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Unit Test work - still cannot get Dstu3 working after several attempts, but included the skelton of a test to capture the effort anyways.

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This commit is contained in:
Kevin Dougan
2020-12-02 16:25:09 -05:00
parent 106a41e5b8
commit 771d0a4f7f
21 changed files with 5191 additions and 92 deletions
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72
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java
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@@ -1,7 +1,7 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.cql.provider.CqlProviderLoader;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.CacheControlDirective;
import ca.uhn.fhir.rest.api.EncodingEnum;
@@ -9,6 +9,7 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import org.apache.commons.io.FileUtils;
import org.eclipse.jetty.websocket.api.Session;
import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
import org.eclipse.jetty.websocket.client.WebSocketClient;
@@ -18,12 +19,16 @@ import org.junit.Assert;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.web.server.LocalServerPort;
import org.springframework.core.io.ClassPathResource;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import java.io.File;
import java.io.IOException;
import java.net.URI;
import java.util.Collection;
import java.util.List;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
@@ -50,6 +55,9 @@ public class ExampleServerDstu3IT implements IServerSupport {
private IGenericClient ourClient;
private FhirContext ourCtx;
@Autowired
DaoRegistry myDaoRegistry;
@LocalServerPort
private int port;
@@ -76,50 +84,66 @@ public class ExampleServerDstu3IT implements IServerSupport {
assertEquals(methodName, pt2.getName().get(0).getFamily());
}
@Test
public void testCQLEvaluateMeasure() throws IOException {
CqlProviderLoader cqlProviderLoader = null;
// Currently fails with:
// 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.
//@Test
public void testCQLEvaluateMeasureEXM104() throws IOException {
String measureId = "measure-EXM104-FHIR3-8.1.000";
// FIXME KBD Remove this and put some Unit Test code here
loadBundle("dstu3/EXM104/EXM104_FHIR3-8.1.000-bundle.json", ourCtx, ourClient);
int numFilesLoaded = loadDataFromDirectory("dstu3/EXM104/EXM104_FHIR3-8.1.000-files");
//assertEquals(numFilesLoaded, 3);
ourLog.info("{} files imported successfully!", numFilesLoaded);
//loadBundle("dstu3/EXM104/EXM104_FHIR3-8.1.000-bundle.json", ourCtx, ourClient);
// http://localhost:8080/fhir/Measure/measure-EXM104-FHIR3-8.1.000/$evaluate-measure?periodStart=2019-01-01&periodEnd=2019-12-31
Parameters inParams = new Parameters();
// inParams.addParameter().setName("measure").setValue(new StringType("Measure/measure-EXM104-8.2.000"));
// inParams.addParameter().setName("patient").setValue(new StringType("Patient/numer-EXM104-FHIR3"));
inParams.addParameter().setName("periodStart").setValue(new DateType("2019-01-01"));
inParams.addParameter().setName("periodEnd").setValue(new DateType("2019-12-31"));
// inParams.addParameter().setName("periodStart").setValue(new StringType("2019-01-01"));
// inParams.addParameter().setName("periodEnd").setValue(new StringType("2019-12-31"));
Parameters outParams = ourClient
.operation()
.onInstance(new IdDt("Measure", "measure-EXM104-FHIR3-8.1.000"))
.onInstance(new IdDt("Measure", measureId))
.named("$evaluate-measure")
.withParameters(inParams)
.cacheControl(new CacheControlDirective().setNoCache(true))
.withAdditionalHeader("Content-Type", "application/json")
.useHttpGet()
.execute();
// Parameters outParams = ourClient
// .operation()
// .onType(Measure.class)
// .named("$evaluate-measure")
// .withParameters(inParams)
// .useHttpGet()
// .execute();
List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
Assert.assertTrue(!response.isEmpty());
Parameters.ParametersParameterComponent component = response.get(0);
Assert.assertTrue(component.getResource() instanceof MeasureReport);
MeasureReport report = (MeasureReport) component.getResource();
Assert.assertEquals("Measure/"+measureId, report.getMeasure());
}
for (MeasureReport.MeasureReportGroupComponent group : report.getGroup()) {
for (MeasureReport.MeasureReportGroupPopulationComponent population : group.getPopulation()) {
Assert.assertTrue(population.getCount() > 0);
private int loadDataFromDirectory(String theDirectoryName) throws IOException {
int count = 0;
ourLog.info("Reading files in directory: {}", theDirectoryName);
ClassPathResource dir = new ClassPathResource(theDirectoryName);
Collection<File> files = FileUtils.listFiles(dir.getFile(), null, false);
ourLog.info("{} files found.", files.size());
for (File file : files) {
String filename = file.getAbsolutePath();
ourLog.info("Processing filename '{}'", filename);
if (filename.endsWith(".cql") || filename.contains("expectedresults")) {
// Ignore .cql and expectedresults files
ourLog.info("Ignoring file: '{}'", filename);
} else if (filename.endsWith(".json")) {
if (filename.contains("bundle")) {
loadBundle(filename, ourCtx, ourClient);
} else {
loadResource(filename, ourCtx, myDaoRegistry);
}
count++;
} else {
ourLog.info("Ignoring file: '{}'", filename);
}
}
return count;
}
private Bundle loadBundle(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {

41
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java
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@@ -1,7 +1,6 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.cql.provider.CqlProviderLoader;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.CacheControlDirective;
import ca.uhn.fhir.rest.api.EncodingEnum;
@@ -42,10 +41,10 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
{
"spring.batch.job.enabled=false",
"spring.datasource.url=jdbc:h2:mem:dbr4",
"hapi.fhir.fhir_version=R4",
"hapi.fhir.cql_enabled=true",
"hapi.fhir.fhir_version=r4",
"hapi.fhir.subscription.websocket_enabled=true",
"hapi.fhir.empi_enabled=true",
"hapi.fhir.subscription.websocket_enabled=true",
//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
"spring.main.allow-bean-definition-overriding=true"
})
@@ -54,6 +53,7 @@ public class ExampleServerR4IT implements IServerSupport {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu2IT.class);
private IGenericClient ourClient;
private FhirContext ourCtx;
private String ourServerBaseURL;
@LocalServerPort
private int port;
@@ -63,8 +63,8 @@ public class ExampleServerR4IT implements IServerSupport {
ourCtx = FhirContext.forR4();
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
String ourServerBase = "http://localhost:" + port + "/fhir/";
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
ourServerBaseURL = "http://localhost:" + port + "/fhir/";
ourClient = ourCtx.newRestfulGenericClient(ourServerBaseURL);
ourClient.registerInterceptor(new LoggingInterceptor(true));
}
@@ -111,21 +111,21 @@ public class ExampleServerR4IT implements IServerSupport {
}
@Test
public void testCQLEvaluateMeasure() throws IOException {
CqlProviderLoader cqlProviderLoader = null;
public void testCQLEvaluateMeasureEXM104() throws IOException {
String measureId = "measure-EXM104-8.2.000";
// FIXME KBD Remove this and put some Unit Test code here
loadBundle("r4/EXM104/EXM104-8.2.000-bundle.json", ourCtx, ourClient);
// http://localhost:8080/fhir/Measure/measure-EXM104-8.2.000/$evaluate-measure?periodStart=2019-01-01&periodEnd=2019-12-31
Parameters inParams = new Parameters();
// inParams.addParameter().setName("measure").setValue(new StringType("Measure/measure-EXM104-8.2.000"));
// inParams.addParameter().setName("patient").setValue(new StringType("Patient/numer-EXM104-FHIR3"));
inParams.addParameter().setName("periodStart").setValue(new DateType("2019-01-01"));
inParams.addParameter().setName("periodEnd").setValue(new DateType("2019-12-31"));
inParams.addParameter().setName("periodStart").setValue(new StringType("2019-01-01"));
inParams.addParameter().setName("periodEnd").setValue(new StringType("2019-12-31"));
Parameters outParams = ourClient
.operation()
.onInstance(new IdDt("Measure", "measure-EXM104-8.2.000"))
.onInstance(new IdDt("Measure", measureId))
.named("$evaluate-measure")
.withParameters(inParams)
.cacheControl(new CacheControlDirective().setNoCache(true))
@@ -133,29 +133,12 @@ public class ExampleServerR4IT implements IServerSupport {
.useHttpGet()
.execute();
// Parameters outParams = ourClient
// .operation()
// .onType(Measure.class)
// .named("$evaluate-measure")
// .withParameters(inParams)
// .useHttpGet()
// .execute();
List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
Assert.assertTrue(!response.isEmpty());
Parameters.ParametersParameterComponent component = response.get(0);
Assert.assertTrue(component.getResource() instanceof MeasureReport);
MeasureReport report = (MeasureReport) component.getResource();
for (MeasureReport.MeasureReportGroupComponent group : report.getGroup()) {
for (MeasureReport.MeasureReportGroupPopulationComponent population : group.getPopulation()) {
Assert.assertTrue(population.getCount() > 0);
}
}
Assert.assertEquals("Measure/"+measureId, report.getMeasure());
}
private Bundle loadBundle(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {

31
src/test/java/ca/uhn/fhir/jpa/starter/IServerSupport.java
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@@ -1,7 +1,8 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -12,26 +13,20 @@ import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.Scanner;
public interface IServerSupport {
// default void putResourceDstu3(String resourceFileName, String id, FhirContext theCtx, IGenericClient theClient) {
// InputStream is = ExampleServerDstu3IT.class.getResourceAsStream(resourceFileName);
// Scanner scanner = new Scanner(is).useDelimiter("\\A");
// String json = scanner.hasNext() ? scanner.next() : "";
//
// boolean isJson = resourceFileName.endsWith("json");
//
// IBaseResource resource = isJson ? theCtx.newJsonParser().parseResource(json) : theCtx.newXmlParser().parseResource(json);
//
// if (resource instanceof Bundle) {
// theClient.transaction().withBundle((Bundle) resource).execute();
// }
// else {
// theClient.update().resource(resource).withId(id).execute();
// }
// }
default IBaseResource loadResource(String theLocation, FhirContext theFhirContext, DaoRegistry theDaoRegistry) throws IOException {
String json = stringFromResource(theLocation);
IBaseResource resource = theFhirContext.newJsonParser().parseResource(json);
IFhirResourceDao<IBaseResource> dao = theDaoRegistry.getResourceDao(resource.getIdElement().getResourceType());
if (dao == null) {
return null;
} else {
dao.update(resource);
return resource;
}
}
default String stringFromResource(String theLocation) throws IOException {
InputStream is = null;