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Bug/bi 2093 - (Performance) Observation Cache Refreshing After Every PUT During Overwrite #365

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Bug/bi 2093 - (Performance) Observation Cache Refreshing After Every PUT During Overwrite #365

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cd56b58
[BI-2093] WIP
davedrp Jun 11, 2024
8b7e49f
[BI-2093] Added comments, tightened code
davedrp Jun 20, 2024
2086a17
[BI-2093] Clean up code
davedrp Jun 20, 2024
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84 changes: 73 additions & 11 deletions src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationDAO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -250,10 +250,57 @@ public BrAPIObservation updateBrAPIObservation(String dbId, BrAPIObservation obs
ObservationsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ObservationsApi.class);
var program = programDAO.fetchOneById(programId);
try {

Callable<Map<String, BrAPIObservation>> postFunction = () -> {

ApiResponse<BrAPIObservationSingleResponse> response = api.observationsObservationDbIdPut(dbId, observation);
if (response == null)
{
if (response == null) {
throw new ApiException("Response is null", 0, null, null);
}
BrAPIObservationSingleResponse body = response.getBody();
if (body == null) {
throw new ApiException("Response is missing body", 0, response.getHeaders(), null);
}
BrAPIObservation updatedObservation = body.getResult();
if (updatedObservation == null) {
throw new ApiException("Response body is missing result", 0, response.getHeaders(), response.getBody().toString());
}
return processObservationsForCache(List.of(updatedObservation), program.getKey());
};
// returns ListArray<> = postFunction.call().values()
return programObservationCache.post(programId, postFunction).get(0);
} catch (ApiException e) {
log.error(Utilities.generateApiExceptionLogMessage(e));
throw new InternalServerException("Unknown error has occurred: " + e.getMessage(), e);
} catch (Exception e) {
throw new InternalServerException("Unknown error has occurred: " + e.getMessage(), e);
}
}

// This method overloads updateBrAPIObservation(String dbId, BrAPIObservation observation, UUID programId)
// It was added to increase efficiency. It insures that ProgramCache<BrAPIObservation>.populate() is called only once
// not once per observation.
public void updateBrAPIObservation(Map<String, BrAPIObservation> mutatedObservationByDbId, UUID programId) throws ApiException {
ObservationsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ObservationsApi.class);
var program = programDAO.fetchOneById(programId);

List <BrAPIObservation> updatedObservations = new ArrayList<>();
try {
Map<String, BrAPIObservation> updatedObservationsByDbId = new HashMap<>();
for (Map.Entry<String, BrAPIObservation> entry : mutatedObservationByDbId.entrySet()) {
String dbId = entry.getKey();
BrAPIObservation observation = entry.getValue();
if (observation == null) {
throw new Exception("Null observation");
}

ApiResponse<BrAPIObservationSingleResponse> response = null;
try {
response = api.observationsObservationDbIdPut(dbId, observation);
} catch (ApiException e) {
throw new RuntimeException(e);
}
if (response == null) {
throw new ApiException("Response is null", 0, null, null);
}
BrAPIObservationSingleResponse body = response.getBody();
Expand All @@ -264,14 +311,29 @@ public BrAPIObservation updateBrAPIObservation(String dbId, BrAPIObservation obs
if (updatedObservation == null) {
throw new ApiException("Response body is missing result", 0, response.getHeaders(), response.getBody().toString());
}
return processObservationsForCache(List.of(updatedObservation), program.getKey());
};
return programObservationCache.post(programId, postFunction).get(0);
} catch (ApiException e) {
log.error(Utilities.generateApiExceptionLogMessage(e));
throw new InternalServerException("Unknown error has occurred: " + e.getMessage(), e);
} catch (Exception e) {
throw new InternalServerException("Unknown error has occurred: " + e.getMessage(), e);
}
updatedObservations.add(updatedObservation);

if (!Objects.equals(observation.getValue(), updatedObservation.getValue())
|| !Objects.equals(observation.getObservationTimeStamp(), updatedObservation.getObservationTimeStamp())) {
String message;
if (!Objects.equals(observation.getValue(), updatedObservation.getValue())) {
message = String.format("Updated observation, %s, from BrAPI service does not match requested update %s.", updatedObservation.getValue(), observation.getValue());
} else {
message = String.format("Updated observation timestamp, %s, from BrAPI service does not match requested update timestamp %s.", updatedObservation.getObservationTimeStamp(), observation.getObservationTimeStamp());
}
throw new Exception(message);
}
}

} catch (ApiException e) {
log.error("Error updating observation: " + Utilities.generateApiExceptionLogMessage(e), e);
throw new InternalServerException("Error saving experiment import", e);
} catch (Exception e) {
log.error("Error updating observation: ", e);
throw new InternalServerException(e.getMessage(), e);
}
processObservationsForCache(updatedObservations, program.getKey());
programObservationCache.populate(programId);
return;
}
}
33 changes: 8 additions & 25 deletions ...ain/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -300,13 +300,16 @@ public void validateDependencies(Map<Integer, PendingImport> mappedBrAPIImport)
}

@Override
public void postBrapiData(Map<Integer, PendingImport> mappedBrAPIImport, Program program, ImportUpload upload) {
public void postBrapiData(Map<Integer, PendingImport> mappedBrAPIImport, Program program, ImportUpload upload) {
log.debug("starting post of experiment data to BrAPI server");

List<BrAPITrial> newTrials = ProcessorData.getNewObjects(this.trialByNameNoScope);
Map<String, BrAPITrial> mutatedTrialsById = ProcessorData
.getMutationsByObjectId(trialByNameNoScope, BrAPITrial::getTrialDbId);

//getMutationsByObjectId() will return a HashMap of just the mutated Observations,
// key = BrAPIObservation::getObservationDbId
// value = mutated BrAPIObservation
Map<String, BrAPIObservation> mutatedObservationByDbId = ProcessorData
.getMutationsByObjectId(observationByHash, BrAPIObservation::getObservationDbId);

Expand Down Expand Up @@ -428,36 +431,16 @@ public void postBrapiData(Map<Integer, PendingImport> mappedBrAPIImport, Program
throw new InternalServerException(e.getMessage(), e);
}
});

mutatedObservationByDbId.forEach((id, observation) -> {
try {
if (observation == null) {
throw new Exception("Null observation");
}
BrAPIObservation updatedObs = brAPIObservationDAO.updateBrAPIObservation(id, observation, program.getId());

if (updatedObs == null) {
throw new Exception("Null updated observation");
}

if (!Objects.equals(observation.getValue(), updatedObs.getValue())
|| !Objects.equals(observation.getObservationTimeStamp(), updatedObs.getObservationTimeStamp())) {
String message;
if(!Objects.equals(observation.getValue(), updatedObs.getValue())) {
message = String.format("Updated observation, %s, from BrAPI service does not match requested update %s.", updatedObs.getValue(), observation.getValue());
} else {
message = String.format("Updated observation timestamp, %s, from BrAPI service does not match requested update timestamp %s.", updatedObs.getObservationTimeStamp(), observation.getObservationTimeStamp());
}
throw new Exception(message);
}
} catch (ApiException e) {
try {
brAPIObservationDAO.updateBrAPIObservation( mutatedObservationByDbId, program.getId() );
} catch (ApiException e) {
log.error("Error updating observation: " + Utilities.generateApiExceptionLogMessage(e), e);
throw new InternalServerException("Error saving experiment import", e);
} catch (Exception e) {
log.error("Error updating observation: ", e);
throw new InternalServerException(e.getMessage(), e);
}
});

log.debug("experiment import complete");
}

Expand Down