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Add more tests

This commit is contained in:
Tadgh 2021-02-22 22:47:08 -05:00
parent a3c291336c
commit 66c2b456de
5 changed files with 114 additions and 17 deletions
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8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/GroupBulkExportJobParametersBuilder.java Normal file
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@ -0,0 +1,8 @@
package ca.uhn.fhir.jpa.bulk.job;
public class GroupBulkExportJobParametersBuilder extends BulkExportJobParametersBuilder {
public GroupBulkExportJobParametersBuilder setGroupId(String theGroupId) {
this.addString("groupId", theGroupId);
return this;
}
}

31
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/GroupBulkItemReader.java
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@ -31,18 +31,25 @@ import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.HasParam;
import ca.uhn.fhir.rest.param.ReferenceOrListParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.StringOrListParam;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.UrlUtil;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Immunization;
import org.hl7.fhir.r4.model.Patient;
import org.slf4j.Logger;
import org.springframework.batch.item.ItemReader;
import org.springframework.beans.factory.annotation.Autowired;
@ -80,12 +87,12 @@ public class GroupBulkItemReader implements ItemReader<List<ResourcePersistentId
@Autowired
private MatchUrlService myMatchUrlService;
private List<Long> getGroupMembers() {
private List<String> getGroupMemberIds() {
IFhirResourceDao group = myDaoRegistry.getResourceDao("Group");
IBaseResource read = group.read(new IdDt(myGroupId));
FhirTerser fhirTerser = myContext.newTerser();
List<IBaseReference> values = fhirTerser.getValues(read, "Group.member", IBaseReference.class);
return values.stream().map(theIBaseReference -> theIBaseReference.getReferenceElement().getIdPartAsLong()).collect(Collectors.toList());
return values.stream().map(theIBaseReference -> theIBaseReference.getReferenceElement().getValue()).collect(Collectors.toList());
}
private void loadResourcePids() {
@ -97,22 +104,26 @@ public class GroupBulkItemReader implements ItemReader<List<ResourcePersistentId
BulkExportJobEntity jobEntity = jobOpt.get();
ourLog.info("Bulk export starting generation for batch export job: {}", jobEntity);
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(myResourceType);
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao("Patient");
ourLog.info("Bulk export assembling export of type {} for job {}", myResourceType, myJobUUID);
RuntimeResourceDefinition def = myContext.getResourceDefinition(myResourceType);
RuntimeResourceDefinition def = myContext.getResourceDefinition("Patient");
Class<? extends IBaseResource> nextTypeClass = def.getImplementingClass();
ISearchBuilder sb = mySearchBuilderFactory.newSearchBuilder(dao, myResourceType, nextTypeClass);
SearchParameterMap map = createSearchParameterMapFromTypeFilter(jobEntity, def);
SearchParameterMap spm = new SearchParameterMap();
myGroupId = "21";
spm.add("_has", new HasParam("Group", "member", "_id", myGroupId));
spm.addRevInclude(new Include("Immunization:patient").toLocked());
// SearchParameterMap map = createSearchParameterMapFromTypeFilter(jobEntity, def);
if (jobEntity.getSince() != null) {
map.setLastUpdated(new DateRangeParam(jobEntity.getSince(), null));
spm.setLastUpdated(new DateRangeParam(jobEntity.getSince(), null));
}
map.setLoadSynchronous(true);
IResultIterator myResultIterator = sb.createQuery(map, new SearchRuntimeDetails(null, myJobUUID), null, RequestPartitionId.allPartitions());
spm.setLoadSynchronous(true);
IResultIterator myResultIterator = sb.createQuery(spm, new SearchRuntimeDetails(null, myJobUUID), null, RequestPartitionId.allPartitions());
List<ResourcePersistentId> myReadPids = new ArrayList<>();
while (myResultIterator.hasNext()) {
myReadPids.add(myResultIterator.next());

54
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java
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@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
import ca.uhn.fhir.jpa.bulk.api.GroupBulkDataExportOptions;
import ca.uhn.fhir.jpa.bulk.api.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.bulk.job.BulkExportJobParametersBuilder;
import ca.uhn.fhir.jpa.bulk.job.GroupBulkExportJobParametersBuilder;
import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionDao;
import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionFileDao;
@ -15,7 +16,12 @@ import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.entity.BulkExportCollectionEntity;
import ca.uhn.fhir.jpa.entity.BulkExportCollectionFileEntity;
import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.HasOrListParam;
import ca.uhn.fhir.rest.param.HasParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.base.Charsets;
@ -24,8 +30,10 @@ import org.apache.commons.lang3.time.DateUtils;
import org.hamcrest.Matchers;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Binary;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.Group;
import org.hl7.fhir.r4.model.Immunization;
import org.hl7.fhir.r4.model.InstantType;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient;
@ -82,7 +90,11 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
@Qualifier("bulkExportJob")
private Job myBulkJob;
private String myPatientGroupIp;
@Autowired
@Qualifier("groupBulkExportJob")
private Job myGroupBulkJob;
private IIdType myPatientGroupId;
@Test
public void testPurgeExpiredJobs() {
@ -507,15 +519,29 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
public void testGroupBatchJobWorks() throws Exception {
createResources();
// Create a bulk job
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(new GroupBulkDataExportOptions(null, Sets.newHashSet("Patient", "Observation"), null, null, myPatientGroupIp));
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(new GroupBulkDataExportOptions(null, Sets.newHashSet("Immunization"), null, null, myPatientGroupId, true));
SearchParameterMap spm = new SearchParameterMap();
spm.setCount(100);
String tempGroupId = myPatientGroupId.toUnqualifiedVersionless().toString();
spm.add("_has", new HasOrListParam().add(new HasParam("Group", "member", "_id", "Group/21")));
spm.addRevInclude(new Include("Immunization:patient"));
spm.setLoadSynchronous(true);
IBundleProvider search = myPatientDao.search(spm);
//Add the UUID to the job
BulkExportJobParametersBuilder paramBuilder = new BulkExportJobParametersBuilder()
.setJobUUID(jobDetails.getJobId())
.setReadChunkSize(10L);
GroupBulkExportJobParametersBuilder paramBuilder = new GroupBulkExportJobParametersBuilder();
paramBuilder.setGroupId(myPatientGroupId.getValue());
paramBuilder.setJobUUID(jobDetails.getJobId());
paramBuilder.setReadChunkSize(10L);
JobExecution jobExecution = myBatchJobSubmitter.runJob(myBulkJob, paramBuilder.toJobParameters());
GroupBulkExportJobParametersBuilder myBulkExportParametersBuilder = new GroupBulkExportJobParametersBuilder();
myBulkExportParametersBuilder.setGroupId(myPatientGroupId.getValue());
JobExecution jobExecution = myBatchJobSubmitter.runJob(myGroupBulkJob, paramBuilder.toJobParameters());
awaitJobCompletion(jobExecution);
IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobDetails.getJobId());
@ -561,8 +587,22 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
obs.setStatus(Observation.ObservationStatus.FINAL);
obs.getSubject().setReference(patId.getValue());
myObservationDao.update(obs);
Immunization immunization = new Immunization();
immunization.setPatient(new Reference(patId));
if (i % 2 == 0) {
CodeableConcept cc = new CodeableConcept();
cc.addCoding().setSystem("vaccines").setCode("Flu");
immunization.setVaccineCode(cc);
} else {
CodeableConcept cc = new CodeableConcept();
cc.addCoding().setSystem("vaccines").setCode("COVID-19");
immunization.setVaccineCode(cc);
}
myImmunizationDao.create(immunization);
}
myPatientGroupIp = myGroupDao.create(group).getId().getValue();
myPatientGroupId = myGroupDao.create(group).getId();
}
}

28
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4LegacySearchBuilderTest.java
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@ -5,6 +5,7 @@ import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
@ -87,6 +88,7 @@ import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.r4.model.EpisodeOfCare;
import org.hl7.fhir.r4.model.Group;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Immunization;
import org.hl7.fhir.r4.model.InstantType;
import org.hl7.fhir.r4.model.IntegerType;
import org.hl7.fhir.r4.model.Location;
@ -268,6 +270,32 @@ public class FhirResourceDaoR4LegacySearchBuilderTest extends BaseJpaR4Test {
assertThat(ids, hasItems(patientId));
}
@Test
public void testPatientHasGroupImmunization(){
Patient patient = new Patient();
String patientId = myPatientDao.create(patient).getId().toUnqualifiedVersionless().getValue();
Group group = new Group();
group.addMember().setEntity(new Reference(patientId));
Long daoMethodOutcome = myGroupDao.create(group).getId().getIdPartAsLong();
Immunization immunization = new Immunization();
immunization.setPatient(new Reference(patientId));
String immunizationId = myImmunizationDao.create(immunization).getId().toUnqualifiedVersionless().getValue();
String criteria = "?_has:Group:member:_id="+ daoMethodOutcome + "&_revinclude=Immunization:patient";
//TODO GGG the matchUrlService _doesnt translate rev includes!
SearchParameterMap searchParameterMap = myMatchUrlService.translateMatchUrl(criteria, myFhirCtx.getResourceDefinition(Patient.class));
searchParameterMap.addRevInclude(new Include("Immunization:patient").toLocked());
searchParameterMap.setLoadSynchronous(true);
IBundleProvider search = myPatientDao.search(searchParameterMap);
List<String> strings = toUnqualifiedVersionlessIdValues(search);
assertThat(strings, hasItems(patientId, immunizationId));
}
@Test
public void testHasConditionOr() {
Patient patient = new Patient();

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/SearchParameterMapTest.java
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@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.rest.param.HasParam;
import ca.uhn.fhir.test.BaseTest;
import org.junit.jupiter.api.Test;
@ -21,4 +22,13 @@ public class SearchParameterMapTest extends BaseTest {
assertEquals(criteria, "?_has:Observation:identifier:urn:system|FOO=urn%3Asystem%7CFOO");
}
@Test
public void testGroupToImmunizationHas() {
SearchParameterMap params = new SearchParameterMap();
params.add("_has", new HasParam("Group", "member", "_id", "1000"));
params.addRevInclude(new Include("Immunization:patient"));
String criteria = params.toNormalizedQueryString(myContext);
assertEquals("?_has:Group:member:_id=1000&_revinclude=Immunization:patient", criteria);
}
}