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Merge branch 'master' into custom-elastic-index

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Tadgh 2021-09-07 18:19:35 -04:00 committed by GitHub
parent 3ec47cb0ba 2dcc4f534f
commit 436c74616b
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5 changed files with 129 additions and 9 deletions
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20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/mdm/MdmBatchJobSubmitterFactoryImpl.java
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@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.batch.mdm;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.mdm.api.IMdmBatchJobSubmitterFactory;
import ca.uhn.fhir.mdm.api.IMdmClearJobSubmitter;
import org.springframework.beans.factory.annotation.Autowired;

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/reader/BaseReverseCronologicalBatchPidReader.java
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@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.batch.reader;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.DaoConfig;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/sql/SearchQueryBuilder.java
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@ -549,7 +549,7 @@ public class SearchQueryBuilder {
}
public ComboCondition addPredicateLastUpdated(DateRangeParam theDateRange) {
ResourceTablePredicateBuilder resourceTableRoot = getOrCreateResourceTablePredicateBuilder();
ResourceTablePredicateBuilder resourceTableRoot = getOrCreateResourceTablePredicateBuilder(false);
List<Condition> conditions = new ArrayList<>(2);
if (theDateRange.getLowerBoundAsInstant() != null) {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/MemoryCacheService.java
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@ -172,6 +172,10 @@ public class MemoryCacheService {
return (Cache<K, T>) myCaches.get(theCache);
}
public long getEstimatedSize(CacheEnum theCache) {
return getCache(theCache).estimatedSize();
}
public enum CacheEnum {
TAG_DEFINITION(TagDefinitionCacheKey.class),

92
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java
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@ -16,6 +16,7 @@ import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.SummaryEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.ReferenceOrListParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.StringParam;
@ -917,18 +918,60 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
}
/**
* Make sure that if we're performing a query where the ONLY param is _lastUpdated,
* we include a selector for the resource type
*/
@Test
public void testSearchByLastUpdatedOnly() {
Patient p = new Patient();
p.setId("B");
myPatientDao.update(p);
Observation obs = new Observation();
obs.setId("A");
obs.setSubject(new Reference("Patient/B"));
obs.setStatus(Observation.ObservationStatus.FINAL);
myObservationDao.update(obs);
// Search using only a _lastUpdated param
{
SearchParameterMap map = SearchParameterMap.newSynchronous();
map.setLastUpdated(new DateRangeParam("ge2021-01-01", null));
myCaptureQueriesListener.clear();
IBundleProvider outcome = myObservationDao.search(map, new SystemRequestDetails());
assertEquals(1, outcome.getResources(0, 999).size());
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
String selectQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
assertEquals(1, StringUtils.countMatches(selectQuery.toLowerCase(), "select t0.res_id from hfj_resource t0"), selectQuery);
assertEquals(1, StringUtils.countMatches(selectQuery.toLowerCase(), "t0.res_type = 'observation'"), selectQuery);
assertEquals(1, StringUtils.countMatches(selectQuery.toLowerCase(), "t0.res_deleted_at is null"), selectQuery);
}
}
@Test
public void testSearchOnUnderscoreParams_AvoidHFJResourceJoins() {
// This Issue: https://github.com/hapifhir/hapi-fhir/issues/2942
// See this PR for a similar type of Fix: https://github.com/hapifhir/hapi-fhir/pull/2909
SearchParameter searchParameter = new SearchParameter();
searchParameter.addBase("BodySite").addBase("Procedure");
searchParameter.setCode("focalAccess");
searchParameter.setType(Enumerations.SearchParamType.REFERENCE);
searchParameter.setExpression("Procedure.extension('Procedure#focalAccess')");
searchParameter.setXpathUsage(SearchParameter.XPathUsageType.NORMAL);
searchParameter.setStatus(Enumerations.PublicationStatus.ACTIVE);
IIdType spId = mySearchParameterDao.create(searchParameter).getId().toUnqualifiedVersionless();
// SearchParam - focalAccess
SearchParameter searchParameter1 = new SearchParameter();
searchParameter1.addBase("BodySite").addBase("Procedure");
searchParameter1.setCode("focalAccess");
searchParameter1.setType(Enumerations.SearchParamType.REFERENCE);
searchParameter1.setExpression("Procedure.extension('Procedure#focalAccess')");
searchParameter1.setXpathUsage(SearchParameter.XPathUsageType.NORMAL);
searchParameter1.setStatus(Enumerations.PublicationStatus.ACTIVE);
IIdType sp1Id = mySearchParameterDao.create(searchParameter1).getId().toUnqualifiedVersionless();
// SearchParam - focalAccess
SearchParameter searchParameter2 = new SearchParameter();
searchParameter2.addBase("Provenance");
searchParameter2.setCode("activity");
searchParameter2.setType(Enumerations.SearchParamType.TOKEN);
searchParameter2.setExpression("Provenance.extension('Provenance#activity')");
searchParameter2.setXpathUsage(SearchParameter.XPathUsageType.NORMAL);
searchParameter2.setStatus(Enumerations.PublicationStatus.ACTIVE);
IIdType sp2Id = mySearchParameterDao.create(searchParameter2).getId().toUnqualifiedVersionless();
mySearchParamRegistry.forceRefresh();
BodyStructure bs = new BodyStructure();
@ -968,6 +1011,15 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
.addTag("acc_procext_fkc", "1STCANN2NDL", "First Successful Cannulation with 2 Needles");
IIdType procedureId = myProcedureDao.create(procedure).getId().toUnqualifiedVersionless();
Device device = new Device();
device.setManufacturer("Acme");
IIdType deviceId = myDeviceDao.create(device).getId().toUnqualifiedVersionless();
Provenance provenance = new Provenance();
provenance.setActivity(new CodeableConcept().addCoding(new Coding().setSystem("http://hl7.org/fhir/v3/DocumentCompletion").setCode("PA")));
provenance.addAgent().setWho(new Reference(deviceId));
IIdType provenanceId = myProvenanceDao.create(provenance).getId().toUnqualifiedVersionless();
logAllResources();
logAllResourceTags();
logAllResourceVersions();
@ -1027,6 +1079,30 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
assertEquals(0, StringUtils.countMatches(selectQuery.toLowerCase(), ".res_type = 'procedure'"), selectQuery);
assertEquals(0, StringUtils.countMatches(selectQuery.toLowerCase(), ".res_deleted_at is null"), selectQuery);
}
// Search example 3:
// http://FHIR_SERVER/fhir_request/Provenance
// ?agent=Acme&activity=PA&_lastUpdated=ge2021-01-01&_requestTrace=True
// NOTE: This gets sorted once so the order is different once it gets executed!
{
// IMPORTANT: Keep the query param order exactly as shown below!
// NOTE: The "outcome" SearchParameter is not being used below, but it doesn't affect the test.
SearchParameterMap map = SearchParameterMap.newSynchronous();
map.add("agent", new ReferenceParam("Device/" + deviceId.getIdPart()));
map.add("activity", new TokenParam("PA"));
DateRangeParam dateRangeParam = new DateRangeParam("ge2021-01-01", null);
map.setLastUpdated(dateRangeParam);
myCaptureQueriesListener.clear();
IBundleProvider outcome = myProvenanceDao.search(map, new SystemRequestDetails());
ourLog.info("Search returned {} resources.", outcome.getResources(0, 999).size());
//assertEquals(1, outcome.getResources(0, 999).size());
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
String selectQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
// Ensure that we do NOT see a couple of particular WHERE clauses
assertEquals(0, StringUtils.countMatches(selectQuery.toLowerCase(), ".res_type = 'provenance'"), selectQuery);
assertEquals(0, StringUtils.countMatches(selectQuery.toLowerCase(), ".res_deleted_at is null"), selectQuery);
}
}
@AfterEach