Permission Performance Optimizations (#2341)

* Implemented permission lookup to bypass hibernate.
* Moved PermissionsDTO to PermissionManager
* Removed GSON to use the app-wide ObjectMapper from Jackson
* Removed unused imports to GSON.

pom.xml

@@ -1024,11 +1024,6 @@
       <artifactId>HikariCP</artifactId>
       <version>4.0.3</version>
     </dependency>
-    <dependency>
-      <groupId>com.google.code.gson</groupId>
-      <artifactId>gson</artifactId>
-      <version>2.9.0</version>
-    </dependency>
     <dependency>
       <groupId>org.jasypt</groupId>
       <artifactId>jasypt-hibernate4</artifactId>

src/main/java/org/ohdsi/webapi/service/UserService.java

@@ -1,5 +1,6 @@
 package org.ohdsi.webapi.service;
 
+import com.fasterxml.jackson.databind.JsonNode;
 import com.odysseusinc.logging.event.*;
 import org.eclipse.collections.impl.block.factory.Comparators;
 import org.ohdsi.webapi.shiro.Entities.PermissionEntity;
@@ -50,6 +51,7 @@ public static class User implements Comparable<User> {
     public String login;
     public String name;
     public List<Permission> permissions;
+    public JsonNode permissionIdx;
 
     public User() {}
 
@@ -114,6 +116,8 @@ public User getCurrentUser() throws Exception {
     user.login = currentUser.getLogin();
     user.name = currentUser.getName();
     user.permissions = convertPermissions(permissions);
+    user.permissionIdx = authorizer.queryUserPermissions(currentUser.getLogin()).permissions;
+
 
     return user;
   }

src/main/java/org/ohdsi/webapi/shiro/PermissionManager.java

@@ -1,5 +1,8 @@
 package org.ohdsi.webapi.shiro;
 
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ArrayNode;
 import com.odysseusinc.logging.event.AddUserEvent;
 import com.odysseusinc.logging.event.DeleteRoleEvent;
 import org.apache.shiro.SecurityUtils;
@@ -25,10 +28,16 @@
 import org.springframework.transaction.annotation.Transactional;
 
 import java.security.Principal;
+import java.util.HashMap;
 import java.util.LinkedHashSet;
+import java.util.List;
 import java.util.Map;
 import java.util.Set;
 import java.util.concurrent.ConcurrentHashMap;
+import org.apache.commons.lang3.StringUtils;
+import org.ohdsi.circe.helper.ResourceHelper;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.jdbc.core.JdbcTemplate;
 
 /**
  *
@@ -38,6 +47,9 @@
 @Transactional
 public class PermissionManager {
 
+  @Value("${datasource.ohdsi.schema}")
+  private String ohdsiSchema;
+
   @Autowired
   private UserRepository userRepository;
 
@@ -55,9 +67,20 @@ public class PermissionManager {
 
   @Autowired
   private ApplicationEventPublisher eventPublisher;
-
+
+  @Autowired
+  private JdbcTemplate jdbcTemplate;
+
+  @Autowired
+  private ObjectMapper objectMapper;
+
   private ThreadLocal<ConcurrentHashMap<String, UserSimpleAuthorizationInfo>> authorizationInfoCache = ThreadLocal.withInitial(ConcurrentHashMap::new);
 
+  public static class PermissionsDTO {
+
+    public JsonNode permissions = null;
+  }
+
   public RoleEntity addRole(String roleName, boolean isSystem) {
     Guard.checkNotEmpty(roleName);
 
@@ -305,7 +328,51 @@ public Set<PermissionEntity> getUserPermissions(UserEntity user) {
 
     return permissions;
   }
+
+  public PermissionsDTO queryUserPermissions(final String login) {
+    String permQuery = StringUtils.replace(
+            ResourceHelper.GetResourceAsString("/resources/security/getPermissionsForUser.sql"),
+            "@ohdsi_schema",
+            this.ohdsiSchema);
+    final UserEntity user = userRepository.findByLogin(login);
+
+    List<String> permissions = this.jdbcTemplate.query(
+            permQuery, 
+            (ps) -> {
+              ps.setLong(1, user.getId());
+            },
+            (rs, rowNum) -> {
+              return rs.getString("value");
+            });
+    PermissionsDTO permDto = new PermissionsDTO();
+    permDto.permissions = permsToJsonNode(permissions);
+    return permDto;
+  }
+
+  /**
+   * This method takes a list of strings and returns a JSObject representing 
+   * the first element of each permission as a key, and the List<String> of 
+   * permissions that start with the key as the value
+  */
+  private JsonNode permsToJsonNode(List<String> permissions) {
+
+    Map<String, ArrayNode> resultMap = new HashMap<>();
+
+    // Process each input string
+    for (String inputString : permissions) {
+      String[] parts = inputString.split(":");
+      String key = parts[0];
+      // Create a new JsonArray for the key if it doesn't exist
+      resultMap.putIfAbsent(key, objectMapper.createArrayNode());
+      // Add the value to the JsonArray
+      resultMap.get(key).add(inputString);
+    }
 
+    // Convert the resultMap to a JsonNode
+
+    return objectMapper.valueToTree(resultMap);
+  }
+
   private Set<PermissionEntity> getRolePermissions(RoleEntity role) {
     Set<PermissionEntity> permissions = new LinkedHashSet<>();
 

src/main/java/org/ohdsi/webapi/shiro/filters/SendTokenInHeaderFilter.java

@@ -1,16 +1,17 @@
 package org.ohdsi.webapi.shiro.filters;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
 import static org.ohdsi.webapi.shiro.management.AtlasSecurity.PERMISSIONS_ATTRIBUTE;
 import static org.ohdsi.webapi.shiro.management.AtlasSecurity.TOKEN_ATTRIBUTE;
 
-import com.google.gson.Gson;
 import java.io.IOException;
 import java.io.PrintWriter;
 import javax.servlet.ServletRequest;
 import javax.servlet.ServletResponse;
 import javax.servlet.http.HttpServletResponse;
 import org.apache.shiro.web.servlet.AdviceFilter;
 import org.apache.shiro.web.util.WebUtils;
+import org.ohdsi.webapi.shiro.PermissionManager;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.http.MediaType;
@@ -25,31 +26,29 @@ public class SendTokenInHeaderFilter extends AdviceFilter {
   private static final String ERROR_WRITING_PERMISSIONS_TO_RESPONSE_LOG = "Error writing permissions to response";
   private static final String TOKEN_HEADER_NAME = "Bearer";
 
+  private final ObjectMapper objectMapper;
+
+  public SendTokenInHeaderFilter(ObjectMapper objectMapper) {
+    this.objectMapper = objectMapper;
+  }
+
+
+
   @Override
   protected boolean preHandle(ServletRequest request, ServletResponse response) {
     String jwt = (String)request.getAttribute(TOKEN_ATTRIBUTE);
-    String permissions = (String)request.getAttribute(PERMISSIONS_ATTRIBUTE);
+    PermissionManager.PermissionsDTO permissions = (PermissionManager.PermissionsDTO)request.getAttribute(PERMISSIONS_ATTRIBUTE);
 
     HttpServletResponse httpResponse = WebUtils.toHttp(response);
     httpResponse.setHeader(TOKEN_HEADER_NAME, jwt);
     httpResponse.setContentType(MediaType.APPLICATION_JSON_UTF8_VALUE);
     httpResponse.setStatus(HttpServletResponse.SC_OK);
 
     try (final PrintWriter responseWriter = response.getWriter()) {
-      responseWriter.print(new Gson().toJson(new PermissionsDTO(permissions)));
+      responseWriter.print(objectMapper.writeValueAsString(permissions));
     } catch (IOException e) {
       LOGGER.error(ERROR_WRITING_PERMISSIONS_TO_RESPONSE_LOG, e);
     }
     return false;
   }
-
-  public static class PermissionsDTO {
-
-    private PermissionsDTO(String permissions) {
-
-      this.permissions = permissions;
-    }
-
-    public final String permissions;
-  }
 }

src/main/java/org/ohdsi/webapi/shiro/filters/UpdateAccessTokenFilter.java

@@ -145,8 +145,8 @@ protected boolean preHandle(ServletRequest request, ServletResponse response) th
     }
 
     request.setAttribute(TOKEN_ATTRIBUTE, jwt);
-    Collection<String> permissions = this.authorizer.getAuthorizationInfo(login).getStringPermissions();
-    request.setAttribute(PERMISSIONS_ATTRIBUTE, StringUtils.join(permissions, "|"));
+    PermissionManager.PermissionsDTO permissions = this.authorizer.queryUserPermissions(login);
+    request.setAttribute(PERMISSIONS_ATTRIBUTE, permissions);
     return true;
   }
 

src/main/java/org/ohdsi/webapi/shiro/management/AtlasRegularSecurity.java

@@ -1,5 +1,6 @@
 package org.ohdsi.webapi.shiro.management;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
 import io.buji.pac4j.filter.CallbackFilter;
 import io.buji.pac4j.filter.SecurityFilter;
 import io.buji.pac4j.realm.Pac4jRealm;
@@ -259,6 +260,9 @@ public class AtlasRegularSecurity extends AtlasSecurity {
 
     @Autowired
     private PermissionManager permissionManager;
+
+    @Autowired
+    private ObjectMapper objectMapper;    
 
     public AtlasRegularSecurity(EntityPermissionSchemaResolver permissionSchemaResolver) {
 
@@ -293,7 +297,7 @@ public Map<FilterTemplates, Filter> getFilters() {
         }
 
         filters.put(SEND_TOKEN_IN_URL, new SendTokenInUrlFilter(this.oauthUiCallback));
-        filters.put(SEND_TOKEN_IN_HEADER, new SendTokenInHeaderFilter());
+        filters.put(SEND_TOKEN_IN_HEADER, new SendTokenInHeaderFilter(this.objectMapper));
 
         filters.put(RUN_AS, new RunAsFilter(userRepository));
 

src/main/resources/resources/security/getPermissionsForUser.sql

@@ -0,0 +1,6 @@
+select distinct sp.value
+from @ohdsi_schema.sec_user_role sur 
+join @ohdsi_schema.sec_role_permission srp on sur.role_id = srp.role_id
+join @ohdsi_schema.sec_permission sp on sp.id = srp.permission_id
+where sur.user_id = ?
+order by value;