Merge master

.github/workflows/ci.yaml

@@ -9,6 +9,11 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
+    env:
+      TESTCONTAINERS_DOCKER_SOCKET_OVERRIDE: /var/run/docker.sock
+      DOCKER_HOST: unix:///var/run/docker.sock
+      TESTCONTAINERS_RYUK_DISABLED: "true"
+      TESTCONTAINERS_CHECKS_DISABLE: "true"
 
     steps:
       - uses: actions/checkout@v3
@@ -19,5 +24,21 @@ jobs:
         with:
           java-version: '17'
           distribution: 'adopt'
+      - name: Debug Docker (Testcontainers)
+        run: |
+          echo "=== whoami ==="
+          whoami
+          echo "=== groups ==="
+          groups
+          echo "=== id ==="
+          id
+          echo "=== DOCKER_HOST ==="
+          echo "${DOCKER_HOST:-<not set>}"
+          echo "=== Docker socket ==="
+          ls -la /var/run/docker.sock 2>&1 || true
+          echo "=== docker info ==="
+          docker info 2>&1 || true
+          echo "=== docker run hello-world ==="
+          docker run --rm hello-world 2>&1 || true
       - name: Build with Maven
         run: mvn --batch-mode package

.github/workflows/release.yaml

@@ -12,6 +12,11 @@ jobs:
     outputs:
       version: ${{ steps.release-outputs.outputs.version }}
       service: ${{ steps.release-outputs.outputs.service }}
+    env:
+      TESTCONTAINERS_DOCKER_SOCKET_OVERRIDE: /var/run/docker.sock
+      DOCKER_HOST: unix:///var/run/docker.sock
+      TESTCONTAINERS_RYUK_DISABLED: "true"
+      TESTCONTAINERS_CHECKS_DISABLE: "true"
 
     steps:
       - name: Login to Docker Hub
@@ -69,6 +74,22 @@ jobs:
           git tag ${{ steps.bump.outputs.new_base_version }}
           git push origin HEAD:${GITHUB_REF##*/}
           git push origin ${{ steps.bump.outputs.new_base_version }}
+      - name: Debug Docker (Testcontainers)
+        run: |
+          echo "=== whoami ==="
+          whoami
+          echo "=== groups ==="
+          groups
+          echo "=== id ==="
+          id
+          echo "=== DOCKER_HOST ==="
+          echo "${DOCKER_HOST:-<not set>}"
+          echo "=== Docker socket ==="
+          ls -la /var/run/docker.sock 2>&1 || true
+          echo "=== docker info ==="
+          docker info 2>&1 || true
+          echo "=== docker run hello-world ==="
+          docker run --rm hello-world 2>&1 || true
       - name: Build package
         run: mvn --batch-mode clean package
       - name: Build and push image

Dockerfile

@@ -1,4 +1,4 @@
-FROM eclipse-temurin:17-jre-jammy
+FROM eclipse-temurin:21-jre
 MAINTAINER protege.stanford.edu
 
 EXPOSE 7777

pom.xml

@@ -70,7 +70,7 @@
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>minio</artifactId>
-            <version>1.19.7</version>
+            <version>1.21.3</version>
             <scope>test</scope>
         </dependency>
 
@@ -97,7 +97,7 @@
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>testcontainers</artifactId>
-            <version>1.18.1</version>
+            <version>1.21.4</version>
             <scope>test</scope>
         </dependency>
         <dependency>
@@ -120,12 +120,13 @@
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>junit-jupiter</artifactId>
+            <version>1.21.4</version>
             <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>rabbitmq</artifactId>
-            <version>1.19.7</version>
+            <version>1.21.4</version>
             <scope>test</scope>
         </dependency>
         <dependency>

src/main/java/edu/stanford/protege/webprotege/gateway/FormsController.java

@@ -39,7 +39,12 @@ public FormsController(RpcClient rpcClient, ObjectMapper objectMapper) {
     @GetMapping("/data/projects/{projectId}/forms")
     public ResponseEntity<Map<String, Object>> getForms(@PathVariable(PROJECT_ID) ProjectId projectId,
                                    @AuthenticationPrincipal Jwt jwt) {
-        return rpcClient.call(jwt, GET_FORM_DESCRIPTORS, Map.of(PROJECT_ID, projectId));
+        try {
+            CorrelationMDCUtil.setCorrelationId(UUID.randomUUID().toString());
+            return rpcClient.call(jwt, GET_FORM_DESCRIPTORS, Map.of(PROJECT_ID, projectId));
+        } finally {
+            CorrelationMDCUtil.clearCorrelationId();
+        }
     }
 
     @PostMapping("/data/projects/{projectId}/forms")
@@ -51,6 +56,7 @@ public ResponseEntity<Map<String, Object>> setForms(@PathVariable(PROJECT_ID) Pr
         // formDescriptors
         // formSelectors
         try {
+            CorrelationMDCUtil.setCorrelationId(UUID.randomUUID().toString());
             var tree = objectMapper.readValue(forms, new TypeReference<Map<String, Object>>() {});
             var params = new LinkedHashMap<>(tree);
             params.put("changeRequestId", ChangeRequestId.generate());
@@ -59,6 +65,8 @@ public ResponseEntity<Map<String, Object>> setForms(@PathVariable(PROJECT_ID) Pr
 
         } catch (JsonProcessingException e) {
             throw new ResponseStatusException(HttpStatus.BAD_REQUEST, e.getMessage());
+        } finally {
+            CorrelationMDCUtil.clearCorrelationId();
         }
     }
 }

src/main/java/edu/stanford/protege/webprotege/gateway/RpcRequestProcessor.java

@@ -10,6 +10,9 @@
 import org.jetbrains.annotations.Nullable;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.amqp.AmqpTimeoutException;
+import org.springframework.amqp.core.AmqpMessageReturnedException;
+import org.springframework.amqp.core.AmqpReplyTimeoutException;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.HttpStatusCode;
@@ -19,6 +22,8 @@
 import java.util.Collections;
 import java.util.Map;
 import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.CompletionException;
+import java.util.concurrent.TimeoutException;
 
 /**
  * Matthew Horridge
@@ -76,11 +81,22 @@ private CompletableFuture<RpcResponse> sendMessage(RpcRequest request, String ac
                     payload, userId);
             return reply
                     .exceptionally(e -> {
+                        if(e instanceof CompletionException completionException) {
+                            if(completionException.getCause() instanceof AmqpReplyTimeoutException timeoutException) {
+                                logger.error("Timeout while waiting for reply to message on channel {}: {}", request.methodName(), timeoutException.getMessage(), e);
+                                throw new ResponseStatusException(HttpStatus.GATEWAY_TIMEOUT, "Timed out while waiting for reply to message on channel " + request.methodName(), timeoutException);
+                            }
+                            else if(completionException.getCause() instanceof AmqpMessageReturnedException messageReturnedException) {
+                                logger.error("Message returned: {}", messageReturnedException.getMessage(), e);
+                                throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR, "Message to channel " + request.methodName() + " was returned");
+                            }
+                        }
                         if (e instanceof ProjectUnderMaintenanceException) {
                             throw (ProjectUnderMaintenanceException) e;
                         }
                         logger.error("Error during send and receive: {}.  Returning failed future with ResponseStatusException HTTP 500 Internal Server Error", e.getMessage(), e);
                         throw new ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR, e.getMessage(), e);
+
                     })
                     .thenCompose(msg -> {
                         try {

src/main/resources/application.yaml

@@ -44,6 +44,6 @@ spring.security.oauth2:
       authorization-grant-type: authorization_code
       scope: openid
     provider.keycloak:
-      issuer-uri: http://webprotege-local.edu/keycloak-admin/realms/webprotege
+      issuer-uri: http://webprotege-local.edu/keycloak/realms/webprotege
       user-name-attribute: preferred_username
-  resourceserver.jwt.issuer-uri: http://webprotege-local.edu/keycloak-admin/realms/webprotege
+  resourceserver.jwt.issuer-uri: http://webprotege-local.edu/keycloak/realms/webprotege