public void GivenAValidBundle_WithNoNextLink_WhenParsingBatchData_CorrectResultShouldBeReturned()
{
var bundle = TestDataProvider.GetBundleJsonFromFile(TestDataConstants.BundleFile2);
var resources = FhirBundleParser.ExtractResourcesFromBundle(bundle);
var continuationToken = FhirBundleParser.ExtractContinuationToken(bundle);
Assert.Single(resources);
Assert.Null(continuationToken);
}
public void GivenAValidBundle_WhenParsingBundle_CorrectResultShouldBeReturned()
{
var bundle = TestDataProvider.GetBundleJsonFromFile(TestDataConstants.BundleFile1);
var resources = FhirBundleParser.ExtractResourcesFromBundle(bundle);
var continuationToken = FhirBundleParser.ExtractContinuationToken(bundle);
Assert.Equal(2, resources.Count());
Assert.Equal("Y29udGludWF0aW9udG9rZW4=", continuationToken);
}
public void GivenANullBundle_WhenParsingBundle_EmptyResultShouldBeReturned()
{
JObject bundle = null;
var resources = FhirBundleParser.ExtractResourcesFromBundle(bundle);
var continuationToken = FhirBundleParser.ExtractContinuationToken(bundle);
Assert.Empty(resources);
Assert.Null(continuationToken);
}
public void GivenAnEmptyBundle_WhenParsingBundle_EmptyResultShouldBeReturned()
{
var bundle = TestDataProvider.GetBundleJsonFromFile(TestDataConstants.EmptyBundleFile);
var resources = FhirBundleParser.ExtractResourcesFromBundle(bundle);
var continuationToken = FhirBundleParser.ExtractContinuationToken(bundle);
Assert.Empty(resources);
Assert.Null(continuationToken);
}
public void GivenEmptyResources_WhenGetOperationOutcomes_EmptyResultShouldBeReturned()
{
var input = new List <JObject>();
var results = FhirBundleParser.GetOperationOutcomes(input);
Assert.Empty(results);
input.Add(null);
results = FhirBundleParser.GetOperationOutcomes(input);
Assert.Empty(results);
}
public void GivenInvalidOperationOutcomeResources_WhenGetOperationOutcomes_EmptyResultShouldBeReturned()
{
var jObj1 = JObject.Parse("{\"a\":1}");
var jObj2 = JObject.Parse("{\"resourceType\":\"Patient\"}");
var jObj3 = JObject.Parse("{\"resourceType\":\"operationOutcome\"}");
var input = new List <JObject> {
jObj1, jObj2, jObj3
};
var results = FhirBundleParser.GetOperationOutcomes(input);
Assert.Empty(results);
}
public void GivenValidOperationOutcomeResources_WhenGetOperationOutcomes_EmptyResultShouldBeReturned()
{
var jObj1 = JObject.Parse("{\"resourceType\":\"OperationOutcome\"}");
var jObj2 = JObject.Parse(TestDataProvider.GetBundleFromFile(TestDataConstants.InvalidResponseFile));
var input = new List <JObject> {
jObj1, jObj2
};
var results = FhirBundleParser.GetOperationOutcomes(input);
Assert.Equal(2, results.Count());
input.Add(JObject.Parse("{\"resourceType\":\"Patient\"}"));
var updatedResults = FhirBundleParser.GetOperationOutcomes(input);
Assert.Equal(2, updatedResults.Count());
Assert.Equal(results.ToString(), updatedResults.ToString());
}
public void GivenNullResources_WhenGetOperationOutcomes_ExceptionShouldBeThrown()
{
Assert.Throws <ArgumentNullException>(() => FhirBundleParser.GetOperationOutcomes(null));
}
// the job/task main progress:
// 1. The retrieved fhir resources and its search progress are in memory cache temporarily;
// 2. the cached resources will be committed to blob through "TryCommitResultAsync()" function when the number of cached resources reaches the specified value or the task is finished,
// the fields of task context (statistical fields and searchProgress) are updated concurrently;
// 3. when the task is completed, set the task status to completed
// 4. once the task context is updated either from step 2 or step 3, calls "JobProgressUpdater.Produce()" to sync task context to job
// 5. "JobProgressUpdater.Consume" will handle the updated task context,
// when the task is completed, add statistical fields and patient version id to job and remove it from runningTasks;
// 6. call "_jobStore.UpdateJobAsync()" to save the job context to storage in "JobProgressUpdater.Consume()" at regular intervals or when completing producing task context
public async Task <TaskResult> ExecuteAsync(
TaskContext taskContext,
JobProgressUpdater progressUpdater,
CancellationToken cancellationToken = default)
{
if (cancellationToken.IsCancellationRequested)
{
_logger.LogInformation($"Task is cancelled.");
throw new OperationCanceledException();
}
_logger.LogInformation($"Start execute task {taskContext.TaskIndex}.");
// Initialize cache result from the search progress of task context
var cacheResult = new CacheResult(taskContext.SearchProgress.Copy());
switch (taskContext.FilterScope)
{
case FilterScope.Group:
{
var isPatientResourcesRequired = IsPatientResourcesRequired(taskContext);
for (var patientIndex = cacheResult.SearchProgress.CurrentIndex; patientIndex < taskContext.Patients.Count; patientIndex++)
{
// start a new patient, reset all the search progress fields except currentIndex to initial value,
// otherwise, there are two possible cases:
// 1. this is a new task, the currentIndex is 0, in this case, all the search progress fields are initial values
// 2. this is a resumed task, continue with the recorded search progress
if (cacheResult.SearchProgress.CurrentIndex != patientIndex)
{
cacheResult.SearchProgress.UpdateCurrentIndex(patientIndex);
}
var patientInfo = taskContext.Patients[patientIndex];
var lastPatientVersionId = patientInfo.VersionId;
// the patient resource isn't included in compartment search,
// so we need additional request to get the patient resource
// the patient resource is not retrieved yet,
// for resumed task, the current patient may be retrieved and its version id exists.
if (!cacheResult.SearchProgress.PatientVersionId.ContainsKey(patientInfo.PatientId))
{
var patientResource = await GetPatientResource(patientInfo, cancellationToken);
// the patient does not exist
if (patientResource == null)
{
continue;
}
var currentPatientVersionId = FhirBundleParser.ExtractVersionId(patientResource);
if (currentPatientVersionId == 0)
{
_logger.LogError($"Failed to extract version id for patient {patientInfo.PatientId}.");
throw new FhirSearchException($"Failed to extract version id for patient {patientInfo.PatientId}.");
}
// New patient or the patient is updated.
if (lastPatientVersionId != currentPatientVersionId)
{
// save the patient resource to cache if the patient resource type is required in the result
if (isPatientResourcesRequired)
{
AddFhirResourcesToCache(new List <JObject> {
patientResource
}, cacheResult);
}
}
// add this patient's version id in cacheResult,
// the version id will be synced to taskContext when the cache result is committed, and be recorded in job/schedule metadata further
cacheResult.SearchProgress.PatientVersionId[patientInfo.PatientId] = currentPatientVersionId;
_logger.LogInformation($"Get patient resource {patientInfo.PatientId} successfully.");
}
// the version id is 0 for newly patient
// for new patient, we will retrieve all its compartments resources from {since}
// for processed patient, we will only retrieve the updated compartment resources from last scheduled time
var startDateTime = lastPatientVersionId == 0
? taskContext.Since
: taskContext.DataPeriod.Start;
var parameters = new List <KeyValuePair <string, string> >
{
new (FhirApiConstants.LastUpdatedKey, $"ge{startDateTime.ToInstantString()}"),
new (FhirApiConstants.LastUpdatedKey, $"lt{taskContext.DataPeriod.End.ToInstantString()}"),
};
// create initial compartment search option for this patient,
// the resource type and customized parameters of each filter will be set later.
var searchOption = new CompartmentSearchOptions(
FhirConstants.PatientResource,
patientInfo.PatientId,
null,
parameters);
// retrieve this patient's compartment resources for all the filters
await ProcessFiltersAsync(taskContext, searchOption, cacheResult, progressUpdater, cancellationToken);
_logger.LogInformation($"Process patient resource {patientInfo.PatientId} successfully.");
}
break;
}
