Improve FENCEAuthenticationService with additional checks and code re…

…factoring

The code has been modified to include an additional check in FENCEAuthenticationService to ensure that FENCEMapping is not empty before creating access rules. This will prevent unnecessary errors and exception handling.

pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/authentication/FENCEAuthenticationService.java

@@ -98,7 +98,7 @@ public FENCEAuthenticationService(UserService userService,
                                       @Value("${fence.parent.consent.group.concept.path}") String fenceParentConceptPath,
                                       @Value("${fence.topmed.consent.group.concept.path}") String fenceTopmedConceptPath,
                                       @Value("${fence.consent.group.concept.path}") String fenceHarmonizedConceptPath,
-                                      AccessRuleService accessRuleService, FenceMappingUtility fenceMappingUtility){
+                                      AccessRuleService accessRuleService, FenceMappingUtility fenceMappingUtility) {
         this.userService = userService;
         this.roleService = roleService;
         this.connectionService = connectionService;
@@ -128,7 +128,7 @@ public void initializeFenceService() {
 
         // We need to set the underscoreFields here so that we can use them in the access rules during PostConstruct
         // If we don't set them here, we will get a NullPointerException when we try to use them in the access rules
-        underscoreFields = new String[] {
+        underscoreFields = new String[]{
                 parentAccessionField,
                 topmedAccessionField,
                 fence_harmonized_consent_group_concept_path,
@@ -154,36 +154,40 @@ public void initializeFenceService() {
         logger.info("fence_harmonized_concept_path: {}", fence_harmonized_concept_path);
         logger.info("underscoreFields: {}", Arrays.toString(underscoreFields));
 
-        // Create all potential access rules using the fence mapping
-        Set<Role> roles = fenceMappingUtility.getFenceMappingByAuthZ().values().parallelStream().map(projectMetadata -> {
-            if (projectMetadata == null) {
-                logger.error("initializeFenceService() -> createAndUpsertRole could not find study in FENCE mapping SKIPPING: {}", projectMetadata);
-                return null;
-            }
+        if (!fenceMappingUtility.getFENCEMapping().isEmpty() && !fenceMappingUtility.getFenceMappingByAuthZ().isEmpty()) {
+            // Create all potential access rules using the fence mapping
+            Set<Role> roles = fenceMappingUtility.getFenceMappingByAuthZ().values().parallelStream().map(projectMetadata -> {
+                if (projectMetadata == null) {
+                    logger.error("initializeFenceService() -> createAndUpsertRole could not find study in FENCE mapping SKIPPING: {}", projectMetadata);
+                    return null;
+                }
 
-            if (projectMetadata.getStudyIdentifier() == null || projectMetadata.getStudyIdentifier().isEmpty()) {
-                logger.error("initializeFenceService() -> createAndUpsertRole could not find study identifier in FENCE mapping SKIPPING: {}", projectMetadata);
-                return null;
-            }
+                if (projectMetadata.getStudyIdentifier() == null || projectMetadata.getStudyIdentifier().isEmpty()) {
+                    logger.error("initializeFenceService() -> createAndUpsertRole could not find study identifier in FENCE mapping SKIPPING: {}", projectMetadata);
+                    return null;
+                }
 
-            if (projectMetadata.getAuthZ() == null || projectMetadata.getAuthZ().isEmpty()) {
-                logger.error("initializeFenceService() -> createAndUpsertRole could not find authZ in FENCE mapping SKIPPING: {}", projectMetadata);
-                return null;
-            }
+                if (projectMetadata.getAuthZ() == null || projectMetadata.getAuthZ().isEmpty()) {
+                    logger.error("initializeFenceService() -> createAndUpsertRole could not find authZ in FENCE mapping SKIPPING: {}", projectMetadata);
+                    return null;
+                }
 
-            String projectId = projectMetadata.getStudyIdentifier();
-            String consentCode = projectMetadata.getConsentGroupCode();
-            String newRoleName = StringUtils.isNotBlank(consentCode) ? "FENCE_"+projectId+"_"+consentCode : "FENCE_"+projectId;
+                String projectId = projectMetadata.getStudyIdentifier();
+                String consentCode = projectMetadata.getConsentGroupCode();
+                String newRoleName = StringUtils.isNotBlank(consentCode) ? "FENCE_" + projectId + "_" + consentCode : "FENCE_" + projectId;
 
-            return createRole(newRoleName, "FENCE role " + newRoleName);
-        }).filter(Objects::nonNull).collect(Collectors.toSet());
+                return createRole(newRoleName, "FENCE role " + newRoleName);
+            }).filter(Objects::nonNull).collect(Collectors.toSet());
 
-        roleService.persistAll(roles);
+            roleService.persistAll(roles);
+        } else {
+            logger.error("initializeFenceService() -> createAndUpsertRole could not find any studies in FENCE mapping");
+        }
     }
 
-    public HashMap<String, String> getFENCEProfile(String callback_url, Map<String, String> authRequest){
+    public HashMap<String, String> getFENCEProfile(String callback_url, Map<String, String> authRequest) {
         logger.debug("getFENCEProfile() starting...");
-        String fence_code  = authRequest.get("code");
+        String fence_code = authRequest.get("code");
 
         // Validate that the fence code is alphanumeric
         if (!fence_code.matches("[a-zA-Z0-9]+")) {
@@ -197,7 +201,7 @@ public HashMap<String, String> getFENCEProfile(String callback_url, Map<String,
             logger.debug("getFENCEProfile() query FENCE for user profile with code");
             fence_user_profile = getFENCEUserProfile(getFENCEAccessToken(callback_url, fence_code).get("access_token").asText());
 
-            if(logger.isTraceEnabled()){
+            if (logger.isTraceEnabled()) {
                 // create object mapper instance
                 ObjectMapper mapper = new ObjectMapper();
                 // `JsonNode` to JSON string
@@ -210,8 +214,8 @@ public HashMap<String, String> getFENCEProfile(String callback_url, Map<String,
             logger.debug("getFENCEProfile() .email:{}", fence_user_profile.get("email"));
         } catch (Exception ex) {
             logger.error("getFENCEProfile() could not retrieve the user profile from the auth provider, because {}", ex.getMessage(), ex);
-            throw new NotAuthorizedException("Could not get the user profile "+
-                    "from the Gen3 authentication provider."+ex.getMessage());
+            throw new NotAuthorizedException("Could not get the user profile " +
+                    "from the Gen3 authentication provider." + ex.getMessage());
         }
 
         User current_user;
@@ -243,7 +247,7 @@ public HashMap<String, String> getFENCEProfile(String callback_url, Map<String,
 
             String projectId = projectMetadata.getStudyIdentifier();
             String consentCode = projectMetadata.getConsentGroupCode();
-            String newRoleName = StringUtils.isNotBlank(consentCode) ? "FENCE_"+projectId+"_"+consentCode : "FENCE_"+projectId;
+            String newRoleName = StringUtils.isNotBlank(consentCode) ? "FENCE_" + projectId + "_" + consentCode : "FENCE_" + projectId;
 
             roleNames.add(newRoleName);
         });
@@ -287,7 +291,7 @@ public HashMap<String, String> getFENCEProfile(String callback_url, Map<String,
         } catch (Exception ex) {
             logger.error("upsertRole() Could not add roles to user, because {}", ex.getMessage());
         }
-        HashMap<String, Object> claims = new HashMap<String,Object>();
+        HashMap<String, Object> claims = new HashMap<String, Object>();
         claims.put("name", fence_user_profile.get("name"));
         claims.put("email", current_user.getEmail());
         claims.put("sub", current_user.getSubject());
@@ -334,7 +338,7 @@ private JsonNode getFENCEUserProfile(String access_token) {
 
         logger.debug("getFENCEUserProfile() getting user profile from uri:{}/user/user", this.idp_provider_uri);
         ResponseEntity<String> fence_user_profile_response = this.restClientUtil.retrieveGetResponse(
-                this.idp_provider_uri+"/user/user",
+                this.idp_provider_uri + "/user/user",
                 headers
         );
 
@@ -363,7 +367,7 @@ private JsonNode getFENCEAccessToken(String callback_url, String fence_code) {
         queryMap.add("code", fence_code);
         queryMap.add("redirect_uri", callback_url);
 
-        String fence_token_url = this.idp_provider_uri+"/user/oauth2/token";
+        String fence_token_url = this.idp_provider_uri + "/user/oauth2/token";
 
         HttpEntity<MultiValueMap<String, String>> request = new HttpEntity<>(queryMap, headers);
         JsonNode respJson = null;
@@ -403,7 +407,7 @@ private User createUserFromFENCEProfile(JsonNode node) {
         logger.debug("createUserFromFENCEProfile() starting...");
 
         User new_user = new User();
-        new_user.setSubject("fence|"+node.get("user_id").asText());
+        new_user.setSubject("fence|" + node.get("user_id").asText());
         // This is not always an email address, but it is the only attribute other than the sub claim
         // that is guaranteed to be populated by Fence and which makes sense as a display name for a
         // user.
@@ -427,12 +431,12 @@ private User createUserFromFENCEProfile(JsonNode node) {
     /**
      * Insert or Update the User object's list of Roles in the database.
      *
-     * @param u The User object the generated Role will be added to
-     * @param roleName Name of the Role
+     * @param u               The User object the generated Role will be added to
+     * @param roleName        Name of the Role
      * @param roleDescription Description of the Role
      * @return boolean Whether the Role was successfully added to the User or not
      */
-    public boolean upsertRole(User u,  String roleName, String roleDescription) {
+    public boolean upsertRole(User u, String roleName, String roleDescription) {
         boolean status = false;
 
         // Get the User's list of Roles. The first time, this will be an empty Set.
@@ -478,7 +482,9 @@ private Set<Privilege> addFENCEPrivileges(Role r) {
         //harmonized has 2 ARs for parent + harminized and harmonized only
         //Topmed has up to three ARs for topmed / topmed + parent / topmed + harmonized
         Set<Privilege> privs = r.getPrivileges();
-        if (privs == null) { privs = new HashSet<Privilege>();}
+        if (privs == null) {
+            privs = new HashSet<Privilege>();
+        }
 
         //e.g. FENCE_phs0000xx_c2 or FENCE_tutorial-biolinc_camp
         String project_name = extractProject(roleName);
@@ -494,7 +500,7 @@ private Set<Privilege> addFENCEPrivileges(Role r) {
         // Look up the metadata by consent group.
         StudyMetaData projectMetadata = getFENCEMappingforProjectAndConsent(project_name, consent_group);
 
-        if(projectMetadata == null){
+        if (projectMetadata == null) {
             //no privileges means no access to this project.  just return existing set of privs.
             logger.warn("No metadata available for project {}.{}", project_name, consent_group);
             return privs;
@@ -509,28 +515,28 @@ private Set<Privilege> addFENCEPrivileges(Role r) {
 
         // we need to add escape sequence back in to the path for parsing later (also need to double escape the regex)
         // we need to do this for the query Template and scopes, but should NOT do this for the rules.
-        if(concept_path != null) {
+        if (concept_path != null) {
             concept_path = concept_path.replaceAll("\\\\", "\\\\\\\\");
         }
 
-        if(dataType != null && dataType.contains("G")) {
+        if (dataType != null && dataType.contains("G")) {
             //insert genomic/topmed privs - this will also add rules for including harmonized & parent data if applicable
             privs.add(upsertTopmedPrivilege(project_name, projectAlias, consent_group, concept_path, isHarmonized));
         }
 
-        if(dataType != null && dataType.contains("P")) {
+        if (dataType != null && dataType.contains("P")) {
             //insert clinical privs
             logger.info("addPrivileges() project:{} consent_group:{} concept_path:{}", project_name, consent_group, concept_path);
             privs.add(upsertClinicalPrivilege(project_name, projectAlias, consent_group, concept_path, false));
 
             //if harmonized study, also create harmonized privileges
-            if(Boolean.TRUE.equals(isHarmonized)) {
+            if (Boolean.TRUE.equals(isHarmonized)) {
                 privs.add(upsertClinicalPrivilege(project_name, projectAlias, consent_group, concept_path, true));
             }
         }
 
         //projects without G or P in data_type are skipped
-        if(dataType == null || (!dataType.contains("P")  && !dataType.contains("G"))){
+        if (dataType == null || (!dataType.contains("P") && !dataType.contains("G"))) {
             logger.warn("Missing study type for {} {}. Skipping.", project_name, consent_group);
         }
 
@@ -544,9 +550,9 @@ private Set<Privilege> addFENCEPrivileges(Role r) {
      * Privileges created with this method will deny access if any genomic filters (topmed data) are included.
      *
      * @param studyIdentifier The study identifier
-     * @param consent_group The consent group
-     * @param conceptPath The concept path
-     * @param isHarmonized Whether the study is harmonized
+     * @param consent_group   The consent group
+     * @param conceptPath     The concept path
+     * @param isHarmonized    Whether the study is harmonized
      * @return The created privilege
      */
     private Privilege upsertClinicalPrivilege(String studyIdentifier, String projectAlias, String consent_group, String conceptPath, boolean isHarmonized) {
@@ -574,7 +580,7 @@ private Privilege upsertClinicalPrivilege(String studyIdentifier, String project
                 logger.debug("Escaped consent concept path: {}", consent_concept_path);
             }
 
-            if(fence_harmonized_concept_path != null && !fence_harmonized_concept_path.contains("\\\\")){
+            if (fence_harmonized_concept_path != null && !fence_harmonized_concept_path.contains("\\\\")) {
                 //these have to be escaped again so that jaxson can convert it correctly
                 fence_harmonized_concept_path = fence_harmonized_concept_path.replaceAll("\\\\", "\\\\\\\\");
                 logger.debug("upsertTopmedPrivilege(): escaped harmonized consent path" + fence_harmonized_concept_path);
@@ -627,14 +633,14 @@ private Privilege upsertClinicalPrivilege(String studyIdentifier, String project
     /**
      * Configures the AccessRule with gates and sub-rules.
      *
-     * @param ar                The AccessRule to configure.
-     * @param studyIdentifier   The study identifier.
-     * @param consent_group     The consent group.
-     * @param conceptPath       The concept path.
-     * @param projectAlias      The project alias.
-     * @param parent            Whether to include parent gates.
-     * @param harmonized        Whether to include harmonized gates.
-     * @param topmed            Whether to include Topmed gates.
+     * @param ar              The AccessRule to configure.
+     * @param studyIdentifier The study identifier.
+     * @param consent_group   The consent group.
+     * @param conceptPath     The concept path.
+     * @param projectAlias    The project alias.
+     * @param parent          Whether to include parent gates.
+     * @param harmonized      Whether to include harmonized gates.
+     * @param topmed          Whether to include Topmed gates.
      */
     private void configureAccessRule(AccessRule ar, String studyIdentifier, String consent_group, String conceptPath, String projectAlias, boolean parent, boolean harmonized, boolean topmed) {
         if (ar.getGates() == null) {
@@ -654,11 +660,11 @@ private void configureAccessRule(AccessRule ar, String studyIdentifier, String c
     /**
      * Configures the harmonized AccessRule with gates and sub-rules.
      *
-     * @param ar                The AccessRule to configure.
-     * @param studyIdentifier   The study identifier.
-     * @param consent_group     The consent group.
-     * @param conceptPath       The concept path.
-     * @param projectAlias      The project alias.
+     * @param ar              The AccessRule to configure.
+     * @param studyIdentifier The study identifier.
+     * @param consent_group   The consent group.
+     * @param conceptPath     The concept path.
+     * @param projectAlias    The project alias.
      */
     private void configureHarmonizedAccessRule(AccessRule ar, String studyIdentifier, String consent_group, String conceptPath, String projectAlias) {
         if (ar.getGates() == null) {
@@ -730,9 +736,10 @@ private Collection<? extends AccessRule> getTopmedRestrictedSubRules() {
     /**
      * Creates and returns a restricted sub-rule AccessRule for Topmed.
      * topmed restriction rules don't need much configuration.  Just deny all access.
-     * @param type  The type of the Topmed restriction.
-     * @param rule  The rule expression.
-     * @return      The created AccessRule.
+     *
+     * @param type The type of the Topmed restriction.
+     * @param rule The rule expression.
+     * @return The created AccessRule.
      */
     private AccessRule upsertTopmedRestrictedSubRule(String type, String rule) {
         // Construct the AccessRule name
@@ -766,16 +773,16 @@ private Collection<? extends AccessRule> getPhenotypeSubRules(String studyIdenti
         //categorical filters will always contain at least one entry (for the consent groups); it will never be empty
         rules.add(createPhenotypeSubRule(fence_parent_consent_group_concept_path, "ALLOW_PARENT_CONSENT", "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "", true));
 
-        for(String underscorePath : underscoreFields) {
+        for (String underscorePath : underscoreFields) {
             rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.fields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "FIELDS", false));
             rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "CATEGORICAL", true));
             rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.requiredFields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "REQ_FIELDS", false));
         }
 
-        rules.add(createPhenotypeSubRule(conceptPath, alias+ "_" + studyIdentifier, "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "CATEGORICAL", true));
-        rules.add(createPhenotypeSubRule(conceptPath, alias+ "_" + studyIdentifier, "$.query.query.numericFilters", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "NUMERIC", true));
-        rules.add(createPhenotypeSubRule(conceptPath, alias+ "_" + studyIdentifier, "$.query.query.fields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "FIELDS", false));
-        rules.add(createPhenotypeSubRule(conceptPath, alias+ "_" + studyIdentifier, "$.query.query.requiredFields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "REQUIRED_FIELDS", false));
+        rules.add(createPhenotypeSubRule(conceptPath, alias + "_" + studyIdentifier, "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "CATEGORICAL", true));
+        rules.add(createPhenotypeSubRule(conceptPath, alias + "_" + studyIdentifier, "$.query.query.numericFilters", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "NUMERIC", true));
+        rules.add(createPhenotypeSubRule(conceptPath, alias + "_" + studyIdentifier, "$.query.query.fields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "FIELDS", false));
+        rules.add(createPhenotypeSubRule(conceptPath, alias + "_" + studyIdentifier, "$.query.query.requiredFields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "REQUIRED_FIELDS", false));
 
         return rules;
     }
@@ -794,7 +801,7 @@ private Collection<? extends AccessRule> getHarmonizedSubRules() {
         rules.add(createPhenotypeSubRule(fence_harmonized_consent_group_concept_path, "ALLOW_HARMONIZED_CONSENT", "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "", true));
         rules.add(createPhenotypeSubRule(fence_topmed_consent_group_concept_path, "ALLOW_TOPMED_CONSENT", "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "", true));
 
-        for(String underscorePath : underscoreFields) {
+        for (String underscorePath : underscoreFields) {
             rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.fields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "FIELDS", false));
             rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "CATEGORICAL", true));
             rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.requiredFields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "REQ_FIELDS", false));
@@ -811,28 +818,30 @@ private Collection<? extends AccessRule> getHarmonizedSubRules() {
 
     /**
      * generate and return a set of rules that disallow access to phenotype data (only genomic filters allowed)
+     *
      * @return
      */
     private Collection<? extends AccessRule> getPhenotypeRestrictedSubRules(String studyIdentifier, String consentCode, String alias) {
         Set<AccessRule> rules = new HashSet<AccessRule>();
         //categorical filters will always contain at least one entry (for the consent groups); it will never be empty
         rules.add(createPhenotypeSubRule(fence_topmed_consent_group_concept_path, "ALLOW_TOPMED_CONSENT", "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "", true));
 
-        for(String underscorePath : underscoreFields ) {
+        for (String underscorePath : underscoreFields) {
             rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.fields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "FIELDS", false));
             rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.categoryFilters", AccessRule.TypeNaming.ALL_CONTAINS, "CATEGORICAL", true));
             rules.add(createPhenotypeSubRule(underscorePath, "ALLOW " + underscorePath, "$.query.query.requiredFields.[*]", AccessRule.TypeNaming.ALL_CONTAINS_OR_EMPTY, "REQ_FIELDS", false));
         }
 
-        rules.add(createPhenotypeSubRule(null, alias + "_" + studyIdentifier+ "_" + consentCode, "$.query.query.numericFilters.[*]", AccessRule.TypeNaming.IS_EMPTY, "DISALLOW_NUMERIC", false));
-        rules.add(createPhenotypeSubRule(null, alias + "_" + studyIdentifier+ "_" + consentCode, "$.query.query.requiredFields.[*]", AccessRule.TypeNaming.IS_EMPTY, "DISALLOW_REQUIRED_FIELDS", false));
+        rules.add(createPhenotypeSubRule(null, alias + "_" + studyIdentifier + "_" + consentCode, "$.query.query.numericFilters.[*]", AccessRule.TypeNaming.IS_EMPTY, "DISALLOW_NUMERIC", false));
+        rules.add(createPhenotypeSubRule(null, alias + "_" + studyIdentifier + "_" + consentCode, "$.query.query.requiredFields.[*]", AccessRule.TypeNaming.IS_EMPTY, "DISALLOW_REQUIRED_FIELDS", false));
 
         return rules;
     }
 
     /**
      * Return a set of gates that identify which consent values have been provided.  the boolean parameters indicate
      * if a value in the specified consent location should allow this gate to pass.
+     *
      * @param parent
      * @param harmonized
      * @param topmed
@@ -850,6 +859,7 @@ private Collection<? extends AccessRule> getGates(boolean parent, boolean harmon
     /**
      * Creates a privilege for Topmed access. This has (up to) three access rules:
      * 1) topmed only 2) topmed + parent 3) topmed + harmonized.
+     *
      * @param studyIdentifier
      * @param projectAlias
      * @param consentGroup
@@ -1001,11 +1011,11 @@ private void addStandardAccessRules(Set<AccessRule> accessRules) {
      * Generates Main rule only; gates & sub-rules attached after calling this
      * prentRule should be null if this is the main rule, or the appropriate value if this is a sub-rule
      *
-     * @param studyIdentifier  The study identifier.
-     * @param consent_group    The consent group.
-     * @param label            The label for the rule.
-     * @param consent_path     The consent path.
-     * @return                 The created AccessRule.
+     * @param studyIdentifier The study identifier.
+     * @param consent_group   The consent group.
+     * @param label           The label for the rule.
+     * @param consent_path    The consent path.
+     * @return The created AccessRule.
      */
     private AccessRule createConsentAccessRule(String studyIdentifier, String consent_group, String label, String consent_path) {
         String ar_name = (consent_group != null && !consent_group.isEmpty()) ? "AR_CONSENT_" + studyIdentifier + "_" + consent_group + "_" + label : "AR_CONSENT_" + studyIdentifier;
@@ -1029,10 +1039,11 @@ private AccessRule createConsentAccessRule(String studyIdentifier, String consen
     /**
      * Creates and returns a Topmed access rule AccessRule.
      * Generates Main Rule only; gates & sub-rules attached by calling method
+     *
      * @param project_name  The name of the project.
      * @param consent_group The consent group.
      * @param label         The label for the rule.
-     * @return              The created AccessRule.
+     * @return The created AccessRule.
      */
     private AccessRule upsertTopmedAccessRule(String project_name, String consent_group, String label) {
         String ar_name = (consent_group != null && !consent_group.isEmpty()) ? "AR_TOPMED_" + project_name + "_" + consent_group + "_" + label : "AR_TOPMED_" + project_name + "_" + label;
@@ -1060,7 +1071,7 @@ private AccessRule upsertTopmedAccessRule(String project_name, String consent_gr
      * @param project_name  The name of the project.
      * @param consent_group The consent group.
      * @param label         The label for the rule.
-     * @return              The created AccessRule.
+     * @return The created AccessRule.
      */
     private AccessRule upsertHarmonizedAccessRule(String project_name, String consent_group, String label) {
         String ar_name = "AR_TOPMED_" + project_name + "_" + consent_group + "_" + label;
@@ -1087,11 +1098,11 @@ private AccessRule upsertHarmonizedAccessRule(String project_name, String consen
      * Insert a new gate (if it doesn't exist yet) to identify if consent values are present in the query.
      * return an existing gate named GATE_{gateName}_(PRESENT|MISSING) if it exists.
      *
-     * @param gateName     The name of the gate.
-     * @param rule         The rule expression.
-     * @param is_present   Whether the gate is for present or missing consent.
-     * @param description  The description of the gate.
-     * @return             The created AccessRule.
+     * @param gateName    The name of the gate.
+     * @param rule        The rule expression.
+     * @param is_present  Whether the gate is for present or missing consent.
+     * @param description The description of the gate.
+     * @return The created AccessRule.
      */
     private AccessRule upsertConsentGate(String gateName, String rule, boolean is_present, String description) {
         gateName = "GATE_" + gateName + "_" + (is_present ? "PRESENT" : "MISSING");