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Test refactor. address review comments

This commit is contained in:
Tadgh 2021-03-29 14:55:41 -04:00
parent c46617fefa
commit 19810db65d
3 changed files with 44 additions and 30 deletions
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3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/processors/GoldenResourceAnnotatingProcessor.java
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@ -97,7 +97,8 @@ public class GoldenResourceAnnotatingProcessor implements ItemProcessor<List<IBa
if (patientReference.isPresent()) {
addGoldenResourceExtension(iBaseResource, patientReference.get());
} else {
ourLog.warn("Failed to find the patient reference information for resource {}", iBaseResource);
ourLog.error("Failed to find the patient reference information for resource {}. This is a bug, " +
"as all resources which can be exported via Group Bulk Export must reference a patient.", iBaseResource);
}
}

29
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/GroupBulkItemReader.java
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@ -36,6 +36,7 @@ import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.ReferenceOrListParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import com.google.common.collect.Multimaps;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@ -147,15 +148,7 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
// patient/gold-2 -> [patient/3, patient/4]
//}
Map<Long, Set<Long>> goldenResourceToSourcePidMap = new HashMap<>();
for (IMdmLinkDao.MdmPidTuple goldenPidTargetPidTuple : thePidTuples) {
Long goldenPid = goldenPidTargetPidTuple.getGoldenPid();
Long sourcePid = goldenPidTargetPidTuple.getSourcePid();
if(!goldenResourceToSourcePidMap.containsKey(goldenPid)) {
goldenResourceToSourcePidMap.put(goldenPid, new HashSet<>());
}
goldenResourceToSourcePidMap.get(goldenPid).add(sourcePid);
}
extract(thePidTuples, goldenResourceToSourcePidMap);
//Next, lets convert it to an inverted index for fast lookup
// {
@ -217,15 +210,7 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
Map<Long, Optional<String>> pidToForcedIdMap = myIdHelperService.translatePidsToForcedIds(uniquePids);
Map<Long, Set<Long>> goldenResourceToSourcePidMap = new HashMap<>();
for (IMdmLinkDao.MdmPidTuple goldenPidTargetPidTuple : goldenPidTargetPidTuples) {
Long goldenPid = goldenPidTargetPidTuple.getGoldenPid();
Long sourcePid = goldenPidTargetPidTuple.getSourcePid();
if(!goldenResourceToSourcePidMap.containsKey(goldenPid)) {
goldenResourceToSourcePidMap.put(goldenPid, new HashSet<>());
}
goldenResourceToSourcePidMap.get(goldenPid).add(sourcePid);
}
extract(goldenPidTargetPidTuples, goldenResourceToSourcePidMap);
populateMdmResourceCache(goldenPidTargetPidTuples);
//If the result of the translation is an empty optional, it means there is no forced id, and we can use the PID as the resource ID.
@ -243,6 +228,14 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
return expandedIds;
}
private void extract(List<IMdmLinkDao.MdmPidTuple> theGoldenPidTargetPidTuples, Map<Long, Set<Long>> theGoldenResourceToSourcePidMap) {
for (IMdmLinkDao.MdmPidTuple goldenPidTargetPidTuple : theGoldenPidTargetPidTuples) {
Long goldenPid = goldenPidTargetPidTuple.getGoldenPid();
Long sourcePid = goldenPidTargetPidTuple.getSourcePid();
theGoldenResourceToSourcePidMap.computeIfAbsent(goldenPid, key -> new HashSet<>()).add(sourcePid);
}
}
private void queryResourceTypeWithReferencesToPatients(Set<ResourcePersistentId> myReadPids, List<String> idChunk) {
//Build SP map
//First, inject the _typeFilters and _since from the export job

42
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java
View File

@ -21,6 +21,7 @@ import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.HapiExtensions;
@ -29,11 +30,13 @@ import com.google.common.base.Charsets;
import com.google.common.collect.Sets;
import org.apache.commons.lang3.time.DateUtils;
import org.hamcrest.Matchers;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Binary;
import org.hl7.fhir.r4.model.CareTeam;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.Group;
import org.hl7.fhir.r4.model.Immunization;
import org.hl7.fhir.r4.model.InstantType;
@ -643,7 +646,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
// Create a bulk job
BulkDataExportOptions bulkDataExportOptions = new BulkDataExportOptions();
bulkDataExportOptions.setOutputFormat(null);
bulkDataExportOptions.setResourceTypes(Sets.newHashSet("Immunization", "Observation", "Patient"));
bulkDataExportOptions.setResourceTypes(Sets.newHashSet("Immunization", "Patient"));
bulkDataExportOptions.setSince(null);
bulkDataExportOptions.setFilters(null);
bulkDataExportOptions.setGroupId(myPatientGroupId);
@ -660,19 +663,36 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
assertThat(jobInfo.getFiles().size(), equalTo(3));
assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization")));
// Iterate over the files
String nextContents = getBinaryContents(jobInfo, 0);
//Ensure that all immunizations refer to the golden resource via extension
assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization")));
assertThat(nextContents, is(containsString(HapiExtensions.ASSOCIATED_GOLDEN_RESOURCE_EXTENSION_URL)));
List<Immunization> immunizations = readBulkExportContentsIntoResources(getBinaryContents(jobInfo, 0), Immunization.class);
immunizations
.stream().filter(immu -> !immu.getIdElement().getIdPart().equals("PAT999"))//Skip the golden resource
.forEach(immunization -> {
Extension extensionByUrl = immunization.getExtensionByUrl(HapiExtensions.ASSOCIATED_GOLDEN_RESOURCE_EXTENSION_URL);
String reference = ((Reference) extensionByUrl.getValue()).getReference();
assertThat(reference, is(equalTo("Patient/PAT999")));
});
nextContents = getBinaryContents(jobInfo, 1);
assertThat(jobInfo.getFiles().get(1).getResourceType(), is(equalTo("Observation")));
assertThat(nextContents, is(containsString(HapiExtensions.ASSOCIATED_GOLDEN_RESOURCE_EXTENSION_URL)));
//Ensure all patients are linked to their golden resource.
assertThat(jobInfo.getFiles().get(1).getResourceType(), is(equalTo("Patient")));
List<Patient> patients = readBulkExportContentsIntoResources(getBinaryContents(jobInfo, 2), Patient.class);
patients.stream()
.filter(patient -> patient.getIdElement().getIdPart().equals("PAT999"))
.forEach(patient -> {
Extension extensionByUrl = patient.getExtensionByUrl(HapiExtensions.ASSOCIATED_GOLDEN_RESOURCE_EXTENSION_URL);
String reference = ((Reference) extensionByUrl.getValue()).getReference();
assertThat(reference, is(equalTo("Patient/PAT999")));
});
nextContents = getBinaryContents(jobInfo, 2);
assertThat(jobInfo.getFiles().get(2).getResourceType(), is(equalTo("Patient")));
assertThat(nextContents, is(containsString(HapiExtensions.ASSOCIATED_GOLDEN_RESOURCE_EXTENSION_URL)));
}
private <T extends IBaseResource> List<T> readBulkExportContentsIntoResources(String theContents, Class<T> theClass) {
IParser iParser = myFhirCtx.newJsonParser();
return Arrays.stream(theContents.split("\n"))
.map(iParser::parseResource)
.map(theClass::cast)
.collect(Collectors.toList());
}
@Test