Examples with Database au.csiro.pathling.io.Database used on opensource projects

Example 1 with Database

use of au.csiro.pathling.io.Database in project pathling by aehrc.

the class ManifestConverterTest method convertsManifest.

@Test
void convertsManifest() {
    database = new Database(configuration, spark, fhirEncoders, executor);
    final PassportScope passportScope = new PassportScope();
    final VisaManifest manifest = new VisaManifest();
    manifest.setPatientIds(Arrays.asList(PATIENT_ID_1, PATIENT_ID_2, PATIENT_ID_3, PATIENT_ID_4));
    final ManifestConverter manifestConverter = new ManifestConverter(configuration, fhirContext);
    manifestConverter.populateScope(passportScope, manifest);
    // Convert the scope to JSON and compare it to a test fixture.
    final Gson gson = new GsonBuilder().create();
    final String json = gson.toJson(passportScope);
    assertJson("responses/ManifestConverterTest/convertsManifest.json", json);
    // our test patients.
    for (final ResourceType resourceType : passportScope.keySet()) {
        if (AVAILABLE_RESOURCE_TYPES.contains(resourceType)) {
            boolean found = false;
            for (final String filter : passportScope.get(resourceType)) {
                final Dataset<Row> dataset = assertThatResultOf(resourceType, filter).isElementPath(BooleanPath.class).selectResult().apply(result -> result.filter(result.columns()[1])).getDataset();
                if (dataset.count() > 0) {
                    found = true;
                }
            }
            assertTrue(found, "No results found for " + resourceType.toCode());
        }
    }
}

Example 2 with Database

use of au.csiro.pathling.io.Database in project pathling by aehrc.

the class EntityTagInterceptorTest method setUp.

@BeforeEach
void setUp() {
    database = mock(Database.class);
    conformanceProvider = mock(ConformanceProvider.class);
    request = mock(HttpServletRequest.class);
    requestDetails = mock(RequestDetails.class);
    response = mock(HttpServletResponse.class);
    final Configuration configuration = mock(Configuration.class);
    final HttpCaching httpCaching = mock(HttpCaching.class);
    when(httpCaching.getVary()).thenReturn(List.of("Accept", "Accept-Encoding", "Prefer", "Authorization"));
    when(httpCaching.getCacheableControl()).thenReturn(List.of("must-revalidate", "max-age=1"));
    when(configuration.getHttpCaching()).thenReturn(httpCaching);
    interceptor = new EntityTagInterceptor(configuration, database, conformanceProvider);
}

Example 3 with Database

use of au.csiro.pathling.io.Database in project pathling by aehrc.

the class CodingLiteralPathTest method setUp.

@BeforeEach
void setUp() {
    final Database database = mock(Database.class);
    final Dataset<Row> inputContextDataset = new ResourceDatasetBuilder(spark).withIdColumn().withRow("observation-1").withRow("observation-2").withRow("observation-3").withRow("observation-4").withRow("observation-5").build();
    when(database.read(ResourceType.OBSERVATION)).thenReturn(inputContextDataset);
    inputContext = new ResourcePathBuilder(spark).expression("Observation").resourceType(ResourceType.OBSERVATION).database(database).singular(true).build();
}

Example 4 with Database

use of au.csiro.pathling.io.Database in project pathling by aehrc.

the class ExtractQueryTest method setUp.

@BeforeEach
void setUp() {
    SharedMocks.resetAll();
    database = mock(Database.class);
    final ResultWriter resultWriter = mock(ResultWriter.class);
    final ResultRegistry resultRegistry = mock(ResultRegistry.class);
    executor = new ExtractExecutor(configuration, fhirContext, spark, database, Optional.ofNullable(terminologyServiceFactory), resultWriter, resultRegistry);
}

Example 5 with Database

use of au.csiro.pathling.io.Database in project pathling by aehrc.

the class AggregateExecutorTest method runFirstGroupingThroughSearch.

/**
 * Test that the drill-down expression from the first grouping from each aggregate result can be
 * successfully executed using the FHIRPath search.
 */
@AfterEach
void runFirstGroupingThroughSearch() {
    if (response != null) {
        final Optional<Grouping> firstGroupingOptional = response.getGroupings().stream().filter(grouping -> grouping.getDrillDown().isPresent()).findFirst();
        if (firstGroupingOptional.isPresent()) {
            final Grouping firstGrouping = firstGroupingOptional.get();
            assertTrue(firstGrouping.getDrillDown().isPresent());
            final String drillDown = firstGrouping.getDrillDown().get();
            final StringAndListParam filters = new StringAndListParam();
            filters.addAnd(new StringParam(drillDown));
            final IBundleProvider searchExecutor = new SearchExecutor(configuration, fhirContext, spark, database, Optional.of(terminologyServiceFactory), fhirEncoders, subjectResource, Optional.of(filters));
            final List<IBaseResource> resources = searchExecutor.getResources(0, 100);
            assertTrue(resources.size() > 0);
        }
    }
}