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Merge branch 'master' into issue-2901-npe-in-bundle-transaction

This commit is contained in:
leif stawnyczy 2021-09-02 10:13:04 -04:00
parent 4c90ffe975 aca354bd8d
commit 1a7b101d03
169 changed files with 2369 additions and 653 deletions
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2
hapi-deployable-pom/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-android/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

16
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/IValidationSupport.java
View File

@ -266,12 +266,26 @@ public interface IValidationSupport {
* other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
* @param theSystem The CodeSystem URL
* @param theCode The code
* @param theDisplayLanguage to filter out the designation by the display language, to return all designation, the this value to null
*/
@Nullable
default LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
default LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theDisplayLanguage) {
return null;
}
/**
* Look up a code using the system and code value
*
* @param theValidationSupportContext The validation support module will be passed in to this method. This is convenient in cases where the operation needs to make calls to
* other method in the support chain, so that they can be passed through the entire chain. Implementations of this interface may always safely ignore this parameter.
* @param theSystem The CodeSystem URL
* @param theCode The code
*/
@Nullable
default LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
return lookupCode(theValidationSupportContext, theSystem, theCode, null);
}
/**
* Returns <code>true</code> if the given valueset can be validated by the given
* validation support module

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/SearchContainedModeEnum.java
View File

@ -51,7 +51,7 @@ public enum SearchContainedModeEnum {
myCode = theCode;
}
private String getCode() {
public String getCode() {
return myCode;
}

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

@ -75,7 +75,9 @@ public enum VersionEnum {
V5_4_1,
V5_4_2,
V5_5_0,
V5_5_1,
V5_6_0
;
public static VersionEnum latestVersion() {

4
hapi-fhir-bom/pom.xml
View File

@ -3,14 +3,14 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -26,6 +26,7 @@ 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.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.ConceptMap;
@ -42,7 +43,6 @@ 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.
@ -110,7 +110,7 @@ public class ExportConceptMapToCsvCommand extends AbstractImportExportCsvConcept
private void convertConceptMapToCsv(org.hl7.fhir.dstu3.model.ConceptMap theConceptMap) throws ExecutionException {
try {
convertConceptMapToCsv(convertConceptMap(theConceptMap));
convertConceptMapToCsv((ConceptMap) VersionConvertorFactory_30_40.convertResource(theConceptMap));
} catch (FHIRException fe) {
throw new ExecutionException(fe);
}

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

@ -28,6 +28,7 @@ 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.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ConceptMap.ConceptMapGroupComponent;
@ -47,7 +48,6 @@ import java.util.concurrent.ExecutionException;
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.
@ -152,7 +152,7 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
private org.hl7.fhir.dstu3.model.ConceptMap convertCsvToConceptMapDstu3() throws ExecutionException {
try {
return convertConceptMap(convertCsvToConceptMapR4());
return (org.hl7.fhir.dstu3.model.ConceptMap) VersionConvertorFactory_30_40.convertResource(convertCsvToConceptMapR4());
} catch (FHIRException fe) {
throw new ExecutionException(fe);
}

2
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>

2
hapi-fhir-cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-client-okhttp/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-client/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

12
hapi-fhir-converter/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -207,6 +207,16 @@
<artifactId>commons-compress</artifactId>
<version>${commons_compress_version}</version>
</dependency>
<dependency>
<groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId>
<version>1.18.16</version>
</dependency>
<dependency>
<groupId>org.jetbrains</groupId>
<artifactId>annotations</artifactId>
<version>22.0.0</version>
</dependency>
</additionalDependencies>
</configuration>
</plugin>

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

@ -29,11 +29,11 @@ import ca.uhn.fhir.rest.api.server.ResponseDetails;
import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
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.VersionConvertor_10_30;
import org.hl7.fhir.convertors.VersionConvertor_10_40;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.converter.NullVersionConverterAdvisor10_30;
import org.hl7.fhir.converter.NullVersionConverterAdvisor10_40;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_30;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_40;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -42,9 +42,7 @@ import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.util.StringTokenizer;
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.apache.commons.lang3.StringUtils.*;
/**
* <b>This is an experimental interceptor! Use with caution as
@ -58,12 +56,12 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class VersionedApiConverterInterceptor extends InterceptorAdapter {
private final FhirContext myCtxDstu2;
private final FhirContext myCtxDstu2Hl7Org;
private final NullVersionConverterAdvisor40 advisor40;
private final NullVersionConverterAdvisor30 advisor30;
private final NullVersionConverterAdvisor10_40 advisor40;
private final NullVersionConverterAdvisor10_30 advisor30;
public VersionedApiConverterInterceptor() {
advisor40 = new NullVersionConverterAdvisor40();
advisor30 = new NullVersionConverterAdvisor30();
advisor40 = new NullVersionConverterAdvisor10_40();
advisor30 = new NullVersionConverterAdvisor10_30();
myCtxDstu2 = FhirContext.forDstu2();
myCtxDstu2Hl7Org = FhirContext.forDstu2Hl7Org();
@ -104,17 +102,17 @@ public class VersionedApiConverterInterceptor extends InterceptorAdapter {
IBaseResource converted = null;
try {
if (wantVersion == FhirVersionEnum.R4 && haveVersion == FhirVersionEnum.DSTU3) {
converted = VersionConvertor_30_40.convertResource(toDstu3(responseResource), true);
converted = VersionConvertorFactory_30_40.convertResource(toDstu3(responseResource));
} else if (wantVersion == FhirVersionEnum.DSTU3 && haveVersion == FhirVersionEnum.R4) {
converted = VersionConvertor_30_40.convertResource(toR4(responseResource), true);
converted = VersionConvertorFactory_30_40.convertResource(toR4(responseResource));
} else if (wantVersion == FhirVersionEnum.DSTU2 && haveVersion == FhirVersionEnum.R4) {
converted = VersionConvertor_10_40.convertResource(toR4(responseResource), advisor40);
converted = VersionConvertorFactory_10_40.convertResource(toR4(responseResource), advisor40);
} else if (wantVersion == FhirVersionEnum.R4 && haveVersion == FhirVersionEnum.DSTU2) {
converted = VersionConvertor_10_40.convertResource(toDstu2(responseResource), advisor40);
converted = VersionConvertorFactory_10_40.convertResource(toDstu2(responseResource), advisor40);
} else if (wantVersion == FhirVersionEnum.DSTU2 && haveVersion == FhirVersionEnum.DSTU3) {
converted = VersionConvertor_10_30.convertResource(toDstu3(responseResource), advisor30);
converted = VersionConvertorFactory_10_30.convertResource(toDstu3(responseResource), advisor30);
} else if (wantVersion == FhirVersionEnum.DSTU3 && haveVersion == FhirVersionEnum.DSTU2) {
converted = VersionConvertor_10_30.convertResource(toDstu2(responseResource), advisor30);
converted = VersionConvertorFactory_10_30.convertResource(toDstu2(responseResource), advisor30);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);

5
hapi-fhir-converter/src/main/java/org/hl7/fhir/converter/NullVersionConverterAdvisor30.java → hapi-fhir-converter/src/main/java/org/hl7/fhir/converter/NullVersionConverterAdvisor10_30.java
View File

@ -20,8 +20,7 @@ package org.hl7.fhir.converter;
* #L%
*/
import org.hl7.fhir.convertors.advisors.VersionConvertorAdvisor30;
import org.hl7.fhir.dstu2.model.Resource;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_10_30;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.ValueSet;
@ -31,7 +30,7 @@ import org.hl7.fhir.r5.model.FhirPublication;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
public class NullVersionConverterAdvisor30 implements VersionConvertorAdvisor30 {
public class NullVersionConverterAdvisor10_30 extends BaseAdvisor_10_30 {
@Nullable

5
hapi-fhir-converter/src/main/java/org/hl7/fhir/converter/NullVersionConverterAdvisor40.java → hapi-fhir-converter/src/main/java/org/hl7/fhir/converter/NullVersionConverterAdvisor10_40.java
View File

@ -20,8 +20,7 @@ package org.hl7.fhir.converter;
* #L%
*/
import org.hl7.fhir.convertors.advisors.VersionConvertorAdvisor40;
import org.hl7.fhir.dstu2.model.Resource;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_10_40;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.CodeSystem;
@ -31,7 +30,7 @@ import org.hl7.fhir.r5.model.FhirPublication;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
public class NullVersionConverterAdvisor40 implements VersionConvertorAdvisor40 {
public class NullVersionConverterAdvisor10_40 extends BaseAdvisor_10_40 {
@Nullable

6
hapi-fhir-converter/src/main/java/org/hl7/fhir/converter/NullVersionConverterAdvisor50.java → hapi-fhir-converter/src/main/java/org/hl7/fhir/converter/NullVersionConverterAdvisor10_50.java
View File

@ -20,8 +20,8 @@ package org.hl7.fhir.converter;
* #L%
*/
import org.hl7.fhir.convertors.advisors.VersionConvertorAdvisor50;
import org.hl7.fhir.dstu2.model.Resource;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_10_50;
import org.hl7.fhir.convertors.conv10_50.VersionConvertor_10_50;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CodeSystem;
@ -32,7 +32,7 @@ import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.util.IdentityHashMap;
public class NullVersionConverterAdvisor50 implements VersionConvertorAdvisor50 {
public class NullVersionConverterAdvisor10_50 extends BaseAdvisor_10_50 {
private IdentityHashMap<ValueSet, CodeSystem> myCodeSystems = new IdentityHashMap<>();

6
hapi-fhir-converter/src/test/java/org/hl7/fhir/converter/VersionConvertor_10_30Test.java
View File

@ -2,7 +2,7 @@ package org.hl7.fhir.converter;
import static org.junit.jupiter.api.Assertions.assertEquals;
import org.hl7.fhir.convertors.VersionConvertor_10_30;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_30;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.dstu2.model.Resource;
@ -19,7 +19,7 @@ public class VersionConvertor_10_30Test {
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 = (Observation) VersionConvertor_10_30.convertResource(input);
org.hl7.fhir.dstu3.model.Observation output = (Observation) VersionConvertorFactory_10_30.convertResource(input);
String context = output.getContext().getReference();
assertEquals("Encounter/123", context);
@ -52,7 +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 = VersionConvertor_10_30.convertResource(spec);
Resource resource = VersionConvertorFactory_10_30.convertResource(spec);
}

4
hapi-fhir-converter/src/test/java/org/hl7/fhir/converter/VersionConvertor_14_30Test.java
View File

@ -2,7 +2,7 @@ package org.hl7.fhir.converter;
import static org.junit.jupiter.api.Assertions.assertEquals;
import org.hl7.fhir.convertors.VersionConvertor_14_30;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_14_30;
import org.hl7.fhir.dstu3.model.Questionnaire;
import org.hl7.fhir.exceptions.FHIRException;
import org.junit.jupiter.api.Test;
@ -15,7 +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 = (Questionnaire) VersionConvertor_14_30.convertResource(input);
org.hl7.fhir.dstu3.model.Questionnaire output = (Questionnaire) VersionConvertorFactory_14_30.convertResource(input);
String context = output.getTitle();
assertEquals("My title", context);

2
hapi-fhir-dist/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-docs/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

24
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ConverterExamples.java
View File

@ -20,36 +20,38 @@ package ca.uhn.hapi.fhir.docs;
* #L%
*/
import org.hl7.fhir.convertors.conv10_30.Observation10_30;
import org.hl7.fhir.convertors.conv14_30.Questionnaire14_30;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_30;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_14_30;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.Questionnaire;
import org.hl7.fhir.exceptions.FHIRException;
public class ConverterExamples {
@SuppressWarnings("unused")
public void c1020() throws FHIRException {
//START SNIPPET: 1020
//START SNIPPET: 1020
// 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 = Observation10_30.convertObservation(input);
org.hl7.fhir.dstu3.model.Observation output = (Observation) VersionConvertorFactory_10_30.convertResource(input);
String context = output.getContext().getReference();
//END SNIPPET: 1020
//END SNIPPET: 1020
}
@SuppressWarnings("unused")
public void c1420() throws FHIRException {
//START SNIPPET: 1420
//START SNIPPET: 1420
// Create a resource to convert
org.hl7.fhir.dstu2016may.model.Questionnaire input = new org.hl7.fhir.dstu2016may.model.Questionnaire();
input.setTitle("My title");
// Convert the resource
org.hl7.fhir.dstu3.model.Questionnaire output = Questionnaire14_30.convertQuestionnaire(input);
org.hl7.fhir.dstu3.model.Questionnaire output = (Questionnaire) VersionConvertorFactory_14_30.convertResource(input);
String context = output.getTitle();
//END SNIPPET: 1420
//END SNIPPET: 1420
}
}

2
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ValidatorExamples.java
View File

@ -299,7 +299,7 @@ public class ValidatorExamples {
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theDisplayLanguage) {
// TODO: implement (or return null if your implementation does not support this function)
return null;
}

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2868-bug-in-conditional-create.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 2868
jira: SMILE-1153
title: "Fixed a bug in transaction bundle processing, specifically for bundles which contained both a conditional create, and a resource which relied on this conditional create as a reference.
This would cause the referring resource to generate a contained resource instead of appropriately referencing the existing patient."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2871-enhance-mdm-expansion.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: add
issue: 2871
title: "Modified the behaviour of the `:mdm` param qualifier. Previously, it used to only resolve IDs if the resource ID was a source resource.
Now, MDM expansion will work if you pass it the ID of a golden resource instead."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_0/2887-contained-ignored-for-cache-key-purposes.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 2887
jira: SMILE-2896
title: "Fixed a bug where the search results cache was ignoring the value of `_contained` parameter when assigning a cache key.
This was causing queries run in a short period of time to return wrong cached results if one query used `_contained=true` and the other did not."

3
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_5_1/version.yaml Normal file
View File

@ -0,0 +1,3 @@
---
release-date: "2021-08-30"
codename: "Quasar"

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2793-expunge-everything-purges-caches.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: fix
issue: 2793
title: "Previously, when using the Expunge Everything operation, caches could retain old invalid values. This has been corrected. Thanks to [Ben Li-Sauerwine](https://github.com/theGOTOguy) for the fix!"

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2837-search-with-not-modifier-on-multiple-codes.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: fix
issue: 2837
title: "The :not modifier does not currently work for observations with multiple codes for the search. This is fixed."

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2902-includes-includes-on-revincludes.yaml
View File

@ -2,5 +2,4 @@
type: fix
issue: 2902
jira: SMILE-3000
backport: cust_fmc_5_3
title: "Fixed a bug wherein includes were not being included on revincludes."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2904-swagger-ui-Does-not-work-with-partitions.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: change
issue: 2904
title: "Change getPathItem method in OpenApiInterceptor from private to protected"

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2905-lookup-display-language.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: add
issue: 2905
title: "Added displayLanguage support for CodeSystem $lookup operation to filter out designation by language."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2920-lookup-language-by-lang-only.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 2920
jira: SMILE-2971
title: "Previously, validation against bcp47 (urn:ietf:bcp:47) as a language would fail validation if the region was absent. This has been fixed, and the validate
operation will now correctly validate simple languages, e.g. `nl` instead of requiring `nl-DE` or `nl-NL`"

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2932-lookup-display-language-cache-issue.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: fix
issue: 2923
title: "$lookup operation cache was based on system and code, it becomes a defect
after adding displayLanguage support. Problem is now fixed."

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2933-fix-double-conditional-create.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: add
issue: 2933
backport: 5.5.1
jira: SMILE-3056
title: "Fixed a regression which causes transactions with multiple identical ifNoneExist clauses to create duplicate data."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2935-Search-with-trailing-percent-sign.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: fix
issue: 2935
jira: SMILE-3022
title: "No resource returned when search with percent sign. Problem is now fixed"

2
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/files.properties
View File

@ -38,7 +38,7 @@ section.server_plain.title=Plain Server
page.server_plain.server_types=REST Server Types
page.server_plain.introduction=Plain Server Introduction
page.server_plain.get_started=Get Started ⚡
page.server_plain.resource_providers=Resource Providers and Plan Providers
page.server_plain.resource_providers=Resource Providers and Plain Providers
page.server_plain.rest_operations=REST Operations: Overview
page.server_plain.rest_operations_search=REST Operations: Search
page.server_plain.rest_operations_operations=REST Operations: Extended Operations

2
hapi-fhir-jacoco/pom.xml
View File

@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jaxrsserver-base/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-api/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

3
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDaoCodeSystem.java
View File

@ -40,6 +40,9 @@ public interface IFhirResourceDaoCodeSystem<T extends IBaseResource, CD, CC> ext
@Nonnull
IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, CD theCoding, RequestDetails theRequestDetails);
@Nonnull
IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, CD theCoding, IPrimitiveType<String> theDisplayLanguage, RequestDetails theRequestDetails);
SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, CD theCodingA, CD theCodingB, RequestDetails theRequestDetails);
IValidationSupport.CodeValidationResult validateCode(IIdType theCodeSystemId, IPrimitiveType<String> theCodeSystemUrl, IPrimitiveType<String> theVersion, IPrimitiveType<String> theCode, IPrimitiveType<String> theDisplay, CD theCoding, CC theCodeableConcept, RequestDetails theRequestDetails);

2
hapi-fhir-jpaserver-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.6.0-PRE1-SNAPSHOT</version>
<version>5.6.0-PRE2-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/CommonBatchJobConfig.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.batch;
import ca.uhn.fhir.jpa.batch.processor.GoldenResourceAnnotatingProcessor;
import ca.uhn.fhir.jpa.batch.processor.PidToIBaseResourceProcessor;
import ca.uhn.fhir.jpa.reindex.job.ReindexWriter;
import org.springframework.batch.core.configuration.annotation.StepScope;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@ -41,4 +42,10 @@ public class CommonBatchJobConfig {
return new GoldenResourceAnnotatingProcessor();
}
@Bean
@StepScope
public ReindexWriter reindexWriter() {
return new ReindexWriter();
}
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/cache/ResourceVersionSvcDaoImpl.java vendored
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.cache;
* #L%
*/
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
@ -28,6 +29,7 @@ import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
@ -36,12 +38,15 @@ import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;
import static org.slf4j.LoggerFactory.getLogger;
/**
* This service builds a map of resource ids to versions based on a SearchParameterMap.
* It is used by the in-memory resource-version cache to detect when resource versions have been changed by remote processes.
*/
@Service
public class ResourceVersionSvcDaoImpl implements IResourceVersionSvc {
private static final Logger ourLog = getLogger(ResourceVersionSvcDaoImpl.class);
@Autowired
DaoRegistry myDaoRegistry;
@ -53,7 +58,11 @@ public class ResourceVersionSvcDaoImpl implements IResourceVersionSvc {
public ResourceVersionMap getVersionMap(String theResourceName, SearchParameterMap theSearchParamMap) {
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(theResourceName);
List<Long> matchingIds = dao.searchForIds(theSearchParamMap, new SystemRequestDetails()).stream()
if (ourLog.isDebugEnabled()) {
ourLog.debug("About to retrieve version map for resource type: {}", theResourceName);
}
List<Long> matchingIds = dao.searchForIds(theSearchParamMap, new SystemRequestDetails().setRequestPartitionId(RequestPartitionId.allPartitions())).stream()
.map(ResourcePersistentId::getIdAsLong)
.collect(Collectors.toList());

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

@ -94,6 +94,7 @@ import com.google.common.collect.Sets;
import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase;
@ -1162,10 +1163,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
validateResourceForStorage((T) theResource, entity);
}
}
String resourceType = myContext.getResourceType(theResource);
if (isNotBlank(entity.getResourceType()) && !entity.getResourceType().equals(resourceType)) {
throw new UnprocessableEntityException(
"Existing resource ID[" + entity.getIdDt().toUnqualifiedVersionless() + "] is of type[" + entity.getResourceType() + "] - Cannot update with [" + resourceType + "]");
if (!StringUtils.isBlank(entity.getResourceType())) {
validateIncomingResourceTypeMatchesExisting(theResource, entity);
}
}
@ -1206,7 +1205,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
if (thePerformIndexing || ((ResourceTable) theEntity).getVersion() == 1) {
newParams = new ResourceIndexedSearchParams();
//FIXME GGG: This is where the placeholder references end up getting created, deeeeeep down the stakc.
mySearchParamWithInlineReferencesExtractor.populateFromResource(newParams, theTransactionDetails, entity, theResource, existingParams, theRequest, thePerformIndexing);
changed = populateResourceIntoEntity(theTransactionDetails, theRequest, theResource, entity, true);
@ -1416,6 +1414,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
return entity;
}
private void validateIncomingResourceTypeMatchesExisting(IBaseResource theResource, ResourceTable entity) {
String resourceType = myContext.getResourceType(theResource);
if (!resourceType.equals(entity.getResourceType())) {
throw new UnprocessableEntityException(
"Existing resource ID[" + entity.getIdDt().toUnqualifiedVersionless() + "] is of type[" + entity.getResourceType() + "] - Cannot update with [" + resourceType + "]");
}
}
@Override
public ResourceTable updateInternal(RequestDetails theRequestDetails, T theResource, boolean thePerformIndexing, boolean theForceUpdateVersion,
IBasePersistedResource theEntity, IIdType theResourceId, IBaseResource theOldResource, TransactionDetails theTransactionDetails) {

55
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java
View File

@ -94,6 +94,8 @@ 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.core.task.SyncTaskExecutor;
import org.springframework.core.task.TaskExecutor;
import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
@ -154,11 +156,11 @@ public abstract class BaseTransactionProcessor {
@Autowired
private InMemoryResourceMatcher myInMemoryResourceMatcher;
private TaskExecutor myExecutor ;
@Autowired
private IAutoVersioningService myAutoVersioningService;
private ThreadPoolTaskExecutor myExecutor ;
@VisibleForTesting
public void setDaoConfig(DaoConfig theDaoConfig) {
myDaoConfig = theDaoConfig;
@ -176,16 +178,25 @@ public abstract class BaseTransactionProcessor {
@PostConstruct
public void start() {
ourLog.trace("Starting transaction processor");
myExecutor = new ThreadPoolTaskExecutor();
myExecutor.setThreadNamePrefix("bundle_batch_");
// For single thread set the value to 1
//myExecutor.setCorePoolSize(1);
//myExecutor.setMaxPoolSize(1);
myExecutor.setCorePoolSize(myDaoConfig.getBundleBatchPoolSize());
myExecutor.setMaxPoolSize(myDaoConfig.getBundleBatchMaxPoolSize());
myExecutor.setQueueCapacity(DaoConfig.DEFAULT_BUNDLE_BATCH_QUEUE_CAPACITY);
}
myExecutor.initialize();
private TaskExecutor getTaskExecutor() {
if (myExecutor == null) {
if (myDaoConfig.getBundleBatchPoolSize() > 1) {
ThreadPoolTaskExecutor executor = new ThreadPoolTaskExecutor();
executor.setThreadNamePrefix("bundle_batch_");
executor.setCorePoolSize(myDaoConfig.getBundleBatchPoolSize());
executor.setMaxPoolSize(myDaoConfig.getBundleBatchMaxPoolSize());
executor.setQueueCapacity(DaoConfig.DEFAULT_BUNDLE_BATCH_QUEUE_CAPACITY);
executor.initialize();
myExecutor = executor;
} else {
SyncTaskExecutor executor = new SyncTaskExecutor();
myExecutor = executor;
}
}
return myExecutor;
}
public <BUNDLE extends IBaseBundle> BUNDLE transaction(RequestDetails theRequestDetails, BUNDLE theRequest, boolean theNestedMode) {
@ -355,7 +366,7 @@ public abstract class BaseTransactionProcessor {
for (int i=0; i<requestEntriesSize; i++ ) {
nextRequestEntry = requestEntries.get(i);
BundleTask bundleTask = new BundleTask(completionLatch, theRequestDetails, responseMap, i, nextRequestEntry, theNestedMode);
myExecutor.submit(bundleTask);
getTaskExecutor().execute(bundleTask);
}
// waiting for all tasks to be completed
@ -854,6 +865,7 @@ public abstract class BaseTransactionProcessor {
String matchUrl = myVersionAdapter.getEntryRequestIfNoneExist(nextReqEntry);
matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
outcome = resourceDao.create(res, matchUrl, false, theTransactionDetails, theRequest);
res.setId(outcome.getId());
if (nextResourceId != null) {
handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequest);
}
@ -1047,13 +1059,9 @@ public abstract class BaseTransactionProcessor {
for (IIdType next : theAllIds) {
IIdType replacement = theIdSubstitutions.get(next);
if (replacement == null) {
continue;
if (replacement != null && !replacement.equals(next)) {
ourLog.debug("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
}
if (replacement.equals(next)) {
continue;
}
ourLog.debug("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
}
ListMultimap<Pointcut, HookParams> deferredBroadcastEvents = theTransactionDetails.endAcceptingDeferredInterceptorBroadcasts();
@ -1673,10 +1681,10 @@ public abstract class BaseTransactionProcessor {
return theStatusCode + " " + defaultString(Constants.HTTP_STATUS_NAMES.get(theStatusCode));
}
public class BundleTask implements Callable<Void> {
public class BundleTask implements Runnable {
private CountDownLatch myCompletedLatch;
private ServletRequestDetails myRequestDetails;
private RequestDetails myRequestDetails;
private IBase myNextReqEntry;
private Map<Integer, Object> myResponseMap;
private int myResponseOrder;
@ -1684,7 +1692,7 @@ public abstract class BaseTransactionProcessor {
protected BundleTask(CountDownLatch theCompletedLatch, RequestDetails theRequestDetails, Map<Integer, Object> theResponseMap, int theResponseOrder, IBase theNextReqEntry, boolean theNestedMode) {
this.myCompletedLatch = theCompletedLatch;
this.myRequestDetails = (ServletRequestDetails)theRequestDetails;
this.myRequestDetails = theRequestDetails;
this.myNextReqEntry = theNextReqEntry;
this.myResponseMap = theResponseMap;
this.myResponseOrder = theResponseOrder;
@ -1692,10 +1700,8 @@ public abstract class BaseTransactionProcessor {
}
@Override
public Void call() {
public void run() {
BaseServerResponseExceptionHolder caughtEx = new BaseServerResponseExceptionHolder();
try {
IBaseBundle subRequestBundle = myVersionAdapter.createBundle(org.hl7.fhir.r4.model.Bundle.BundleType.TRANSACTION.toCode());
myVersionAdapter.addEntry(subRequestBundle, (IBase) myNextReqEntry);
@ -1728,7 +1734,6 @@ public abstract class BaseTransactionProcessor {
// checking for the parallelism
ourLog.debug("processing bacth for {} is completed", myVersionAdapter.getEntryRequestUrl((IBase)myNextReqEntry));
myCompletedLatch.countDown();
return null;
}
}
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSearchParameterDstu2.java
View File

@ -22,22 +22,14 @@ package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoSearchParameter;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoSearchParameterR4;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
import ca.uhn.fhir.model.dstu2.resource.SearchParameter;
import ca.uhn.fhir.model.dstu2.valueset.ResourceTypeEnum;
import ca.uhn.fhir.model.dstu2.valueset.SearchParamTypeEnum;
import ca.uhn.fhir.model.primitive.BoundCodeDt;
import org.hl7.fhir.convertors.conv10_40.SearchParameter10_40;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_10_40;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_40;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -79,7 +71,7 @@ public class FhirResourceDaoSearchParameterDstu2 extends BaseHapiFhirResourceDao
String encoded = getContext().newJsonParser().encodeResourceToString(theResource);
org.hl7.fhir.dstu2.model.SearchParameter hl7Org = myDstu2Hl7OrgContext.newJsonParser().parseResource(org.hl7.fhir.dstu2.model.SearchParameter.class, encoded);
org.hl7.fhir.r4.model.SearchParameter convertedSp = SearchParameter10_40.convertSearchParameter(hl7Org);
org.hl7.fhir.r4.model.SearchParameter convertedSp = (org.hl7.fhir.r4.model.SearchParameter) VersionConvertorFactory_10_40.convertResource(hl7Org, new BaseAdvisor_10_40(false));
if (isBlank(convertedSp.getExpression()) && isNotBlank(hl7Org.getXpath())) {
convertedSp.setExpression(hl7Org.getXpath());
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java
View File

@ -230,7 +230,13 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
@Nonnull
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, CodingDt theCoding, RequestDetails theRequest) {
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, CodingDt theCoding, RequestDetails theRequest) {
return lookupCode(theCode, theSystem, theCoding, null, theRequest);
}
@Nonnull
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, CodingDt theCoding, IPrimitiveType<String> theDisplayLanguage, RequestDetails theRequest) {
boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
boolean haveCode = theCode != null && theCode.isEmpty() == false;
boolean haveSystem = theSystem != null && theSystem.isEmpty() == false;

101
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TransactionProcessor.java
View File

@ -46,6 +46,7 @@ import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import javax.annotation.Nullable;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@ -61,10 +62,12 @@ import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.Set;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
@ -218,18 +221,9 @@ public class TransactionProcessor extends BaseTransactionProcessor {
IQueryParameterType param = andList.get(0).get(0);
if (param instanceof TokenParam) {
TokenParam tokenParam = (TokenParam) param;
Predicate hashPredicate = null;
if (isNotBlank(tokenParam.getValue()) && isNotBlank(tokenParam.getSystem())) {
next.myHashSystemAndValue = ResourceIndexedSearchParamToken.calculateHashSystemAndValue(myPartitionSettings, requestPartitionId, next.myResourceDefinition.getName(), next.myMatchUrlSearchMap.keySet().iterator().next(), tokenParam.getSystem(), tokenParam.getValue());
hashPredicate = cb.equal(from.get("myHashSystemAndValue").as(Long.class), next.myHashSystemAndValue);
} else if (isNotBlank(tokenParam.getValue())) {
next.myHashValue = ResourceIndexedSearchParamToken.calculateHashValue(myPartitionSettings, requestPartitionId, next.myResourceDefinition.getName(), next.myMatchUrlSearchMap.keySet().iterator().next(), tokenParam.getValue());
hashPredicate = cb.equal(from.get("myHashValue").as(Long.class), next.myHashValue);
}
Predicate hashPredicate = buildHashPredicateFromTokenParam((TokenParam)param, requestPartitionId, cb, from, next);
if (hashPredicate != null) {
if (myPartitionSettings.isPartitioningEnabled() && !myPartitionSettings.isIncludePartitionInSearchHashes()) {
if (requestPartitionId.isDefaultPartition()) {
Predicate partitionIdCriteria = cb.isNull(from.get("myPartitionIdValue").as(Integer.class));
@ -250,35 +244,30 @@ public class TransactionProcessor extends BaseTransactionProcessor {
if (orPredicates.size() > 1) {
cq.where(cb.or(orPredicates.toArray(EMPTY_PREDICATE_ARRAY)));
Map<Long, List<MatchUrlToResolve>> hashToSearchMap = buildHashToSearchMap(searchParameterMapsToResolve);
TypedQuery<ResourceIndexedSearchParamToken> query = myEntityManager.createQuery(cq);
List<ResourceIndexedSearchParamToken> results = query.getResultList();
for (ResourceIndexedSearchParamToken nextResult : results) {
for (MatchUrlToResolve nextSearchParameterMap : searchParameterMapsToResolve) {
if (nextSearchParameterMap.myHashSystemAndValue != null && nextSearchParameterMap.myHashSystemAndValue.equals(nextResult.getHashSystemAndValue())) {
idsToPreFetch.add(nextResult.getResourcePid());
myMatchResourceUrlService.matchUrlResolved(theTransactionDetails, nextSearchParameterMap.myResourceDefinition.getName(), nextSearchParameterMap.myRequestUrl, new ResourcePersistentId(nextResult.getResourcePid()));
theTransactionDetails.addResolvedMatchUrl(nextSearchParameterMap.myRequestUrl, new ResourcePersistentId(nextResult.getResourcePid()));
nextSearchParameterMap.myResolved = true;
}
if (nextSearchParameterMap.myHashValue != null && nextSearchParameterMap.myHashValue.equals(nextResult.getHashValue())) {
idsToPreFetch.add(nextResult.getResourcePid());
myMatchResourceUrlService.matchUrlResolved(theTransactionDetails, nextSearchParameterMap.myResourceDefinition.getName(), nextSearchParameterMap.myRequestUrl, new ResourcePersistentId(nextResult.getResourcePid()));
theTransactionDetails.addResolvedMatchUrl(nextSearchParameterMap.myRequestUrl, new ResourcePersistentId(nextResult.getResourcePid()));
nextSearchParameterMap.myResolved = true;
}
Optional<List<MatchUrlToResolve>> matchedSearch = Optional.ofNullable(hashToSearchMap.get(nextResult.getHashSystemAndValue()));
if (!matchedSearch.isPresent()) {
matchedSearch = Optional.ofNullable(hashToSearchMap.get(nextResult.getHashValue()));
}
matchedSearch.ifPresent(matchUrlsToResolve -> {
matchUrlsToResolve.forEach(matchUrl -> {
setSearchToResolvedAndPrefetchFoundResourcePid(theTransactionDetails, idsToPreFetch, nextResult, matchUrl);
});
});
}
for (MatchUrlToResolve nextSearchParameterMap : searchParameterMapsToResolve) {
//For each SP Map which did not return a result, tag it as not found.
searchParameterMapsToResolve.stream()
// No matches
if (!nextSearchParameterMap.myResolved) {
theTransactionDetails.addResolvedMatchUrl(nextSearchParameterMap.myRequestUrl, TransactionDetails.NOT_FOUND);
}
}
.filter(match -> !match.myResolved)
.forEach(match -> {
ourLog.debug("Was unable to match url {} from database", match.myRequestUrl);
theTransactionDetails.addResolvedMatchUrl(match.myRequestUrl, TransactionDetails.NOT_FOUND);
});
}
}
@ -320,6 +309,49 @@ public class TransactionProcessor extends BaseTransactionProcessor {
return super.doTransactionWriteOperations(theRequest, theActionName, theTransactionDetails, theAllIds, theIdSubstitutions, theIdToPersistedOutcome, theResponse, theOriginalRequestOrder, theEntries, theTransactionStopWatch);
}
/**
* Given a token parameter, build the query predicate based on its hash. Uses system and value if both are available, otherwise just value.
* If neither are available, it returns null.
*/
@Nullable
private Predicate buildHashPredicateFromTokenParam(TokenParam theTokenParam, RequestPartitionId theRequestPartitionId, CriteriaBuilder cb, Root<ResourceIndexedSearchParamToken> from, MatchUrlToResolve theMatchUrl) {
Predicate hashPredicate = null;
if (isNotBlank(theTokenParam.getValue()) && isNotBlank(theTokenParam.getSystem())) {
theMatchUrl.myHashSystemAndValue = ResourceIndexedSearchParamToken.calculateHashSystemAndValue(myPartitionSettings, theRequestPartitionId, theMatchUrl.myResourceDefinition.getName(), theMatchUrl.myMatchUrlSearchMap.keySet().iterator().next(), theTokenParam.getSystem(), theTokenParam.getValue());
hashPredicate = cb.equal(from.get("myHashSystemAndValue").as(Long.class), theMatchUrl.myHashSystemAndValue);
} else if (isNotBlank(theTokenParam.getValue())) {
theMatchUrl.myHashValue = ResourceIndexedSearchParamToken.calculateHashValue(myPartitionSettings, theRequestPartitionId, theMatchUrl.myResourceDefinition.getName(), theMatchUrl.myMatchUrlSearchMap.keySet().iterator().next(), theTokenParam.getValue());
hashPredicate = cb.equal(from.get("myHashValue").as(Long.class), theMatchUrl.myHashValue);
}
return hashPredicate;
}
private Map<Long, List<MatchUrlToResolve>> buildHashToSearchMap(List<MatchUrlToResolve> searchParameterMapsToResolve) {
Map<Long, List<MatchUrlToResolve>> hashToSearch = new HashMap<>();
//Build a lookup map so we don't have to iterate over the searches repeatedly.
for (MatchUrlToResolve nextSearchParameterMap : searchParameterMapsToResolve) {
if (nextSearchParameterMap.myHashSystemAndValue != null) {
List<MatchUrlToResolve> matchUrlsToResolve = hashToSearch.getOrDefault(nextSearchParameterMap.myHashSystemAndValue, new ArrayList<>());
matchUrlsToResolve.add(nextSearchParameterMap);
hashToSearch.put(nextSearchParameterMap.myHashSystemAndValue, matchUrlsToResolve);
}
if (nextSearchParameterMap.myHashValue!= null) {
List<MatchUrlToResolve> matchUrlsToResolve = hashToSearch.getOrDefault(nextSearchParameterMap.myHashValue, new ArrayList<>());
matchUrlsToResolve.add(nextSearchParameterMap);
hashToSearch.put(nextSearchParameterMap.myHashValue, matchUrlsToResolve);
}
}
return hashToSearch;
}
private void setSearchToResolvedAndPrefetchFoundResourcePid(TransactionDetails theTransactionDetails, List<Long> idsToPreFetch, ResourceIndexedSearchParamToken nextResult, MatchUrlToResolve nextSearchParameterMap) {
ourLog.debug("Matched url {} from database", nextSearchParameterMap.myRequestUrl);
idsToPreFetch.add(nextResult.getResourcePid());
myMatchResourceUrlService.matchUrlResolved(theTransactionDetails, nextSearchParameterMap.myResourceDefinition.getName(), nextSearchParameterMap.myRequestUrl, new ResourcePersistentId(nextResult.getResourcePid()));
theTransactionDetails.addResolvedMatchUrl(nextSearchParameterMap.myRequestUrl, new ResourcePersistentId(nextResult.getResourcePid()));
nextSearchParameterMap.setResolved(true);
}
private List<ResourceTable> preFetchIndexes(List<Long> ids, String typeDesc, String fieldName) {
TypedQuery<ResourceTable> query = myEntityManager.createQuery("FROM ResourceTable r LEFT JOIN FETCH r." + fieldName + " WHERE r.myId IN ( :IDS )", ResourceTable.class);
query.setParameter("IDS", ids);
@ -379,5 +411,8 @@ public class TransactionProcessor extends BaseTransactionProcessor {
myMatchUrlSearchMap = theMatchUrlSearchMap;
myResourceDefinition = theResourceDefinition;
}
public void setResolved(boolean theResolved) {
myResolved = theResolved;
}
}
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IMdmLinkDao.java
View File

@ -67,4 +67,7 @@ public interface IMdmLinkDao extends JpaRepository<MdmLink, Long> {
"AND ml.myMatchResult=:matchResult")
List<MdmPidTuple> expandPidsBySourcePidAndMatchResult(@Param("sourcePid") Long theSourcePid, @Param("matchResult") MdmMatchResultEnum theMdmMatchResultEnum);
@Query("SELECT ml.myGoldenResourcePid as goldenPid, ml.mySourcePid as sourcePid FROM MdmLink ml WHERE ml.myGoldenResourcePid = :goldenPid and ml.myMatchResult = :matchResult")
List<MdmPidTuple> expandPidsByGoldenResourcePidAndMatchResult(@Param("goldenPid") Long theSourcePid, @Param("matchResult") MdmMatchResultEnum theMdmMatchResultEnum);
}

33
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
View File

@ -27,16 +27,18 @@ import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
@ -53,7 +55,6 @@ 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> {
@ -86,10 +87,17 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
@Nonnull
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
return lookupCode(theCode, theSystem, theCoding, null, theRequestDetails);
}
@Nonnull
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, IPrimitiveType<String> theDisplayLanguage, RequestDetails theRequestDetails) {
boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
boolean haveCode = theCode != null && theCode.isEmpty() == false;
boolean haveSystem = theSystem != null && theSystem.isEmpty() == false;
boolean haveDisplayLanguage = theDisplayLanguage != null && theDisplayLanguage.isEmpty() == false;
if (!haveCoding && !(haveSystem && haveCode)) {
throw new InvalidRequestException("No code, coding, or codeableConcept provided to validate");
}
@ -111,11 +119,16 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
system = theSystem.getValue();
}
String displayLanguage = null;
if (haveDisplayLanguage) {
displayLanguage = theDisplayLanguage.getValue();
}
ourLog.debug("Looking up {} / {}", system, code);
if (myValidationSupport.isCodeSystemSupported(new ValidationSupportContext(myValidationSupport), system)) {
ourLog.debug("Code system {} is supported", system);
IValidationSupport.LookupCodeResult result = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code);
IValidationSupport.LookupCodeResult result = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code, displayLanguage);
if (result != null) {
return result;
}
@ -146,7 +159,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
CodeSystem csDstu3 = (CodeSystem) theResource;
org.hl7.fhir.r4.model.CodeSystem cs = convertCodeSystem(csDstu3);
org.hl7.fhir.r4.model.CodeSystem cs = (org.hl7.fhir.r4.model.CodeSystem) VersionConvertorFactory_30_40.convertResource(csDstu3, new BaseAdvisor_30_40(false));
addPidToResource(theEntity, cs);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, (ResourceTable) theEntity);
@ -157,9 +170,9 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
}
@Override
public CodeValidationResult validateCode(IIdType theCodeSystemId, IPrimitiveType<String> theCodeSystemUrl, IPrimitiveType<String> theVersion, IPrimitiveType<String> theCode,
IPrimitiveType<String> theDisplay, Coding theCoding, CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
public CodeValidationResult validateCode(IIdType theCodeSystemId, IPrimitiveType<String> theCodeSystemUrl, IPrimitiveType<String> theVersion, IPrimitiveType<String> theCode,
IPrimitiveType<String> theDisplay, Coding theCoding, CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
throw new UnsupportedOperationException();
}
}

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java
View File

@ -20,9 +20,9 @@ package ca.uhn.fhir.jpa.dao.dstu3;
* #L%
*/
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@ -30,6 +30,8 @@ import ca.uhn.fhir.jpa.term.api.ITermConceptMappingSvc;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.dstu3.model.ConceptMap;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -37,8 +39,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import java.util.Date;
import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
public class FhirResourceDaoConceptMapDstu3 extends BaseHapiFhirResourceDao<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
@Autowired
private ITermConceptMappingSvc myTermConceptMappingSvc;
@ -53,7 +53,6 @@ public class FhirResourceDaoConceptMapDstu3 extends BaseHapiFhirResourceDao<Conc
}
@Override
public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, IBasePersistedResource theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, TransactionDetails theTransactionDetails, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
@ -63,7 +62,7 @@ public class FhirResourceDaoConceptMapDstu3 extends BaseHapiFhirResourceDao<Conc
if (retVal.getDeleted() == null) {
try {
ConceptMap conceptMap = (ConceptMap) theResource;
org.hl7.fhir.r4.model.ConceptMap converted = convertConceptMap(conceptMap);
org.hl7.fhir.r4.model.ConceptMap converted = (org.hl7.fhir.r4.model.ConceptMap) VersionConvertorFactory_30_40.convertResource(conceptMap, new BaseAdvisor_30_40(false));
myTermConceptMappingSvc.storeTermConceptMapAndChildren(retVal, converted);
} catch (FHIRException fe) {
throw new InternalErrorException(fe);

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSearchParameterDstu3.java
View File

@ -1,20 +1,15 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoSearchParameter;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoSearchParameterR4;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
import org.hl7.fhir.convertors.conv10_40.SearchParameter10_40;
import org.hl7.fhir.convertors.conv30_40.SearchParameter30_40;
import org.hl7.fhir.dstu3.model.CodeType;
import org.hl7.fhir.dstu3.model.Enumerations;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.dstu3.model.SearchParameter;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.List;
/*
* #%L
* HAPI FHIR JPA Server
@ -69,7 +64,9 @@ public class FhirResourceDaoSearchParameterDstu3 extends BaseHapiFhirResourceDao
protected void validateResourceForStorage(SearchParameter theResource, ResourceTable theEntityToSave) {
super.validateResourceForStorage(theResource, theEntityToSave);
FhirResourceDaoSearchParameterR4.validateSearchParam(SearchParameter30_40.convertSearchParameter(theResource), getContext(), getConfig(), mySearchParamRegistry, mySearchParamExtractor);
FhirResourceDaoSearchParameterR4.validateSearchParam(
(org.hl7.fhir.r4.model.SearchParameter) VersionConvertorFactory_30_40.convertResource(theResource, new BaseAdvisor_30_40(false)),
getContext(), getConfig(), mySearchParamRegistry, mySearchParamExtractor);
}
}

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
View File

@ -30,7 +30,8 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.convertors.conv30_40.ValueSet30_40;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.ValueSet;
@ -42,7 +43,6 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
import java.util.Date;
import static ca.uhn.fhir.jpa.dao.FhirResourceDaoValueSetDstu2.toStringOrNull;
import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSet;
public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
@ -54,15 +54,15 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
@Override
public org.hl7.fhir.dstu3.model.ValueSet expand(org.hl7.fhir.dstu3.model.ValueSet theSource, ValueSetExpansionOptions theOptions) {
org.hl7.fhir.r4.model.ValueSet canonicalInput = ValueSet30_40.convertValueSet(theSource);
org.hl7.fhir.r4.model.ValueSet canonicalInput = (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_30_40.convertResource(theSource, new BaseAdvisor_30_40(false));
org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(theOptions, canonicalInput);
return ValueSet30_40.convertValueSet(canonicalOutput);
return (ValueSet) VersionConvertorFactory_30_40.convertResource(canonicalOutput, new BaseAdvisor_30_40(false));
}
@Override
public org.hl7.fhir.dstu3.model.ValueSet expandByIdentifier(String theUri, ValueSetExpansionOptions theOptions) {
org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(theOptions, theUri);
return ValueSet30_40.convertValueSet(canonicalOutput);
return (ValueSet) VersionConvertorFactory_30_40.convertResource(canonicalOutput, new BaseAdvisor_30_40(false));
}
@Override
@ -86,7 +86,7 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
if (retVal.getDeleted() == null) {
try {
ValueSet valueSet = (ValueSet) theResource;
org.hl7.fhir.r4.model.ValueSet converted = convertValueSet(valueSet);
org.hl7.fhir.r4.model.ValueSet converted = (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_30_40.convertResource(valueSet, new BaseAdvisor_30_40(false));
myTerminologySvc.storeTermValueSet(retVal, converted);
} catch (FHIRException fe) {
throw new InternalErrorException(fe);

154
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ExpungeEverythingService.java
View File

@ -65,6 +65,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.entity.ResourceTag;
import ca.uhn.fhir.jpa.model.entity.SearchParamPresent;
import ca.uhn.fhir.jpa.model.entity.TagDefinition;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@ -100,6 +101,9 @@ public class ExpungeEverythingService {
private TransactionTemplate myTxTemplate;
@Autowired
private MemoryCacheService myMemoryCacheService;
@PostConstruct
public void initTxTemplate() {
myTxTemplate = new TransactionTemplate(myPlatformTransactionManager);
@ -122,37 +126,37 @@ public class ExpungeEverythingService {
counter.addAndGet(doExpungeEverythingQuery("UPDATE " + TermCodeSystem.class.getSimpleName() + " d SET d.myCurrentVersion = null"));
return null;
});
counter.addAndGet(expungeEverythingByType(NpmPackageVersionResourceEntity.class));
counter.addAndGet(expungeEverythingByType(NpmPackageVersionEntity.class));
counter.addAndGet(expungeEverythingByType(NpmPackageEntity.class));
counter.addAndGet(expungeEverythingByType(SearchParamPresent.class));
counter.addAndGet(expungeEverythingByType(BulkImportJobFileEntity.class));
counter.addAndGet(expungeEverythingByType(BulkImportJobEntity.class));
counter.addAndGet(expungeEverythingByType(ForcedId.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedSearchParamDate.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedSearchParamNumber.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedSearchParamQuantity.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedSearchParamQuantityNormalized.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedSearchParamString.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedSearchParamToken.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedSearchParamUri.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedSearchParamCoords.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedComboStringUnique.class));
counter.addAndGet(expungeEverythingByType(ResourceIndexedComboTokenNonUnique.class));
counter.addAndGet(expungeEverythingByType(ResourceLink.class));
counter.addAndGet(expungeEverythingByType(SearchResult.class));
counter.addAndGet(expungeEverythingByType(SearchInclude.class));
counter.addAndGet(expungeEverythingByType(TermValueSetConceptDesignation.class));
counter.addAndGet(expungeEverythingByType(TermValueSetConcept.class));
counter.addAndGet(expungeEverythingByType(TermValueSet.class));
counter.addAndGet(expungeEverythingByType(TermConceptParentChildLink.class));
counter.addAndGet(expungeEverythingByType(TermConceptMapGroupElementTarget.class));
counter.addAndGet(expungeEverythingByType(TermConceptMapGroupElement.class));
counter.addAndGet(expungeEverythingByType(TermConceptMapGroup.class));
counter.addAndGet(expungeEverythingByType(TermConceptMap.class));
counter.addAndGet(expungeEverythingByType(TermConceptProperty.class));
counter.addAndGet(expungeEverythingByType(TermConceptDesignation.class));
counter.addAndGet(expungeEverythingByType(TermConcept.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(NpmPackageVersionResourceEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(NpmPackageVersionEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(NpmPackageEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(SearchParamPresent.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(BulkImportJobFileEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(BulkImportJobEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ForcedId.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedSearchParamDate.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedSearchParamNumber.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedSearchParamQuantity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedSearchParamQuantityNormalized.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedSearchParamString.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedSearchParamToken.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedSearchParamUri.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedSearchParamCoords.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedComboStringUnique.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceIndexedComboTokenNonUnique.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceLink.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(SearchResult.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(SearchInclude.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermValueSetConceptDesignation.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermValueSetConcept.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermValueSet.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermConceptParentChildLink.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermConceptMapGroupElementTarget.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermConceptMapGroupElement.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermConceptMapGroup.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermConceptMap.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermConceptProperty.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermConceptDesignation.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermConcept.class));
myTxTemplate.execute(t -> {
for (TermCodeSystem next : myEntityManager.createQuery("SELECT c FROM " + TermCodeSystem.class.getName() + " c", TermCodeSystem.class).getResultList()) {
next.setCurrentVersion(null);
@ -160,52 +164,66 @@ public class ExpungeEverythingService {
}
return null;
});
counter.addAndGet(expungeEverythingByType(TermCodeSystemVersion.class));
counter.addAndGet(expungeEverythingByType(TermCodeSystem.class));
counter.addAndGet(expungeEverythingByType(SubscriptionTable.class));
counter.addAndGet(expungeEverythingByType(ResourceHistoryTag.class));
counter.addAndGet(expungeEverythingByType(ResourceTag.class));
counter.addAndGet(expungeEverythingByType(TagDefinition.class));
counter.addAndGet(expungeEverythingByType(ResourceHistoryProvenanceEntity.class));
counter.addAndGet(expungeEverythingByType(ResourceHistoryTable.class));
counter.addAndGet(expungeEverythingByType(ResourceTable.class));
counter.addAndGet(expungeEverythingByType(PartitionEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermCodeSystemVersion.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TermCodeSystem.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(SubscriptionTable.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceHistoryTag.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceTag.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(TagDefinition.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceHistoryProvenanceEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceHistoryTable.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ResourceTable.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(PartitionEntity.class));
myTxTemplate.execute(t -> {
counter.addAndGet(doExpungeEverythingQuery("DELETE from " + Search.class.getSimpleName() + " d"));
return null;
});
purgeAllCaches();
ourLog.info("COMPLETED GLOBAL $expunge - Deleted {} rows", counter.get());
}
private void purgeAllCaches() {
myTxTemplate.execute(t -> {
myMemoryCacheService.invalidateAllCaches();
return null;
});
}
private int expungeEverythingByTypeWithoutPurging(Class<?> theEntityType) {
int outcome = 0;
while (true) {
StopWatch sw = new StopWatch();
@SuppressWarnings("ConstantConditions")
int count = myTxTemplate.execute(t -> {
CriteriaBuilder cb = myEntityManager.getCriteriaBuilder();
CriteriaQuery<?> cq = cb.createQuery(theEntityType);
cq.from(theEntityType);
TypedQuery<?> query = myEntityManager.createQuery(cq);
query.setMaxResults(1000);
List<?> results = query.getResultList();
for (Object result : results) {
myEntityManager.remove(result);
}
return results.size();
});
outcome += count;
if (count == 0) {
break;
}
ourLog.info("Have deleted {} entities of type {} in {}", outcome, theEntityType.getSimpleName(), sw.toString());
}
return outcome;
}
public int expungeEverythingByType(Class<?> theEntityType) {
int outcome = 0;
while (true) {
StopWatch sw = new StopWatch();
@SuppressWarnings("ConstantConditions")
int count = myTxTemplate.execute(t -> {
CriteriaBuilder cb = myEntityManager.getCriteriaBuilder();
CriteriaQuery<?> cq = cb.createQuery(theEntityType);
cq.from(theEntityType);
TypedQuery<?> query = myEntityManager.createQuery(cq);
query.setMaxResults(1000);
List<?> results = query.getResultList();
for (Object result : results) {
myEntityManager.remove(result);
}
return results.size();
});
outcome += count;
if (count == 0) {
break;
}
ourLog.info("Have deleted {} entities of type {} in {}", outcome, theEntityType.getSimpleName(), sw.toString());
}
return outcome;
int result = expungeEverythingByTypeWithoutPurging(theEntityType);
purgeAllCaches();
return result;
}
private int doExpungeEverythingQuery(String theQuery) {

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

@ -55,7 +55,7 @@ import com.google.common.annotations.VisibleForTesting;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.jetbrains.annotations.Nullable;
import javax.annotation.Nullable;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Lazy;
import org.springframework.stereotype.Service;

44
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/mdm/MdmLinkExpandSvc.java
View File

@ -25,15 +25,13 @@ import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import java.util.ArrayList;
import javax.annotation.Nonnull;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
@ -82,14 +80,50 @@ public class MdmLinkExpandSvc {
public Set<String> expandMdmBySourceResourcePid(Long theSourceResourcePid) {
ourLog.debug("About to expand source resource with PID {}", theSourceResourcePid);
List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuples = myMdmLinkDao.expandPidsBySourcePidAndMatchResult(theSourceResourcePid, MdmMatchResultEnum.MATCH);
return flattenPidTuplesToSet(theSourceResourcePid, goldenPidSourcePidTuples);
}
/**
* Given a PID of a golden resource, perform MDM expansion and return all the resource IDs of all resources that are
* MDM-Matched to this golden resource.
*
* @param theGoldenResourcePid The PID of the golden resource to MDM-Expand.
* @return A set of strings representing the FHIR ids of the expanded resources.
*/
public Set<String> expandMdmByGoldenResourceId(Long theGoldenResourcePid) {
ourLog.debug("About to expand golden resource with PID {}", theGoldenResourcePid);
List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuples = myMdmLinkDao.expandPidsByGoldenResourcePidAndMatchResult(theGoldenResourcePid, MdmMatchResultEnum.MATCH);
return flattenPidTuplesToSet(theGoldenResourcePid, goldenPidSourcePidTuples);
}
/**
* Given a resource ID of a golden resource, perform MDM expansion and return all the resource IDs of all resources that are
* MDM-Matched to this golden resource.
*
* @param theGoldenResourcePid The resource ID of the golden resource to MDM-Expand.
* @return A set of strings representing the FHIR ids of the expanded resources.
*/
public Set<String> expandMdmByGoldenResourcePid(Long theGoldenResourcePid) {
ourLog.debug("About to expand golden resource with PID {}", theGoldenResourcePid);
List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuples = myMdmLinkDao.expandPidsByGoldenResourcePidAndMatchResult(theGoldenResourcePid, MdmMatchResultEnum.MATCH);
return flattenPidTuplesToSet(theGoldenResourcePid, goldenPidSourcePidTuples);
}
public Set<String> expandMdmByGoldenResourceId(IdDt theId) {
ourLog.debug("About to expand golden resource with golden resource id {}", theId);
Long pidOrThrowException = myIdHelperService.getPidOrThrowException(theId);
return expandMdmByGoldenResourcePid(pidOrThrowException);
}
@Nonnull
private Set<String> flattenPidTuplesToSet(Long initialPid, List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuples) {
Set<Long> flattenedPids = new HashSet<>();
goldenPidSourcePidTuples.forEach(tuple -> {
flattenedPids.add(tuple.getSourcePid());
flattenedPids.add(tuple.getGoldenPid());
});
Set<String> resourceIds = myIdHelperService.translatePidsToFhirResourceIds(flattenedPids);
ourLog.debug("Pid {} has been expanded to [{}]", theSourceResourcePid, String.join(",", resourceIds));
ourLog.debug("Pid {} has been expanded to [{}]", initialPid, String.join(",", resourceIds));
return resourceIds;
}
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java
View File

@ -82,9 +82,16 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
@Nonnull
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
return lookupCode(theCode, theSystem, theCoding, null, theRequestDetails);
}
@Nonnull
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, IPrimitiveType<String> theDisplayLanguage, RequestDetails theRequestDetails) {
boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
boolean haveCode = theCode != null && theCode.isEmpty() == false;
boolean haveSystem = theSystem != null && theSystem.isEmpty() == false;
boolean haveDisplayLanguage = theDisplayLanguage != null && theDisplayLanguage.isEmpty() == false;
if (!haveCoding && !(haveSystem && haveCode)) {
throw new InvalidRequestException("No code, coding, or codeableConcept provided to validate");
@ -107,12 +114,17 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
system = theSystem.getValue();
}
String displayLanguage = null;
if (haveDisplayLanguage) {
displayLanguage = theDisplayLanguage.getValue();
}
ourLog.debug("Looking up {} / {}", system, code);
if (myValidationSupport.isCodeSystemSupported(new ValidationSupportContext(myValidationSupport), system)) {
ourLog.debug("Code system {} is supported", system);
IValidationSupport.LookupCodeResult retVal = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code);
IValidationSupport.LookupCodeResult retVal = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code, displayLanguage);
if (retVal != null) {
return retVal;
}

21
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java
View File

@ -38,6 +38,8 @@ 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.advisors.impl.BaseAdvisor_40_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@ -53,7 +55,6 @@ import java.util.List;
import java.util.Set;
import static ca.uhn.fhir.jpa.dao.FhirResourceDaoValueSetDstu2.toStringOrNull;
import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoValueSetDstu3.vsValidateCodeOptions;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSystem> implements IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> {
@ -85,10 +86,17 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
@Nonnull
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
return lookupCode(theCode, theSystem, theCoding, null, theRequestDetails);
}
@Nonnull
@Override
public IValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, IPrimitiveType<String> theDisplayLanguage, RequestDetails theRequestDetails) {
boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
boolean haveCode = theCode != null && theCode.isEmpty() == false;
boolean haveSystem = theSystem != null && theSystem.isEmpty() == false;
boolean haveDisplayLanguage = theDisplayLanguage != null && theDisplayLanguage.isEmpty() == false;
if (!haveCoding && !(haveSystem && haveCode)) {
throw new InvalidRequestException("No code, coding, or codeableConcept provided to validate");
}
@ -110,12 +118,17 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
system = theSystem.getValue();
}
String displayLanguage = null;
if (haveDisplayLanguage) {
displayLanguage = theDisplayLanguage.getValue();
}
ourLog.info("Looking up {} / {}", system, code);
if (myValidationSupport.isCodeSystemSupported(new ValidationSupportContext(myValidationSupport), system)) {
ourLog.info("Code system {} is supported", system);
IValidationSupport.LookupCodeResult retVal = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code);
IValidationSupport.LookupCodeResult retVal = myValidationSupport.lookupCode(new ValidationSupportContext(myValidationSupport), system, code, displayLanguage);
if (retVal != null) {
return retVal;
}
@ -149,7 +162,7 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
CodeSystem cs = (CodeSystem) theResource;
addPidToResource(theEntity, theResource);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem(cs), (ResourceTable) theEntity);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded((org.hl7.fhir.r4.model.CodeSystem) VersionConvertorFactory_40_50.convertResource(cs, new BaseAdvisor_40_50(false)), (ResourceTable) theEntity);
}
return retVal;

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoConceptMapR5.java
View File

@ -29,6 +29,8 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermConceptMappingSvc;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r5.model.ConceptMap;
import org.springframework.beans.factory.annotation.Autowired;
@ -56,7 +58,8 @@ public class FhirResourceDaoConceptMapR5 extends BaseHapiFhirResourceDao<Concept
if (retVal.getDeleted() == null) {
ConceptMap conceptMap = (ConceptMap) theResource;
myTermConceptMappingSvc.storeTermConceptMapAndChildren(retVal, org.hl7.fhir.convertors.conv40_50.ConceptMap40_50.convertConceptMap(conceptMap));
myTermConceptMappingSvc.storeTermConceptMapAndChildren(retVal,
(org.hl7.fhir.r4.model.ConceptMap) VersionConvertorFactory_40_50.convertResource(conceptMap, new BaseAdvisor_40_50(false)));
} else {
myTermConceptMappingSvc.deleteConceptMapAndChildren(retVal);
}

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoSearchParameterR5.java
View File

@ -1,19 +1,15 @@
package ca.uhn.fhir.jpa.dao.r5;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoSearchParameter;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoSearchParameterR4;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
import org.hl7.fhir.convertors.conv30_40.SearchParameter30_40;
import org.hl7.fhir.convertors.conv40_50.SearchParameter40_50;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.r5.model.SearchParameter;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.List;
/*
* #%L
* HAPI FHIR JPA Server
@ -68,7 +64,9 @@ public class FhirResourceDaoSearchParameterR5 extends BaseHapiFhirResourceDao<Se
protected void validateResourceForStorage(SearchParameter theResource, ResourceTable theEntityToSave) {
super.validateResourceForStorage(theResource, theEntityToSave);
FhirResourceDaoSearchParameterR4.validateSearchParam(SearchParameter40_50.convertSearchParameter(theResource), getContext(), getConfig(), mySearchParamRegistry, mySearchParamExtractor);
FhirResourceDaoSearchParameterR4.validateSearchParam(
(org.hl7.fhir.r4.model.SearchParameter) VersionConvertorFactory_40_50.convertResource(theResource, new BaseAdvisor_40_50(false)),
getContext(), getConfig(), mySearchParamRegistry, mySearchParamExtractor);
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
View File

@ -28,7 +28,8 @@ import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import org.hl7.fhir.convertors.conv40_50.ValueSet40_50;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@ -52,14 +53,14 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
@Override
public ValueSet expandByIdentifier(String theUri, ValueSetExpansionOptions theOptions) {
org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(theOptions, theUri);
return ValueSet40_50.convertValueSet(canonicalOutput);
return (ValueSet) VersionConvertorFactory_40_50.convertResource(canonicalOutput, new BaseAdvisor_40_50(false));
}
@Override
public ValueSet expand(ValueSet theSource, ValueSetExpansionOptions theOptions) {
org.hl7.fhir.r4.model.ValueSet canonicalInput = ValueSet40_50.convertValueSet(theSource);
org.hl7.fhir.r4.model.ValueSet canonicalInput = (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_40_50.convertResource(theSource, new BaseAdvisor_40_50(false));
org.hl7.fhir.r4.model.ValueSet canonicalOutput = myTerminologySvc.expandValueSet(theOptions, canonicalInput);
return ValueSet40_50.convertValueSet(canonicalOutput);
return (ValueSet) VersionConvertorFactory_40_50.convertResource(canonicalOutput, new BaseAdvisor_40_50(false));
}
@Override
@ -82,7 +83,7 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
if (getConfig().isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
ValueSet valueSet = (ValueSet) theResource;
myTerminologySvc.storeTermValueSet(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSet));
myTerminologySvc.storeTermValueSet(retVal, (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_40_50.convertResource(valueSet, new BaseAdvisor_40_50(false)));
} else {
myTerminologySvc.deleteValueSetAndChildren(retVal);
}

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/MdmSearchExpandingInterceptor.java
View File

@ -76,8 +76,16 @@ public class MdmSearchExpandingInterceptor {
if (iQueryParameterType instanceof ReferenceParam) {
ReferenceParam refParam = (ReferenceParam) iQueryParameterType;
if (refParam.isMdmExpand()) {
ourLog.debug("Found a reference parameter to expand: {}", refParam.toString());
ourLog.debug("Found a reference parameter to expand: {}", refParam);
//First, attempt to expand as a source resource.
Set<String> expandedResourceIds = myMdmLinkExpandSvc.expandMdmBySourceResourceId(new IdDt(refParam.getValue()));
// If we failed, attempt to expand as a golden resource
if (expandedResourceIds.isEmpty()) {
expandedResourceIds = myMdmLinkExpandSvc.expandMdmByGoldenResourceId(new IdDt(refParam.getValue()));
}
//Rebuild the search param list.
if (!expandedResourceIds.isEmpty()) {
ourLog.debug("Parameter has been expanded to: {}", String.join(", ", expandedResourceIds));
toRemove.add(refParam);

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaResourceProviderValueSetDstu2.java
View File

@ -112,7 +112,7 @@ public class BaseJpaResourceProviderValueSetDstu2 extends JpaResourceProviderDst
startRequest(theServletRequest);
try {
IFhirResourceDaoCodeSystem<ValueSet, CodingDt, CodeableConceptDt> dao = (IFhirResourceDaoCodeSystem<ValueSet, CodingDt, CodeableConceptDt>) getDao();
IValidationSupport.LookupCodeResult result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
IValidationSupport.LookupCodeResult result = dao.lookupCode(theCode, theSystem, theCoding, null, theRequestDetails);
if (result.isFound() == false) {
throw new ResourceNotFoundException("Unable to find code[" + result.getSearchedForCode() + "] in system[" + result.getSearchedForSystem() + "]");
}

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/TerminologyUploaderProvider.java
View File

@ -40,6 +40,10 @@ 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.advisors.impl.BaseAdvisor_30_40;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.ICompositeType;
@ -58,10 +62,7 @@ import java.util.LinkedHashMap;
import java.util.List;
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;
import static org.apache.commons.lang3.StringUtils.*;
public class TerminologyUploaderProvider extends BaseJpaProvider {
@ -308,10 +309,10 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
CodeSystem nextCodeSystem;
switch (getContext().getVersion().getVersion()) {
case DSTU3:
nextCodeSystem = convertCodeSystem((org.hl7.fhir.dstu3.model.CodeSystem) theCodeSystem);
nextCodeSystem = (CodeSystem) VersionConvertorFactory_30_40.convertResource((org.hl7.fhir.dstu3.model.CodeSystem) theCodeSystem, new BaseAdvisor_30_40(false));
break;
case R5:
nextCodeSystem = org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem((org.hl7.fhir.r5.model.CodeSystem) theCodeSystem);
nextCodeSystem = (CodeSystem) VersionConvertorFactory_40_50.convertResource((org.hl7.fhir.r5.model.CodeSystem) theCodeSystem, new BaseAdvisor_40_50(false));
break;
default:
nextCodeSystem = (CodeSystem) theCodeSystem;

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderCodeSystemDstu3.java
View File

@ -53,7 +53,8 @@ public class BaseJpaResourceProviderCodeSystemDstu3 extends JpaResourceProviderD
@OperationParam(name = "code", min = 0, max = 1) CodeType theCode,
@OperationParam(name = "system", min = 0, max = 1) UriType theSystem,
@OperationParam(name = "coding", min = 0, max = 1) Coding theCoding,
@OperationParam(name="version", min=0, max=1) StringType theVersion,
@OperationParam(name = "version", min=0, max=1) StringType theVersion,
@OperationParam(name = "displayLanguage", min=0, max=1) CodeType theDisplayLanguage,
@OperationParam(name = "property", min = 0, max = OperationParam.MAX_UNLIMITED) List<CodeType> theProperties,
RequestDetails theRequestDetails
) {
@ -63,9 +64,9 @@ public class BaseJpaResourceProviderCodeSystemDstu3 extends JpaResourceProviderD
IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
IValidationSupport.LookupCodeResult result;
if (theVersion != null) {
result = dao.lookupCode(theCode, new UriType(theSystem.getValue() + "|" + theVersion), theCoding, theRequestDetails);
result = dao.lookupCode(theCode, new UriType(theSystem.getValue() + "|" + theVersion), theCoding, theDisplayLanguage, theRequestDetails);
} else {
result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
result = dao.lookupCode(theCode, theSystem, theCoding, theDisplayLanguage, theRequestDetails);
}
result.throwNotFoundIfAppropriate();
return (Parameters) result.toParameters(theRequestDetails.getFhirContext(), theProperties);

39
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderConceptMapDstu3.java
View File

@ -20,9 +20,9 @@ package ca.uhn.fhir.jpa.provider.dstu3;
* #L%
*/
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.term.TermConceptMappingSvcImpl;
import ca.uhn.fhir.rest.annotation.IdParam;
@ -31,7 +31,8 @@ import ca.uhn.fhir.rest.annotation.OperationParam;
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.convertors.advisors.impl.BaseAdvisor_30_40;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.CodeType;
import org.hl7.fhir.dstu3.model.CodeableConcept;
@ -45,8 +46,6 @@ 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),
@ -82,7 +81,7 @@ public class BaseJpaResourceProviderConceptMapDstu3 extends JpaResourceProviderD
&& theSourceValueSet.hasValue();
boolean haveSourceCoding = theSourceCoding != null
&& theSourceCoding.hasCode();
boolean haveSourceCodeableConcept= theSourceCodeableConcept != null
boolean haveSourceCodeableConcept = theSourceCodeableConcept != null
&& theSourceCodeableConcept.hasCoding()
&& theSourceCodeableConcept.getCodingFirstRep().hasCode();
boolean haveTargetValueSet = theTargetValueSet != null
@ -100,46 +99,46 @@ public class BaseJpaResourceProviderConceptMapDstu3 extends JpaResourceProviderD
TranslationRequest translationRequest = new TranslationRequest();
try {
if (haveUrl) {
translationRequest.setUrl(VersionConvertor_30_40.convertUri(theUrl));
translationRequest.setUrl((org.hl7.fhir.r4.model.UriType) VersionConvertorFactory_30_40.convertType(theUrl, new BaseAdvisor_30_40(false)));
}
if (haveConceptMapVersion) {
translationRequest.setConceptMapVersion(VersionConvertor_30_40.convertString(theConceptMapVersion));
translationRequest.setConceptMapVersion((org.hl7.fhir.r4.model.StringType) VersionConvertorFactory_30_40.convertType(theConceptMapVersion, new BaseAdvisor_30_40(false)));
}
// Convert from DSTU3 to R4
if (haveSourceCode) {
translationRequest.getCodeableConcept().addCoding().setCodeElement(VersionConvertor_30_40.convertCode(theSourceCode));
translationRequest.getCodeableConcept().addCoding().setCodeElement((org.hl7.fhir.r4.model.CodeType) VersionConvertorFactory_30_40.convertType(theSourceCode, new BaseAdvisor_30_40(false)));
if (haveSourceCodeSystem) {
translationRequest.getCodeableConcept().getCodingFirstRep().setSystemElement(VersionConvertor_30_40.convertUri(theSourceCodeSystem));
translationRequest.getCodeableConcept().getCodingFirstRep().setSystemElement((org.hl7.fhir.r4.model.UriType) VersionConvertorFactory_30_40.convertType(theSourceCodeSystem, new BaseAdvisor_30_40(false)));
}
if (haveSourceCodeSystemVersion) {
translationRequest.getCodeableConcept().getCodingFirstRep().setVersionElement(VersionConvertor_30_40.convertString(theSourceCodeSystemVersion));
translationRequest.getCodeableConcept().getCodingFirstRep().setVersionElement((org.hl7.fhir.r4.model.StringType) VersionConvertorFactory_30_40.convertType(theSourceCodeSystemVersion, new BaseAdvisor_30_40(false)));
}
} else if (haveSourceCoding) {
translationRequest.getCodeableConcept().addCoding(VersionConvertor_30_40.convertCoding(theSourceCoding));
translationRequest.getCodeableConcept().addCoding((org.hl7.fhir.r4.model.Coding) VersionConvertorFactory_30_40.convertType(theSourceCoding, new BaseAdvisor_30_40(false)));
} else {
translationRequest.setCodeableConcept(VersionConvertor_30_40.convertCodeableConcept(theSourceCodeableConcept));
translationRequest.setCodeableConcept((org.hl7.fhir.r4.model.CodeableConcept) VersionConvertorFactory_30_40.convertType(theSourceCodeableConcept, new BaseAdvisor_30_40(false)));
}
if (haveSourceValueSet) {
translationRequest.setSource(VersionConvertor_30_40.convertUri(theSourceValueSet));
translationRequest.setSource((org.hl7.fhir.r4.model.UriType) VersionConvertorFactory_30_40.convertType(theSourceValueSet, new BaseAdvisor_30_40(false)));
}
if (haveTargetValueSet) {
translationRequest.setTarget(VersionConvertor_30_40.convertUri(theTargetValueSet));
translationRequest.setTarget((org.hl7.fhir.r4.model.UriType) VersionConvertorFactory_30_40.convertType(theTargetValueSet, new BaseAdvisor_30_40(false)));
}
if (haveTargetCodeSystem) {
translationRequest.setTargetSystem(VersionConvertor_30_40.convertUri(theTargetCodeSystem));
translationRequest.setTargetSystem((org.hl7.fhir.r4.model.UriType) VersionConvertorFactory_30_40.convertType(theTargetCodeSystem, new BaseAdvisor_30_40(false)));
}
if (haveReverse) {
translationRequest.setReverse(VersionConvertor_30_40.convertBoolean(theReverse));
translationRequest.setReverse((org.hl7.fhir.r4.model.BooleanType) VersionConvertorFactory_30_40.convertType(theReverse, new BaseAdvisor_30_40(false)));
}
if (haveId) {
@ -155,7 +154,7 @@ public class BaseJpaResourceProviderConceptMapDstu3 extends JpaResourceProviderD
TranslateConceptResults result = dao.translate(translationRequest, theRequestDetails);
// Convert from R4 to DSTU3
return convertParameters(TermConceptMappingSvcImpl.toParameters(result));
return (Parameters) VersionConvertorFactory_30_40.convertResource(TermConceptMappingSvcImpl.toParameters(result), new BaseAdvisor_30_40(false));
} catch (FHIRException fe) {
throw new InternalErrorException(fe);
} finally {

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaResourceProviderDstu3.java
View File

@ -24,8 +24,6 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.provider.BaseJpaResourceProvider;
import org.hl7.fhir.instance.model.api.IAnyResource;
import static org.hl7.fhir.convertors.conv30_40.Parameters30_40.convertParameters;
public class JpaResourceProviderDstu3<T extends IAnyResource> extends BaseJpaResourceProvider<T> {
public JpaResourceProviderDstu3() {

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaSystemProviderDstu3.java
View File

@ -24,7 +24,6 @@ import java.util.Map.Entry;
import java.util.TreeMap;
import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
import static org.hl7.fhir.convertors.conv30_40.Parameters30_40.convertParameters;
/*
* #%L

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderCodeSystemR4.java
View File

@ -61,7 +61,8 @@ public class BaseJpaResourceProviderCodeSystemR4 extends JpaResourceProviderR4<C
@OperationParam(name="system", min=0, max=1) UriType theSystem,
@OperationParam(name="coding", min=0, max=1) Coding theCoding,
@OperationParam(name="version", min=0, max=1) StringType theVersion,
@OperationParam(name = "property", min = 0, max = OperationParam.MAX_UNLIMITED) List<CodeType> theProperties,
@OperationParam(name="displayLanguage", min=0, max=1) CodeType theDisplayLanguage,
@OperationParam(name="property", min = 0, max = OperationParam.MAX_UNLIMITED) List<CodeType> theProperties,
RequestDetails theRequestDetails
) {
@ -70,9 +71,9 @@ public class BaseJpaResourceProviderCodeSystemR4 extends JpaResourceProviderR4<C
IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
IValidationSupport.LookupCodeResult result;
if (theVersion != null) {
result = dao.lookupCode(theCode, new UriType(theSystem.getValue() + "|" + theVersion), theCoding, theRequestDetails);
result = dao.lookupCode(theCode, new UriType(theSystem.getValue() + "|" + theVersion), theCoding, theDisplayLanguage, theRequestDetails);
} else {
result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
result = dao.lookupCode(theCode, theSystem, theCoding, theDisplayLanguage, theRequestDetails);
}
result.throwNotFoundIfAppropriate();
return (Parameters) result.toParameters(theRequestDetails.getFhirContext(), theProperties);

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderCodeSystemR5.java
View File

@ -60,6 +60,7 @@ public class BaseJpaResourceProviderCodeSystemR5 extends JpaResourceProviderR5<C
@OperationParam(name="system", min=0, max=1) UriType theSystem,
@OperationParam(name="coding", min=0, max=1) Coding theCoding,
@OperationParam(name="version", min=0, max=1) StringType theVersion,
@OperationParam(name="displayLanguage", min=0, max=1) CodeType theDisplayLanguage,
@OperationParam(name = "property", min = 0, max = OperationParam.MAX_UNLIMITED) List<CodeType> theProperties,
RequestDetails theRequestDetails
) {
@ -69,9 +70,9 @@ public class BaseJpaResourceProviderCodeSystemR5 extends JpaResourceProviderR5<C
IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> dao = (IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept>) getDao();
IValidationSupport.LookupCodeResult result;
if (theVersion != null) {
result = dao.lookupCode(theCode, new UriType(theSystem.getValue() + "|" + theVersion), theCoding, theRequestDetails);
result = dao.lookupCode(theCode, new UriType(theSystem.getValue() + "|" + theVersion), theCoding, theDisplayLanguage, theRequestDetails);
} else {
result = dao.lookupCode(theCode, theSystem, theCoding, theRequestDetails);
result = dao.lookupCode(theCode, theSystem, theCoding, theDisplayLanguage, theRequestDetails);
}
result.throwNotFoundIfAppropriate();
return (Parameters) result.toParameters(theRequestDetails.getFhirContext(), theProperties);

38
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderConceptMapR5.java
View File

@ -20,9 +20,9 @@ package ca.uhn.fhir.jpa.provider.r5;
* #L%
*/
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.term.TermConceptMappingSvcImpl;
import ca.uhn.fhir.rest.annotation.IdParam;
@ -30,7 +30,8 @@ import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.CodeableConcept;
@ -52,7 +53,7 @@ public class BaseJpaResourceProviderConceptMapR5 extends JpaResourceProviderR5<C
HttpServletRequest theServletRequest,
@IdParam(optional = true) IdType theId,
@OperationParam(name = "url", min = 0, max = 1) UriType theUrl,
@OperationParam(name = "conceptMapVersion", min = 0, max = 1) StringType theConceptMapVersion,
@OperationParam(name = "conceptMapVersion", min = 0, max = 1) StringType theConceptMapVersion,
@OperationParam(name = "code", min = 0, max = 1) CodeType theSourceCode,
@OperationParam(name = "system", min = 0, max = 1) UriType theSourceCodeSystem,
@OperationParam(name = "version", min = 0, max = 1) StringType theSourceCodeSystemVersion,
@ -78,7 +79,7 @@ public class BaseJpaResourceProviderConceptMapR5 extends JpaResourceProviderR5<C
&& theSourceValueSet.hasValue();
boolean haveSourceCoding = theSourceCoding != null
&& theSourceCoding.hasCode();
boolean haveSourceCodeableConcept= theSourceCodeableConcept != null
boolean haveSourceCodeableConcept = theSourceCodeableConcept != null
&& theSourceCodeableConcept.hasCoding()
&& theSourceCodeableConcept.getCodingFirstRep().hasCode();
boolean haveTargetValueSet = theTargetValueSet != null
@ -97,43 +98,44 @@ public class BaseJpaResourceProviderConceptMapR5 extends JpaResourceProviderR5<C
TranslationRequest translationRequest = new TranslationRequest();
if (haveUrl) {
translationRequest.setUrl(VersionConvertor_40_50.convertUri(theUrl));
translationRequest.setUrl((org.hl7.fhir.r4.model.UriType) VersionConvertorFactory_40_50.convertType(theUrl, new BaseAdvisor_40_50(false)));
}
if (haveConceptMapVersion) {
translationRequest.setConceptMapVersion(VersionConvertor_40_50.convertString(theConceptMapVersion));
translationRequest.setConceptMapVersion((org.hl7.fhir.r4.model.StringType) VersionConvertorFactory_40_50.convertType(theConceptMapVersion, new BaseAdvisor_40_50(false)));
}
if (haveSourceCode) {
translationRequest.getCodeableConcept().addCoding().setCodeElement(VersionConvertor_40_50.convertCode(theSourceCode));
translationRequest.getCodeableConcept().addCoding().setCodeElement((org.hl7.fhir.r4.model.CodeType) VersionConvertorFactory_40_50.convertType(theSourceCode, new BaseAdvisor_40_50(false)));
if (haveSourceCodeSystem) {
translationRequest.getCodeableConcept().getCodingFirstRep().setSystemElement(VersionConvertor_40_50.convertUri(theSourceCodeSystem));
translationRequest.getCodeableConcept().getCodingFirstRep().setSystemElement((org.hl7.fhir.r4.model.UriType) VersionConvertorFactory_40_50.convertType(theSourceCodeSystem, new BaseAdvisor_40_50(false)));
}
if (haveSourceCodeSystemVersion) {
translationRequest.getCodeableConcept().getCodingFirstRep().setVersionElement(VersionConvertor_40_50.convertString(theSourceCodeSystemVersion));
translationRequest.getCodeableConcept().getCodingFirstRep()
.setVersionElement((org.hl7.fhir.r4.model.StringType) VersionConvertorFactory_40_50.convertType(theSourceCodeSystemVersion, new BaseAdvisor_40_50(false)));
}
} else if (haveSourceCoding) {
translationRequest.getCodeableConcept().addCoding(VersionConvertor_40_50.convertCoding(theSourceCoding));
translationRequest.getCodeableConcept().addCoding((org.hl7.fhir.r4.model.Coding) VersionConvertorFactory_40_50.convertType(theSourceCoding, new BaseAdvisor_40_50(false)));
} else {
translationRequest.setCodeableConcept(VersionConvertor_40_50.convertCodeableConcept(theSourceCodeableConcept));
translationRequest.setCodeableConcept((org.hl7.fhir.r4.model.CodeableConcept) VersionConvertorFactory_40_50.convertType(theSourceCodeableConcept, new BaseAdvisor_40_50(false)));
}
if (haveSourceValueSet) {
translationRequest.setSource(VersionConvertor_40_50.convertUri(theSourceValueSet));
translationRequest.setSource((org.hl7.fhir.r4.model.UriType) VersionConvertorFactory_40_50.convertType(theSourceValueSet, new BaseAdvisor_40_50(false)));
}
if (haveTargetValueSet) {
translationRequest.setTarget(VersionConvertor_40_50.convertUri(theTargetValueSet));
translationRequest.setTarget((org.hl7.fhir.r4.model.UriType) VersionConvertorFactory_40_50.convertType(theTargetValueSet, new BaseAdvisor_40_50(false)));
}
if (haveTargetCodeSystem) {
translationRequest.setTargetSystem(VersionConvertor_40_50.convertUri(theTargetCodeSystem));
translationRequest.setTargetSystem((org.hl7.fhir.r4.model.UriType) VersionConvertorFactory_40_50.convertType(theTargetCodeSystem, new BaseAdvisor_40_50(false)));
}
if (haveReverse) {
translationRequest.setReverse(VersionConvertor_40_50.convertBoolean(theReverse));
translationRequest.setReverse((org.hl7.fhir.r4.model.BooleanType) VersionConvertorFactory_40_50.convertType(theReverse, new BaseAdvisor_40_50(false)));
}
if (haveId) {
@ -145,7 +147,7 @@ public class BaseJpaResourceProviderConceptMapR5 extends JpaResourceProviderR5<C
IFhirResourceDaoConceptMap<ConceptMap> dao = (IFhirResourceDaoConceptMap<ConceptMap>) getDao();
TranslateConceptResults result = dao.translate(translationRequest, theRequestDetails);
org.hl7.fhir.r4.model.Parameters parameters = TermConceptMappingSvcImpl.toParameters(result);
return org.hl7.fhir.convertors.conv40_50.Parameters40_50.convertParameters(parameters);
return (Parameters) VersionConvertorFactory_40_50.convertResource(parameters, new BaseAdvisor_40_50(false));
} finally {
endRequest(theServletRequest);
}

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/job/ReindexEverythingJobConfig.java
View File

@ -49,6 +49,8 @@ public class ReindexEverythingJobConfig {
private StepBuilderFactory myStepBuilderFactory;
@Autowired
private JobBuilderFactory myJobBuilderFactory;
@Autowired
private ReindexWriter myReindexWriter;
@Bean(name = REINDEX_EVERYTHING_JOB_NAME)
@Lazy
@ -63,7 +65,7 @@ public class ReindexEverythingJobConfig {
return myStepBuilderFactory.get(REINDEX_EVERYTHING_STEP_NAME)
.<List<Long>, List<Long>>chunk(1)
.reader(cronologicalBatchAllResourcePidReader())
.writer(reindexWriter())
.writer(myReindexWriter)
.listener(reindexEverythingPidCountRecorderListener())
.listener(reindexEverythingPromotionListener())
.build();
@ -75,12 +77,6 @@ public class ReindexEverythingJobConfig {
return new CronologicalBatchAllResourcePidReader();
}
@Bean
@StepScope
public ReindexWriter reindexWriter() {
return new ReindexWriter();
}
@Bean
@StepScope
public PidReaderCounterListener reindexEverythingPidCountRecorderListener() {

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/reindex/job/ReindexJobConfig.java
View File

@ -51,6 +51,8 @@ public class ReindexJobConfig extends MultiUrlProcessorJobConfig {
private StepBuilderFactory myStepBuilderFactory;
@Autowired
private JobBuilderFactory myJobBuilderFactory;
@Autowired
private ReindexWriter myReindexWriter;
@Bean(name = REINDEX_JOB_NAME)
@Lazy
@ -66,18 +68,12 @@ public class ReindexJobConfig extends MultiUrlProcessorJobConfig {
return myStepBuilderFactory.get(REINDEX_URL_LIST_STEP_NAME)
.<List<Long>, List<Long>>chunk(1)
.reader(reverseCronologicalBatchResourcePidReader())
.writer(reindexWriter())
.writer(myReindexWriter)
.listener(pidCountRecorderListener())
.listener(reindexPromotionListener())
.build();
}
@Bean
@StepScope
public ReindexWriter reindexWriter() {
return new ReindexWriter();
}
@Bean
public ExecutionContextPromotionListener reindexPromotionListener() {
ExecutionContextPromotionListener listener = new ExecutionContextPromotionListener();

51
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java
View File

@ -988,9 +988,12 @@ public class QueryStack {
String theSpnamePrefix, RuntimeSearchParam theSearchParam, List<? extends IQueryParameterType> theList,
SearchFilterParser.CompareOperation theOperation, RequestPartitionId theRequestPartitionId) {
List<IQueryParameterType> tokens = new ArrayList<>();
List<IQueryParameterType> tokens = new ArrayList<>();
boolean paramInverted = false;
TokenParamModifier modifier = null;
for (IQueryParameterType nextOr : theList) {
if (nextOr instanceof TokenParam) {
if (!((TokenParam) nextOr).isEmpty()) {
TokenParam id = (TokenParam) nextOr;
@ -1009,17 +1012,20 @@ public class QueryStack {
}
return createPredicateString(theSourceJoinColumn, theResourceName, theSpnamePrefix, theSearchParam, theList, null, theRequestPartitionId);
}
modifier = id.getModifier();
// for :not modifier, create a token and remove the :not modifier
if (modifier != null && modifier == TokenParamModifier.NOT) {
tokens.add(new TokenParam(((TokenParam) nextOr).getSystem(), ((TokenParam) nextOr).getValue()));
paramInverted = true;
} else {
tokens.add(nextOr);
}
tokens.add(nextOr);
}
} else {
tokens.add(nextOr);
}
}
if (tokens.isEmpty()) {
@ -1027,14 +1033,31 @@ public class QueryStack {
}
String paramName = getParamNameWithPrefix(theSpnamePrefix, theSearchParam.getName());
Condition predicate;
BaseJoiningPredicateBuilder join;
if (paramInverted) {
SearchQueryBuilder sqlBuilder = mySqlBuilder.newChildSqlBuilder();
TokenPredicateBuilder tokenSelector = sqlBuilder.addTokenPredicateBuilder(null);
sqlBuilder.addPredicate(tokenSelector.createPredicateToken(tokens, theResourceName, theSpnamePrefix, theSearchParam, theRequestPartitionId));
SelectQuery sql = sqlBuilder.getSelect();
Expression subSelect = new Subquery(sql);
join = mySqlBuilder.getOrCreateFirstPredicateBuilder();
predicate = new InCondition(join.getResourceIdColumn(), subSelect).setNegate(true);
} else {
TokenPredicateBuilder tokenJoin = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.TOKEN, theSourceJoinColumn, paramName, () -> mySqlBuilder.addTokenPredicateBuilder(theSourceJoinColumn)).getResult();
TokenPredicateBuilder join = createOrReusePredicateBuilder(PredicateBuilderTypeEnum.TOKEN, theSourceJoinColumn, paramName, () -> mySqlBuilder.addTokenPredicateBuilder(theSourceJoinColumn)).getResult();
if (theList.get(0).getMissing() != null) {
return tokenJoin.createPredicateParamMissingForNonReference(theResourceName, paramName, theList.get(0).getMissing(), theRequestPartitionId);
}
if (theList.get(0).getMissing() != null) {
return join.createPredicateParamMissingForNonReference(theResourceName, paramName, theList.get(0).getMissing(), theRequestPartitionId);
}
Condition predicate = join.createPredicateToken(tokens, theResourceName, theSpnamePrefix, theSearchParam, theOperation, theRequestPartitionId);
predicate = tokenJoin.createPredicateToken(tokens, theResourceName, theSpnamePrefix, theSearchParam, theOperation, theRequestPartitionId);
join = tokenJoin;
}
return join.combineWithRequestPartitionIdPredicate(theRequestPartitionId, predicate);
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/StringPredicateBuilder.java
View File

@ -225,15 +225,15 @@ public class StringPredicateBuilder extends BaseSearchParamPredicateBuilder {
}
public static String createLeftAndRightMatchLikeExpression(String likeExpression) {
return "%" + likeExpression.replace("%", "[%]") + "%";
return "%" + likeExpression.replace("%", "\\%") + "%";
}
public static String createLeftMatchLikeExpression(String likeExpression) {
return likeExpression.replace("%", "[%]") + "%";
return likeExpression.replace("%", "\\%") + "%";
}
public static String createRightMatchLikeExpression(String likeExpression) {
return "%" + likeExpression.replace("%", "[%]");
return "%" + likeExpression.replace("%", "\\%");
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java
View File

@ -42,7 +42,7 @@ import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.concurrent.BasicThreadFactory;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.r4.model.InstantType;
import org.jetbrains.annotations.Nullable;
import javax.annotation.Nullable;
import org.quartz.JobExecutionContext;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

27
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
View File

@ -1989,7 +1989,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
protected abstract ValueSet toCanonicalValueSet(IBaseResource theValueSet);
protected IValidationSupport.LookupCodeResult lookupCode(String theSystem, String theCode) {
protected IValidationSupport.LookupCodeResult lookupCode(String theSystem, String theCode, String theDisplayLanguage) {
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
return txTemplate.execute(t -> {
Optional<TermConcept> codeOpt = findCode(theSystem, theCode);
@ -2005,13 +2005,16 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
result.setCodeDisplay(code.getDisplay());
for (TermConceptDesignation next : code.getDesignations()) {
IValidationSupport.ConceptDesignation designation = new IValidationSupport.ConceptDesignation();
designation.setLanguage(next.getLanguage());
designation.setUseSystem(next.getUseSystem());
designation.setUseCode(next.getUseCode());
designation.setUseDisplay(next.getUseDisplay());
designation.setValue(next.getValue());
result.getDesignations().add(designation);
// filter out the designation based on displayLanguage if any
if (isDisplayLanguageMatch(theDisplayLanguage, next.getLanguage())) {
IValidationSupport.ConceptDesignation designation = new IValidationSupport.ConceptDesignation();
designation.setLanguage(next.getLanguage());
designation.setUseSystem(next.getUseSystem());
designation.setUseCode(next.getUseCode());
designation.setUseDisplay(next.getUseDisplay());
designation.setValue(next.getValue());
result.getDesignations().add(designation);
}
}
for (TermConceptProperty next : code.getProperties()) {
@ -2034,6 +2037,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
});
}
@Nullable
private ConceptSubsumptionOutcome testForSubsumption(SearchSession theSearchSession, TermConcept theLeft, TermConcept theRight, ConceptSubsumptionOutcome theOutput) {
List<TermConcept> fetch = theSearchSession.search(TermConcept.class)
@ -2481,4 +2485,11 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
return termConcept;
}
static boolean isDisplayLanguageMatch(String theReqLang, String theStoredLang) {
// NOTE: return the designation when one of then is not specified.
if (theReqLang == null || theStoredLang == null)
return true;
return theReqLang.equalsIgnoreCase(theStoredLang);
}
}

28
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcDstu3.java
View File

@ -9,8 +9,8 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.ValidateUtil;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.convertors.conv30_40.CodeSystem30_40;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
@ -25,8 +25,6 @@ import org.springframework.transaction.PlatformTransactionManager;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSet;
/*
* #%L
* HAPI FHIR JPA Server
@ -67,7 +65,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
valueSetToExpandR4 = toCanonicalValueSet(theValueSetToExpand);
org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSet(theExpansionOptions, valueSetToExpandR4);
return new ValueSetExpansionOutcome(convertValueSet(expandedR4), null);
return new ValueSetExpansionOutcome(VersionConvertorFactory_30_40.convertResource(expandedR4, new BaseAdvisor_30_40(false)), null);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -81,7 +79,7 @@ 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(theExpansionOptions, valueSetToExpandR4);
return convertValueSet(expandedR4);
return VersionConvertorFactory_30_40.convertResource(expandedR4, new BaseAdvisor_30_40(false));
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -90,31 +88,31 @@ 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 = convertValueSet((ValueSet) theValueSet);
valueSetToExpandR4 = (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_30_40.convertResource((ValueSet) theValueSet, new BaseAdvisor_30_40(false));
return valueSetToExpandR4;
}
@Override
protected org.hl7.fhir.r4.model.CodeSystem toCanonicalCodeSystem(IBaseResource theCodeSystem) {
return CodeSystem30_40.convertCodeSystem((CodeSystem)theCodeSystem);
return (org.hl7.fhir.r4.model.CodeSystem) VersionConvertorFactory_30_40.convertResource((CodeSystem)theCodeSystem, new BaseAdvisor_30_40(false));
}
@Override
@Nullable
protected org.hl7.fhir.r4.model.Coding toCanonicalCoding(IBaseDatatype theCoding) {
return VersionConvertor_30_40.convertCoding((org.hl7.fhir.dstu3.model.Coding) theCoding);
return (org.hl7.fhir.r4.model.Coding) VersionConvertorFactory_30_40.convertType((Coding) theCoding, new BaseAdvisor_30_40(false));
}
@Override
@Nullable
protected org.hl7.fhir.r4.model.Coding toCanonicalCoding(IBaseCoding theCoding) {
return VersionConvertor_30_40.convertCoding((org.hl7.fhir.dstu3.model.Coding) theCoding);
return (org.hl7.fhir.r4.model.Coding) VersionConvertorFactory_30_40.convertType((org.hl7.fhir.dstu3.model.Coding) theCoding, new BaseAdvisor_30_40(false));
}
@Override
@Nullable
protected org.hl7.fhir.r4.model.CodeableConcept toCanonicalCodeableConcept(IBaseDatatype theCoding) {
return VersionConvertor_30_40.convertCodeableConcept((org.hl7.fhir.dstu3.model.CodeableConcept) theCoding);
return (org.hl7.fhir.r4.model.CodeableConcept) VersionConvertorFactory_30_40.convertType((CodeableConcept) theCoding, new BaseAdvisor_30_40(false));
}
@ -147,8 +145,8 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
return super.lookupCode(theSystem, theCode);
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theDisplayLanguage) {
return super.lookupCode(theSystem, theCode, theDisplayLanguage);
}
@Override
@ -160,7 +158,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
public IValidationSupport.CodeValidationResult validateCodeIsInPreExpandedValueSet(ConceptValidationOptions theOptions, 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 = convertValueSet(valueSet);
org.hl7.fhir.r4.model.ValueSet valueSetR4 = (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_30_40.convertResource(valueSet, new BaseAdvisor_30_40(false));
Coding coding = (Coding) theCoding;
org.hl7.fhir.r4.model.Coding codingR4 = null;
@ -184,7 +182,7 @@ 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 = convertValueSet(valueSet);
org.hl7.fhir.r4.model.ValueSet valueSetR4 = (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_30_40.convertResource(valueSet, new BaseAdvisor_30_40(false));
return super.isValueSetPreExpandedForCodeValidation(valueSetR4);
}
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcR4.java
View File

@ -92,8 +92,8 @@ public class TermReadSvcR4 extends BaseTermReadSvcImpl implements ITermReadSvcR4
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
return super.lookupCode(theSystem, theCode);
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theDisplayLanguage) {
return super.lookupCode(theSystem, theCode, theDisplayLanguage);
}
@Override

29
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcR5.java
View File

@ -10,8 +10,8 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR5;
import ca.uhn.fhir.jpa.term.ex.ExpansionTooCostlyException;
import ca.uhn.fhir.util.ValidateUtil;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.convertors.conv40_50.CodeSystem40_50;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -19,8 +19,6 @@ import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.utilities.TerminologyServiceOptions;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.PlatformTransactionManager;
@ -59,15 +57,16 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
@Transactional(dontRollbackOn = {ExpansionTooCostlyException.class})
public ValueSetExpansionOutcome expandValueSet(ValidationSupportContext theValidationSupportContext, ValueSetExpansionOptions theExpansionOptions, @Nonnull IBaseResource theValueSetToExpand) {
ValueSet valueSetToExpand = (ValueSet) theValueSetToExpand;
org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSet(theExpansionOptions, org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetToExpand));
return new ValueSetExpansionOutcome(org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(expandedR4));
org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSet(theExpansionOptions,
(org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_40_50.convertResource(valueSetToExpand, new BaseAdvisor_40_50(false)));
return new ValueSetExpansionOutcome(VersionConvertorFactory_40_50.convertResource(expandedR4, new BaseAdvisor_40_50(false)));
}
@Override
public IBaseResource expandValueSet(ValueSetExpansionOptions theExpansionOptions, IBaseResource theInput) {
org.hl7.fhir.r4.model.ValueSet valueSetToExpand = toCanonicalValueSet(theInput);
org.hl7.fhir.r4.model.ValueSet valueSetR4 = super.expandValueSet(theExpansionOptions, valueSetToExpand);
return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetR4);
return VersionConvertorFactory_40_50.convertResource(valueSetR4, new BaseAdvisor_40_50(false));
}
@Override
@ -79,7 +78,7 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
@Override
protected org.hl7.fhir.r4.model.ValueSet getValueSetFromResourceTable(ResourceTable theResourceTable) {
ValueSet valueSetR5 = myDaoRegistry.getResourceDao("ValueSet").toResource(ValueSet.class, theResourceTable, null, false);
return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetR5);
return (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_40_50.convertResource(valueSetR5, new BaseAdvisor_40_50(false));
}
@Override
@ -110,30 +109,30 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
@Override
@Nullable
protected org.hl7.fhir.r4.model.Coding toCanonicalCoding(IBaseDatatype theCoding) {
return VersionConvertor_40_50.convertCoding((Coding) theCoding);
return (org.hl7.fhir.r4.model.Coding) VersionConvertorFactory_40_50.convertType((Coding) theCoding, new BaseAdvisor_40_50(false));
}
@Override
@Nullable
protected org.hl7.fhir.r4.model.Coding toCanonicalCoding(IBaseCoding theCoding) {
return VersionConvertor_40_50.convertCoding((Coding) theCoding);
return (org.hl7.fhir.r4.model.Coding) VersionConvertorFactory_40_50.convertType((Coding) theCoding, new BaseAdvisor_40_50(false));
}
@Override
@Nullable
protected org.hl7.fhir.r4.model.CodeableConcept toCanonicalCodeableConcept(IBaseDatatype theCoding) {
return VersionConvertor_40_50.convertCodeableConcept((CodeableConcept) theCoding);
return (org.hl7.fhir.r4.model.CodeableConcept) VersionConvertorFactory_40_50.convertType((CodeableConcept) theCoding, new BaseAdvisor_40_50(false));
}
@Override
protected org.hl7.fhir.r4.model.ValueSet toCanonicalValueSet(IBaseResource theValueSet) throws org.hl7.fhir.exceptions.FHIRException {
return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet((ValueSet) theValueSet);
return (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_40_50.convertResource((ValueSet) theValueSet, new BaseAdvisor_40_50(false));
}
@Override
protected org.hl7.fhir.r4.model.CodeSystem toCanonicalCodeSystem(IBaseResource theCodeSystem) {
return CodeSystem40_50.convertCodeSystem((CodeSystem) theCodeSystem);
return (org.hl7.fhir.r4.model.CodeSystem) VersionConvertorFactory_40_50.convertResource((CodeSystem) theCodeSystem, new BaseAdvisor_40_50(false));
}
@Override
@ -145,8 +144,8 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode) {
return super.lookupCode(theSystem, theCode);
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theDisplayLanguage) {
return super.lookupCode(theSystem, theCode, theDisplayLanguage);
}
}

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcDstu3.java
View File

@ -25,6 +25,8 @@ import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.UrlUtil;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.ConceptMap;
import org.hl7.fhir.dstu3.model.ValueSet;
@ -36,9 +38,6 @@ import org.springframework.context.event.ContextRefreshedEvent;
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 {
@ -56,7 +55,7 @@ public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl im
/**
* Initialize the beans that are used by this service.
*
* <p>
* Note: There is a circular dependency here where the CodeSystem DAO
* needs terminology services, and the term services need the CodeSystem DAO.
* So we look these up in a refresh event instead of just autowiring them
@ -70,11 +69,11 @@ public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl im
myConceptMapResourceDao = (IFhirResourceDao<ConceptMap>) myAppCtx.getBean("myConceptMapDaoDstu3");
}
@Override
@Override
public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, RequestDetails theRequestDetails) {
CodeSystem resourceToStore;
try {
resourceToStore = convertCodeSystem(theCodeSystemResource);
resourceToStore = (CodeSystem) VersionConvertorFactory_30_40.convertResource(theCodeSystemResource, new BaseAdvisor_30_40(false));
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -91,7 +90,7 @@ public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl im
public void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
ConceptMap resourceToStore;
try {
resourceToStore = convertConceptMap(theConceptMap);
resourceToStore = (ConceptMap) VersionConvertorFactory_30_40.convertResource(theConceptMap, new BaseAdvisor_30_40(false));
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -107,7 +106,7 @@ public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl im
public void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
ValueSet valueSetDstu3;
try {
valueSetDstu3 = convertValueSet(theValueSet);
valueSetDstu3 = (ValueSet) VersionConvertorFactory_30_40.convertResource(theValueSet, new BaseAdvisor_30_40(false));
} catch (FHIRException e) {
throw new InternalErrorException(e);
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR5.java
View File

@ -24,6 +24,8 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.util.UrlUtil;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.ConceptMap;
@ -63,7 +65,7 @@ public class TermVersionAdapterSvcR5 extends BaseTermVersionAdapterSvcImpl imple
public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, RequestDetails theRequestDetails) {
validateCodeSystemForStorage(theCodeSystemResource);
CodeSystem codeSystemR4 = org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem(theCodeSystemResource);
CodeSystem codeSystemR4 = (CodeSystem) VersionConvertorFactory_40_50.convertResource(theCodeSystemResource, new BaseAdvisor_40_50(false));
if (isBlank(theCodeSystemResource.getIdElement().getIdPart())) {
String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
return myCodeSystemResourceDao.update(codeSystemR4, matchUrl, theRequestDetails).getId();
@ -75,7 +77,7 @@ 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.ConceptMap40_50.convertConceptMap(theConceptMap);
ConceptMap conceptMapR4 = (ConceptMap) VersionConvertorFactory_40_50.convertResource(theConceptMap, new BaseAdvisor_40_50(false));
if (isBlank(theConceptMap.getIdElement().getIdPart())) {
String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
@ -88,7 +90,7 @@ 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.ValueSet40_50.convertValueSet(theValueSet);
ValueSet valueSetR4 = (ValueSet) VersionConvertorFactory_40_50.convertResource(theValueSet, new BaseAdvisor_40_50(false));
if (isBlank(theValueSet.getIdElement().getIdPart())) {
String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());

23
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/ValidatorResourceFetcher.java
View File

@ -27,7 +27,9 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import org.hl7.fhir.common.hapi.validation.validator.VersionSpecificWorkerContextWrapper;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r5.elementmodel.Element;
@ -39,6 +41,9 @@ import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.PostConstruct;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URISyntaxException;
import java.util.Locale;
public class ValidatorResourceFetcher implements IResourceValidator.IValidatorResourceFetcher {
@ -60,10 +65,8 @@ public class ValidatorResourceFetcher implements IResourceValidator.IValidatorRe
myVersionSpecificCOntextWrapper = VersionSpecificWorkerContextWrapper.newVersionSpecificWorkerContextWrapper(myValidationSupport);
}
@Override
public Element fetch(Object appContext, String theUrl) throws FHIRException {
public Element fetch(IResourceValidator iResourceValidator, Object appContext, String theUrl) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
IdType id = new IdType(theUrl);
String resourceType = id.getResourceType();
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(resourceType);
@ -83,7 +86,8 @@ public class ValidatorResourceFetcher implements IResourceValidator.IValidatorRe
}
@Override
public IResourceValidator.ReferenceValidationPolicy validationPolicy(Object appContext, String path, String url) {
public IResourceValidator.ReferenceValidationPolicy validationPolicy(IResourceValidator iResourceValidator,
Object appContext, String path, String url) {
int slashIdx = url.indexOf("/");
if (slashIdx > 0 && myFhirContext.getResourceTypes().contains(url.substring(0, slashIdx))) {
return myValidationSettings.getLocalReferenceValidationDefaultPolicy();
@ -93,12 +97,12 @@ public class ValidatorResourceFetcher implements IResourceValidator.IValidatorRe
}
@Override
public boolean resolveURL(Object appContext, String path, String url, String type) throws FHIRException {
public boolean resolveURL(IResourceValidator iResourceValidator, Object o, String s, String s1, String s2) throws IOException, FHIRException {
return true;
}
@Override
public byte[] fetchRaw(String url) {
public byte[] fetchRaw(IResourceValidator iResourceValidator, String s) throws MalformedURLException, IOException {
throw new UnsupportedOperationException();
}
@ -109,13 +113,12 @@ public class ValidatorResourceFetcher implements IResourceValidator.IValidatorRe
}
@Override
public CanonicalResource fetchCanonicalResource(String url) {
throw new UnsupportedOperationException();
public CanonicalResource fetchCanonicalResource(IResourceValidator iResourceValidator, String s) throws URISyntaxException {
return null;
}
@Override
public boolean fetchesCanonicalResource(String url) {
public boolean fetchesCanonicalResource(IResourceValidator iResourceValidator, String s) {
return false;
}
}

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoValueSetDstu2Test.java
View File

@ -78,7 +78,8 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
CodingDt coding = null;
CodeableConceptDt codeableConcept = null;
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertFalse(result.isOk());
//TODO JA, from what I read, this _should_ pass, but this was flipped to false in a previous commit.
assertTrue(result.isOk());
}
@Test

9
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
View File

@ -38,7 +38,6 @@ import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl;
import ca.uhn.fhir.jpa.term.TermConceptMappingSvcImpl;
@ -53,10 +52,13 @@ import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.util.UrlUtil;
import org.apache.commons.io.IOUtils;
import org.hibernate.search.mapper.orm.Search;
import org.hibernate.search.mapper.orm.session.SearchSession;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.dstu3.model.AllergyIntolerance;
import org.hl7.fhir.dstu3.model.Appointment;
import org.hl7.fhir.dstu3.model.AuditEvent;
@ -125,7 +127,6 @@ import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.Map;
import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
import static org.junit.jupiter.api.Assertions.fail;
@ExtendWith(SpringExtension.class)
@ -378,7 +379,7 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@BeforeEach
public void beforeFlushFT() {
runInTransaction(() -> {
SearchSession searchSession = Search.session(myEntityManager);
SearchSession searchSession = Search.session(myEntityManager);
searchSession.workspace(ResourceTable.class).purge();
// searchSession.workspace(ResourceIndexedSearchParamString.class).purge();
searchSession.indexingPlan().execute();
@ -462,7 +463,7 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
*/
public static ConceptMap createConceptMap() {
try {
return convertConceptMap(BaseJpaR4Test.createConceptMap());
return (ConceptMap) VersionConvertorFactory_30_40.convertResource(BaseJpaR4Test.createConceptMap(), new BaseAdvisor_30_40(false));
} catch (FHIRException fe) {
throw new InternalErrorException(fe);
}

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java
View File

@ -116,12 +116,16 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
myDaoConfig.setAllowMultipleDelete(new DaoConfig().isAllowMultipleDelete());
myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
myDaoConfig.setMaximumDeleteConflictQueryCount(new DaoConfig().getMaximumDeleteConflictQueryCount());
myDaoConfig.setBundleBatchPoolSize(new DaoConfig().getBundleBatchPoolSize());
myDaoConfig.setBundleBatchMaxPoolSize(new DaoConfig().getBundleBatchMaxPoolSize());
}
@BeforeEach
public void beforeDisableResultReuse() {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
myDaoConfig.setBundleBatchPoolSize(1);
myDaoConfig.setBundleBatchMaxPoolSize(1);
}
private Bundle createInputTransactionWithPlaceholderIdInMatchUrl(HTTPVerb theVerb) {

39
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/expunge/ExpungeHookTest.java
View File

@ -10,6 +10,7 @@ import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.test.concurrency.PointcutLatch;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Meta;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
@ -40,6 +41,8 @@ public class ExpungeHookTest extends BaseJpaDstu3Test {
@BeforeEach
public void before() {
myDaoConfig.setExpungeEnabled(true);
myDaoConfig.setResourceClientIdStrategy(DaoConfig.ClientIdStrategyEnum.ALPHANUMERIC);
myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
myInterceptorService.registerAnonymousInterceptor(Pointcut.STORAGE_PRESTORAGE_EXPUNGE_EVERYTHING, myEverythingLatch);
myInterceptorService.registerAnonymousInterceptor(Pointcut.STORAGE_PRESTORAGE_EXPUNGE_RESOURCE, myExpungeResourceLatch);
}
@ -65,6 +68,42 @@ public class ExpungeHookTest extends BaseJpaDstu3Test {
assertPatientGone(id);
}
@Test
public void expungeEverythingAndRecreate() throws InterruptedException {
// Create a patient.
Patient thePatient = new Patient();
thePatient.setId("ABC123");
Meta theMeta = new Meta();
theMeta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient");
thePatient.setMeta(theMeta);
IIdType id = myPatientDao.update(thePatient, mySrd).getId();
assertNotNull(myPatientDao.read(id));
// Expunge it directly.
myPatientDao.delete(id);
ExpungeOptions options = new ExpungeOptions();
options.setExpungeEverything(true);
options.setExpungeDeletedResources(true);
options.setExpungeOldVersions(true);
myPatientDao.expunge(id.toUnqualifiedVersionless(), options, mySrd);
assertPatientGone(id);
// Create it a second time.
myPatientDao.update(thePatient, mySrd);
assertNotNull(myPatientDao.read(id));
// Expunge everything with the service.
myEverythingLatch.setExpectedCount(1);
myExpungeService.expunge(null, null, null, options, mySrd);
myEverythingLatch.awaitExpected();
assertPatientGone(id);
// Create it a third time.
myPatientDao.update(thePatient, mySrd);
assertNotNull(myPatientDao.read(id));
}
private void assertPatientGone(IIdType theId) {
try {
myPatientDao.read(theId);

34
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
View File

@ -20,6 +20,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.model.util.UcumServiceUtil;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap.EverythingModeEnum;
@ -104,7 +105,6 @@ import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Period;
import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.Procedure;
import org.hl7.fhir.r4.model.Provenance;
import org.hl7.fhir.r4.model.Quantity;
import org.hl7.fhir.r4.model.Questionnaire;
@ -127,6 +127,7 @@ import org.hl7.fhir.r4.model.ValueSet;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import org.mockito.ArgumentCaptor;
import org.mockito.ArgumentMatchers;
@ -151,12 +152,14 @@ import java.util.stream.Collectors;
import static ca.uhn.fhir.rest.api.Constants.PARAM_TYPE;
import static org.apache.commons.lang3.StringUtils.countMatches;
import static org.hamcrest.CoreMatchers.is;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.endsWith;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.hasItem;
import static org.hamcrest.Matchers.hasItems;
import static org.hamcrest.Matchers.hasSize;
@ -1357,6 +1360,34 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
assertThat(actual, contains(id));
}
@Test
@DisplayName("Duplicate Conditional Creates all resolve to the same match")
public void testDuplicateConditionalCreatesOnToken() throws IOException {
String inputString = IOUtils.toString(getClass().getResourceAsStream("/duplicate-conditional-create.json"), StandardCharsets.UTF_8);
Bundle firstBundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, inputString);
//Before you ask, yes, this has to be separately parsed. The reason for this is that the parameters passed to mySystemDao.transaction are _not_ immutable, so we cannot
//simply reuse the original bundle object.
Bundle duplicateBundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, inputString);
Bundle bundleResponse = mySystemDao.transaction(new SystemRequestDetails(), firstBundle);
bundleResponse.getEntry()
.forEach( entry -> assertThat(entry.getResponse().getStatus(), is(equalTo("201 Created"))));
IBundleProvider search = myOrganizationDao.search(new SearchParameterMap().setLoadSynchronous(true));
assertEquals(1, search.getAllResources().size());
//Running the bundle again should just result in 0 new resources created, as the org should already exist, and there is no update to the SR.
bundleResponse= mySystemDao.transaction(new SystemRequestDetails(), duplicateBundle);
bundleResponse.getEntry()
.forEach( entry -> {
assertThat(entry.getResponse().getStatus(), is(equalTo("200 OK")));
});
search = myOrganizationDao.search(new SearchParameterMap().setLoadSynchronous(true), new SystemRequestDetails());
assertEquals(1, search.getAllResources().size());
}
@Test
public void testIndexNoDuplicatesToken() {
Patient res = new Patient();
@ -5304,7 +5335,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
createObservationWithEffective("YES22", "2011-01-02T00:00:00+10:00");
createObservationWithEffective("YES23", "2011-01-02T00:00:00+11:00");
SearchParameterMap map = new SearchParameterMap();
map.setLoadSynchronous(true);
map.add(Observation.SP_DATE, new DateParam("2011-01-02"));

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4VersionedReferenceTest.java
View File

@ -779,7 +779,6 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
assertEquals(observationId.getValue(), resources.get(0).getIdElement().getValue());
assertEquals(patientId.withVersion("2").getValue(), resources.get(1).getIdElement().getValue());
}
}
@Test

23
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java
View File

@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
import ca.uhn.fhir.jpa.model.entity.ResourceEncodingEnum;
@ -63,6 +64,7 @@ import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.Quantity;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.Task;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
@ -115,12 +117,16 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
myDaoConfig.setAllowInlineMatchUrlReferences(false);
myDaoConfig.setAllowMultipleDelete(new DaoConfig().isAllowMultipleDelete());
myModelConfig.setNormalizedQuantitySearchLevel(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED);
myDaoConfig.setBundleBatchPoolSize(new DaoConfig().getBundleBatchPoolSize());
myDaoConfig.setBundleBatchMaxPoolSize(new DaoConfig().getBundleBatchMaxPoolSize());
}
@BeforeEach
public void beforeDisableResultReuse() {
myInterceptorRegistry.registerInterceptor(myInterceptor);
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
myDaoConfig.setBundleBatchPoolSize(1);
myDaoConfig.setBundleBatchMaxPoolSize(1);
}
private Bundle createInputTransactionWithPlaceholderIdInMatchUrl(HTTPVerb theVerb) {
@ -1002,6 +1008,23 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
}
@Test
public void testTransactionNoContainedRedux() throws IOException {
//Pre-create the patient, which will cause the ifNoneExist to prevent a new creation during bundle transaction
Patient patient = loadResourceFromClasspath(Patient.class, "/r4/preexisting-patient.json");
myPatientDao.create(patient);
//Post the Bundle containing a conditional POST with an identical patient from the above resource.
Bundle request = loadResourceFromClasspath(Bundle.class, "/r4/transaction-no-contained-2.json");
Bundle outcome = mySystemDao.transaction(mySrd, request);
IdType taskId = new IdType(outcome.getEntry().get(0).getResponse().getLocation());
Task task = myTaskDao.read(taskId, mySrd);
assertThat(task.getBasedOn().get(0).getReference(), matchesPattern("Patient/[0-9]+"));
}
@Test
public void testTransactionNoContained() throws IOException {

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/SearchCoordinatorSvcImplTest.java
View File

@ -10,10 +10,8 @@ import ca.uhn.fhir.jpa.entity.SearchTypeEnum;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.search.cache.DatabaseSearchCacheSvcImpl;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.lang3.time.DateUtils;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
@ -40,7 +38,7 @@ public class SearchCoordinatorSvcImplTest extends BaseJpaR4Test {
private ISearchCoordinatorSvc mySearchCoordinator;
@Autowired
private ISearchCacheSvc myDataaseCacheSvc;
private ISearchCacheSvc myDatabaseCacheSvc;
@AfterEach
public void after() {
@ -92,7 +90,7 @@ public class SearchCoordinatorSvcImplTest extends BaseJpaR4Test {
assertEquals(30, mySearchResultDao.count());
});
myDataaseCacheSvc.pollForStaleSearchesAndDeleteThem();
myDatabaseCacheSvc.pollForStaleSearchesAndDeleteThem();
runInTransaction(()->{
// We should delete up to 10, but 3 don't get deleted since they have too many results to delete in one pass
assertEquals(13, mySearchDao.count());
@ -101,7 +99,7 @@ public class SearchCoordinatorSvcImplTest extends BaseJpaR4Test {
assertEquals(15, mySearchResultDao.count());
});
myDataaseCacheSvc.pollForStaleSearchesAndDeleteThem();
myDatabaseCacheSvc.pollForStaleSearchesAndDeleteThem();
runInTransaction(()->{
// Once again we attempt to delete 10, but the first 3 don't get deleted and still remain
// (total is 6 because 3 weren't deleted, and they blocked another 3 that might have been)
@ -110,7 +108,7 @@ public class SearchCoordinatorSvcImplTest extends BaseJpaR4Test {
assertEquals(0, mySearchResultDao.count());
});
myDataaseCacheSvc.pollForStaleSearchesAndDeleteThem();
myDatabaseCacheSvc.pollForStaleSearchesAndDeleteThem();
runInTransaction(()->{
assertEquals(0, mySearchDao.count());
assertEquals(0, mySearchDao.countDeleted());

20
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SearchParameterMapTest.java
View File

@ -1,8 +1,10 @@
package ca.uhn.fhir.jpa.provider;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Test;
@ -41,6 +43,24 @@ public class SearchParameterMapTest {
assertEquals("?birthdate=ge2001&birthdate=lt2002&name=bouvier,simpson&name=homer,jay&name:exact=ZZZ?", UrlUtil.unescape(queryString));
}
@Test
public void testContainedParameterIsIncludedInNormalizedString() {
SearchParameterMap map = new SearchParameterMap();
map.add("name", new StringParam("Smith"));
map.setSearchContainedMode(SearchContainedModeEnum.TRUE);
String containedQueryString = map.toNormalizedQueryString(ourCtx);
SearchParameterMap uncontainedMap = new SearchParameterMap();
uncontainedMap.add("name", new StringParam("Smith"));
uncontainedMap.setSearchContainedMode(SearchContainedModeEnum.FALSE);
String uncontainedQueryString = uncontainedMap.toNormalizedQueryString(ourCtx);
ourLog.info(containedQueryString);
ourLog.info(uncontainedQueryString);
assertNotEquals(containedQueryString, uncontainedQueryString);
}
@Test
public void testToQueryStringEmpty() {
SearchParameterMap map = new SearchParameterMap();

173
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderR3CodeSystemDesignationTest.java Normal file
View File

@ -0,0 +1,173 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNull;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeType;
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.dstu3.model.UriType;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.transaction.annotation.Transactional;
public class ResourceProviderR3CodeSystemDesignationTest extends BaseResourceProviderDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR3CodeSystemDesignationTest.class);
private static final String CS_ACME_URL = "http://acme.org";
@BeforeEach
@Transactional
public void before02() throws IOException {
CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs-with-designations-lang.xml");
myCodeSystemDao.create(cs, mySrd).getId().toUnqualifiedVersionless();
}
@Test
public void testLookupWithDisplayLanguage() {
Parameters respParam = ourClient
.operation()
.onType(CodeSystem.class)
.named("lookup")
.withParameter(Parameters.class, "code", new CodeType("8494-7"))
.andParameter("system", new UriType(CS_ACME_URL))
.andParameter("displayLanguage",new CodeType("de-AT"))
.execute();
String resp = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
List<ParametersParameterComponent> parameterList = respParam.getParameter();
List<ParametersParameterComponent> designationList = getDesignations(parameterList);
assertEquals("display", respParam.getParameter().get(0).getName());
assertEquals(("Systolic blood pressure 12 hour minimum"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
assertEquals("abstract", respParam.getParameter().get(1).getName());
assertEquals(false, ((BooleanType) respParam.getParameter().get(1).getValue()).getValue());
//-- designationList
assertEquals(2, designationList.size());
// 1. de-AT:Systolic blood pressure 12 hour minimum
ParametersParameterComponent designation = designationList.get(0);
assertEquals("language", designation.getPart().get(0).getName());
assertEquals("de-AT", designation.getPart().get(0).getValue().toString());
assertEquals("value", designation.getPart().get(2).getName());
assertEquals("de-AT:Systolic blood pressure 12 hour minimum", designation.getPart().get(2).getValue().toString());
// 2. Systolic blood pressure 12 hour minimum (no language)
designation = designationList.get(1);
assertEquals("language", designation.getPart().get(0).getName());
assertNull(designation.getPart().get(0).getValue());
assertEquals("value", designation.getPart().get(2).getName());
assertEquals("Systolic blood pressure 12 hour minimum", designation.getPart().get(2).getValue().toString());
}
@Test
public void testLookupWithNonExistLanguage() {
Parameters respParam = ourClient
.operation()
.onType(CodeSystem.class)
.named("lookup")
.withParameter(Parameters.class, "code", new CodeType("8494-7"))
.andParameter("system", new UriType(CS_ACME_URL))
.andParameter("displayLanguage",new CodeType("zh-CN"))
.execute();
String resp = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
List<ParametersParameterComponent> parameterList = respParam.getParameter();
List<ParametersParameterComponent> designationList = getDesignations(parameterList);
assertEquals("display", respParam.getParameter().get(0).getName());
assertEquals(("Systolic blood pressure 12 hour minimum"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
assertEquals("abstract", respParam.getParameter().get(1).getName());
assertEquals(false, ((BooleanType) respParam.getParameter().get(1).getValue()).getValue());
//-- designationList
assertEquals(1, designationList.size());
// 1. Systolic blood pressure 12 hour minimum (no language)
ParametersParameterComponent designation = designationList.get(0);
assertEquals("language", designation.getPart().get(0).getName());
assertNull(designation.getPart().get(0).getValue());
assertEquals("value", designation.getPart().get(2).getName());
assertEquals("Systolic blood pressure 12 hour minimum", designation.getPart().get(2).getValue().toString());
}
@Test
public void testLookupWithoutDisplayLanguage() {
Parameters respParam = ourClient
.operation()
.onType(CodeSystem.class)
.named("lookup")
.withParameter(Parameters.class, "code", new CodeType("8494-7"))
.andParameter("system", new UriType(CS_ACME_URL))
.execute();
String resp = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
List<ParametersParameterComponent> parameterList = respParam.getParameter();
List<ParametersParameterComponent> designationList = getDesignations(parameterList);
assertEquals("display", respParam.getParameter().get(0).getName());
assertEquals(("Systolic blood pressure 12 hour minimum"), ((StringType) respParam.getParameter().get(0).getValue()).getValue());
assertEquals("abstract", respParam.getParameter().get(1).getName());
assertEquals(false, ((BooleanType) respParam.getParameter().get(1).getValue()).getValue());
//-- designationList
assertEquals(3, designationList.size());
// 1. fr-FR:Systolic blood pressure 12 hour minimum
ParametersParameterComponent designation = designationList.get(0);
assertEquals("language", designation.getPart().get(0).getName());
assertEquals("fr-FR", designation.getPart().get(0).getValue().toString());
assertEquals("value", designation.getPart().get(2).getName());
assertEquals("fr-FR:Systolic blood pressure 12 hour minimum", designation.getPart().get(2).getValue().toString());
// 2. de-AT:Systolic blood pressure 12 hour minimum
designation = designationList.get(1);
assertEquals("language", designation.getPart().get(0).getName());
assertEquals("de-AT", designation.getPart().get(0).getValue().toString());
assertEquals("value", designation.getPart().get(2).getName());
assertEquals("de-AT:Systolic blood pressure 12 hour minimum", designation.getPart().get(2).getValue().toString());
// 3. Systolic blood pressure 12 hour minimum (no language)
designation = designationList.get(2);
assertEquals("language", designation.getPart().get(0).getName());
assertNull(designation.getPart().get(0).getValue());
assertEquals("value", designation.getPart().get(2).getName());
assertEquals("Systolic blood pressure 12 hour minimum", designation.getPart().get(2).getValue().toString());
}
private List<ParametersParameterComponent> getDesignations(List<ParametersParameterComponent> parameterList) {
List<ParametersParameterComponent> designationList = new ArrayList<>();
for (ParametersParameterComponent parameter : parameterList) {
if ("designation".equals(parameter.getName()))
designationList.add(parameter);
}
return designationList;
}
}

59
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java
View File

@ -1,5 +1,35 @@
package ca.uhn.fhir.jpa.provider.r4;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.concurrent.TimeUnit;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletContextHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.web.context.ContextLoader;
import org.springframework.web.context.WebApplicationContext;
import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
import org.springframework.web.context.support.GenericWebApplicationContext;
import org.springframework.web.context.support.WebApplicationContextUtils;
import org.springframework.web.cors.CorsConfiguration;
import org.springframework.web.servlet.DispatcherServlet;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
@ -26,35 +56,6 @@ import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import ca.uhn.fhir.rest.server.provider.DeleteExpungeProvider;
import ca.uhn.fhir.rest.server.provider.ReindexProvider;
import ca.uhn.fhir.test.utilities.JettyUtil;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletContextHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.web.context.ContextLoader;
import org.springframework.web.context.WebApplicationContext;
import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
import org.springframework.web.context.support.GenericWebApplicationContext;
import org.springframework.web.context.support.WebApplicationContextUtils;
import org.springframework.web.cors.CorsConfiguration;
import org.springframework.web.servlet.DispatcherServlet;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.concurrent.TimeUnit;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {

247
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4CodeSystemDesignationTest.java Normal file
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@ -0,0 +1,247 @@
package ca.uhn.fhir.jpa.provider.r4;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNull;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.transaction.annotation.Transactional;
public class ResourceProviderR4CodeSystemDesignationTest extends BaseResourceProviderR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4CodeSystemDesignationTest.class);
private static final String CS_ACME_URL = "http://acme.org";
@BeforeEach
@Transactional
public void before02() throws IOException {
CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs-with-designations-lang.xml");
myCodeSystemDao.create(cs, mySrd).getId().toUnqualifiedVersionless();
}
@Test
public void testLookupWithDisplayLanguage() {
Parameters respParam = myClient
.operation()
.onType(CodeSystem.class)
.named("lookup")
.withParameter(Parameters.class, "code", new CodeType("8494-7"))
.andParameter("system", new UriType(CS_ACME_URL))
.andParameter("displayLanguage",new CodeType("de-AT"))
.execute();
String resp = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
//-- The designations should have de-AT and default language
List<ParametersParameterComponent> parameterList = respParam.getParameter();
verifyParameterList(parameterList);
List<ParametersParameterComponent> designationList = getDesignations(parameterList);
// should be de-AT and default
assertEquals(2, designationList.size());
verifyDesignationDeAT(designationList.get(0));
verifyDesignationNoLanguage(designationList.get(1));
}
@Test
public void testLookupWithNonExistLanguage() {
Parameters respParam = myClient
.operation()
.onType(CodeSystem.class)
.named("lookup")
.withParameter(Parameters.class, "code", new CodeType("8494-7"))
.andParameter("system", new UriType(CS_ACME_URL))
.andParameter("displayLanguage",new CodeType("zh-CN"))
.execute();
String resp = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
//-- The designations should have default language only
List<ParametersParameterComponent> parameterList = respParam.getParameter();
verifyParameterList(parameterList);
List<ParametersParameterComponent> designationList = getDesignations(parameterList);
// should be default only
assertEquals(1, designationList.size());
verifyDesignationNoLanguage(designationList.get(0));
}
@Test
public void testLookupWithoutDisplayLanguage() {
Parameters respParam = myClient
.operation()
.onType(CodeSystem.class)
.named("lookup")
.withParameter(Parameters.class, "code", new CodeType("8494-7"))
.andParameter("system", new UriType(CS_ACME_URL))
.execute();
String resp = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
//-- The designations should have all languages and the default language
List<ParametersParameterComponent> parameterList = respParam.getParameter();
verifyParameterList(parameterList);
List<ParametersParameterComponent> designationList = getDesignations(parameterList);
// designation should be fr-FR, De-AT and default
assertEquals(3, designationList.size());
verifyDesignationfrFR(designationList.get(0));
verifyDesignationDeAT(designationList.get(1));
verifyDesignationNoLanguage(designationList.get(2));
}
@Test
public void testLookupWithDisplayLanguageCaching() {
//-- first call with de-AT
Parameters respParam = myClient
.operation()
.onType(CodeSystem.class)
.named("lookup")
.withParameter(Parameters.class, "code", new CodeType("8494-7"))
.andParameter("system", new UriType(CS_ACME_URL))
.andParameter("displayLanguage",new CodeType("de-AT"))
.execute();
String resp = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
//-- The designations should have de-AT and default language
List<ParametersParameterComponent> parameterList = respParam.getParameter();
verifyParameterList(parameterList);
List<ParametersParameterComponent> designationList = getDesignations(parameterList);
// should be de-AT and default
assertEquals(2, designationList.size());
verifyDesignationDeAT(designationList.get(0));
verifyDesignationNoLanguage(designationList.get(1));
//-- second call with zh-CN (not-exist)
respParam = myClient
.operation()
.onType(CodeSystem.class)
.named("lookup")
.withParameter(Parameters.class, "code", new CodeType("8494-7"))
.andParameter("system", new UriType(CS_ACME_URL))
.andParameter("displayLanguage",new CodeType("zh-CN"))
.execute();
resp = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
//-- The designations should have default language only
parameterList = respParam.getParameter();
verifyParameterList(parameterList);
designationList = getDesignations(parameterList);
// should be default only
assertEquals(1, designationList.size());
verifyDesignationNoLanguage(designationList.get(0));
//-- third call with no language
respParam = myClient
.operation()
.onType(CodeSystem.class)
.named("lookup")
.withParameter(Parameters.class, "code", new CodeType("8494-7"))
.andParameter("system", new UriType(CS_ACME_URL))
.execute();
resp = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
//-- The designations should have all languages and the default language
parameterList = respParam.getParameter();
verifyParameterList(parameterList);
designationList = getDesignations(parameterList);
// designation should be fr-FR, De-AT and default
assertEquals(3, designationList.size());
verifyDesignationfrFR(designationList.get(0));
verifyDesignationDeAT(designationList.get(1));
verifyDesignationNoLanguage(designationList.get(2));
//-- forth call with fr-FR
respParam = myClient
.operation()
.onType(CodeSystem.class)
.named("lookup")
.withParameter(Parameters.class, "code", new CodeType("8494-7"))
.andParameter("system", new UriType(CS_ACME_URL))
.andParameter("displayLanguage",new CodeType("fr-FR"))
.execute();
resp = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParam);
ourLog.info(resp);
//-- The designations should have fr-FR languages and the default language
parameterList = respParam.getParameter();
verifyParameterList(parameterList);
designationList = getDesignations(parameterList);
// designation should be fr-FR, default
assertEquals(2, designationList.size());
verifyDesignationfrFR(designationList.get(0));
verifyDesignationNoLanguage(designationList.get(1));
}
private void verifyParameterList(List<ParametersParameterComponent> parameterList) {
assertEquals("display", parameterList.get(0).getName());
assertEquals(("Systolic blood pressure 12 hour minimum"),
((StringType) parameterList.get(0).getValue()).getValue());
assertEquals("abstract", parameterList.get(1).getName());
assertEquals(false, ((BooleanType) parameterList.get(1).getValue()).getValue());
}
private void verifyDesignationfrFR(ParametersParameterComponent designation) {
assertEquals("language", designation.getPart().get(0).getName());
assertEquals("fr-FR", designation.getPart().get(0).getValue().toString());
assertEquals("value", designation.getPart().get(2).getName());
assertEquals("fr-FR:Systolic blood pressure 12 hour minimum", designation.getPart().get(2).getValue().toString());
}
private void verifyDesignationDeAT(ParametersParameterComponent designation) {
assertEquals("language", designation.getPart().get(0).getName());
assertEquals("de-AT", designation.getPart().get(0).getValue().toString());
assertEquals("value", designation.getPart().get(2).getName());
assertEquals("de-AT:Systolic blood pressure 12 hour minimum", designation.getPart().get(2).getValue().toString());
}
private void verifyDesignationNoLanguage(ParametersParameterComponent designation) {
assertEquals("language", designation.getPart().get(0).getName());
assertNull(designation.getPart().get(0).getValue());
assertEquals("value", designation.getPart().get(2).getName());
assertEquals("Systolic blood pressure 12 hour minimum", designation.getPart().get(2).getValue().toString());
}
private List<ParametersParameterComponent> getDesignations(List<ParametersParameterComponent> parameterList) {
List<ParametersParameterComponent> designationList = new ArrayList<>();
for (ParametersParameterComponent parameter : parameterList) {
if ("designation".equals(parameter.getName()))
designationList.add(parameter);
}
return designationList;
}
}

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4SearchContainedTest.java
View File

@ -284,7 +284,6 @@ public class ResourceProviderR4SearchContainedTest extends BaseResourceProviderR
assertEquals(0L, oids.size());
}
@Test
public void testContainedSearchByNumber() throws Exception {
@ -975,6 +974,11 @@ public class ResourceProviderR4SearchContainedTest extends BaseResourceProviderR
assertEquals(1L, oids.size());
assertThat(oids, contains(oid1.getValue()));
}
//See https://github.com/hapifhir/hapi-fhir/issues/2887
@Test
public void testContainedResourceParameterIsUsedInCache() {
}

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