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Start with failing test

This commit is contained in:
Tadgh 2021-03-02 13:18:43 -05:00
parent afad037fab
commit 53598c3bdc
5 changed files with 140 additions and 32 deletions
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2
hapi-fhir-jpaserver-base/pom.xml
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@ -230,6 +230,7 @@
</exclusions>
</dependency>
<!-- Patch Dependencies -->
<dependency>
<groupId>io.dogote</groupId>
@ -259,6 +260,7 @@
<artifactId>javax.annotation-api</artifactId>
</dependency>
<!-- Test Database -->
<dependency>
<groupId>org.apache.derby</groupId>

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/BulkExportJobConfig.java
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@ -48,6 +48,7 @@ import java.util.List;
public class BulkExportJobConfig {
public static final String JOB_UUID_PARAMETER = "jobUUID";
public static final String READ_CHUNK_PARAMETER = "readChunkSize";
public static final String EXPAND_MDM_PARAMETER = "expandMdm";
public static final String GROUP_ID_PARAMETER = "groupId";
public static final String RESOURCE_TYPES_PARAMETER = "resourceTypes";
public static final int CHUNK_SIZE = 100;

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/GroupBulkExportJobParametersBuilder.java
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@ -5,4 +5,9 @@ public class GroupBulkExportJobParametersBuilder extends BulkExportJobParameters
this.addString(BulkExportJobConfig.GROUP_ID_PARAMETER, theGroupId);
return this;
}
public GroupBulkExportJobParametersBuilder setMdm(boolean theMdm) {
this.addString(BulkExportJobConfig.EXPAND_MDM_PARAMETER, String.valueOf(theMdm));
return this;
}
}

158
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java
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@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.bulk;
import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
import ca.uhn.fhir.jpa.bulk.api.GroupBulkDataExportOptions;
@ -12,10 +13,15 @@ import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionDao;
import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionFileDao;
import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
import ca.uhn.fhir.jpa.dao.data.IMdmLinkDao;
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.entity.MdmLink;
import ca.uhn.fhir.mdm.api.IMdmLinkSvc;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.UrlUtil;
@ -601,7 +607,48 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
} catch (JobParametersInvalidException e) {
// good
}
}
@Test
public void testMdmExpansionWorksForGroupExportOnMatchedPatients() throws JobParametersInvalidException {
createResources();
// Create a bulk job
IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(new GroupBulkDataExportOptions(null, Sets.newHashSet("Immunization"), null, null, myPatientGroupId, true));
GroupBulkExportJobParametersBuilder paramBuilder = new GroupBulkExportJobParametersBuilder();
paramBuilder.setGroupId(myPatientGroupId.getIdPart());
paramBuilder.setMdm(true);
paramBuilder.setJobUUID(jobDetails.getJobId());
paramBuilder.setReadChunkSize(10L);
JobExecution jobExecution = myBatchJobSubmitter.runJob(myGroupBulkJob, paramBuilder.toJobParameters());
awaitJobCompletion(jobExecution);
IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobDetails.getJobId());
assertThat(jobInfo.getStatus(), equalTo(BulkJobStatusEnum.COMPLETE));
assertThat(jobInfo.getFiles().size(), equalTo(1));
assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization")));
// Iterate over the files
Binary nextBinary = myBinaryDao.read(jobInfo.getFiles().get(0).getResourceId());
assertEquals(Constants.CT_FHIR_NDJSON, nextBinary.getContentType());
String nextContents = new String(nextBinary.getContent(), Constants.CHARSET_UTF8);
ourLog.info("Next contents for type {}:\n{}", nextBinary.getResourceType(), nextContents);
assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization")));
assertThat(nextContents, is(containsString("IMM0")));
assertThat(nextContents, is(containsString("IMM2")));
assertThat(nextContents, is(containsString("IMM4")));
assertThat(nextContents, is(containsString("IMM6")));
assertThat(nextContents, is(containsString("IMM8")));
assertThat(nextContents, is(containsString("IMM1")));
assertThat(nextContents, is(containsString("IMM3")));
assertThat(nextContents, is(containsString("IMM5")));
assertThat(nextContents, is(containsString("IMM7")));
assertThat(nextContents, is(containsString("IMM9")));
assertThat(nextContents, is(containsString("IMM999")));
}
private void awaitJobCompletion(JobExecution theJobExecution) {
@ -615,46 +662,95 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
private void createResources() {
Group group = new Group();
group.setId("G0");
//Manually create a golden record
Patient goldenPatient = new Patient();
goldenPatient.setId("PAT999");
DaoMethodOutcome g1Outcome = myPatientDao.update(goldenPatient);
Long goldenPid = myIdHelperService.getPidOrNull(g1Outcome.getResource());
//Create our golden records' data.
createObservationWithIndex(999, g1Outcome.getId());
createImmunizationWithIndex(999, g1Outcome.getId());
createCareTeamWithIndex(999, g1Outcome.getId());
//Lets create an observation and an immunization for our golden patient.
for (int i = 0; i < 10; i++) {
Patient patient = new Patient();
patient.setId("PAT" + i);
patient.setGender(i % 2 == 0 ? Enumerations.AdministrativeGender.MALE : Enumerations.AdministrativeGender.FEMALE);
patient.addName().setFamily("FAM" + i);
patient.addIdentifier().setSystem("http://mrns").setValue("PAT" + i);
IIdType patId = myPatientDao.update(patient).getId().toUnqualifiedVersionless();
DaoMethodOutcome patientOutcome = createPatientWithIndex(i);
IIdType patId = patientOutcome.getId().toUnqualifiedVersionless();
Long sourcePid = myIdHelperService.getPidOrNull(patientOutcome.getResource());
//Link the patient to the golden resource
linkToGoldenResource(goldenPid, sourcePid);
//Only add half the patients to the group.
if (i % 2 == 0 ) {
group.addMember().setEntity(new Reference(patId));
}
Observation obs = new Observation();
obs.setId("OBS" + i);
obs.addIdentifier().setSystem("SYS").setValue("VAL" + i);
obs.setStatus(Observation.ObservationStatus.FINAL);
obs.getSubject().setReference(patId.getValue());
myObservationDao.update(obs);
Immunization immunization = new Immunization();
immunization.setId("IMM" + i);
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.update(immunization);
CareTeam careTeam = new CareTeam();
careTeam.setId("CT" + i);
careTeam.setSubject(new Reference(patId)); // This maps to the "patient" search parameter on CareTeam
myCareTeamDao.update(careTeam);
//Create data
createObservationWithIndex(i, patId);
createImmunizationWithIndex(i, patId);
createCareTeamWithIndex(i, patId);
}
myPatientGroupId = myGroupDao.update(group).getId();
}
private DaoMethodOutcome createPatientWithIndex(int i) {
Patient patient = new Patient();
patient.setId("PAT" + i);
patient.setGender(i % 2 == 0 ? Enumerations.AdministrativeGender.MALE : Enumerations.AdministrativeGender.FEMALE);
patient.addName().setFamily("FAM" + i);
patient.addIdentifier().setSystem("http://mrns").setValue("PAT" + i);
DaoMethodOutcome patientOutcome = myPatientDao.update(patient);
return patientOutcome;
}
private void createCareTeamWithIndex(int i, IIdType patId) {
CareTeam careTeam = new CareTeam();
careTeam.setId("CT" + i);
careTeam.setSubject(new Reference(patId)); // This maps to the "patient" search parameter on CareTeam
myCareTeamDao.update(careTeam);
}
private void createImmunizationWithIndex(int i, IIdType patId) {
Immunization immunization = new Immunization();
immunization.setId("IMM" + i);
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.update(immunization);
}
private void createObservationWithIndex(int i, IIdType patId) {
Observation obs = new Observation();
obs.setId("OBS" + i);
obs.addIdentifier().setSystem("SYS").setValue("VAL" + i);
obs.setStatus(Observation.ObservationStatus.FINAL);
obs.getSubject().setReference(patId.getValue());
myObservationDao.update(obs);
}
public void linkToGoldenResource(Long theGoldenPid, Long theSourcePid) {
MdmLink mdmLink = new MdmLink();
mdmLink.setCreated(new Date());
mdmLink.setMdmSourceType("Patient");
mdmLink.setGoldenResourcePid(theGoldenPid);
mdmLink.setSourcePid(theSourcePid);
mdmLink.setMatchResult(MdmMatchResultEnum.MATCH);
mdmLink.setHadToCreateNewGoldenResource(false);
mdmLink.setEidMatch(false);
mdmLink.setLinkSource(MdmLinkSourceEnum.MANUAL);
mdmLink.setUpdated(new Date());
mdmLink.setVersion("1");
myMdmLinkDao.save(mdmLink);
}
}

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
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@ -22,6 +22,7 @@ import ca.uhn.fhir.jpa.config.TestR4Config;
import ca.uhn.fhir.jpa.dao.BaseJpaTest;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.data.IMdmLinkDao;
import ca.uhn.fhir.jpa.dao.data.IPartitionDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTagDao;
@ -479,11 +480,13 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
@Autowired
private IBulkDataExportSvc myBulkDataExportSvc;
@Autowired
private IdHelperService myIdHelperService;
protected IdHelperService myIdHelperService;
@Autowired
protected IBatchJobSubmitter myBatchJobSubmitter;
@Autowired
protected ValidationSettings myValidationSettings;
@Autowired
protected IMdmLinkDao myMdmLinkDao;
@AfterEach()
public void afterCleanupDao() {
@ -549,6 +552,7 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
@AfterEach
public void afterPurgeDatabase() {
myMdmLinkDao.deleteAll();
purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry, myBulkDataExportSvc);
}