Merge pull request #255 from hapifhir/bugfix/mdm-fix

Bugfix/mdm fix

pom.xml

@@ -20,6 +20,7 @@
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>
 
     <properties>
+        <spring_boot_version>2.5.2</spring_boot_version>
         <java.version>8</java.version>
     </properties>
 

src/main/java/ca/uhn/fhir/jpa/starter/Application.java

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.jpa.starter;
 
-import ca.uhn.fhir.jpa.mdm.MdmConfig;
+import ca.uhn.fhir.jpa.starter.mdm.MdmConfig;
 import ca.uhn.fhir.jpa.starter.annotations.OnEitherVersion;
 import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
 import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
@@ -29,6 +29,15 @@ public class Application extends SpringBootServletInitializer {
 
   public static void main(String[] args) {
 
+  	 /*
+  	 * https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/246
+  	 * This will be allowed for a short period until we know how MDM should be configured
+  	 * or don't have multiple equal bean instantiations.
+  	 *
+  	 * This will require changes in the main project as stated in the Github comment
+  	 * */
+  	 System.setProperty("spring.main.allow-bean-definition-overriding","true");
+
     System.setProperty("spring.batch.job.enabled", "false");
     SpringApplication.run(Application.class, args);
 

src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java

@@ -24,6 +24,7 @@ import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
+import ca.uhn.fhir.mdm.provider.MdmProviderLoader;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.narrative.INarrativeGenerator;
 import ca.uhn.fhir.narrative2.NullNarrativeGenerator;
@@ -46,19 +47,18 @@ import ca.uhn.fhir.validation.IValidatorModule;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 import com.google.common.base.Strings;
 import com.google.common.collect.ImmutableList;
-import org.hl7.fhir.r4.model.Bundle.BundleType;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.ApplicationContext;
-import org.springframework.http.HttpHeaders;
-import org.springframework.web.cors.CorsConfiguration;
-
-import javax.servlet.ServletException;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
 import java.util.stream.Collectors;
+import javax.servlet.ServletException;
+import org.hl7.fhir.r4.model.Bundle.BundleType;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.ApplicationContext;
+import org.springframework.http.HttpHeaders;
+import org.springframework.web.cors.CorsConfiguration;
 
 public class BaseJpaRestfulServer extends RestfulServer {
   private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaRestfulServer.class);
@@ -73,7 +73,7 @@ public class BaseJpaRestfulServer extends RestfulServer {
   @Autowired
   IFhirSystemDao fhirSystemDao;
   @Autowired
-  ResourceProviderFactory resourceProviders;
+  ResourceProviderFactory resourceProviderFactory;
   @Autowired
   IJpaSystemProvider jpaSystemProvider;
   @Autowired
@@ -101,9 +101,13 @@ public class BaseJpaRestfulServer extends RestfulServer {
   @Autowired(required = false)
   IRepositoryValidationInterceptorFactory factory;
   // These are set only if the features are enabled
-  private CqlProviderLoader cqlProviderLoader;
+  @Autowired
-	@Autowired
+  Optional<CqlProviderLoader> cqlProviderLoader;
-	private IValidationSupport myValidationSupport;
+  @Autowired
+  Optional<MdmProviderLoader> mdmProviderProvider;
+
+  @Autowired
+  private IValidationSupport myValidationSupport;
 
   public BaseJpaRestfulServer() {
   }
@@ -127,7 +131,14 @@ public class BaseJpaRestfulServer extends RestfulServer {
 
     setFhirContext(fhirSystemDao.getContext());
 
-    registerProviders(resourceProviders.createProviders());
+    /*
+     * Order matters - the MDM provider registers itself on the resourceProviderFactory - hence the loading must be done
+     * ahead of provider registration
+     */
+    if(appProperties.getMdm_enabled())
+    	mdmProviderProvider.get().loadProvider();
+
+    registerProviders(resourceProviderFactory.createProviders());
     registerProvider(jpaSystemProvider);
 
     /*

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java

@@ -5,18 +5,23 @@ import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
 import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition;
+import ca.uhn.fhir.jpa.starter.cql.StarterCqlDstu3Config;
+import javax.annotation.PostConstruct;
+import javax.persistence.EntityManagerFactory;
+import javax.sql.DataSource;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.annotation.*;
+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.core.env.ConfigurableEnvironment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
-import javax.annotation.PostConstruct;
-import javax.persistence.EntityManagerFactory;
-import javax.sql.DataSource;
-
 @Configuration
 @Conditional(OnDSTU3Condition.class)
+@Import(StarterCqlDstu3Config.class)
 public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
 
   @Autowired

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

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.mdm;
+package ca.uhn.fhir.jpa.starter.mdm;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.mdm.config.MdmConsumerConfig;
@@ -9,6 +9,7 @@ import ca.uhn.fhir.mdm.rules.config.MdmRuleValidator;
 import ca.uhn.fhir.mdm.rules.config.MdmSettings;
 import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 import com.google.common.base.Charsets;
+import java.io.IOException;
 import org.apache.commons.io.IOUtils;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
@@ -18,12 +19,6 @@ import org.springframework.context.annotation.Import;
 import org.springframework.core.io.DefaultResourceLoader;
 import org.springframework.core.io.Resource;
 
-import java.io.IOException;
-
-/**
- * TODO: Move this to package "ca.uhn.fhir.jpa.starter" in HAPI FHIR 5.2.0+. The lousy component scan
- * in 5.1.0 picks this up even if MDM is disabled currently.
- */
 @Configuration
 @Conditional(MdmConfigCondition.class)
 @Import({MdmConsumerConfig.class, MdmSubmitterConfig.class})

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

@@ -1,4 +1,4 @@
-package ca.uhn.fhir.jpa.mdm;
+package ca.uhn.fhir.jpa.starter.mdm;
 
 import org.springframework.context.annotation.Condition;
 import org.springframework.context.annotation.ConditionContext;

src/main/resources/application.yaml

@@ -81,6 +81,7 @@ hapi:
 #    filter_search_enabled: true
 #    graphql_enabled: true
 #    narrative_enabled: true
+#    mdm_enabled: true
 #    partitioning:
 #      allow_references_across_partitions: false
 #      partitioning_include_in_search_hashes: false
@@ -125,7 +126,7 @@ hapi:
 #    binary_storage_enabled: true
 #    bulk_export_enabled: true
 #    subscription:
-#      resthook_enabled: false
+#      resthook_enabled: true
 #      websocket_enabled: false
 #      email:
 #        from: some@test.com