Examples with IntegerParameter com.ibm.cohort.cql.evaluation.parameters.IntegerParameter used on opensource projects

Example 11 with IntegerParameter

use of com.ibm.cohort.cql.evaluation.parameters.IntegerParameter in project quality-measure-and-cohort-service by Alvearie.

the class MeasureEvaluatorTest method measure_report_generated___java_overrides_overwrite_measure_params.

@Test
public void measure_report_generated___java_overrides_overwrite_measure_params() throws Exception {
    CapabilityStatement metadata = getCapabilityStatement();
    mockFhirResourceRetrieval("/metadata?_format=json", metadata);
    Patient patient = getPatient("123", AdministrativeGender.MALE, "1970-10-10");
    mockFhirResourceRetrieval(patient);
    Library library = mockLibraryRetrieval("TestDummyPopulations", DEFAULT_VERSION, "cql/fhir-measure/test-dummy-populations.xml", ELM_MIME_TYPE);
    Measure measure = getCohortMeasure("CohortMeasureName", library, INITIAL_POPULATION);
    String duplicateParamName = "duplicateParam";
    int fhirMeasureIntValue = 10;
    int javaParameterIntValue = 99;
    measure.addExtension(createParameterExtension(duplicateParamName, new IntegerType(fhirMeasureIntValue)));
    mockFhirResourceRetrieval(measure);
    Map<String, Parameter> parameterMap = new HashMap<>();
    parameterMap.put(duplicateParamName, new IntegerParameter(javaParameterIntValue));
    MeasureReport report = evaluator.evaluatePatientMeasure(measure.getId(), patient.getId(), parameterMap);
    assertNotNull(report);
    // Make sure report only contained one entry for the duplicate parameter
    List<Type> filteredReportParams = report.getExtension().stream().filter(x -> x.getUrl().equals(MEASURE_PARAMETER_VALUE_URL)).map(x -> (ParameterDefinition) x.getValue()).filter(x -> x.getName().equals(duplicateParamName)).map(x -> x.getExtensionByUrl(PARAMETER_VALUE_URL).getValue()).collect(Collectors.toList());
    assertEquals(1, filteredReportParams.size());
    // Sanity check input parameter values were different before checking for correct value
    assertNotEquals(fhirMeasureIntValue, javaParameterIntValue);
    assertEquals(javaParameterIntValue, ((IntegerType) filteredReportParams.get(0)).getValue().intValue());
}

Example 12 with IntegerParameter

use of com.ibm.cohort.cql.evaluation.parameters.IntegerParameter in project quality-measure-and-cohort-service by Alvearie.

the class SparkCqlEvaluatorTest method testReadCqlJobsSuccess.

@Test
public void testReadCqlJobsSuccess() throws Exception {
    IntervalParameter measurementPeriod = new IntervalParameter();
    measurementPeriod.setStart(new DateParameter("2020-01-01")).setEnd(new DateParameter("2021-01-01"));
    IntegerParameter minimumAge = new IntegerParameter(17);
    evaluator.hadoopConfiguration = new SerializableConfiguration(SparkHadoopUtil.get().conf());
    CqlEvaluationRequests requests = evaluator.readJobSpecification("src/test/resources/simple-job/cql-jobs.json");
    assertNotNull(requests);
    assertEquals(measurementPeriod, requests.getGlobalParameters().get("Measurement Period"));
    assertEquals(1, requests.getEvaluations().size());
    assertEquals(minimumAge, requests.getEvaluations().get(0).getParameters().get("MinimumAge"));
}

Example 13 with IntegerParameter

use of com.ibm.cohort.cql.evaluation.parameters.IntegerParameter in project quality-measure-and-cohort-service by Alvearie.

the class SparkCqlEvaluatorTest method testGetFilteredRequestsGlobalParametersApplied.

@Test
public void testGetFilteredRequestsGlobalParametersApplied() {
    CqlEvaluationRequests requests = new CqlEvaluationRequests();
    requests.setGlobalParameters(new HashMap<String, Parameter>() {

        {
            put("param1", new IntegerParameter(10));
            put("param2", new StringParameter("10"));
            put("globalParam", new DecimalParameter("10.0"));
        }
    });
    CqlEvaluationRequest request = makeEvaluationRequest("context", "lib1", "1.0.0");
    request.setExpressionsByNames(new HashSet<>(Collections.singletonList("cohortOrig")));
    request.setParameters(new HashMap<String, Parameter>() {

        {
            put("param1", new IntegerParameter(1));
            put("param2", new StringParameter("1"));
            put("param3", new DecimalParameter("1.0"));
        }
    });
    CqlEvaluationRequest request2 = makeEvaluationRequest("context", "lib2", "1.0.0");
    request2.setExpressionsByNames(new HashSet<>(Collections.singletonList("cohortOrig")));
    List<CqlEvaluationRequest> evaluations = Arrays.asList(request, request2);
    requests.setEvaluations(evaluations);
    CqlEvaluationRequests actual = evaluator.getFilteredRequests(requests, null, null);
    for (CqlEvaluationRequest evaluation : actual.getEvaluations()) {
        if (evaluation.getDescriptor().getLibraryId().equals("lib1")) {
            assertEquals(4, evaluation.getParameters().size());
            assertEquals(new IntegerParameter(1), evaluation.getParameters().get("param1"));
            assertEquals(new StringParameter("1"), evaluation.getParameters().get("param2"));
            assertEquals(new DecimalParameter("1.0"), evaluation.getParameters().get("param3"));
            assertEquals(new DecimalParameter("10.0"), evaluation.getParameters().get("globalParam"));
        } else if (evaluation.getDescriptor().getLibraryId().equals("lib2")) {
            assertEquals(3, evaluation.getParameters().size());
            assertEquals(new IntegerParameter(10), evaluation.getParameters().get("param1"));
            assertEquals(new StringParameter("10"), evaluation.getParameters().get("param2"));
            assertEquals(new DecimalParameter("10.0"), evaluation.getParameters().get("globalParam"));
        } else {
            fail("Unexpected library encountered. Expected only lib1 and lib2.");
        }
    }
}

Example 14 with IntegerParameter

use of com.ibm.cohort.cql.evaluation.parameters.IntegerParameter in project quality-measure-and-cohort-service by Alvearie.

the class SparkCqlEvaluatorTest method testParameterMatrixOutputWithKeyParametersSpecifiedSuccess.

@Test
public void testParameterMatrixOutputWithKeyParametersSpecifiedSuccess() throws Exception {
    String outputLocation = "target/output/param-matrix-key-params/patient_cohort";
    CqlEvaluationRequest template = new CqlEvaluationRequest();
    template.setDescriptor(new CqlLibraryDescriptor().setLibraryId("SampleLibrary").setVersion("1.0.0"));
    template.setExpressionsByNames(Collections.singleton("IsFemale"));
    template.setContextKey("Patient");
    template.setContextValue("NA");
    CqlEvaluationRequests requests = new CqlEvaluationRequests();
    requests.setEvaluations(new ArrayList<>());
    List<Integer> ages = Arrays.asList(15, 17, 18);
    for (Integer age : ages) {
        Map<String, Parameter> parameters = new HashMap<>();
        parameters.put("MinimumAge", new IntegerParameter(age));
        CqlEvaluationRequest request = new CqlEvaluationRequest(template);
        request.setParameters(parameters);
        requests.getEvaluations().add(request);
        CqlExpressionConfiguration renamed = new CqlExpressionConfiguration();
        renamed.setName("IsFemale");
        renamed.setOutputColumn("Renamed");
        Map<String, Parameter> parametersWithExtraneous = new HashMap<>(parameters);
        parametersWithExtraneous.put("Extraneous", new IntegerParameter(0));
        request = new CqlEvaluationRequest(template);
        request.setExpressions(Collections.singleton(renamed));
        request.setParameters(parametersWithExtraneous);
        requests.getEvaluations().add(request);
    }
    ObjectMapper om = new ObjectMapper();
    File jobsFile = new File("target/param-matrix/cql-jobs.json");
    if (!jobsFile.exists()) {
        jobsFile.getParentFile().mkdirs();
    }
    FileUtils.write(jobsFile, om.writeValueAsString(requests), StandardCharsets.UTF_8);
    try {
        String[] args = new String[] { "-d", "src/test/resources/simple-job/context-definitions.json", "-j", jobsFile.getPath(), "-m", "src/test/resources/simple-job/modelinfo/simple-modelinfo-1.0.0.xml", "-c", "src/test/resources/simple-job/cql", "-i", "Patient=" + new File("src/test/resources/simple-job/testdata/patient").toURI().toString(), "-o", "Patient=" + new File(outputLocation).toURI().toString(), "--output-format", "delta", "--overwrite-output-for-contexts", "--metadata-output-path", outputLocation, "--key-parameters", "MinimumAge" };
        SparkCqlEvaluator.main(args);
        validateOutputCountsAndColumns(outputLocation, new HashSet<>(Arrays.asList("id", "parameters", "SampleLibrary|IsFemale", "Renamed")), 10 * ages.size(), "delta");
    } finally {
        jobsFile.delete();
    }
}

Example 15 with IntegerParameter

use of com.ibm.cohort.cql.evaluation.parameters.IntegerParameter in project quality-measure-and-cohort-service by Alvearie.

the class SparkCqlEvaluatorTest method testParameterMatrixOutputNonOverlappingParamsSuccess.

@Test
public void testParameterMatrixOutputNonOverlappingParamsSuccess() throws Exception {
    String outputLocation = "target/output/param-matrix-non-overlap/patient_cohort";
    CqlEvaluationRequest template = new CqlEvaluationRequest();
    template.setDescriptor(new CqlLibraryDescriptor().setLibraryId("SampleLibrary").setVersion("1.0.0"));
    template.setExpressionsByNames(Collections.singleton("IsFemale"));
    template.setContextKey("Patient");
    template.setContextValue("NA");
    CqlEvaluationRequests requests = new CqlEvaluationRequests();
    requests.setEvaluations(new ArrayList<>());
    List<Integer> ages = Arrays.asList(15, 17, 18);
    for (Integer age : ages) {
        Map<String, Parameter> parameters = new HashMap<>();
        parameters.put("MinimumAge", new IntegerParameter(age));
        CqlEvaluationRequest request = new CqlEvaluationRequest(template);
        request.setParameters(parameters);
        requests.getEvaluations().add(request);
        CqlExpressionConfiguration renamed = new CqlExpressionConfiguration();
        renamed.setName("IsFemale");
        renamed.setOutputColumn("Renamed");
        Map<String, Parameter> parametersWithExtraneous = new HashMap<>(parameters);
        parametersWithExtraneous.put("Extraneous", new IntegerParameter(0));
        request = new CqlEvaluationRequest(template);
        request.setExpressions(Collections.singleton(renamed));
        request.setParameters(parametersWithExtraneous);
        requests.getEvaluations().add(request);
    }
    ObjectMapper om = new ObjectMapper();
    File jobsFile = new File("target/output/param-matrix/cql-jobs.json");
    if (!jobsFile.exists()) {
        jobsFile.getParentFile().mkdirs();
    }
    FileUtils.write(jobsFile, om.writeValueAsString(requests), StandardCharsets.UTF_8);
    try {
        String[] args = new String[] { "-d", "src/test/resources/simple-job/context-definitions.json", "-j", jobsFile.getPath(), "-m", "src/test/resources/simple-job/modelinfo/simple-modelinfo-1.0.0.xml", "-c", "src/test/resources/simple-job/cql", "-i", "Patient=" + new File("src/test/resources/simple-job/testdata/patient").toURI().toString(), "-o", "Patient=" + new File(outputLocation).toURI().toString(), "--output-format", "delta", "--overwrite-output-for-contexts", "--metadata-output-path", outputLocation };
        SparkCqlEvaluator.main(args);
        // Because we've got a mismatch in the parameters in the first and second columns, each context
        // has a set of rows for the first parameter set where one column is populated and the other is null
        // and another set of rows where the first column is null and the second is populated.
        validateOutputCountsAndColumns(outputLocation, new HashSet<>(Arrays.asList("id", "parameters", "SampleLibrary|IsFemale", "Renamed")), 10 * ages.size() * /*outputColumns=*/
        2, "delta");
    } finally {
        jobsFile.delete();
    }
}