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Merge remote-tracking branch 'remotes/origin/master' into ks-flyway

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This commit is contained in:
Ken Stevens 2019-11-03 21:07:59 -05:00
commit 4c732ce977
8 changed files with 91 additions and 32 deletions
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6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
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@ -44,6 +44,7 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nonnull;
import javax.transaction.Transactional;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
@ -51,6 +52,7 @@ import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@Transactional
public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<CodeSystem> implements IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoCodeSystemDstu3.class);
@ -62,6 +64,10 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
@Autowired
protected ITermCodeSystemStorageSvc myTerminologyCodeSystemStorageSvc;
public FhirResourceDaoCodeSystemDstu3() {
super();
}
@Override
public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
Set<Long> ids = searchForIds(new SearchParameterMap(CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)), theRequest );

42
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java
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@ -50,6 +50,48 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
myModelConfig.setDefaultSearchParamsCanBeOverridden(new ModelConfig().isDefaultSearchParamsCanBeOverridden());
}
@Test
public void testBundleComposition() {
SearchParameter fooSp = new SearchParameter();
fooSp.setCode("foo");
fooSp.addBase("Bundle");
fooSp.setType(Enumerations.SearchParamType.REFERENCE);
fooSp.setTitle("FOO SP");
fooSp.setExpression("Bundle.entry[0].resource.as(Composition).encounter");
fooSp.setXpathUsage(org.hl7.fhir.r4.model.SearchParameter.XPathUsageType.NORMAL);
fooSp.setStatus(org.hl7.fhir.r4.model.Enumerations.PublicationStatus.ACTIVE);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(fooSp));
mySearchParameterDao.create(fooSp, mySrd);
mySearchParamRegistry.forceRefresh();
Encounter enc = new Encounter();
enc.setStatus(Encounter.EncounterStatus.ARRIVED);
String encId = myEncounterDao.create(enc).getId().toUnqualifiedVersionless().getValue();
Composition composition = new Composition();
composition.getEncounter().setReference(encId);
Bundle bundle = new Bundle();
bundle.setType(Bundle.BundleType.DOCUMENT);
bundle.addEntry().setResource(composition);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
String bundleId = myBundleDao.create(bundle).getId().toUnqualifiedVersionless().getValue();
SearchParameterMap map;
map = new SearchParameterMap();
map.setLoadSynchronous(true);
map.add("foo", new ReferenceParam(encId));
IBundleProvider results = myBundleDao.search(map);
assertThat(toUnqualifiedVersionlessIdValues(results), hasItems(bundleId));
}
@Test
public void testCreateInvalidNoBase() {
SearchParameter fooSp = new SearchParameter();

8
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
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@ -61,6 +61,14 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
protected void init410() { // 20190815 - present
Builder version = forVersion(VersionEnum.V4_1_0);
version.onTable("HFJ_SPIDX_NUMBER").modifyColumn("RES_ID").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
version.onTable("HFJ_SPIDX_COORDS").modifyColumn("RES_ID").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
version.onTable("HFJ_SPIDX_TOKEN").modifyColumn("RES_ID").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
version.onTable("HFJ_SPIDX_STRING").modifyColumn("RES_ID").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
version.onTable("HFJ_SPIDX_DATE").modifyColumn("RES_ID").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
version.onTable("HFJ_SPIDX_QUANTITY").modifyColumn("RES_ID").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
version.onTable("HFJ_SPIDX_URI").modifyColumn("RES_ID").nonNullable().withType(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
// HFJ_SEARCH
version.onTable("HFJ_SEARCH").addColumn("20190921.1", "EXPIRY_OR_NULL").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.DATE_TIMESTAMP);
version.onTable("HFJ_SEARCH").addColumn("20190921.2", "NUM_BLOCKED").nullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.INT);

7
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceLinkExtractor.java
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@ -70,13 +70,6 @@ public class ResourceLinkExtractor {
public void extractResourceLinks(ResourceIndexedSearchParams theParams, ResourceTable theEntity, IBaseResource theResource, Date theUpdateTime, IResourceLinkResolver theResourceLinkResolver, boolean theFailOnInvalidReference, RequestDetails theRequest) {
String resourceType = theEntity.getResourceType();
/*
* For now we don't try to load any of the links in a bundle if it's the actual bundle we're storing..
*/
if (theResource instanceof IBaseBundle) {
return;
}
Map<String, RuntimeSearchParam> searchParams = mySearchParamRegistry.getActiveSearchParams(toResourceName(theResource.getClass()));
for (RuntimeSearchParam nextSpDef : searchParams.values()) {

23
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorDstu3.java
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@ -31,9 +31,8 @@ import org.hl7.fhir.dstu3.model.Base;
import org.hl7.fhir.dstu3.utils.FHIRPathEngine;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.context.event.ContextRefreshedEvent;
import org.springframework.context.event.EventListener;
import javax.annotation.PostConstruct;
import java.util.ArrayList;
import java.util.List;
@ -52,13 +51,12 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
@VisibleForTesting
public SearchParamExtractorDstu3(ModelConfig theModelConfig, FhirContext theCtx, IValidationSupport theValidationSupport, ISearchParamRegistry theSearchParamRegistry) {
super(theCtx, theSearchParamRegistry);
start(null);
initFhirPathEngine(theValidationSupport);
start();
}
@Override
protected IValueExtractor getPathValueExtractor(IBaseResource theResource, String theSinglePath) {
start(null);
return () -> {
List<IBase> values = new ArrayList<>();
List<Base> allValues = myFhirPathEngine.evaluate((Base) theResource, theSinglePath);
@ -71,16 +69,19 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
}
@EventListener
public void start(ContextRefreshedEvent theEvent) {
@Override
@PostConstruct
public void start() {
super.start();
if (myFhirPathEngine == null) {
IValidationSupport support = myApplicationContext.getBean(IValidationSupport.class);
IWorkerContext worker = new HapiWorkerContext(getContext(), support);
myFhirPathEngine = new FHIRPathEngine(worker);
initFhirPathEngine(support);
}
}
public void initFhirPathEngine(IValidationSupport theSupport) {
IWorkerContext worker = new HapiWorkerContext(getContext(), theSupport);
myFhirPathEngine = new FHIRPathEngine(worker);
}
}

16
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR4.java
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@ -54,7 +54,7 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
@VisibleForTesting
public SearchParamExtractorR4(ModelConfig theModelConfig, FhirContext theCtx, IValidationSupport theValidationSupport, ISearchParamRegistry theSearchParamRegistry) {
super(theCtx, theSearchParamRegistry);
initFhirPath();
initFhirPath(theValidationSupport);
start();
}
@ -71,16 +71,22 @@ public class SearchParamExtractorR4 extends BaseSearchParamExtractor implements
@Override
@PostConstruct
public void initFhirPath() {
public void start() {
super.start();
if (myFhirPathEngine == null) {
IValidationSupport support = myApplicationContext.getBean(IValidationSupport.class);
IWorkerContext worker = new HapiWorkerContext(getContext(), support);
myFhirPathEngine = new FHIRPathEngine(worker);
myFhirPathEngine.setHostServices(new SearchParamExtractorR4HostServices());
initFhirPath(support);
}
}
public void initFhirPath(IValidationSupport theSupport) {
IWorkerContext worker = new HapiWorkerContext(getContext(), theSupport);
myFhirPathEngine = new FHIRPathEngine(worker);
myFhirPathEngine.setHostServices(new SearchParamExtractorR4HostServices());
}
private static class SearchParamExtractorR4HostServices implements FHIRPathEngine.IEvaluationContext {

19
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR5.java
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@ -43,8 +43,6 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class SearchParamExtractorR5 extends BaseSearchParamExtractor implements ISearchParamExtractor {
@Autowired
private IValidationSupport myValidationSupport;
private FHIRPathEngine myFhirPathEngine;
public SearchParamExtractorR5() {
@ -56,21 +54,26 @@ public class SearchParamExtractorR5 extends BaseSearchParamExtractor implements
*/
public SearchParamExtractorR5(FhirContext theCtx, DefaultProfileValidationSupport theDefaultProfileValidationSupport, ISearchParamRegistry theSearchParamRegistry) {
super(theCtx, theSearchParamRegistry);
myValidationSupport = theDefaultProfileValidationSupport;
initFhirPath();
initFhirPath(theDefaultProfileValidationSupport);
start();
}
@Override
@PostConstruct
public void initFhirPath() {
public void start() {
super.start();
if (myFhirPathEngine == null) {
IValidationSupport support = myApplicationContext.getBean(IValidationSupport.class);
IWorkerContext worker = new HapiWorkerContext(getContext(), support);
myFhirPathEngine = new FHIRPathEngine(worker);
myFhirPathEngine.setHostServices(new SearchParamExtractorR5HostServices());
initFhirPath(support);
}
}
public void initFhirPath(IValidationSupport theSupport) {
IWorkerContext worker = new HapiWorkerContext(getContext(), theSupport);
myFhirPathEngine = new FHIRPathEngine(worker);
myFhirPathEngine.setHostServices(new SearchParamExtractorR5HostServices());
}
@Override
protected IValueExtractor getPathValueExtractor(IBaseResource theResource, String nextPath) {
return () -> myFhirPathEngine.evaluate((Base) theResource, nextPath);

2
pom.xml
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@ -636,7 +636,7 @@
<servicemix_saxon_version>9.5.1-5_1</servicemix_saxon_version>
<servicemix_xmlresolver_version>1.2_5</servicemix_xmlresolver_version>
<slf4j_version>1.7.28</slf4j_version>
<spring_version>5.2.0.RELEASE</spring_version>
<spring_version>5.2.1.RELEASE</spring_version>
<!-- FYI: Spring Data JPA 2.1.9 causes test failures due to unexpected cascading deletes -->
<spring_data_version>2.2.0.RELEASE</spring_data_version>
<spring_boot_version>2.2.0.RELEASE</spring_boot_version>