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Example 1 with ClasspathCqlLibraryProvider

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;
}
Also used : TranslatingCqlLibraryProvider(com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider) CohortEvaluation(com.ibm.cohort.engine.api.service.model.CohortEvaluation) IGenericClient(ca.uhn.fhir.rest.client.api.IGenericClient) R4RestFhirTerminologyProvider(com.ibm.cohort.engine.terminology.R4RestFhirTerminologyProvider) DefaultRetrieveCacheContext(com.ibm.cohort.engine.measure.cache.DefaultRetrieveCacheContext) RetrieveCacheContext(com.ibm.cohort.engine.measure.cache.RetrieveCacheContext) CqlToElmTranslator(com.ibm.cohort.cql.translation.CqlToElmTranslator) CqlLibraryProvider(com.ibm.cohort.cql.library.CqlLibraryProvider) PriorityCqlLibraryProvider(com.ibm.cohort.cql.library.PriorityCqlLibraryProvider) TranslatingCqlLibraryProvider(com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) IAttachment(com.ibm.websphere.jaxrs20.multipart.IAttachment) MapCqlLibraryProviderFactory(com.ibm.cohort.cql.library.MapCqlLibraryProviderFactory) CqlTerminologyProvider(com.ibm.cohort.cql.terminology.CqlTerminologyProvider) ObjectMapper(com.fasterxml.jackson.databind.ObjectMapper) FhirClientBuilder(com.ibm.cohort.fhir.client.config.FhirClientBuilder) ZipInputStream(java.util.zip.ZipInputStream) InputStream(java.io.InputStream) CohortResult(com.ibm.cohort.engine.api.service.model.CohortResult) DefaultRetrieveCacheContext(com.ibm.cohort.engine.measure.cache.DefaultRetrieveCacheContext) PriorityCqlLibraryProvider(com.ibm.cohort.cql.library.PriorityCqlLibraryProvider) Response(javax.ws.rs.core.Response) ApiResponse(io.swagger.annotations.ApiResponse) ZipInputStream(java.util.zip.ZipInputStream) FhirClientBuilderFactory(com.ibm.cohort.fhir.client.config.FhirClientBuilderFactory) FhirServerConfig(com.ibm.cohort.fhir.client.config.FhirServerConfig) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) Path(javax.ws.rs.Path) ApiImplicitParams(io.swagger.annotations.ApiImplicitParams) POST(javax.ws.rs.POST) Consumes(javax.ws.rs.Consumes) Produces(javax.ws.rs.Produces) ApiOperation(io.swagger.annotations.ApiOperation) ApiResponses(io.swagger.annotations.ApiResponses)

Example 2 with ClasspathCqlLibraryProvider

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());
}
Also used : FileInputStream(java.io.FileInputStream) InputStream(java.io.InputStream) MapCqlLibraryProvider(com.ibm.cohort.cql.library.MapCqlLibraryProvider) CqlToElmTranslator(com.ibm.cohort.cql.translation.CqlToElmTranslator) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) PriorityCqlLibraryProvider(com.ibm.cohort.cql.library.PriorityCqlLibraryProvider) CqlLibraryProvider(com.ibm.cohort.cql.library.CqlLibraryProvider) MapCqlLibraryProvider(com.ibm.cohort.cql.library.MapCqlLibraryProvider) FileInputStream(java.io.FileInputStream) PriorityCqlLibraryProvider(com.ibm.cohort.cql.library.PriorityCqlLibraryProvider) CqlLibrary(com.ibm.cohort.cql.library.CqlLibrary) ProviderBasedCqlLibrarySourceProvider(com.ibm.cohort.cql.provider.ProviderBasedCqlLibrarySourceProvider) MapCqlLibraryProviderFactory(com.ibm.cohort.cql.library.MapCqlLibraryProviderFactory) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) CqlLibraryDescriptor(com.ibm.cohort.cql.library.CqlLibraryDescriptor) CqlTranslationResult(com.ibm.cohort.cql.translation.CqlTranslationResult)

Example 3 with ClasspathCqlLibraryProvider

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;
}
Also used : FhirClientBuilder(com.ibm.cohort.fhir.client.config.FhirClientBuilder) TranslatingCqlLibraryProvider(com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider) IGenericClient(ca.uhn.fhir.rest.client.api.IGenericClient) R4RestFhirTerminologyProvider(com.ibm.cohort.engine.terminology.R4RestFhirTerminologyProvider) FhirClientBuilderFactory(com.ibm.cohort.fhir.client.config.FhirClientBuilderFactory) CqlToElmTranslator(com.ibm.cohort.cql.translation.CqlToElmTranslator) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) CqlLibraryProvider(com.ibm.cohort.cql.library.CqlLibraryProvider) TranslatingCqlLibraryProvider(com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) CqlTerminologyProvider(com.ibm.cohort.cql.terminology.CqlTerminologyProvider) CqlDataProvider(com.ibm.cohort.cql.data.CqlDataProvider) CqlEvaluator(com.ibm.cohort.cql.evaluation.CqlEvaluator)

Example 4 with ClasspathCqlLibraryProvider

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());
}
Also used : CqlLibrary(com.ibm.cohort.cql.library.CqlLibrary) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) CqlLibrarySourceProvider(com.ibm.cohort.cql.provider.CqlLibrarySourceProvider) Assert.assertThrows(org.junit.Assert.assertThrows) CqlLibrary(com.ibm.cohort.cql.library.CqlLibrary) CqlLibraryProvider(com.ibm.cohort.cql.library.CqlLibraryProvider) Test(org.junit.Test) Reader(java.io.Reader) Format(com.ibm.cohort.cql.library.Format) File(java.io.File) CqlLibraryDescriptor(com.ibm.cohort.cql.library.CqlLibraryDescriptor) CqlTranslatorException(org.cqframework.cql.cql2elm.CqlTranslatorException) FileReader(java.io.FileReader) Assert.assertEquals(org.junit.Assert.assertEquals) CqlLibrarySourceProvider(com.ibm.cohort.cql.provider.CqlLibrarySourceProvider) Reader(java.io.Reader) FileReader(java.io.FileReader) FileReader(java.io.FileReader) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) CqlLibraryProvider(com.ibm.cohort.cql.library.CqlLibraryProvider) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) CqlLibraryDescriptor(com.ibm.cohort.cql.library.CqlLibraryDescriptor) File(java.io.File) Test(org.junit.Test)

Example 5 with ClasspathCqlLibraryProvider

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");
    }
}
Also used : ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) CqlLibraryProvider(com.ibm.cohort.cql.library.CqlLibraryProvider) ClasspathCqlLibraryProvider(com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider) CqlLibraryDescriptor(com.ibm.cohort.cql.library.CqlLibraryDescriptor) Test(org.junit.Test)

Aggregations

ClasspathCqlLibraryProvider (com.ibm.cohort.cql.library.ClasspathCqlLibraryProvider)16 CqlLibraryProvider (com.ibm.cohort.cql.library.CqlLibraryProvider)14 TranslatingCqlLibraryProvider (com.ibm.cohort.cql.translation.TranslatingCqlLibraryProvider)11 CqlToElmTranslator (com.ibm.cohort.cql.translation.CqlToElmTranslator)10 Test (org.junit.Test)9 PriorityCqlLibraryProvider (com.ibm.cohort.cql.library.PriorityCqlLibraryProvider)6 File (java.io.File)6 HashMap (java.util.HashMap)6 CqlTerminologyProvider (com.ibm.cohort.cql.terminology.CqlTerminologyProvider)5 ObjectMapper (com.fasterxml.jackson.databind.ObjectMapper)4 CqlDataProvider (com.ibm.cohort.cql.data.CqlDataProvider)4 CqlLibrary (com.ibm.cohort.cql.library.CqlLibrary)4 CqlLibraryDescriptor (com.ibm.cohort.cql.library.CqlLibraryDescriptor)4 MapCqlLibraryProviderFactory (com.ibm.cohort.cql.library.MapCqlLibraryProviderFactory)4 IGenericClient (ca.uhn.fhir.rest.client.api.IGenericClient)3 CqlEvaluationRequests (com.ibm.cohort.cql.evaluation.CqlEvaluationRequests)3 CqlEvaluator (com.ibm.cohort.cql.evaluation.CqlEvaluator)3 CqlVersionedIdentifier (com.ibm.cohort.cql.library.CqlVersionedIdentifier)3 EqualsStringMatcher (com.ibm.cohort.cql.util.EqualsStringMatcher)3 R4RestFhirTerminologyProvider (com.ibm.cohort.engine.terminology.R4RestFhirTerminologyProvider)3