Upgrade dependencies ⬆️

- Upgrade FHIR Gateway
- Upgrade 3rd party dependencies
- Update workflow configuration JDK version

.github/workflows/ci.yml

@@ -17,10 +17,10 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Set up JDK 11
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
-          java-version: 11
+          java-version: '17'
 
       - name: Run Unit tests and generate report
         run: mvn -B clean test jacoco:report --file pom.xml --file README.md --file LICENSE

exec/pom.xml

@@ -12,7 +12,7 @@
 
   <properties>
     <root.basedir>${project.parent.basedir}</root.basedir>
-    <spring-boot.version>2.7.5</spring-boot.version>
+    <spring-boot.version>3.3.4</spring-boot.version>
     <!-- We do not want to deploy the `exec` uber jar. -->
     <maven.deploy.skip>true</maven.deploy.skip>
   </properties>
@@ -46,13 +46,13 @@
     <dependency>
       <groupId>com.google.fhir.gateway</groupId>
       <artifactId>server</artifactId>
-      <version>0.3.1</version>
+      <version>${fhir.gateway.version}</version>
     </dependency>
 
     <dependency>
       <groupId>com.google.fhir.gateway</groupId>
       <artifactId>plugins</artifactId>
-      <version>0.3.1</version>
+      <version>${fhir.gateway.version}</version>
     </dependency>
 
     <!-- For Spring -->
@@ -98,7 +98,7 @@
             </goals>
             <configuration>
               <mainClass>org.smartregister.fhir.gateway.MainApp</mainClass>
-              <!-- We use ZIP layout such that PropertiesLauncher is used and we
+              <!-- We use ZIP layout such that PropertiesLauncher is used, and we
               can add extra jars through `loader.path` property:
               https://docs.spring.io/spring-boot/docs/current/reference/html/executable-jar.html#appendix.executable-jar.property-launcher
               This is useful for when people want to inject other plugins into

plugins/pom.xml

@@ -11,31 +11,31 @@
 
   <properties>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-    <maven.compiler.source>11</maven.compiler.source>
-    <maven.compiler.target>11</maven.compiler.target>
+    <maven.compiler.source>17</maven.compiler.source>
+    <maven.compiler.target>17</maven.compiler.target>
     <project.basedir>${project.basedir}</project.basedir>
-    <hapifhir.version>6.8.3</hapifhir.version>
+    <hapifhir.version>7.4.3</hapifhir.version>
     <fhir.proxy-plugin.version>0.2.0</fhir.proxy-plugin.version>
+    <sentry.version>7.15.0</sentry.version>
+    <jakarta-servlet.version>6.0.0</jakarta-servlet.version>
   </properties>
 
   <dependencies>
-
     <dependency>
       <groupId>com.google.fhir.gateway</groupId>
       <artifactId>server</artifactId>
-      <version>0.3.2</version>
+      <version>${fhir.gateway.version}</version>
     </dependency>
     <dependency>
       <groupId>com.google.fhir.gateway</groupId>
       <artifactId>plugins</artifactId>
-      <version>0.3.1</version>
+      <version>${fhir.gateway.version}</version>
     </dependency>
     <!-- Needed for JEE/Servlet support -->
     <dependency>
-      <groupId>javax.servlet</groupId>
-      <artifactId>javax.servlet-api</artifactId>
-      <version>4.0.1</version>
-      <scope>provided</scope>
+      <groupId>jakarta.servlet</groupId>
+      <artifactId>jakarta.servlet-api</artifactId>
+      <version>${jakarta-servlet.version}</version>
     </dependency>
     <dependency>
       <groupId>ca.uhn.hapi.fhir</groupId>
@@ -51,12 +51,12 @@
     <dependency>
       <groupId>io.sentry</groupId>
       <artifactId>sentry-logback</artifactId>
-      <version>7.6.0</version>
+      <version>${sentry.version}</version>
     </dependency>
     <dependency>
       <groupId>io.sentry</groupId>
-      <artifactId>sentry-spring-boot-starter</artifactId>
-      <version>7.6.0</version>
+      <artifactId>sentry-spring-boot-starter-jakarta</artifactId>
+      <version>${sentry.version}</version>
     </dependency>
   </dependencies>
 

plugins/src/main/java/org/smartregister/fhir/gateway/plugins/LocationHierarchyEndpointHelper.java

@@ -10,9 +10,6 @@
 import java.util.Map;
 import java.util.stream.Collectors;
 
-import javax.annotation.Nullable;
-import javax.servlet.http.HttpServletRequest;
-
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.r4.model.Binary;
 import org.hl7.fhir.r4.model.Bundle;
@@ -37,6 +34,8 @@
 import ca.uhn.fhir.rest.gclient.TokenClientParam;
 import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import jakarta.annotation.Nullable;
+import jakarta.servlet.http.HttpServletRequest;
 
 public class LocationHierarchyEndpointHelper {
 

plugins/src/main/java/org/smartregister/fhir/gateway/plugins/PermissionAccessChecker.java

@@ -17,7 +17,6 @@
 import org.hl7.fhir.r4.model.CareTeam;
 import org.hl7.fhir.r4.model.Composition;
 import org.hl7.fhir.r4.model.Organization;
-import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.smartregister.fhir.gateway.plugins.interfaces.ResourceFinder;
@@ -40,6 +39,7 @@
 import ca.uhn.fhir.rest.api.SearchStyleEnum;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
+import jakarta.annotation.Nonnull;
 
 public class PermissionAccessChecker implements AccessChecker {
     private static final Logger logger = LoggerFactory.getLogger(PermissionAccessChecker.class);
@@ -282,7 +282,7 @@ private List<String> getLocationUuids(String[] syncLocations) {
         return locationUuids;
     }
 
-    @NotNull
+    @Nonnull
     private Map<String, List<String>> collateSyncStrategyIds(
             String syncStrategy,
             PractitionerDetails practitionerDetails,

plugins/src/main/java/org/smartregister/fhir/gateway/plugins/PractitionerDetailsEndpointHelper.java

@@ -23,7 +23,6 @@
 import org.hl7.fhir.r4.model.OrganizationAffiliation;
 import org.hl7.fhir.r4.model.Practitioner;
 import org.hl7.fhir.r4.model.PractitionerRole;
-import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.smartregister.model.location.LocationHierarchy;
@@ -37,6 +36,7 @@
 import ca.uhn.fhir.rest.api.SearchStyleEnum;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.gclient.ReferenceClientParam;
+import jakarta.annotation.Nonnull;
 
 public class PractitionerDetailsEndpointHelper {
     private static final Logger logger =
@@ -160,7 +160,7 @@ protected Bundle getAttributedPractitionerDetailsByPractitioner(Practitioner pra
         return responseBundle;
     }
 
-    @NotNull
+    @Nonnull
     public static Set<String> getAttributedLocations(List<LocationHierarchy> locationHierarchies) {
         List<ParentChildrenMap> parentChildrenList =
                 locationHierarchies.stream()

plugins/src/main/java/org/smartregister/fhir/gateway/plugins/RestUtils.java

@@ -2,16 +2,15 @@
 
 import static org.smartregister.fhir.gateway.plugins.Constants.AUTHORIZATION;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import com.google.fhir.gateway.ExceptionUtil;
 import com.google.fhir.gateway.TokenVerifier;
 
 import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 
 public class RestUtils {
 

plugins/src/main/java/org/smartregister/fhir/gateway/plugins/SyncAccessDecision.java

@@ -13,8 +13,6 @@
 import java.util.Map;
 import java.util.stream.Collectors;
 
-import javax.annotation.Nullable;
-
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.http.HttpResponse;
@@ -25,7 +23,6 @@
 import org.hl7.fhir.r4.model.ListResource;
 import org.hl7.fhir.r4.model.OperationOutcome;
 import org.hl7.fhir.r4.model.Resource;
-import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -42,6 +39,8 @@
 import ca.uhn.fhir.rest.api.RequestTypeEnum;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
+import jakarta.annotation.Nonnull;
+import jakarta.annotation.Nullable;
 import lombok.Getter;
 
 public class SyncAccessDecision implements AccessDecision {
@@ -152,7 +151,7 @@ public RequestMutation getRequestMutation(RequestDetailsReader requestDetailsRea
 
             requestMutation =
                     RequestMutation.builder()
-                            .queryParams(
+                            .additionalQueryParams(
                                     Map.of(
                                             Constants.TAG_SEARCH_PARAM,
                                             List.of(
@@ -359,7 +358,7 @@ private boolean includeAttributedPractitioners(String requestPath) {
                 && SyncAccessDecisionConstants.ENDPOINT_PRACTITIONER_DETAILS.equals(requestPath);
     }
 
-    @NotNull
+    @Nonnull
     private static OperationOutcome createOperationOutcome(String exception) {
         OperationOutcome operationOutcome = new OperationOutcome();
         OperationOutcome.OperationOutcomeIssueComponent operationOutcomeIssueComponent =
@@ -371,7 +370,7 @@ private static OperationOutcome createOperationOutcome(String exception) {
         return operationOutcome;
     }
 
-    @NotNull
+    @Nonnull
     private static Bundle processListEntriesGatewayModeByListResource(
             ListResource responseListResource, int start, int count) {
         Bundle requestBundle = new Bundle();
@@ -418,7 +417,7 @@ private Bundle processListEntriesGatewayModeByBundle(
         return requestBundle.setEntry(bundleEntryComponentList);
     }
 
-    @NotNull
+    @Nonnull
     static Bundle.BundleEntryComponent createBundleEntryComponent(
             Bundle.HTTPVerb method, String requestPath, @Nullable String condition) {
 

plugins/src/main/java/org/smartregister/fhir/gateway/plugins/endpoint/BaseEndpoint.java

@@ -6,10 +6,6 @@
 import java.io.PrintWriter;
 import java.nio.charset.StandardCharsets;
 
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.smartregister.fhir.gateway.plugins.RestUtils;
@@ -18,6 +14,9 @@
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.parser.IParser;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 
 public abstract class BaseEndpoint extends HttpServlet {
     private static final Logger logger = LoggerFactory.getLogger(BaseEndpoint.class);

plugins/src/main/java/org/smartregister/fhir/gateway/plugins/endpoint/LocationHierarchyEndpoint.java

@@ -4,10 +4,6 @@
 
 import java.io.IOException;
 
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
 import org.apache.http.HttpStatus;
 import org.hl7.fhir.r4.model.Bundle;
 import org.smartregister.fhir.gateway.plugins.Constants;
@@ -18,6 +14,9 @@
 import com.auth0.jwt.interfaces.DecodedJWT;
 
 import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
+import jakarta.servlet.annotation.WebServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 
 @WebServlet("/LocationHierarchy")
 public class LocationHierarchyEndpoint extends BaseEndpoint {

plugins/src/main/java/org/smartregister/fhir/gateway/plugins/endpoint/PractitionerDetailEndpoint.java

@@ -5,10 +5,6 @@
 import java.io.IOException;
 import java.util.Collections;
 
-import javax.servlet.annotation.WebServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
 import org.apache.http.HttpStatus;
 import org.smartregister.fhir.gateway.plugins.Constants;
 import org.smartregister.fhir.gateway.plugins.PractitionerDetailsEndpointHelper;
@@ -17,6 +13,9 @@
 import org.smartregister.model.practitioner.PractitionerDetails;
 
 import ca.uhn.fhir.rest.server.exceptions.AuthenticationException;
+import jakarta.servlet.annotation.WebServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 
 @WebServlet("/PractitionerDetail")
 public class PractitionerDetailEndpoint extends BaseEndpoint {

plugins/src/test/java/org/smartregister/fhir/gateway/plugins/LocationHierarchyEndpointHelperTest.java

@@ -12,8 +12,6 @@
 import java.util.List;
 import java.util.Map;
 
-import javax.servlet.http.HttpServletRequest;
-
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.CodeableConcept;
@@ -37,6 +35,7 @@
 import ca.uhn.fhir.rest.gclient.IQuery;
 import ca.uhn.fhir.rest.gclient.IUntypedQuery;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import jakarta.servlet.http.HttpServletRequest;
 
 public class LocationHierarchyEndpointHelperTest {
 

plugins/src/test/java/org/smartregister/fhir/gateway/plugins/RestUtilTest.java

@@ -5,14 +5,14 @@
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.verify;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
 import org.junit.Test;
 import org.mockito.Mockito;
 
 import com.google.fhir.gateway.TokenVerifier;
 
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
+
 public class RestUtilTest {
 
     @Test(expected = RuntimeException.class)