Got examples .... sort of

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

@@ -0,0 +1,379 @@
+package ca.uhn.fhir.jpa.starter;
+
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.jpa.api.config.DaoConfig.ClientIdStrategyEnum;
+import ca.uhn.fhir.rest.api.EncodingEnum;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
+import org.springframework.context.annotation.Configuration;
+
+
+@ConfigurationProperties(prefix = "hapi.fhir")
+@Configuration
+@EnableConfigurationProperties
+public class AppProperties {
+
+
+  private Boolean allow_cascading_deletes = false;
+  private Boolean allow_contains_searches = true;
+  private Boolean allow_external_references = false;
+  private Boolean allow_multiple_delete = false;
+  private Boolean allow_override_default_search_params = true;
+  private Boolean allow_placeholder_references = true;
+  private Boolean auto_create_placeholder_reference_targets = true;
+  private Integer default_page_size = 20;
+  private Boolean enable_index_missing_fields = false;
+  private Boolean enforce_referential_integrity_on_delete = true;
+  private Boolean enforce_referential_integrity_on_write = true;
+  private Boolean etag_support_enabled = true;
+  private Boolean expunge_enabled = true;
+  private Boolean fhirpath_interceptor_enabled = false;
+  private Boolean filter_search_enabled = true;
+  private Boolean graphql_enabled = true;
+  private Boolean binary_storage_enabled = true;
+  private Boolean bulk_export_enabled = true;
+  private EncodingEnum default_encoding = EncodingEnum.JSON;
+  private FhirVersionEnum fhir_version = FhirVersionEnum.R4;
+  private Integer max_binary_size = 104857600;
+  private Integer max_page_size = 200;
+  private Integer retain_cached_searches_mins = 60;
+  private Integer reuse_cached_search_results_millis = 60000;
+  private ClientIdStrategyEnum client_id_strategy = ClientIdStrategyEnum.ALPHANUMERIC;
+
+
+  private Validation validation;
+  private Server server;
+  private Logger logger;
+
+  public Validation getValidation() {
+    return validation;
+  }
+
+  public void setValidation(Validation validation) {
+    this.validation = validation;
+  }
+
+  public Server getServer() {
+    return server;
+  }
+
+  public void setServer(Server server) {
+    this.server = server;
+  }
+
+  public Logger getLogger() {
+    return logger;
+  }
+
+  public void setLogger(Logger logger) {
+    this.logger = logger;
+  }
+
+  public ClientIdStrategyEnum getClient_id_strategy() {
+    return client_id_strategy;
+  }
+
+  public void setClient_id_strategy(
+    ClientIdStrategyEnum client_id_strategy) {
+    this.client_id_strategy = client_id_strategy;
+  }
+
+  public Boolean getAllow_cascading_deletes() {
+    return allow_cascading_deletes;
+  }
+
+  public void setAllow_cascading_deletes(Boolean allow_cascading_deletes) {
+    this.allow_cascading_deletes = allow_cascading_deletes;
+  }
+
+  public Boolean getAllow_contains_searches() {
+    return allow_contains_searches;
+  }
+
+  public void setAllow_contains_searches(Boolean allow_contains_searches) {
+    this.allow_contains_searches = allow_contains_searches;
+  }
+
+  public Boolean getAllow_external_references() {
+    return allow_external_references;
+  }
+
+  public void setAllow_external_references(Boolean allow_external_references) {
+    this.allow_external_references = allow_external_references;
+  }
+
+  public Boolean getAllow_multiple_delete() {
+    return allow_multiple_delete;
+  }
+
+  public void setAllow_multiple_delete(Boolean allow_multiple_delete) {
+    this.allow_multiple_delete = allow_multiple_delete;
+  }
+
+  public Boolean getAllow_override_default_search_params() {
+    return allow_override_default_search_params;
+  }
+
+  public void setAllow_override_default_search_params(
+    Boolean allow_override_default_search_params) {
+    this.allow_override_default_search_params = allow_override_default_search_params;
+  }
+
+  public Boolean getAllow_placeholder_references() {
+    return allow_placeholder_references;
+  }
+
+  public void setAllow_placeholder_references(Boolean allow_placeholder_references) {
+    this.allow_placeholder_references = allow_placeholder_references;
+  }
+
+  public Boolean getAuto_create_placeholder_reference_targets() {
+    return auto_create_placeholder_reference_targets;
+  }
+
+  public void setAuto_create_placeholder_reference_targets(
+    Boolean auto_create_placeholder_reference_targets) {
+    this.auto_create_placeholder_reference_targets = auto_create_placeholder_reference_targets;
+  }
+
+  public Integer getDefault_page_size() {
+    return default_page_size;
+  }
+
+  public void setDefault_page_size(Integer default_page_size) {
+    this.default_page_size = default_page_size;
+  }
+
+  public Boolean getEnable_index_missing_fields() {
+    return enable_index_missing_fields;
+  }
+
+  public void setEnable_index_missing_fields(Boolean enable_index_missing_fields) {
+    this.enable_index_missing_fields = enable_index_missing_fields;
+  }
+
+  public Boolean getEnforce_referential_integrity_on_delete() {
+    return enforce_referential_integrity_on_delete;
+  }
+
+  public void setEnforce_referential_integrity_on_delete(
+    Boolean enforce_referential_integrity_on_delete) {
+    this.enforce_referential_integrity_on_delete = enforce_referential_integrity_on_delete;
+  }
+
+  public Boolean getEnforce_referential_integrity_on_write() {
+    return enforce_referential_integrity_on_write;
+  }
+
+  public void setEnforce_referential_integrity_on_write(
+    Boolean enforce_referential_integrity_on_write) {
+    this.enforce_referential_integrity_on_write = enforce_referential_integrity_on_write;
+  }
+
+  public Boolean getEtag_support_enabled() {
+    return etag_support_enabled;
+  }
+
+  public void setEtag_support_enabled(Boolean etag_support_enabled) {
+    this.etag_support_enabled = etag_support_enabled;
+  }
+
+  public Boolean getExpunge_enabled() {
+    return expunge_enabled;
+  }
+
+  public void setExpunge_enabled(Boolean expunge_enabled) {
+    this.expunge_enabled = expunge_enabled;
+  }
+
+  public Boolean getFhirpath_interceptor_enabled() {
+    return fhirpath_interceptor_enabled;
+  }
+
+  public void setFhirpath_interceptor_enabled(Boolean fhirpath_interceptor_enabled) {
+    this.fhirpath_interceptor_enabled = fhirpath_interceptor_enabled;
+  }
+
+  public Boolean getFilter_search_enabled() {
+    return filter_search_enabled;
+  }
+
+  public void setFilter_search_enabled(Boolean filter_search_enabled) {
+    this.filter_search_enabled = filter_search_enabled;
+  }
+
+  public Boolean getGraphql_enabled() {
+    return graphql_enabled;
+  }
+
+  public void setGraphql_enabled(Boolean graphql_enabled) {
+    this.graphql_enabled = graphql_enabled;
+  }
+
+  public Boolean getBinary_storage_enabled() {
+    return binary_storage_enabled;
+  }
+
+  public void setBinary_storage_enabled(Boolean binary_storage_enabled) {
+    this.binary_storage_enabled = binary_storage_enabled;
+  }
+
+  public Boolean getBulk_export_enabled() {
+    return bulk_export_enabled;
+  }
+
+  public void setBulk_export_enabled(Boolean bulk_export_enabled) {
+    this.bulk_export_enabled = bulk_export_enabled;
+  }
+
+  public EncodingEnum getDefault_encoding() {
+    return default_encoding;
+  }
+
+  public void setDefault_encoding(EncodingEnum default_encoding) {
+    this.default_encoding = default_encoding;
+  }
+
+  public FhirVersionEnum getFhir_version() {
+    return fhir_version;
+  }
+
+  public void setFhir_version(FhirVersionEnum fhir_version) {
+    this.fhir_version = fhir_version;
+  }
+
+  public Integer getMax_binary_size() {
+    return max_binary_size;
+  }
+
+  public void setMax_binary_size(Integer max_binary_size) {
+    this.max_binary_size = max_binary_size;
+  }
+
+  public Integer getMax_page_size() {
+    return max_page_size;
+  }
+
+  public void setMax_page_size(Integer max_page_size) {
+    this.max_page_size = max_page_size;
+  }
+
+  public Integer getRetain_cached_searches_mins() {
+    return retain_cached_searches_mins;
+  }
+
+  public void setRetain_cached_searches_mins(Integer retain_cached_searches_mins) {
+    this.retain_cached_searches_mins = retain_cached_searches_mins;
+  }
+
+  public Integer getReuse_cached_search_results_millis() {
+    return reuse_cached_search_results_millis;
+  }
+
+  public void setReuse_cached_search_results_millis(Integer reuse_cached_search_results_millis) {
+    this.reuse_cached_search_results_millis = reuse_cached_search_results_millis;
+  }
+
+  public static class Logger {
+
+    private String name = "fhirtest.access";
+    private String error_format = "ERROR - ${requestVerb} ${requestUrl}";
+    private String format = "Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]";
+    private Boolean log_exceptions = true;
+
+    public String getName() {
+      return name;
+    }
+
+    public void setName(String name) {
+      this.name = name;
+    }
+
+    public String getError_format() {
+      return error_format;
+    }
+
+    public void setError_format(String error_format) {
+      this.error_format = error_format;
+    }
+
+    public String getFormat() {
+      return format;
+    }
+
+    public void setFormat(String format) {
+      this.format = format;
+    }
+
+    public Boolean getLog_exceptions() {
+      return log_exceptions;
+    }
+
+    public void setLog_exceptions(Boolean log_exceptions) {
+      this.log_exceptions = log_exceptions;
+    }
+  }
+
+
+  public static class Server {
+
+    private String id = "home";
+    private String name = "Local Tester";
+    private String address = "http://localhost:8080/fhir";
+    private Boolean refuse_to_fetch_third_party_urls = true;
+
+    public String getId() {
+      return id;
+    }
+
+    public void setId(String id) {
+      this.id = id;
+    }
+
+    public String getName() {
+      return name;
+    }
+
+    public void setName(String name) {
+      this.name = name;
+    }
+
+    public String getAddress() {
+      return address;
+    }
+
+    public void setAddress(String address) {
+      this.address = address;
+    }
+
+    public Boolean getRefuse_to_fetch_third_party_urls() {
+      return refuse_to_fetch_third_party_urls;
+    }
+
+    public void setRefuse_to_fetch_third_party_urls(Boolean refuse_to_fetch_third_party_urls) {
+      this.refuse_to_fetch_third_party_urls = refuse_to_fetch_third_party_urls;
+    }
+  }
+
+  public static class Validation {
+
+    private Boolean requests_enabled = false;
+    private Boolean responses_enabled = false;
+
+    public Boolean getRequests_enabled() {
+      return requests_enabled;
+    }
+
+    public void setRequests_enabled(Boolean requests_enabled) {
+      this.requests_enabled = requests_enabled;
+    }
+
+    public Boolean getResponses_enabled() {
+      return responses_enabled;
+    }
+
+    public void setResponses_enabled(Boolean responses_enabled) {
+      this.responses_enabled = responses_enabled;
+    }
+  }
+}

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

@@ -1,16 +1,20 @@
 package ca.uhn.fhir.jpa.starter;
 
 import org.springframework.boot.SpringApplication;
+import org.springframework.boot.autoconfigure.EnableAutoConfiguration;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.autoconfigure.elasticsearch.ElasticsearchRestClientAutoConfiguration;
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
 import org.springframework.boot.web.servlet.ServletComponentScan;
 import org.springframework.boot.web.servlet.ServletRegistrationBean;
 import org.springframework.context.annotation.Bean;
 import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
 import org.springframework.web.servlet.DispatcherServlet;
 
-@ServletComponentScan(basePackageClasses = {JpaRestfulServer.class})
+@ServletComponentScan(basePackageClasses = {JpaRestfulServer.class}, basePackages = "ca.uhn.fhir.jpa.starter")
 @SpringBootApplication(exclude = ElasticsearchRestClientAutoConfiguration.class)
+@EnableConfigurationProperties
+@EnableAutoConfiguration
 public class Application {
 
   public static void main(String[] args) {

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

@@ -11,7 +11,11 @@ import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
 import ca.uhn.fhir.jpa.bulk.provider.BulkDataExportProvider;
 import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
 import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
-import ca.uhn.fhir.jpa.provider.*;
+import ca.uhn.fhir.jpa.provider.GraphQLProvider;
+import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
+import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
+import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
+import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
 import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4;
@@ -25,12 +29,23 @@ import ca.uhn.fhir.model.dstu2.composite.MetaDt;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
 import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.rest.server.interceptor.*;
+import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.FhirPathFilterInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
 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.validation.IValidatorModule;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.TreeSet;
+import javax.servlet.ServletException;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.Meta;
 import org.hl7.fhir.r4.model.Bundle.BundleType;
@@ -38,12 +53,15 @@ import org.springframework.context.ApplicationContext;
 import org.springframework.http.HttpHeaders;
 import org.springframework.web.cors.CorsConfiguration;
 
-import javax.servlet.ServletException;
-import java.util.*;
-
 
 public class BaseJpaRestfulServer extends RestfulServer {
 
+  AppProperties hapiProperties;
+
+  public BaseJpaRestfulServer(AppProperties appProperties) {
+    this.hapiProperties = appProperties;
+  }
+
   private static final long serialVersionUID = 1L;
 
   @SuppressWarnings("unchecked")
@@ -107,24 +125,32 @@ public class BaseJpaRestfulServer extends RestfulServer {
     DaoConfig daoConfig = appCtx.getBean(DaoConfig.class);
     ISearchParamRegistry searchParamRegistry = appCtx.getBean(ISearchParamRegistry.class);
     if (fhirVersion == FhirVersionEnum.DSTU2) {
-      IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle, MetaDt> systemDao = appCtx.getBean("mySystemDaoDstu2", IFhirSystemDao.class);
+      IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle, MetaDt> systemDao = appCtx
-      JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao, daoConfig);
+        .getBean("mySystemDaoDstu2", IFhirSystemDao.class);
+      JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao,
+        daoConfig);
       confProvider.setImplementationDescription("HAPI FHIR DSTU2 Server");
       setServerConformanceProvider(confProvider);
     } else {
       if (fhirVersion == FhirVersionEnum.DSTU3) {
-        IFhirSystemDao<Bundle, Meta> systemDao = appCtx.getBean("mySystemDaoDstu3", IFhirSystemDao.class);
+        IFhirSystemDao<Bundle, Meta> systemDao = appCtx
-        JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao, daoConfig, searchParamRegistry);
+          .getBean("mySystemDaoDstu3", IFhirSystemDao.class);
+        JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao,
+          daoConfig, searchParamRegistry);
         confProvider.setImplementationDescription("HAPI FHIR DSTU3 Server");
         setServerConformanceProvider(confProvider);
       } else if (fhirVersion == FhirVersionEnum.R4) {
-        IFhirSystemDao<org.hl7.fhir.r4.model.Bundle, org.hl7.fhir.r4.model.Meta> systemDao = appCtx.getBean("mySystemDaoR4", IFhirSystemDao.class);
+        IFhirSystemDao<org.hl7.fhir.r4.model.Bundle, org.hl7.fhir.r4.model.Meta> systemDao = appCtx
-        JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(this, systemDao, daoConfig, searchParamRegistry);
+          .getBean("mySystemDaoR4", IFhirSystemDao.class);
+        JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(this, systemDao,
+          daoConfig, searchParamRegistry);
         confProvider.setImplementationDescription("HAPI FHIR R4 Server");
         setServerConformanceProvider(confProvider);
       } else if (fhirVersion == FhirVersionEnum.R5) {
-        IFhirSystemDao<org.hl7.fhir.r5.model.Bundle, org.hl7.fhir.r5.model.Meta> systemDao = appCtx.getBean("mySystemDaoR5", IFhirSystemDao.class);
+        IFhirSystemDao<org.hl7.fhir.r5.model.Bundle, org.hl7.fhir.r5.model.Meta> systemDao = appCtx
-        JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(this, systemDao, daoConfig, searchParamRegistry);
+          .getBean("mySystemDaoR5", IFhirSystemDao.class);
+        JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(this, systemDao,
+          daoConfig, searchParamRegistry);
         confProvider.setImplementationDescription("HAPI FHIR R5 Server");
         setServerConformanceProvider(confProvider);
       } else {
@@ -257,7 +283,8 @@ public class BaseJpaRestfulServer extends RestfulServer {
     DaoRegistry daoRegistry = appCtx.getBean(DaoRegistry.class);
     IInterceptorBroadcaster interceptorBroadcaster = appCtx.getBean(IInterceptorBroadcaster.class);
     if (HapiProperties.getAllowCascadingDeletes()) {
-      CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(ctx, daoRegistry, interceptorBroadcaster);
+      CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(ctx,
+        daoRegistry, interceptorBroadcaster);
       getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
     }
 

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

@@ -2,12 +2,18 @@ package ca.uhn.fhir.jpa.starter;
 
 import javax.servlet.ServletException;
 import javax.servlet.annotation.WebServlet;
+import org.springframework.context.annotation.Import;
 
 @WebServlet(urlPatterns = {"/fhir/*"})
+@Import(AppProperties.class)
 public class JpaRestfulServer extends BaseJpaRestfulServer {
 
   private static final long serialVersionUID = 1L;
 
+  public JpaRestfulServer(AppProperties appProperties) {
+    super(appProperties);
+  }
+
   @Override
   protected void initialize() throws ServletException {
     super.initialize();

src/main/resources/application.yaml

@@ -0,0 +1,62 @@
+spring:
+  datasource:
+    url: 'jdbc:h2:file:./target/database/h2'
+    username: sa
+    password:
+    driverClassName: org.h2.Driver
+    max-active: 15
+hapi:
+  fhir:
+    allow_cascading_deletes: true
+    allow_contains_searches: true
+    allow_external_references: true
+    allow_multiple_delete: true
+    allow_override_default_search_params: true
+    allow_placeholder_references: true
+    auto_create_placeholder_reference_targets: false
+    default_encoding: JSON
+    default_page_size: 20
+    enable_index_missing_fields: false
+    enforce_referential_integrity_on_delete: false
+    enforce_referential_integrity_on_write: false
+    etag_support_enabled: true
+    expunge_enabled: true
+    fhir_version: DSTU3
+    daoconfig_client_id_strategy:
+    fhirpath_interceptor_enabled: false
+    filter_search_enabled: true
+    graphql_enabled: true
+    logger:
+      error_format: 'ERROR - ${requestVerb} ${requestUrl}'
+      format: >-
+        Path[${servletPath}] Source[${requestHeader.x-forwarded-for}]
+        Operation[${operationType} ${operationName} ${idOrResourceName}]
+        UA[${requestHeader.user-agent}] Params[${requestParameters}]
+        ResponseEncoding[${responseEncodingNoDefault}]
+      log_exceptions: true
+      name: fhirtest.access
+    max_binary_size: 104857600
+    max_page_size: 200
+    retain_cached_searches_mins: 60
+    reuse_cached_search_results_millis: 60000
+    server:
+      id: home
+      name: Local Tester
+      server_address: 'http://localhost:8080/fhir'
+      refuse_to_fetch_third_party_urls: false
+    validation:
+      requests_enabled: false
+      responses_enabled: false
+
+    binary_storage_enabled: true
+    bulk_export_enabled: true
+elasticsearch:
+  debug:
+    pretty_print_json_log: false
+    refresh_after_write: false
+  enabled: false
+  password: SomePassword
+  required_index_status: YELLOW
+  rest_url: 'http://localhost:9200'
+  schema_management_strategy: CREATE
+  username: SomeUsername