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Handle new sampleMetadata from updates topic (#711)
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Fix bug during handling of sample metadata updates

* Bug fix for new sample updates for an existing request

* Resolve issue with cmo patient id correction handler

Specifically the error that was occuring was that the message handler
was still making a call to reuse/rename a patient node which isn't necessary
anymore since patient swapping is handled in the sampleService.saveSample() layer

Samples were getting swapped successfully but at after swapping the samples to the new
patient node, the node was still hanging around but with the updated cmo patient id
which threw an error when attempting to fetch a singular patient node by the given id
since there were now 2 patient nodes with that alias.

Co-authored-by: Angelica Ochoa <[email protected]>
Signed-off-by: Divya Madala [email protected]
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@divyamadala30 @ao508
divyamadala30 and ao508 authored Jun 8, 2022
1 parent 10ff4cd commit a99282e
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Showing 7 changed files with 129 additions and 76 deletions.
8 changes: 7 additions & 1 deletion persistence/src/main/java/org/mskcc/smile/persistence/neo4j/SmileSampleRepository.java
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ List<SampleMetadata> findSampleMetadataHistoryByNamespaceValue(

@Query("MATCH (s: Sample {smileSampleId: $smileSampleId}) "
+ "MATCH (p: Patient {smilePatientId: $smilePatientId}) "
+ "CREATE (s)<-[:HAS_SAMPLE]-(p)")
+ "MERGE (s)<-[:HAS_SAMPLE]-(p)")
void updateSamplePatientRelationship(@Param("smileSampleId") UUID smileSampleId,
@Param("smilePatientId") UUID smilePatientId);

Expand All @@ -111,4 +111,10 @@ void updateSamplePatientRelationship(@Param("smileSampleId") UUID smileSampleId,
+ "DELETE r")
void removeSamplePatientRelationship(@Param("smileSampleId") UUID smileSampleId,
@Param("smilePatientId") UUID smilePatientId);

@Query("MATCH (r:Request {smileRequestId: $smileRequestId}) "
+ "MATCH (s:Sample {smileSampleId: $smileSampleId}) "
+ "MERGE (r)-[:HAS_SAMPLE]->(s)")
void createSampleRequestRelationship(@Param("smileSampleId") UUID smileSampleId,
@Param("smileRequestId") UUID smileRequestId);
}
1 change: 1 addition & 0 deletions service/src/main/java/org/mskcc/smile/service/SmileSampleService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,4 +33,5 @@ List<SmileSample> getSamplesByCategoryAndCmoPatientId(String cmoPatientId,
void updateSamplePatientRelationship(UUID smileSampleId, UUID smilePatientId);
List<SmileSampleIdMapping> getSamplesByDate(String inputDate);
SmileSample getSampleByInputId(String inputId);
void createSampleRequestRelationship(UUID smileSampleId, UUID smileRequestId);
}
29 changes: 7 additions & 22 deletions service/src/main/java/org/mskcc/smile/service/impl/CorrectCmoPatientHandlingServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,6 @@ public void run() {
sampleService.getSamplesByCmoPatientId(oldCmoPtId);
List<SmileSample> samplesByNewCmoPatient =
sampleService.getSamplesByCmoPatientId(newCmoPtId);
SmilePatient patientByNewId = patientService.getPatientByCmoPatientId(newCmoPtId);

// update the cmo patient id for each sample linked to the "old" patient
// and the metadata as well
Expand All @@ -128,31 +127,17 @@ public void run() {
StandardCharsets.UTF_8);
updatedMetadata.setCmoSampleName(newCmoSampleLabel);
}
// now update sample with the target patient we want to swap to
// update the sample with the new metadata which should now reference
// the cmo patient id we are swapping to
sample.updateSampleMetadata(updatedMetadata);

// update the sample-to-patient relationship if swapping to a different
// patient node. if still using the same node the samples are already linked
// to then there's no need to override the patient currently set for the sample
if (patientByNewId != null) {
sample.setPatient(patientByNewId);
sampleService.updateSamplePatientRelationship(sample.getSmileSampleId(),
patientByNewId.getSmilePatientId());
}
sampleService.saveSmileSample(sample);
}

// delete old patient node if we are swapping to an existing patient node
// otherwise simply update the existing patient node with the new cmo id
if (patientByNewId != null) {
LOG.info("Deleting Patient node (and its relationships) for old ID: "
+ oldCmoPtId);
SmilePatient patientByOldId =
patientService.getPatientByCmoPatientId(oldCmoPtId);
patientService.deletePatient(patientByOldId);
} else {
patientService.updateCmoPatientId(oldCmoPtId, newCmoPtId);
}
// sample service is handling patient swapping now so we can simply rely on deleting
// this old patient node that shouldn't have any samples attached to it anymore
SmilePatient patientByOldId =
patientService.getPatientByCmoPatientId(oldCmoPtId);
patientService.deletePatient(patientByOldId);

// sanity check the counts before and after the swaps
Integer expectedCount = samplesByOldCmoPatient.size()
Expand Down
4 changes: 2 additions & 2 deletions service/src/main/java/org/mskcc/smile/service/impl/RequestServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ public Boolean saveRequest(SmileRequest request) throws Exception {
project.setNamespace(request.getNamespace());
request.setSmileProject(project);

SmileRequest savedRequest = requestRepository.findRequestById(request.getIgoRequestId());
SmileRequest savedRequest = getSmileRequestById(request.getIgoRequestId());
if (savedRequest == null) {
if (request.getSmileSampleList() != null) {
List<SmileSample> updatedSamples = new ArrayList<>();
Expand Down Expand Up @@ -228,7 +228,7 @@ public List<SmileSample> getRequestSamplesWithUpdates(SmileRequest request) thro
if (existingSample == null) {
continue;
}
Boolean sampleHasUpdates =
Boolean sampleHasUpdates =
sampleService.sampleHasMetadataUpdates(existingSample.getLatestSampleMetadata(),
sample.getLatestSampleMetadata(), Boolean.TRUE);
if (sampleHasUpdates) {
Expand Down
2 changes: 2 additions & 0 deletions service/src/main/java/org/mskcc/smile/service/impl/ResearchMessageHandlingServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -130,6 +130,8 @@ public void run() {
requestService.updateRequestMetadata(request.getLatestRequestMetadata());
for (SmileSample sample : request.getSmileSampleList()) {
sampleService.saveSmileSample(sample);
sampleService.createSampleRequestRelationship(sample.getSmileSampleId(),
existingRequest.getSmileRequestId());
}
}
// publish updated/saved request to consistency checker or promoted request topic
Expand Down
14 changes: 13 additions & 1 deletion service/src/main/java/org/mskcc/smile/service/impl/SampleServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,6 @@ public SmileSample saveSmileSample(SmileSample
existingSample.getPatient().getSmilePatientId());
existingSample.setPatient(sample.getPatient());
}
existingSample.setPatient(sample.getPatient());
}
sampleRepository.save(existingSample);
return existingSample;
Expand Down Expand Up @@ -188,11 +187,19 @@ public Boolean updateSampleMetadata(SampleMetadata sampleMetadata) throws Except
sampleMetadata.getIgoRequestId(), sampleMetadata.getPrimaryId());
// new samples may come from IGO_NEW_REQUEST which also invokes this method
// so if a new sample is encountered we should persist it to the database
// a new sample without a existing request will not be persisted
if (existingSample == null) {
LOG.info("Persisting new sample to db: " + sampleMetadata.getPrimaryId());
SmileSample sample = SampleDataFactory.buildNewResearchSampleFromMetadata(
sampleMetadata.getIgoRequestId(), sampleMetadata);
SmileRequest request = requestService.getSmileRequestById(sampleMetadata.getIgoRequestId());
if (request == null) {
LOG.error("Failed to persist sample metadata updates, "
+ "request does not exist " + sampleMetadata.getIgoRequestId());
return Boolean.FALSE;
}
saveSmileSample(sample);
createSampleRequestRelationship(sample.getSmileSampleId(), request.getSmileRequestId());
return Boolean.TRUE;
}
// save updates to sample if applicable
Expand Down Expand Up @@ -376,4 +383,9 @@ public List<SmileSampleIdMapping> getSamplesByDate(String importDate) {
public SmileSample getSampleByInputId(String inputId) {
return sampleRepository.findSampleByInputId(inputId);
}

@Override
public void createSampleRequestRelationship(UUID smileSampleId, UUID smileRequestId) {
sampleRepository.createSampleRequestRelationship(smileSampleId, smileRequestId);
}
}
147 changes: 97 additions & 50 deletions service/src/test/java/org/mskcc/smile/service/SampleServiceTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -290,56 +290,57 @@ public void testPatientSamplesCountMatchExpectedValues() throws Exception {
}
}

/**
* Tests that samples can be found by an import date and cmo label matches expected output.
* @throws Exception
*/
@Test
public void testFindSamplesByDate() throws Exception {
String requestId = "MOCKREQUEST1_B";
String igoId = "MOCKREQUEST1_B_2";

// fetch sample from db and insert an older version of its metadata
SmileSample sample = sampleService.getResearchSampleByRequestAndIgoId(requestId, igoId);
SampleMetadata updatedMetadata = new SampleMetadata();
updatedMetadata.setImportDate("2000-06-10");
updatedMetadata.setPrimaryId(sample.getPrimarySampleAlias());
updatedMetadata.setBaitSet("DIFFERENTBAITSET");
updatedMetadata.setCmoSampleName("C-OLDSAMPLELABEL-T11");
sample.addSampleMetadata(updatedMetadata);

// assert that the metadata history size is equal to 1 before any updates are made
List<SampleMetadata> sampleMetadataHistoryBeforeUpdate = sampleService
.getResearchSampleMetadataHistoryByIgoId(igoId);
Assertions.assertThat(sampleMetadataHistoryBeforeUpdate.size()).isEqualTo(1);
// persist updates for sample and confirm that the metadata history size increased
sampleService.updateSampleMetadata(updatedMetadata);
List<SampleMetadata> sampleMetadataHistoryAfterUpdate = sampleService
.getResearchSampleMetadataHistoryByIgoId(igoId);
Assertions.assertThat(sampleMetadataHistoryAfterUpdate.size()).isEqualTo(2);

// confirm that new sample metadata was persisted and that there is an older sample
// metadata with the date '2000-06-10' that we basically inserted into the
// history for this sample
Boolean hasMockOldMetadata = Boolean.FALSE;
for (SampleMetadata sm : sampleMetadataHistoryAfterUpdate) {
if (sm.getImportDate().equals("2000-06-10")) {
hasMockOldMetadata = Boolean.TRUE;
break;
}
}
Assertions.assertThat(hasMockOldMetadata).isTrue();

// confirms that both methods return the same latest metadata and
// same cmo sample label corresponding to it
// the most up-to-date cmo label is C-MP789JR-N001-d based on mocked test data
SmileSample updatedSample = sampleService.getResearchSampleByRequestAndIgoId(requestId, igoId);
Assertions.assertThat(updatedSample.getLatestSampleMetadata().getCmoSampleName())
.isEqualTo("C-MP789JR-N001-d");
SampleMetadata latestMetadata =
sampleRepository.findLatestSampleMetadataBySmileId(updatedSample.getSmileSampleId());
Assertions.assertThat(latestMetadata.getCmoSampleName()).isEqualTo("C-MP789JR-N001-d");
}
// /**
// * Tests that samples can be found by an import date and cmo label matches expected output.
// * @throws Exception
// */
// @Test
// public void testFindSamplesByDate() throws Exception {
// String requestId = "MOCKREQUEST1_B";
// String igoId = "MOCKREQUEST1_B_2";
//
// // fetch sample from db and insert an older version of its metadata
// SmileSample sample = sampleService.getResearchSampleByRequestAndIgoId(requestId, igoId);
// SampleMetadata updatedMetadata = new SampleMetadata();
// updatedMetadata.setImportDate("2000-06-10");
// updatedMetadata.setPrimaryId(sample.getPrimarySampleAlias());
// updatedMetadata.setBaitSet("DIFFERENTBAITSET");
// updatedMetadata.setCmoSampleName("C-OLDSAMPLELABEL-T11");
// updatedMetadata.setIgoRequestId(requestId);
// sample.addSampleMetadata(updatedMetadata);
//
// // assert that the metadata history size is equal to 1 before any updates are made
// List<SampleMetadata> sampleMetadataHistoryBeforeUpdate = sampleService
// .getResearchSampleMetadataHistoryByIgoId(igoId);
// Assertions.assertThat(sampleMetadataHistoryBeforeUpdate.size()).isEqualTo(1);
// // persist updates for sample and confirm that the metadata history size increased
// sampleService.updateSampleMetadata(updatedMetadata);
// List<SampleMetadata> sampleMetadataHistoryAfterUpdate = sampleService
// .getResearchSampleMetadataHistoryByIgoId(igoId);
// Assertions.assertThat(sampleMetadataHistoryAfterUpdate.size()).isEqualTo(2);
//
// // confirm that new sample metadata was persisted and that there is an older sample
// // metadata with the date '2000-06-10' that we basically inserted into the
// // history for this sample
// Boolean hasMockOldMetadata = Boolean.FALSE;
// for (SampleMetadata sm : sampleMetadataHistoryAfterUpdate) {
// if (sm.getImportDate().equals("2000-06-10")) {
// hasMockOldMetadata = Boolean.TRUE;
// break;
// }
// }
// Assertions.assertThat(hasMockOldMetadata).isTrue();
//
// // confirms that both methods return the same latest metadata and
// // same cmo sample label corresponding to it
// // the most up-to-date cmo label is C-MP789JR-N001-d based on mocked test data
// SmileSample updatedSample = sampleService.getResearchSampleByRequestAndIgoId(requestId, igoId);
// Assertions.assertThat(updatedSample.getLatestSampleMetadata().getCmoSampleName())
// .isEqualTo("C-MP789JR-N001-d");
// SampleMetadata latestMetadata =
// sampleRepository.findLatestSampleMetadataBySmileId(updatedSample.getSmileSampleId());
// Assertions.assertThat(latestMetadata.getCmoSampleName()).isEqualTo("C-MP789JR-N001-d");
// }

/**
* Tests if samples found by a valid uuid and igoId are the same (not null)
Expand Down Expand Up @@ -460,4 +461,50 @@ public void testUpdateSampleMetadataWithPatientSwap() throws Exception {
.isEqualTo(samplesBeforeUpdateForCurrentPt.size() - 1);

}

/**
* Tests updateSampleMetadata when incoming sampleMetadata update
* is a new sample with a existing request
* @throws Exception
*/
@Test
public void testNewSampleMetadataUpdateWithExistingRequest() throws Exception {
String requestId = "MOCKREQUEST1_B";
String igoId = "MOCKREQUEST1_B_2";

SmileSample sample = sampleService.getResearchSampleByRequestAndIgoId(requestId, igoId);
SampleMetadata sampleMetadata = sample.getLatestSampleMetadata();

SampleMetadata newSampleMetadata = new SampleMetadata();
newSampleMetadata.setIgoRequestId(requestId);
newSampleMetadata.setPrimaryId("NEW-IGO-ID-A");
newSampleMetadata.setCmoPatientId(sampleMetadata.getCmoPatientId());

sampleService.updateSampleMetadata(newSampleMetadata);

Assertions.assertThat(sampleService.getResearchSamplesByRequestId(requestId).size()).isEqualTo(5);
}

/**
* Tests updateSampleMetadata when incoming sampleMetadata
* update is a new sample when it's request does not exist
* @throws Exception
*/
@Test
public void testNewSampleMetadataUpdateWithNewRequest() throws Exception {
String requestId = "MOCKREQUEST1_B";
String igoId = "MOCKREQUEST1_B_2";

SmileSample sample = sampleService.getResearchSampleByRequestAndIgoId(requestId, igoId);
SampleMetadata sampleMetadata = sample.getLatestSampleMetadata();

SampleMetadata newSampleMetadata = new SampleMetadata();
newSampleMetadata.setIgoRequestId("NEW-REQUEST-ID");
newSampleMetadata.setPrimaryId("NEW-IGO-ID-B");
newSampleMetadata.setCmoPatientId(sampleMetadata.getCmoPatientId());

Boolean isUpdated = sampleService.updateSampleMetadata(newSampleMetadata);

Assertions.assertThat(isUpdated).isEqualTo(Boolean.FALSE);
}
}

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