application dev config changed with two profiles dev-r4 & dev-r5, Sup…

…port for summary improved with custom organization/ author === Tenant, Summary restrained to Immunization, now supported with

R5

pom.xml

@@ -814,9 +814,19 @@
             </properties>
         </profile>
         <profile>
-            <id>dev</id>
+            <id>dev-r4</id>
             <properties>
-                <spring.profiles.active>dev</spring.profiles.active>
+                <spring.profiles.active>dev-r4</spring.profiles.active>
+                <IIS_MYSQL_URL>jdbc:mysql://localhost/iis_alongside_jpa</IIS_MYSQL_URL>
+<!--                <mysql.hibernate.connection.url>jdbc:mysql://localhost/iis_alongside_jpa</mysql.hibernate.connection.url>-->
+                <jpa.properties.hibernate.dialect>ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect</jpa.properties.hibernate.dialect>
+                <maven.test.skip>true</maven.test.skip>
+            </properties>
+        </profile>
+        <profile>
+            <id>dev-r5</id>
+            <properties>
+                <spring.profiles.active>dev-r5</spring.profiles.active>
                 <IIS_MYSQL_URL>jdbc:mysql://localhost/iis_alongside_jpa</IIS_MYSQL_URL>
 <!--                <mysql.hibernate.connection.url>jdbc:mysql://localhost/iis_alongside_jpa</mysql.hibernate.connection.url>-->
                 <jpa.properties.hibernate.dialect>ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect</jpa.properties.hibernate.dialect>

src/main/java/org/immregistries/iis/kernal/fhir/ips/IpsConfig.java

@@ -19,7 +19,7 @@ public class IpsConfig {
 	@Bean
 	@Conditional(OnR4Condition.class)
 	public IIpsGenerationStrategy ipsGenerationStrategyR4() {
-		return new DefaultIpsGenerationStrategy();
+		return new IpsGenerationStrategyR4();
 	}
 
 	@Bean
@@ -30,13 +30,11 @@ public IIpsGenerationStrategy ipsGenerationStrategyR5() {
 
 	@Bean
 	public IpsGeneratorSvcImpl ipsGeneratorSvc(FhirContext fhirContext, IIpsGenerationStrategy ipsGenerationStrategy,DaoRegistry daoRegistry) {
-		IpsGeneratorSvcImpl ipsGeneratorSvc = new IpsGeneratorSvcIIS(fhirContext, ipsGenerationStrategy, daoRegistry);
-		return ipsGeneratorSvc;
+		return new IpsGeneratorSvcIIS(fhirContext, ipsGenerationStrategy, daoRegistry);
 	}
 
 	@Bean
 	public IpsOperationProvider ipsOperationProvider(IIpsGeneratorSvc iIpsGeneratorSvc) {
-		IpsOperationProvider ipsOperationProvider = new IpsOperationProvider(iIpsGeneratorSvc);
-		return ipsOperationProvider;
+		return new IpsOperationProvider(iIpsGeneratorSvc);
 	}
 }

src/main/java/org/immregistries/iis/kernal/fhir/ips/IpsGenerationStrategyR4.java

@@ -0,0 +1,35 @@
+package org.immregistries.iis.kernal.fhir.ips;
+
+import ca.uhn.fhir.jpa.ips.api.SectionRegistry;
+import ca.uhn.fhir.jpa.ips.strategy.DefaultIpsGenerationStrategy;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Address;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Organization;
+import org.immregistries.iis.kernal.fhir.security.ServletHelper;
+import org.immregistries.iis.kernal.mapping.forR4.OrganizationMapperR4;
+import org.immregistries.iis.kernal.model.Tenant;
+import org.springframework.beans.factory.annotation.Autowired;
+
+public class IpsGenerationStrategyR4 extends DefaultIpsGenerationStrategy {
+
+	@Autowired
+	OrganizationMapperR4 organizationMapper;
+
+	/**
+	 * Constructor
+	 */
+	public IpsGenerationStrategyR4() {
+		super();
+		this.setSectionRegistry(new SectionRegistryR4());
+	}
+
+	@Override
+	public IBaseResource createAuthor() {
+		Tenant tenant = ServletHelper.getTenant();
+
+		Organization organization = organizationMapper.getFhirResource(tenant);
+		return organization;
+	}
+
+}

src/main/java/org/immregistries/iis/kernal/fhir/ips/IpsGenerationStrategyR5.java

@@ -1,14 +1,16 @@
 package org.immregistries.iis.kernal.fhir.ips;
 
 import ca.uhn.fhir.jpa.ips.api.IpsContext;
-import ca.uhn.fhir.jpa.ips.api.SectionRegistry;
 import ca.uhn.fhir.jpa.ips.strategy.DefaultIpsGenerationStrategy;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.model.api.Include;
 import com.google.common.collect.Sets;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r5.model.*;
+import org.immregistries.iis.kernal.fhir.security.ServletHelper;
+import org.immregistries.iis.kernal.mapping.forR5.OrganizationMapperR5;
+import org.springframework.beans.factory.annotation.Autowired;
 
 import java.time.LocalDate;
 import java.time.format.DateTimeFormatter;
@@ -22,94 +24,23 @@
  * prototype, unusable
  */
 public class IpsGenerationStrategyR5 extends DefaultIpsGenerationStrategy {
+
+	@Autowired
+	OrganizationMapperR5 organizationMapper;
 	/**
 	 * Constructor
 	 */
 	public IpsGenerationStrategyR5() {
 		super();
+		this.setSectionRegistry(new SectionRegistryR5());
 	}
 
 	@Override
 	public IBaseResource createAuthor() {
-		Organization organization = new Organization();
-		organization
-			.setName("eHealthLab - University of Cyprus")
-			.setId(IdType.newRandomUuid());
-		organization.addContact().setAddress(new Address()
-				.addLine("1 University Avenue")
-				.setCity("Nicosia")
-				.setPostalCode("2109")
-				.setCountry("CY"));
+		Organization organization = organizationMapper.getFhirResource(ServletHelper.getTenant());
 		return organization;
 	}
 
-	@Override
-	public String createTitle(IpsContext theContext) {
-		return "Patient Summary as of "
-			+ DateTimeFormatter.ofPattern("MM/dd/yyyy").format(LocalDate.now());
-	}
-
-	@Override
-	public IIdType massageResourceId(@Nullable IpsContext theIpsContext, @Nonnull IBaseResource theResource) {
-		return IdType.newRandomUuid();
-	}
-
-	@Override
-	public void massageResourceSearch(
-		IpsContext.IpsSectionContext theIpsSectionContext, SearchParameterMap theSearchParameterMap) {
-		switch (theIpsSectionContext.getSection()) {
-			case ALLERGY_INTOLERANCE:
-			case PROBLEM_LIST:
-			case IMMUNIZATIONS:
-			case PROCEDURES:
-			case MEDICAL_DEVICES:
-			case ILLNESS_HISTORY:
-			case FUNCTIONAL_STATUS:
-			default:
-				return;
-
-		}
-		// Shouldn't happen: This means none of the above switches handled the Section+resourceType combination
-//		assert false
-//			: "Don't know how to handle " + theIpsSectionContext.getSection() + "/"
-//			+ theIpsSectionContext.getResourceType();
-	}
-
-	@Nonnull
-	@Override
-	public Set<Include> provideResourceSearchIncludes(IpsContext.IpsSectionContext theIpsSectionContext) {
-		switch (theIpsSectionContext.getSection()) {
-			case MEDICATION_SUMMARY:
-				if (ResourceType.MedicationStatement.name().equals(theIpsSectionContext.getResourceType())) {
-					return Sets.newHashSet(MedicationStatement.INCLUDE_MEDICATION);
-				}
-				if (ResourceType.MedicationRequest.name().equals(theIpsSectionContext.getResourceType())) {
-					return Sets.newHashSet(MedicationRequest.INCLUDE_MEDICATION);
-				}
-				if (ResourceType.MedicationAdministration.name().equals(theIpsSectionContext.getResourceType())) {
-					return Sets.newHashSet(MedicationAdministration.INCLUDE_MEDICATION);
-				}
-				if (ResourceType.MedicationDispense.name().equals(theIpsSectionContext.getResourceType())) {
-					return Sets.newHashSet(MedicationDispense.INCLUDE_MEDICATION);
-				}
-				break;
-			case MEDICAL_DEVICES:
-			case ALLERGY_INTOLERANCE:
-			case PROBLEM_LIST:
-			case IMMUNIZATIONS:
-			case PROCEDURES:
-			case DIAGNOSTIC_RESULTS:
-			case VITAL_SIGNS:
-			case ILLNESS_HISTORY:
-			case PREGNANCY:
-			case SOCIAL_HISTORY:
-			case FUNCTIONAL_STATUS:
-			case PLAN_OF_CARE:
-			case ADVANCE_DIRECTIVES:
-				break;
-		}
-		return Collections.emptySet();
-	}
 
 	@SuppressWarnings("EnhancedSwitchMigration")
 	@Override

src/main/java/org/immregistries/iis/kernal/fhir/ips/IpsGeneratorSvcIIS.java

@@ -352,18 +352,36 @@ private String createSectionNarrative(
 		ResourceInclusionCollection theGlobalResourceCollection) {
 		CustomThymeleafNarrativeGenerator generator = newNarrativeGenerator(theGlobalResourceCollection);
 
-		org.hl7.fhir.r4.model.Bundle bundle = new org.hl7.fhir.r4.model.Bundle();
-		for (IBaseResource resource : theResources.getResources()) {
-			BundleEntrySearchModeEnum searchMode = ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.get(resource);
-			if (searchMode == BundleEntrySearchModeEnum.MATCH) {
-				bundle.addEntry().setResource((org.hl7.fhir.r4.model.Resource) resource);
+		if (myFhirContext.getVersion().getVersion().equals(FhirVersionEnum.R4)) {
+			org.hl7.fhir.r4.model.Bundle bundle = new org.hl7.fhir.r4.model.Bundle();
+			for (IBaseResource resource : theResources.getResources()) {
+				BundleEntrySearchModeEnum searchMode = ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.get(resource);
+				if (searchMode == BundleEntrySearchModeEnum.MATCH) {
+					bundle.addEntry().setResource((org.hl7.fhir.r4.model.Resource) resource);
+				}
+			}
+			String profile = theSection.getProfile();
+			bundle.getMeta().addProfile(profile);
+
+			// Generate the narrative
+			return generator.generateResourceNarrative(myFhirContext, bundle);
+		} else if (myFhirContext.getVersion().getVersion().equals(FhirVersionEnum.R5)) {
+			org.hl7.fhir.r5.model.Bundle bundle = new org.hl7.fhir.r5.model.Bundle();
+			for (IBaseResource resource : theResources.getResources()) {
+				BundleEntrySearchModeEnum searchMode = ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.get(resource);
+				if (searchMode == BundleEntrySearchModeEnum.MATCH) {
+					bundle.addEntry().setResource((org.hl7.fhir.r5.model.Resource) resource);
+				}
 			}
+			String profile = theSection.getProfile();
+			bundle.getMeta().addProfile(profile);
+
+			// Generate the narrative
+			return generator.generateResourceNarrative(myFhirContext, bundle);
+		} else {
+			return "";
 		}
-		String profile = theSection.getProfile();
-		bundle.getMeta().addProfile(profile);
 
-		// Generate the narrative
-		return generator.generateResourceNarrative(myFhirContext, bundle);
 	}
 
 	@Nonnull

src/main/java/org/immregistries/iis/kernal/fhir/ips/SectionRegistryR4.java

@@ -0,0 +1,28 @@
+package org.immregistries.iis.kernal.fhir.ips;
+
+import ca.uhn.fhir.jpa.ips.api.SectionRegistry;
+
+public class SectionRegistryR4 extends SectionRegistry {
+
+	@Override
+	/**
+	 * Add the various sections to the registry in order. overridden for
+	 * customization.
+	 */
+	protected void addSections() {
+//		addSectionAllergyIntolerance();
+//		addSectionMedicationSummary();
+//		addSectionProblemList();
+		addSectionImmunizations();
+//		addSectionProcedures();
+//		addSectionMedicalDevices();
+//		addSectionDiagnosticResults();
+//		addSectionVitalSigns();
+//		addSectionPregnancy();
+//		addSectionSocialHistory();
+//		addSectionIllnessHistory();
+//		addSectionFunctionalStatus();
+//		addSectionPlanOfCare();
+//		addSectionAdvanceDirectives();
+	}
+}

src/main/java/org/immregistries/iis/kernal/fhir/ips/SectionRegistryR5.java

@@ -0,0 +1,28 @@
+package org.immregistries.iis.kernal.fhir.ips;
+
+import ca.uhn.fhir.jpa.ips.api.SectionRegistry;
+
+public class SectionRegistryR5  extends SectionRegistry {
+
+	@Override
+	/**
+	 * Add the various sections to the registry in order. overridden for
+	 * customization.
+	 */
+	protected void addSections() {
+//		addSectionAllergyIntolerance();
+//		addSectionMedicationSummary();
+//		addSectionProblemList();
+		addSectionImmunizations();
+//		addSectionProcedures();
+//		addSectionMedicalDevices();
+//		addSectionDiagnosticResults();
+//		addSectionVitalSigns();
+//		addSectionPregnancy();
+//		addSectionSocialHistory();
+//		addSectionIllnessHistory();
+//		addSectionFunctionalStatus();
+//		addSectionPlanOfCare();
+//		addSectionAdvanceDirectives();
+	}
+}

src/main/java/org/immregistries/iis/kernal/fhir/mdm/CustomSubscriptionCanonicalizer.java

@@ -42,7 +42,7 @@
 public class CustomSubscriptionCanonicalizer extends SubscriptionCanonicalizer {
 	private static final Logger ourLog = LoggerFactory.getLogger(SubscriptionCanonicalizer.class);
 
-	final FhirContext myFhirContext;
+	private final FhirContext myFhirContext;
 	@Autowired
 	public CustomSubscriptionCanonicalizer(FhirContext theFhirContext) {
 		super(theFhirContext);