Initial commit

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ExtensionUtil.java

@@ -28,6 +28,7 @@ import org.hl7.fhir.instance.model.api.IBaseExtension;
 import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
 
 import java.util.List;
+import java.util.function.Predicate;
 import java.util.stream.Collectors;
 
 /**
@@ -103,14 +104,44 @@ public class ExtensionUtil {
 	 * @param theExtensionUrl URL of the extension to get. Must be non-null
 	 * @return Returns the first available extension with the specified URL, or null if such extension doesn't exist
 	 */
-	public static IBaseExtension<?, ?> getExtension(IBaseHasExtensions theBase, String theExtensionUrl) {
+	public static IBaseExtension<?, ?> getExtension(IBase theBase, String theExtensionUrl) {
-		return theBase.getExtension()
+		return validateExtensionSupport(theBase)
+			.getExtension()
 			.stream()
 			.filter(e -> theExtensionUrl.equals(e.getUrl()))
 			.findFirst()
 			.orElse(null);
 	}
 
+	/**
+	 * Gets all extensions that match the specified filter predicate
+	 *
+	 * @param theBase   The resource to get the extension for
+	 * @param theFilter Predicate to match the extension against
+	 * @return Returns all extension with the specified URL, or an empty list if such extensions do not exist
+	 */
+	public static List<IBaseExtension<?, ?>> getExtensions(IBase theBase, Predicate<? super IBaseExtension> theFilter) {
+		return validateExtensionSupport(theBase)
+			.getExtension()
+			.stream()
+			.filter(theFilter)
+			.collect(Collectors.toList());
+	}
+
+	/**
+	 * Gets all extensions with the specified URL
+	 *
+	 * @param theBase The resource to get the extension for
+	 * @return Returns all extension with the specified URL, or an empty list if such extensions do not exist
+	 */
+	public static List<IBaseExtension<?, ?>> clearExtensions(IBase theBase, Predicate<? super IBaseExtension> theFilter) {
+		List<IBaseExtension<?, ?>> retVal = getExtensions(theBase, theFilter);
+		validateExtensionSupport(theBase)
+			.getExtension()
+			.removeIf(theFilter);
+		return retVal;
+	}
+
 	/**
 	 * Gets all extensions with the specified URL
 	 *
@@ -119,10 +150,8 @@ public class ExtensionUtil {
 	 * @return Returns all extension with the specified URL, or an empty list if such extensions do not exist
 	 */
 	public static List<IBaseExtension<?, ?>> getExtensions(IBaseHasExtensions theBase, String theExtensionUrl) {
-		return theBase.getExtension()
+		Predicate<IBaseExtension> urlEqualityPredicate = e -> theExtensionUrl.equals(e.getUrl());
-			.stream()
+		return getExtensions(theBase, urlEqualityPredicate);
-			.filter(e -> theExtensionUrl.equals(e.getUrl()))
-			.collect(Collectors.toList());
 	}
 
 	/**

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TerserUtil.java

@@ -97,12 +97,12 @@ public final class TerserUtil {
 	}
 
 	/**
-	 * get the Values of a specified field.
+	 * Gets all values of the specified field.
 	 *
 	 * @param theFhirContext Context holding resource definition
 	 * @param theResource    Resource to check if the specified field is set
 	 * @param theFieldName   name of the field to check
-	 * @return Returns true if field exists and has any values set, and false otherwise
+	 * @return Returns all values for the specified field or null if field with the provided name doesn't exist
 	 */
 	public static List<IBase> getValues(FhirContext theFhirContext, IBaseResource theResource, String theFieldName) {
 		RuntimeResourceDefinition resourceDefinition = theFhirContext.getResourceDefinition(theResource);
@@ -114,6 +114,23 @@ public final class TerserUtil {
 		return resourceIdentifier.getAccessor().getValues(theResource);
 	}
 
+	/**
+	 * Gets the first available value for the specified field.
+	 *
+	 * @param theFhirContext Context holding resource definition
+	 * @param theResource    Resource to check if the specified field is set
+	 * @param theFieldName   name of the field to check
+	 * @return Returns the first value for the specified field or null if field with the provided name doesn't exist or
+	 * has no values
+	 */
+	public static IBase getValue(FhirContext theFhirContext, IBaseResource theResource, String theFieldName) {
+		List<IBase> values = getValues(theFhirContext, theResource, theFieldName);
+		if (values == null || values.isEmpty()) {
+			return null;
+		}
+		return values.get(0);
+	}
+
 	/**
 	 * Clones specified composite field (collection). Composite field values must conform to the collections
 	 * contract.
@@ -256,6 +273,20 @@ public final class TerserUtil {
 		childDefinition.getAccessor().getValues(theResource).clear();
 	}
 
+	/**
+	 * Sets the provided field with the given values. This method will add to the collection of existing field values
+	 * in case of multiple cardinality. Use {@link #clearField(FhirContext, FhirTerser, String, IBaseResource, IBase...)}
+	 * to remove values before setting
+	 *
+	 * @param theFhirContext Context holding resource definition
+	 * @param theFieldName   Child field name of the resource to set
+	 * @param theResource    The resource to set the values on
+	 * @param theValues      The values to set on the resource child field name
+	 */
+	public static void setField(FhirContext theFhirContext, String theFieldName, IBaseResource theResource, IBase... theValues) {
+		setField(theFhirContext, theFhirContext.newTerser(), theFieldName, theResource, theValues);
+	}
+
 	/**
 	 * Sets the provided field with the given values. This method will add to the collection of existing field values
 	 * in case of multiple cardinality. Use {@link #clearField(FhirContext, FhirTerser, String, IBaseResource, IBase...)}
@@ -303,6 +334,18 @@ public final class TerserUtil {
 		setFieldByFhirPath(theFhirContext.newTerser(), theFhirPath, theResource, theValue);
 	}
 
+	public static List<IBase> getFieldByFhirPath(FhirContext theFhirContext, String theFhirPath, IBaseResource theResource) {
+		return theFhirContext.newTerser().getValues(theResource, theFhirPath, false, false);
+	}
+
+	public static IBase getFirstFieldByFhirPath(FhirContext theFhirContext, String theFhirPath, IBaseResource theResource) {
+		List<IBase> values = getFieldByFhirPath(theFhirContext, theFhirPath, theResource);
+		if (values == null || values.isEmpty()) {
+			return null;
+		}
+		return values.get(0);
+	}
+
 	private static void replaceField(IBaseResource theFrom, IBaseResource theTo, BaseRuntimeChildDefinition childDefinition) {
 		childDefinition.getAccessor().getFirstValueOrNull(theFrom).ifPresent(v -> {
 				childDefinition.getMutator().setValue(theTo, v);

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TerserUtilHelper.java

@@ -111,12 +111,27 @@ public class TerserUtilHelper {
 	 * Gets values of the specified field.
 	 *
 	 * @param theField The field to get values from
-	 * @return Returns a collection of values containing values or null if the spefied field doesn't exist
+	 * @return Returns a collection of values containing values or null if the specified field doesn't exist
 	 */
 	public List<IBase> getFieldValues(String theField) {
 		return TerserUtil.getValues(myContext, myResource, theField);
 	}
 
+	/**
+	 * Gets first available values of the specified field.
+	 *
+	 * @param theField The field to get values from
+	 * @return Returns the first available value for the field name or null if the
+	 * specified field doesn't exist or has no values
+	 */
+	public IBase getFieldValue(String theField) {
+		List<IBase> values = getFieldValues(theField);
+		if (values == null || values.isEmpty()) {
+			return null;
+		}
+		return values.get(0);
+	}
+
 	/**
 	 * Gets the terser instance, creating one if necessary.
 	 *

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/ResourceFlatteningInterceptor.java

@@ -0,0 +1,148 @@
+package ca.uhn.fhir.jpa.interceptor;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.interceptor.api.Hook;
+import ca.uhn.fhir.interceptor.api.Interceptor;
+import ca.uhn.fhir.interceptor.api.Pointcut;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.model.primitive.CodeDt;
+import ca.uhn.fhir.model.primitive.StringDt;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.util.ExtensionUtil;
+import ca.uhn.fhir.util.TerserUtil;
+import ca.uhn.fhir.util.TerserUtilHelper;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseExtension;
+import org.hl7.fhir.instance.model.api.IBaseReference;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.List;
+
+@Interceptor
+public class ResourceFlatteningInterceptor {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(ResourceFlatteningInterceptor.class);
+
+	@Autowired
+	private FhirContext myFhirContext;
+
+	@Autowired
+	private DaoRegistry myDaoRegistry;
+
+	public ResourceFlatteningInterceptor(FhirContext theFhirContext, DaoRegistry theDaoRegistry) {
+		myFhirContext = theFhirContext;
+		myDaoRegistry = theDaoRegistry;
+	}
+
+
+	@Hook(Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED)
+	public void resourceUpdatedPreCommit(RequestDetails theRequest, IBaseResource theResource) {
+		ourLog.debug("Validating address on for create {}, {}", theResource, theRequest);
+		handleRequest(theRequest, theResource);
+	}
+
+	@Hook(Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED)
+	public void resourceCreatedPreCommit(RequestDetails theRequest, IBaseResource theResource) {
+		ourLog.debug("Validating address on for create {}, {}", theResource, theRequest);
+		handleRequest(theRequest, theResource);
+	}
+
+	private void handleRequest(RequestDetails theRequest, IBaseResource theResource) {
+		switch (myFhirContext.getResourceType(theResource)) {
+			case "Location":
+				flattenLocation(theResource);
+				return;
+			case "Account":
+				flattenAccount(theResource);
+				return;
+			case "Role":
+				flattenRole(theResource);
+				return;
+			default:
+				return;
+		}
+	}
+
+	private void flattenLocation(IBaseResource theResource) {
+		TerserUtilHelper helper = TerserUtilHelper.newHelper(myFhirContext, theResource);
+		IBase managingOrganizationsRef = helper.getFieldValue("managingOrganization");
+		if (managingOrganizationsRef == null) {
+			ourLog.info("No organization is associated with {}", theResource);
+			return;
+		}
+
+		IBaseResource referencedOrg = ((IBaseReference) managingOrganizationsRef).getResource();
+		if (referencedOrg == null) {
+			ourLog.warn("Missing value for reference {}", referencedOrg);
+			return;
+		}
+		TerserUtil.getValues(myFhirContext, referencedOrg, "address").clear();
+
+		IBase newAddress = helper.getFieldValue("address");
+		TerserUtil.setFieldByFhirPath(myFhirContext, "address", referencedOrg, newAddress);
+
+		IFhirResourceDao dao = getDao(referencedOrg);
+		dao.update(referencedOrg);
+	}
+
+	private void flattenAccount(IBaseResource theAccount) {
+		TerserUtilHelper account = TerserUtilHelper.newHelper(myFhirContext, theAccount);
+		List<IBase> owner = account.getFieldValues("owner");
+		if (owner.isEmpty()) {
+			ourLog.info("No organization is associated with {}", theAccount);
+			return;
+		}
+
+		for (IBase o : owner) {
+			IBaseResource org = ((IBaseReference) o).getResource();
+			if (org == null) {
+				ourLog.warn("Missing value for reference {}", o);
+				continue;
+			}
+
+			IBaseExtension ext = ExtensionUtil.getOrCreateExtension(org, "http://hapifhir.org/Flattener/Account");
+			IPrimitiveType status = (IPrimitiveType) TerserUtil.getFirstFieldByFhirPath(myFhirContext, "status", theAccount);
+			ExtensionUtil.setExtension(myFhirContext, ext, status.getValueAsString());
+
+			IFhirResourceDao dao = getDao(org);
+			dao.update(org);
+		}
+	}
+
+	// PractitionerRole.specialty becomes Practitioner.Extension.valueCode
+	private void flattenRole(IBaseResource theRole) {
+		TerserUtilHelper role = TerserUtilHelper.newHelper(myFhirContext, theRole);
+
+		List<IBase> specialties = role.getFieldValues("specialty");
+		if (specialties.isEmpty()) {
+			ourLog.info("No specialties are associated with {}", theRole);
+			return;
+		}
+
+		for (IBase o : specialties) {
+			IBaseResource practitioner = (IBaseResource) TerserUtil.getValue(myFhirContext, theRole, "practitioner");
+			if (practitioner == null) {
+				ourLog.warn("Practitioner is not set on {}", theRole);
+				continue;
+			}
+
+			String roleUrl = "http://hapifhir.org/Flattener/Role/" + theRole.toString();
+
+			IBaseExtension ext = ExtensionUtil.getOrCreateExtension(practitioner, roleUrl);
+			ext.setValue(new CodeDt(String.valueOf(role.getFieldValue("status"))));
+
+			IFhirResourceDao dao = getDao(practitioner);
+			dao.update(practitioner);
+		}
+	}
+
+	private IFhirResourceDao getDao(IBaseResource theReferencedOrg) {
+		String resourceType = myFhirContext.getResourceType(theReferencedOrg);
+		return myDaoRegistry.getResourceDao(resourceType);
+	}
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/ResourceFlatteningInterceptorTest.java

@@ -0,0 +1,124 @@
+package ca.uhn.fhir.jpa.interceptor;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.provider.r4.BaseResourceProviderR4Test;
+import ca.uhn.fhir.util.TerserUtilHelper;
+import org.checkerframework.checker.units.qual.A;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Account;
+import org.hl7.fhir.r4.model.Address;
+import org.hl7.fhir.r4.model.CodeableConcept;
+import org.hl7.fhir.r4.model.Location;
+import org.hl7.fhir.r4.model.Organization;
+import org.hl7.fhir.r4.model.PractitionerRole;
+import org.hl7.fhir.r4.model.Reference;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import javax.annotation.Nonnull;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+class ResourceFlatteningInterceptorTest extends BaseResourceProviderR4Test {
+
+	private ResourceFlatteningInterceptor myInterceptor;
+
+	@Autowired
+	private DaoRegistry myDaoRegistry;
+	@Autowired
+	private FhirContext myFhirContext;
+
+	@BeforeEach
+	public void init() {
+		myInterceptor = new ResourceFlatteningInterceptor(myFhirContext, myDaoRegistry);
+	}
+
+	public <T extends IBaseResource> IFhirResourceDao<T> getDao(IBaseResource theResource) {
+		String type = myFhirContext.getResourceType(theResource);
+		return myDaoRegistry.getResourceDao(type);
+	}
+
+	@Test
+	public void testFlatteningOfLocation() {
+		// Location.address becomes Organization.address
+		Organization newOrganization = newPersistentOrganization();
+
+		Location location = new Location();
+		Address newAddress = new Address();
+		newAddress.addLine("NEW LINE 1").setCity("NEW CITY");
+		location.setAddress(newAddress);
+		location.setManagingOrganization(new Reference(newOrganization));
+
+		myInterceptor.resourceCreatedPreCommit(null, location);
+
+		Organization savedOrganization = (Organization) getDao(newOrganization)
+			.read(newOrganization.getIdElement());
+		assertEquals(1, savedOrganization.getAddress().size(), "Expect old addresses cleared up");
+
+		Address savedAddress = savedOrganization.getAddressFirstRep();
+		assertTrue(newAddress.equalsDeep(savedAddress), "Expect organization address replaced");
+	}
+
+	@Nonnull
+	private Organization newPersistentOrganization() {
+		Organization newOrganization = newOrganization();
+		return (Organization) getDao(newOrganization).create(newOrganization).getResource();
+	}
+
+	@Nonnull
+	private Organization newOrganization() {
+		Organization retVal = new Organization();
+		retVal.addAddress()
+			.addLine("Address 1 Line 1")
+			.setCity("Address 1 City");
+		retVal.addAddress()
+			.addLine("Address 2 Line 1")
+			.setCity("Address 2 City");
+		return retVal;
+	}
+
+	@Test
+	public void testFlatteningOfLocationWithEmptyManagingOrg() {
+		try {
+			myInterceptor.resourceCreatedPreCommit(null, new Location());
+		} catch (Exception e) {
+			fail("Expected no errors");
+		}
+	}
+
+	@Test
+	public void testFlatteningOfAccount() {
+		// Account.status become Organization.Extension.valueCode
+		Organization organization = newPersistentOrganization();
+		assertTrue(organization.getExtension().isEmpty());
+
+		Account account = new Account();
+		account.setName("Test Account");
+		account.setStatus(Account.AccountStatus.ACTIVE);
+		account.setDescription("Test Active Account");
+		account.setOwner(new Reference(organization));
+
+		myInterceptor.resourceCreatedPreCommit(null, account);
+
+		Organization savedOrganization = (Organization) getDao(organization).read(organization.getIdElement());
+		assertFalse(organization.getExtension().isEmpty());
+
+		assertEquals(Account.AccountStatus.ACTIVE.toCode(), organization.getExtension().get(0).getValue().primitiveValue());
+	}
+
+	@Test
+	public void testFlatteningOfAnEmptyAccout() {
+		myInterceptor.resourceCreatedPreCommit(null, new Account());
+	}
+
+	public void testFlatteningOfPractitionerRole() {
+		// PractitionerRole.specialty becomes Practitioner.Extension.valueCode
+		PractitionerRole role = new PractitionerRole();
+		CodeableConcept specialty = role.addSpecialty();
+	}
+
+}

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/util/TerserUtilTest.java

@@ -57,9 +57,11 @@ class TerserUtilTest {
 		assertEquals(1, p2Helper.getFieldValues("identifier").size());
 
 		Identifier id1 = (Identifier) p1Helper.getFieldValues("identifier").get(0);
-		Identifier id2 = (Identifier) p2Helper.getFieldValues("identifier").get(0);
+		Identifier id2 = (Identifier) p2Helper.getFieldValue("identifier");
 		assertTrue(id1.equalsDeep(id2));
 		assertFalse(id1.equals(id2));
+
+		assertNull(p2Helper.getFieldValue("address"));
 	}
 
 	@Test