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Updated utils

This commit is contained in:
Nick Goupinets 2021-03-19 18:14:48 -04:00
parent 5747d5d841
commit 142fd4c108
5 changed files with 75 additions and 282 deletions
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57
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ExtensionUtil.java
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@ -27,6 +27,7 @@ import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseExtension; import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions; import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import javax.annotation.Nonnull;
import java.util.List; import java.util.List;
import java.util.function.Predicate; import java.util.function.Predicate;
import java.util.stream.Collectors; import java.util.stream.Collectors;
@ -54,6 +55,34 @@ public class ExtensionUtil {
return extension; return extension;
} }
/**
* Returns an new empty extension.
*
* @param theBase Base resource to add the extension to
* @return Returns a new extension
* @throws IllegalArgumentException IllegalArgumentException is thrown in case resource doesn't support extensions
*/
public static IBaseExtension<?, ?> addExtension(IBase theBase) {
return addExtension(theBase, null);
}
/**
* Returns an extension with the specified URL
*
* @param theBase Base resource to add the extension to
* @param theUrl URL for the extension
* @return Returns a new extension with the specified URL.
* @throws IllegalArgumentException IllegalArgumentException is thrown in case resource doesn't support extensions
*/
public static IBaseExtension<?, ?> addExtension(IBase theBase, String theUrl) {
IBaseHasExtensions baseHasExtensions = validateExtensionSupport(theBase);
IBaseExtension extension = baseHasExtensions.addExtension();
if (theUrl != null) {
extension.setUrl(theUrl);
}
return extension;
}
private static IBaseHasExtensions validateExtensionSupport(IBase theBase) { private static IBaseHasExtensions validateExtensionSupport(IBase theBase) {
if (!(theBase instanceof IBaseHasExtensions)) { if (!(theBase instanceof IBaseHasExtensions)) {
throw new IllegalArgumentException(String.format("Expected instance that supports extensions, but got %s", theBase)); throw new IllegalArgumentException(String.format("Expected instance that supports extensions, but got %s", theBase));
@ -105,10 +134,15 @@ public class ExtensionUtil {
* @return Returns the first available extension with the specified URL, or null if such extension doesn't exist * @return Returns the first available extension with the specified URL, or null if such extension doesn't exist
*/ */
public static IBaseExtension<?, ?> getExtension(IBase theBase, String theExtensionUrl) { public static IBaseExtension<?, ?> getExtension(IBase theBase, String theExtensionUrl) {
return validateExtensionSupport(theBase) Predicate<IBaseExtension> filter;
.getExtension() if (theExtensionUrl == null) {
filter = (e -> true);
} else {
filter = (e -> theExtensionUrl.equals(e.getUrl()));
}
return getExtensions(theBase, filter)
.stream() .stream()
.filter(e -> theExtensionUrl.equals(e.getUrl()))
.findFirst() .findFirst()
.orElse(null); .orElse(null);
} }
@ -129,10 +163,21 @@ public class ExtensionUtil {
} }
/** /**
* Gets all extensions with the specified URL * Removes all extensions.
* *
* @param theBase The resource to get the extension for * @param theBase The resource to clear the extension for
* @return Returns all extension with the specified URL, or an empty list if such extensions do not exist * @return Returns all extension that were removed
*/
public static List<IBaseExtension<?, ?>> clearExtensions(IBase theBase) {
return clearExtensions(theBase, (e -> true));
}
/**
* Removes all extensions that match the specified predicate
*
* @param theBase The base object to clear the extension for
* @param theFilter Defines which extensions should be cleared
* @return Returns all extension that were removed
*/ */
public static List<IBaseExtension<?, ?>> clearExtensions(IBase theBase, Predicate<? super IBaseExtension> theFilter) { public static List<IBaseExtension<?, ?>> clearExtensions(IBase theBase, Predicate<? super IBaseExtension> theFilter) {
List<IBaseExtension<?, ?>> retVal = getExtensions(theBase, theFilter); List<IBaseExtension<?, ?>> retVal = getExtensions(theBase, theFilter);

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TerserUtil.java
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@ -334,11 +334,11 @@ public final class TerserUtil {
setFieldByFhirPath(theFhirContext.newTerser(), theFhirPath, theResource, theValue); setFieldByFhirPath(theFhirContext.newTerser(), theFhirPath, theResource, theValue);
} }
public static List<IBase> getFieldByFhirPath(FhirContext theFhirContext, String theFhirPath, IBaseResource theResource) { public static List<IBase> getFieldByFhirPath(FhirContext theFhirContext, String theFhirPath, IBase theResource) {
return theFhirContext.newTerser().getValues(theResource, theFhirPath, false, false); return theFhirContext.newTerser().getValues(theResource, theFhirPath, false, false);
} }
public static IBase getFirstFieldByFhirPath(FhirContext theFhirContext, String theFhirPath, IBaseResource theResource) { public static IBase getFirstFieldByFhirPath(FhirContext theFhirContext, String theFhirPath, IBase theResource) {
List<IBase> values = getFieldByFhirPath(theFhirContext, theFhirPath, theResource); List<IBase> values = getFieldByFhirPath(theFhirContext, theFhirPath, theResource);
if (values == null || values.isEmpty()) { if (values == null || values.isEmpty()) {
return null; return null;

24
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TerserUtilHelper.java
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@ -108,15 +108,35 @@ public class TerserUtilHelper {
} }
/** /**
* Gets values of the specified field. * Gets values for the specified child field.
* *
* @param theField The field to get values from * @param theField The field to get values from
* @return Returns a collection of values containing values or null if the specified field doesn't exist * @return Returns a list of retrieved values or null if the specified field doesn't exist
*/ */
public List<IBase> getFieldValues(String theField) { public List<IBase> getFieldValues(String theField) {
return TerserUtil.getValues(myContext, myResource, theField); return TerserUtil.getValues(myContext, myResource, theField);
} }
/**
* Gets values for the specified field values by FHIRPath.
*
* @param theFhirPath The FHIR path expression to get the values from
* @return Returns a collection of values or null if the specified field doesn't exist
*/
public List<IBase> getFieldValuesByFhirPath(String theFhirPath) {
return TerserUtil.getFieldByFhirPath(myContext, theFhirPath, myResource);
}
/**
* Gets first available value for the specified field values by FHIRPath.
*
* @param theFhirPath The FHIR path expression to get the values from
* @return Returns the value or null if the specified field doesn't exist or is empty
*/
public IBase getFieldValueByFhirPath(String theFhirPath) {
return TerserUtil.getFirstFieldByFhirPath(myContext, theFhirPath, myResource);
}
/** /**
* Gets first available values of the specified field. * Gets first available values of the specified field.
* *

148
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/ResourceFlatteningInterceptor.java
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@ -1,148 +0,0 @@
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);
}
}

124
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/ResourceFlatteningInterceptorTest.java
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@ -1,124 +0,0 @@
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();
}
}