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

Example 26 with Parameter

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

the class SparkCqlEvaluatorTest method testParameterMatrixOutputSimpleSuccess.

@Test
public void testParameterMatrixOutputSimpleSuccess() throws Exception {
    String outputLocation = "target/output/param-matrix/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);
    }
    ObjectMapper om = new ObjectMapper();
    File jobsFile = new File("target/output/param-matrix-simple/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);
        validateOutputCountsAndColumns(outputLocation, new HashSet<>(Arrays.asList("id", "parameters", "SampleLibrary|IsFemale")), 10 * ages.size(), "delta");
    } finally {
        jobsFile.delete();
    }
}

Example 27 with Parameter

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

the class SparkCqlEvaluatorTest method testParameterMatrixOutputDisabledRowsGroupingSuccess.

@Test
public void testParameterMatrixOutputDisabledRowsGroupingSuccess() throws Exception {
    String outputLocation = "target/output/param-matrix-group-disabled/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));
        CqlExpressionConfiguration renamed = new CqlExpressionConfiguration();
        renamed.setName("IsFemale");
        renamed.setOutputColumn("IsFemale" + age);
        CqlEvaluationRequest request = new CqlEvaluationRequest(template);
        request.setExpressions(Collections.singleton(renamed));
        request.setParameters(parameters);
        requests.getEvaluations().add(request);
    }
    ObjectMapper om = new ObjectMapper();
    File jobsFile = new File("target/output/param-matrix-simple/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, "--disable-result-grouping" };
        SparkCqlEvaluator.main(args);
        validateOutputCountsAndColumns(outputLocation, new HashSet<>(Arrays.asList("id", "parameters", "IsFemale15", "IsFemale17", "IsFemale18")), 10, "delta");
    } finally {
        jobsFile.delete();
    }
}

Example 28 with Parameter

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

the class CqlEvaluator method evaluate.

public List<Pair<CqlEvaluationRequest, CqlEvaluationResult>> evaluate(CqlEvaluationRequests requests, CqlDebug debug) {
    List<Pair<CqlEvaluationRequest, CqlEvaluationResult>> results = new ArrayList<>(requests.getEvaluations().size());
    ZonedDateTime batchDateTime = ZonedDateTime.now();
    for (CqlEvaluationRequest request : requests.getEvaluations()) {
        Map<String, Parameter> parameters = new HashMap<>();
        if (requests.getGlobalParameters() != null) {
            parameters.putAll(requests.getGlobalParameters());
        }
        if (request.getParameters() != null) {
            parameters.putAll(request.getParameters());
        }
        CqlEvaluationRequest withGlobals = new CqlEvaluationRequest(request);
        withGlobals.setParameters(parameters);
        results.add(Pair.of(request, evaluate(withGlobals, debug, batchDateTime)));
    }
    return results;
}

Example 29 with Parameter

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

the class ParameterHelperTest method testResolveCodeParameter.

@Test
public void testResolveCodeParameter() {
    Map<String, Parameter> params = ParameterHelper.parseParameterArguments(Arrays.asList("test:code:1.2.3:SNOMEDCT:Hernia"));
    assertEquals(1, params.size());
    CodeParameter p = (CodeParameter) params.get("test");
    assertNotNull("Parameter with expected name not found", p);
    assertEquals("Unexpected value", "1.2.3", p.getValue());
    assertEquals("Unexpected value", "SNOMEDCT", p.getSystem());
    assertEquals("Unexpected value", "Hernia", p.getDisplay());
}

Example 30 with Parameter

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

the class ParameterHelper method parseParameterArguments.

/**
 * Conversion routine for CQL parameter values encoded for command line
 * interaction.
 *
 * @param arguments list of CQL parameter values encoded as strings
 * @return decoded parameter values formatted for consumption by the CQL engine
 */
public static Map<String, Parameter> parseParameterArguments(List<String> arguments) {
    Map<String, Parameter> result = new HashMap<>();
    Pattern p = Pattern.compile("(?<name>[^:]+):(?<type>[^:]+):(?<value>.*)");
    for (String arg : arguments) {
        Matcher m = p.matcher(arg);
        if (m.matches()) {
            String name = m.group("name");
            String type = m.group("type");
            String value = m.group("value");
            String subType = null;
            String start = null;
            String end = null;
            if (type.equals("interval")) {
                String[] parts = value.split(",");
                if (parts.length != 3) {
                    throw new IllegalArgumentException("Invalid interval format. Must contain exactly 3 fields separated by commas");
                }
                subType = parts[0];
                start = parts[1];
                end = parts[2];
            }
            Map.Entry<String, Parameter> stringObjectEntry = convertParameter(name, type, value, subType, start, end);
            result.put(stringObjectEntry.getKey(), stringObjectEntry.getValue());
        } else {
            throw new IllegalArgumentException(String.format("Invalid parameter string %s", arg));
        }
    }
    return result;
}