Examples with Library org.hl7.fhir.r5.model.Library used on opensource projects

Example 36 with Library

use of org.hl7.fhir.r5.model.Library in project quality-measure-and-cohort-service by Alvearie.

the class MeasureCLITest method testCohortMeasureByURLSinglePatientCommandLineInput.

@Test
public void testCohortMeasureByURLSinglePatientCommandLineInput() throws Exception {
    mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
    Patient patient = getPatient("123", AdministrativeGender.MALE, "1592-14-03");
    mockFhirResourceRetrieval(patient);
    Library library = mockLibraryRetrieval("Test", DEFAULT_RESOURCE_VERSION, "cql/basic/Test-1.0.0.cql");
    Measure measure = getCohortMeasure("Test", library, "Female");
    mockMeasureRetrieval(measure);
    File tmpFile = new File("target/fhir-stub.json");
    ObjectMapper om = new ObjectMapper();
    try (Writer w = new FileWriter(tmpFile)) {
        w.write(om.writeValueAsString(getFhirServerConfig()));
    }
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    PrintStream out = new PrintStream(baos);
    try {
        MeasureCLI cli = new MeasureCLI();
        cli.runWithArgs(new String[] { "-d", tmpFile.getAbsolutePath(), "-p", "p1:interval:decimal,1.0,100.5", "-p", "p2:integer:1", "-r", CanonicalHelper.toCanonicalUrl(measure.getUrl(), measure.getVersion()), "-c", patient.getId() }, out);
    } finally {
        tmpFile.delete();
    }
    String output = new String(baos.toByteArray());
    String[] lines = output.split(System.getProperty("line.separator"));
    assertEquals(output, 4, lines.length);
}

Example 37 with Library

use of org.hl7.fhir.r5.model.Library in project quality-measure-and-cohort-service by Alvearie.

the class MeasureCLITest method testProportionRatioSinglePatient.

@Test
public void testProportionRatioSinglePatient() throws Exception {
    mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
    Patient patient = new Patient();
    patient.setId("123");
    patient.setGender(AdministrativeGender.MALE);
    OffsetDateTime birthDate = OffsetDateTime.now().minusYears(30);
    patient.setBirthDate(Date.from(birthDate.toInstant()));
    mockFhirResourceRetrieval(patient);
    Library library = mockLibraryRetrieval("Test", DEFAULT_RESOURCE_VERSION, "cql/basic/Test-1.0.0.cql");
    expressionsByPopulationType.clear();
    expressionsByPopulationType.put(MeasurePopulationType.INITIALPOPULATION, "Male");
    expressionsByPopulationType.put(MeasurePopulationType.DENOMINATOR, "Male");
    expressionsByPopulationType.put(MeasurePopulationType.NUMERATOR, "Over the hill");
    expectationsByPopulationType.clear();
    expectationsByPopulationType.put(MeasurePopulationType.INITIALPOPULATION, 1);
    expectationsByPopulationType.put(MeasurePopulationType.DENOMINATOR, 1);
    expectationsByPopulationType.put(MeasurePopulationType.NUMERATOR, 0);
    Measure measure = getProportionMeasure("Test", library, expressionsByPopulationType);
    mockFhirResourceRetrieval(measure);
    File tmpFile = new File("target/fhir-stub.json");
    ObjectMapper om = new ObjectMapper();
    try (Writer w = new FileWriter(tmpFile)) {
        w.write(om.writeValueAsString(getFhirServerConfig()));
    }
    File tmpMeasureConfigurationsFile = createTmpConfigurationsFileForSingleMeasure(measure.getId());
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    PrintStream out = new PrintStream(baos);
    try {
        MeasureCLI cli = new MeasureCLI();
        cli.runWithArgs(new String[] { "-d", tmpFile.getAbsolutePath(), "-j", tmpMeasureConfigurationsFile.getAbsolutePath(), "-c", patient.getId() }, out);
    } finally {
        tmpFile.delete();
        tmpMeasureConfigurationsFile.delete();
    }
    String output = new String(baos.toByteArray());
    System.out.println(output);
    String[] lines = output.split(System.getProperty("line.separator"));
    assertEquals(output, 6, lines.length);
    assertTextPopulationExpectations(lines);
}

Example 38 with Library

use of org.hl7.fhir.r5.model.Library in project quality-measure-and-cohort-service by Alvearie.

the class MeasureCLITest method testJsonFormattedOutput.

@Test
public void testJsonFormattedOutput() throws Exception {
    mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
    Patient patient = getPatient("123", AdministrativeGender.MALE, "1592-14-03");
    mockFhirResourceRetrieval(patient);
    Library library = mockLibraryRetrieval("Test", DEFAULT_RESOURCE_VERSION, "cql/basic/Test-1.0.0.cql");
    Measure measure = getCohortMeasure("Test", library, "Male");
    mockFhirResourceRetrieval(measure);
    File tmpFile = new File("target/fhir-stub.json");
    ObjectMapper om = new ObjectMapper();
    try (Writer w = new FileWriter(tmpFile)) {
        w.write(om.writeValueAsString(getFhirServerConfig()));
    }
    File tmpMeasureConfigurationsFile = createTmpConfigurationsFileForSingleMeasure(measure.getId());
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    PrintStream out = new PrintStream(baos);
    try {
        MeasureCLI cli = new MeasureCLI();
        cli.runWithArgs(new String[] { "-d", tmpFile.getAbsolutePath(), "-j", tmpMeasureConfigurationsFile.getAbsolutePath(), "-c", patient.getId(), "-f", "JSON" }, out);
    } finally {
        tmpFile.delete();
        tmpMeasureConfigurationsFile.delete();
    }
    String output = new String(baos.toByteArray());
    System.out.println(output);
    assertTrue(output.contains("\"resourceType\": \"MeasureReport\""));
}

Example 39 with Library

use of org.hl7.fhir.r5.model.Library in project quality-measure-and-cohort-service by Alvearie.

the class MeasureCLITest method testCohortMeasureSinglePatientJsonInputWithCacheDisabled.

@Test
public void testCohortMeasureSinglePatientJsonInputWithCacheDisabled() throws Exception {
    mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
    Patient patient = getPatient("123", AdministrativeGender.MALE, "1592-14-03");
    mockFhirResourceRetrieval(patient);
    Library library = mockLibraryRetrieval("Test", DEFAULT_RESOURCE_VERSION, "cql/basic/Test-1.0.0.cql");
    Measure measure = getCohortMeasure("Test", library, "Female");
    mockFhirResourceRetrieval(measure);
    File tmpFile = new File("target/fhir-stub.json");
    ObjectMapper om = new ObjectMapper();
    try (Writer w = new FileWriter(tmpFile)) {
        w.write(om.writeValueAsString(getFhirServerConfig()));
    }
    File tmpMeasureConfigurationsFile = createTmpConfigurationsFileForSingleMeasure(measure.getId());
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    PrintStream out = new PrintStream(baos);
    try {
        MeasureCLI cli = new MeasureCLI();
        cli.runWithArgs(new String[] { "-d", tmpFile.getAbsolutePath(), "-j", tmpMeasureConfigurationsFile.getAbsolutePath(), "-c", patient.getId(), "--disable-retrieve-cache" }, out);
    } finally {
        tmpFile.delete();
        tmpMeasureConfigurationsFile.delete();
    }
    String output = new String(baos.toByteArray());
    String[] lines = output.split(System.lineSeparator());
    assertEquals(output, 4, lines.length);
}

Example 40 with Library

use of org.hl7.fhir.r5.model.Library in project quality-measure-and-cohort-service by Alvearie.

the class MeasureCLITest method testCohortMeasureByIDSinglePatientCommandLineInput.

@Test
public void testCohortMeasureByIDSinglePatientCommandLineInput() throws Exception {
    mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
    Patient patient = getPatient("123", AdministrativeGender.MALE, "1592-14-03");
    mockFhirResourceRetrieval(patient);
    Library library = mockLibraryRetrieval("Test", DEFAULT_RESOURCE_VERSION, "cql/basic/Test-1.0.0.cql");
    Measure measure = getCohortMeasure("Test", library, "Female");
    mockFhirResourceRetrieval(measure);
    File tmpFile = new File("target/fhir-stub.json");
    ObjectMapper om = new ObjectMapper();
    try (Writer w = new FileWriter(tmpFile)) {
        w.write(om.writeValueAsString(getFhirServerConfig()));
    }
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    PrintStream out = new PrintStream(baos);
    try {
        MeasureCLI cli = new MeasureCLI();
        cli.runWithArgs(new String[] { "-d", tmpFile.getAbsolutePath(), "-p", "p1:interval:decimal,1.0,100.5", "-p", "p2:integer:1", "-r", measure.getId(), "-c", patient.getId() }, out);
    } finally {
        tmpFile.delete();
    }
    String output = new String(baos.toByteArray());
    String[] lines = output.split(System.getProperty("line.separator"));
    assertEquals(output, 4, lines.length);
}