Merge remote-tracking branch 'origin/master' into rel_8_3_tracking
This commit is contained in:
dotasek
1
.gitignore
vendored
1
.gitignore
vendored
@@ -124,7 +124,6 @@ local.properties
|
||||
.factorypath
|
||||
.project
|
||||
.settings
|
||||
.springBeans
|
||||
.sts4-cache
|
||||
|
||||
# Code Recommenders
|
||||
|
||||
16
README.md
16
README.md
@@ -51,7 +51,7 @@ HAPI looks in the environment variables for properties in the [application.yaml]
|
||||
|
||||
### Configuration via overridden application.yaml file and using Docker
|
||||
|
||||
You can customize HAPI by telling HAPI to look for the configuration file in a different location, eg.:
|
||||
You can customize HAPI by telling HAPI to look for the configuration file in a different location, e.g.:
|
||||
|
||||
```
|
||||
docker run -p 8090:8080 -v $(pwd)/yourLocalFolder:/configs -e "--spring.config.location=file:///configs/another.application.yaml" hapiproject/hapi:latest
|
||||
@@ -237,7 +237,7 @@ The Server will then be accessible at http://localhost:8888/fhir and the Capabil
|
||||
```bash
|
||||
mvn clean spring-boot:run -Pboot
|
||||
```
|
||||
Server will then be accessible at http://localhost:8080/ and eg. http://localhost:8080/fhir/metadata. Remember to adjust you overlay configuration in the application.yaml to the following:
|
||||
Server will then be accessible at http://localhost:8080/ and e.g. http://localhost:8080/fhir/metadata. Remember to adjust you overlay configuration in the application.yaml to the following:
|
||||
|
||||
```yaml
|
||||
tester:
|
||||
@@ -253,7 +253,7 @@ Server will then be accessible at http://localhost:8080/ and eg. http://localhos
|
||||
```bash
|
||||
mvn clean package spring-boot:repackage -DskipTests=true -Pboot && java -jar target/ROOT.war
|
||||
```
|
||||
Server will then be accessible at http://localhost:8080/ and eg. http://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to the following:
|
||||
Server will then be accessible at http://localhost:8080/ and e.g. http://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to the following:
|
||||
|
||||
```yaml
|
||||
tester:
|
||||
@@ -268,7 +268,7 @@ Server will then be accessible at http://localhost:8080/ and eg. http://localhos
|
||||
```bash
|
||||
mvn clean package com.google.cloud.tools:jib-maven-plugin:dockerBuild -Dimage=distroless-hapi && docker run -p 8080:8080 distroless-hapi
|
||||
```
|
||||
Server will then be accessible at http://localhost:8080/ and eg. http://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to the following:
|
||||
Server will then be accessible at http://localhost:8080/ and e.g. http://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to the following:
|
||||
|
||||
```yaml
|
||||
tester:
|
||||
@@ -284,7 +284,7 @@ Server will then be accessible at http://localhost:8080/ and eg. http://localhos
|
||||
```bash
|
||||
./build-docker-image.sh && docker run -p 8080:8080 hapi-fhir/hapi-fhir-jpaserver-starter:latest
|
||||
```
|
||||
Server will then be accessible at http://localhost:8080/ and eg. http://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to the following:
|
||||
Server will then be accessible at http://localhost:8080/ and e.g. http://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to the following:
|
||||
|
||||
```yaml
|
||||
tester:
|
||||
@@ -384,7 +384,7 @@ Several template files that can be customized are found in the following directo
|
||||
|
||||
Using the Maven-Embedded Jetty method above is convenient, but it is not a good solution if you want to leave the server running in the background.
|
||||
|
||||
Most people who are using HAPI FHIR JPA as a server that is accessible to other people (whether internally on your network or publically hosted) will do so using an Application Server, such as [Apache Tomcat](http://tomcat.apache.org/) or [Jetty](https://www.eclipse.org/jetty/). Note that any Servlet 3.0+ compatible Web Container will work (e.g Wildfly, Websphere, etc.).
|
||||
Most people who are using HAPI FHIR JPA as a server that is accessible to other people (whether internally on your network or publicly hosted) will do so using an Application Server, such as [Apache Tomcat](http://tomcat.apache.org/) or [Jetty](https://www.eclipse.org/jetty/). Note that any Servlet 3.0+ compatible Web Container will work (e.g. Wildfly, Websphere, etc.).
|
||||
|
||||
Tomcat is very popular, so it is a good choice simply because you will be able to find many tutorials online. Jetty is a great alternative due to its fast startup time and good overall performance.
|
||||
|
||||
@@ -402,7 +402,7 @@ Again, browse to the following link to use the server (note that the port 8080 m
|
||||
|
||||
You will then be able to access the JPA server e.g. using http://localhost:8080/fhir/metadata.
|
||||
|
||||
If you would like it to be hosted at eg. hapi-fhir-jpaserver, eg. http://localhost:8080/hapi-fhir-jpaserver/ or http://localhost:8080/hapi-fhir-jpaserver/fhir/metadata - then rename the WAR file to ```hapi-fhir-jpaserver.war``` and adjust the overlay configuration accordingly e.g.
|
||||
If you would like it to be hosted at e.g. hapi-fhir-jpaserver, e.g. http://localhost:8080/hapi-fhir-jpaserver/ or http://localhost:8080/hapi-fhir-jpaserver/fhir/metadata - then rename the WAR file to ```hapi-fhir-jpaserver.war``` and adjust the overlay configuration accordingly e.g.
|
||||
|
||||
```yaml
|
||||
tester:
|
||||
@@ -525,7 +525,7 @@ Set `hapi.fhir.store_resource_in_lucene_index_enabled` in the [application.yaml]
|
||||
|
||||
## Changing cached search results time
|
||||
|
||||
It is possible to change the cached search results time. The option `reuse_cached_search_results_millis` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) is 6000 miliseconds by default.
|
||||
It is possible to change the cached search results time. The option `reuse_cached_search_results_millis` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) is 6000 milliseconds by default.
|
||||
Set `reuse_cached_search_results_millis: -1` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to ignore the cache time every search.
|
||||
|
||||
## Build the distroless variant of the image (for lower footprint and improved security)
|
||||
|
||||
@@ -14,7 +14,7 @@ dependencies:
|
||||
repository: oci://registry-1.docker.io/bitnamicharts
|
||||
version: 2.31.3
|
||||
appVersion: 8.2.0
|
||||
version: 0.20.0
|
||||
version: 0.20.1
|
||||
annotations:
|
||||
artifacthub.io/license: Apache-2.0
|
||||
artifacthub.io/containsSecurityUpdates: "false"
|
||||
@@ -27,14 +27,4 @@ annotations:
|
||||
# When using the list of objects option the valid supported kinds are
|
||||
# added, changed, deprecated, removed, fixed, and security.
|
||||
- kind: changed
|
||||
description: "updated postgresql sub-chart to 16.7.11"
|
||||
- kind: changed
|
||||
description: "updated common sub-chart to 2.31.3"
|
||||
- kind: changed
|
||||
description: "updated curlimages/curl to 8.14.1"
|
||||
- kind: changed
|
||||
description: "updated hapiproject/hapi to v8.2.0-1"
|
||||
- kind: changed
|
||||
description: "use ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect dialect"
|
||||
- kind: changed
|
||||
description: "made the init container waiting for the database to be ready configurable"
|
||||
description: "fixed typo in README.md"
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
# HAPI FHIR JPA Server Starter Helm Chart
|
||||
|
||||
  
|
||||
  
|
||||
|
||||
This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes environment.
|
||||
|
||||
@@ -98,7 +98,7 @@ INFO[2021-11-20T12:38:04Z] Found Chart directories [charts/hapi-fhir-jpaserver]
|
||||
INFO[2021-11-20T12:38:04Z] Generating README Documentation for chart /usr/src/app/charts/hapi-fhir-jpaserver
|
||||
```
|
||||
|
||||
## Enable Distributed Tracing based on the OpenTelemtry Java Agent
|
||||
## Enable Distributed Tracing based on the OpenTelemetry Java Agent
|
||||
|
||||
The container image includes the [OpenTelemetry Java agent JAR](https://github.com/open-telemetry/opentelemetry-java-instrumentation)
|
||||
which can be used to enable distributed tracing. It can be configured entirely using environment variables,
|
||||
|
||||
@@ -27,7 +27,7 @@ INFO[2021-11-20T12:38:04Z] Found Chart directories [charts/hapi-fhir-jpaserver]
|
||||
INFO[2021-11-20T12:38:04Z] Generating README Documentation for chart /usr/src/app/charts/hapi-fhir-jpaserver
|
||||
```
|
||||
|
||||
## Enable Distributed Tracing based on the OpenTelemtry Java Agent
|
||||
## Enable Distributed Tracing based on the OpenTelemetry Java Agent
|
||||
|
||||
The container image includes the [OpenTelemetry Java agent JAR](https://github.com/open-telemetry/opentelemetry-java-instrumentation)
|
||||
which can be used to enable distributed tracing. It can be configured entirely using environment variables,
|
||||
|
||||
4
pom.xml
4
pom.xml
@@ -6,7 +6,7 @@
|
||||
<properties>
|
||||
<java.version>17</java.version>
|
||||
<hapi.fhir.jpa.server.starter.revision>1</hapi.fhir.jpa.server.starter.revision>
|
||||
<clinical-reasoning.version>3.23.0</clinical-reasoning.version>
|
||||
<clinical-reasoning.version>3.24.0</clinical-reasoning.version>
|
||||
</properties>
|
||||
|
||||
<!-- one-liner to take you to the cloud with settings form the application.yaml file: -->
|
||||
@@ -195,7 +195,7 @@
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
|
||||
<!-- If you are using HAPI narrative generation, you will need to include Thymeleaf as well. Otherwise the following can be omitted. -->
|
||||
<!-- If you are using HAPI narrative generation, you will need to include Thymeleaf as well. Otherwise, the following can be omitted. -->
|
||||
<dependency>
|
||||
<groupId>org.thymeleaf</groupId>
|
||||
<artifactId>thymeleaf</artifactId>
|
||||
|
||||
@@ -45,7 +45,7 @@ public class Application extends SpringBootServletInitializer {
|
||||
|
||||
SpringApplication.run(Application.class, args);
|
||||
|
||||
// Server is now accessible at eg. http://localhost:8080/fhir/metadata
|
||||
// Server is now accessible at e.g. http://localhost:8080/fhir/metadata
|
||||
// UI is now accessible at http://localhost:8080/
|
||||
}
|
||||
|
||||
|
||||
@@ -22,6 +22,7 @@ import org.springframework.beans.factory.annotation.Configurable;
|
||||
import org.springframework.beans.factory.annotation.Qualifier;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.io.Serial;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static org.opencds.cqf.fhir.cr.hapi.config.test.TestCdsHooksConfig.CDS_HOOKS_OBJECT_MAPPER_FACTORY;
|
||||
@@ -29,6 +30,8 @@ import static org.opencds.cqf.fhir.cr.hapi.config.test.TestCdsHooksConfig.CDS_HO
|
||||
@Configurable
|
||||
public class CdsHooksServlet extends HttpServlet {
|
||||
private static final Logger logger = LoggerFactory.getLogger(CdsHooksServlet.class);
|
||||
|
||||
@Serial
|
||||
private static final long serialVersionUID = 1L;
|
||||
|
||||
@Autowired
|
||||
|
||||
@@ -179,9 +179,8 @@ public class ModuleConfigurationPrefetchSvc extends CdsPrefetchSvc {
|
||||
return true;
|
||||
}
|
||||
if (resource instanceof IBaseBundle) {
|
||||
return BundleUtil.toListOfEntries(fhirContext, (IBaseBundle) resource)
|
||||
.size()
|
||||
> 0;
|
||||
return !BundleUtil.toListOfEntries(fhirContext, (IBaseBundle) resource)
|
||||
.isEmpty();
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
@@ -41,24 +41,28 @@ public class FhirServerConfigCommon {
|
||||
private static final Logger ourLog = 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");
|
||||
"Server configured to {} contains searches",
|
||||
appProperties.getAllow_contains_searches() ? "allow" : "deny");
|
||||
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");
|
||||
"Server configured to {} multiple deletes",
|
||||
appProperties.getAllow_multiple_delete() ? "allow" : "deny");
|
||||
ourLog.info(
|
||||
"Server configured to {} external references",
|
||||
appProperties.getAllow_external_references() ? "allow" : "deny");
|
||||
ourLog.info(
|
||||
"Server configured to {} DAO scheduling",
|
||||
appProperties.getDao_scheduling_enabled() ? "enable" : "disable");
|
||||
ourLog.info(
|
||||
"Server configured to {} delete expunges",
|
||||
appProperties.getDelete_expunge_enabled() ? "enable" : "disable");
|
||||
ourLog.info("Server configured to {} expunges", appProperties.getExpunge_enabled() ? "enable" : "disable");
|
||||
ourLog.info(
|
||||
"Server configured to {} overriding default search params",
|
||||
appProperties.getAllow_override_default_search_params() ? "allow" : "deny");
|
||||
ourLog.info(
|
||||
"Server configured to {} auto-creating placeholder references",
|
||||
appProperties.getAuto_create_placeholder_reference_targets() ? "allow" : "disable");
|
||||
ourLog.info(
|
||||
"Server configured to auto-version references at paths {}",
|
||||
appProperties.getAuto_version_reference_at_paths());
|
||||
@@ -66,12 +70,14 @@ public class FhirServerConfigCommon {
|
||||
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");
|
||||
ourLog.info(
|
||||
"Server is configured to enable email with host '{}' and port {}",
|
||||
email.getHost(),
|
||||
email.getPort());
|
||||
ourLog.info("Server will use '{}' as the from email address", email.getFrom());
|
||||
|
||||
if (!Strings.isNullOrEmpty(email.getUsername())) {
|
||||
ourLog.info("Server is configured to use username '" + email.getUsername() + "' for email");
|
||||
ourLog.info("Server is configured to use username '{}' for email", email.getUsername());
|
||||
}
|
||||
|
||||
if (!Strings.isNullOrEmpty(email.getPassword())) {
|
||||
@@ -91,17 +97,19 @@ public class FhirServerConfigCommon {
|
||||
ourLog.info("Indexed on contained resource enabled");
|
||||
}
|
||||
|
||||
ourLog.info("Server configured to " + (appProperties.getPre_expand_value_sets() ? "enable" : "disable")
|
||||
+ " value set pre-expansion");
|
||||
ourLog.info(
|
||||
"Server configured to " + (appProperties.getEnable_task_pre_expand_value_sets() ? "enable" : "disable")
|
||||
+ " value set pre-expansion task");
|
||||
ourLog.info("Server configured for pre-expand value set default count of "
|
||||
+ (appProperties.getPre_expand_value_sets_default_count().toString()));
|
||||
ourLog.info("Server configured for pre-expand value set max count of "
|
||||
+ (appProperties.getPre_expand_value_sets_max_count().toString()));
|
||||
ourLog.info("Server configured for maximum expansion size of "
|
||||
+ (appProperties.getMaximum_expansion_size().toString()));
|
||||
"Server configured to {} value set pre-expansion",
|
||||
appProperties.getPre_expand_value_sets() ? "enable" : "disable");
|
||||
ourLog.info(
|
||||
"Server configured to {} value set pre-expansion task",
|
||||
appProperties.getEnable_task_pre_expand_value_sets() ? "enable" : "disable");
|
||||
ourLog.info(
|
||||
"Server configured for pre-expand value set default count of {}",
|
||||
appProperties.getPre_expand_value_sets_default_count());
|
||||
ourLog.info(
|
||||
"Server configured for pre-expand value set max count of {}",
|
||||
appProperties.getPre_expand_value_sets_max_count());
|
||||
ourLog.info("Server configured for maximum expansion size of {}", appProperties.getMaximum_expansion_size());
|
||||
}
|
||||
|
||||
@Bean
|
||||
@@ -194,8 +202,9 @@ public class FhirServerConfigCommon {
|
||||
|
||||
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));
|
||||
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);
|
||||
@@ -237,19 +246,21 @@ public class FhirServerConfigCommon {
|
||||
// Set and/or recommend default Server ID Strategy of UUID when using the ANY Client ID Strategy
|
||||
if (appProperties.getClient_id_strategy() == JpaStorageSettings.ClientIdStrategyEnum.ANY) {
|
||||
if (appProperties.getServer_id_strategy() == null) {
|
||||
ourLog.info("Defaulting server to use '" + JpaStorageSettings.IdStrategyEnum.UUID
|
||||
+ "' Server ID Strategy when using the '" + JpaStorageSettings.ClientIdStrategyEnum.ANY
|
||||
+ "' Client ID Strategy");
|
||||
ourLog.info(
|
||||
"Defaulting server to use '{}' Server ID Strategy when using the '{}' Client ID Strategy",
|
||||
JpaStorageSettings.IdStrategyEnum.UUID,
|
||||
JpaStorageSettings.ClientIdStrategyEnum.ANY);
|
||||
appProperties.setServer_id_strategy(JpaStorageSettings.IdStrategyEnum.UUID);
|
||||
} else if (appProperties.getServer_id_strategy() != JpaStorageSettings.IdStrategyEnum.UUID) {
|
||||
ourLog.warn("WARNING: '" + JpaStorageSettings.IdStrategyEnum.UUID
|
||||
+ "' Server ID Strategy is highly recommended when using the '"
|
||||
+ JpaStorageSettings.ClientIdStrategyEnum.ANY + "' Client ID Strategy");
|
||||
ourLog.warn(
|
||||
"WARNING: '{}' Server ID Strategy is highly recommended when using the '{}' Client ID Strategy",
|
||||
JpaStorageSettings.IdStrategyEnum.UUID,
|
||||
JpaStorageSettings.ClientIdStrategyEnum.ANY);
|
||||
}
|
||||
}
|
||||
if (appProperties.getServer_id_strategy() != null) {
|
||||
jpaStorageSettings.setResourceServerIdStrategy(appProperties.getServer_id_strategy());
|
||||
ourLog.info("Server configured to use '" + appProperties.getServer_id_strategy() + "' Server ID Strategy");
|
||||
ourLog.info("Server configured to use '{}' Server ID Strategy", appProperties.getServer_id_strategy());
|
||||
}
|
||||
|
||||
// to Disable the Resource History
|
||||
|
||||
@@ -248,7 +248,7 @@ public class StarterJpaConfig {
|
||||
|
||||
List<String> allAllowedCORSOrigins = appProperties.getCors().getAllowed_origin();
|
||||
allAllowedCORSOrigins.forEach(config::addAllowedOriginPattern);
|
||||
ourLog.info("CORS allows the following origins: " + String.join(", ", allAllowedCORSOrigins));
|
||||
ourLog.info("CORS allows the following origins: {}", String.join(", ", allAllowedCORSOrigins));
|
||||
|
||||
config.addExposedHeader("Location");
|
||||
config.addExposedHeader("Content-Location");
|
||||
@@ -467,9 +467,7 @@ public class StarterJpaConfig {
|
||||
registerCustomInterceptors(fhirServer, appContext, appProperties.getCustomInterceptorClasses());
|
||||
|
||||
// register the IPS Provider
|
||||
if (!theIpsOperationProvider.isEmpty()) {
|
||||
fhirServer.registerProvider(theIpsOperationProvider.get());
|
||||
}
|
||||
theIpsOperationProvider.ifPresent(fhirServer::registerProvider);
|
||||
|
||||
if (appProperties.getUserRequestRetryVersionConflictsInterceptorEnabled()) {
|
||||
fhirServer.registerInterceptor(new UserRequestRetryVersionConflictsInterceptor());
|
||||
@@ -500,7 +498,7 @@ public class StarterJpaConfig {
|
||||
throw new ConfigurationException("Interceptor class was not found on classpath: " + className, e);
|
||||
}
|
||||
|
||||
// first check if the class a Bean in the app context
|
||||
// first check if the class is a Bean in the app context
|
||||
Object interceptor = null;
|
||||
try {
|
||||
interceptor = theAppContext.getBean(clazz);
|
||||
@@ -541,7 +539,7 @@ public class StarterJpaConfig {
|
||||
throw new ConfigurationException("Provider class was not found on classpath: " + className, e);
|
||||
}
|
||||
|
||||
// first check if the class a Bean in the app context
|
||||
// first check if the class is a Bean in the app context
|
||||
Object provider = null;
|
||||
try {
|
||||
provider = theAppContext.getBean(clazz);
|
||||
|
||||
@@ -50,11 +50,11 @@ public class RepositoryValidationInterceptorFactoryR4 implements IRepositoryVali
|
||||
IBundleProvider results = structureDefinitionResourceProvider.search(new SearchParameterMap()
|
||||
.setLoadSynchronous(true)
|
||||
.add(StructureDefinition.SP_KIND, new TokenParam("resource")));
|
||||
Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size()).stream()
|
||||
Map<String, List<StructureDefinition>> structureDefinitions = results.getResources(0, results.size()).stream()
|
||||
.map(StructureDefinition.class::cast)
|
||||
.collect(Collectors.groupingBy(StructureDefinition::getType));
|
||||
|
||||
structureDefintions.forEach((key, value) -> {
|
||||
structureDefinitions.forEach((key, value) -> {
|
||||
String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
|
||||
repositoryValidatingRuleBuilder
|
||||
.forResourcesOfType(key)
|
||||
|
||||
@@ -50,11 +50,11 @@ public class RepositoryValidationInterceptorFactoryR4B implements IRepositoryVal
|
||||
IBundleProvider results = structureDefinitionResourceProvider.search(new SearchParameterMap()
|
||||
.setLoadSynchronous(true)
|
||||
.add(StructureDefinition.SP_KIND, new TokenParam("resource")));
|
||||
Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size()).stream()
|
||||
Map<String, List<StructureDefinition>> structureDefinitions = results.getResources(0, results.size()).stream()
|
||||
.map(StructureDefinition.class::cast)
|
||||
.collect(Collectors.groupingBy(StructureDefinition::getType));
|
||||
|
||||
structureDefintions.forEach((key, value) -> {
|
||||
structureDefinitions.forEach((key, value) -> {
|
||||
String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
|
||||
repositoryValidatingRuleBuilder
|
||||
.forResourcesOfType(key)
|
||||
|
||||
@@ -49,11 +49,11 @@ public class RepositoryValidationInterceptorFactoryR5 implements IRepositoryVali
|
||||
IBundleProvider results = structureDefinitionResourceProvider.search(new SearchParameterMap()
|
||||
.setLoadSynchronous(true)
|
||||
.add(StructureDefinition.SP_KIND, new TokenParam("resource")));
|
||||
Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size()).stream()
|
||||
Map<String, List<StructureDefinition>> structureDefinitions = results.getResources(0, results.size()).stream()
|
||||
.map(StructureDefinition.class::cast)
|
||||
.collect(Collectors.groupingBy(StructureDefinition::getType));
|
||||
|
||||
structureDefintions.forEach((key, value) -> {
|
||||
structureDefinitions.forEach((key, value) -> {
|
||||
String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
|
||||
repositoryValidatingRuleBuilder
|
||||
.forResourcesOfType(key)
|
||||
|
||||
@@ -22,6 +22,7 @@ import org.opencds.cqf.fhir.cr.hapi.common.ElmCacheResourceChangeListener;
|
||||
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.opencds.cqf.fhir.utility.client.TerminologyServerClientSettings;
|
||||
import org.springframework.boot.context.properties.ConfigurationProperties;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
import org.springframework.context.annotation.Conditional;
|
||||
@@ -57,6 +58,11 @@ public class CrCommonConfig {
|
||||
return theCrProperties.getCql().getTerminology();
|
||||
}
|
||||
|
||||
@Bean
|
||||
TerminologyServerClientSettings terminologyServerClientSettings(CrProperties theCrProperties) {
|
||||
return theCrProperties.getTerminologyServerClientSettings();
|
||||
}
|
||||
|
||||
@Bean
|
||||
public EvaluationSettings evaluationSettings(
|
||||
CrProperties theCrProperties,
|
||||
|
||||
@@ -1,11 +1,15 @@
|
||||
package ca.uhn.fhir.jpa.starter.cr;
|
||||
|
||||
import org.opencds.cqf.fhir.utility.client.TerminologyServerClientSettings;
|
||||
|
||||
public class CrProperties {
|
||||
private Boolean enabled;
|
||||
|
||||
private CareGapsProperties careGaps = new CareGapsProperties();
|
||||
private CqlProperties cql = new CqlProperties();
|
||||
|
||||
private TerminologyServerClientSettings terminologyServerClientSettings = new TerminologyServerClientSettings();
|
||||
|
||||
public Boolean getEnabled() {
|
||||
return enabled;
|
||||
}
|
||||
@@ -29,4 +33,12 @@ public class CrProperties {
|
||||
public void setCql(CqlProperties cql) {
|
||||
this.cql = cql;
|
||||
}
|
||||
|
||||
public TerminologyServerClientSettings getTerminologyServerClientSettings() {
|
||||
return terminologyServerClientSettings;
|
||||
}
|
||||
|
||||
public void setTerminologyServerClientSettings(TerminologyServerClientSettings terminologyServerClientSettings) {
|
||||
this.terminologyServerClientSettings = terminologyServerClientSettings;
|
||||
}
|
||||
}
|
||||
|
||||
@@ -11,7 +11,7 @@ public class PostInitProviderRegisterer {
|
||||
resourceProviderFactory.attach(new Observer(restfulServer));
|
||||
}
|
||||
|
||||
private class Observer implements IResourceProviderFactoryObserver {
|
||||
private static class Observer implements IResourceProviderFactoryObserver {
|
||||
private RestfulServer restfulServer;
|
||||
|
||||
public Observer(RestfulServer restfulServer) {
|
||||
|
||||
@@ -188,14 +188,12 @@ public class EnvironmentHelper {
|
||||
public static Map<String, Object> getAllProperties(PropertySource<?> aPropSource) {
|
||||
Map<String, Object> result = new HashMap<>();
|
||||
|
||||
if (aPropSource instanceof CompositePropertySource) {
|
||||
CompositePropertySource cps = (CompositePropertySource) aPropSource;
|
||||
if (aPropSource instanceof CompositePropertySource cps) {
|
||||
cps.getPropertySources().forEach(ps -> addAll(result, getAllProperties(ps)));
|
||||
return result;
|
||||
}
|
||||
|
||||
if (aPropSource instanceof EnumerablePropertySource<?>) {
|
||||
EnumerablePropertySource<?> ps = (EnumerablePropertySource<?>) aPropSource;
|
||||
if (aPropSource instanceof EnumerablePropertySource<?> ps) {
|
||||
Arrays.asList(ps.getPropertyNames()).forEach(key -> result.put(key, ps.getProperty(key)));
|
||||
return result;
|
||||
}
|
||||
|
||||
@@ -6,7 +6,7 @@ server:
|
||||
tomcat:
|
||||
# allow | as a separator in the URL
|
||||
relaxed-query-chars: "|"
|
||||
#Adds the option to go to eg. http://localhost:8080/actuator/health for seeing the running configuration
|
||||
#Adds the option to go to e.g. http://localhost:8080/actuator/health for seeing the running configuration
|
||||
#see https://docs.spring.io/spring-boot/docs/current/reference/html/actuator.html#actuator.endpoints
|
||||
management:
|
||||
#The following configuration will enable the actuator endpoints at /actuator/health, /actuator/info, /actuator/prometheus, /actuator/metrics. For security purposes, only /actuator/health is enabled by default.
|
||||
@@ -14,7 +14,7 @@ management:
|
||||
enabled-by-default: false
|
||||
web:
|
||||
exposure:
|
||||
include: 'health' # or e.g. 'info,health,prometheus,metrics' or '*' for all'
|
||||
include: 'health' # or e.g. 'info,health,prometheus,metrics' or '*' for all
|
||||
endpoint:
|
||||
info:
|
||||
enabled: true
|
||||
@@ -89,6 +89,11 @@ hapi:
|
||||
caregaps:
|
||||
reporter: "default"
|
||||
section_author: "default"
|
||||
terminologyServerClientSettings:
|
||||
maxRetryCount: 3
|
||||
retryIntervalMillis: 1000
|
||||
timeoutSeconds: 30
|
||||
socketTimeout: 60
|
||||
cql:
|
||||
use_embedded_libraries: true
|
||||
compiler:
|
||||
@@ -288,12 +293,12 @@ hapi:
|
||||
|
||||
# comma-separated list of fully qualified interceptor classes.
|
||||
# classes listed here will be fetched from the Spring context when combined with 'custom-bean-packages',
|
||||
# or will be instantiated via reflection using an no-arg contructor; then registered with the server
|
||||
# or will be instantiated via reflection using a no-arg constructor; then registered with the server
|
||||
#custom-interceptor-classes:
|
||||
|
||||
# comma-separated list of fully qualified provider classes.
|
||||
# classes listed here will be fetched from the Spring context when combined with 'custom-bean-packages',
|
||||
# or will be instantiated via reflection using an no-arg contructor; then registered with the server
|
||||
# or will be instantiated via reflection using a no-arg constructor; then registered with the server
|
||||
#custom-provider-classes:
|
||||
# specify what should be stored in meta.source based on StoreMetaSourceInformationEnum defaults to NONE
|
||||
# store_meta_source_information: NONE
|
||||
|
||||
@@ -3,7 +3,7 @@ server:
|
||||
# servlet:
|
||||
# context-path: /example/path
|
||||
port: 8080
|
||||
#Adds the option to go to eg. http://localhost:8080/actuator/health for seeing the running configuration
|
||||
#Adds the option to go to e.g. http://localhost:8080/actuator/health for seeing the running configuration
|
||||
#see https://docs.spring.io/spring-boot/docs/current/reference/html/actuator.html#actuator.endpoints
|
||||
management:
|
||||
#The following configuration will enable the actuator endpoints at /actuator/health, /actuator/info, /actuator/prometheus, /actuator/metrics. For security purposes, only /actuator/health is enabled by default.
|
||||
@@ -11,7 +11,7 @@ management:
|
||||
enabled-by-default: false
|
||||
web:
|
||||
exposure:
|
||||
include: 'health' # or e.g. 'info,health,prometheus,metrics' or '*' for all'
|
||||
include: 'health' # or e.g. 'info,health,prometheus,metrics' or '*' for all
|
||||
endpoint:
|
||||
info:
|
||||
enabled: true
|
||||
@@ -87,6 +87,11 @@ hapi:
|
||||
caregaps:
|
||||
reporter: "default"
|
||||
section_author: "default"
|
||||
terminologyServerClientSettings:
|
||||
maxRetryCount: 3
|
||||
retryIntervalMillis: 1000
|
||||
timeoutSeconds: 30
|
||||
socketTimeout: 60
|
||||
cql:
|
||||
use_embedded_libraries: true
|
||||
compiler:
|
||||
@@ -144,7 +149,7 @@ hapi:
|
||||
### forces the use of the https:// protocol for the returned server address.
|
||||
### alternatively, it may be set using the X-Forwarded-Proto header.
|
||||
# use_apache_address_strategy_https: false
|
||||
### enables the server to overwrite defaults on HTML, css, etc. under the url pattern of eg. /content/custom **
|
||||
### enables the server to overwrite defaults on HTML, css, etc. under the url pattern of e.g. /content/custom **
|
||||
### Folder with custom content MUST be named custom. If omitted then default content applies
|
||||
#custom_content_path: ./custom
|
||||
### enables the server host custom content. If e.g. the value ./configs/app is supplied then the content
|
||||
@@ -193,7 +198,7 @@ hapi:
|
||||
# enable_index_of_type: true
|
||||
# enable_index_contained_resource: false
|
||||
# resource_dbhistory_enabled: false
|
||||
### !!Extended Lucene/Elasticsearch Indexing is still a experimental feature, expect some features (e.g. _total=accurate) to not work as expected!!
|
||||
### !!Extended Lucene/Elasticsearch Indexing is still an experimental feature, expect some features (e.g. _total=accurate) to not work as expected!!
|
||||
### more information here: https://hapifhir.io/hapi-fhir/docs/server_jpa/elastic.html
|
||||
advanced_lucene_indexing: false
|
||||
search_index_full_text_enabled: false
|
||||
@@ -252,12 +257,12 @@ hapi:
|
||||
|
||||
# comma-separated list of fully qualified interceptor classes.
|
||||
# classes listed here will be fetched from the Spring context when combined with 'custom-bean-packages',
|
||||
# or will be instantiated via reflection using an no-arg contructor; then registered with the server
|
||||
# or will be instantiated via reflection using a no-arg constructor; then registered with the server
|
||||
#custom-interceptor-classes:
|
||||
|
||||
# comma-separated list of fully qualified provider classes.
|
||||
# classes listed here will be fetched from the Spring context when combined with 'custom-bean-packages',
|
||||
# or will be instantiated via reflection using an no-arg contructor; then registered with the server
|
||||
# or will be instantiated via reflection using a no-arg constructor; then registered with the server
|
||||
#custom-provider-classes:
|
||||
|
||||
# Threadpool size for BATCH'ed GETs in a bundle.
|
||||
|
||||
@@ -47,7 +47,7 @@
|
||||
<p>
|
||||
This UI can be customized!
|
||||
You might want to put rules on who can use this server here, or
|
||||
notices about privacy, or whatever else you want..
|
||||
notices about privacy, or whatever else you want.
|
||||
</p>
|
||||
</div>
|
||||
</div>
|
||||
@@ -63,7 +63,7 @@
|
||||
<script>
|
||||
// Function to check if a file exists using AJAX
|
||||
function fileExists(filePath, callback) {
|
||||
var xhr = new XMLHttpRequest();
|
||||
let xhr = new XMLHttpRequest();
|
||||
xhr.onreadystatechange = function() {
|
||||
if (xhr.readyState === 4) {
|
||||
callback(xhr.status === 200);
|
||||
@@ -77,7 +77,7 @@
|
||||
fileExists("content/custom/about.html", function(exists) {
|
||||
if (exists) {
|
||||
loadFile("content/custom/about.html", function(content) {
|
||||
var replacementContainer = document.getElementById("replacementAbout");
|
||||
let replacementContainer = document.getElementById("replacementAbout");
|
||||
replacementContainer.innerHTML = content;
|
||||
});
|
||||
}
|
||||
@@ -85,7 +85,7 @@
|
||||
|
||||
// Function to load file content using AJAX
|
||||
function loadFile(filePath, callback) {
|
||||
var xhr = new XMLHttpRequest();
|
||||
let xhr = new XMLHttpRequest();
|
||||
xhr.onreadystatechange = function() {
|
||||
if (xhr.readyState === 4 && xhr.status === 200) {
|
||||
callback(xhr.responseText);
|
||||
|
||||
@@ -80,7 +80,7 @@ class CdsHooksServletIT implements IServerSupport {
|
||||
ourCdsBase = "http://localhost:" + port + "/cds-services";
|
||||
|
||||
var cdsServicesJson = myCdsServiceRegistry.getCdsServicesJson();
|
||||
if (cdsServicesJson != null && cdsServicesJson.getServices() != null && !cdsServicesJson.getServices().isEmpty()) {
|
||||
if (cdsServicesJson != null && cdsServicesJson.getServices() != null) {
|
||||
var services = cdsServicesJson.getServices();
|
||||
for (int i = 0; i < services.size(); i++) {
|
||||
myCdsServiceRegistry.unregisterService(services.get(i).getId(), "CR");
|
||||
@@ -91,12 +91,12 @@ class CdsHooksServletIT implements IServerSupport {
|
||||
private Boolean hasCdsServices() throws IOException {
|
||||
var response = callCdsServicesDiscovery();
|
||||
|
||||
// NOTE: this is looking for a repsonse that indicates there are CDS services availalble.
|
||||
// NOTE: this is looking for a response that indicates there are CDS services available.
|
||||
// And empty response looks like: {"services": []}
|
||||
// Looking at the actual response string consumes the InputStream which has side-effects, making it tricky to compare the actual contents.
|
||||
// Hence the test just looks at the length to make this determination.
|
||||
// Looking at the actual response string consumes the InputStream which has side effects, making it tricky to compare the actual contents.
|
||||
// Hence, the test just looks at the length to make this determination.
|
||||
// The actual response has newlines in it which vary in size on some systems, but a value of 25 seems to work across linux/mac/windows
|
||||
// to ensure the repsonse actually contains CDS services in it
|
||||
// to ensure the response actually contains CDS services in it
|
||||
return response.getEntity().getContentLength() > 25 || response.getEntity().isChunked();
|
||||
}
|
||||
|
||||
@@ -120,23 +120,24 @@ class CdsHooksServletIT implements IServerSupport {
|
||||
@Test
|
||||
void testCdsHooks() throws IOException {
|
||||
loadBundle("r4/HelloWorld-Bundle.json", ourCtx, ourClient);
|
||||
await().atMost(10000, TimeUnit.MILLISECONDS).until(() -> hasCdsServices());
|
||||
var cdsRequest = "{\n" +
|
||||
" \"hookInstance\": \"12345\",\n" +
|
||||
" \"hook\": \"patient-view\",\n" +
|
||||
" \"context\": {\n" +
|
||||
" \"userId\": \"Practitioner/example\",\n" +
|
||||
" \"patientId\": \"Patient/example-hello-world\"\n" +
|
||||
" },\n" +
|
||||
" \"prefetch\": {\n" +
|
||||
" \"item1\": {\n" +
|
||||
" \"resourceType\": \"Patient\",\n" +
|
||||
" \"id\": \"example-hello-world\",\n" +
|
||||
" \"gender\": \"male\",\n" +
|
||||
" \"birthDate\": \"2000-01-01\"\n" +
|
||||
" }\n" +
|
||||
" }\n" +
|
||||
"}";
|
||||
await().atMost(10000, TimeUnit.MILLISECONDS).until(this::hasCdsServices);
|
||||
var cdsRequest = """
|
||||
{
|
||||
"hookInstance": "12345",
|
||||
"hook": "patient-view",
|
||||
"context": {
|
||||
"userId": "Practitioner/example",
|
||||
"patientId": "Patient/example-hello-world"
|
||||
},
|
||||
"prefetch": {
|
||||
"item1": {
|
||||
"resourceType": "Patient",
|
||||
"id": "example-hello-world",
|
||||
"gender": "male",
|
||||
"birthDate": "2000-01-01"
|
||||
}
|
||||
}
|
||||
}""";
|
||||
try (CloseableHttpClient httpClient = HttpClients.createDefault()) {
|
||||
HttpPost request = new HttpPost(ourCdsBase + "/hello-world");
|
||||
request.setEntity(new StringEntity(cdsRequest));
|
||||
@@ -158,7 +159,7 @@ class CdsHooksServletIT implements IServerSupport {
|
||||
@Test
|
||||
void testRec10() throws IOException {
|
||||
loadBundle("r4/opioidcds-10-order-sign-bundle.json", ourCtx, ourClient);
|
||||
await().atMost(20000, TimeUnit.MILLISECONDS).until(() -> hasCdsServices());
|
||||
await().atMost(20000, TimeUnit.MILLISECONDS).until(this::hasCdsServices);
|
||||
var fhirServer = " \"fhirServer\": " + "\"" + ourServerBase + "\"" + ",\n";
|
||||
var cdsRequest = "{\n" +
|
||||
" \"hookInstance\": \"055b009c-4a7d-4db4-a35e-0e5198918ed1\",\n" +
|
||||
|
||||
@@ -13,13 +13,10 @@ import java.io.IOException;
|
||||
|
||||
import java.util.Date;
|
||||
import java.util.GregorianCalendar;
|
||||
import java.util.List;
|
||||
|
||||
import co.elastic.clients.elasticsearch.ElasticsearchClient;
|
||||
import co.elastic.clients.elasticsearch.indices.IndexSettings;
|
||||
import co.elastic.clients.json.JsonData;
|
||||
import jakarta.annotation.PreDestroy;
|
||||
import org.elasticsearch.client.RequestOptions;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.model.Bundle;
|
||||
import org.hl7.fhir.r4.model.DateTimeType;
|
||||
@@ -68,8 +65,7 @@ import org.testcontainers.junit.jupiter.Testcontainers;
|
||||
"spring.jpa.properties.hibernate.search.backend.analysis.configurer=ca.uhn.fhir.jpa.search.elastic.HapiElasticsearchAnalysisConfigurer"
|
||||
})
|
||||
@ContextConfiguration(initializers = ElasticsearchLastNR4IT.Initializer.class)
|
||||
public class ElasticsearchLastNR4IT {
|
||||
|
||||
class ElasticsearchLastNR4IT {
|
||||
private IGenericClient ourClient;
|
||||
private FhirContext ourCtx;
|
||||
|
||||
|
||||
@@ -33,7 +33,7 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
"hapi.fhir.partitioning.database_partition_mode_enabled=true",
|
||||
"hapi.fhir.partitioning.patient_id_partitioning_mode=true"
|
||||
})
|
||||
public class ExampleServerDbpmR5IT {
|
||||
class ExampleServerDbpmR5IT {
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu2IT.class);
|
||||
private IGenericClient ourClient;
|
||||
|
||||
@@ -51,8 +51,6 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
"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(ExampleServerDstu3IT.class);
|
||||
|
||||
@@ -39,7 +39,7 @@ class ExampleServerR4BIT {
|
||||
@Order(0)
|
||||
void testCreateAndRead() {
|
||||
String methodName = "testCreateAndRead";
|
||||
ourLog.info("Entering " + methodName + "()...");
|
||||
ourLog.info("Entering {}()...", methodName);
|
||||
|
||||
Patient pt = new Patient();
|
||||
pt.setActive(true);
|
||||
@@ -56,51 +56,52 @@ class ExampleServerR4BIT {
|
||||
|
||||
@Test
|
||||
void testBatchPutWithIdenticalTags() {
|
||||
String batchPuts = "{\n" +
|
||||
"\t\"resourceType\": \"Bundle\",\n" +
|
||||
"\t\"id\": \"patients\",\n" +
|
||||
"\t\"type\": \"batch\",\n" +
|
||||
"\t\"entry\": [\n" +
|
||||
"\t\t{\n" +
|
||||
"\t\t\t\"request\": {\n" +
|
||||
"\t\t\t\t\"method\": \"PUT\",\n" +
|
||||
"\t\t\t\t\"url\": \"Patient/pat-1\"\n" +
|
||||
"\t\t\t},\n" +
|
||||
"\t\t\t\"resource\": {\n" +
|
||||
"\t\t\t\t\"resourceType\": \"Patient\",\n" +
|
||||
"\t\t\t\t\"id\": \"pat-1\",\n" +
|
||||
"\t\t\t\t\"meta\": {\n" +
|
||||
"\t\t\t\t\t\"tag\": [\n" +
|
||||
"\t\t\t\t\t\t{\n" +
|
||||
"\t\t\t\t\t\t\t\"system\": \"http://mysystem.org\",\n" +
|
||||
"\t\t\t\t\t\t\t\"code\": \"value2\"\n" +
|
||||
"\t\t\t\t\t\t}\n" +
|
||||
"\t\t\t\t\t]\n" +
|
||||
"\t\t\t\t}\n" +
|
||||
"\t\t\t},\n" +
|
||||
"\t\t\t\"fullUrl\": \"/Patient/pat-1\"\n" +
|
||||
"\t\t},\n" +
|
||||
"\t\t{\n" +
|
||||
"\t\t\t\"request\": {\n" +
|
||||
"\t\t\t\t\"method\": \"PUT\",\n" +
|
||||
"\t\t\t\t\"url\": \"Patient/pat-2\"\n" +
|
||||
"\t\t\t},\n" +
|
||||
"\t\t\t\"resource\": {\n" +
|
||||
"\t\t\t\t\"resourceType\": \"Patient\",\n" +
|
||||
"\t\t\t\t\"id\": \"pat-2\",\n" +
|
||||
"\t\t\t\t\"meta\": {\n" +
|
||||
"\t\t\t\t\t\"tag\": [\n" +
|
||||
"\t\t\t\t\t\t{\n" +
|
||||
"\t\t\t\t\t\t\t\"system\": \"http://mysystem.org\",\n" +
|
||||
"\t\t\t\t\t\t\t\"code\": \"value2\"\n" +
|
||||
"\t\t\t\t\t\t}\n" +
|
||||
"\t\t\t\t\t]\n" +
|
||||
"\t\t\t\t}\n" +
|
||||
"\t\t\t},\n" +
|
||||
"\t\t\t\"fullUrl\": \"/Patient/pat-2\"\n" +
|
||||
"\t\t}\n" +
|
||||
"\t]\n" +
|
||||
"}";
|
||||
String batchPuts = """
|
||||
{
|
||||
\t"resourceType": "Bundle",
|
||||
\t"id": "patients",
|
||||
\t"type": "batch",
|
||||
\t"entry": [
|
||||
\t\t{
|
||||
\t\t\t"request": {
|
||||
\t\t\t\t"method": "PUT",
|
||||
\t\t\t\t"url": "Patient/pat-1"
|
||||
\t\t\t},
|
||||
\t\t\t"resource": {
|
||||
\t\t\t\t"resourceType": "Patient",
|
||||
\t\t\t\t"id": "pat-1",
|
||||
\t\t\t\t"meta": {
|
||||
\t\t\t\t\t"tag": [
|
||||
\t\t\t\t\t\t{
|
||||
\t\t\t\t\t\t\t"system": "http://mysystem.org",
|
||||
\t\t\t\t\t\t\t"code": "value2"
|
||||
\t\t\t\t\t\t}
|
||||
\t\t\t\t\t]
|
||||
\t\t\t\t}
|
||||
\t\t\t},
|
||||
\t\t\t"fullUrl": "/Patient/pat-1"
|
||||
\t\t},
|
||||
\t\t{
|
||||
\t\t\t"request": {
|
||||
\t\t\t\t"method": "PUT",
|
||||
\t\t\t\t"url": "Patient/pat-2"
|
||||
\t\t\t},
|
||||
\t\t\t"resource": {
|
||||
\t\t\t\t"resourceType": "Patient",
|
||||
\t\t\t\t"id": "pat-2",
|
||||
\t\t\t\t"meta": {
|
||||
\t\t\t\t\t"tag": [
|
||||
\t\t\t\t\t\t{
|
||||
\t\t\t\t\t\t\t"system": "http://mysystem.org",
|
||||
\t\t\t\t\t\t\t"code": "value2"
|
||||
\t\t\t\t\t\t}
|
||||
\t\t\t\t\t]
|
||||
\t\t\t\t}
|
||||
\t\t\t},
|
||||
\t\t\t"fullUrl": "/Patient/pat-2"
|
||||
\t\t}
|
||||
\t]
|
||||
}""";
|
||||
Bundle bundle = FhirContext.forR4B().newJsonParser().parseResource(Bundle.class, batchPuts);
|
||||
ourClient.transaction().withBundle(bundle).execute();
|
||||
}
|
||||
|
||||
@@ -18,7 +18,6 @@ import org.apache.http.client.methods.CloseableHttpResponse;
|
||||
import org.apache.http.client.methods.HttpGet;
|
||||
import org.apache.http.impl.client.CloseableHttpClient;
|
||||
import org.apache.http.impl.client.HttpClients;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.model.*;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
@@ -34,7 +33,6 @@ import org.springframework.boot.test.web.server.LocalServerPort;
|
||||
import java.io.IOException;
|
||||
import java.net.URI;
|
||||
import java.net.URISyntaxException;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
import java.util.concurrent.TimeUnit;
|
||||
|
||||
@@ -44,6 +42,7 @@ import static org.hamcrest.Matchers.equalTo;
|
||||
import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertFalse;
|
||||
import static org.junit.jupiter.api.Assertions.assertInstanceOf;
|
||||
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;
|
||||
@@ -92,7 +91,7 @@ class ExampleServerR4IT implements IServerSupport {
|
||||
@Order(0)
|
||||
void testCreateAndRead() {
|
||||
String methodName = "testCreateAndRead";
|
||||
ourLog.info("Entering " + methodName + "()...");
|
||||
ourLog.info("Entering {}()...", methodName);
|
||||
|
||||
Patient pt = new Patient();
|
||||
pt.setActive(true);
|
||||
@@ -132,7 +131,7 @@ class ExampleServerR4IT implements IServerSupport {
|
||||
List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
|
||||
assertFalse(response.isEmpty());
|
||||
Parameters.ParametersParameterComponent component = response.get(0);
|
||||
assertTrue(component.getResource() instanceof MeasureReport);
|
||||
assertInstanceOf(MeasureReport.class, component.getResource());
|
||||
MeasureReport report = (MeasureReport) component.getResource();
|
||||
assertEquals(measureUrl + "|0.0.003", report.getMeasure());
|
||||
}
|
||||
@@ -150,66 +149,57 @@ class ExampleServerR4IT implements IServerSupport {
|
||||
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);
|
||||
assertInstanceOf(Period.class, results.getParameter("return").getValue());
|
||||
}
|
||||
|
||||
@Test
|
||||
void testBatchPutWithIdenticalTags() {
|
||||
String batchPuts = "{\n" +
|
||||
"\t\"resourceType\": \"Bundle\",\n" +
|
||||
"\t\"id\": \"patients\",\n" +
|
||||
"\t\"type\": \"batch\",\n" +
|
||||
"\t\"entry\": [\n" +
|
||||
"\t\t{\n" +
|
||||
"\t\t\t\"request\": {\n" +
|
||||
"\t\t\t\t\"method\": \"PUT\",\n" +
|
||||
"\t\t\t\t\"url\": \"Patient/pat-1\"\n" +
|
||||
"\t\t\t},\n" +
|
||||
"\t\t\t\"resource\": {\n" +
|
||||
"\t\t\t\t\"resourceType\": \"Patient\",\n" +
|
||||
"\t\t\t\t\"id\": \"pat-1\",\n" +
|
||||
"\t\t\t\t\"meta\": {\n" +
|
||||
"\t\t\t\t\t\"tag\": [\n" +
|
||||
"\t\t\t\t\t\t{\n" +
|
||||
"\t\t\t\t\t\t\t\"system\": \"http://mysystem.org\",\n" +
|
||||
"\t\t\t\t\t\t\t\"code\": \"value2\"\n" +
|
||||
"\t\t\t\t\t\t}\n" +
|
||||
"\t\t\t\t\t]\n" +
|
||||
"\t\t\t\t}\n" +
|
||||
"\t\t\t},\n" +
|
||||
"\t\t\t\"fullUrl\": \"/Patient/pat-1\"\n" +
|
||||
"\t\t},\n" +
|
||||
"\t\t{\n" +
|
||||
"\t\t\t\"request\": {\n" +
|
||||
"\t\t\t\t\"method\": \"PUT\",\n" +
|
||||
"\t\t\t\t\"url\": \"Patient/pat-2\"\n" +
|
||||
"\t\t\t},\n" +
|
||||
"\t\t\t\"resource\": {\n" +
|
||||
"\t\t\t\t\"resourceType\": \"Patient\",\n" +
|
||||
"\t\t\t\t\"id\": \"pat-2\",\n" +
|
||||
"\t\t\t\t\"meta\": {\n" +
|
||||
"\t\t\t\t\t\"tag\": [\n" +
|
||||
"\t\t\t\t\t\t{\n" +
|
||||
"\t\t\t\t\t\t\t\"system\": \"http://mysystem.org\",\n" +
|
||||
"\t\t\t\t\t\t\t\"code\": \"value2\"\n" +
|
||||
"\t\t\t\t\t\t}\n" +
|
||||
"\t\t\t\t\t]\n" +
|
||||
"\t\t\t\t}\n" +
|
||||
"\t\t\t},\n" +
|
||||
"\t\t\t\"fullUrl\": \"/Patient/pat-2\"\n" +
|
||||
"\t\t}\n" +
|
||||
"\t]\n" +
|
||||
"}";
|
||||
String batchPuts = """
|
||||
{
|
||||
\t"resourceType": "Bundle",
|
||||
\t"id": "patients",
|
||||
\t"type": "batch",
|
||||
\t"entry": [
|
||||
\t\t{
|
||||
\t\t\t"request": {
|
||||
\t\t\t\t"method": "PUT",
|
||||
\t\t\t\t"url": "Patient/pat-1"
|
||||
\t\t\t},
|
||||
\t\t\t"resource": {
|
||||
\t\t\t\t"resourceType": "Patient",
|
||||
\t\t\t\t"id": "pat-1",
|
||||
\t\t\t\t"meta": {
|
||||
\t\t\t\t\t"tag": [
|
||||
\t\t\t\t\t\t{
|
||||
\t\t\t\t\t\t\t"system": "http://mysystem.org",
|
||||
\t\t\t\t\t\t\t"code": "value2"
|
||||
\t\t\t\t\t\t}
|
||||
\t\t\t\t\t]
|
||||
\t\t\t\t}
|
||||
\t\t\t},
|
||||
\t\t\t"fullUrl": "/Patient/pat-1"
|
||||
\t\t},
|
||||
\t\t{
|
||||
\t\t\t"request": {
|
||||
\t\t\t\t"method": "PUT",
|
||||
\t\t\t\t"url": "Patient/pat-2"
|
||||
\t\t\t},
|
||||
\t\t\t"resource": {
|
||||
\t\t\t\t"resourceType": "Patient",
|
||||
\t\t\t\t"id": "pat-2",
|
||||
\t\t\t\t"meta": {
|
||||
\t\t\t\t\t"tag": [
|
||||
\t\t\t\t\t\t{
|
||||
\t\t\t\t\t\t\t"system": "http://mysystem.org",
|
||||
\t\t\t\t\t\t\t"code": "value2"
|
||||
\t\t\t\t\t\t}
|
||||
\t\t\t\t\t]
|
||||
\t\t\t\t}
|
||||
\t\t\t},
|
||||
\t\t\t"fullUrl": "/Patient/pat-2"
|
||||
\t\t}
|
||||
\t]
|
||||
}""";
|
||||
Bundle bundle = FhirContext.forR4().newJsonParser().parseResource(Bundle.class, batchPuts);
|
||||
ourClient.transaction().withBundle(bundle).execute();
|
||||
}
|
||||
@@ -277,8 +267,8 @@ class ExampleServerR4IT implements IServerSupport {
|
||||
var reporter = crProperties.getCareGaps().getReporter();
|
||||
var author = crProperties.getCareGaps().getSection_author();
|
||||
|
||||
assertTrue(reporter.equals("Organization/alphora"));
|
||||
assertTrue(author.equals("Organization/alphora-author"));
|
||||
assertEquals("Organization/alphora", reporter);
|
||||
assertEquals("Organization/alphora-author", author);
|
||||
|
||||
String periodStartValid = "2019-01-01";
|
||||
String periodEndValid = "2019-12-31";
|
||||
@@ -327,7 +317,7 @@ class ExampleServerR4IT implements IServerSupport {
|
||||
@Test
|
||||
void testDiffOperationIsRegistered() {
|
||||
String methodName = "testDiff";
|
||||
ourLog.info("Entering " + methodName + "()...");
|
||||
ourLog.info("Entering {}()...", methodName);
|
||||
|
||||
Patient pt = new Patient();
|
||||
pt.setActive(true);
|
||||
|
||||
@@ -4,7 +4,6 @@ import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
||||
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
|
||||
import ca.uhn.fhir.rest.client.api.IGenericClient;
|
||||
import com.google.common.base.Charsets;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.hl7.fhir.instance.model.api.IBaseBundle;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
@@ -15,6 +14,7 @@ import java.io.File;
|
||||
import java.io.FileInputStream;
|
||||
import java.io.IOException;
|
||||
import java.io.InputStream;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
|
||||
public interface IServerSupport {
|
||||
|
||||
@@ -45,6 +45,6 @@ public interface IServerSupport {
|
||||
Resource resource = resourceLoader.getResource(theLocation);
|
||||
is = resource.getInputStream();
|
||||
}
|
||||
return IOUtils.toString(is, Charsets.UTF_8);
|
||||
return IOUtils.toString(is, StandardCharsets.UTF_8);
|
||||
}
|
||||
}
|
||||
|
||||
@@ -1,13 +1,9 @@
|
||||
package ca.uhn.fhir.jpa.starter;
|
||||
|
||||
import org.opencds.cqf.fhir.cql.EvaluationSettings;
|
||||
import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
|
||||
import org.opencds.cqf.fhir.utility.ValidationProfile;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
import org.springframework.context.annotation.Configuration;
|
||||
|
||||
import java.util.Map;
|
||||
|
||||
@Configuration
|
||||
public class MeasureEvaluationConfig {
|
||||
|
||||
|
||||
@@ -17,12 +17,10 @@ import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
|
||||
import org.junit.jupiter.api.Assertions;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.boot.test.context.SpringBootTest;
|
||||
import org.springframework.boot.test.web.server.LocalServerPort;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
|
||||
import ca.uhn.fhir.rest.api.MethodOutcome;
|
||||
import ca.uhn.fhir.rest.client.api.IGenericClient;
|
||||
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
|
||||
@@ -100,11 +98,9 @@ public class ParallelUpdatesVersionConflictTest {
|
||||
List<Callable<Integer>> callables = new ArrayList<>();
|
||||
for (int i = 0; i < threadCnt; i++) {
|
||||
final int cnt = i;
|
||||
Callable<Integer> callable = new Callable<>() {
|
||||
@Override
|
||||
public Integer call() throws Exception {
|
||||
Callable<Integer> callable = () -> {
|
||||
Patient pat = new Patient();
|
||||
//make sure to change something so the server doesnt short circuit on a no-op
|
||||
//make sure to change something so the server doesn't short circuit on a no-op
|
||||
pat.addName().setFamily("fam-" + cnt);
|
||||
pat.setId(patientId);
|
||||
|
||||
@@ -135,10 +131,9 @@ public class ParallelUpdatesVersionConflictTest {
|
||||
MethodOutcome outcome = client.update().resource(pat).withId(patientId)
|
||||
.withAdditionalHeader(headerName, "retry; max-retries=10")
|
||||
.execute();
|
||||
ourLog.trace("updated patient: " + outcome.getResponseStatusCode());
|
||||
ourLog.trace("updated patient: {}", outcome.getResponseStatusCode());
|
||||
return outcome.getResponseStatusCode();
|
||||
}
|
||||
}
|
||||
};
|
||||
callables.add(callable);
|
||||
}
|
||||
|
||||
@@ -43,7 +43,7 @@ public class SocketImplementation {
|
||||
|
||||
/**
|
||||
* This method is executed when the client is connecting to the server.
|
||||
* In this case, we are sending a message to create the subscription dynamiclly
|
||||
* In this case, we are sending a message to create the subscription dynamically
|
||||
*
|
||||
* @param session
|
||||
*/
|
||||
@@ -58,7 +58,6 @@ public class SocketImplementation {
|
||||
|
||||
ourLog.info("Connection: DONE");
|
||||
} catch (Throwable t) {
|
||||
t.printStackTrace();
|
||||
ourLog.error("Failure", t);
|
||||
}
|
||||
}
|
||||
@@ -70,7 +69,7 @@ public class SocketImplementation {
|
||||
*/
|
||||
@OnMessage
|
||||
public void onMessage(String theMsg) {
|
||||
ourLog.info("Got msg: " + theMsg);
|
||||
ourLog.info("Got msg: {}", theMsg);
|
||||
myMessages.add(theMsg);
|
||||
|
||||
if (theMsg.startsWith("bound ")) {
|
||||
@@ -78,7 +77,7 @@ public class SocketImplementation {
|
||||
mySubsId = (theMsg.substring("bound ".length()));
|
||||
} else if (myGotBound && theMsg.startsWith("add " + mySubsId + "\n")) {
|
||||
String text = theMsg.substring(("add " + mySubsId + "\n").length());
|
||||
ourLog.info("text: " + text);
|
||||
ourLog.info("text: {}", text);
|
||||
} else if (theMsg.startsWith("ping ")) {
|
||||
myPingCount++;
|
||||
} else {
|
||||
|
||||
@@ -21,8 +21,7 @@ public class CustomInterceptorBean {
|
||||
IBaseResource resource = servletRequestDetails.getResource();
|
||||
|
||||
// add an extension before saving the resource to mark it
|
||||
if (opType == RestOperationTypeEnum.CREATE && resource instanceof Patient) {
|
||||
Patient pat = (Patient) resource;
|
||||
if (opType == RestOperationTypeEnum.CREATE && resource instanceof Patient pat) {
|
||||
Extension ext = pat.addExtension();
|
||||
ext.setUrl("http://some.custom.pkg1/CustomInterceptorBean");
|
||||
ext.setValue(new StringType("CustomInterceptorBean wuz here"));
|
||||
|
||||
@@ -16,8 +16,7 @@ public class CustomInterceptorPojo {
|
||||
IBaseResource resource = servletRequestDetails.getResource();
|
||||
|
||||
// add an extension before saving the resource to mark it
|
||||
if (opType == RestOperationTypeEnum.CREATE && resource instanceof Patient) {
|
||||
Patient pat = (Patient) resource;
|
||||
if (opType == RestOperationTypeEnum.CREATE && resource instanceof Patient pat) {
|
||||
Extension ext = pat.addExtension();
|
||||
ext.setUrl("http://some.custom.pkg1/CustomInterceptorPojo");
|
||||
ext.setValue(new StringType("CustomInterceptorPojo wuz here"));
|
||||
|
||||
@@ -4,7 +4,7 @@ management:
|
||||
enabled-by-default: false
|
||||
web:
|
||||
exposure:
|
||||
include: 'info,health,prometheus,metrics' # or '*' for all'
|
||||
include: 'info,health,prometheus,metrics' # or '*' for all
|
||||
endpoint:
|
||||
info:
|
||||
enabled: true
|
||||
@@ -31,7 +31,7 @@ spring:
|
||||
allow-bean-definition-overriding: true
|
||||
flyway:
|
||||
enabled: false
|
||||
check-location: false
|
||||
fail-on-missing-locations: false
|
||||
baselineOnMigrate: true
|
||||
datasource:
|
||||
url: jdbc:h2:mem:test_mem
|
||||
@@ -126,7 +126,7 @@ hapi:
|
||||
# enable_index_missing_fields: false
|
||||
# enable_index_of_type: true
|
||||
# enable_index_contained_resource: false
|
||||
### !!Extended Lucene/Elasticsearch Indexing is still a experimental feature, expect some features (e.g. _total=accurate) to not work as expected!!
|
||||
### !!Extended Lucene/Elasticsearch Indexing is still an experimental feature, expect some features (e.g. _total=accurate) to not work as expected!!
|
||||
### more information here: https://hapifhir.io/hapi-fhir/docs/server_jpa/elastic.html
|
||||
advanced_lucene_indexing: false
|
||||
search_index_full_text_enabled: false
|
||||
|
||||
@@ -15,7 +15,7 @@ on the jetbrains website, in addition to the [API reference][Link-HTTP-Client-Re
|
||||
|
||||
### Formatting
|
||||
Each test file corresponds to a given section within the hapifhir documentation as close as possible. For
|
||||
example, there is a `plain_server.rest` file, which attemps to smoke test all basic functionality outlined in the section
|
||||
example, there is a `plain_server.rest` file, which attempts to smoke test all basic functionality outlined in the section
|
||||
[within the docs][Link-HAPI-FHIR-docs-plain-server].
|
||||
|
||||
Individual tests are formatted as follows:
|
||||
@@ -38,7 +38,7 @@ To run these tests against a specific server, configure the server details withi
|
||||
```
|
||||
|
||||
### Running the Tests
|
||||
Within IntelliJ, right click the file you wish to run tests in and select the `Run All` option from the menu.
|
||||
Within IntelliJ, right-click the file you wish to run tests in and select the `Run All` option from the menu.
|
||||
|
||||
**Important:** Tests may not work individually when run. Often times, tests need to be run sequentially, as they depend
|
||||
on resources/references from previous tests to complete. _(An example of this would be adding a Patient, saving the id,
|
||||
|
||||
@@ -81,13 +81,13 @@ Content-Type: application/json
|
||||
client.assert(resourceType === "Bundle", "Expected 'Bundle' but received '" + resourceType + "'");
|
||||
});
|
||||
client.test("All patient additions successful", function() {
|
||||
for (var index = 0; index < response.body.entry.length; index++) {
|
||||
for (let index = 0; index < response.body.entry.length; index++) {
|
||||
client.assert(response.body.entry[index].response.status === "201 Created", "Expected '201 Created' for patient index " + index + " but received '" + response.body.entry[index].response.status + "'");
|
||||
}
|
||||
});
|
||||
const batch_patient_location = response.body.entry[0].response.location;
|
||||
const indexOfHistory = batch_patient_location.lastIndexOf("/_history");
|
||||
var trimmed_location = batch_patient_location.substring(0, indexOfHistory);
|
||||
let trimmed_location = batch_patient_location.substring(0, indexOfHistory);
|
||||
trimmed_location = trimmed_location.replace("Patient/", "")
|
||||
client.global.set("batch_patient_id", trimmed_location);
|
||||
%}
|
||||
|
||||
Reference in New Issue
Block a user