Update Clinical Reasoning plugin

.vscode/launch.json

@@ -7,7 +7,18 @@
  "cwd": "${workspaceFolder}",
  "mainClass": "ca.uhn.fhir.jpa.starter.Application",
  "projectName": "hapi-fhir-jpaserver-starter",
- "args": "",
+ "vmArgs": [
+ "-XX:TieredStopAtLevel=1",
+ // "-Ddebug=true",
+ // "-Dloader.debug=true",
+ "-Dhapi.fhir.bulk_export_enabled=false",
+ "-Dspring.batch.job.enabled=false",
+ "-Dspring.main.allow-bean-definition-overriding=true",
+ "-Dhapi.fhir.cdshooks.enabled=true",
+ "-Dhapi.fhir.cr.enabled=true",
+ "-Dspring.main.allow-bean-definition-overriding=true"
+
+ ],
  "envFile": "${workspaceFolder}/.env"
  }
  ]

.vscode/settings.json

@@ -5,5 +5,6 @@
  "**/.settings": true,
  "**/.factorypath": true
  },
- "java.compile.nullAnalysis.mode": "disabled"
+ "java.compile.nullAnalysis.mode": "disabled",
+ "java.configuration.updateBuildConfiguration": "automatic"
 }

README.md

@@ -483,7 +483,11 @@ The server may be configured with subscription support by enabling properties in
 
 ## Enabling Clinical Reasoning
 
-Set `hapi.fhir.cr_enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable [Clinical Quality Language](https://cql.hl7.org/) on this server.
+Set `hapi.fhir.cr_enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable [Clinical Quality Language](https://cql.hl7.org/) on this server. An alternate settings file, [cds.application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/cds.application.yaml), exists with the Clinical Reasoning module enabled and default settings that have been found to work with most CDS and dQM test cases.
+
+## Enabling CDS Hooks
+
+Set `hapi.fhir.cdshooks.enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable [CDS Hooks](https://cds-hooks.org/) on this server. The Clinical Reasoning module must also be enabled because this implementation of CDS Hooks includes [CDS on FHIR](https://build.fhir.org/clinicalreasoning-cds-on-fhir.html). An example CDS Service using CDS on FHIR is available in the CdsHooksServletIT test class.
 
 ## Enabling MDM (EMPI)
 

pom.xml

@@ -42,6 +42,15 @@
 
  <dependencyManagement>
  <dependencies>
+
+ <!-- Temporarily override CR depedencies for debugging -->
+<!-- <dependency>-->
+<!-- <groupId>org.opencds.cqf.fhir</groupId>-->
+<!-- <artifactId>cqf-fhir-bom</artifactId>-->
+<!-- <version>3.4.0</version>-->
+<!-- <type>pom</type>-->
+<!-- <scope>import</scope>-->
+<!-- </dependency>-->
  <dependency>
  <groupId>org.glassfish.jaxb</groupId>
  <artifactId>jaxb-runtime</artifactId>

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/ProviderConfiguration.java

@@ -3,10 +3,6 @@
 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;
 
@@ -16,8 +12,7 @@ public ProviderConfiguration(boolean cqlLoggingEnabled, String clientIdHeaderNam
  }
 
  public ProviderConfiguration(CdsHooksProperties cdsProperties, CrProperties crProperties) {
- this.clientIdHeaderName = cdsProperties.getClientIdHeaderName();
- this.cqlLoggingEnabled = crProperties.isCqlRuntimeDebugLoggingEnabled();
+ this(crProperties.getCql().getRuntime().isDebugLoggingEnabled(), cdsProperties.getClientIdHeaderName());
  }
 
  public String getClientIdHeaderName() {

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/StarterCdsHooksConfig.java

@@ -1,11 +1,21 @@
 package ca.uhn.fhir.jpa.starter.cdshooks;
 
+import ca.uhn.fhir.jpa.starter.cr.CrCommonConfig;
 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 ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrServiceRegistry;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.ICdsCrServiceRegistry;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.CdsCrDiscoveryServiceRegistry;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.ICdsCrDiscoveryServiceRegistry;
+import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsPrefetchDaoSvc;
+import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsPrefetchFhirClientSvc;
+import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsPrefetchSvc;
+import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsResolutionStrategySvc;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
 import org.springframework.boot.web.servlet.ServletRegistrationBean;
@@ -16,8 +26,38 @@
 
 @Configuration
 @Conditional({CdsHooksConfigCondition.class, CrConfigCondition.class})
-@Import(CdsHooksConfig.class)
+@Import({CdsHooksConfig.class, CrCommonConfig.class})
 public class StarterCdsHooksConfig {
+
+// @Bean
+// CdsPrefetchSvc cdsPrefetchSvc(
+// CdsResolutionStrategySvc theCdsResolutionStrategySvc,
+// CdsPrefetchDaoSvc theResourcePrefetchDao,
+// CdsPrefetchFhirClientSvc theResourcePrefetchFhirClient,
+// ICdsHooksDaoAuthorizationSvc theCdsHooksDaoAuthorizationSvc) {
+// return new ModuleConfigurationPrefetchSvc(
+// theCdsResolutionStrategySvc,
+// theResourcePrefetchDao,
+// theResourcePrefetchFhirClient,
+// theCdsHooksDaoAuthorizationSvc);
+// }
+
+ @Bean
+ public ICdsCrDiscoveryServiceRegistry cdsCrDiscoveryServiceRegistry() {
+ CdsCrDiscoveryServiceRegistry registry = new CdsCrDiscoveryServiceRegistry();
+ registry.unregister(FhirVersionEnum.R4);
+ registry.register(FhirVersionEnum.R4, UpdatedCrDiscoveryServiceR4.class);
+ return registry;
+ }
+
+ @Bean
+ public ICdsCrServiceRegistry cdsCrServiceRegistry() {
+ CdsCrServiceRegistry registry = new CdsCrServiceRegistry();
+ registry.unregister(FhirVersionEnum.R4);
+ registry.register(FhirVersionEnum.R4, UpdatedCdsCrServiceR4.class);
+ return registry;
+ }
+
  @Bean
  public CdsHooksProperties cdsHooksProperties() {
  return new CdsHooksProperties();

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/UpdatedCdsCrServiceR4.java

@@ -0,0 +1,30 @@
+package ca.uhn.fhir.jpa.starter.cdshooks;
+
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.hapi.fhir.cdshooks.api.ICdsConfigService;
+import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceRequestJson;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrServiceR4;
+import org.hl7.fhir.r4.model.BooleanType;
+import org.hl7.fhir.r4.model.Parameters;
+import org.opencds.cqf.fhir.api.Repository;
+
+import java.util.stream.Collectors;
+
+import static ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrConstants.APPLY_PARAMETER_DATA;
+import static ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrConstants.APPLY_PARAMETER_DATA_ENDPOINT;
+import static org.opencds.cqf.fhir.utility.r4.Parameters.part;
+
+public class UpdatedCdsCrServiceR4 extends CdsCrServiceR4 {
+ public UpdatedCdsCrServiceR4(RequestDetails theRequestDetails, Repository theRepository, ICdsConfigService theCdsConfigService) {
+ super(theRequestDetails, theRepository, theCdsConfigService);
+ }
+
+ @Override
+ public Parameters encodeParams(CdsServiceRequestJson theJson) {
+ Parameters parameters = super.encodeParams(theJson);
+ if (parameters.hasParameter(APPLY_PARAMETER_DATA)) {
+ parameters.addParameter(part("useServerData", new BooleanType(false)));
+ }
+ return parameters;
+ }
+}

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/UpdatedCrDiscoveryServiceR4.java

@@ -0,0 +1,12 @@
+package ca.uhn.fhir.jpa.starter.cdshooks;
+
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.CrDiscoveryServiceR4;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.opencds.cqf.fhir.api.Repository;
+
+public class UpdatedCrDiscoveryServiceR4 extends CrDiscoveryServiceR4 {
+ public UpdatedCrDiscoveryServiceR4(IIdType thePlanDefinitionId, Repository theRepository) {
+ super(thePlanDefinitionId, theRepository);
+ myMaxUriLength = 6000;
+ }
+}

src/main/java/ca/uhn/fhir/jpa/starter/cr/CareGapsProperties.java

@@ -0,0 +1,22 @@
+package ca.uhn.fhir.jpa.starter.cr;
+
+public class CareGapsProperties {
+ private String reporter = "default";
+ private String section_author = "default";
+
+ public String getReporter() {
+ return reporter;
+ }
+
+ public void setReporter(String reporter) {
+ this.reporter = reporter;
+ }
+
+ public String getSection_author() {
+ return section_author;
+ }
+
+ public void setSection_author(String section_author) {
+ this.section_author = section_author;
+ }
+}