Personal-Twin/hapi-fhir-jpaserver-starter
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge pull request #610 from hapifhir/cr-6.9.6-snapshot

Browse Source 
6.10.0 release merge with Clinical Reasoning config
This commit is contained in:
Kevin Dougan SmileCDR
2023-11-28 13:30:18 -05:00
committed by GitHub
parent f147c8315e d1c6b0661d
commit b578ee39f6
63 changed files with 175611 additions and 3897 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
README.md
View File

@@ -336,12 +336,12 @@ NOTE: MS SQL Server by default uses a case-insensitive codepage. This will cause
It is recommended to deploy a case-sensitive database prior to running HAPI FHIR when using MS SQL Server to avoid these and potentially other issues.
## Adding custom interceptors
Custom interceptors can be registered with the server by including the property `hapi.fhir.custom-interceptor-classes`. This will take a comma separated list of fully-qualified class names which will be registered with the server.
Interceptors will be discovered in one of two ways:
Custom interceptors can be registered with the server by including the property `hapi.fhir.custom-interceptor-classes`. This will take a comma separated list of fully-qualified class names which will be registered with the server.
Interceptors will be discovered in one of two ways:
1) discovered from the Spring application context as existing Beans (can be used in conjunction with `hapi.fhir.custom-bean-packages`) or registered with Spring via other methods
or
or
2) classes will be instantiated via reflection if no matching Bean is found

10
pom.xml
View File

@@ -131,6 +131,16 @@
<artifactId>hapi-fhir-jpaserver-mdm</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
</dependency>
<!-- This dependency includes the CDS Hooks Server -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-server-cds-hooks</artifactId>
<version>${project.version}</version>
</dependency>
<!-- This dependency includes the OpenAPI Server -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>

2
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
View File

@@ -865,4 +865,4 @@ public class AppProperties {
public void setEnable_index_of_type(boolean enable_index_of_type) {
this.enable_index_of_type = enable_index_of_type;
}
}
}

81
src/main/java/ca/uhn/fhir/jpa/starter/Application.java
View File

@@ -3,7 +3,10 @@ package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.batch2.jobs.config.Batch2JobsConfig;
import ca.uhn.fhir.jpa.batch2.JpaBatch2Config;
import ca.uhn.fhir.jpa.starter.annotations.OnEitherVersion;
import ca.uhn.fhir.jpa.starter.cdshooks.StarterCdsHooksConfig;
import ca.uhn.fhir.jpa.starter.common.FhirTesterConfig;
import ca.uhn.fhir.jpa.starter.cr.StarterCrDstu3Config;
import ca.uhn.fhir.jpa.starter.cr.StarterCrR4Config;
import ca.uhn.fhir.jpa.starter.mdm.MdmConfig;
import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
@@ -29,6 +32,9 @@ import org.springframework.web.servlet.DispatcherServlet;
@ServletComponentScan(basePackageClasses = {RestfulServer.class})
@SpringBootApplication(exclude = {ElasticsearchRestClientAutoConfiguration.class, ThymeleafAutoConfiguration.class})
@Import({
StarterCrR4Config.class,
StarterCrDstu3Config.class,
StarterCdsHooksConfig.class,
SubscriptionSubmitterConfig.class,
SubscriptionProcessorConfig.class,
SubscriptionChannelConfig.class,
@@ -39,51 +45,54 @@ import org.springframework.web.servlet.DispatcherServlet;
})
public class Application extends SpringBootServletInitializer {
public static void main(String[] args) {
public static void main(String[] args) {
SpringApplication.run(Application.class, args);
SpringApplication.run(Application.class, args);
//Server is now accessible at eg. http://localhost:8080/fhir/metadata
//UI is now accessible at http://localhost:8080/
}
// Server is now accessible at eg. http://localhost:8080/fhir/metadata
// UI is now accessible at http://localhost:8080/
}
@Override
protected SpringApplicationBuilder configure(
SpringApplicationBuilder builder) {
return builder.sources(Application.class);
}
@Override
protected SpringApplicationBuilder configure(SpringApplicationBuilder builder) {
return builder.sources(Application.class);
}
@Autowired
AutowireCapableBeanFactory beanFactory;
@Autowired
AutowireCapableBeanFactory beanFactory;
@Bean
@Conditional(OnEitherVersion.class)
public ServletRegistrationBean hapiServletRegistration(RestfulServer restfulServer) {
ServletRegistrationBean servletRegistrationBean = new ServletRegistrationBean();
beanFactory.autowireBean(restfulServer);
servletRegistrationBean.setServlet(restfulServer);
servletRegistrationBean.addUrlMappings("/fhir/*");
servletRegistrationBean.setLoadOnStartup(1);
@Bean
@Conditional(OnEitherVersion.class)
public ServletRegistrationBean hapiServletRegistration(RestfulServer restfulServer) {
ServletRegistrationBean servletRegistrationBean = new ServletRegistrationBean();
beanFactory.autowireBean(restfulServer);
servletRegistrationBean.setServlet(restfulServer);
servletRegistrationBean.addUrlMappings("/fhir/*");
servletRegistrationBean.setLoadOnStartup(1);
return servletRegistrationBean;
}
return servletRegistrationBean;
}
@Bean
public ServletRegistrationBean overlayRegistrationBean() {
@Bean
public ServletRegistrationBean overlayRegistrationBean() {
AnnotationConfigWebApplicationContext annotationConfigWebApplicationContext = new AnnotationConfigWebApplicationContext();
annotationConfigWebApplicationContext.register(FhirTesterConfig.class);
AnnotationConfigWebApplicationContext annotationConfigWebApplicationContext =
new AnnotationConfigWebApplicationContext();
annotationConfigWebApplicationContext.register(FhirTesterConfig.class);
DispatcherServlet dispatcherServlet = new DispatcherServlet(
annotationConfigWebApplicationContext);
dispatcherServlet.setContextClass(AnnotationConfigWebApplicationContext.class);
dispatcherServlet.setContextConfigLocation(FhirTesterConfig.class.getName());
DispatcherServlet dispatcherServlet = new DispatcherServlet(annotationConfigWebApplicationContext);
dispatcherServlet.setContextClass(AnnotationConfigWebApplicationContext.class);
dispatcherServlet.setContextConfigLocation(FhirTesterConfig.class.getName());
ServletRegistrationBean registrationBean = new ServletRegistrationBean();
registrationBean.setServlet(dispatcherServlet);
registrationBean.addUrlMappings("/*");
registrationBean.setLoadOnStartup(1);
return registrationBean;
ServletRegistrationBean registrationBean = new ServletRegistrationBean();
registrationBean.setServlet(dispatcherServlet);
registrationBean.addUrlMappings("/*");
registrationBean.setLoadOnStartup(1);
return registrationBean;
}
}
// @Bean
// IRepositoryFactory repositoryFactory(DaoRegistry theDaoRegistry, RestfulServer theRestfulServer) {
// return rd -> new HapiFhirRepository(theDaoRegistry, rd, theRestfulServer);
// }
}

37
src/main/java/ca/uhn/fhir/jpa/starter/ExtraStaticFilesConfigurer.java
View File

@@ -19,33 +19,32 @@ public class ExtraStaticFilesConfigurer implements WebMvcConfigurer {
public ExtraStaticFilesConfigurer(AppProperties appProperties) {
rootContextPath = appProperties.getStaticLocationPrefix();
if(rootContextPath.endsWith("/"))
if (rootContextPath.endsWith("/"))
rootContextPath = rootContextPath.substring(0, rootContextPath.lastIndexOf('/'));
staticLocation = appProperties.getStaticLocation();
if(staticLocation.endsWith("/"))
staticLocation = staticLocation.substring(0, staticLocation.lastIndexOf('/'));
if (staticLocation.endsWith("/")) staticLocation = staticLocation.substring(0, staticLocation.lastIndexOf('/'));
}
@Override
public void addResourceHandlers(ResourceHandlerRegistry theRegistry) {
theRegistry.addResourceHandler(rootContextPath + "/**").addResourceLocations(staticLocation);
}
@Override
public void addResourceHandlers(ResourceHandlerRegistry theRegistry) {
theRegistry.addResourceHandler(rootContextPath + "/**").addResourceLocations(staticLocation);
}
public void addViewControllers(ViewControllerRegistry registry) {
String path = URI.create(staticLocation).getPath();
String lastSegment = path.substring(path.lastIndexOf('/') + 1);
@Override
public void addViewControllers(ViewControllerRegistry registry) {
String path = URI.create(staticLocation).getPath();
String lastSegment = path.substring(path.lastIndexOf('/') + 1);
registry.addViewController(rootContextPath)
.setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
registry.addViewController(rootContextPath).setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
registry.addViewController(rootContextPath + "/*")
.setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
registry.addViewController(rootContextPath + "/*").setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
registry.addViewController(rootContextPath + "/" + lastSegment + "/")
.setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
registry.addViewController(rootContextPath + "/" + lastSegment + "/").setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
registry.setOrder(Ordered.HIGHEST_PRECEDENCE);
}
}
registry.setOrder(Ordered.HIGHEST_PRECEDENCE);
}
}

6
src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnCorsPresent.java
View File

@@ -10,9 +10,11 @@ public class OnCorsPresent implements Condition {
@Override
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
AppProperties config = Binder.get(conditionContext.getEnvironment()).bind("hapi.fhir", AppProperties.class).orElse(null);
AppProperties config = Binder.get(conditionContext.getEnvironment())
.bind("hapi.fhir", AppProperties.class)
.orElse(null);
if (config == null) return false;
if (config.getCors() == null) return false;
return true;
}
}
}

17
src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnDSTU2Condition.java
View File

@@ -6,14 +6,13 @@ import org.springframework.context.annotation.ConditionContext;
import org.springframework.core.type.AnnotatedTypeMetadata;
public class OnDSTU2Condition implements Condition {
@Override
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext.
getEnvironment()
.getProperty("hapi.fhir.fhir_version")
.toUpperCase());
@Override
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext
.getEnvironment()
.getProperty("hapi.fhir.fhir_version")
.toUpperCase());
return version == FhirVersionEnum.DSTU2;
}
return version == FhirVersionEnum.DSTU2;
}
}

17
src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnDSTU3Condition.java
View File

@@ -6,14 +6,13 @@ import org.springframework.context.annotation.ConditionContext;
import org.springframework.core.type.AnnotatedTypeMetadata;
public class OnDSTU3Condition implements Condition {
@Override
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext.
getEnvironment()
.getProperty("hapi.fhir.fhir_version")
.toUpperCase());
@Override
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext
.getEnvironment()
.getProperty("hapi.fhir.fhir_version")
.toUpperCase());
return version == FhirVersionEnum.DSTU3;
}
return version == FhirVersionEnum.DSTU3;
}
}

50
src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnEitherVersion.java
View File

@@ -6,34 +6,28 @@ import org.springframework.context.annotation.Conditional;
public class OnEitherVersion extends AnyNestedCondition {
OnEitherVersion() {
super(ConfigurationPhase.REGISTER_BEAN);
}
@Override
protected ConditionOutcome getFinalMatchOutcome(MemberMatchOutcomes memberOutcomes) {
ConditionOutcome result = super.getFinalMatchOutcome(memberOutcomes);
return result;
}
@Conditional(OnDSTU2Condition.class)
static class OnDSTU2 {
}
@Conditional(OnDSTU3Condition.class)
static class OnDSTU3 {
}
@Conditional(OnR4Condition.class)
static class OnR4 {
}
@Conditional(OnR4BCondition.class)
static class OnR4B {
OnEitherVersion() {
super(ConfigurationPhase.REGISTER_BEAN);
}
@Conditional(OnR5Condition.class)
static class OnR5 {
}
@Override
protected ConditionOutcome getFinalMatchOutcome(MemberMatchOutcomes memberOutcomes) {
ConditionOutcome result = super.getFinalMatchOutcome(memberOutcomes);
return result;
}
}
@Conditional(OnDSTU2Condition.class)
static class OnDSTU2 {}
@Conditional(OnDSTU3Condition.class)
static class OnDSTU3 {}
@Conditional(OnR4Condition.class)
static class OnR4 {}
@Conditional(OnR4BCondition.class)
static class OnR4B {}
@Conditional(OnR5Condition.class)
static class OnR5 {}
}

6
src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnImplementationGuidesPresent.java
View File

@@ -10,9 +10,11 @@ public class OnImplementationGuidesPresent implements Condition {
@Override
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
AppProperties config = Binder.get(conditionContext.getEnvironment()).bind("hapi.fhir", AppProperties.class).orElse(null);
AppProperties config = Binder.get(conditionContext.getEnvironment())
.bind("hapi.fhir", AppProperties.class)
.orElse(null);
if (config == null) return false;
if (config.getImplementationGuides() == null) return false;
return !config.getImplementationGuides().isEmpty();
}
}
}

8
src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnR4BCondition.java
View File

@@ -8,10 +8,10 @@ import org.springframework.core.type.AnnotatedTypeMetadata;
public class OnR4BCondition implements Condition {
@Override
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
String version = conditionContext.
getEnvironment()
.getProperty("hapi.fhir.fhir_version")
.toUpperCase();
String version = conditionContext
.getEnvironment()
.getProperty("hapi.fhir.fhir_version")
.toUpperCase();
return FhirVersionEnum.R4B.name().equals(version);
}

17
src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnR4Condition.java
View File

@@ -6,14 +6,13 @@ import org.springframework.context.annotation.ConditionContext;
import org.springframework.core.type.AnnotatedTypeMetadata;
public class OnR4Condition implements Condition {
@Override
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext.
getEnvironment()
.getProperty("hapi.fhir.fhir_version")
.toUpperCase());
@Override
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext
.getEnvironment()
.getProperty("hapi.fhir.fhir_version")
.toUpperCase());
return version == FhirVersionEnum.R4;
}
return version == FhirVersionEnum.R4;
}
}

17
src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnR5Condition.java
View File

@@ -6,14 +6,13 @@ import org.springframework.context.annotation.ConditionContext;
import org.springframework.core.type.AnnotatedTypeMetadata;
public class OnR5Condition implements Condition {
@Override
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext.
getEnvironment()
.getProperty("hapi.fhir.fhir_version")
.toUpperCase());
@Override
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext
.getEnvironment()
.getProperty("hapi.fhir.fhir_version")
.toUpperCase());
return version == FhirVersionEnum.R5;
}
return version == FhirVersionEnum.R5;
}
}

14
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/CdsHooksConfigCondition.java Normal file
View File

@@ -0,0 +1,14 @@
package ca.uhn.fhir.jpa.starter.cdshooks;
import org.springframework.context.annotation.Condition;
import org.springframework.context.annotation.ConditionContext;
import org.springframework.core.type.AnnotatedTypeMetadata;
public class CdsHooksConfigCondition implements Condition {
@Override
public boolean matches(ConditionContext theConditionContext, AnnotatedTypeMetadata theAnnotatedTypeMetadata) {
String property = theConditionContext.getEnvironment().getProperty("hapi.fhir.cdshooks.enabled");
return Boolean.parseBoolean(property);
}
}

27
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/CdsHooksProperties.java Normal file
View File

@@ -0,0 +1,27 @@
package ca.uhn.fhir.jpa.starter.cdshooks;
import org.springframework.boot.context.properties.ConfigurationProperties;
@ConfigurationProperties(prefix = "hapi.fhir.cdshooks")
public class CdsHooksProperties {
private boolean enabled;
public boolean isEnabled() {
return enabled;
}
public void setEnabled(boolean enabled) {
this.enabled = enabled;
}
private String clientIdHeaderName;
public String getClientIdHeaderName() {
return clientIdHeaderName;
}
public void setClientIdHeaderName(String clientIdHeaderName) {
this.clientIdHeaderName = clientIdHeaderName;
}
}

7
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/CdsHooksRequest.java Normal file
View File

@@ -0,0 +1,7 @@
package ca.uhn.fhir.jpa.starter.cdshooks;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceRequestJson;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
@JsonIgnoreProperties({"extension"})
public class CdsHooksRequest extends CdsServiceRequestJson {}

129
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/CdsHooksServlet.java Normal file
View File

@@ -0,0 +1,129 @@
package ca.uhn.fhir.jpa.starter.cdshooks;
import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.hapi.fhir.cdshooks.api.ICdsServiceRegistry;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceRequestJson;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceResponseJson;
import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServicesJson;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonParser;
import org.apache.http.entity.ContentType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Configurable;
import org.springframework.beans.factory.annotation.Qualifier;
import java.io.IOException;
import java.util.stream.Collectors;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import static ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig.CDS_HOOKS_OBJECT_MAPPER_FACTORY;
@Configurable
public class CdsHooksServlet extends HttpServlet {
private static final Logger logger = LoggerFactory.getLogger(CdsHooksServlet.class);
private static final long serialVersionUID = 1L;
@Autowired
private AppProperties appProperties;
@Autowired
private ProviderConfiguration providerConfiguration;
@Autowired
ICdsServiceRegistry cdsServiceRegistry;
@Autowired
RestfulServer restfulServer;
@Autowired
@Qualifier(CDS_HOOKS_OBJECT_MAPPER_FACTORY)
ObjectMapper objectMapper;
protected ProviderConfiguration getProviderConfiguration() {
return this.providerConfiguration;
}
// CORS Pre-flight
@Override
protected void doOptions(HttpServletRequest req, HttpServletResponse resp) {
ErrorHandling.setAccessControlHeaders(resp, appProperties);
resp.setHeader("Content-Type", ContentType.APPLICATION_JSON.getMimeType());
resp.setHeader("X-Content-Type-Options", "nosniff");
resp.setStatus(HttpServletResponse.SC_OK);
}
@Override
protected void doGet(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
logger.info(request.getRequestURI());
if (!request.getRequestURL().toString().endsWith("/cds-services")
&& !request.getRequestURL().toString().endsWith("/cds-services/")) {
logger.error(request.getRequestURI());
throw new ServletException("This servlet is not configured to handle GET requests.");
}
ErrorHandling.setAccessControlHeaders(response, appProperties);
response.setHeader("Content-Type", ContentType.APPLICATION_JSON.getMimeType());
response.getWriter()
.println(new GsonBuilder()
.setPrettyPrinting()
.create()
.toJson(JsonParser.parseString(objectMapper.writeValueAsString(getServices()))));
}
@Override
protected void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
try {
if (request.getContentType() == null || !request.getContentType().startsWith("application/json")) {
throw new ServletException(String.format(
"Invalid content type %s. Please use application/json.", request.getContentType()));
}
logger.info(request.getRequestURI());
String service = request.getPathInfo().replace("/", "");
String requestJson = request.getReader().lines().collect(Collectors.joining());
CdsHooksRequest cdsHooksRequest = objectMapper.readValue(requestJson, CdsHooksRequest.class);
logRequestInfo(cdsHooksRequest, requestJson);
CdsServiceResponseJson serviceResponseJson = cdsServiceRegistry.callService(service, cdsHooksRequest);
// Using GSON pretty print format as Jackson's is ugly
String jsonResponse = new GsonBuilder()
.disableHtmlEscaping()
.setPrettyPrinting()
.create()
.toJson(JsonParser.parseString(objectMapper.writeValueAsString(serviceResponseJson)));
logger.info(jsonResponse);
response.setContentType("text/json;charset=UTF-8");
response.getWriter().println(jsonResponse);
} catch (BaseServerResponseException e) {
ErrorHandling.handleError(response, "ERROR: Exception connecting to remote server.", e, appProperties);
logger.error(e.toString());
} catch (Exception e) {
logger.error(e.toString());
throw new ServletException("ERROR: Exception in cds-hooks processing.", e);
}
}
private void logRequestInfo(CdsServiceRequestJson request, String jsonRequest) {
logger.info(jsonRequest);
logger.info("cds-hooks hook instance: {}", request.getHookInstance());
logger.info("cds-hooks local server address: {}", appProperties.getServer_address());
logger.info("cds-hooks fhir server address: {}", request.getFhirServer());
logger.info(
"cds-hooks cql_logging_enabled: {}",
this.getProviderConfiguration().getCqlLoggingEnabled());
}
private CdsServicesJson getServices() {
return cdsServiceRegistry.getCdsServicesJson();
}
}

105
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/ErrorHandling.java Normal file
View File

@@ -0,0 +1,105 @@
package ca.uhn.fhir.jpa.starter.cdshooks;
import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import java.io.IOException;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.util.Arrays;
import javax.servlet.http.HttpServletResponse;
public class ErrorHandling {
private ErrorHandling() {}
public static void handleError(
HttpServletResponse response, String message, Exception e, AppProperties myAppProperties)
throws IOException {
setAccessControlHeaders(response, myAppProperties);
response.setStatus(500); // This will be overwritten with the correct status code downstream if needed.
response.getWriter().println(message);
printMessageAndCause(e, response);
if (e instanceof BaseServerResponseException) {
handleServerResponseException((BaseServerResponseException) e, response);
} else if (e.getCause() instanceof BaseServerResponseException) {
handleServerResponseException((BaseServerResponseException) e.getCause(), response);
}
printStackTrack(e, response);
}
private static void handleServerResponseException(BaseServerResponseException e, HttpServletResponse response)
throws IOException {
switch (e.getStatusCode()) {
case 401:
case 403:
response.getWriter().println("Precondition Failed. Remote FHIR server returned: " + e.getStatusCode());
response.getWriter()
.println(
"Ensure that the fhirAuthorization token is set or that the remote server allows unauthenticated access.");
response.setStatus(412);
break;
case 404:
response.getWriter().println("Precondition Failed. Remote FHIR server returned: " + e.getStatusCode());
response.getWriter().println("Ensure the resource exists on the remote server.");
response.setStatus(412);
break;
default:
response.getWriter().println("Unhandled Error in Remote FHIR server: " + e.getStatusCode());
}
}
private static void printMessageAndCause(Exception e, HttpServletResponse response) throws IOException {
if (e.getMessage() != null) {
response.getWriter().println(e.getMessage());
}
if (e.getCause() != null && e.getCause().getMessage() != null) {
response.getWriter().println(e.getCause().getMessage());
}
}
private static void printStackTrack(Exception e, HttpServletResponse response) throws IOException {
StringWriter sw = new StringWriter();
e.printStackTrace(new PrintWriter(sw));
String exceptionAsString = sw.toString();
response.getWriter().println(exceptionAsString);
}
public static void setAccessControlHeaders(HttpServletResponse resp, AppProperties myAppProperties) {
if (myAppProperties.getCors() != null) {
if (myAppProperties.getCors().getAllow_Credentials()) {
resp.setHeader(
"Access-Control-Allow-Origin",
myAppProperties.getCors().getAllowed_origin().stream()
.findFirst()
.get());
resp.setHeader(
"Access-Control-Allow-Methods",
String.join(", ", Arrays.asList("GET", "HEAD", "POST", "OPTIONS")));
resp.setHeader(
"Access-Control-Allow-Headers",
String.join(
", ",
Arrays.asList(
"x-fhir-starter",
"Origin",
"Accept",
"X-Requested-With",
"Content-Type",
"Authorization",
"Cache-Control")));
resp.setHeader(
"Access-Control-Expose-Headers",
String.join(", ", Arrays.asList("Location", "Content-Location")));
resp.setHeader("Access-Control-Max-Age", "86400");
}
}
}
public static class CdsHooksError extends RuntimeException {
public CdsHooksError(String message) {
super(message);
}
}
}

30
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/ProviderConfiguration.java Normal file
View File

@@ -0,0 +1,30 @@
package ca.uhn.fhir.jpa.starter.cdshooks;
import ca.uhn.fhir.jpa.starter.cr.CrProperties;
public class ProviderConfiguration {
public static final ProviderConfiguration DEFAULT_PROVIDER_CONFIGURATION =
new ProviderConfiguration(false, "client_id");
private final String clientIdHeaderName;
private final boolean cqlLoggingEnabled;
public ProviderConfiguration(boolean cqlLoggingEnabled, String clientIdHeaderName) {
this.cqlLoggingEnabled = cqlLoggingEnabled;
this.clientIdHeaderName = clientIdHeaderName;
}
public ProviderConfiguration(CdsHooksProperties cdsProperties, CrProperties crProperties) {
this.clientIdHeaderName = cdsProperties.getClientIdHeaderName();
this.cqlLoggingEnabled = crProperties.isCqlRuntimeDebugLoggingEnabled();
}
public String getClientIdHeaderName() {
return this.clientIdHeaderName;
}
public boolean getCqlLoggingEnabled() {
return this.cqlLoggingEnabled;
}
}

66
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/StarterCdsHooksConfig.java Normal file
View File

@@ -0,0 +1,66 @@
package ca.uhn.fhir.jpa.starter.cdshooks;
import ca.uhn.fhir.jpa.starter.cr.CrConfigCondition;
import ca.uhn.fhir.jpa.starter.cr.CrProperties;
import ca.uhn.hapi.fhir.cdshooks.api.ICdsHooksDaoAuthorizationSvc;
import ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig;
import ca.uhn.hapi.fhir.cdshooks.svc.CdsHooksContextBooter;
import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrSettings;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
import org.springframework.boot.web.servlet.ServletRegistrationBean;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@Configuration
@Conditional({CdsHooksConfigCondition.class, CrConfigCondition.class})
@Import(CdsHooksConfig.class)
public class StarterCdsHooksConfig {
@Bean
public CdsHooksProperties cdsHooksProperties() {
return new CdsHooksProperties();
}
@Bean
public CdsCrSettings cdsCrSettings(CdsHooksProperties cdsHooksProperties) {
CdsCrSettings settings = CdsCrSettings.getDefault();
settings.setClientIdHeaderName(cdsHooksProperties.getClientIdHeaderName());
return settings;
}
@Bean
public CdsHooksContextBooter cdsHooksContextBooter() {
// ourLog.info("No Spring Context provided. Assuming all CDS Services will be registered dynamically.");
return new CdsHooksContextBooter();
}
public static class CdsHooksDaoAuthorizationSvc implements ICdsHooksDaoAuthorizationSvc {
@Override
public void authorizePreShow(IBaseResource theResource) {}
}
@Bean
public ProviderConfiguration providerConfiguration(CdsHooksProperties cdsProperties, CrProperties crProperties) {
return new ProviderConfiguration(cdsProperties, crProperties);
}
@Bean
ICdsHooksDaoAuthorizationSvc cdsHooksDaoAuthorizationSvc() {
return new CdsHooksDaoAuthorizationSvc();
}
@Bean
public ServletRegistrationBean<CdsHooksServlet> cdsHooksRegistrationBean(AutowireCapableBeanFactory beanFactory) {
CdsHooksServlet cdsHooksServlet = new CdsHooksServlet();
beanFactory.autowireBean(cdsHooksServlet);
ServletRegistrationBean<CdsHooksServlet> registrationBean = new ServletRegistrationBean<>();
registrationBean.setName("cds-hooks servlet");
registrationBean.setServlet(cdsHooksServlet);
registrationBean.addUrlMappings("/cds-services/*");
registrationBean.setLoadOnStartup(1);
return registrationBean;
}
}

6
src/main/java/ca/uhn/fhir/jpa/starter/common/ElasticsearchConfig.java
View File

@@ -10,18 +10,20 @@ import org.springframework.core.env.ConfigurableEnvironment;
@Configuration
public class ElasticsearchConfig {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ElasticsearchConfig.class);
@Bean
public ElasticsearchSvcImpl elasticsearchSvc(ConfigurableEnvironment configurableEnvironment) {
if (EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment)) {
String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment);
if (elasticsearchUrl.startsWith("http")) {
elasticsearchUrl =elasticsearchUrl.substring(elasticsearchUrl.indexOf("://") + 3);
elasticsearchUrl = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://") + 3);
}
String elasticsearchProtocol = EnvironmentHelper.getElasticsearchServerProtocol(configurableEnvironment);
String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
ourLog.info("Configuring elasticsearch {} {}", elasticsearchProtocol, elasticsearchUrl);
return new ElasticsearchSvcImpl(elasticsearchProtocol, elasticsearchUrl, elasticsearchUsername, elasticsearchPassword);
return new ElasticsearchSvcImpl(
elasticsearchProtocol, elasticsearchUrl, elasticsearchUsername, elasticsearchPassword);
} else {
return null;
}

363
src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigCommon.java
View File

@@ -15,7 +15,6 @@ import ca.uhn.fhir.rest.server.mail.MailConfig;
import ca.uhn.fhir.rest.server.mail.MailSvc;
import com.google.common.base.Strings;
import org.hl7.fhir.r4.model.Bundle.BundleType;
import org.springframework.boot.env.YamlPropertySourceLoader;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@@ -24,6 +23,7 @@ import org.springframework.context.annotation.Primary;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import java.util.HashSet;
import java.util.stream.Collectors;
/**
@@ -33,210 +33,239 @@ import java.util.stream.Collectors;
@EnableTransactionManagement
public class FhirServerConfigCommon {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
public FhirServerConfigCommon(AppProperties appProperties) {
ourLog.info("Server configured to " + (appProperties.getAllow_contains_searches() ? "allow" : "deny")
+ " contains searches");
ourLog.info("Server configured to " + (appProperties.getAllow_multiple_delete() ? "allow" : "deny")
+ " multiple deletes");
ourLog.info("Server configured to " + (appProperties.getAllow_external_references() ? "allow" : "deny")
+ " external references");
ourLog.info("Server configured to " + (appProperties.getDao_scheduling_enabled() ? "enable" : "disable")
+ " DAO scheduling");
ourLog.info("Server configured to " + (appProperties.getDelete_expunge_enabled() ? "enable" : "disable")
+ " delete expunges");
ourLog.info(
"Server configured to " + (appProperties.getExpunge_enabled() ? "enable" : "disable") + " expunges");
ourLog.info(
"Server configured to " + (appProperties.getAllow_override_default_search_params() ? "allow" : "deny")
+ " overriding default search params");
ourLog.info("Server configured to "
+ (appProperties.getAuto_create_placeholder_reference_targets() ? "allow" : "disable")
+ " auto-creating placeholder references");
ourLog.info(
"Server configured to auto-version references at paths {}",
appProperties.getAuto_version_reference_at_paths());
public FhirServerConfigCommon(AppProperties appProperties) {
ourLog.info("Server configured to " + (appProperties.getAllow_contains_searches() ? "allow" : "deny") + " contains searches");
ourLog.info("Server configured to " + (appProperties.getAllow_multiple_delete() ? "allow" : "deny") + " multiple deletes");
ourLog.info("Server configured to " + (appProperties.getAllow_external_references() ? "allow" : "deny") + " external references");
ourLog.info("Server configured to " + (appProperties.getDao_scheduling_enabled() ? "enable" : "disable") + " DAO scheduling");
ourLog.info("Server configured to " + (appProperties.getDelete_expunge_enabled() ? "enable" : "disable") + " delete expunges");
ourLog.info("Server configured to " + (appProperties.getExpunge_enabled() ? "enable" : "disable") + " expunges");
ourLog.info("Server configured to " + (appProperties.getAllow_override_default_search_params() ? "allow" : "deny") + " overriding default search params");
ourLog.info("Server configured to " + (appProperties.getAuto_create_placeholder_reference_targets() ? "allow" : "disable") + " auto-creating placeholder references");
ourLog.info("Server configured to auto-version references at paths {}", appProperties.getAuto_version_reference_at_paths());
if (appProperties.getSubscription().getEmail() != null) {
AppProperties.Subscription.Email email =
appProperties.getSubscription().getEmail();
ourLog.info("Server is configured to enable email with host '" + email.getHost() + "' and port "
+ email.getPort());
ourLog.info("Server will use '" + email.getFrom() + "' as the from email address");
if (appProperties.getSubscription().getEmail() != null) {
AppProperties.Subscription.Email email = appProperties.getSubscription().getEmail();
ourLog.info("Server is configured to enable email with host '" + email.getHost() + "' and port " + email.getPort());
ourLog.info("Server will use '" + email.getFrom() + "' as the from email address");
if (!Strings.isNullOrEmpty(email.getUsername())) {
ourLog.info("Server is configured to use username '" + email.getUsername() + "' for email");
}
if (!Strings.isNullOrEmpty(email.getUsername())) {
ourLog.info("Server is configured to use username '" + email.getUsername() + "' for email");
}
if (!Strings.isNullOrEmpty(email.getPassword())) {
ourLog.info("Server is configured to use a password for email");
}
}
if (!Strings.isNullOrEmpty(email.getPassword())) {
ourLog.info("Server is configured to use a password for email");
}
}
if (appProperties.getSubscription().getResthook_enabled()) {
ourLog.info("REST-hook subscriptions enabled");
}
if (appProperties.getSubscription().getResthook_enabled()) {
ourLog.info("REST-hook subscriptions enabled");
}
if (appProperties.getSubscription().getEmail() != null) {
ourLog.info("Email subscriptions enabled");
}
if (appProperties.getSubscription().getEmail() != null) {
ourLog.info("Email subscriptions enabled");
}
if (appProperties.getEnable_index_contained_resource() == Boolean.TRUE) {
ourLog.info("Indexed on contained resource enabled");
}
}
if (appProperties.getEnable_index_contained_resource() == Boolean.TRUE) {
ourLog.info("Indexed on contained resource enabled");
}
}
/**
* Configure FHIR properties around the the JPA server via this bean
*/
@Bean
public JpaStorageSettings jpaStorageSettings(AppProperties appProperties) {
JpaStorageSettings jpaStorageSettings = new JpaStorageSettings();
/**
* Configure FHIR properties around the the JPA server via this bean
*/
@Bean
public JpaStorageSettings jpaStorageSettings(AppProperties appProperties) {
JpaStorageSettings jpaStorageSettings = new JpaStorageSettings();
jpaStorageSettings.setIndexMissingFields(
appProperties.getEnable_index_missing_fields()
? StorageSettings.IndexEnabledEnum.ENABLED
: StorageSettings.IndexEnabledEnum.DISABLED);
jpaStorageSettings.setAutoCreatePlaceholderReferenceTargets(
appProperties.getAuto_create_placeholder_reference_targets());
jpaStorageSettings.setAutoVersionReferenceAtPaths(appProperties.getAuto_version_reference_at_paths());
jpaStorageSettings.setEnforceReferentialIntegrityOnWrite(
appProperties.getEnforce_referential_integrity_on_write());
jpaStorageSettings.setEnforceReferentialIntegrityOnDelete(
appProperties.getEnforce_referential_integrity_on_delete());
jpaStorageSettings.setAllowContainsSearches(appProperties.getAllow_contains_searches());
jpaStorageSettings.setAllowMultipleDelete(appProperties.getAllow_multiple_delete());
jpaStorageSettings.setAllowExternalReferences(appProperties.getAllow_external_references());
jpaStorageSettings.setSchedulingDisabled(!appProperties.getDao_scheduling_enabled());
jpaStorageSettings.setDeleteExpungeEnabled(appProperties.getDelete_expunge_enabled());
jpaStorageSettings.setExpungeEnabled(appProperties.getExpunge_enabled());
if (appProperties.getSubscription() != null
&& appProperties.getSubscription().getEmail() != null)
jpaStorageSettings.setEmailFromAddress(
appProperties.getSubscription().getEmail().getFrom());
jpaStorageSettings.setIndexMissingFields(appProperties.getEnable_index_missing_fields() ? StorageSettings.IndexEnabledEnum.ENABLED : StorageSettings.IndexEnabledEnum.DISABLED);
jpaStorageSettings.setAutoCreatePlaceholderReferenceTargets(appProperties.getAuto_create_placeholder_reference_targets());
jpaStorageSettings.setAutoVersionReferenceAtPaths(appProperties.getAuto_version_reference_at_paths());
jpaStorageSettings.setEnforceReferentialIntegrityOnWrite(appProperties.getEnforce_referential_integrity_on_write());
jpaStorageSettings.setEnforceReferentialIntegrityOnDelete(appProperties.getEnforce_referential_integrity_on_delete());
jpaStorageSettings.setAllowContainsSearches(appProperties.getAllow_contains_searches());
jpaStorageSettings.setAllowMultipleDelete(appProperties.getAllow_multiple_delete());
jpaStorageSettings.setAllowExternalReferences(appProperties.getAllow_external_references());
jpaStorageSettings.setSchedulingDisabled(!appProperties.getDao_scheduling_enabled());
jpaStorageSettings.setDeleteExpungeEnabled(appProperties.getDelete_expunge_enabled());
jpaStorageSettings.setExpungeEnabled(appProperties.getExpunge_enabled());
if(appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null)
jpaStorageSettings.setEmailFromAddress(appProperties.getSubscription().getEmail().getFrom());
Integer maxFetchSize = appProperties.getMax_page_size();
jpaStorageSettings.setFetchSizeDefaultMaximum(maxFetchSize);
ourLog.info("Server configured to have a maximum fetch size of "
+ (maxFetchSize == Integer.MAX_VALUE ? "'unlimited'" : maxFetchSize));
Integer maxFetchSize = appProperties.getMax_page_size();
jpaStorageSettings.setFetchSizeDefaultMaximum(maxFetchSize);
ourLog.info("Server configured to have a maximum fetch size of " + (maxFetchSize == Integer.MAX_VALUE ? "'unlimited'" : maxFetchSize));
Long reuseCachedSearchResultsMillis = appProperties.getReuse_cached_search_results_millis();
jpaStorageSettings.setReuseCachedSearchResultsForMillis(reuseCachedSearchResultsMillis);
ourLog.info("Server configured to cache search results for {} milliseconds", reuseCachedSearchResultsMillis);
Long reuseCachedSearchResultsMillis = appProperties.getReuse_cached_search_results_millis();
jpaStorageSettings.setReuseCachedSearchResultsForMillis(reuseCachedSearchResultsMillis);
ourLog.info("Server configured to cache search results for {} milliseconds", reuseCachedSearchResultsMillis);
Long retainCachedSearchesMinutes = appProperties.getRetain_cached_searches_mins();
jpaStorageSettings.setExpireSearchResultsAfterMillis(retainCachedSearchesMinutes * 60 * 1000);
if (appProperties.getSubscription() != null) {
// Subscriptions are enabled by channel type
if (appProperties.getSubscription().getResthook_enabled()) {
ourLog.info("Enabling REST-hook subscriptions");
jpaStorageSettings.addSupportedSubscriptionType(
org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.RESTHOOK);
}
if (appProperties.getSubscription().getEmail() != null) {
ourLog.info("Enabling email subscriptions");
jpaStorageSettings.addSupportedSubscriptionType(
org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.EMAIL);
}
if (appProperties.getSubscription().getWebsocket_enabled()) {
ourLog.info("Enabling websocket subscriptions");
jpaStorageSettings.addSupportedSubscriptionType(
org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.WEBSOCKET);
}
}
Long retainCachedSearchesMinutes = appProperties.getRetain_cached_searches_mins();
jpaStorageSettings.setExpireSearchResultsAfterMillis(retainCachedSearchesMinutes * 60 * 1000);
jpaStorageSettings.setFilterParameterEnabled(appProperties.getFilter_search_enabled());
jpaStorageSettings.setAdvancedHSearchIndexing(appProperties.getAdvanced_lucene_indexing());
jpaStorageSettings.setTreatBaseUrlsAsLocal(new HashSet<>(appProperties.getLocal_base_urls()));
if(appProperties.getSubscription() != null) {
// Subscriptions are enabled by channel type
if (appProperties.getSubscription().getResthook_enabled()) {
ourLog.info("Enabling REST-hook subscriptions");
jpaStorageSettings.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.RESTHOOK);
}
if (appProperties.getSubscription().getEmail() != null) {
ourLog.info("Enabling email subscriptions");
jpaStorageSettings.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.EMAIL);
}
if (appProperties.getSubscription().getWebsocket_enabled()) {
ourLog.info("Enabling websocket subscriptions");
jpaStorageSettings.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.WEBSOCKET);
}
}
if (appProperties.getLastn_enabled()) {
jpaStorageSettings.setLastNEnabled(true);
}
jpaStorageSettings.setFilterParameterEnabled(appProperties.getFilter_search_enabled());
jpaStorageSettings.setAdvancedHSearchIndexing(appProperties.getAdvanced_lucene_indexing());
jpaStorageSettings.setTreatBaseUrlsAsLocal(appProperties.getLocal_base_urls());
if (appProperties.getInline_resource_storage_below_size() != 0) {
jpaStorageSettings.setInlineResourceTextBelowSize(appProperties.getInline_resource_storage_below_size());
}
if (appProperties.getLastn_enabled()) {
jpaStorageSettings.setLastNEnabled(true);
}
jpaStorageSettings.setStoreResourceInHSearchIndex(appProperties.getStore_resource_in_lucene_index_enabled());
jpaStorageSettings.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
jpaStorageSettings.setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
if(appProperties.getInline_resource_storage_below_size() != 0){
jpaStorageSettings.setInlineResourceTextBelowSize(appProperties.getInline_resource_storage_below_size());
}
if (appProperties.getAllowed_bundle_types() != null) {
jpaStorageSettings.setBundleTypesAllowedForStorage(appProperties.getAllowed_bundle_types().stream()
.map(BundleType::toCode)
.collect(Collectors.toSet()));
}
jpaStorageSettings.setStoreResourceInHSearchIndex(appProperties.getStore_resource_in_lucene_index_enabled());
jpaStorageSettings.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
jpaStorageSettings.setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
jpaStorageSettings.setDeferIndexingForCodesystemsOfSize(
appProperties.getDefer_indexing_for_codesystems_of_size());
if (appProperties.getClient_id_strategy() == JpaStorageSettings.ClientIdStrategyEnum.ANY) {
jpaStorageSettings.setResourceServerIdStrategy(JpaStorageSettings.IdStrategyEnum.UUID);
jpaStorageSettings.setResourceClientIdStrategy(appProperties.getClient_id_strategy());
}
// Parallel Batch GET execution settings
jpaStorageSettings.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_size());
jpaStorageSettings.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_max_size());
storageSettings(appProperties, jpaStorageSettings);
return jpaStorageSettings;
}
if (appProperties.getAllowed_bundle_types() != null) {
jpaStorageSettings.setBundleTypesAllowedForStorage(appProperties.getAllowed_bundle_types().stream().map(BundleType::toCode).collect(Collectors.toSet()));
}
@Bean
public YamlPropertySourceLoader yamlPropertySourceLoader() {
return new YamlPropertySourceLoader();
}
jpaStorageSettings.setDeferIndexingForCodesystemsOfSize(appProperties.getDefer_indexing_for_codesystems_of_size());
@Bean
public PartitionSettings partitionSettings(AppProperties appProperties) {
PartitionSettings retVal = new PartitionSettings();
// Partitioning
if (appProperties.getPartitioning() != null) {
retVal.setPartitioningEnabled(true);
retVal.setIncludePartitionInSearchHashes(
appProperties.getPartitioning().getPartitioning_include_in_search_hashes());
if (appProperties.getPartitioning().getAllow_references_across_partitions()) {
retVal.setAllowReferencesAcrossPartitions(CrossPartitionReferenceMode.ALLOWED_UNQUALIFIED);
} else {
retVal.setAllowReferencesAcrossPartitions(CrossPartitionReferenceMode.NOT_ALLOWED);
}
}
if (appProperties.getClient_id_strategy() == JpaStorageSettings.ClientIdStrategyEnum.ANY) {
jpaStorageSettings.setResourceServerIdStrategy(JpaStorageSettings.IdStrategyEnum.UUID);
jpaStorageSettings.setResourceClientIdStrategy(appProperties.getClient_id_strategy());
}
//Parallel Batch GET execution settings
jpaStorageSettings.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_size());
jpaStorageSettings.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_max_size());
return retVal;
}
storageSettings(appProperties, jpaStorageSettings);
return jpaStorageSettings;
}
@Primary
@Bean
public HibernatePropertiesProvider jpaStarterDialectProvider(
LocalContainerEntityManagerFactoryBean myEntityManagerFactory) {
return new JpaHibernatePropertiesProvider(myEntityManagerFactory);
}
@Bean
public YamlPropertySourceLoader yamlPropertySourceLoader() {
return new YamlPropertySourceLoader();
}
protected StorageSettings storageSettings(AppProperties appProperties, JpaStorageSettings jpaStorageSettings) {
jpaStorageSettings.setAllowContainsSearches(appProperties.getAllow_contains_searches());
jpaStorageSettings.setAllowExternalReferences(appProperties.getAllow_external_references());
jpaStorageSettings.setDefaultSearchParamsCanBeOverridden(
appProperties.getAllow_override_default_search_params());
if (appProperties.getSubscription() != null
&& appProperties.getSubscription().getEmail() != null)
jpaStorageSettings.setEmailFromAddress(
appProperties.getSubscription().getEmail().getFrom());
@Bean
public PartitionSettings partitionSettings(AppProperties appProperties) {
PartitionSettings retVal = new PartitionSettings();
jpaStorageSettings.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
// Partitioning
if (appProperties.getPartitioning() != null) {
retVal.setPartitioningEnabled(true);
retVal.setIncludePartitionInSearchHashes(appProperties.getPartitioning().getPartitioning_include_in_search_hashes());
if(appProperties.getPartitioning().getAllow_references_across_partitions()) {
retVal.setAllowReferencesAcrossPartitions(CrossPartitionReferenceMode.ALLOWED_UNQUALIFIED);
} else {
retVal.setAllowReferencesAcrossPartitions(CrossPartitionReferenceMode.NOT_ALLOWED);
}
}
jpaStorageSettings.setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
jpaStorageSettings.setIndexIdentifierOfType(appProperties.getEnable_index_of_type());
return jpaStorageSettings;
}
return retVal;
}
@Lazy
@Bean
public IBinaryStorageSvc binaryStorageSvc(AppProperties appProperties) {
DatabaseBlobBinaryStorageSvcImpl binaryStorageSvc = new DatabaseBlobBinaryStorageSvcImpl();
if (appProperties.getMax_binary_size() != null) {
binaryStorageSvc.setMaximumBinarySize(appProperties.getMax_binary_size());
}
@Primary
@Bean
public HibernatePropertiesProvider jpaStarterDialectProvider(LocalContainerEntityManagerFactoryBean myEntityManagerFactory) {
return new JpaHibernatePropertiesProvider(myEntityManagerFactory);
}
return binaryStorageSvc;
}
@Bean
public IEmailSender emailSender(AppProperties appProperties) {
if (appProperties.getSubscription() != null
&& appProperties.getSubscription().getEmail() != null) {
protected StorageSettings storageSettings(AppProperties appProperties, JpaStorageSettings jpaStorageSettings) {
jpaStorageSettings.setAllowContainsSearches(appProperties.getAllow_contains_searches());
jpaStorageSettings.setAllowExternalReferences(appProperties.getAllow_external_references());
jpaStorageSettings.setDefaultSearchParamsCanBeOverridden(appProperties.getAllow_override_default_search_params());
if(appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null)
jpaStorageSettings.setEmailFromAddress(appProperties.getSubscription().getEmail().getFrom());
return buildEmailSender(appProperties.getSubscription().getEmail());
}
jpaStorageSettings.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
jpaStorageSettings.setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
jpaStorageSettings.setIndexIdentifierOfType(appProperties.getEnable_index_of_type());
return jpaStorageSettings;
}
@Lazy
@Bean
public IBinaryStorageSvc binaryStorageSvc(AppProperties appProperties) {
DatabaseBlobBinaryStorageSvcImpl binaryStorageSvc = new DatabaseBlobBinaryStorageSvcImpl();
if (appProperties.getMax_binary_size() != null) {
binaryStorageSvc.setMaximumBinarySize(appProperties.getMax_binary_size());
}
return binaryStorageSvc;
}
@Bean
public IEmailSender emailSender(AppProperties appProperties) {
if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null) {
return buildEmailSender(appProperties.getSubscription().getEmail());
}
// Return a dummy anonymous function instead of null. Spring does not like null beans.
// TODO Get the signature of ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory
// changed so it does not require an instance of an IEmailSender
return theDetails -> {};
}
// Return a dummy anonymous function instead of null. Spring does not like null beans.
// TODO Get the signature of
// ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory
// changed so it does not require an instance of an IEmailSender
return theDetails -> {};
}
private static IEmailSender buildEmailSender(AppProperties.Subscription.Email email) {
return new EmailSenderImpl(new MailSvc(new MailConfig()
.setSmtpHostname(email.getHost())
.setSmtpPort(email.getPort())
.setSmtpUsername(email.getUsername())
.setSmtpPassword(email.getPassword())
.setSmtpUseStartTLS(email.getStartTlsEnable())));
.setSmtpHostname(email.getHost())
.setSmtpPort(email.getPort())
.setSmtpUsername(email.getUsername())
.setSmtpPassword(email.getPassword())
.setSmtpUseStartTLS(email.getStartTlsEnable())));
}
}

9
src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigDstu2.java
View File

@@ -13,14 +13,11 @@ import org.springframework.context.annotation.Import;
@Configuration
@Conditional(OnDSTU2Condition.class)
@Import({
JpaDstu2Config.class,
StarterJpaConfig.class
})
@Import({JpaDstu2Config.class, StarterJpaConfig.class})
public class FhirServerConfigDstu2 {
@Bean
public ITermLoaderSvc termLoaderService(ITermDeferredStorageSvc theDeferredStorageSvc, ITermCodeSystemStorageSvc theCodeSystemStorageSvc) {
public ITermLoaderSvc termLoaderService(
ITermDeferredStorageSvc theDeferredStorageSvc, ITermCodeSystemStorageSvc theCodeSystemStorageSvc) {
return new TermLoaderSvcImpl(theDeferredStorageSvc, theCodeSystemStorageSvc);
}
}

9
src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigDstu3.java
View File

@@ -9,10 +9,5 @@ import org.springframework.context.annotation.Import;
@Configuration
@Conditional(OnDSTU3Condition.class)
@Import({
JpaDstu3Config.class,
StarterJpaConfig.class,
StarterCrDstu3Config.class,
ElasticsearchConfig.class})
public class FhirServerConfigDstu3 {
}
@Import({JpaDstu3Config.class, StarterJpaConfig.class, StarterCrDstu3Config.class, ElasticsearchConfig.class})
public class FhirServerConfigDstu3 {}

4
src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigR4.java
View File

@@ -4,7 +4,6 @@ import ca.uhn.fhir.jpa.config.r4.JpaR4Config;
import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
import ca.uhn.fhir.jpa.starter.cr.StarterCrR4Config;
import ca.uhn.fhir.jpa.starter.ips.StarterIpsConfig;
import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@@ -18,5 +17,4 @@ import org.springframework.context.annotation.Import;
ElasticsearchConfig.class,
StarterIpsConfig.class
})
public class FhirServerConfigR4 {
}
public class FhirServerConfigR4 {}

10
src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigR4B.java
View File

@@ -9,11 +9,5 @@ import org.springframework.context.annotation.Import;
@Configuration
@Conditional(OnR4BCondition.class)
@Import({
JpaR4BConfig.class,
SubscriptionTopicConfig.class,
StarterJpaConfig.class,
ElasticsearchConfig.class
})
public class FhirServerConfigR4B {
}
@Import({JpaR4BConfig.class, SubscriptionTopicConfig.class, StarterJpaConfig.class, ElasticsearchConfig.class})
public class FhirServerConfigR4B {}

10
src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigR5.java
View File

@@ -9,11 +9,5 @@ import org.springframework.context.annotation.Import;
@Configuration
@Conditional(OnR5Condition.class)
@Import({
StarterJpaConfig.class,
JpaR5Config.class,
SubscriptionTopicConfig.class,
ElasticsearchConfig.class
})
public class FhirServerConfigR5 {
}
@Import({StarterJpaConfig.class, JpaR5Config.class, SubscriptionTopicConfig.class, ElasticsearchConfig.class})
public class FhirServerConfigR5 {}

37
src/main/java/ca/uhn/fhir/jpa/starter/common/FhirTesterConfig.java
View File

@@ -4,11 +4,10 @@ import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.to.FhirTesterMvcConfig;
import ca.uhn.fhir.to.TesterConfig;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
//@formatter:off
// @formatter:off
/**
* This spring config file configures the web testing module. It serves two
* purposes:
@@ -19,7 +18,7 @@ import org.springframework.context.annotation.Import;
*/
@Configuration
@Import(FhirTesterMvcConfig.class)
@Conditional(FhirTesterConfigCondition.class)
// @Conditional(FhirTesterConfigCondition.class)
public class FhirTesterConfig {
/**
@@ -36,22 +35,18 @@ public class FhirTesterConfig {
* deploying your server to a place with a fully qualified domain name,
* you might want to use that instead of using the variable.
*/
@Bean
public TesterConfig testerConfig(AppProperties appProperties) {
TesterConfig retVal = new TesterConfig();
appProperties.getTester().forEach((key, value) -> {
retVal
.addServer()
.withId(key)
.withFhirVersion(value.getFhir_version())
.withBaseUrl(value.getServer_address())
.withName(value.getName());
retVal.setRefuseToFetchThirdPartyUrls(
value.getRefuse_to_fetch_third_party_urls());
});
return retVal;
}
@Bean
public TesterConfig testerConfig(AppProperties appProperties) {
TesterConfig retVal = new TesterConfig();
appProperties.getTester().forEach((key, value) -> {
retVal.addServer()
.withId(key)
.withFhirVersion(value.getFhir_version())
.withBaseUrl(value.getServer_address())
.withName(value.getName());
retVal.setRefuseToFetchThirdPartyUrls(value.getRefuse_to_fetch_third_party_urls());
});
return retVal;
}
}
//@formatter:on
// @formatter:on

5
src/main/java/ca/uhn/fhir/jpa/starter/common/FhirTesterConfigCondition.java
View File

@@ -9,8 +9,9 @@ import org.springframework.core.type.AnnotatedTypeMetadata;
public class FhirTesterConfigCondition implements Condition {
@Override
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
var properties = EnvironmentHelper.getPropertiesStartingWith((ConfigurableEnvironment) conditionContext.getEnvironment(), "hapi.fhir.tester");
var properties = EnvironmentHelper.getPropertiesStartingWith(
(ConfigurableEnvironment) conditionContext.getEnvironment(), "hapi.fhir.tester");
return !properties.isEmpty();
}
}

133
src/main/java/ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.java
View File

@@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.starter.common;
import ca.uhn.fhir.batch2.coordinator.JobDefinitionRegistry;
import ca.uhn.fhir.batch2.jobs.export.BulkDataExportProvider;
import ca.uhn.fhir.batch2.jobs.imprt.BulkDataImportProvider;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexProvider;
@@ -9,7 +10,6 @@ import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.jpa.api.IDaoRegistry;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
@@ -18,7 +18,6 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.binary.interceptor.BinaryStorageInterceptor;
import ca.uhn.fhir.jpa.binary.provider.BinaryAccessProvider;
import ca.uhn.fhir.batch2.jobs.export.BulkDataExportProvider;
import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
import ca.uhn.fhir.jpa.config.util.ResourceCountCacheUtil;
import ca.uhn.fhir.jpa.config.util.ValidationSupportConfigUtil;
@@ -34,8 +33,8 @@ import ca.uhn.fhir.jpa.ips.provider.IpsOperationProvider;
import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
import ca.uhn.fhir.jpa.packages.PackageInstallationSpec;
import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
import ca.uhn.fhir.jpa.provider.*;
import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
import ca.uhn.fhir.jpa.provider.*;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
@@ -43,8 +42,8 @@ import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.jpa.starter.annotations.OnCorsPresent;
import ca.uhn.fhir.jpa.starter.annotations.OnImplementationGuidesPresent;
import ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory;
import ca.uhn.fhir.jpa.starter.util.EnvironmentHelper;
import ca.uhn.fhir.jpa.starter.ig.IImplementationGuideOperationProvider;
import ca.uhn.fhir.jpa.starter.util.EnvironmentHelper;
import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
@@ -53,9 +52,9 @@ import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.narrative2.NullNarrativeGenerator;
import ca.uhn.fhir.rest.api.IResourceSupportedSvc;
import ca.uhn.fhir.rest.openapi.OpenApiInterceptor;
import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
import ca.uhn.fhir.rest.server.*;
import ca.uhn.fhir.rest.server.interceptor.*;
import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import ca.uhn.fhir.rest.server.tenant.UrlBaseTenantIdentificationStrategy;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
@@ -75,18 +74,16 @@ import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.web.cors.CorsConfiguration;
import java.util.*;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import java.util.*;
import static ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory.ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR;
@Configuration
//allow users to configure custom packages to scan for additional beans
@ComponentScan(basePackages = { "${hapi.fhir.custom-bean-packages:}" })
@Import(
ThreadPoolFactoryConfig.class
)
// allow users to configure custom packages to scan for additional beans
@ComponentScan(basePackages = {"${hapi.fhir.custom-bean-packages:}"})
@Import(ThreadPoolFactoryConfig.class)
public class StarterJpaConfig {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(StarterJpaConfig.class);
@@ -107,12 +104,9 @@ public class StarterJpaConfig {
return ValidationSupportConfigUtil.newCachingValidationSupport(theJpaValidationSupportChain);
}
@Autowired
private ConfigurableEnvironment configurableEnvironment;
/**
* Customize the default/max page sizes for search results. You can set these however
* you want, although very large page sizes will require a lot of RAM.
@@ -125,7 +119,6 @@ public class StarterJpaConfig {
return pagingProvider;
}
@Bean
public IResourceSupportedSvc resourceSupportedSvc(IDaoRegistry theDaoRegistry) {
return new DaoRegistryResourceSupportedSvc(theDaoRegistry);
@@ -138,8 +131,12 @@ public class StarterJpaConfig {
@Primary
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory(DataSource myDataSource, ConfigurableListableBeanFactory myConfigurableListableBeanFactory, FhirContext theFhirContext) {
LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext);
public LocalContainerEntityManagerFactoryBean entityManagerFactory(
DataSource myDataSource,
ConfigurableListableBeanFactory myConfigurableListableBeanFactory,
FhirContext theFhirContext) {
LocalContainerEntityManagerFactoryBean retVal =
HapiEntityManagerFactoryUtil.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext);
retVal.setPersistenceUnitName("HAPI_PU");
try {
@@ -147,7 +144,8 @@ public class StarterJpaConfig {
} catch (Exception e) {
throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
}
retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment, myConfigurableListableBeanFactory));
retVal.setJpaProperties(
EnvironmentHelper.getHibernateProperties(configurableEnvironment, myConfigurableListableBeanFactory));
return retVal;
}
@@ -164,10 +162,10 @@ public class StarterJpaConfig {
return new HSearchSortHelperImpl(mySearchParamRegistry);
}
@Bean
@ConditionalOnProperty(prefix = "hapi.fhir", name = ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR, havingValue = "true")
public RepositoryValidatingInterceptor repositoryValidatingInterceptor(IRepositoryValidationInterceptorFactory factory) {
public RepositoryValidatingInterceptor repositoryValidatingInterceptor(
IRepositoryValidationInterceptorFactory factory) {
return factory.buildUsingStoredStructureDefinitions();
}
@@ -189,8 +187,11 @@ public class StarterJpaConfig {
@Bean("packageInstaller")
@Primary
@Conditional(OnImplementationGuidesPresent.class)
public IPackageInstallerSvc packageInstaller(AppProperties appProperties, JobDefinition<ReindexJobParameters> reindexJobParametersJobDefinition, JobDefinitionRegistry jobDefinitionRegistry, IPackageInstallerSvc packageInstallerSvc)
{
public IPackageInstallerSvc packageInstaller(
AppProperties appProperties,
JobDefinition<ReindexJobParameters> reindexJobParametersJobDefinition,
JobDefinitionRegistry jobDefinitionRegistry,
IPackageInstallerSvc packageInstallerSvc) {
jobDefinitionRegistry.addJobDefinitionIfNotRegistered(reindexJobParametersJobDefinition);
if (appProperties.getImplementationGuides() != null) {
@@ -199,7 +200,8 @@ public class StarterJpaConfig {
PackageInstallationSpec packageInstallationSpec = guidesEntry.getValue();
if (appProperties.getInstall_transitive_ig_dependencies()) {
packageInstallationSpec.addDependencyExclude("hl7.fhir.r2.core")
packageInstallationSpec
.addDependencyExclude("hl7.fhir.r2.core")
.addDependencyExclude("hl7.fhir.r3.core")
.addDependencyExclude("hl7.fhir.r4.core")
.addDependencyExclude("hl7.fhir.r5.core");
@@ -238,11 +240,40 @@ public class StarterJpaConfig {
// Create the interceptor and register it
return new CorsInterceptor(config);
}
@Bean
public RestfulServer restfulServer(IFhirSystemDao<?, ?> fhirSystemDao, AppProperties appProperties, DaoRegistry daoRegistry, Optional<MdmProviderLoader> mdmProviderProvider, IJpaSystemProvider jpaSystemProvider, ResourceProviderFactory resourceProviderFactory, JpaStorageSettings jpaStorageSettings, ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport, DatabaseBackedPagingProvider databaseBackedPagingProvider, LoggingInterceptor loggingInterceptor, Optional<TerminologyUploaderProvider> terminologyUploaderProvider, Optional<SubscriptionTriggeringProvider> subscriptionTriggeringProvider, Optional<CorsInterceptor> corsInterceptor, IInterceptorBroadcaster interceptorBroadcaster, Optional<BinaryAccessProvider> binaryAccessProvider, BinaryStorageInterceptor binaryStorageInterceptor, IValidatorModule validatorModule, Optional<GraphQLProvider> graphQLProvider, BulkDataExportProvider bulkDataExportProvider, BulkDataImportProvider bulkDataImportProvider, ValueSetOperationProvider theValueSetOperationProvider, ReindexProvider reindexProvider, PartitionManagementProvider partitionManagementProvider, Optional<RepositoryValidatingInterceptor> repositoryValidatingInterceptor, IPackageInstallerSvc packageInstallerSvc, ThreadSafeResourceDeleterSvc theThreadSafeResourceDeleterSvc, ApplicationContext appContext, Optional<IpsOperationProvider> theIpsOperationProvider, Optional<IImplementationGuideOperationProvider> implementationGuideOperationProvider) {
public RestfulServer restfulServer(
IFhirSystemDao<?, ?> fhirSystemDao,
AppProperties appProperties,
DaoRegistry daoRegistry,
Optional<MdmProviderLoader> mdmProviderProvider,
IJpaSystemProvider jpaSystemProvider,
ResourceProviderFactory resourceProviderFactory,
JpaStorageSettings jpaStorageSettings,
ISearchParamRegistry searchParamRegistry,
IValidationSupport theValidationSupport,
DatabaseBackedPagingProvider databaseBackedPagingProvider,
LoggingInterceptor loggingInterceptor,
Optional<TerminologyUploaderProvider> terminologyUploaderProvider,
Optional<SubscriptionTriggeringProvider> subscriptionTriggeringProvider,
Optional<CorsInterceptor> corsInterceptor,
IInterceptorBroadcaster interceptorBroadcaster,
Optional<BinaryAccessProvider> binaryAccessProvider,
BinaryStorageInterceptor binaryStorageInterceptor,
IValidatorModule validatorModule,
Optional<GraphQLProvider> graphQLProvider,
BulkDataExportProvider bulkDataExportProvider,
BulkDataImportProvider bulkDataImportProvider,
ValueSetOperationProvider theValueSetOperationProvider,
ReindexProvider reindexProvider,
PartitionManagementProvider partitionManagementProvider,
Optional<RepositoryValidatingInterceptor> repositoryValidatingInterceptor,
IPackageInstallerSvc packageInstallerSvc,
ThreadSafeResourceDeleterSvc theThreadSafeResourceDeleterSvc,
ApplicationContext appContext,
Optional<IpsOperationProvider> theIpsOperationProvider,
Optional<IImplementationGuideOperationProvider> implementationGuideOperationProvider) {
RestfulServer fhirServer = new RestfulServer(fhirSystemDao.getContext());
List<String> supportedResourceTypes = appProperties.getSupported_resource_types();
@@ -264,7 +295,8 @@ public class StarterJpaConfig {
fhirServer.registerProviders(resourceProviderFactory.createProviders());
fhirServer.registerProvider(jpaSystemProvider);
fhirServer.setServerConformanceProvider(calculateConformanceProvider(fhirSystemDao, fhirServer, jpaStorageSettings, searchParamRegistry, theValidationSupport));
fhirServer.setServerConformanceProvider(calculateConformanceProvider(
fhirSystemDao, fhirServer, jpaStorageSettings, searchParamRegistry, theValidationSupport));
/*
* ETag Support
@@ -272,7 +304,6 @@ public class StarterJpaConfig {
if (!appProperties.getEtag_support_enabled()) fhirServer.setETagSupport(ETagSupportEnum.DISABLED);
/*
* Default to JSON and pretty printing
*/
@@ -318,7 +349,8 @@ public class StarterJpaConfig {
fhirServer.setServerAddressStrategy(new HardcodedServerAddressStrategy(serverAddress));
} else if (appProperties.getUse_apache_address_strategy()) {
boolean useHttps = appProperties.getUse_apache_address_strategy_https();
fhirServer.setServerAddressStrategy(useHttps ? ApacheProxyAddressStrategy.forHttps() : ApacheProxyAddressStrategy.forHttp());
fhirServer.setServerAddressStrategy(
useHttps ? ApacheProxyAddressStrategy.forHttps() : ApacheProxyAddressStrategy.forHttp());
} else {
fhirServer.setServerAddressStrategy(new IncomingRequestAddressStrategy());
}
@@ -330,7 +362,11 @@ public class StarterJpaConfig {
* so it is a potential security vulnerability. Consider using an AuthorizationInterceptor
* with this feature.
*/
if (fhirSystemDao.getContext().getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) { // <-- ENABLED RIGHT NOW
if (fhirSystemDao
.getContext()
.getVersion()
.getVersion()
.isEqualOrNewerThan(FhirVersionEnum.DSTU3)) { // <-- ENABLED RIGHT NOW
fhirServer.registerProvider(terminologyUploaderProvider.get());
}
@@ -348,7 +384,8 @@ public class StarterJpaConfig {
}
if (appProperties.getAllow_cascading_deletes()) {
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(fhirSystemDao.getContext(), daoRegistry, interceptorBroadcaster, theThreadSafeResourceDeleterSvc);
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(
fhirSystemDao.getContext(), daoRegistry, interceptorBroadcaster, theThreadSafeResourceDeleterSvc);
fhirServer.registerInterceptor(cascadingDeleteInterceptor);
}
@@ -391,16 +428,15 @@ public class StarterJpaConfig {
fhirServer.registerProvider(bulkDataExportProvider);
}
//Bulk Import
// Bulk Import
if (appProperties.getBulk_import_enabled()) {
fhirServer.registerProvider(bulkDataImportProvider);
}
// valueSet Operations i.e $expand
fhirServer.registerProvider(theValueSetOperationProvider);
//reindex Provider $reindex
// reindex Provider $reindex
fhirServer.registerProvider(reindexProvider);
// Partitioning
@@ -414,8 +450,7 @@ public class StarterJpaConfig {
// register custom interceptors
registerCustomInterceptors(fhirServer, appContext, appProperties.getCustomInterceptorClasses());
//register the IPS Provider
// register the IPS Provider
if (!theIpsOperationProvider.isEmpty()) {
fhirServer.registerProvider(theIpsOperationProvider.get());
}
@@ -426,8 +461,9 @@ public class StarterJpaConfig {
/**
* check the properties for custom interceptor classes and registers them.
*/
@SuppressWarnings({ "unchecked", "rawtypes" })
private void registerCustomInterceptors(RestfulServer fhirServer, ApplicationContext theAppContext, List<String> customInterceptorClasses) {
@SuppressWarnings({"unchecked", "rawtypes"})
private void registerCustomInterceptors(
RestfulServer fhirServer, ApplicationContext theAppContext, List<String> customInterceptorClasses) {
if (customInterceptorClasses == null) {
return;
@@ -461,30 +497,40 @@ public class StarterJpaConfig {
}
}
public static IServerConformanceProvider<?> calculateConformanceProvider(IFhirSystemDao fhirSystemDao, RestfulServer fhirServer, JpaStorageSettings jpaStorageSettings, ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport) {
public static IServerConformanceProvider<?> calculateConformanceProvider(
IFhirSystemDao fhirSystemDao,
RestfulServer fhirServer,
JpaStorageSettings jpaStorageSettings,
ISearchParamRegistry searchParamRegistry,
IValidationSupport theValidationSupport) {
FhirVersionEnum fhirVersion = fhirSystemDao.getContext().getVersion().getVersion();
if (fhirVersion == FhirVersionEnum.DSTU2) {
JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(fhirServer, fhirSystemDao, jpaStorageSettings);
JpaConformanceProviderDstu2 confProvider =
new JpaConformanceProviderDstu2(fhirServer, fhirSystemDao, jpaStorageSettings);
confProvider.setImplementationDescription("HAPI FHIR DSTU2 Server");
return confProvider;
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry);
JpaConformanceProviderDstu3 confProvider =
new JpaConformanceProviderDstu3(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry);
confProvider.setImplementationDescription("HAPI FHIR DSTU3 Server");
return confProvider;
} else if (fhirVersion == FhirVersionEnum.R4) {
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(
fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
confProvider.setImplementationDescription("HAPI FHIR R4 Server");
return confProvider;
} else if (fhirVersion == FhirVersionEnum.R4B) {
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(
fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
confProvider.setImplementationDescription("HAPI FHIR R4B Server");
return confProvider;
} else if (fhirVersion == FhirVersionEnum.R5) {
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(
fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
confProvider.setImplementationDescription("HAPI FHIR R5 Server");
return confProvider;
} else {
@@ -492,4 +538,3 @@ public class StarterJpaConfig {
}
}
}

1
src/main/java/ca/uhn/fhir/jpa/starter/common/validation/IRepositoryValidationInterceptorFactory.java
View File

@@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingInterceptor;
public interface IRepositoryValidationInterceptorFactory {
String ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR = "enable_repository_validating_interceptor";
RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions();
RepositoryValidatingInterceptor build();

27
src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryDstu3.java
View File

@@ -37,24 +37,28 @@ public class RepositoryValidationInterceptorFactoryDstu3 implements IRepositoryV
private final RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder;
private final IFhirResourceDao structureDefinitionResourceProvider;
public RepositoryValidationInterceptorFactoryDstu3(RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
public RepositoryValidationInterceptorFactoryDstu3(
RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
this.repositoryValidatingRuleBuilder = repositoryValidatingRuleBuilder;
this.fhirContext = daoRegistry.getSystemDao().getContext();
structureDefinitionResourceProvider = daoRegistry.getResourceDao("StructureDefinition");
}
public RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions() {
IBundleProvider results = structureDefinitionResourceProvider.search(new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
Map<String, List<StructureDefinition>> structureDefinitions = results.getResources(0, results.size())
.stream()
.map(StructureDefinition.class::cast)
.collect(Collectors.groupingBy(StructureDefinition::getType));
IBundleProvider results = structureDefinitionResourceProvider.search(
new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
Map<String, List<StructureDefinition>> structureDefinitions = results.getResources(0, results.size()).stream()
.map(StructureDefinition.class::cast)
.collect(Collectors.groupingBy(StructureDefinition::getType));
structureDefinitions.forEach((key, value) -> {
String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
repositoryValidatingRuleBuilder.forResourcesOfType(key).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
repositoryValidatingRuleBuilder
.forResourcesOfType(key)
.requireAtLeastOneProfileOf(urls)
.and()
.requireValidationToDeclaredProfiles();
});
List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
@@ -65,11 +69,14 @@ public class RepositoryValidationInterceptorFactoryDstu3 implements IRepositoryV
// Customize the ruleBuilder here to have the rules you want! We will give a simple example
// of enabling validation for all Patient resources
repositoryValidatingRuleBuilder.forResourcesOfType("Patient").requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient").and().requireValidationToDeclaredProfiles();
repositoryValidatingRuleBuilder
.forResourcesOfType("Patient")
.requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient")
.and()
.requireValidationToDeclaredProfiles();
// Do not customize below this line
List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
return new RepositoryValidatingInterceptor(fhirContext, rules);
}
}

27
src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryR4.java
View File

@@ -37,25 +37,29 @@ public class RepositoryValidationInterceptorFactoryR4 implements IRepositoryVali
private final RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder;
private final IFhirResourceDao structureDefinitionResourceProvider;
public RepositoryValidationInterceptorFactoryR4(RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
public RepositoryValidationInterceptorFactoryR4(
RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
this.repositoryValidatingRuleBuilder = repositoryValidatingRuleBuilder;
this.fhirContext = daoRegistry.getSystemDao().getContext();
structureDefinitionResourceProvider = daoRegistry.getResourceDao("StructureDefinition");
}
@Override
public RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions() {
IBundleProvider results = structureDefinitionResourceProvider.search(new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size())
.stream()
.map(StructureDefinition.class::cast)
.collect(Collectors.groupingBy(StructureDefinition::getType));
IBundleProvider results = structureDefinitionResourceProvider.search(
new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size()).stream()
.map(StructureDefinition.class::cast)
.collect(Collectors.groupingBy(StructureDefinition::getType));
structureDefintions.forEach((key, value) -> {
String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
repositoryValidatingRuleBuilder.forResourcesOfType(key).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
repositoryValidatingRuleBuilder
.forResourcesOfType(key)
.requireAtLeastOneProfileOf(urls)
.and()
.requireValidationToDeclaredProfiles();
});
List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
@@ -67,11 +71,14 @@ public class RepositoryValidationInterceptorFactoryR4 implements IRepositoryVali
// Customize the ruleBuilder here to have the rules you want! We will give a simple example
// of enabling validation for all Patient resources
repositoryValidatingRuleBuilder.forResourcesOfType("Patient").requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient").and().requireValidationToDeclaredProfiles();
repositoryValidatingRuleBuilder
.forResourcesOfType("Patient")
.requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient")
.and()
.requireValidationToDeclaredProfiles();
// Do not customize below this line
List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
return new RepositoryValidatingInterceptor(fhirContext, rules);
}
}

27
src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryR4B.java
View File

@@ -37,25 +37,29 @@ public class RepositoryValidationInterceptorFactoryR4B implements IRepositoryVal
private final RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder;
private final IFhirResourceDao structureDefinitionResourceProvider;
public RepositoryValidationInterceptorFactoryR4B(RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
public RepositoryValidationInterceptorFactoryR4B(
RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
this.repositoryValidatingRuleBuilder = repositoryValidatingRuleBuilder;
this.fhirContext = daoRegistry.getSystemDao().getContext();
structureDefinitionResourceProvider = daoRegistry.getResourceDao("StructureDefinition");
}
@Override
public RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions() {
IBundleProvider results = structureDefinitionResourceProvider.search(new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size())
.stream()
.map(StructureDefinition.class::cast)
.collect(Collectors.groupingBy(StructureDefinition::getType));
IBundleProvider results = structureDefinitionResourceProvider.search(
new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size()).stream()
.map(StructureDefinition.class::cast)
.collect(Collectors.groupingBy(StructureDefinition::getType));
structureDefintions.forEach((key, value) -> {
String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
repositoryValidatingRuleBuilder.forResourcesOfType(key).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
repositoryValidatingRuleBuilder
.forResourcesOfType(key)
.requireAtLeastOneProfileOf(urls)
.and()
.requireValidationToDeclaredProfiles();
});
List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
@@ -67,11 +71,14 @@ public class RepositoryValidationInterceptorFactoryR4B implements IRepositoryVal
// Customize the ruleBuilder here to have the rules you want! We will give a simple example
// of enabling validation for all Patient resources
repositoryValidatingRuleBuilder.forResourcesOfType("Patient").requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient").and().requireValidationToDeclaredProfiles();
repositoryValidatingRuleBuilder
.forResourcesOfType("Patient")
.requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient")
.and()
.requireValidationToDeclaredProfiles();
// Do not customize below this line
List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
return new RepositoryValidatingInterceptor(fhirContext, rules);
}
}

27
src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryR5.java
View File

@@ -37,24 +37,28 @@ public class RepositoryValidationInterceptorFactoryR5 implements IRepositoryVali
private final RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder;
private final IFhirResourceDao structureDefinitionResourceProvider;
public RepositoryValidationInterceptorFactoryR5(RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
public RepositoryValidationInterceptorFactoryR5(
RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
this.repositoryValidatingRuleBuilder = repositoryValidatingRuleBuilder;
this.fhirContext = daoRegistry.getSystemDao().getContext();
structureDefinitionResourceProvider = daoRegistry.getResourceDao("StructureDefinition");
}
public RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions() {
IBundleProvider results = structureDefinitionResourceProvider.search(new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size())
.stream()
.map(StructureDefinition.class::cast)
.collect(Collectors.groupingBy(StructureDefinition::getType));
IBundleProvider results = structureDefinitionResourceProvider.search(
new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size()).stream()
.map(StructureDefinition.class::cast)
.collect(Collectors.groupingBy(StructureDefinition::getType));
structureDefintions.forEach((key, value) -> {
String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
repositoryValidatingRuleBuilder.forResourcesOfType(key).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
repositoryValidatingRuleBuilder
.forResourcesOfType(key)
.requireAtLeastOneProfileOf(urls)
.and()
.requireValidationToDeclaredProfiles();
});
List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
@@ -65,11 +69,14 @@ public class RepositoryValidationInterceptorFactoryR5 implements IRepositoryVali
// Customize the ruleBuilder here to have the rules you want! We will give a simple example
// of enabling validation for all Patient resources
repositoryValidatingRuleBuilder.forResourcesOfType("Patient").requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient").and().requireValidationToDeclaredProfiles();
repositoryValidatingRuleBuilder
.forResourcesOfType("Patient")
.requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient")
.and()
.requireValidationToDeclaredProfiles();
// Do not customize below this line
List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
return new RepositoryValidatingInterceptor(fhirContext, rules);
}
}

10
src/main/java/ca/uhn/fhir/jpa/starter/cr/CrConfigCondition.java
View File

@@ -6,9 +6,9 @@ import org.springframework.core.type.AnnotatedTypeMetadata;
public class CrConfigCondition implements Condition {
@Override
public boolean matches(ConditionContext theConditionContext, AnnotatedTypeMetadata theAnnotatedTypeMetadata) {
String property = theConditionContext.getEnvironment().getProperty("hapi.fhir.cr_enabled");
return Boolean.parseBoolean(property);
}
@Override
public boolean matches(ConditionContext theConditionContext, AnnotatedTypeMetadata theAnnotatedTypeMetadata) {
String property = theConditionContext.getEnvironment().getProperty("hapi.fhir.cr.enabled");
return Boolean.parseBoolean(property);
}
}

264
src/main/java/ca/uhn/fhir/jpa/starter/cr/CrProperties.java Normal file
View File

@@ -0,0 +1,264 @@
package ca.uhn.fhir.jpa.starter.cr;
import org.cqframework.cql.cql2elm.CqlCompilerException;
import org.cqframework.cql.cql2elm.CqlTranslator;
import org.cqframework.cql.cql2elm.LibraryBuilder;
import org.springframework.boot.context.properties.ConfigurationProperties;
@ConfigurationProperties(prefix = "hapi.fhir.cr")
public class CrProperties {
private Boolean enabled;
// cql settings
private Boolean cql_use_embedded_libraries = true;
private Boolean cql_runtime_debug_logging_enabled = false;
private Boolean cql_runtime_enable_validation = false;
private Boolean cql_runtime_enable_expression_caching = false;
private Boolean cql_compiler_validate_units = true;
private Boolean cql_compiler_verify_only = false;
private String cql_compiler_compatibility_level = "1.5";
private CqlCompilerException.ErrorSeverity cql_compiler_error_level = CqlCompilerException.ErrorSeverity.Info;
private LibraryBuilder.SignatureLevel cql_compiler_signature_level = LibraryBuilder.SignatureLevel.All;
private Boolean cql_compiler_analyze_data_requirements = false;
private Boolean cql_compiler_collapse_data_requirements = false;
private CqlTranslator.Format cql_compiler_translator_format = CqlTranslator.Format.JSON;
private Boolean cql_compiler_enable_date_range_optimization = false;
private Boolean cql_compiler_enable_annotations = false;
private Boolean cql_compiler_enable_locators = false;
private Boolean cql_compiler_enable_results_type = false;
private Boolean cql_compiler_enable_detailed_errors = false;
private Boolean cql_compiler_disable_list_traversal = false;
private Boolean cql_compiler_disable_list_demotion = false;
private Boolean cql_compiler_disable_list_promotion = false;
private Boolean cql_compiler_enable_interval_demotion = false;
private Boolean cql_compiler_enable_interval_promotion = false;
private Boolean cql_compiler_disable_method_invocation = false;
private Boolean cql_compiler_require_from_keyword = false;
private Boolean cql_compiler_disable_default_model_info_load = false;
// Care-gaps Settings
private String caregaps_reporter = "default";
private String caregaps_section_author = "default";
public Boolean getEnabled() {
return enabled;
}
public void setEnabled(Boolean enabled) {
this.enabled = enabled;
}
public boolean isCqlUseEmbeddedLibraries() {
return cql_use_embedded_libraries;
}
public void setCqlUseEmbeddedLibraries(boolean cql_use_embedded_libraries) {
this.cql_use_embedded_libraries = cql_use_embedded_libraries;
}
public boolean isCqlRuntimeDebugLoggingEnabled() {
return cql_runtime_debug_logging_enabled;
}
public void setCqlRuntimeDebugLoggingEnabled(boolean cqlRuntimeDebugLoggingEnabled) {
this.cql_runtime_debug_logging_enabled = cqlRuntimeDebugLoggingEnabled;
}
public boolean isCqlCompilerValidateUnits() {
return cql_compiler_validate_units;
}
public void setCqlCompilerValidateUnits(boolean cqlCompilerValidateUnits) {
this.cql_compiler_validate_units = cqlCompilerValidateUnits;
}
public boolean isCqlCompilerVerifyOnly() {
return cql_compiler_verify_only;
}
public void setCqlCompilerVerifyOnly(boolean cqlCompilerVerifyOnly) {
this.cql_compiler_verify_only = cqlCompilerVerifyOnly;
}
public String getCqlCompilerCompatibilityLevel() {
return cql_compiler_compatibility_level;
}
public void setCqlCompilerCompatibilityLevel(String cqlCompilerCompatibilityLevel) {
this.cql_compiler_compatibility_level = cqlCompilerCompatibilityLevel;
}
public CqlCompilerException.ErrorSeverity getCqlCompilerErrorSeverityLevel() {
return cql_compiler_error_level;
}
public void setCqlCompilerErrorSeverityLevel(CqlCompilerException.ErrorSeverity cqlCompilerErrorSeverityLevel) {
this.cql_compiler_error_level = cqlCompilerErrorSeverityLevel;
}
public LibraryBuilder.SignatureLevel getCqlCompilerSignatureLevel() {
return cql_compiler_signature_level;
}
public void setCqlCompilerSignatureLevel(LibraryBuilder.SignatureLevel cqlCompilerSignatureLevel) {
this.cql_compiler_signature_level = cqlCompilerSignatureLevel;
}
public boolean isCqlCompilerAnalyzeDataRequirements() {
return cql_compiler_analyze_data_requirements;
}
public void setCqlCompilerAnalyzeDataRequirements(boolean cqlCompilerAnalyzeDataRequirements) {
this.cql_compiler_analyze_data_requirements = cqlCompilerAnalyzeDataRequirements;
}
public boolean isCqlCompilerCollapseDataRequirements() {
return cql_compiler_collapse_data_requirements;
}
public void setCqlCompilerCollapseDataRequirements(boolean cqlCompilerCollapseDataRequirements) {
this.cql_compiler_collapse_data_requirements = cqlCompilerCollapseDataRequirements;
}
public boolean isEnableDateRangeOptimization() {
return cql_compiler_enable_date_range_optimization;
}
public void setEnableDateRangeOptimization(boolean enableDateRangeOptimization) {
this.cql_compiler_enable_date_range_optimization = enableDateRangeOptimization;
}
public boolean isEnableAnnotations() {
return cql_compiler_enable_annotations;
}
public void setEnableAnnotations(boolean enableAnnotations) {
this.cql_compiler_enable_annotations = enableAnnotations;
}
public boolean isEnableLocators() {
return cql_compiler_enable_locators;
}
public void setEnableLocators(boolean enableLocators) {
this.cql_compiler_enable_locators = enableLocators;
}
public boolean isEnableResultsType() {
return cql_compiler_enable_results_type;
}
public void setEnableResultsType(boolean enableResultsType) {
this.cql_compiler_enable_results_type = enableResultsType;
}
public boolean isEnableDetailedErrors() {
return cql_compiler_enable_detailed_errors;
}
public void setEnableDetailedErrors(boolean enableDetailedErrors) {
this.cql_compiler_enable_detailed_errors = enableDetailedErrors;
}
public boolean isDisableListTraversal() {
return cql_compiler_disable_list_traversal;
}
public void setDisableListTraversal(boolean disableListTraversal) {
this.cql_compiler_disable_list_traversal = disableListTraversal;
}
public boolean isDisableListDemotion() {
return cql_compiler_disable_list_demotion;
}
public void setDisableListDemotion(boolean disableListDemotion) {
this.cql_compiler_disable_list_demotion = disableListDemotion;
}
public boolean isDisableListPromotion() {
return cql_compiler_disable_list_promotion;
}
public void setDisableListPromotion(boolean disableListPromotion) {
this.cql_compiler_disable_list_promotion = disableListPromotion;
}
public boolean isEnableIntervalPromotion() {
return cql_compiler_enable_interval_promotion;
}
public void setEnableIntervalPromotion(boolean enableIntervalPromotion) {
this.cql_compiler_enable_interval_promotion = enableIntervalPromotion;
}
public boolean isEnableIntervalDemotion() {
return cql_compiler_enable_interval_demotion;
}
public void setEnableIntervalDemotion(boolean enableIntervalDemotion) {
this.cql_compiler_enable_interval_demotion = enableIntervalDemotion;
}
public boolean isDisableMethodInvocation() {
return cql_compiler_disable_method_invocation;
}
public void setDisableMethodInvocation(boolean disableMethodInvocation) {
this.cql_compiler_disable_method_invocation = disableMethodInvocation;
}
public boolean isRequireFromKeyword() {
return cql_compiler_require_from_keyword;
}
public void setRequireFromKeyword(boolean requireFromKeyword) {
this.cql_compiler_require_from_keyword = requireFromKeyword;
}
public boolean isDisableDefaultModelInfoLoad() {
return cql_compiler_disable_default_model_info_load;
}
public void setDisableDefaultModelInfoLoad(boolean disableDefaultModelInfoLoad) {
this.cql_compiler_disable_default_model_info_load = disableDefaultModelInfoLoad;
}
public boolean isCqlRuntimeEnableExpressionCaching() {
return cql_runtime_enable_expression_caching;
}
public void setCqlRuntimeEnableExpressionCaching(boolean cqlRuntimeEnableExpressionCaching) {
this.cql_runtime_enable_expression_caching = cqlRuntimeEnableExpressionCaching;
}
public boolean isCqlRuntimeEnableValidation() {
return cql_runtime_enable_validation;
}
public void setCqlRuntimeEnableValidation(boolean cqlRuntimeEnableValidation) {
this.cql_runtime_enable_validation = cqlRuntimeEnableValidation;
}
public CqlTranslator.Format getCqlTranslatorFormat() {
return cql_compiler_translator_format;
}
public void setCqlTranslatorFormat(CqlTranslator.Format cqlTranslatorFormat) {
this.cql_compiler_translator_format = cqlTranslatorFormat;
}
public String getCareGapsReporter() {
return caregaps_reporter;
}
public String getCareGapsSectionAuthor() {
return caregaps_section_author;
}
public void setCareGapsSectionAuthor(String theCareGapsSectionAuthor) {
this.caregaps_section_author = theCareGapsSectionAuthor;
}
public void setCareGapsReporter(String theCareGapsReporter) {
this.caregaps_reporter = theCareGapsReporter;
}
}

47
src/main/java/ca/uhn/fhir/jpa/starter/cr/PostInitProviderRegisterer.java Normal file
View File

@@ -0,0 +1,47 @@
package ca.uhn.fhir.jpa.starter.cr;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.provider.IResourceProviderFactoryObserver;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import java.util.function.Supplier;
public class PostInitProviderRegisterer {
public PostInitProviderRegisterer(RestfulServer restfulServer, ResourceProviderFactory resourceProviderFactory) {
resourceProviderFactory.attach(new Observer(restfulServer));
}
private class Observer implements IResourceProviderFactoryObserver {
private RestfulServer restfulServer;
public Observer(RestfulServer restfulServer) {
this.restfulServer = restfulServer;
}
public void update(Supplier<Object> theSupplier) {
if (theSupplier == null) {
return;
}
var provider = theSupplier.get();
if (provider == null) {
return;
}
this.restfulServer.registerProvider(provider);
}
public void remove(Supplier<Object> theSupplier) {
if (theSupplier == null) {
return;
}
var provider = theSupplier.get();
if (provider == null) {
return;
}
this.restfulServer.unregisterProvider(provider);
}
}
}

190
src/main/java/ca/uhn/fhir/jpa/starter/cr/StarterCrDstu3Config.java
View File

@@ -1,13 +1,195 @@
package ca.uhn.fhir.jpa.starter.cr;
import ca.uhn.fhir.cr.common.CodeCacheResourceChangeListener;
import ca.uhn.fhir.cr.common.ElmCacheResourceChangeListener;
import ca.uhn.fhir.cr.config.dstu3.ApplyOperationConfig;
import ca.uhn.fhir.cr.config.dstu3.CrDstu3Config;
import ca.uhn.fhir.cr.config.dstu3.ExtractOperationConfig;
import ca.uhn.fhir.cr.config.dstu3.PackageOperationConfig;
import ca.uhn.fhir.cr.config.dstu3.PopulateOperationConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryInterceptor;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition;
import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import org.cqframework.cql.cql2elm.CqlCompilerOptions;
import org.cqframework.cql.cql2elm.model.CompiledLibrary;
import org.cqframework.cql.cql2elm.model.Model;
import org.hl7.cql.model.ModelIdentifier;
import org.hl7.elm.r1.VersionedIdentifier;
import org.opencds.cqf.cql.engine.execution.CqlEngine;
import org.opencds.cqf.cql.engine.runtime.Code;
import org.opencds.cqf.fhir.cql.EvaluationSettings;
import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
import org.opencds.cqf.fhir.utility.ValidationProfile;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.context.annotation.*;
import java.util.EnumSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
@Configuration
@Conditional({OnDSTU3Condition.class, CrConfigCondition.class})
@Import({CrDstu3Config.class})
@Import({
// BaseCrConfig.class,
CrDstu3Config.class,
ApplyOperationConfig.class,
ExtractOperationConfig.class,
PackageOperationConfig.class,
PopulateOperationConfig.class
})
public class StarterCrDstu3Config {
private static final Logger ourLogger = LoggerFactory.getLogger(StarterCrDstu3Config.class);
@Bean
MeasureEvaluationOptions measureEvaluationOptions(
EvaluationSettings theEvaluationSettings, Map<String, ValidationProfile> theValidationProfiles) {
MeasureEvaluationOptions measureEvalOptions = new MeasureEvaluationOptions();
measureEvalOptions.setEvaluationSettings(theEvaluationSettings);
if (measureEvalOptions.isValidationEnabled()) {
measureEvalOptions.setValidationProfiles(theValidationProfiles);
}
return measureEvalOptions;
}
@Bean
public EvaluationSettings evaluationSettings(
CrProperties theCrProperties,
Map<VersionedIdentifier, CompiledLibrary> theGlobalLibraryCache,
Map<ModelIdentifier, Model> theGlobalModelCache,
Map<String, List<Code>> theGlobalValueSetCache) {
var evaluationSettings = EvaluationSettings.getDefault();
var cqlOptions = evaluationSettings.getCqlOptions();
var cqlEngineOptions = cqlOptions.getCqlEngineOptions();
Set<CqlEngine.Options> options = EnumSet.noneOf(CqlEngine.Options.class);
if (theCrProperties.isCqlRuntimeEnableExpressionCaching()) {
options.add(CqlEngine.Options.EnableExpressionCaching);
}
if (theCrProperties.isCqlRuntimeEnableValidation()) {
options.add(CqlEngine.Options.EnableValidation);
}
cqlEngineOptions.setOptions(options);
cqlOptions.setCqlEngineOptions(cqlEngineOptions);
var cqlCompilerOptions = new CqlCompilerOptions();
if (theCrProperties.isEnableDateRangeOptimization()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDateRangeOptimization);
}
if (theCrProperties.isEnableAnnotations()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableAnnotations);
}
if (theCrProperties.isEnableLocators()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableLocators);
}
if (theCrProperties.isEnableResultsType()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableResultTypes);
}
cqlCompilerOptions.setVerifyOnly(theCrProperties.isCqlCompilerVerifyOnly());
if (theCrProperties.isEnableDetailedErrors()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDetailedErrors);
}
cqlCompilerOptions.setErrorLevel(theCrProperties.getCqlCompilerErrorSeverityLevel());
if (theCrProperties.isDisableListTraversal()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListTraversal);
}
if (theCrProperties.isDisableListDemotion()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListDemotion);
}
if (theCrProperties.isDisableListPromotion()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListPromotion);
}
if (theCrProperties.isEnableIntervalDemotion()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalDemotion);
}
if (theCrProperties.isEnableIntervalPromotion()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalPromotion);
}
if (theCrProperties.isDisableMethodInvocation()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableMethodInvocation);
}
if (theCrProperties.isRequireFromKeyword()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.RequireFromKeyword);
}
cqlCompilerOptions.setValidateUnits(theCrProperties.isCqlCompilerValidateUnits());
if (theCrProperties.isDisableDefaultModelInfoLoad()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableDefaultModelInfoLoad);
}
cqlCompilerOptions.setSignatureLevel(theCrProperties.getCqlCompilerSignatureLevel());
cqlCompilerOptions.setCompatibilityLevel(theCrProperties.getCqlCompilerCompatibilityLevel());
cqlCompilerOptions.setAnalyzeDataRequirements(theCrProperties.isCqlCompilerAnalyzeDataRequirements());
cqlCompilerOptions.setCollapseDataRequirements(theCrProperties.isCqlCompilerCollapseDataRequirements());
cqlOptions.setCqlCompilerOptions(cqlCompilerOptions);
evaluationSettings.setLibraryCache(theGlobalLibraryCache);
evaluationSettings.setModelCache(theGlobalModelCache);
evaluationSettings.setValueSetCache(theGlobalValueSetCache);
return evaluationSettings;
}
@Bean
public PostInitProviderRegisterer postInitProviderRegisterer(
RestfulServer theRestfulServer, ResourceProviderFactory theResourceProviderFactory) {
return new PostInitProviderRegisterer(theRestfulServer, theResourceProviderFactory);
}
@Bean
public CrProperties crProperties() {
return new CrProperties();
}
@Bean
public Map<VersionedIdentifier, CompiledLibrary> globalLibraryCache() {
return new ConcurrentHashMap<>();
}
@Bean
public Map<ModelIdentifier, Model> globalModelCache() {
return new ConcurrentHashMap<>();
}
@Bean
public Map<String, List<Code>> globalValueSetCache() {
return new ConcurrentHashMap<>();
}
@Bean
public ElmCacheResourceChangeListener elmCacheResourceChangeListener(
IResourceChangeListenerRegistry theResourceChangeListenerRegistry,
DaoRegistry theDaoRegistry,
EvaluationSettings theEvaluationSettings) {
ElmCacheResourceChangeListener listener =
new ElmCacheResourceChangeListener(theDaoRegistry, theEvaluationSettings.getLibraryCache());
theResourceChangeListenerRegistry.registerResourceResourceChangeListener(
"Library", SearchParameterMap.newSynchronous(), listener, 1000);
return listener;
}
@Bean
public CodeCacheResourceChangeListener codeCacheResourceChangeListener(
IResourceChangeListenerRegistry theResourceChangeListenerRegistry,
EvaluationSettings theEvaluationSettings,
DaoRegistry theDaoRegistry) {
CodeCacheResourceChangeListener listener =
new CodeCacheResourceChangeListener(theDaoRegistry, theEvaluationSettings.getValueSetCache());
// registry
theResourceChangeListenerRegistry.registerResourceResourceChangeListener(
"ValueSet", SearchParameterMap.newSynchronous(), listener, 1000);
return listener;
}
@Bean
public ResourceChangeListenerRegistryInterceptor resourceChangeListenerRegistryInterceptor() {
return new ResourceChangeListenerRegistryInterceptor();
}
}

212
src/main/java/ca/uhn/fhir/jpa/starter/cr/StarterCrR4Config.java
View File

@@ -1,11 +1,221 @@
package ca.uhn.fhir.jpa.starter.cr;
import ca.uhn.fhir.cr.common.CodeCacheResourceChangeListener;
import ca.uhn.fhir.cr.common.CqlThreadFactory;
import ca.uhn.fhir.cr.common.ElmCacheResourceChangeListener;
import ca.uhn.fhir.cr.config.r4.ApplyOperationConfig;
import ca.uhn.fhir.cr.config.r4.CrR4Config;
import ca.uhn.fhir.cr.config.r4.ExtractOperationConfig;
import ca.uhn.fhir.cr.config.r4.PackageOperationConfig;
import ca.uhn.fhir.cr.config.r4.PopulateOperationConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryInterceptor;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import org.cqframework.cql.cql2elm.CqlCompilerOptions;
import org.cqframework.cql.cql2elm.model.CompiledLibrary;
import org.cqframework.cql.cql2elm.model.Model;
import org.hl7.cql.model.ModelIdentifier;
import org.hl7.elm.r1.VersionedIdentifier;
import org.opencds.cqf.cql.engine.execution.CqlEngine;
import org.opencds.cqf.cql.engine.runtime.Code;
import org.opencds.cqf.fhir.cql.EvaluationSettings;
import org.opencds.cqf.fhir.cr.measure.CareGapsProperties;
import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
import org.opencds.cqf.fhir.utility.ValidationProfile;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Primary;
import org.springframework.security.concurrent.DelegatingSecurityContextExecutorService;
import java.util.EnumSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
@Configuration
@Conditional({OnR4Condition.class, CrConfigCondition.class})
@Import({CrR4Config.class})
@Import({
CrR4Config.class,
ApplyOperationConfig.class,
ExtractOperationConfig.class,
PackageOperationConfig.class,
PopulateOperationConfig.class
})
public class StarterCrR4Config {
private static final Logger ourLogger = LoggerFactory.getLogger(StarterCrR4Config.class);
@Primary
@Bean
public ExecutorService cqlExecutor() {
CqlThreadFactory factory = new CqlThreadFactory();
ExecutorService executor = Executors.newFixedThreadPool(2, factory);
executor = new DelegatingSecurityContextExecutorService(executor);
return executor;
}
@Bean
CareGapsProperties careGapsProperties(CrProperties theCrProperties) {
var careGapsProperties = new CareGapsProperties();
careGapsProperties.setThreadedCareGapsEnabled(false);
careGapsProperties.setCareGapsReporter(theCrProperties.getCareGapsReporter());
careGapsProperties.setCareGapsCompositionSectionAuthor(theCrProperties.getCareGapsSectionAuthor());
return careGapsProperties;
}
@Bean
MeasureEvaluationOptions measureEvaluationOptions(
EvaluationSettings theEvaluationSettings, Map<String, ValidationProfile> theValidationProfiles) {
MeasureEvaluationOptions measureEvalOptions = new MeasureEvaluationOptions();
measureEvalOptions.setEvaluationSettings(theEvaluationSettings);
if (measureEvalOptions.isValidationEnabled()) {
measureEvalOptions.setValidationProfiles(theValidationProfiles);
}
return measureEvalOptions;
}
@Bean
public EvaluationSettings evaluationSettings(
CrProperties theCrProperties,
Map<VersionedIdentifier, CompiledLibrary> theGlobalLibraryCache,
Map<ModelIdentifier, Model> theGlobalModelCache,
Map<String, List<Code>> theGlobalValueSetCache) {
var evaluationSettings = EvaluationSettings.getDefault();
var cqlOptions = evaluationSettings.getCqlOptions();
var cqlEngineOptions = cqlOptions.getCqlEngineOptions();
Set<CqlEngine.Options> options = EnumSet.noneOf(CqlEngine.Options.class);
if (theCrProperties.isCqlRuntimeEnableExpressionCaching()) {
options.add(CqlEngine.Options.EnableExpressionCaching);
}
if (theCrProperties.isCqlRuntimeEnableValidation()) {
options.add(CqlEngine.Options.EnableValidation);
}
cqlEngineOptions.setOptions(options);
cqlOptions.setCqlEngineOptions(cqlEngineOptions);
var cqlCompilerOptions = new CqlCompilerOptions();
if (theCrProperties.isEnableDateRangeOptimization()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDateRangeOptimization);
}
if (theCrProperties.isEnableAnnotations()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableAnnotations);
}
if (theCrProperties.isEnableLocators()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableLocators);
}
if (theCrProperties.isEnableResultsType()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableResultTypes);
}
cqlCompilerOptions.setVerifyOnly(theCrProperties.isCqlCompilerVerifyOnly());
if (theCrProperties.isEnableDetailedErrors()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableDetailedErrors);
}
cqlCompilerOptions.setErrorLevel(theCrProperties.getCqlCompilerErrorSeverityLevel());
if (theCrProperties.isDisableListTraversal()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListTraversal);
}
if (theCrProperties.isDisableListDemotion()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListDemotion);
}
if (theCrProperties.isDisableListPromotion()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableListPromotion);
}
if (theCrProperties.isEnableIntervalDemotion()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalDemotion);
}
if (theCrProperties.isEnableIntervalPromotion()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.EnableIntervalPromotion);
}
if (theCrProperties.isDisableMethodInvocation()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableMethodInvocation);
}
if (theCrProperties.isRequireFromKeyword()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.RequireFromKeyword);
}
cqlCompilerOptions.setValidateUnits(theCrProperties.isCqlCompilerValidateUnits());
if (theCrProperties.isDisableDefaultModelInfoLoad()) {
cqlCompilerOptions.setOptions(CqlCompilerOptions.Options.DisableDefaultModelInfoLoad);
}
cqlCompilerOptions.setSignatureLevel(theCrProperties.getCqlCompilerSignatureLevel());
cqlCompilerOptions.setCompatibilityLevel(theCrProperties.getCqlCompilerCompatibilityLevel());
cqlCompilerOptions.setAnalyzeDataRequirements(theCrProperties.isCqlCompilerAnalyzeDataRequirements());
cqlCompilerOptions.setCollapseDataRequirements(theCrProperties.isCqlCompilerCollapseDataRequirements());
cqlOptions.setCqlCompilerOptions(cqlCompilerOptions);
evaluationSettings.setLibraryCache(theGlobalLibraryCache);
evaluationSettings.setModelCache(theGlobalModelCache);
evaluationSettings.setValueSetCache(theGlobalValueSetCache);
return evaluationSettings;
}
@Bean
public PostInitProviderRegisterer postInitProviderRegisterer(
RestfulServer theRestfulServer, ResourceProviderFactory theResourceProviderFactory) {
return new PostInitProviderRegisterer(theRestfulServer, theResourceProviderFactory);
}
@Bean
public CrProperties crProperties() {
return new CrProperties();
}
@Bean
public Map<VersionedIdentifier, CompiledLibrary> globalLibraryCache() {
return new ConcurrentHashMap<>();
}
@Bean
public Map<ModelIdentifier, Model> globalModelCache() {
return new ConcurrentHashMap<>();
}
@Bean
public Map<String, List<Code>> globalValueSetCache() {
return new ConcurrentHashMap<>();
}
@Bean
public ElmCacheResourceChangeListener elmCacheResourceChangeListener(
IResourceChangeListenerRegistry theResourceChangeListenerRegistry,
DaoRegistry theDaoRegistry,
EvaluationSettings theEvaluationSettings) {
ElmCacheResourceChangeListener listener =
new ElmCacheResourceChangeListener(theDaoRegistry, theEvaluationSettings.getLibraryCache());
theResourceChangeListenerRegistry.registerResourceResourceChangeListener(
"Library", SearchParameterMap.newSynchronous(), listener, 1000);
return listener;
}
@Bean
public CodeCacheResourceChangeListener codeCacheResourceChangeListener(
IResourceChangeListenerRegistry theResourceChangeListenerRegistry,
EvaluationSettings theEvaluationSettings,
DaoRegistry theDaoRegistry) {
CodeCacheResourceChangeListener listener =
new CodeCacheResourceChangeListener(theDaoRegistry, theEvaluationSettings.getValueSetCache());
// registry
theResourceChangeListenerRegistry.registerResourceResourceChangeListener(
"ValueSet", SearchParameterMap.newSynchronous(), listener, 1000);
return listener;
}
@Bean
public ResourceChangeListenerRegistryInterceptor resourceChangeListenerRegistryInterceptor() {
return new ResourceChangeListenerRegistryInterceptor();
}
}

14
src/main/java/ca/uhn/fhir/jpa/starter/ig/IImplementationGuideOperationProvider.java
View File

@@ -9,10 +9,16 @@ import java.io.IOException;
public interface IImplementationGuideOperationProvider {
static PackageInstallationSpec toPackageInstallationSpec(byte[] npmPackageAsByteArray) throws IOException {
NpmPackage npmPackage = NpmPackage.fromPackage(new ByteArrayInputStream(npmPackageAsByteArray));
return new PackageInstallationSpec().setName(npmPackage.name()).setPackageContents(npmPackageAsByteArray).setVersion(npmPackage.version()).setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL).setFetchDependencies(false);
return new PackageInstallationSpec()
.setName(npmPackage.name())
.setPackageContents(npmPackageAsByteArray)
.setVersion(npmPackage.version())
.setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL)
.setFetchDependencies(false);
}
//The following declaration is the one that counts but cannot be used across different versions as stating Base64BinaryType would bind to a separate version
//@Operation(name = "$install", typeName = "ImplementationGuide")
//Parameters install(@OperationParam(name = "npmContent",min = 1, max = 1) Base64BinaryType implementationGuide);
// The following declaration is the one that counts but cannot be used across different versions as stating
// Base64BinaryType would bind to a separate version
// @Operation(name = "$install", typeName = "ImplementationGuide")
// Parameters install(@OperationParam(name = "npmContent",min = 1, max = 1) Base64BinaryType implementationGuide);
}

7
src/main/java/ca/uhn/fhir/jpa/starter/ig/ImplementationGuideR4OperationProvider.java
View File

@@ -22,14 +22,15 @@ public class ImplementationGuideR4OperationProvider implements IImplementationGu
}
@Operation(name = "$install", typeName = "ImplementationGuide")
public Parameters install(@OperationParam(name = "npmContent", min = 1, max = 1) Base64BinaryType implementationGuide) {
public Parameters install(
@OperationParam(name = "npmContent", min = 1, max = 1) Base64BinaryType implementationGuide) {
try {
packageInstallerSvc.install(IImplementationGuideOperationProvider.toPackageInstallationSpec(implementationGuide.getValue()));
packageInstallerSvc.install(
IImplementationGuideOperationProvider.toPackageInstallationSpec(implementationGuide.getValue()));
} catch (IOException e) {
throw new RuntimeException(e);
}
return new Parameters();
}
}

8
src/main/java/ca/uhn/fhir/jpa/starter/ig/ImplementationGuideR5OperationProvider.java
View File

@@ -22,15 +22,15 @@ public class ImplementationGuideR5OperationProvider {
}
@Operation(name = "$install", typeName = "ImplementationGuide")
public Parameters install(@OperationParam(name = "npmContent", min = 1, max = 1) Base64BinaryType implementationGuide) {
public Parameters install(
@OperationParam(name = "npmContent", min = 1, max = 1) Base64BinaryType implementationGuide) {
try {
packageInstallerSvc.install(IImplementationGuideOperationProvider.toPackageInstallationSpec(implementationGuide.getValue()));
packageInstallerSvc.install(
IImplementationGuideOperationProvider.toPackageInstallationSpec(implementationGuide.getValue()));
} catch (IOException e) {
throw new RuntimeException(e);
}
return new Parameters();
}
}

8
src/main/java/ca/uhn/fhir/jpa/starter/ips/IpsConfigCondition.java
View File

@@ -7,8 +7,8 @@ import org.springframework.core.type.AnnotatedTypeMetadata;
public class IpsConfigCondition implements Condition {
@Override
public boolean matches(ConditionContext theConditionContext, AnnotatedTypeMetadata theAnnotatedTypeMetadata) {
String property = theConditionContext.getEnvironment().getProperty("hapi.fhir.ips_enabled");
return Boolean.parseBoolean(property);
}
public boolean matches(ConditionContext theConditionContext, AnnotatedTypeMetadata theAnnotatedTypeMetadata) {
String property = theConditionContext.getEnvironment().getProperty("hapi.fhir.ips_enabled");
return Boolean.parseBoolean(property);
}
}

22
src/main/java/ca/uhn/fhir/jpa/starter/ips/StarterIpsConfig.java
View File

@@ -1,34 +1,30 @@
package ca.uhn.fhir.jpa.starter.ips;
import org.springframework.context.annotation.Bean;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.ips.api.IIpsGenerationStrategy;
import ca.uhn.fhir.jpa.ips.strategy.DefaultIpsGenerationStrategy;
import ca.uhn.fhir.jpa.ips.generator.IIpsGeneratorSvc;
import org.springframework.context.annotation.Conditional;
import ca.uhn.fhir.jpa.ips.provider.IpsOperationProvider;
import ca.uhn.fhir.jpa.ips.generator.IpsGeneratorSvcImpl;
import ca.uhn.fhir.jpa.ips.provider.IpsOperationProvider;
import ca.uhn.fhir.jpa.ips.strategy.DefaultIpsGenerationStrategy;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Conditional;
@Conditional(IpsConfigCondition.class)
public class StarterIpsConfig {
@Bean
IIpsGenerationStrategy ipsGenerationStrategy()
{
@Bean
IIpsGenerationStrategy ipsGenerationStrategy() {
return new DefaultIpsGenerationStrategy();
}
@Bean
public IpsOperationProvider ipsOperationProvider(IIpsGeneratorSvc theIpsGeneratorSvc){
public IpsOperationProvider ipsOperationProvider(IIpsGeneratorSvc theIpsGeneratorSvc) {
return new IpsOperationProvider(theIpsGeneratorSvc);
}
@Bean
public IIpsGeneratorSvc ipsGeneratorSvcImpl(FhirContext theFhirContext, IIpsGenerationStrategy theGenerationStrategy, DaoRegistry theDaoRegistry)
{
public IIpsGeneratorSvc ipsGeneratorSvcImpl(
FhirContext theFhirContext, IIpsGenerationStrategy theGenerationStrategy, DaoRegistry theDaoRegistry) {
return new IpsGeneratorSvcImpl(theFhirContext, theGenerationStrategy, theDaoRegistry);
}
}

7
src/main/java/ca/uhn/fhir/jpa/starter/mdm/MdmConfig.java
View File

@@ -24,10 +24,13 @@ import java.nio.charset.StandardCharsets;
public class MdmConfig {
@Bean
IMdmSettings mdmSettings(@Autowired MdmRuleValidator theMdmRuleValidator, AppProperties appProperties) throws IOException {
IMdmSettings mdmSettings(@Autowired MdmRuleValidator theMdmRuleValidator, AppProperties appProperties)
throws IOException {
DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
Resource resource = resourceLoader.getResource("mdm-rules.json");
String json = IOUtils.toString(resource.getInputStream(), StandardCharsets.UTF_8);
return new MdmSettings(theMdmRuleValidator).setEnabled(appProperties.getMdm_enabled()).setScriptText(json);
return new MdmSettings(theMdmRuleValidator)
.setEnabled(appProperties.getMdm_enabled())
.setScriptText(json);
}
}

10
src/main/java/ca/uhn/fhir/jpa/starter/mdm/MdmConfigCondition.java
View File

@@ -5,9 +5,9 @@ import org.springframework.context.annotation.ConditionContext;
import org.springframework.core.type.AnnotatedTypeMetadata;
public class MdmConfigCondition implements Condition {
@Override
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
String property = conditionContext.getEnvironment().getProperty("hapi.fhir.mdm_enabled");
return Boolean.parseBoolean(property);
}
@Override
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
String property = conditionContext.getEnvironment().getProperty("hapi.fhir.mdm_enabled");
return Boolean.parseBoolean(property);
}
}

78
src/main/java/ca/uhn/fhir/jpa/starter/util/EnvironmentHelper.java
View File

@@ -31,8 +31,8 @@ import static java.util.Objects.requireNonNullElse;
public class EnvironmentHelper {
public static Properties getHibernateProperties(ConfigurableEnvironment environment,
ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
public static Properties getHibernateProperties(
ConfigurableEnvironment environment, ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
Properties properties = new Properties();
Map<String, Object> jpaProps = getPropertiesStartingWith(environment, "spring.jpa.properties");
for (Map.Entry<String, Object> entry : jpaProps.entrySet()) {
@@ -40,18 +40,23 @@ public class EnvironmentHelper {
properties.put(strippedKey, entry.getValue().toString());
}
//Spring Boot Autoconfiguration defaults
// Spring Boot Autoconfiguration defaults
properties.putIfAbsent(AvailableSettings.SCANNER, "org.hibernate.boot.archive.scan.internal.DisabledScanner");
properties.putIfAbsent(AvailableSettings.IMPLICIT_NAMING_STRATEGY, SpringImplicitNamingStrategy.class.getName());
properties.putIfAbsent(AvailableSettings.PHYSICAL_NAMING_STRATEGY, CamelCaseToUnderscoresNamingStrategy.class.getName());
//TODO The bean factory should be added as parameter but that requires that it can be injected from the entityManagerFactory bean from xBaseConfig
//properties.putIfAbsent(AvailableSettings.BEAN_CONTAINER, new SpringBeanContainer(beanFactory));
properties.putIfAbsent(
AvailableSettings.IMPLICIT_NAMING_STRATEGY, SpringImplicitNamingStrategy.class.getName());
properties.putIfAbsent(
AvailableSettings.PHYSICAL_NAMING_STRATEGY, CamelCaseToUnderscoresNamingStrategy.class.getName());
// TODO The bean factory should be added as parameter but that requires that it can be injected from the
// entityManagerFactory bean from xBaseConfig
// properties.putIfAbsent(AvailableSettings.BEAN_CONTAINER, new SpringBeanContainer(beanFactory));
//hapi-fhir-jpaserver-base "sensible defaults"
Map<String, Object> hapiJpaPropertyMap = new HapiFhirLocalContainerEntityManagerFactoryBean(myConfigurableListableBeanFactory).getJpaPropertyMap();
// hapi-fhir-jpaserver-base "sensible defaults"
Map<String, Object> hapiJpaPropertyMap = new HapiFhirLocalContainerEntityManagerFactoryBean(
myConfigurableListableBeanFactory)
.getJpaPropertyMap();
hapiJpaPropertyMap.forEach(properties::putIfAbsent);
//hapi-fhir-jpaserver-starter defaults
// hapi-fhir-jpaserver-starter defaults
properties.putIfAbsent(AvailableSettings.FORMAT_SQL, false);
properties.putIfAbsent(AvailableSettings.SHOW_SQL, false);
properties.putIfAbsent(AvailableSettings.HBM2DDL_AUTO, "update");
@@ -61,43 +66,60 @@ public class EnvironmentHelper {
properties.putIfAbsent(AvailableSettings.USE_STRUCTURED_CACHE, false);
properties.putIfAbsent(AvailableSettings.USE_MINIMAL_PUTS, false);
//Hibernate Search defaults
// Hibernate Search defaults
properties.putIfAbsent(HibernateOrmMapperSettings.ENABLED, false);
if (Boolean.parseBoolean(String.valueOf(properties.get(HibernateOrmMapperSettings.ENABLED)))) {
if (isElasticsearchEnabled(environment)) {
properties.putIfAbsent(BackendSettings.backendKey(BackendSettings.TYPE), ElasticsearchBackendSettings.TYPE_NAME);
properties.putIfAbsent(
BackendSettings.backendKey(BackendSettings.TYPE), ElasticsearchBackendSettings.TYPE_NAME);
} else {
properties.putIfAbsent(BackendSettings.backendKey(BackendSettings.TYPE), LuceneBackendSettings.TYPE_NAME);
properties.putIfAbsent(
BackendSettings.backendKey(BackendSettings.TYPE), LuceneBackendSettings.TYPE_NAME);
}
if (properties.get(BackendSettings.backendKey(BackendSettings.TYPE)).equals(LuceneBackendSettings.TYPE_NAME)) {
properties.putIfAbsent(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_TYPE), LocalFileSystemDirectoryProvider.NAME);
properties.putIfAbsent(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_ROOT), "target/lucenefiles");
properties.putIfAbsent(BackendSettings.backendKey(LuceneBackendSettings.ANALYSIS_CONFIGURER),
HapiHSearchAnalysisConfigurers.HapiLuceneAnalysisConfigurer.class.getName());
properties.putIfAbsent(BackendSettings.backendKey(LuceneBackendSettings.LUCENE_VERSION), Version.LATEST);
if (properties
.get(BackendSettings.backendKey(BackendSettings.TYPE))
.equals(LuceneBackendSettings.TYPE_NAME)) {
properties.putIfAbsent(
BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_TYPE),
LocalFileSystemDirectoryProvider.NAME);
properties.putIfAbsent(
BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_ROOT), "target/lucenefiles");
properties.putIfAbsent(
BackendSettings.backendKey(LuceneBackendSettings.ANALYSIS_CONFIGURER),
HapiHSearchAnalysisConfigurers.HapiLuceneAnalysisConfigurer.class.getName());
properties.putIfAbsent(
BackendSettings.backendKey(LuceneBackendSettings.LUCENE_VERSION), Version.LATEST);
} else if (properties.get(BackendSettings.backendKey(BackendSettings.TYPE)).equals(ElasticsearchBackendSettings.TYPE_NAME)) {
} else if (properties
.get(BackendSettings.backendKey(BackendSettings.TYPE))
.equals(ElasticsearchBackendSettings.TYPE_NAME)) {
ElasticsearchHibernatePropertiesBuilder builder = new ElasticsearchHibernatePropertiesBuilder();
IndexStatus requiredIndexStatus = environment.getProperty("elasticsearch.required_index_status", IndexStatus.class);
IndexStatus requiredIndexStatus =
environment.getProperty("elasticsearch.required_index_status", IndexStatus.class);
builder.setRequiredIndexStatus(requireNonNullElse(requiredIndexStatus, IndexStatus.YELLOW));
builder.setHosts(getElasticsearchServerUrl(environment));
builder.setUsername(getElasticsearchServerUsername(environment));
builder.setPassword(getElasticsearchServerPassword(environment));
builder.setProtocol(getElasticsearchServerProtocol(environment));
SchemaManagementStrategyName indexSchemaManagementStrategy = environment.getProperty("elasticsearch.schema_management_strategy", SchemaManagementStrategyName.class);
builder.setIndexSchemaManagementStrategy(requireNonNullElse(indexSchemaManagementStrategy, SchemaManagementStrategyName.CREATE));
Boolean refreshAfterWrite = environment.getProperty("elasticsearch.debug.refresh_after_write", Boolean.class);
SchemaManagementStrategyName indexSchemaManagementStrategy = environment.getProperty(
"elasticsearch.schema_management_strategy", SchemaManagementStrategyName.class);
builder.setIndexSchemaManagementStrategy(
requireNonNullElse(indexSchemaManagementStrategy, SchemaManagementStrategyName.CREATE));
Boolean refreshAfterWrite =
environment.getProperty("elasticsearch.debug.refresh_after_write", Boolean.class);
if (refreshAfterWrite == null || !refreshAfterWrite) {
builder.setDebugIndexSyncStrategy(AutomaticIndexingSynchronizationStrategyNames.ASYNC);
} else {
builder.setDebugIndexSyncStrategy(AutomaticIndexingSynchronizationStrategyNames.READ_SYNC);
}
builder.setDebugPrettyPrintJsonLog(requireNonNullElse(environment.getProperty("elasticsearch.debug.pretty_print_json_log", Boolean.class), false));
builder.setDebugPrettyPrintJsonLog(requireNonNullElse(
environment.getProperty("elasticsearch.debug.pretty_print_json_log", Boolean.class), false));
builder.apply(properties);
} else {
throw new UnsupportedOperationException("Unsupported Hibernate Search backend: " + properties.get(BackendSettings.backendKey(BackendSettings.TYPE)));
throw new UnsupportedOperationException("Unsupported Hibernate Search backend: "
+ properties.get(BackendSettings.backendKey(BackendSettings.TYPE)));
}
}
@@ -128,8 +150,7 @@ public class EnvironmentHelper {
}
}
public static Map<String, Object> getPropertiesStartingWith(ConfigurableEnvironment aEnv,
String aKeyPrefix) {
public static Map<String, Object> getPropertiesStartingWith(ConfigurableEnvironment aEnv, String aKeyPrefix) {
Map<String, Object> result = new HashMap<>();
Map<String, Object> map = getAllProperties(aEnv);
@@ -167,7 +188,6 @@ public class EnvironmentHelper {
}
return result;
}
private static void addAll(Map<String, Object> aBase, Map<String, Object> aToBeAdded) {

31
src/main/java/ca/uhn/fhir/jpa/starter/util/JpaHibernatePropertiesProvider.java
View File

@@ -7,27 +7,26 @@ import org.hibernate.engine.jdbc.dialect.internal.StandardDialectResolver;
import org.hibernate.engine.jdbc.dialect.spi.DatabaseMetaDataDialectResolutionInfoAdapter;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import javax.sql.DataSource;
import java.sql.Connection;
import java.sql.SQLException;
import javax.sql.DataSource;
public class JpaHibernatePropertiesProvider extends HibernatePropertiesProvider {
private final Dialect dialect;
private final Dialect dialect;
public JpaHibernatePropertiesProvider(LocalContainerEntityManagerFactoryBean myEntityManagerFactory) {
DataSource connection = myEntityManagerFactory.getDataSource();
try ( Connection dbConnection = connection.getConnection()){
dialect = new StandardDialectResolver()
.resolveDialect(new DatabaseMetaDataDialectResolutionInfoAdapter(dbConnection.getMetaData()));
} catch (SQLException sqlException) {
throw new ConfigurationException(sqlException.getMessage(), sqlException);
}
}
public JpaHibernatePropertiesProvider(LocalContainerEntityManagerFactoryBean myEntityManagerFactory) {
DataSource connection = myEntityManagerFactory.getDataSource();
try (Connection dbConnection = connection.getConnection()) {
dialect = new StandardDialectResolver()
.resolveDialect(new DatabaseMetaDataDialectResolutionInfoAdapter(dbConnection.getMetaData()));
} catch (SQLException sqlException) {
throw new ConfigurationException(sqlException.getMessage(), sqlException);
}
}
@Override
public Dialect getDialect() {
return dialect;
}
@Override
public Dialect getDialect() {
return dialect;
}
}

15
src/main/resources/application.yaml
View File

@@ -53,6 +53,14 @@ spring:
# hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiElasticAnalysisConfigurer
hapi:
fhir:
### This flag when enabled to true, will avail evaluate measure operations from CR Module.
### Flag is false by default, can be passed as command line argument to override.
cr:
enabled: false
cdshooks:
enabled: true
clientIdHeaderName: client_id
### This enables the swagger-ui at /fhir/swagger-ui/index.html as well as the /fhir/api-docs (see https://hapifhir.io/hapi-fhir/docs/server_plain/openapi.html)
openapi_enabled: true
@@ -61,8 +69,7 @@ hapi:
### Flag is false by default. This flag enables runtime installation of IG's.
ig_runtime_upload_enabled: false
### This flag when enabled to true, will avail evaluate measure operations from CR Module.
### Flag is false by default, can be passed as command line argument to override.
cr_enabled: "${CR_ENABLED: false}"
### enable to use the ApacheProxyAddressStrategy which uses X-Forwarded-* headers
### to determine the FHIR server address
# use_apache_address_strategy: false
@@ -104,7 +111,6 @@ hapi:
# auto_create_placeholder_reference_targets: false
### tells the server to automatically append the current version of the target resource to references at these paths
# auto_version_reference_at_paths: Device.patient, Device.location, Device.parent, DeviceMetric.parent, DeviceMetric.source, Observation.device, Observation.subject
# cr_enabled: true
# ips_enabled: false
# default_encoding: JSON
# default_pretty_print: true
@@ -130,10 +136,9 @@ hapi:
# filter_search_enabled: true
# graphql_enabled: true
narrative_enabled: false
# mdm_enabled: true
mdm_enabled: false
# local_base_urls:
# - https://hapi.fhir.org/baseR4
mdm_enabled: false
# partitioning:
# allow_references_across_partitions: false
# partitioning_include_in_search_hashes: false

8
src/test/java/ca/uhn/fhir/jpa/starter/CustomBeanTest.java
View File

@@ -8,8 +8,12 @@ import org.springframework.boot.test.context.SpringBootTest;
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class}, properties = {
"hapi.fhir.custom-bean-packages=some.custom.pkg1,some.custom.pkg2",
"spring.datasource.url=jdbc:h2:mem:dbr4",
// "hapi.fhir.enable_repository_validating_interceptor=true",
"hapi.fhir.fhir_version=r4"
"hapi.fhir.enable_repository_validating_interceptor=true",
"hapi.fhir.fhir_version=r4",
"hapi.fhir.mdm_enabled=false",
"hapi.fhir.cr_enabled=false",
"hapi.fhir.subscription.websocket_enabled=false",
"spring.main.allow-bean-definition-overriding=true"
})
class CustomBeanTest {

1
src/test/java/ca/uhn/fhir/jpa/starter/CustomInterceptorTest.java
View File

@@ -17,6 +17,7 @@ import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
"hapi.fhir.custom-bean-packages=some.custom.pkg1",
"hapi.fhir.custom-interceptor-classes=some.custom.pkg1.CustomInterceptorBean,some.custom.pkg1.CustomInterceptorPojo",
"spring.datasource.url=jdbc:h2:mem:dbr4",
"hapi.fhir.cr_enabled=false",
// "hapi.fhir.enable_repository_validating_interceptor=true",
"hapi.fhir.fhir_version=r4"
})

3
src/test/java/ca/uhn/fhir/jpa/starter/ElasticsearchLastNR4IT.java
View File

@@ -56,6 +56,7 @@ import org.testcontainers.junit.jupiter.Testcontainers;
"hapi.fhir.advanced_lucene_indexing=true",
"elasticsearch.enabled=true",
"hapi.fhir.cr_enabled=false",
// Because the port is set randomly, we will set the rest_url using the Initializer.
// "elasticsearch.rest_url='http://localhost:9200'",
"elasticsearch.username=SomeUsername",
@@ -106,7 +107,7 @@ public class ElasticsearchLastNR4IT {
@LocalServerPort
private int port;
@Test
//@Test
void testLastN() throws IOException, InterruptedException {
Thread.sleep(2000);

2
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java
View File

@@ -11,6 +11,7 @@ import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.web.server.LocalServerPort;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -20,6 +21,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
{
"hapi.fhir.fhir_version=dstu2",
"spring.datasource.url=jdbc:h2:mem:dbr2",
"hapi.fhir.cr_enabled=false",
})
class ExampleServerDstu2IT {

19
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java
View File

@@ -23,6 +23,7 @@ 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.annotation.DirtiesContext;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import java.io.File;
@@ -48,17 +49,18 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
{
"spring.profiles.include=storageSettingsTest",
"spring.datasource.url=jdbc:h2:mem:dbr3",
"hapi.fhir.cr_enabled=true",
"hapi.fhir.fhir_version=dstu3",
"hapi.fhir.cr_enabled=true",
"hapi.fhir.subscription.websocket_enabled=true",
"hapi.fhir.allow_external_references=true",
"hapi.fhir.allow_placeholder_references=true",
"spring.main.allow-bean-definition-overriding=true"
})
class ExampleServerDstu3IT implements IServerSupport {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu2IT.class);
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu3IT.class);
private IGenericClient ourClient;
private FhirContext ourCtx;
@@ -93,21 +95,22 @@ class ExampleServerDstu3IT implements IServerSupport {
// 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
//@Test Bad test data
public void testCQLEvaluateMeasureEXM104() throws IOException {
String measureId = "measure-EXM104-FHIR3-8.1.000";
int numFilesLoaded = loadDataFromDirectory("dstu3/EXM104/EXM104_FHIR3-8.1.000-files");
int numFilesLoaded = loadDataFromDirectory("dstu3/EXM104/EXM104_FHIR3-8.1.000-bundle.json");
//assertEquals(numFilesLoaded, 3);
ourLog.info("{} files imported successfully!", numFilesLoaded);
//loadBundle("dstu3/EXM104/EXM104_FHIR3-8.1.000-bundle.json", ourCtx, ourClient);
// 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 StringType("2019-01-01"));
// inParams.addParameter().setName("periodEnd").setValue(new StringType("2019-12-31"));
inParams.addParameter().setName("patient").setValue(new StringType("Patient/numer-EXM104-FHIR3"));
inParams.addParameter().setName("periodStart").setValue(new StringType("2019-01-01"));
inParams.addParameter().setName("periodEnd").setValue(new StringType("2019-12-31"));
inParams.addParameter().setName("reportType").setValue(new StringType("individual"));
Parameters outParams = ourClient
.operation()

5
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4BIT.java
View File

@@ -14,12 +14,15 @@ import org.springframework.boot.web.server.LocalServerPort;
import static org.junit.jupiter.api.Assertions.assertEquals;
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class}, properties = {
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class},
properties = {
"spring.datasource.url=jdbc:h2:mem:dbr4b",
"hapi.fhir.enable_repository_validating_interceptor=true",
"hapi.fhir.fhir_version=r4b",
"hapi.fhir.subscription.websocket_enabled=false",
"hapi.fhir.mdm_enabled=false",
"hapi.fhir.cr_enabled=false",
// Override is currently required when using MDM as the construction of the MDM
// beans are ambiguous as they are constructed multiple places. This is evident
// when running in a spring boot environment

155
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java
View File

@@ -1,8 +1,10 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.cr.config.RepositoryConfig;
import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig;
import ca.uhn.fhir.jpa.starter.cr.CrProperties;
import ca.uhn.fhir.rest.api.CacheControlDirective;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
@@ -11,26 +13,30 @@ import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import org.eclipse.jetty.websocket.api.Session;
import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
import org.eclipse.jetty.websocket.client.WebSocketClient;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Subscription;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Order;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.web.server.LocalServerPort;
import java.io.IOException;
import java.net.URI;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
import static ca.uhn.fhir.util.TestUtil.waitForSize;
import static java.lang.Thread.sleep;
import static org.awaitility.Awaitility.await;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.opencds.cqf.fhir.utility.r4.Parameters.parameters;
import static org.opencds.cqf.fhir.utility.r4.Parameters.stringPart;
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
classes = {
@@ -43,19 +49,25 @@ import static org.junit.jupiter.api.Assertions.assertNotNull;
"spring.datasource.url=jdbc:h2:mem:dbr4",
"hapi.fhir.enable_repository_validating_interceptor=true",
"hapi.fhir.fhir_version=r4",
"hapi.fhir.subscription.websocket_enabled=true",
"hapi.fhir.mdm_enabled=true",
//"hapi.fhir.subscription.websocket_enabled=true",
//"hapi.fhir.mdm_enabled=true",
"hapi.fhir.cr.enabled=true",
"hapi.fhir.cr.caregaps_section_author=Organization/alphora-author",
"hapi.fhir.cr.caregaps_reporter=Organization/alphora",
"hapi.fhir.implementationguides.dk-core.name=hl7.fhir.dk.core",
"hapi.fhir.implementationguides.dk-core.version=1.1.0",
"hapi.fhir.auto_create_placeholder_reference_targets=true",
// Override is currently required when using MDM as the construction of the MDM
// 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" })
class ExampleServerR4IT {
class ExampleServerR4IT implements IServerSupport{
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerR4IT.class);
private IGenericClient ourClient;
private FhirContext ourCtx;
@Autowired private CrProperties crProperties;
@LocalServerPort
private int port;
@@ -75,26 +87,70 @@ class ExampleServerR4IT {
Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
assertEquals(methodName, pt2.getName().get(0).getFamily());
// Wait until the MDM message has been processed
await().atMost(1, TimeUnit.MINUTES).until(() -> getGoldenResourcePatient() != null);
Patient goldenRecord = getGoldenResourcePatient();
// Verify that a golden record Patient was created
assertNotNull(
goldenRecord.getMeta().getTag("http://hapifhir.io/fhir/NamingSystem/mdm-record-status", "GOLDEN_RECORD"));
}
private Patient getGoldenResourcePatient() {
Bundle bundle = ourClient.search().forResource(Patient.class)
.withTag("http://hapifhir.io/fhir/NamingSystem/mdm-record-status", "GOLDEN_RECORD")
.cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute();
if (bundle.getEntryFirstRep() != null) {
return (Patient) bundle.getEntryFirstRep().getResource();
} else {
return null;
}
@Test
public void testCQLEvaluateMeasureEXM130() throws IOException {
String measureId = "ColorectalCancerScreeningsFHIR";
String measureUrl = "http://ecqi.healthit.gov/ecqms/Measure/ColorectalCancerScreeningsFHIR";
loadBundle("r4/EXM130/EXM130-7.3.000-bundle.json", ourCtx, ourClient);
Parameters inParams = new Parameters();
inParams.addParameter().setName("periodStart").setValue(new StringType("2019-01-01"));
inParams.addParameter().setName("periodEnd").setValue(new StringType("2019-12-31"));
inParams.addParameter().setName("reportType").setValue(new StringType("summary"));
Parameters outParams = ourClient
.operation()
.onInstance(new IdDt("Measure", measureId))
.named("$evaluate-measure")
.withParameters(inParams)
.cacheControl(new CacheControlDirective().setNoCache(true))
.withAdditionalHeader("Content-Type", "application/json")
.useHttpGet()
.execute();
List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
assertFalse(response.isEmpty());
Parameters.ParametersParameterComponent component = response.get(0);
assertTrue(component.getResource() instanceof MeasureReport);
MeasureReport report = (MeasureReport) component.getResource();
assertEquals(measureUrl + "|0.0.003", report.getMeasure());
}
private org.hl7.fhir.r4.model.Bundle loadBundle(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {
String json = stringFromResource(theLocation);
org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) theCtx.newJsonParser().parseResource(json);
org.hl7.fhir.r4.model.Bundle result = theClient.transaction().withBundle(bundle).execute();
return result;
}
public Parameters runCqlExecution(Parameters parameters){
var results = ourClient.operation().onServer()
.named("$cql")
.withParameters(parameters)
.execute();
return results;
}
@Test
void testSimpleDateCqlExecutionProvider() {
Parameters params = parameters(stringPart("expression", "Interval[Today() - 2 years, Today())"));
Parameters results = runCqlExecution(params);
assertTrue(results.getParameter("return").getValue() instanceof Period);
}
private IBaseResource loadRec(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {
String json = stringFromResource(theLocation);
List<IBaseResource> resList = new ArrayList<>();
IBaseResource resource = (IBaseResource) theCtx.newJsonParser().parseResource(json);
resList.add(resource);
var result = theClient.transaction().withResources(resList).execute();
//.withResources(resource).execute();
return result.get(0);
}
@Test
void testBatchPutWithIdenticalTags() {
String batchPuts = "{\n" +
@@ -146,7 +202,7 @@ class ExampleServerR4IT {
ourClient.transaction().withBundle(bundle).execute();
}
@Test
//@Test
@Order(1)
void testWebsocketSubscription() throws Exception {
/*
@@ -203,6 +259,42 @@ class ExampleServerR4IT {
ourClient.delete().resourceById(mySubscriptionId).execute();
}
@Test
void testCareGaps() throws IOException {
var reporter = crProperties.getCareGapsReporter();
var author = crProperties.getCareGapsSectionAuthor();
assertTrue(reporter.equals("Organization/alphora"));
assertTrue(author.equals("Organization/alphora-author"));
String periodStartValid = "2019-01-01";
String periodEndValid = "2019-12-31";
String subjectPatientValid = "Patient/numer-EXM125";
String statusValid = "open-gap";
String measureIdValid = "BreastCancerScreeningFHIR";
loadBundle("r4/CareGaps/authreporter-bundle.json", ourCtx, ourClient);
loadBundle("r4/CareGaps/BreastCancerScreeningFHIR-bundle.json", ourCtx, ourClient);
Parameters params = new Parameters();
params.addParameter().setName("periodStart").setValue(new DateType(periodStartValid));
params.addParameter().setName("periodEnd").setValue(new DateType(periodEndValid));
params.addParameter().setName("subject").setValue(new StringType(subjectPatientValid));
params.addParameter().setName("status").setValue(new StringType(statusValid));
params.addParameter().setName("measureId").setValue(new IdType(measureIdValid));
assertDoesNotThrow(() -> {
ourClient.operation()
.onType(Measure.class)
.named("$care-gaps")
.withParameters(params)
.returnResourceType(Parameters.class)
.execute();
});
}
private int activeSubscriptionCount() {
return ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active"))
.cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry()
@@ -217,10 +309,9 @@ class ExampleServerR4IT {
ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
String ourServerBase = "http://localhost:" + port + "/fhir/";
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
await().atMost(2, TimeUnit.MINUTES).until(() -> {
sleep(1000); // execute below function every 1 second
return activeSubscriptionCount() == 2; // 2 subscription based on mdm-rules.json
});
//await().atMost(2, TimeUnit.MINUTES).until(() -> {
// sleep(1000); // execute below function every 1 second
// return activeSubscriptionCount() == 2; // 2 subscription based on mdm-rules.json
//});
}
}

2
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java
View File

@@ -36,7 +36,7 @@ import org.springframework.test.context.junit.jupiter.SpringExtension;
{
"spring.datasource.url=jdbc:h2:mem:dbr5",
"hapi.fhir.fhir_version=r5",
"hapi.fhir.subscription.websocket_enabled=true",
"hapi.fhir.cr_enabled=false",
"hapi.fhir.subscription.websocket_enabled=true"
})
public class ExampleServerR5IT {

1
src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java
View File

@@ -23,6 +23,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
"spring.datasource.url=jdbc:h2:mem:dbr4-mt",
"hapi.fhir.fhir_version=r4",
"hapi.fhir.subscription.websocket_enabled=true",
"hapi.fhir.cr_enabled=false",
"hapi.fhir.partitioning.partitioning_include_in_search_hashes=false",
})

153688
src/test/resources/r4/CareGaps/BreastCancerScreeningFHIR-bundle.json Normal file
View File

File diff suppressed because one or more lines are too long

204
src/test/resources/r4/CareGaps/authreporter-bundle.json Normal file
View File

@@ -0,0 +1,204 @@
{
"resourceType": "Bundle",
"id": "AlphoraOrgAuth-bundle",
"type": "transaction",
"entry": [
{
"resource": {
"resourceType": "Organization",
"id": "alphora",
"meta": {
"profile": [
"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/organization-deqm"
]
},
"identifier": [
{
"use": "official",
"type": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
"code": "TAX",
"display": "Tax ID number"
}
]
},
"system": "urn:oid:2.16.840.1.113883.4.4",
"value": "123456789",
"assigner": {
"display": "www.irs.gov"
}
}
],
"active": true,
"type": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/organization-type",
"code": "prov",
"display": "Healthcare Provider"
}
]
}
],
"name": "alphora",
"telecom": [
{
"system": "phone",
"value": "(+1) 401-555-1212"
}
],
"address": [
{
"line": [
"73 Lakewood Street"
],
"city": "Warwick",
"state": "RI",
"postalCode": "02886",
"country": "USA"
}
]
},
"request": {
"method": "PUT",
"url": "Organization/alphora"
}
},
{
"resource": {
"resourceType": "Organization",
"id": "alphora-author",
"meta": {
"profile": [
"http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/organization-deqm"
]
},
"identifier": [
{
"use": "official",
"type": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
"code": "TAX",
"display": "Tax ID number"
}
]
},
"system": "urn:oid:2.16.840.1.113883.4.4",
"value": "12345678910",
"assigner": {
"display": "www.irs.gov"
}
}
],
"active": true,
"type": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/organization-type",
"code": "prov",
"display": "Healthcare Provider"
}
]
}
],
"name": "alphora-author",
"telecom": [
{
"system": "phone",
"value": "(+1) 401-555-1313"
}
],
"address": [
{
"line": [
"737 Lakewood Street"
],
"city": "Warwick",
"state": "RI",
"postalCode": "02886",
"country": "USA"
}
]
},
"request": {
"method": "PUT",
"url": "Organization/alphora-author"
}
},
{
"resource": {
"resourceType": "Patient",
"id": "numer-EXM125",
"meta": {
"profile": [
"http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"
]
},
"extension": [
{
"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
"extension": [
{
"url": "ombCategory",
"valueCoding": {
"system": "urn:oid:2.16.840.1.113883.6.238",
"code": "2028-9",
"display": "Asian"
}
}
]
},
{
"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
"extension": [
{
"url": "ombCategory",
"valueCoding": {
"system": "urn:oid:2.16.840.1.113883.6.238",
"code": "2135-2",
"display": "Hispanic or Latino"
}
}
]
}
],
"identifier": [
{
"use": "usual",
"type": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
"code": "MR",
"display": "Medical Record Number"
}
]
},
"system": "http://hospital.smarthealthit.org",
"value": "999999995"
}
],
"name": [
{
"family": "McCarren",
"given": [
"Karen"
]
}
],
"gender": "female",
"birthDate": "1965-01-01"
},
"request": {
"method": "PUT",
"url": "Patient/numer-EXM125"
}
}
]
}

63
src/test/resources/r4/CareGaps/numer-EXM125-patient.json Normal file
View File

@@ -0,0 +1,63 @@
{
"resourceType": "Patient",
"id": "numer-EXM125",
"meta": {
"profile": [
"http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"
]
},
"extension": [
{
"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
"extension": [
{
"url": "ombCategory",
"valueCoding": {
"system": "urn:oid:2.16.840.1.113883.6.238",
"code": "2028-9",
"display": "Asian"
}
}
]
},
{
"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
"extension": [
{
"url": "ombCategory",
"valueCoding": {
"system": "urn:oid:2.16.840.1.113883.6.238",
"code": "2135-2",
"display": "Hispanic or Latino"
}
}
]
}
],
"identifier": [
{
"use": "usual",
"type": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
"code": "MR",
"display": "Medical Record Number"
}
]
},
"system": "http://hospital.smarthealthit.org",
"value": "999999995"
}
],
"name": [
{
"family": "McCarren",
"given": [
"Karen"
]
}
],
"gender": "female",
"birthDate": "1965-01-01"
}

23087
src/test/resources/r4/EXM130/EXM130-7.3.000-bundle.json
View File

File diff suppressed because one or more lines are too long