use of com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider 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.cql.library.ClasspathCqlLibraryProvider in project quality-measure-and-cohort-service by Alvearie.
the class TranslationCLI method runWithArgs.
public void runWithArgs(TranslationOptions options, PrintStream out) throws Exception {
CqlLibraryProvider libraryProvider;
if (options.directory != null && options.directory.exists()) {
MapCqlLibraryProviderFactory libraryProviderFactory = new MapCqlLibraryProviderFactory();
libraryProvider = libraryProviderFactory.fromDirectory(options.directory.toPath());
} else {
libraryProvider = new MapCqlLibraryProvider(Collections.emptyMap());
}
CqlLibraryProvider fhirClasspathProvider = new ClasspathCqlLibraryProvider();
libraryProvider = new PriorityCqlLibraryProvider(libraryProvider, fhirClasspathProvider);
CqlToElmTranslator translator = new CqlToElmTranslator();
if (options.modelInfoFile != null && options.modelInfoFile.exists()) {
translator.registerModelInfo(options.modelInfoFile);
}
String content;
try (InputStream is = new FileInputStream(options.cqlPath)) {
content = IOUtils.toString(is, StandardCharsets.UTF_8);
}
// The values in the descriptor are not relevant for the translation CLI.
CqlLibraryDescriptor descriptor = new CqlLibraryDescriptor().setFormat(Format.CQL).setLibraryId("TranslationCLI").setVersion("TranslationCLI");
CqlLibrary library = new CqlLibrary().setDescriptor(descriptor).setContent(content);
CqlTranslationResult result = translator.translate(library, new ProviderBasedCqlLibrarySourceProvider(libraryProvider));
out.println("Translated Library: ");
out.println(result.getMainLibrary().getContent());
}
use of com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider in project quality-measure-and-cohort-service by Alvearie.
the class PatientTestBase method setupTestFor.
protected CqlEvaluator setupTestFor(DomainResource resource, FhirServerConfig fhirConfig, String firstPackage, String... packages) {
mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
mockFhirResourceRetrieval(resource);
CqlEvaluator evaluator = null;
if (firstPackage != null) {
FhirClientBuilderFactory factory = FhirClientBuilderFactory.newInstance();
FhirClientBuilder fhirClientBuilder = factory.newFhirClientBuilder();
CqlLibraryProvider classpathCqlLibraryProvider = new ClasspathCqlLibraryProvider(firstPackage, packages);
CqlToElmTranslator translator = new CqlToElmTranslator();
CqlLibraryProvider libraryProvider = new TranslatingCqlLibraryProvider(classpathCqlLibraryProvider, translator);
IGenericClient testClient = fhirClientBuilder.createFhirClient(fhirConfig);
CqlTerminologyProvider termProvider = new R4RestFhirTerminologyProvider(testClient);
CqlDataProvider dataProvider = R4DataProviderFactory.createDataProvider(testClient, termProvider, null, R4FhirModelResolverFactory.createCachingResolver(), true, null);
evaluator = new CqlEvaluator().setLibraryProvider(libraryProvider).setDataProvider(dataProvider).setTerminologyProvider(termProvider).setCacheContexts(false);
}
return evaluator;
}
use of com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider in project quality-measure-and-cohort-service by Alvearie.
the class CqlToElmTranslatorTest method testTranslationWithIncludes.
@Test
public void testTranslationWithIncludes() throws Exception {
CqlLibraryProvider provider = new ClasspathCqlLibraryProvider("cql");
CqlLibraryDescriptor descriptor = new CqlLibraryDescriptor().setLibraryId("SampleLibrary").setVersion("1.0.0").setFormat(Format.CQL);
CqlLibrary primaryLibrary = provider.getLibrary(descriptor);
CqlLibrarySourceProvider sourceProvider = vid -> {
CqlLibraryDescriptor d = new CqlLibraryDescriptor().setLibraryId(vid.getId()).setVersion(vid.getVersion()).setFormat(Format.CQL);
return provider.getLibrary(d).getContentAsStream();
};
CqlToElmTranslator translator = new CqlToElmTranslator();
try (Reader modelInfoXML = new FileReader(new File("src/test/resources/modelinfo/mock-modelinfo-1.0.0.xml"))) {
translator.registerModelInfo(modelInfoXML);
}
CqlTranslationResult result = translator.translate(primaryLibrary, sourceProvider);
assertEquals(1, result.getDependencies().size());
}
use of com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider in project quality-measure-and-cohort-service by Alvearie.
the class CqlTranslationIntegrationTest method exceptionCausedByNotIncludingFHIRHelpers.
@Test
public void exceptionCausedByNotIncludingFHIRHelpers() {
CqlLibraryProvider backingLibraryProvider = new ClasspathCqlLibraryProvider("cql.failure");
CqlToElmTranslator translator = new CqlToElmTranslator();
CqlLibraryProvider translatingLibraryProvider = new TranslatingCqlLibraryProvider(backingLibraryProvider, translator, true);
boolean failed = false;
CqlLibraryDescriptor descriptor = new CqlLibraryDescriptor().setLibraryId("MissingFhirHelpers").setVersion("1.0.0").setFormat(Format.ELM);
try {
translatingLibraryProvider.getLibrary(descriptor);
} catch (Exception e) {
failed = true;
Assert.assertTrue("Unexpected exception message: " + e.getMessage(), e.getMessage().startsWith("There were exceptions during cql translation:"));
}
if (!failed) {
Assert.fail("Did not fail translation");
}
}
Aggregations