refactor extracting jwt roles for superadmin.

src/main/java/edu/stanford/protege/webprotege/authorization/AccessManager.java

@@ -69,7 +69,8 @@ Set<Capability> getCapabilityClosure(@Nonnull Subject subject,
      */
     boolean hasPermission(@Nonnull Subject subject,
                           @Nonnull Resource resource,
-                          @Nonnull Capability capability);
+                          @Nonnull Capability capability,
+                          String jwt);
 
     Collection<Subject> getSubjectsWithAccessToResource(Resource resource);
 

src/main/java/edu/stanford/protege/webprotege/authorization/AccessManagerImpl.java

@@ -5,6 +5,7 @@
 import edu.stanford.protege.webprotege.common.ProjectId;
 import edu.stanford.protege.webprotege.ipc.EventDispatcher;
 import org.bson.Document;
+import org.keycloak.common.VerificationException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.data.mongodb.core.MongoTemplate;
@@ -49,19 +50,29 @@ public class AccessManagerImpl implements AccessManager {
 
     private final EventDispatcher eventDispatcher;
 
+    private final TokenValidator tokenValidator;
+
+    private final BuiltInRoleOracle builtInRoleOracle;
+
     /**
      * Constructs an {@link AccessManager} that is backed by MongoDb.
      *
      * @param mongoTemplate A {@link MongoTemplate} that is used to access MongoDb.
      */
     public AccessManagerImpl(ObjectMapper objectMapper,
                              MongoTemplate mongoTemplate,
-                             ProjectRoleDefinitionsManager projectRoleDefinitionsManager, RoleDefinitionsManager roleDefinitionsManager, EventDispatcher eventDispatcher) {
+                             ProjectRoleDefinitionsManager projectRoleDefinitionsManager,
+                             RoleDefinitionsManager roleDefinitionsManager,
+                             EventDispatcher eventDispatcher,
+                             TokenValidator tokenValidator,
+                             BuiltInRoleOracle builtInRoleOracle) {
         this.objectMapper = objectMapper;
         this.mongoTemplate = mongoTemplate;
         this.projectRoleDefinitionsManager = projectRoleDefinitionsManager;
         this.roleDefinitionsManager = roleDefinitionsManager;
         this.eventDispatcher = eventDispatcher;
+        this.tokenValidator = tokenValidator;
+        this.builtInRoleOracle = builtInRoleOracle;
     }
 
     /**
@@ -241,12 +252,31 @@ public Set<Capability> getCapabilityClosure(@Nonnull Subject subject, @Nonnull R
     }
 
     @Override
-    public boolean hasPermission(@Nonnull Subject subject, @Nonnull Resource resource, @Nonnull Capability capability) {
+    public boolean hasPermission(@Nonnull Subject subject, @Nonnull Resource resource, @Nonnull Capability capability, String jwt) {
+        logger.info("Checking permission for subject {} and resource {} with capability: {}", subject, resource, capability);
+
         lock.readLock().lock();
         try {
-            return find(withUserOrAnyUserAndTarget(subject, resource))
+            List<Capability> capabilities = new ArrayList<>(find(withUserOrAnyUserAndTarget(subject, resource))
                     .map(d -> objectMapper.convertValue(d, RoleAssignment.class))
-                    .anyMatch(roleAssignment -> roleAssignment.getCapabilityClosure().contains(capability));
+                    .flatMap(roleAssignment -> roleAssignment.getCapabilityClosure().stream())
+                    .toList());
+
+            if (jwt != null && !jwt.isEmpty()) {
+                try {
+                    List<RoleId> roleIds = tokenValidator.extractClaimsWithoutVerification(jwt).stream()
+                            .map(RoleId::new)
+                            .toList();
+                    capabilities.addAll(builtInRoleOracle.getCapabilitiesAssociatedToRoles(roleIds));
+                } catch (VerificationException e) {
+                    logger.error("Error getting token claims", e);
+                    throw new RuntimeException(e);
+                }
+            }
+
+
+            return capabilities.contains(capability);
+
         } finally {
             lock.readLock().unlock();
         }
@@ -285,7 +315,8 @@ public Collection<Resource> getResourcesAccessibleToSubject(Subject subject, Cap
         lock.readLock().lock();
         try {
             var userName = toUserName(subject);
-            var query = query(where(USER_NAME).is(userName).and(CAPABILITY_CLOSURE).is(capability.id()));
+            logger.info("Trying to fetch resources {} and capability {}", userName, capability.id());
+            var query = query(where(USER_NAME).is(userName).and(CAPABILITY_CLOSURE + ".id").is(capability.id()));
             return find(query)
                     .map(f -> objectMapper.convertValue(f, RoleAssignment.class))
                     .map(ra -> {
@@ -331,7 +362,7 @@ public void rebuild() {
     public void rebuild(ProjectId projectId) {
         lock.writeLock().lock();
         try {
-            logger.info("Rebuilding permissions for project: {}" , projectId);
+            logger.info("Rebuilding permissions for project: {}", projectId);
             var criteria = where(PROJECT_ID).is(projectId.value());
             var queryObject = new Query(criteria).getQueryObject();
             rebuildMatchingRoleAssignments(queryObject);
@@ -345,7 +376,7 @@ private void rebuildMatchingRoleAssignments(Document queryObject) {
         var collection = mongoTemplate.getCollection(COLLECTION_NAME);
         collection.find(queryObject)
                 .forEach(roleAssignmentDoc -> {
-                    final var roleAssignmentId = roleAssignmentDoc.get("_id" );
+                    final var roleAssignmentId = roleAssignmentDoc.get("_id");
                     var roleAssignment = objectMapper.convertValue(roleAssignmentDoc, RoleAssignment.class);
 
                     // For each role assignment we compute the role closure and then
@@ -373,8 +404,8 @@ private void rebuildMatchingRoleAssignments(Document queryObject) {
                             sortedCapabilityClosure);
 
                     var updatedRoleAssignmentDoc = objectMapper.convertValue(updatedRoleAssignment, Document.class);
-                    updatedRoleAssignmentDoc.put("_id" , roleAssignmentId);
-                    collection.replaceOne(new Document("_id" , roleAssignmentId), updatedRoleAssignmentDoc);
+                    updatedRoleAssignmentDoc.put("_id", roleAssignmentId);
+                    collection.replaceOne(new Document("_id", roleAssignmentId), updatedRoleAssignmentDoc);
                 });
     }
 

src/main/java/edu/stanford/protege/webprotege/authorization/AuthorizationCommandsService.java

@@ -24,25 +24,11 @@ public AuthorizationCommandsService(AccessManager accessManager, TokenValidator
     }
     // TODO:  Update this when Alex has committed the code
     public GetAuthorizationStatusResponse handleAuthorizationStatusCommand(GetAuthorizationStatusRequest request, ExecutionContext executionContext) {
-        var hasPermission = false;
-        if(request.resource().isApplication()) {
-            List<RoleId> roleIds;
-            try {
-                roleIds = tokenValidator.getTokenClaims(executionContext.jwt()).stream()
-                        .map(RoleId::new)
-                        .toList();
-                Set<Capability> capabilities  = new HashSet<>(builtInRoleOracle.getCapabilitiesAssociatedToRoles(roleIds));
-                hasPermission = capabilities.contains(request.capability());
-
-            } catch (VerificationException e) {
-                throw new RuntimeException(e);
-            }
-
-        }else {
-            hasPermission = accessManager.hasPermission(request.subject(),
+        var hasPermission = accessManager.hasPermission(request.subject(),
                     request.resource(),
-                    request.capability());
-        }
+                    request.capability(),
+                executionContext.jwt());
+
         if(hasPermission) {
             return new GetAuthorizationStatusResponse(request.resource(),
                     request.subject(),

src/main/java/edu/stanford/protege/webprotege/authorization/GetAuthorizationStatusHandler.java

@@ -20,7 +20,7 @@
  */
 @WebProtegeHandler
 public class GetAuthorizationStatusHandler implements CommandHandler<GetAuthorizationStatusRequest, GetAuthorizationStatusResponse> {
-    private final static Logger logger = LoggerFactory.getLogger(GetAuthorizedCapabilitiesHandler.class);
+    private final static Logger logger = LoggerFactory.getLogger(GetAuthorizationStatusHandler.class);
 
     private final AccessManager accessManager;
 
@@ -47,26 +47,11 @@ public Class<GetAuthorizationStatusRequest> getRequestClass() {
 
     @Override
     public Mono<GetAuthorizationStatusResponse> handleRequest(GetAuthorizationStatusRequest request, ExecutionContext executionContext) {
-        var hasPermission = false;
-        if(request.resource().isApplication()) {
-            List<RoleId> roleIds;
-            try {
-                roleIds = tokenValidator.getTokenClaims(executionContext.jwt()).stream()
-                        .map(RoleId::new)
-                        .toList();
-                Set<Capability> capabilities  = new HashSet<>(builtInRoleOracle.getCapabilitiesAssociatedToRoles(roleIds));
-                hasPermission = capabilities.contains(request.capability());
+        var hasPermission = accessManager.hasPermission(request.subject(),
+                request.resource(),
+                request.capability(),
+                executionContext.jwt());
 
-            } catch (VerificationException e) {
-                logger.error("Error getting token claims", e);
-                throw new RuntimeException(e);
-            }
-
-        }else {
-            hasPermission = accessManager.hasPermission(request.subject(),
-                    request.resource(),
-                    request.capability());
-        }
         if(hasPermission) {
             return Mono.just(new GetAuthorizationStatusResponse(request.resource(),
                     request.subject(),

src/main/java/edu/stanford/protege/webprotege/authorization/GetAuthorizedCapabilitiesHandler.java

@@ -48,7 +48,7 @@ public Mono<GetAuthorizedCapabilitiesResponse> handleRequest(GetAuthorizedCapabi
 
         try {
             //extract any SUPER admin capabilities from token
-            var roleIds = tokenValidator.getTokenClaims(executionContext.jwt()).stream()
+            var roleIds = tokenValidator.extractClaimsWithoutVerification(executionContext.jwt()).stream()
                     .map(RoleId::new)
                     .toList();
             capabilities.addAll(new HashSet<>(builtInRoleOracle.getCapabilitiesAssociatedToRoles(roleIds)));

src/main/java/edu/stanford/protege/webprotege/authorization/TokenValidator.java

@@ -47,18 +47,18 @@ public Map<String,PublicKey> setUpPublicKey(RestTemplate restTemplate) throws IO
         return publicKeys;
     }
 
-    public Set<String> getTokenClaims(String jwt) throws VerificationException {
-
+    /**
+     * Extracts claims from a JWT token without verification.
+     * Note: This method should only be used when token verification is not critical.
+     * For security-critical operations, use getTokenClaims() instead.
+     *
+     * @param jwt The JWT token to extract claims from
+     * @return Set of roles from the token's resource access
+     * @throws VerificationException if the token is malformed
+     */
+    public Set<String> extractClaimsWithoutVerification(String jwt) throws VerificationException {
         TokenVerifier<AccessToken> verifier = TokenVerifier.create(jwt, AccessToken.class);
-
-        PublicKey publicKey = publicKeys.get(verifier.getHeader().getKeyId());
-        if(publicKey == null) {
-            throw new VerificationException();
-        }
-        verifier.publicKey(publicKey);
-        verifier.verify().withDefaultChecks();
         AccessToken token = verifier.getToken();
         return token.getResourceAccess().get("webprotege").getRoles();
-
     }
 }