Unit Test work - still cannot get Dstu3 working after several attempts, but included the skelton of a test to capture the effort anyways.
This commit is contained in:
Kevin Dougan
@@ -1,7 +1,7 @@
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package ca.uhn.fhir.jpa.starter;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.cql.provider.CqlProviderLoader;
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import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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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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@@ -9,6 +9,7 @@ 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 ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
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import org.apache.commons.io.FileUtils;
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import org.eclipse.jetty.websocket.api.Session;
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import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
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import org.eclipse.jetty.websocket.client.WebSocketClient;
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@@ -18,12 +19,16 @@ import org.junit.Assert;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.ExtendWith;
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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.web.server.LocalServerPort;
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import org.springframework.core.io.ClassPathResource;
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import org.springframework.test.context.junit.jupiter.SpringExtension;
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import java.io.File;
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import java.io.IOException;
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import java.net.URI;
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import java.util.Collection;
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import java.util.List;
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import java.util.concurrent.Future;
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import java.util.concurrent.TimeUnit;
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@@ -50,6 +55,9 @@ public class ExampleServerDstu3IT implements IServerSupport {
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private IGenericClient ourClient;
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private FhirContext ourCtx;
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@Autowired
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DaoRegistry myDaoRegistry;
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@LocalServerPort
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private int port;
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@@ -76,50 +84,66 @@ public class ExampleServerDstu3IT implements IServerSupport {
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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 testCQLEvaluateMeasure() throws IOException {
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CqlProviderLoader cqlProviderLoader = null;
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// Currently fails with:
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// ca.uhn.fhir.rest.server.exceptions.InternalErrorException: HTTP 500 : Failed to call access method: java.lang.IllegalArgumentException: Could not load library source for libraries referenced in Measure/Measure/measure-EXM104-FHIR3-8.1.000/_history/1.
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//@Test
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public void testCQLEvaluateMeasureEXM104() throws IOException {
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String measureId = "measure-EXM104-FHIR3-8.1.000";
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// FIXME KBD Remove this and put some Unit Test code here
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loadBundle("dstu3/EXM104/EXM104_FHIR3-8.1.000-bundle.json", ourCtx, ourClient);
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int numFilesLoaded = loadDataFromDirectory("dstu3/EXM104/EXM104_FHIR3-8.1.000-files");
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//assertEquals(numFilesLoaded, 3);
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ourLog.info("{} files imported successfully!", numFilesLoaded);
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//loadBundle("dstu3/EXM104/EXM104_FHIR3-8.1.000-bundle.json", ourCtx, ourClient);
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// http://localhost:8080/fhir/Measure/measure-EXM104-FHIR3-8.1.000/$evaluate-measure?periodStart=2019-01-01&periodEnd=2019-12-31
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Parameters inParams = new Parameters();
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// inParams.addParameter().setName("measure").setValue(new StringType("Measure/measure-EXM104-8.2.000"));
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// inParams.addParameter().setName("patient").setValue(new StringType("Patient/numer-EXM104-FHIR3"));
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inParams.addParameter().setName("periodStart").setValue(new DateType("2019-01-01"));
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inParams.addParameter().setName("periodEnd").setValue(new DateType("2019-12-31"));
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// inParams.addParameter().setName("periodStart").setValue(new StringType("2019-01-01"));
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// inParams.addParameter().setName("periodEnd").setValue(new StringType("2019-12-31"));
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Parameters outParams = ourClient
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.operation()
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.onInstance(new IdDt("Measure", "measure-EXM104-FHIR3-8.1.000"))
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.onInstance(new IdDt("Measure", measureId))
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.named("$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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// Parameters outParams = ourClient
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// .operation()
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// .onType(Measure.class)
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// .named("$evaluate-measure")
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// .withParameters(inParams)
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// .useHttpGet()
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// .execute();
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List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
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Assert.assertTrue(!response.isEmpty());
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Parameters.ParametersParameterComponent component = response.get(0);
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Assert.assertTrue(component.getResource() instanceof MeasureReport);
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MeasureReport report = (MeasureReport) component.getResource();
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Assert.assertEquals("Measure/"+measureId, report.getMeasure());
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}
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for (MeasureReport.MeasureReportGroupComponent group : report.getGroup()) {
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for (MeasureReport.MeasureReportGroupPopulationComponent population : group.getPopulation()) {
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Assert.assertTrue(population.getCount() > 0);
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private int loadDataFromDirectory(String theDirectoryName) throws IOException {
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int count = 0;
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ourLog.info("Reading files in directory: {}", theDirectoryName);
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ClassPathResource dir = new ClassPathResource(theDirectoryName);
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Collection<File> files = FileUtils.listFiles(dir.getFile(), null, false);
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ourLog.info("{} files found.", files.size());
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for (File file : files) {
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String filename = file.getAbsolutePath();
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ourLog.info("Processing filename '{}'", filename);
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if (filename.endsWith(".cql") || filename.contains("expectedresults")) {
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// Ignore .cql and expectedresults files
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ourLog.info("Ignoring file: '{}'", filename);
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} else if (filename.endsWith(".json")) {
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if (filename.contains("bundle")) {
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loadBundle(filename, ourCtx, ourClient);
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} else {
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loadResource(filename, ourCtx, myDaoRegistry);
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}
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count++;
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} else {
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ourLog.info("Ignoring file: '{}'", filename);
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}
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}
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return count;
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}
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private Bundle loadBundle(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {
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@@ -1,7 +1,6 @@
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package ca.uhn.fhir.jpa.starter;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.cql.provider.CqlProviderLoader;
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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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@@ -42,10 +41,10 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
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{
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"spring.batch.job.enabled=false",
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"spring.datasource.url=jdbc:h2:mem:dbr4",
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"hapi.fhir.fhir_version=R4",
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"hapi.fhir.cql_enabled=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.empi_enabled=true",
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"hapi.fhir.subscription.websocket_enabled=true",
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//Override is currently required when using Empi as the construction of the Empi beans are ambiguous as they are constructed multiple places. This is evident when running in a spring boot environment
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"spring.main.allow-bean-definition-overriding=true"
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})
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@@ -54,6 +53,7 @@ public class ExampleServerR4IT implements IServerSupport {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu2IT.class);
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private IGenericClient ourClient;
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private FhirContext ourCtx;
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private String ourServerBaseURL;
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@LocalServerPort
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private int port;
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@@ -63,8 +63,8 @@ public class ExampleServerR4IT implements IServerSupport {
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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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ourServerBaseURL = "http://localhost:" + port + "/fhir/";
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ourClient = ourCtx.newRestfulGenericClient(ourServerBaseURL);
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ourClient.registerInterceptor(new LoggingInterceptor(true));
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}
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@@ -111,21 +111,21 @@ public class ExampleServerR4IT implements IServerSupport {
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}
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@Test
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public void testCQLEvaluateMeasure() throws IOException {
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CqlProviderLoader cqlProviderLoader = null;
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public void testCQLEvaluateMeasureEXM104() throws IOException {
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String measureId = "measure-EXM104-8.2.000";
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// FIXME KBD Remove this and put some Unit Test code here
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loadBundle("r4/EXM104/EXM104-8.2.000-bundle.json", ourCtx, ourClient);
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// http://localhost:8080/fhir/Measure/measure-EXM104-8.2.000/$evaluate-measure?periodStart=2019-01-01&periodEnd=2019-12-31
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Parameters inParams = new Parameters();
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// inParams.addParameter().setName("measure").setValue(new StringType("Measure/measure-EXM104-8.2.000"));
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// inParams.addParameter().setName("patient").setValue(new StringType("Patient/numer-EXM104-FHIR3"));
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inParams.addParameter().setName("periodStart").setValue(new DateType("2019-01-01"));
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inParams.addParameter().setName("periodEnd").setValue(new DateType("2019-12-31"));
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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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Parameters outParams = ourClient
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.operation()
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.onInstance(new IdDt("Measure", "measure-EXM104-8.2.000"))
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.onInstance(new IdDt("Measure", measureId))
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.named("$evaluate-measure")
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.withParameters(inParams)
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.cacheControl(new CacheControlDirective().setNoCache(true))
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@@ -133,29 +133,12 @@ public class ExampleServerR4IT implements IServerSupport {
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.useHttpGet()
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.execute();
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// Parameters outParams = ourClient
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// .operation()
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// .onType(Measure.class)
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// .named("$evaluate-measure")
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// .withParameters(inParams)
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// .useHttpGet()
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// .execute();
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List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
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Assert.assertTrue(!response.isEmpty());
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Parameters.ParametersParameterComponent component = response.get(0);
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Assert.assertTrue(component.getResource() instanceof MeasureReport);
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MeasureReport report = (MeasureReport) component.getResource();
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for (MeasureReport.MeasureReportGroupComponent group : report.getGroup()) {
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for (MeasureReport.MeasureReportGroupPopulationComponent population : group.getPopulation()) {
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Assert.assertTrue(population.getCount() > 0);
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}
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}
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Assert.assertEquals("Measure/"+measureId, report.getMeasure());
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}
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private Bundle loadBundle(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {
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@@ -1,7 +1,8 @@
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package ca.uhn.fhir.jpa.starter;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.rest.client.api.IGenericClient;
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import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
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import com.google.common.base.Charsets;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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@@ -12,26 +13,20 @@ import java.io.File;
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import java.io.FileInputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.util.Scanner;
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public interface IServerSupport {
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// default void putResourceDstu3(String resourceFileName, String id, FhirContext theCtx, IGenericClient theClient) {
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// InputStream is = ExampleServerDstu3IT.class.getResourceAsStream(resourceFileName);
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// Scanner scanner = new Scanner(is).useDelimiter("\\A");
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// String json = scanner.hasNext() ? scanner.next() : "";
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//
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// boolean isJson = resourceFileName.endsWith("json");
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//
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// IBaseResource resource = isJson ? theCtx.newJsonParser().parseResource(json) : theCtx.newXmlParser().parseResource(json);
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//
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// if (resource instanceof Bundle) {
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// theClient.transaction().withBundle((Bundle) resource).execute();
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// }
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// else {
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// theClient.update().resource(resource).withId(id).execute();
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// }
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// }
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default IBaseResource loadResource(String theLocation, FhirContext theFhirContext, DaoRegistry theDaoRegistry) throws IOException {
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String json = stringFromResource(theLocation);
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IBaseResource resource = theFhirContext.newJsonParser().parseResource(json);
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IFhirResourceDao<IBaseResource> dao = theDaoRegistry.getResourceDao(resource.getIdElement().getResourceType());
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if (dao == null) {
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return null;
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} else {
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dao.update(resource);
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return resource;
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}
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}
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default String stringFromResource(String theLocation) throws IOException {
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InputStream is = null;
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@@ -22,6 +22,7 @@ hapi:
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# allow_placeholder_references: true
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# auto_create_placeholder_reference_targets: false
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# cql_enabled: false
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# empi_enabled: false
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# default_encoding: JSON
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# default_pretty_print: true
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# default_page_size: 20
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@@ -183,7 +183,7 @@
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"type": {
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"coding": [
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{
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"system": "http://hl7.org/fhir/codesystem-library-type.html",
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"system": "http://hl7.org/fhir/library-type",
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"code": "logic-library"
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}
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]
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@@ -338,7 +338,7 @@
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"type": {
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"coding": [
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{
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"system": "http://hl7.org/fhir/codesystem-library-type.html",
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"system": "http://hl7.org/fhir/library-type",
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"code": "logic-library"
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}
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]
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@@ -1610,7 +1610,7 @@
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"type": {
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"coding": [
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{
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"system": "http://hl7.org/fhir/codesystem-library-type.html",
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"system": "http://hl7.org/fhir/library-type",
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"code": "logic-library"
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}
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]
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@@ -2177,7 +2177,7 @@
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"type": {
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"coding": [
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{
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"system": "http://hl7.org/fhir/codesystem-library-type.html",
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"system": "http://hl7.org/fhir/library-type",
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"code": "logic-library"
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}
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]
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@@ -2265,7 +2265,7 @@
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"type": {
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"coding": [
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{
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"system": "http://hl7.org/fhir/codesystem-library-type.html",
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"system": "http://hl7.org/fhir/library-type",
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"code": "logic-library"
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}
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]
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File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
@@ -0,0 +1,303 @@
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{
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"resourceType": "MeasureReport",
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"id": "measurereport-denom-EXM104-FHIR3-8.1.000-expectedresults",
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"contained": [
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{
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"resourceType": "Bundle",
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"id": "b20ba55e-a72e-493d-868d-e9f6c007d11a",
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"type": "collection",
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"entry": [
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{
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"fullUrl": "Condition/denom-EXM104-FHIR3-1",
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"resource": {
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"resourceType": "Condition",
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"id": "denom-EXM104-FHIR3-1",
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"meta": {
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"versionId": "1",
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"lastUpdated": "2019-12-18T22:42:17.748-07:00",
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"profile": [
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"http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition"
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]
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},
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"verificationStatus": "confirmed",
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"category": [
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{
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"coding": [
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{
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"system": "http://terminology.hl7.org/CodeSystem/condition-category",
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"code": "encounter-diagnosis",
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"display": "Encounter Diagnosis"
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}
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]
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}
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],
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"code": {
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "116288000",
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"display": "Paralytic stroke (disorder)"
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}
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]
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},
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"subject": {
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"reference": "Patient/denom-EXM104-FHIR3"
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}
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}
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},
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{
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"fullUrl": "Encounter/denom-EXM104-FHIR3-2",
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"resource": {
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"resourceType": "Encounter",
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"id": "denom-EXM104-FHIR3-2",
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"meta": {
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"versionId": "1",
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"lastUpdated": "2019-12-18T22:42:17.748-07:00",
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"profile": [
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"http://hl7.org/fhir/us/core/StructureDefinition/us-core-encounter"
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]
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},
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"status": "finished",
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"class": {
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"system": "http://terminology.hl7.org/CodeSystem/v3-ActCode",
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"code": "IMP",
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"display": "inpatient encounter"
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},
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"type": [
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{
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"coding": [
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{
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"system": "http://snomed.info/sct",
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"code": "32485007",
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"display": "Hospital admission (procedure)"
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}
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]
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}
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],
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"subject": {
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"reference": "Patient/denom-EXM104-FHIR3"
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},
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"period": {
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"start": "2019-08-21T00:00:00-06:00",
|
||||
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|
||||
"system": "http://hospital.smarthealthit.org",
|
||||
"value": "9999999911"
|
||||
}
|
||||
],
|
||||
"name": [
|
||||
{
|
||||
"family": "Jones",
|
||||
"given": [
|
||||
"Louise"
|
||||
]
|
||||
}
|
||||
],
|
||||
"gender": "female",
|
||||
"birthDate": "1971-11-21"
|
||||
},
|
||||
"request": {
|
||||
"method": "PUT",
|
||||
"url": "Patient/numer-EXM104-FHIR3"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user