d762c18765
unrequested changes: commons-logging dependency marked provided (to avoid redundant jar inclusion), removed unused imports in classes that were modified
331 lines
12 KiB
Java
331 lines
12 KiB
Java
package ca.uhn.fhir.jpa.starter;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.cr.config.RepositoryConfig;
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import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig;
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import ca.uhn.fhir.jpa.starter.cr.CrProperties;
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import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.rest.api.CacheControlDirective;
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import ca.uhn.fhir.rest.api.EncodingEnum;
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import ca.uhn.fhir.rest.api.MethodOutcome;
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import ca.uhn.fhir.rest.client.api.IGenericClient;
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import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
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import jakarta.websocket.ContainerProvider;
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import jakarta.websocket.Session;
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import jakarta.websocket.WebSocketContainer;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.Bundle;
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import org.hl7.fhir.r4.model.DateType;
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import org.hl7.fhir.r4.model.IdType;
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import org.hl7.fhir.r4.model.Measure;
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import org.hl7.fhir.r4.model.MeasureReport;
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import org.hl7.fhir.r4.model.Observation;
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import org.hl7.fhir.r4.model.Parameters;
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import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.Period;
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import org.hl7.fhir.r4.model.StringType;
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import org.hl7.fhir.r4.model.Subscription;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Order;
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import org.junit.jupiter.api.Test;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.boot.test.context.SpringBootTest;
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import org.springframework.boot.test.web.server.LocalServerPort;
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import java.io.IOException;
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import java.net.URI;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.concurrent.TimeUnit;
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import static ca.uhn.fhir.util.TestUtil.waitForSize;
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import static org.awaitility.Awaitility.await;
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import static org.hamcrest.Matchers.equalTo;
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import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertFalse;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import static org.opencds.cqf.fhir.utility.r4.Parameters.parameters;
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import static org.opencds.cqf.fhir.utility.r4.Parameters.stringPart;
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@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
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classes = {
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Application.class,
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NicknameServiceConfig.class,
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RepositoryConfig.class
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}, properties = {
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"spring.profiles.include=storageSettingsTest",
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"spring.datasource.url=jdbc:h2:mem:dbr4",
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"hapi.fhir.enable_repository_validating_interceptor=true",
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"hapi.fhir.fhir_version=r4",
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//"hapi.fhir.subscription.websocket_enabled=true",
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//"hapi.fhir.mdm_enabled=true",
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"hapi.fhir.cr.enabled=true",
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"hapi.fhir.cr.caregaps_section_author=Organization/alphora-author",
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"hapi.fhir.cr.caregaps_reporter=Organization/alphora",
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"hapi.fhir.implementationguides.dk-core.name=hl7.fhir.dk.core",
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"hapi.fhir.implementationguides.dk-core.version=1.1.0",
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"hapi.fhir.auto_create_placeholder_reference_targets=true",
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// Override is currently required when using MDM as the construction of the MDM
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// beans are ambiguous as they are constructed multiple places. This is evident
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// when running in a spring boot environment
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"spring.main.allow-bean-definition-overriding=true"})
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class ExampleServerR4IT implements IServerSupport {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerR4IT.class);
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private IGenericClient ourClient;
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private FhirContext ourCtx;
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@Autowired
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private CrProperties crProperties;
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@LocalServerPort
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private int port;
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@Test
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@Order(0)
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void testCreateAndRead() {
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String methodName = "testCreateAndRead";
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ourLog.info("Entering " + methodName + "()...");
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Patient pt = new Patient();
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pt.setActive(true);
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pt.getBirthDateElement().setValueAsString("2020-01-01");
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pt.addIdentifier().setSystem("http://foo").setValue("12345");
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pt.addName().setFamily(methodName);
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IIdType id = ourClient.create().resource(pt).execute().getId();
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Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
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assertEquals(methodName, pt2.getName().get(0).getFamily());
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}
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@Test
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public void testCQLEvaluateMeasureEXM130() throws IOException {
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String measureId = "ColorectalCancerScreeningsFHIR";
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String measureUrl = "http://ecqi.healthit.gov/ecqms/Measure/ColorectalCancerScreeningsFHIR";
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loadBundle("r4/EXM130/EXM130-7.3.000-bundle.json", ourCtx, ourClient);
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Parameters inParams = new Parameters();
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inParams.addParameter().setName("periodStart").setValue(new StringType("2019-01-01"));
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inParams.addParameter().setName("periodEnd").setValue(new StringType("2019-12-31"));
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inParams.addParameter().setName("reportType").setValue(new StringType("summary"));
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Parameters outParams = ourClient
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.operation()
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.onInstance(new IdDt("Measure", measureId))
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.named("$evaluate-measure")
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.withParameters(inParams)
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.cacheControl(new CacheControlDirective().setNoCache(true))
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.withAdditionalHeader("Content-Type", "application/json")
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.useHttpGet()
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.execute();
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List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
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assertFalse(response.isEmpty());
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Parameters.ParametersParameterComponent component = response.get(0);
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assertTrue(component.getResource() instanceof MeasureReport);
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MeasureReport report = (MeasureReport) component.getResource();
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assertEquals(measureUrl + "|0.0.003", report.getMeasure());
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}
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private org.hl7.fhir.r4.model.Bundle loadBundle(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {
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String json = stringFromResource(theLocation);
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org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) theCtx.newJsonParser().parseResource(json);
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org.hl7.fhir.r4.model.Bundle result = theClient.transaction().withBundle(bundle).execute();
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return result;
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}
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public Parameters runCqlExecution(Parameters parameters) {
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var results = ourClient.operation().onServer()
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.named("$cql")
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.withParameters(parameters)
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.execute();
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return results;
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}
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@Test
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void testSimpleDateCqlExecutionProvider() {
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Parameters params = parameters(stringPart("expression", "Interval[Today() - 2 years, Today())"));
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Parameters results = runCqlExecution(params);
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assertTrue(results.getParameter("return").getValue() instanceof Period);
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}
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private IBaseResource loadRec(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {
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String json = stringFromResource(theLocation);
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List<IBaseResource> resList = new ArrayList<>();
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IBaseResource resource = (IBaseResource) theCtx.newJsonParser().parseResource(json);
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resList.add(resource);
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var result = theClient.transaction().withResources(resList).execute();
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//.withResources(resource).execute();
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return result.get(0);
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}
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@Test
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void testBatchPutWithIdenticalTags() {
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String batchPuts = "{\n" +
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"\t\"resourceType\": \"Bundle\",\n" +
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"\t\"id\": \"patients\",\n" +
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"\t\"type\": \"batch\",\n" +
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"\t\"entry\": [\n" +
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"\t\t{\n" +
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"\t\t\t\"request\": {\n" +
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"\t\t\t\t\"method\": \"PUT\",\n" +
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"\t\t\t\t\"url\": \"Patient/pat-1\"\n" +
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"\t\t\t},\n" +
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"\t\t\t\"resource\": {\n" +
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"\t\t\t\t\"resourceType\": \"Patient\",\n" +
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"\t\t\t\t\"id\": \"pat-1\",\n" +
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"\t\t\t\t\"meta\": {\n" +
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"\t\t\t\t\t\"tag\": [\n" +
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"\t\t\t\t\t\t{\n" +
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"\t\t\t\t\t\t\t\"system\": \"http://mysystem.org\",\n" +
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"\t\t\t\t\t\t\t\"code\": \"value2\"\n" +
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"\t\t\t\t\t\t}\n" +
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"\t\t\t\t\t]\n" +
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"\t\t\t\t}\n" +
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"\t\t\t},\n" +
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"\t\t\t\"fullUrl\": \"/Patient/pat-1\"\n" +
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"\t\t},\n" +
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"\t\t{\n" +
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"\t\t\t\"request\": {\n" +
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"\t\t\t\t\"method\": \"PUT\",\n" +
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"\t\t\t\t\"url\": \"Patient/pat-2\"\n" +
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"\t\t\t},\n" +
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"\t\t\t\"resource\": {\n" +
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"\t\t\t\t\"resourceType\": \"Patient\",\n" +
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"\t\t\t\t\"id\": \"pat-2\",\n" +
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"\t\t\t\t\"meta\": {\n" +
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"\t\t\t\t\t\"tag\": [\n" +
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"\t\t\t\t\t\t{\n" +
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"\t\t\t\t\t\t\t\"system\": \"http://mysystem.org\",\n" +
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"\t\t\t\t\t\t\t\"code\": \"value2\"\n" +
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"\t\t\t\t\t\t}\n" +
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"\t\t\t\t\t]\n" +
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"\t\t\t\t}\n" +
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"\t\t\t},\n" +
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"\t\t\t\"fullUrl\": \"/Patient/pat-2\"\n" +
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"\t\t}\n" +
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"\t]\n" +
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"}";
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Bundle bundle = FhirContext.forR4().newJsonParser().parseResource(Bundle.class, batchPuts);
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ourClient.transaction().withBundle(bundle).execute();
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}
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@Test
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@Order(1)
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void testWebsocketSubscription() throws Exception {
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/*
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* Create subscription
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*/
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Subscription subscription = new Subscription();
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subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
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subscription.setStatus(Subscription.SubscriptionStatus.REQUESTED);
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subscription.setCriteria("Observation?status=final");
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Subscription.SubscriptionChannelComponent channel = new Subscription.SubscriptionChannelComponent();
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channel.setType(Subscription.SubscriptionChannelType.WEBSOCKET);
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channel.setPayload("application/json");
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subscription.setChannel(channel);
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int initialActiveSubscriptionCount = activeSubscriptionCount();
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MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
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IIdType mySubscriptionId = methodOutcome.getId();
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// Wait for the subscription to be activated
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await().atMost(1, TimeUnit.MINUTES).until(()->activeSubscriptionCount(), equalTo(initialActiveSubscriptionCount + 1));
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/*
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* Attach websocket
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*/
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SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(),
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EncodingEnum.JSON);
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URI echoUri = new URI("ws://localhost:" + port + "/websocket");
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WebSocketContainer container = ContainerProvider.getWebSocketContainer();
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ourLog.info("Connecting to : {}", echoUri);
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Session session = container.connectToServer(mySocketImplementation, echoUri);
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ourLog.info("Connected to WS: {}", session.isOpen());
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/*
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* Create a matching resource
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*/
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Observation obs = new Observation();
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obs.setStatus(Observation.ObservationStatus.FINAL);
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ourClient.create().resource(obs).execute();
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/*
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* Ensure that we receive a ping on the websocket
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*/
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waitForSize(1, () -> mySocketImplementation.myPingCount);
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/*
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* Clean up
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*/
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ourClient.delete().resourceById(mySubscriptionId).execute();
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}
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@Test
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void testCareGaps() throws IOException {
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var reporter = crProperties.getCareGapsReporter();
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var author = crProperties.getCareGapsSectionAuthor();
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assertTrue(reporter.equals("Organization/alphora"));
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assertTrue(author.equals("Organization/alphora-author"));
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String periodStartValid = "2019-01-01";
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String periodEndValid = "2019-12-31";
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String subjectPatientValid = "Patient/numer-EXM125";
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String statusValid = "open-gap";
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String measureIdValid = "BreastCancerScreeningFHIR";
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loadBundle("r4/CareGaps/authreporter-bundle.json", ourCtx, ourClient);
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loadBundle("r4/CareGaps/BreastCancerScreeningFHIR-bundle.json", ourCtx, ourClient);
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Parameters params = new Parameters();
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params.addParameter().setName("periodStart").setValue(new DateType(periodStartValid));
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params.addParameter().setName("periodEnd").setValue(new DateType(periodEndValid));
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params.addParameter().setName("subject").setValue(new StringType(subjectPatientValid));
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params.addParameter().setName("status").setValue(new StringType(statusValid));
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params.addParameter().setName("measureId").setValue(new IdType(measureIdValid));
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assertDoesNotThrow(() -> {
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ourClient.operation()
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.onType(Measure.class)
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.named("$care-gaps")
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.withParameters(params)
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.returnResourceType(Parameters.class)
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.execute();
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});
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}
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private int activeSubscriptionCount() {
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return ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active"))
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.cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry()
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.size();
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}
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@BeforeEach
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void beforeEach() {
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ourCtx = FhirContext.forR4();
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ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
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ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
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String ourServerBase = "http://localhost:" + port + "/fhir/";
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ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
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//await().atMost(2, TimeUnit.MINUTES).until(() -> {
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// sleep(1000); // execute below function every 1 second
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// return activeSubscriptionCount() == 2; // 2 subscription based on mdm-rules.json
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//});
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}
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}
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