Springify all the providers and cds-hooks servlet

common/src/main/java/org/opencds/cqf/common/config/FhirServerConfig.java

@@ -4,11 +4,15 @@
 import java.sql.Driver;
 
 import org.apache.commons.dbcp2.BasicDataSource;
+import org.opencds.cqf.cds.providers.ProviderConfiguration;
+import org.opencds.cqf.cql.engine.fhir.searchparam.SearchParameterResolver;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.ComponentScan;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
@@ -17,6 +21,7 @@
 
 @Configuration
 @EnableTransactionManagement
+@ComponentScan(basePackages = "org.opencds.cqf.common")
 public class FhirServerConfig {
 
     private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfig.class);
@@ -123,5 +128,19 @@ public ResponseHighlighterInterceptor responseHighlighterInterceptor() {
     @Bean
 	public PartitionSettings partitionSettings() {
 		return new PartitionSettings();
-	}
+    }
+
+    @Bean()
+    public ProviderConfiguration providerConfiguration() {
+        return new ProviderConfiguration(
+                HapiProperties.getCdsHooksFhirServerExpandValueSets(),
+                HapiProperties.getCdsHooksFhirServerMaxCodesPerQuery(),
+                HapiProperties.getCdsHooksFhirServerSearchStyleEnum(),
+                HapiProperties.getCdsHooksPreFetchMaxUriLength());
+    }
+
+    @Bean()
+    public SearchParameterResolver searchParameterResolver(FhirContext fhirContext) {
+        return new SearchParameterResolver(fhirContext);
+    }
 }

common/src/main/java/org/opencds/cqf/common/retrieve/JpaFhirRetrieveProvider.java

@@ -9,24 +9,29 @@
 import java.util.Map;
 import java.util.stream.Collectors;
 
+import javax.inject.Inject;
+
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.opencds.cqf.cql.engine.fhir.retrieve.SearchParamFhirRetrieveProvider;
 import org.opencds.cqf.cql.engine.fhir.searchparam.SearchParameterMap;
 import org.opencds.cqf.cql.engine.fhir.searchparam.SearchParameterResolver;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.stereotype.Component;
 
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 
+@Component
 public class JpaFhirRetrieveProvider extends SearchParamFhirRetrieveProvider {
 
     private static final Logger logger = LoggerFactory.getLogger(JpaFhirRetrieveProvider.class);
 
     DaoRegistry registry;
 
+    @Inject
     public JpaFhirRetrieveProvider(DaoRegistry registry, SearchParameterResolver searchParameterResolver) {
         super(searchParameterResolver);
         this.registry = registry;

dstu3/pom.xml

@@ -18,5 +18,11 @@
             <artifactId>common</artifactId>
             <version>${project.version}</version>
         </dependency>
+
+      <dependency>
+        <groupId>javax</groupId>
+        <artifactId>javaee-api</artifactId>
+        <version>8.0.1</version>
+      </dependency>
     </dependencies>
 </project>

dstu3/src/main/java/org/opencds/cqf/dstu3/config/FhirServerConfigDstu3.java

@@ -1,11 +1,26 @@
 package org.opencds.cqf.dstu3.config;
 
+import java.util.ArrayList;
+import java.util.List;
+
 import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
 import org.opencds.cqf.common.config.HapiProperties;
+import org.opencds.cqf.dstu3.providers.ActivityDefinitionApplyProvider;
+import org.opencds.cqf.dstu3.providers.ApplyCqlOperationProvider;
+import org.opencds.cqf.dstu3.providers.CacheValueSetsProvider;
+import org.opencds.cqf.dstu3.providers.CodeSystemUpdateProvider;
+import org.opencds.cqf.dstu3.providers.CqlExecutionProvider;
+import org.opencds.cqf.dstu3.providers.LibraryOperationsProvider;
+import org.opencds.cqf.dstu3.providers.MeasureOperationsProvider;
+import org.opencds.cqf.dstu3.providers.ObservationProvider;
+import org.opencds.cqf.dstu3.providers.PlanDefinitionApplyProvider;
+import org.opencds.cqf.dstu3.providers.QuestionnaireProvider;
+import org.opencds.cqf.tooling.library.stu3.NarrativeProvider;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.ComponentScan;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
@@ -17,6 +32,7 @@
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 
 @Configuration
+@ComponentScan(basePackages = "org.opencds.cqf.dstu3")
 public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
     protected final DataSource myDataSource;
 
@@ -71,4 +87,37 @@ public JpaTransactionManager transactionManager(EntityManagerFactory entityManag
         retVal.setEntityManagerFactory(entityManagerFactory);
         return retVal;
     }
+
+    @Bean(name= "myOperationProvidersDstu3")
+    public List<Class<?>> operationProviders() {
+        // TODO: Make this registry dynamic
+        // Scan an interface, create a plugin-api, etc.
+        // Basically, anything that's not included in base HAPI and implements an operation.
+        List<Class<?>> classes = new ArrayList<>();
+        classes.add(ActivityDefinitionApplyProvider.class);
+        classes.add(ApplyCqlOperationProvider.class);
+        classes.add(CacheValueSetsProvider.class);
+        classes.add(CodeSystemUpdateProvider.class);
+        classes.add(CqlExecutionProvider.class);
+        classes.add(LibraryOperationsProvider.class);
+        classes.add(MeasureOperationsProvider.class);
+        classes.add(PlanDefinitionApplyProvider.class);
+
+        // The plugin API will need to a way to determine whether a particular
+        // service should be registered
+        if(HapiProperties.getQuestionnaireResponseExtractEnabled()) { 
+            classes.add(QuestionnaireProvider.class);
+        };        
+
+        if (HapiProperties.getObservationTransformEnabled()) {
+            classes.add(ObservationProvider.class);
+        }
+
+        return classes;
+    }
+
+    @Bean() 
+    public NarrativeProvider narrativeProvider() {
+        return new NarrativeProvider();
+    }
 }

dstu3/src/main/java/org/opencds/cqf/dstu3/evaluation/ProviderFactory.java

@@ -1,5 +1,7 @@
 package org.opencds.cqf.dstu3.evaluation;
 
+import javax.inject.Inject;
+
 import org.opencds.cqf.common.evaluation.EvaluationProviderFactory;
 import org.opencds.cqf.common.helpers.ClientHelper;
 import org.opencds.cqf.common.providers.Dstu3ApelonFhirTerminologyProvider;
@@ -10,6 +12,7 @@
 import org.opencds.cqf.cql.engine.fhir.searchparam.SearchParameterResolver;
 import org.opencds.cqf.cql.engine.fhir.terminology.Dstu3FhirTerminologyProvider;
 import org.opencds.cqf.cql.engine.terminology.TerminologyProvider;
+import org.springframework.stereotype.Component;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
@@ -18,13 +21,15 @@
 
 // This class is a relatively dumb factory for data providers. It supports only
 // creating JPA providers for FHIR and only basic auth for terminology
+@Component
 public class ProviderFactory implements EvaluationProviderFactory {
 
     DaoRegistry registry;
     TerminologyProvider defaultTerminologyProvider;
     FhirContext fhirContext;
     ISearchParamRegistry searchParamRegistry;
 
+    @Inject
     public ProviderFactory(FhirContext fhirContext, DaoRegistry registry,
             TerminologyProvider defaultTerminologyProvider) {
         this.defaultTerminologyProvider = defaultTerminologyProvider;

dstu3/src/main/java/org/opencds/cqf/dstu3/providers/ActivityDefinitionApplyProvider.java

@@ -4,6 +4,8 @@
 import java.util.Collections;
 import java.util.List;
 
+import javax.inject.Inject;
+
 import org.hl7.fhir.dstu3.model.ActivityDefinition;
 import org.hl7.fhir.dstu3.model.Attachment;
 import org.hl7.fhir.dstu3.model.BooleanType;
@@ -24,6 +26,7 @@
 import org.opencds.cqf.cql.engine.fhir.model.Dstu3FhirModelResolver;
 import org.opencds.cqf.cql.engine.model.ModelResolver;
 import org.opencds.cqf.dstu3.helpers.Helper;
+import org.springframework.stereotype.Component;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
@@ -35,12 +38,14 @@
 /**
  * Created by Bryn on 1/16/2017.
  */
+@Component
 public class ActivityDefinitionApplyProvider {
 
     private CqlExecutionProvider executionProvider;
     private ModelResolver modelResolver;
     private IFhirResourceDao<ActivityDefinition> activityDefinitionDao;
 
+    @Inject
     public ActivityDefinitionApplyProvider(FhirContext fhirContext, CqlExecutionProvider executionProvider,
             IFhirResourceDao<ActivityDefinition> activityDefinitionDao) {
         this.modelResolver = new Dstu3FhirModelResolver();

dstu3/src/main/java/org/opencds/cqf/dstu3/providers/ApplyCqlOperationProvider.java

@@ -5,6 +5,8 @@
 import java.util.Date;
 import java.util.List;
 
+import javax.inject.Inject;
+
 import org.cqframework.cql.cql2elm.LibraryManager;
 import org.cqframework.cql.cql2elm.ModelManager;
 import org.cqframework.cql.elm.execution.Library;
@@ -26,19 +28,22 @@
 import org.opencds.cqf.common.helpers.TranslatorHelper;
 import org.opencds.cqf.cql.engine.execution.Context;
 import org.opencds.cqf.cql.engine.runtime.DateTime;
+import org.springframework.stereotype.Component;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.rest.annotation.IdParam;
 import ca.uhn.fhir.rest.annotation.Operation;
 import ca.uhn.fhir.rest.annotation.OperationParam;
 
+@Component
 public class ApplyCqlOperationProvider {
 
     private EvaluationProviderFactory providerFactory;
     private IFhirResourceDao<Bundle> bundleDao;
     FhirContext context;
 
+    @Inject
     public ApplyCqlOperationProvider(EvaluationProviderFactory providerFactory, IFhirResourceDao<Bundle> bundleDao, FhirContext context) {
         this.providerFactory = providerFactory;
         this.bundleDao = bundleDao;

dstu3/src/main/java/org/opencds/cqf/dstu3/providers/CacheValueSetsProvider.java

@@ -4,13 +4,16 @@
 import java.util.HashMap;
 import java.util.Map;
 
+import javax.inject.Inject;
+
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.hl7.fhir.dstu3.model.Endpoint;
 import org.hl7.fhir.dstu3.model.IdType;
 import org.hl7.fhir.dstu3.model.Parameters;
 import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.dstu3.model.ValueSet;
 import org.opencds.cqf.dstu3.helpers.Helper;
+import org.springframework.stereotype.Component;
 
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
@@ -24,11 +27,13 @@
 import ca.uhn.fhir.rest.param.StringOrListParam;
 import ca.uhn.fhir.rest.param.StringParam;
 
+@Component
 public class CacheValueSetsProvider {
 
     private IFhirSystemDao<Bundle, ?> systemDao;
     private IFhirResourceDao<Endpoint> endpointDao;
 
+    @Inject
     public CacheValueSetsProvider(IFhirSystemDao<Bundle, ?> systemDao, IFhirResourceDao<Endpoint> endpointDao) {
         this.systemDao = systemDao;
         this.endpointDao = endpointDao;

dstu3/src/main/java/org/opencds/cqf/dstu3/providers/CodeSystemUpdateProvider.java

@@ -9,13 +9,16 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
+import javax.inject.Inject;
+
 import org.hl7.fhir.dstu3.model.CodeSystem;
 import org.hl7.fhir.dstu3.model.Enumerations;
 import org.hl7.fhir.dstu3.model.IdType;
 import org.hl7.fhir.dstu3.model.OperationOutcome;
 import org.hl7.fhir.dstu3.model.ValueSet;
 import org.opencds.cqf.dstu3.builders.OperationOutcomeBuilder;
 import org.opencds.cqf.dstu3.builders.RandomIdBuilder;
+import org.springframework.stereotype.Component;
 
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@@ -24,10 +27,12 @@
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.UriParam;
 
+@Component
 public class CodeSystemUpdateProvider {
     private IFhirResourceDao<ValueSet> valueSetDao;
     private IFhirResourceDao<CodeSystem> codeSystemDao;
 
+    @Inject
     public CodeSystemUpdateProvider(IFhirResourceDao<ValueSet> valueSetDao,
             IFhirResourceDao<CodeSystem> codeSystemDao) {
         this.valueSetDao = valueSetDao;

dstu3/src/main/java/org/opencds/cqf/dstu3/providers/CqlExecutionProvider.java

@@ -7,6 +7,8 @@
 import java.util.List;
 import java.util.Map;
 
+import javax.inject.Inject;
+
 import org.apache.commons.lang3.tuple.Triple;
 import org.cqframework.cql.cql2elm.CqlTranslator;
 import org.cqframework.cql.cql2elm.CqlTranslatorException;
@@ -37,17 +39,20 @@
 import org.opencds.cqf.cql.engine.terminology.TerminologyProvider;
 import org.opencds.cqf.dstu3.helpers.FhirMeasureBundler;
 import org.opencds.cqf.dstu3.helpers.LibraryHelper;
+import org.springframework.stereotype.Component;
 
 import ca.uhn.fhir.rest.annotation.Operation;
 import ca.uhn.fhir.rest.annotation.OperationParam;
 
 /**
  * Created by Bryn on 1/16/2017.
  */
+@Component
 public class CqlExecutionProvider {
     private EvaluationProviderFactory providerFactory;
     private LibraryResolutionProvider<Library> libraryResolutionProvider;
 
+    @Inject
     public CqlExecutionProvider(LibraryResolutionProvider<Library> libraryResolutionProvider,
             EvaluationProviderFactory providerFactory) {
         this.providerFactory = providerFactory;

dstu3/src/main/java/org/opencds/cqf/dstu3/providers/DataRequirementsProvider.java

@@ -67,8 +67,10 @@
 import org.opencds.cqf.tooling.measure.stu3.CqfMeasure;
 import org.opencds.cqf.tooling.measure.stu3.TerminologyRef;
 import org.opencds.cqf.tooling.measure.stu3.TerminologyRef.TerminologyRefType;
+import org.springframework.stereotype.Component;
 import org.opencds.cqf.tooling.measure.stu3.VersionedTerminologyRef;
 
+@Component
 public class DataRequirementsProvider {
 
     // For creating the CQF measure we need to:

dstu3/src/main/java/org/opencds/cqf/dstu3/providers/HQMFProvider.java

@@ -47,11 +47,13 @@
 import org.opencds.cqf.tooling.measure.stu3.CqfMeasure;
 import org.opencds.cqf.tooling.measure.stu3.TerminologyRef;
 import org.opencds.cqf.tooling.measure.stu3.TerminologyRef.TerminologyRefType;
+import org.springframework.stereotype.Component;
 import org.w3c.dom.Document;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.parser.IParser;
 
+@Component
 public class HQMFProvider {
 
     private static Map<String, String> measureTypeValueSetMap = new HashMap<String, String>() {