Add MSSql Support, fix multiple versions dialects of Postgres being used

.vscode/launch.json

@@ -17,17 +17,6 @@
 				"-Dhapi.fhir.bulk_export_enabled=false",
 				"-Dspring.batch.job.enabled=false"
 			],
-			"stepFilters": {
-				"classNameFilters": [
-					"java.*",
-					"javax.*",
-					"com.sun.*",
-					"sun.*",
-					"sunw.*",
-					"org.omg.*",
-					"org.springframework.aop.*"
-				]
-			}
 		},
 		{
 			"type": "java",
@@ -42,17 +31,6 @@
 				"-Dhapi.fhir.bulk_export_enabled=false",
 				"-Dspring.batch.job.enabled=false"
 			],
-			"stepFilters": {
-				"classNameFilters": [
-					"java.*",
-					"javax.*",
-					"com.sun.*",
-					"sun.*",
-					"sunw.*",
-					"org.omg.*",
-					"org.springframework.aop.*"
-				]
-			},
 			"classPaths": [
 				"$Auto",
 				"$Runtime"
@@ -65,25 +43,17 @@
 			"mainClass": "org.opencds.cqf.ruler.Application",
 			"projectName": "cqf-ruler-server",
 			"vmArgs": [
+				"-XX:TieredStopAtLevel=1",
+				"-Ddebug=true",
+				"-Dloader.debug=true",
 				"-Dspring.datasource.url=jdbc:postgresql://localhost:5432/postgres",
 				"-Dspring.datasource.username=postgres",
 				"-Dspring.datasource.password=",
 				"-Dspring.datasource.driverClassName=org.postgresql.Driver",
-				"-Dspring.jpa.properties.hibernate.dialect=org.hibernate.dialect.PostgreSQL10Dialect",
+				"-Dspring.jpa.properties.hibernate.dialect=ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect",
 				"-Dhapi.fhir.bulk_export_enabled=false",
 				"-Dspring.batch.job.enabled=false"
 			],
-			"stepFilters": {
-				"classNameFilters": [
-					"java.*",
-					"javax.*",
-					"com.sun.*",
-					"sun.*",
-					"sunw.*",
-					"org.omg.*",
-					"org.springframework.aop.*"
-				]
-			},
 			"classPaths": [
 				"$Auto",
 				"$Runtime"
@@ -103,17 +73,6 @@
 				"-Dhapi.fhir.bulk_export_enabled=false",
 				"-Dspring.batch.job.enabled=false"
 			],
-			"stepFilters": {
-				"classNameFilters": [
-					"java.*",
-					"javax.*",
-					"com.sun.*",
-					"sun.*",
-					"sunw.*",
-					"org.omg.*",
-					"org.springframework.aop.*"
-				]
-			},
 			"classPaths": [
 				"$Auto",
 				"$Runtime"
@@ -124,35 +83,13 @@
 			"name": "Attach",
 			"request": "attach",
 			"hostName": "localhost",
-			"port": "5005",
-			"stepFilters": {
-				"classNameFilters": [
-					"java.*",
-					"javax.*",
-					"com.sun.*",
-					"sun.*",
-					"sunw.*",
-					"org.omg.*",
-					"org.springframework.aop.*"
-				]
-			}
+			"port": "5005"
 		},
 		{
 			"type": "java",
 			"name": "Launch Current File",
 			"request": "launch",
 			"mainClass": "${file}",
-			"stepFilters": {
-				"classNameFilters": [
-					"java.*",
-					"javax.*",
-					"com.sun.*",
-					"sun.*",
-					"sunw.*",
-					"org.omg.*",
-					"org.springframework.aop.*"
-				]
-			}
 		}
 	]
 }

.vscode/settings.json

@@ -1,5 +1,10 @@
 {
 	"java.configuration.updateBuildConfiguration": "automatic",
+	"java.debug.settings.stepping.skipClasses": [
+		"$JDK",
+		"java.lang.ClassLoader",
+		"org.springframework.aop.*"
+	],
 	"java.errors.incompleteClasspath.severity": "ignore",
 	"java.test.config": [
 		{

core/src/main/java/org/opencds/cqf/ruler/config/FhirServerConfigCommon.java

@@ -0,0 +1,262 @@
+package org.opencds.cqf.ruler.config;
+
+import java.util.HashSet;
+import java.util.Optional;
+
+import org.hl7.fhir.dstu2.model.Subscription;
+import org.opencds.cqf.external.AppProperties;
+import org.opencds.cqf.ruler.provider.PatchedJpaHibernatePropertiesProvider;
+import org.springframework.boot.env.YamlPropertySourceLoader;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Lazy;
+import org.springframework.context.annotation.Primary;
+import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
+import org.springframework.transaction.annotation.EnableTransactionManagement;
+
+import com.google.common.base.Strings;
+
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.binary.api.IBinaryStorageSvc;
+import ca.uhn.fhir.jpa.binstore.DatabaseBlobBinaryStorageSvcImpl;
+import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
+import ca.uhn.fhir.jpa.model.config.PartitionSettings;
+import ca.uhn.fhir.jpa.model.config.PartitionSettings.CrossPartitionReferenceMode;
+import ca.uhn.fhir.jpa.model.entity.ModelConfig;
+import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory;
+import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailSenderImpl;
+import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
+import ca.uhn.fhir.rest.server.mail.IMailSvc;
+import ca.uhn.fhir.rest.server.mail.MailConfig;
+import ca.uhn.fhir.rest.server.mail.MailSvc;
+
+@Configuration
+@EnableTransactionManagement
+public class FhirServerConfigCommon {
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.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");
+		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");
+
+		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");
+
+			if (!Strings.isNullOrEmpty(email.getUsername())) {
+				ourLog.info("Server is configured to use username '" + email.getUsername() + "' for email");
+			}
+
+			if (!Strings.isNullOrEmpty(email.getPassword())) {
+				ourLog.info("Server is configured to use a password for email");
+			}
+		}
+
+		if (appProperties.getSubscription().getResthook_enabled()) {
+			ourLog.info("REST-hook subscriptions enabled");
+		}
+
+		if (appProperties.getSubscription().getEmail() != null) {
+			ourLog.info("Email subscriptions enabled");
+		}
+
+		if (appProperties.getEnable_index_contained_resource() == Boolean.TRUE) {
+			ourLog.info("Indexed on contained resource enabled");
+		}
+	}
+
+	/**
+	 * Configure FHIR properties around the the JPA server via this bean
+	 */
+	@Bean
+	public DaoConfig daoConfig(AppProperties appProperties) {
+		DaoConfig retVal = new DaoConfig();
+
+		retVal.setIndexMissingFields(appProperties.getEnable_index_missing_fields() ? DaoConfig.IndexEnabledEnum.ENABLED
+				: DaoConfig.IndexEnabledEnum.DISABLED);
+		retVal.setAutoCreatePlaceholderReferenceTargets(appProperties.getAuto_create_placeholder_reference_targets());
+		retVal.setEnforceReferentialIntegrityOnWrite(appProperties.getEnforce_referential_integrity_on_write());
+		retVal.setEnforceReferentialIntegrityOnDelete(appProperties.getEnforce_referential_integrity_on_delete());
+		retVal.setAllowContainsSearches(appProperties.getAllow_contains_searches());
+		retVal.setAllowMultipleDelete(appProperties.getAllow_multiple_delete());
+		retVal.setAllowExternalReferences(appProperties.getAllow_external_references());
+		retVal.setSchedulingDisabled(!appProperties.getDao_scheduling_enabled());
+		retVal.setDeleteExpungeEnabled(appProperties.getDelete_expunge_enabled());
+		retVal.setExpungeEnabled(appProperties.getExpunge_enabled());
+		if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null)
+			retVal.setEmailFromAddress(appProperties.getSubscription().getEmail().getFrom());
+
+		Integer maxFetchSize = appProperties.getMax_page_size();
+		retVal.setFetchSizeDefaultMaximum(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();
+		retVal.setReuseCachedSearchResultsForMillis(reuseCachedSearchResultsMillis);
+		ourLog.info("Server configured to cache search results for {} milliseconds", reuseCachedSearchResultsMillis);
+
+		Long retainCachedSearchesMinutes = appProperties.getRetain_cached_searches_mins();
+		retVal.setExpireSearchResultsAfterMillis(retainCachedSearchesMinutes * 60 * 1000);
+
+		if (appProperties.getSubscription() != null) {
+			// Subscriptions are enabled by channel type
+			if (appProperties.getSubscription().getResthook_enabled()) {
+				ourLog.info("Enabling REST-hook subscriptions");
+				retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.RESTHOOK);
+			}
+			if (appProperties.getSubscription().getEmail() != null) {
+				ourLog.info("Enabling email subscriptions");
+				retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.EMAIL);
+			}
+			if (appProperties.getSubscription().getWebsocket_enabled()) {
+				ourLog.info("Enabling websocket subscriptions");
+				retVal.addSupportedSubscriptionType(
+						org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.WEBSOCKET);
+			}
+		}
+
+		retVal.setFilterParameterEnabled(appProperties.getFilter_search_enabled());
+		retVal.setAdvancedHSearchIndexing(appProperties.getAdvanced_lucene_indexing());
+		retVal.setTreatBaseUrlsAsLocal(new HashSet<>(appProperties.getLocal_base_urls()));
+
+		return retVal;
+	}
+
+	@Bean
+	public YamlPropertySourceLoader yamlPropertySourceLoader() {
+		return new YamlPropertySourceLoader();
+	}
+
+	@Bean
+	public PartitionSettings partitionSettings(AppProperties appProperties) {
+		PartitionSettings retVal = new PartitionSettings();
+
+		// Partitioning
+		if (appProperties.getPartitioning() != null) {
+			retVal.setPartitioningEnabled(true);
+			retVal.setIncludePartitionInSearchHashes(
+					appProperties.getPartitioning().getPartitioning_include_in_search_hashes());
+			if (appProperties.getPartitioning().getAllow_references_across_partitions()) {
+				retVal.setAllowReferencesAcrossPartitions(CrossPartitionReferenceMode.ALLOWED_UNQUALIFIED);
+			} else {
+				retVal.setAllowReferencesAcrossPartitions(CrossPartitionReferenceMode.NOT_ALLOWED);
+			}
+		}
+
+		return retVal;
+	}
+
+	@Primary
+	@Bean
+	public HibernatePropertiesProvider jpaStarterDialectProvider(
+			LocalContainerEntityManagerFactoryBean myEntityManagerFactory) {
+		return new PatchedJpaHibernatePropertiesProvider(myEntityManagerFactory);
+	}
+
+	@Bean
+	public ModelConfig modelConfig(AppProperties appProperties, DaoConfig daoConfig) {
+		ModelConfig modelConfig = daoConfig.getModelConfig();
+		modelConfig.setAllowContainsSearches(appProperties.getAllow_contains_searches());
+		modelConfig.setAllowExternalReferences(appProperties.getAllow_external_references());
+		modelConfig.setDefaultSearchParamsCanBeOverridden(appProperties.getAllow_override_default_search_params());
+		if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null)
+			modelConfig.setEmailFromAddress(appProperties.getSubscription().getEmail().getFrom());
+
+		// You can enable these if you want to support Subscriptions from your server
+		if (appProperties.getSubscription() != null && appProperties.getSubscription().getResthook_enabled() != null) {
+			modelConfig.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.RESTHOOK);
+		}
+
+		if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null) {
+			modelConfig.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.EMAIL);
+		}
+
+		modelConfig.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
+
+		modelConfig.setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
+		modelConfig.setIndexIdentifierOfType(appProperties.getEnable_index_of_type());
+		return modelConfig;
+	}
+
+	/**
+	 * The following bean configures the database connection. The 'url' property
+	 * value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates
+	 * that the server should save resources in a
+	 * directory called "jpaserver_derby_files".
+	 * <p>
+	 * A URL to a remote database could also be placed here, along with login
+	 * credentials and other properties supported by BasicDataSource.
+	 */
+	/*
+	 * @Bean(destroyMethod = "close")
+	 * public BasicDataSource dataSource() throws ClassNotFoundException,
+	 * NoSuchMethodException, IllegalAccessException, InvocationTargetException,
+	 * InstantiationException {
+	 * BasicDataSource retVal = new BasicDataSource();
+	 * Driver driver = (Driver)
+	 * Class.forName(HapiProperties.getDataSourceDriver()).getConstructor().
+	 * newInstance();
+	 * retVal.setDriver(driver);
+	 * retVal.setUrl(HapiProperties.getDataSourceUrl());
+	 * retVal.setUsername(HapiProperties.getDataSourceUsername());
+	 * retVal.setPassword(HapiProperties.getDataSourcePassword());
+	 * retVal.setMaxTotal(HapiProperties.getDataSourceMaxPoolSize());
+	 * return retVal;
+	 * }
+	 */
+
+	@Lazy
+	@Bean
+	public IBinaryStorageSvc binaryStorageSvc(AppProperties appProperties) {
+		DatabaseBlobBinaryStorageSvcImpl binaryStorageSvc = new DatabaseBlobBinaryStorageSvcImpl();
+
+		if (appProperties.getMax_binary_size() != null) {
+			binaryStorageSvc.setMaximumBinarySize(appProperties.getMax_binary_size());
+		}
+
+		return binaryStorageSvc;
+	}
+
+	@Bean
+	public IEmailSender emailSender(AppProperties appProperties,
+			Optional<SubscriptionDeliveryHandlerFactory> subscriptionDeliveryHandlerFactory) {
+		if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null) {
+			MailConfig mailConfig = new MailConfig();
+
+			AppProperties.Subscription.Email email = appProperties.getSubscription().getEmail();
+			mailConfig.setSmtpHostname(email.getHost());
+			mailConfig.setSmtpPort(email.getPort());
+			mailConfig.setSmtpUsername(email.getUsername());
+			mailConfig.setSmtpPassword(email.getPassword());
+			mailConfig.setSmtpUseStartTLS(email.getStartTlsEnable());
+
+			IMailSvc mailSvc = new MailSvc(mailConfig);
+			IEmailSender emailSender = new EmailSenderImpl(mailSvc);
+
+			subscriptionDeliveryHandlerFactory
+					.ifPresent(theSubscriptionDeliveryHandlerFactory -> theSubscriptionDeliveryHandlerFactory
+							.setEmailSender(emailSender));
+
+			return emailSender;
+		}
+
+		return null;
+	}
+}