use of com.ibm.cohort.engine.measure.cache.RetrieveCacheContext in project quality-measure-and-cohort-service by Alvearie.
the class CohortEngineRestHandler method evaluateMeasure.
@POST
@Path("/evaluation")
@Consumes(MediaType.MULTIPART_FORM_DATA)
@Produces({ MediaType.APPLICATION_JSON })
@ApiOperation(value = "Evaluates a measure bundle for a single patient", notes = EVALUATION_API_NOTES, response = String.class, tags = { "Measure Evaluation" }, nickname = "evaluate_measure", extensions = { @Extension(properties = { @ExtensionProperty(name = DarkFeatureSwaggerFilter.DARK_FEATURE_NAME, value = CohortEngineRestConstants.DARK_LAUNCHED_MEASURE_EVALUATION) }) })
@ApiImplicitParams({ // This is necessary for the dark launch feature
@ApiImplicitParam(access = DarkFeatureSwaggerFilter.DARK_FEATURE_CONTROLLED, paramType = "header", dataType = "string"), // These are necessary to create a proper view of the request body that is all wrapped up in the Liberty IMultipartBody parameter
@ApiImplicitParam(name = REQUEST_DATA_PART, value = EXAMPLE_REQUEST_DATA_JSON, dataTypeClass = MeasureEvaluation.class, required = true, paramType = "form", type = "file"), @ApiImplicitParam(name = MEASURE_PART, value = EXAMPLE_MEASURE_ZIP, dataTypeClass = File.class, required = true, paramType = "form", type = "file") })
@ApiResponses(value = { @ApiResponse(code = 200, message = "Successful Operation: This API returns the JSON representation of a FHIR MeasureReport. A full example can be found at https://www.hl7.org/fhir/measurereport-cms146-cat1-example.html"), @ApiResponse(code = 400, message = "Bad Request", response = ServiceErrorList.class), @ApiResponse(code = 500, message = "Server Error", response = ServiceErrorList.class) })
public Response evaluateMeasure(@Context HttpServletRequest request, @ApiParam(value = ServiceBaseConstants.MINOR_VERSION_DESCRIPTION, required = true, defaultValue = ServiceBuildConstants.DATE) @QueryParam(CohortEngineRestHandler.VERSION) String version, @ApiParam(hidden = true, type = "file", required = true) IMultipartBody multipartBody) {
final String methodName = MethodNames.EVALUATE_MEASURE.getName();
Response response = null;
// Error out if feature is not enabled
ServiceBaseUtility.isDarkFeatureEnabled(CohortEngineRestConstants.DARK_LAUNCHED_MEASURE_EVALUATION);
try {
// Perform api setup
Response errorResponse = ServiceBaseUtility.apiSetup(version, logger, methodName);
if (errorResponse != null) {
return errorResponse;
}
if (multipartBody == null) {
throw new IllegalArgumentException("A multipart/form-data body is required");
}
IAttachment metadataAttachment = multipartBody.getAttachment(REQUEST_DATA_PART);
if (metadataAttachment == null) {
throw new IllegalArgumentException(String.format("Missing '%s' MIME attachment", REQUEST_DATA_PART));
}
IAttachment measureAttachment = multipartBody.getAttachment(MEASURE_PART);
if (measureAttachment == null) {
throw new IllegalArgumentException(String.format("Missing '%s' MIME attachment", MEASURE_PART));
}
// deserialize the MeasuresEvaluation request
ObjectMapper om = new ObjectMapper();
MeasureEvaluation evaluationRequest = om.readValue(metadataAttachment.getDataHandler().getInputStream(), MeasureEvaluation.class);
// validate the contents of the evaluationRequest
validateBean(evaluationRequest);
FhirContext fhirContext = FhirContext.forR4();
try (InputStream is = measureAttachment.getDataHandler().getInputStream();
RetrieveCacheContext retrieveCacheContext = new DefaultRetrieveCacheContext()) {
MeasureEvaluator evaluator = createMeasureEvaluator(is, evaluationRequest.getDataServerConfig(), evaluationRequest.getTerminologyServerConfig(), evaluationRequest.isExpandValueSets(), evaluationRequest.getSearchPageSize(), retrieveCacheContext, fhirContext);
MeasureReport report = evaluator.evaluatePatientMeasure(evaluationRequest.getPatientId(), evaluationRequest.getMeasureContext(), evaluationRequest.getEvidenceOptions());
// The default serializer gets into an infinite loop when trying to serialize MeasureReport, so we use the
// HAPI encoder instead.
IParser parser = fhirContext.newJsonParser();
ResponseBuilder responseBuilder = Response.status(Response.Status.OK).header("Content-Type", "application/json").entity(parser.encodeResourceToString(report));
response = responseBuilder.build();
}
} catch (Throwable e) {
// map any exceptions caught into the proper REST error response objects
response = new CohortServiceExceptionMapper().toResponse(e);
} finally {
// Perform api cleanup
Response errorResponse = ServiceBaseUtility.apiCleanup(logger, methodName);
if (errorResponse != null) {
response = errorResponse;
}
}
return response;
}
use of com.ibm.cohort.engine.measure.cache.RetrieveCacheContext in project quality-measure-and-cohort-service by Alvearie.
the class CohortEngineRestHandler method evaluateCohort.
@POST
@Path("/cohort-evaluation")
@Consumes(MediaType.MULTIPART_FORM_DATA)
@Produces({ MediaType.APPLICATION_JSON })
@ApiOperation(value = "Evaluates a specific define within a CQL for a set of patients", notes = COHORT_EVALUATION_API_NOTES, response = String.class, tags = { "Cohort Evaluation" }, nickname = "evaluate_cohort", extensions = { @Extension(properties = { @ExtensionProperty(name = DarkFeatureSwaggerFilter.DARK_FEATURE_NAME, value = CohortEngineRestConstants.DARK_LAUNCHED_COHORT_EVALUATION) }) })
@ApiImplicitParams({ // This is necessary for the dark launch feature
@ApiImplicitParam(access = DarkFeatureSwaggerFilter.DARK_FEATURE_CONTROLLED, paramType = "header", dataType = "string"), @ApiImplicitParam(name = REQUEST_DATA_PART, value = EXAMPLE_COHORT_REQUEST_DATA_JSON, dataTypeClass = CohortEvaluation.class, required = true, paramType = "form", type = "file"), @ApiImplicitParam(name = CQL_DEFINITION, value = CQL_REQUIREMENTS, dataTypeClass = File.class, required = true, paramType = "form", type = "file") })
@ApiResponses(value = { @ApiResponse(code = 200, message = "Successful Operation", response = CohortResult.class), @ApiResponse(code = 400, message = "Bad Request", response = ServiceErrorList.class), @ApiResponse(code = 500, message = "Server Error", response = ServiceErrorList.class) })
public Response evaluateCohort(@Context HttpServletRequest request, @ApiParam(value = ServiceBaseConstants.MINOR_VERSION_DESCRIPTION, required = true, defaultValue = ServiceBuildConstants.DATE) @QueryParam(CohortEngineRestHandler.VERSION) String version, @ApiParam(hidden = true, type = "file", required = true) IMultipartBody multipartBody) {
final String methodName = MethodNames.EVALUATE_COHORT.getName();
Response response = null;
// Error out if feature is not enabled
ServiceBaseUtility.isDarkFeatureEnabled(CohortEngineRestConstants.DARK_LAUNCHED_MEASURE_EVALUATION);
try {
// Perform api setup
Response errorResponse = ServiceBaseUtility.apiSetup(version, logger, methodName);
if (errorResponse != null) {
return errorResponse;
}
if (multipartBody == null) {
throw new IllegalArgumentException("A multipart/form-data body is required");
}
IAttachment metadataAttachment = multipartBody.getAttachment(REQUEST_DATA_PART);
if (metadataAttachment == null) {
throw new IllegalArgumentException(String.format("Missing '%s' MIME attachment", REQUEST_DATA_PART));
}
// deserialize the MeasuresEvaluation request
ObjectMapper om = new ObjectMapper();
CohortEvaluation evaluationRequest = om.readValue(metadataAttachment.getDataHandler().getInputStream(), CohortEvaluation.class);
FhirServerConfig dataServerConfig = evaluationRequest.getDataServerConfig();
FhirServerConfig terminologyServerConfig = evaluationRequest.getTerminologyServerConfig() == null ? evaluationRequest.getDataServerConfig() : evaluationRequest.getTerminologyServerConfig();
IAttachment cqlAttachment = multipartBody.getAttachment(CQL_DEFINITION);
if (cqlAttachment == null) {
throw new IllegalArgumentException(String.format("Missing '%s' MIME attachment", CQL_DEFINITION));
}
// validate the contents of the fhirServerConfig
validateBean(dataServerConfig);
validateBean(terminologyServerConfig);
FhirClientBuilderFactory clientBuilderFactory = FhirClientBuilderFactory.newInstance();
FhirClientBuilder clientBuilder = clientBuilderFactory.newFhirClientBuilder();
CqlLibraryProvider libraryProvider;
try (InputStream is = cqlAttachment.getDataHandler().getInputStream()) {
ZipInputStream zis = new ZipInputStream(is);
MapCqlLibraryProviderFactory libraryProviderFactory = new MapCqlLibraryProviderFactory();
String[] attachmentHeaders = cqlAttachment.getHeader("Content-Disposition").split(";");
String filename = null;
for (String header : attachmentHeaders) {
if (header.contains("filename")) {
filename = FilenameUtils.removeExtension(header.split("=")[1].replaceAll("\"", ""));
}
}
String[] searchPaths = new String[] { "cql", filename + "/cql" };
libraryProvider = libraryProviderFactory.fromZipStream(zis, searchPaths);
}
CqlLibraryProvider fhirClasspathProvider = new ClasspathCqlLibraryProvider();
libraryProvider = new PriorityCqlLibraryProvider(libraryProvider, fhirClasspathProvider);
CqlToElmTranslator translator = new CqlToElmTranslator();
libraryProvider = new TranslatingCqlLibraryProvider(libraryProvider, translator);
IGenericClient dataClient = clientBuilder.createFhirClient(dataServerConfig);
IGenericClient termClient = clientBuilder.createFhirClient(terminologyServerConfig);
CqlTerminologyProvider termProvider = new R4RestFhirTerminologyProvider(termClient);
List<String> passingPatients;
try (RetrieveCacheContext retrieveCacheContext = new DefaultRetrieveCacheContext()) {
passingPatients = evaluateCohort(dataClient, termProvider, libraryProvider, retrieveCacheContext, evaluationRequest);
}
response = Response.status(Response.Status.OK).header("Content-Type", "application/json").entity(new CohortResult(passingPatients)).build();
} catch (Throwable e) {
// map any exceptions caught into the proper REST error response objects
response = new CohortServiceExceptionMapper().toResponse(e);
} finally {
// Perform api cleanup
Response errorResponse = ServiceBaseUtility.apiCleanup(logger, methodName);
if (errorResponse != null) {
response = errorResponse;
}
}
return response;
}
use of com.ibm.cohort.engine.measure.cache.RetrieveCacheContext in project quality-measure-and-cohort-service by Alvearie.
the class R4MeasureEvaluatorBuilderTest method build_withPageSizeOverride_withExpandValueSetsFalse.
@Test
public void build_withPageSizeOverride_withExpandValueSetsFalse() throws Exception {
try (RetrieveCacheContext cacheContext = new DefaultRetrieveCacheContext(new CaffeineConfiguration<>())) {
MeasureEvaluator evaluator = new R4MeasureEvaluatorBuilder().withClientContext(clientContext).withRetrieveCacheContext(cacheContext).withExpandValueSets(false).withPageSize(500).build();
validateMeasureEvaluator(evaluator);
}
verify(0, getRequestedFor(urlMatching("/ValueSet/Type2Diabetes/\\$expand.*")));
verify(0, getRequestedFor(urlMatching("/Condition\\?code=" + DIABETES_CODESYSTEM + ".*")));
verify(1, getRequestedFor(urlMatching("/Condition\\?code%3Ain=Type2Diabetes.*_count=500&_format=json")));
}
use of com.ibm.cohort.engine.measure.cache.RetrieveCacheContext in project quality-measure-and-cohort-service by Alvearie.
the class CohortCLI method runWithArgs.
/**
* Simulate main method behavior in a non-static context for use in testing
* tools. This method is intended to be called only once. Multiple calls for the
* same library path will attempt duplicate library loading.
*
* @param args parameter values
* @param out location where contents that would normally go to stdout should
* be written
* @return CQLEvaluator
* @throws IOException IOException
*/
public CqlEvaluator runWithArgs(String[] args, PrintStream out) throws IOException {
Arguments arguments = new Arguments();
Console console = new DefaultConsole(out);
JCommander jc = JCommander.newBuilder().programName("cql-engine").console(console).addObject(arguments).build();
jc.parse(args);
CqlEvaluator wrapper = null;
if (arguments.isDisplayHelp) {
jc.usage();
} else {
FhirClientBuilderFactory factory = FhirClientBuilderFactory.newInstance();
FhirClientBuilder fhirClientBuilder = factory.newFhirClientBuilder();
readConnectionConfiguration(arguments);
MapCqlLibraryProviderFactory libraryProviderFactory = new MapCqlLibraryProviderFactory();
String[] filters = null;
if (arguments.filters != null) {
filters = arguments.filters.toArray(new String[arguments.filters.size()]);
}
CqlLibraryProvider backingLibraryProvider;
Path libraryFolder = Paths.get(arguments.libraryPath);
if (libraryFolder.toFile().isDirectory()) {
out.println(String.format("Loading libraries from folder '%s'", libraryFolder.toString()));
backingLibraryProvider = libraryProviderFactory.fromDirectory(libraryFolder, filters);
} else if (FileHelpers.isZip(libraryFolder.toFile())) {
out.println(String.format("Loading libraries from ZIP '%s'", libraryFolder.toString()));
backingLibraryProvider = libraryProviderFactory.fromZipFile(libraryFolder, filters);
} else {
out.println(String.format("Loading libraries from FHIR Library '%s'", libraryFolder.toString()));
IGenericClient measureClient = fhirClientBuilder.createFhirClient(measureServerConfig);
FhirResourceResolver<Library> libraryResolver = R4FhirServerResourceResolverFactory.createLibraryResolver(measureClient);
R4LibraryDependencyGatherer dependencyGatherer = new R4LibraryDependencyGatherer(libraryResolver);
List<Library> cqlLibraries = dependencyGatherer.gatherForLibraryId(arguments.libraryPath);
Map<CqlLibraryDescriptor, CqlLibrary> cqlLibraryMap = toCqlLibraryMap(cqlLibraries);
backingLibraryProvider = new MapCqlLibraryProvider(cqlLibraryMap);
}
CqlLibraryProvider fhirClasspathProvider = new ClasspathCqlLibraryProvider();
backingLibraryProvider = new PriorityCqlLibraryProvider(backingLibraryProvider, fhirClasspathProvider);
CqlToElmTranslator translator = new CqlToElmTranslator();
if (arguments.modelInfoFile != null && arguments.modelInfoFile.exists()) {
translator.registerModelInfo(arguments.modelInfoFile);
}
boolean isForceTranslation = arguments.sourceFormat == Format.CQL;
CqlLibraryProvider libraryProvider = new TranslatingCqlLibraryProvider(backingLibraryProvider, translator, isForceTranslation);
IGenericClient dataClient = fhirClientBuilder.createFhirClient(dataServerConfig);
IGenericClient termClient = fhirClientBuilder.createFhirClient(terminologyServerConfig);
CqlTerminologyProvider termProvider = new R4RestFhirTerminologyProvider(termClient);
Map<String, com.ibm.cohort.cql.evaluation.parameters.Parameter> parameters = null;
if (arguments.parameters != null) {
parameters = parseParameterArguments(arguments.parameters);
}
CqlVersionedIdentifier libraryIdentifier = new CqlVersionedIdentifier(arguments.libraryName, arguments.libraryVersion);
List<Pair<String, String>> contexts;
if (arguments.contextIds == null || arguments.contextIds.isEmpty()) {
// If no context ids are provided, perform one run using a null context
contexts = Collections.singletonList(null);
} else {
contexts = arguments.contextIds.stream().map(x -> new ImmutablePair<>(arguments.contextName, x)).collect(Collectors.toList());
}
try (RetrieveCacheContext cacheContext = new DefaultRetrieveCacheContext()) {
CqlDataProvider dataProvider = R4DataProviderFactory.createDataProvider(dataClient, termProvider, cacheContext, R4FhirModelResolverFactory.createCachingResolver(), !arguments.enableTerminologyOptimization, arguments.searchPageSize);
wrapper = new CqlEvaluator().setLibraryProvider(libraryProvider).setDataProvider(dataProvider).setTerminologyProvider(termProvider);
ZonedDateTime evaluationDateTime = ZonedDateTime.now();
for (Pair<String, String> context : contexts) {
String contextLabel = context == null ? "null" : context.getRight();
out.println("Context: " + contextLabel);
CqlEvaluationResult result = wrapper.evaluate(libraryIdentifier, parameters, context, arguments.expressions, arguments.loggingLevel, evaluationDateTime);
out.print(prettyPrintResult(result));
out.println("---");
}
}
}
return wrapper;
}
use of com.ibm.cohort.engine.measure.cache.RetrieveCacheContext in project quality-measure-and-cohort-service by Alvearie.
the class MeasureCLI method runWithArgs.
public MeasureEvaluator runWithArgs(String[] args, PrintStream out) throws IOException {
MeasureEvaluator evaluator = null;
Arguments arguments = new Arguments();
Console console = new DefaultConsole(out);
JCommander jc = JCommander.newBuilder().programName("measure-engine").console(console).addObject(arguments).build();
jc.parse(args);
if (arguments.isDisplayHelp) {
jc.usage();
} else {
arguments.validate();
readDataServerConfiguration(arguments);
readTerminologyServerConfiguration(arguments);
FhirClientBuilderFactory fhirClientBuilderFactory = getFhirClientBuilderFactory();
IGenericClient dataServerClient = fhirClientBuilderFactory.newFhirClientBuilder().createFhirClient(dataServerConfig);
IGenericClient terminologyServerClient = fhirClientBuilderFactory.newFhirClientBuilder().createFhirClient(terminologyServerConfig);
String[] filters = (arguments.filters != null) ? arguments.filters.toArray(new String[arguments.filters.size()]) : null;
IParser parser = getFhirContext().newJsonParser().setPrettyPrint(true);
R4QualityMeasureResolverFactory resolverFactory = new R4QualityMeasureResolverFactory(parser);
FhirResourceResolver<Library> libraryResolver;
FhirResourceResolver<Measure> measureResolver;
if (arguments.measureServerConfigFile != null && FileHelpers.isZip(arguments.measureServerConfigFile)) {
R4QualityMeasureResolvers resolvers = resolverFactory.fromZipFile(arguments.measureServerConfigFile.toPath(), filters);
libraryResolver = resolvers.getLibraryResolver();
measureResolver = resolvers.getMeasureResolver();
} else if (arguments.measureServerConfigFile != null && arguments.measureServerConfigFile.isDirectory()) {
R4QualityMeasureResolvers resolvers = resolverFactory.fromDirectory(arguments.measureServerConfigFile.toPath(), filters);
libraryResolver = resolvers.getLibraryResolver();
measureResolver = resolvers.getMeasureResolver();
} else {
readMeasureServerConfiguration(arguments);
IGenericClient measureServerClient = fhirClientBuilderFactory.newFhirClientBuilder().createFhirClient(measureServerConfig);
libraryResolver = R4FhirServerResourceResolverFactory.createLibraryResolver(measureServerClient);
measureResolver = R4FhirServerResourceResolverFactory.createMeasureResolver(measureServerClient);
}
List<MeasureContext> measureContexts;
if (arguments.measureConfigurationFile != null) {
measureContexts = MeasureContextProvider.getMeasureContexts(arguments.measureConfigurationFile);
} else {
measureContexts = MeasureContextProvider.getMeasureContexts(arguments.resourceId, arguments.parameters);
}
validateMeasureContexts(measureContexts);
R4LibraryDependencyGatherer libraryDependencyGatherer = new R4LibraryDependencyGatherer(libraryResolver);
CqlTerminologyProvider terminologyProvider = new R4RestFhirTerminologyProvider(terminologyServerClient);
try (RetrieveCacheContext retrieveCacheContext = arguments.disableRetrieveCache ? null : new DefaultRetrieveCacheContext()) {
Map<String, CqlDataProvider> dataProviders = R4DataProviderFactory.createDataProviderMap(dataServerClient, terminologyProvider, retrieveCacheContext, R4FhirModelResolverFactory.createCachingResolver(), !arguments.enableTerminologyOptimization, arguments.searchPageSize);
evaluator = new MeasureEvaluator(measureResolver, libraryResolver, libraryDependencyGatherer, terminologyProvider, dataProviders);
for (String contextId : arguments.contextIds) {
out.println("Evaluating: " + contextId);
// Reports only returned for measures where patient is in initial population
List<MeasureReport> reports = evaluator.evaluatePatientMeasures(contextId, measureContexts, new MeasureEvidenceOptions(arguments.includeEvaluatedResources, arguments.defineReturnOption));
for (MeasureReport report : reports) {
if (arguments.reportFormat == ReportFormat.TEXT) {
out.println("Result for " + report.getMeasure());
for (MeasureReport.MeasureReportGroupComponent group : report.getGroup()) {
for (MeasureReport.MeasureReportGroupPopulationComponent pop : group.getPopulation()) {
String popCode = pop.getCode().getCodingFirstRep().getCode();
if (pop.getId() != null) {
popCode += "(" + pop.getId() + ")";
}
out.println(String.format("Population: %s = %d", popCode, pop.getCount()));
}
}
} else {
out.println(parser.encodeResourceToString(report));
}
out.println("---");
}
if (reports.isEmpty()) {
out.println("---");
}
}
}
}
return evaluator;
}
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