerContext, theValidationCtx);
}
public IResourceValidator.IValidatorResourceFetcher getValidatorResourceFetcher() {
return validatorResourceFetcher;
}
public void setValidatorResourceFetcher(IResourceValidator.IValidatorResourceFetcher validatorResourceFetcher) {
this.validatorResourceFetcher = validatorResourceFetcher;
}
public boolean isAssumeValidRestReferences() {
return assumeValidRestReferences;
}
public void setAssumeValidRestReferences(boolean assumeValidRestReferences) {
this.assumeValidRestReferences = assumeValidRestReferences;
}
private static class WorkerContextWrapper implements IWorkerContext {
private final HapiWorkerContext myWrap;
@ -514,6 +534,11 @@ public class FhirInstanceValidator extends org.hl7.fhir.r5.hapi.validation.BaseV
return fetchResource(org.hl7.fhir.r5.model.StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + typeName);
}
@Override
public StructureDefinition fetchRawProfile(String url) {
return myWrap.fetchRawProfile(url);
}
@Override
public List<String> getTypeNames() {
return myWrap.getTypeNames();
@ -706,7 +731,7 @@ public class FhirInstanceValidator extends org.hl7.fhir.r5.hapi.validation.BaseV
}
@Override
public Base resolveReference(Object appContext, String url) throws FHIRException {
public Base resolveReference(Object appContext, String url, Base refContext) throws FHIRException {
return null;
}

21
hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidatorDstu3Test.java
View File

@ -24,10 +24,12 @@ import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.dstu3.utils.FHIRPathEngine;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.junit.*;
import org.junit.rules.TestRule;
import org.junit.rules.TestWatcher;
import org.junit.runner.Description;
import org.mockito.internal.matchers.Any;
import org.mockito.invocation.InvocationOnMock;
import org.mockito.stubbing.Answer;
@ -41,8 +43,7 @@ import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.nullable;
import static org.mockito.Matchers.any;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
import static org.mockito.Mockito.*;
public class FhirInstanceValidatorDstu3Test {
@ -975,7 +976,7 @@ public class FhirInstanceValidatorDstu3Test {
myInstanceVal.setValidationSupport(myMockSupport);
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertThat(errors.toString(), containsString("StructureDefinition reference \"http://foo/structuredefinition/myprofile\" could not be resolved"));
assertThat(errors.toString(), containsString("Profile reference 'http://foo/structuredefinition/myprofile' could not be resolved, so has not been checked"));
}
@Test
@ -1145,6 +1146,20 @@ public class FhirInstanceValidatorDstu3Test {
ourLog.info(output.getMessages().get(0).getMessage());
}
@Test
public void testInvocationOfValidatorFetcher() throws IOException {
String input = IOUtils.toString(FhirInstanceValidatorDstu3Test.class.getResourceAsStream("/dstu3-rick-test.json"), Charsets.UTF_8);
IResourceValidator.IValidatorResourceFetcher resourceFetcher = mock(IResourceValidator.IValidatorResourceFetcher.class);
when(resourceFetcher.validationPolicy(any(),anyString(), anyString())).thenReturn(IResourceValidator.ReferenceValidationPolicy.CHECK_TYPE_IF_EXISTS);
myInstanceVal.setValidatorResourceFetcher(resourceFetcher);
myVal.validateWithResult(input);
verify(resourceFetcher, times(3)).resolveURL(any(), anyString(), anyString());
verify(resourceFetcher, times(4)).validationPolicy(any(), anyString(), anyString());
verify(resourceFetcher, times(4)).fetch(any(), anyString());
}
@Test
public void testValueWithWhitespace() throws IOException {
String input = IOUtils.toString(FhirInstanceValidatorDstu3Test.class.getResourceAsStream("/dstu3-rick-test.json"), Charsets.UTF_8);

2
hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/QuestionnaireResponseValidatorDstu3Test.java
View File

@ -704,7 +704,7 @@ public class QuestionnaireResponseValidatorDstu3Test {
coding.setCode("1293");
QuestionnaireResponseItemAnswerComponent answer = qrItem.addAnswer();
answer.setValue(coding);
coding.addExtension("http://hl7.org/fhir/StructureDefinition/questionnaire-hidden", new BooleanType(true));
coding.addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-CO-value", new DecimalType("1.0"));
qr.addItem().setLinkId("2B").addAnswer().setValue(new BooleanType(true));
String reference = qr.getQuestionnaire().getReference();

3
hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/QuestionnaireValidatorDstu3Test.java
View File

@ -20,6 +20,7 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.Collections;
import java.util.stream.Collectors;
import static org.hamcrest.CoreMatchers.containsString;
import static org.junit.Assert.assertEquals;
@ -71,7 +72,7 @@ public class QuestionnaireValidatorDstu3Test {
ValidationResult errors = myVal.validateWithResult(q);
ourLog.info(errors.toString());
assertThat(errors.isSuccessful(), Matchers.is(true));
assertThat(errors.getMessages(), Matchers.empty());
assertThat(errors.getMessages().stream().filter(t->t.getSeverity().ordinal() > ResultSeverityEnum.INFORMATION.ordinal()).collect(Collectors.toList()), Matchers.empty());
}
}

36
hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java
View File

@ -66,9 +66,10 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import static org.mockito.ArgumentMatchers.nullable;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
import static org.mockito.ArgumentMatchers.*;
import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.Mockito.*;
import static org.mockito.Mockito.times;
public class FhirInstanceValidatorR4Test extends BaseTest {
@ -397,7 +398,11 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
ValidationResult output = myVal.validateWithResult(encoded);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertEquals(46, errors.size());
errors = errors
.stream()
.filter(t->t.getMessage().contains("Bundle entry missing fullUrl"))
.collect(Collectors.toList());
assertEquals(5, errors.size());
}
@Test
@ -633,8 +638,8 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
CachingValidationSupport support = new CachingValidationSupport(new ValidationSupportChain(defaultSupport, valSupport));
// Prepopulate SDs
valSupport.addStructureDefinition(loadStructureDefinition(defaultSupport, "/dstu3/myconsent-profile.xml"));
valSupport.addStructureDefinition(loadStructureDefinition(defaultSupport, "/dstu3/myconsent-ext.xml"));
valSupport.addStructureDefinition(loadStructureDefinition(defaultSupport, "/r4/myconsent-profile.xml"));
valSupport.addStructureDefinition(loadStructureDefinition(defaultSupport, "/r4/myconsent-ext.xml"));
FhirValidator val = ourCtx.newValidator();
val.registerValidatorModule(new FhirInstanceValidator(support));
@ -652,6 +657,8 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
.setSystem("http://terminology.hl7.org/CodeSystem/consentcategorycodes")
.setCode("acd");
// Should pass
ValidationResult output = val.validateWithResult(input);
List<SingleValidationMessage> all = logResultsAndReturnErrorOnes(output);
@ -1031,7 +1038,7 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
myInstanceVal.setValidationSupport(myMockSupport);
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertThat(errors.toString(), containsString("StructureDefinition reference \"http://foo/structuredefinition/myprofile\" could not be resolved"));
assertThat(errors.toString(), containsString("Profile reference 'http://foo/structuredefinition/myprofile' could not be resolved, so has not been checked"));
}
@Test
@ -1250,6 +1257,21 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
assertEquals(0, all.size());
}
@Test
public void testInvocationOfValidatorFetcher() throws IOException {
String encoded = loadResource("/r4/r4-caredove-bundle.json");
IResourceValidator.IValidatorResourceFetcher resourceFetcher = mock(IResourceValidator.IValidatorResourceFetcher.class);
when(resourceFetcher.validationPolicy(any(),anyString(), anyString())).thenReturn(IResourceValidator.ReferenceValidationPolicy.CHECK_TYPE_IF_EXISTS);
myInstanceVal.setValidatorResourceFetcher(resourceFetcher);
myVal.validateWithResult(encoded);
verify(resourceFetcher, times(14)).resolveURL(any(), anyString(), anyString());
verify(resourceFetcher, times(12)).validationPolicy(any(), anyString(), anyString());
verify(resourceFetcher, times(12)).fetch(any(), anyString());
}
@Test
@Ignore
public void testValidateStructureDefinition() throws IOException {

4
hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/QuestionnaireValidatorR4Test.java
View File

@ -23,6 +23,8 @@ import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.stream.Collectors;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.mockito.Mockito.mock;
@ -72,7 +74,7 @@ public class QuestionnaireValidatorR4Test {
ValidationResult errors = myVal.validateWithResult(q);
ourLog.info(errors.toString());
assertThat(errors.isSuccessful(), Matchers.is(true));
assertThat(errors.getMessages(), Matchers.empty());
assertThat(errors.getMessages().stream().filter(t->t.getSeverity().ordinal() > ResultSeverityEnum.INFORMATION.ordinal()).collect(Collectors.toList()), Matchers.empty());
}
}

26
hapi-fhir-validation/src/test/java/org/hl7/fhir/r5/validation/FhirInstanceValidatorR5Test.java
View File

@ -53,9 +53,10 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import static org.mockito.ArgumentMatchers.nullable;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
import static org.mockito.ArgumentMatchers.*;
import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.Mockito.*;
import static org.mockito.Mockito.times;
public class FhirInstanceValidatorR5Test {
@ -415,6 +416,23 @@ public class FhirInstanceValidatorR5Test {
assertThat(nonInfo, empty());
}
@Test
public void testInvocationOfValidatorFetcher() throws IOException {
String input = IOUtils.toString(FhirInstanceValidator.class.getResourceAsStream("/vitals.json"), Charsets.UTF_8);
IResourceValidator.IValidatorResourceFetcher resourceFetcher = mock(IResourceValidator.IValidatorResourceFetcher.class);
when(resourceFetcher.validationPolicy(any(),anyString(), anyString())).thenReturn(IResourceValidator.ReferenceValidationPolicy.CHECK_TYPE_IF_EXISTS);
myInstanceVal.setValidatorResourceFetcher(resourceFetcher);
myVal.validateWithResult(input);
verify(resourceFetcher, times(12)).resolveURL(any(), anyString(), anyString());
verify(resourceFetcher, times(3)).validationPolicy(any(), anyString(), anyString());
verify(resourceFetcher, times(3)).fetch(any(), anyString());
}
@Test
public void testIsNoTerminologyChecks() {
assertFalse(myInstanceVal.isNoTerminologyChecks());
@ -774,7 +792,7 @@ public class FhirInstanceValidatorR5Test {
myInstanceVal.setValidationSupport(myMockSupport);
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertThat(errors.toString(), containsString("StructureDefinition reference \"http://foo/structuredefinition/myprofile\" could not be resolved"));
assertThat(errors.toString(), containsString("Profile reference 'http://foo/structuredefinition/myprofile' could not be resolved, so has not been checked"));
}
@Test

34
hapi-fhir-validation/src/test/resources/r4/myconsent-ext.xml Normal file
View File

@ -0,0 +1,34 @@
<StructureDefinition xmlns="http://hl7.org/fhir">
<id value="PruebaExtension" />
<meta>
<lastUpdated value="2017-12-19T16:53:11.296+01:00" />
</meta>
<url value="http://hl7.org/fhir/StructureDefinition/PruebaExtension" />
<name value="PruebaExtension" />
<status value="draft" />
<date value="2017-12-19T16:51:07.089+01:00" />
<fhirVersion value="3.0.1" />
<kind value="complex-type" />
<abstract value="false" />
<context>
<type value="fhirpath" />
<expression value="Consent" />
</context>
<type value="Extension" />
<baseDefinition value="http://hl7.org/fhir/StructureDefinition/Extension" />
<derivation value="constraint" />
<differential>
<element id="Extension.url">
<path value="Extension.url" />
<fixedUri value="http://hl7.org/fhir/StructureDefinition/PruebaExtension" />
</element>
<element id="Extension.value[x]:valueString">
<path value="Extension.valueString" />
<sliceName value="valueString" />
<min value="1" />
<type>
<code value="string" />
</type>
</element>
</differential>
</StructureDefinition>

42
hapi-fhir-validation/src/test/resources/r4/myconsent-profile.xml Normal file
View File

@ -0,0 +1,42 @@
<StructureDefinition xmlns="http://hl7.org/fhir">
<id value="Consent" />
<meta>
<lastUpdated value="2017-12-21T17:22:27.087+01:00" />
</meta>
<url value="http://hl7.org/fhir/StructureDefinition/MyConsent" />
<name value="Consent" />
<status value="draft" />
<date value="2017-12-19T09:08:41.006+01:00" />
<description value="prueba&#xD;&#xA;" />
<fhirVersion value="3.0.1" />
<kind value="resource" />
<abstract value="false" />
<type value="Consent" />
<baseDefinition value="http://hl7.org/fhir/StructureDefinition/Consent" />
<derivation value="constraint" />
<differential>
<element id="Consent.extension">
<path value="Consent.extension" />
<slicing>
<discriminator>
<type value="value" />
<path value="url" />
</discriminator>
<rules value="open" />
</slicing>
</element>
<element id="Consent.extension:pruebaExtension">
<path value="Consent.extension" />
<sliceName value="pruebaExtension" />
<min value="1" />
<type>
<code value="Extension" />
<profile value="http://hl7.org/fhir/StructureDefinition/PruebaExtension" />
</type>
</element>
<element id="Consent.identifier">
<path value="Consent.identifier" />
<min value="1" />
</element>
</differential>
</StructureDefinition>

97
hapi-fhir-validation/src/test/resources/vitals.json Normal file
View File

@ -0,0 +1,97 @@
{
"resourceType": "Observation",
"id": "satO2",
"meta": {
"profile": [
"http://hl7.org/fhir/StructureDefinition/vitalsigns"
]
},
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: satO2</p><p><b>meta</b>: </p><p><b>identifier</b>: o1223435-10</p><p><b>partOf</b>: <a>Procedure/ob</a></p><p><b>status</b>: final</p><p><b>category</b>: Vital Signs <span>(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'vital-signs' = 'Vital Signs', given as 'Vital Signs'})</span></p><p><b>code</b>: Oxygen saturation in Arterial blood <span>(Details : {LOINC code '2708-6' = 'Oxygen saturation in Arterial blood', given as 'Oxygen saturation in Arterial blood'}; {LOINC code '59408-5' = 'Oxygen saturation in Arterial blood by Pulse oximetry', given as 'Oxygen saturation in Arterial blood by Pulse oximetry'}; {urn:iso:std:iso:11073:10101 code '150456' = '150456', given as 'MDC_PULS_OXIM_SAT_O2'})</span></p><p><b>subject</b>: <a>Patient/example</a></p><p><b>effective</b>: Dec 5, 2014 9:30:10 AM</p><p><b>value</b>: 95 %<span> (Details: UCUM code % = '%')</span></p><p><b>interpretation</b>: Normal (applies to non-numeric results) <span>(Details : {http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation code 'N' = 'Normal', given as 'Normal'})</span></p><p><b>device</b>: <a>DeviceMetric/example</a></p><h3>ReferenceRanges</h3><table><tr><td>-</td><td><b>Low</b></td><td><b>High</b></td></tr><tr><td>*</td><td>90 %<span> (Details: UCUM code % = '%')</span></td><td>99 %<span> (Details: UCUM code % = '%')</span></td></tr></table></div>"
},
"identifier": [
{
"system": "http://goodcare.org/observation/id",
"value": "o1223435-10"
}
],
"partOf": [
{
"reference": "Procedure/ob"
}
],
"status": "final",
"category": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "vital-signs",
"display": "Vital Signs"
}
],
"text": "Vital Signs"
}
],
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "2708-6",
"display": "Oxygen saturation in Arterial blood"
},
{
"system": "http://loinc.org",
"code": "59408-5",
"display": "Oxygen saturation in Arterial blood by Pulse oximetry"
},
{
"system": "urn:iso:std:iso:11073:10101",
"code": "150456",
"display": "MDC_PULS_OXIM_SAT_O2"
}
]
},
"subject": {
"reference": "Patient/example"
},
"effectiveDateTime": "2014-12-05T09:30:10+01:00",
"valueQuantity": {
"value": 95,
"unit": "%",
"system": "http://unitsofmeasure.org",
"code": "%"
},
"interpretation": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation",
"code": "N",
"display": "Normal"
}
],
"text": "Normal (applies to non-numeric results)"
}
],
"device": {
"reference": "DeviceMetric/example"
},
"referenceRange": [
{
"low": {
"value": 90,
"unit": "%",
"system": "http://unitsofmeasure.org",
"code": "%"
},
"high": {
"value": 99,
"unit": "%",
"system": "http://unitsofmeasure.org",
"code": "%"
}
}
]
}

2
pom.xml
View File

@ -606,7 +606,7 @@
<properties>
<fhir_core_version>4.2.0</fhir_core_version>
<fhir_core_version>4.2.1-SNAPSHOT</fhir_core_version>
<ucum_version>1.0.2</ucum_version>
<surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx2048m</surefire_jvm_args>