Feat/prototype teamproject parser

.github/workflows/image_build_push.yaml

@@ -8,6 +8,7 @@ jobs:
     uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master
     with:
       OVERRIDE_REPO_NAME: "ohdsi-webapi"
+      BUILD_PLATFORMS: "linux/amd64"
     secrets:
       ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }}
       ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }}

pom.xml

@@ -82,6 +82,7 @@
     <spring.batch.repository.isolationLevelForCreate>ISOLATION_READ_COMMITTED</spring.batch.repository.isolationLevelForCreate>
     <spring.profiles.active>default</spring.profiles.active>
 
+    <security.ohdsi.custom.authorization.mode>teamproject</security.ohdsi.custom.authorization.mode>
     <security.provider>DisabledSecurity</security.provider>
     <security.token.expiration>43200</security.token.expiration>
     <security.origin>http://localhost</security.origin>
@@ -227,7 +228,7 @@
     <spring.jpa.properties.hibernate.jdbc.batch_size>200</spring.jpa.properties.hibernate.jdbc.batch_size>
     <spring.jpa.properties.hibernate.order_inserts>true</spring.jpa.properties.hibernate.order_inserts>
     <logging.level.root>info</logging.level.root>
-    <logging.level.org.ohdsi>info</logging.level.org.ohdsi>
+    <logging.level.org.ohdsi>debug</logging.level.org.ohdsi>
     <logging.level.org.springframework.orm>info</logging.level.org.springframework.orm>
     <logging.level.org.springframework.jdbc>info</logging.level.org.springframework.jdbc>
     <logging.level.org.springframework.web>info</logging.level.org.springframework.web>

src/main/java/org/ohdsi/webapi/shiro/Entities/UserRoleEntity.java

@@ -87,4 +87,9 @@ public UserOrigin getOrigin() {
   public void setOrigin(UserOrigin origin) {
     this.origin = origin;
   }
+
+  public String toString() {
+    role = this.getRole();
+    return (role != null ? role.getName() : "");
+  }
 }

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

@@ -19,6 +19,8 @@
 import org.ohdsi.webapi.shiro.Entities.UserRepository;
 import org.ohdsi.webapi.shiro.Entities.UserRoleEntity;
 import org.ohdsi.webapi.shiro.Entities.UserRoleRepository;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationEventPublisher;
 import org.springframework.stereotype.Component;
@@ -37,6 +39,7 @@
 @Component
 @Transactional
 public class PermissionManager {
+  private final Logger logger = LoggerFactory.getLogger(PermissionManager.class);
 
   @Autowired
   private UserRepository userRepository;
@@ -59,6 +62,8 @@ public class PermissionManager {
   private ThreadLocal<ConcurrentHashMap<String, UserSimpleAuthorizationInfo>> authorizationInfoCache = ThreadLocal.withInitial(ConcurrentHashMap::new);
 
   public RoleEntity addRole(String roleName, boolean isSystem) {
+    logger.debug("Called addRole: {}", roleName);
+
     Guard.checkNotEmpty(roleName);
 
     checkRoleIsAbsent(roleName, isSystem, "Can't create role - it already exists");
@@ -96,8 +101,32 @@ public void removeUserFromRole(String roleName, String login, UserOrigin origin)
     UserEntity user = this.getUserByLogin(login);
 
     UserRoleEntity userRole = this.userRoleRepository.findByUserAndRole(user, role);
-    if (userRole != null && (origin == null || origin.equals(userRole.getOrigin())))
+    if (userRole != null && (origin == null || origin.equals(userRole.getOrigin()))) {
+      logger.debug("Removing user from role: {}, {}, {}", user.getLogin(), role.getName(), userRole.getOrigin());
       this.userRoleRepository.delete(userRole);
+    }
+  }
+
+  public void removeUserFromUserRole(String roleName, String login) {
+    Guard.checkNotEmpty(roleName);
+    Guard.checkNotEmpty(login);
+
+    if (roleName.equalsIgnoreCase(login))
+      throw new RuntimeException("Can't remove user from personal role");
+
+    logger.debug("Checking if role exists: {}", roleName);
+    RoleEntity role = this.roleRepository.findByNameAndSystemRole(roleName, false);
+    if (role != null) {
+      UserEntity user = this.getUserByLogin(login);
+
+      UserRoleEntity userRole = this.userRoleRepository.findByUserAndRole(user, role);
+      if (userRole != null) {
+        logger.debug("Removing user from USER role: {}, {}", user.getLogin(), roleName);
+        this.userRoleRepository.delete(userRole);
+      }
+    } else {
+          logger.debug("Role {} not found", roleName);
+    }
   }
 
   public Iterable<RoleEntity> getRoles(boolean includePersonalRoles) {
@@ -141,14 +170,29 @@ public void clearAuthorizationInfoCache() {
     this.authorizationInfoCache.set(new ConcurrentHashMap<>());
   }
 
+
+  @Transactional
+  public void registerUser(String login, String name, Set<String> defaultRoles, Set<String> newUserRoles,
+      boolean resetRoles) {
+        registerUser(login, name, UserOrigin.SYSTEM, defaultRoles, newUserRoles, resetRoles);
+  }
+
   @Transactional
   public UserEntity registerUser(final String login, final String name, final Set<String> defaultRoles) {
-    return registerUser(login, name, UserOrigin.SYSTEM, defaultRoles);
+    return registerUser(login, name, UserOrigin.SYSTEM, defaultRoles, null, false);
   }
 
   @Transactional
   public UserEntity registerUser(final String login, final String name, final UserOrigin userOrigin,
                                  final Set<String> defaultRoles) {
+    return registerUser(login, name, userOrigin, defaultRoles, null, false);
+  }
+
+  @Transactional
+  public UserEntity registerUser(final String login, final String name, final UserOrigin userOrigin,
+                                 final Set<String> defaultRoles, final Set<String> newUserRoles, boolean resetRoles) {
+    logger.debug("Called registerUser with resetRoles: login={}, reset roles={}, default roles={}, new user roles={}",
+      login, resetRoles, defaultRoles, newUserRoles);
     Guard.checkNotEmpty(login);
 
     UserEntity user = userRepository.findByLogin(login);
@@ -162,6 +206,14 @@ public UserEntity registerUser(final String login, final String name, final User
         user.setOrigin(userOrigin);
         user = userRepository.save(user);
       }
+      if (resetRoles) {
+        // remove all user roles:
+        removeAllUserRolesFromUser(login, user);
+        // add back just the given newUserRoles:
+        addRolesForUser(login, userOrigin, user, newUserRoles, false);
+      }
+      // get user again, fresh from db with all new roles:
+      user = userRepository.findOne(user.getId());
       return user;
     }
 
@@ -176,18 +228,46 @@ public UserEntity registerUser(final String login, final String name, final User
 
     RoleEntity personalRole = this.addRole(login, false);
     this.addUser(user, personalRole, userOrigin, null);
+    addRolesForUser(login, userOrigin, user, newUserRoles, false);
+    addDefaultRolesForUser(login, userOrigin, user, defaultRoles);
+    // // get user again, fresh from db with all new roles:
+    user = userRepository.findOne(user.getId());
+    return user;
+  }
 
-    if (defaultRoles != null) {
-      for (String roleName: defaultRoles) {
-        RoleEntity defaultRole = this.getSystemRoleByName(roleName);
-        if (defaultRole != null) {
-          this.addUser(user, defaultRole, userOrigin, null);
+  private void addRolesForUser(String login, UserOrigin userOrigin, UserEntity user, Set<String> roles, boolean isSystemRole) {
+    if (roles != null) {
+      for (String roleName: roles) {
+        // Temporary patch/workaround (in reality the role should have been added by sysadmin?):
+        pocAddUserRole(roleName);
+        // end temporary patch
+        RoleEntity role = this.getRoleByName(roleName, isSystemRole);
+        if (role != null) {
+          this.addUser(user, role, userOrigin, null);
         }
       }
     }
+  }
 
-    user = userRepository.findOne(user.getId());
-    return user;
+  private void addDefaultRolesForUser(String login, UserOrigin userOrigin, UserEntity user, Set<String> roles) {
+    addRolesForUser(login, userOrigin, user, roles,true);
+  }
+
+  private void removeAllUserRolesFromUser(String login, UserEntity user) {
+    Set<RoleEntity> userRoles = this.getUserRoles(user);
+    // remove all roles except the personal role:
+    userRoles.stream().filter(role -> !role.getName().equalsIgnoreCase(login)).forEach(userRole -> {
+        this.removeUserFromUserRole(userRole.getName(), login);
+    });
+  }
+
+  private RoleEntity pocAddUserRole(String roleName) {
+    RoleEntity role = this.roleRepository.findByNameAndSystemRole(roleName, false);
+    if (role != null) {
+      return role;
+    } else {
+      return addRole(roleName, false);
+    }
   }
 
   public Iterable<UserEntity> getUsers() {
@@ -322,6 +402,7 @@ private Set<PermissionEntity> getRolePermissions(RoleEntity role) {
 
   private Set<RoleEntity> getUserRoles(UserEntity user) {
     Set<UserRoleEntity> userRoles = user.getUserRoles();
+    logger.debug("Called getUserRoles. Found: {}", userRoles);
     Set<RoleEntity> roles = new LinkedHashSet<>();
     for (UserRoleEntity userRole : userRoles) {
       if (isRelationAllowed(userRole.getStatus())) {

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

@@ -11,10 +11,13 @@
 import java.util.Calendar;
 import java.util.Collection;
 import java.util.Date;
+import java.util.Enumeration;
+import java.util.HashSet;
 import java.util.Objects;
 import java.util.Set;
 import javax.servlet.ServletRequest;
 import javax.servlet.ServletResponse;
+import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 import javax.servlet.http.HttpSession;
 import javax.ws.rs.core.UriBuilder;
@@ -31,27 +34,34 @@
 import org.ohdsi.webapi.shiro.TokenManager;
 import org.ohdsi.webapi.util.UserUtils;
 import org.pac4j.core.profile.CommonProfile;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  *
  * @author gennadiy.anisimov
  */
 public class UpdateAccessTokenFilter extends AdviceFilter {
-
+  private final Logger logger = LoggerFactory.getLogger(UpdateAccessTokenFilter.class);
+
   private final PermissionManager authorizer;
   private final int tokenExpirationIntervalInSeconds;
   private final Set<String> defaultRoles;
   private final String onFailRedirectUrl;
+  private final String authorizationMode;
 
   public UpdateAccessTokenFilter(
           PermissionManager authorizer,
           Set<String> defaultRoles,
           int tokenExpirationIntervalInSeconds,
-          String onFailRedirectUrl) {
+          String onFailRedirectUrl,
+          String authorizationMode) {
     this.authorizer = authorizer;
     this.tokenExpirationIntervalInSeconds = tokenExpirationIntervalInSeconds;
     this.defaultRoles = defaultRoles;
     this.onFailRedirectUrl = onFailRedirectUrl;
+    this.authorizationMode = authorizationMode;
+    logger.debug("AUTHORIZATION_MODE in UpdateAccessTokenFilter constructor == '{}'", this.authorizationMode);
   }
 
   @Override
@@ -121,12 +131,29 @@ protected boolean preHandle(ServletRequest request, ServletResponse response) th
       session.stop();
     }
 
-    if (jwt == null) {
+    if (jwt == null) { // dead check...jwt is always null...
       if (name == null) {
         name = login;
       }
       try {
-        this.authorizer.registerUser(login, name, defaultRoles);
+        logger.debug("AUTHORIZATION_MODE in UpdateAccessTokenFilter == '{}'", this.authorizationMode);
+        boolean resetRoles = false;
+        Set<String> newUserRoles = new HashSet<String>();
+        if (this.authorizationMode.equals("teamproject")) {
+          // in case of "teamproject" mode, we want all roles to be reset always, and
+          // set to only the one requested/found in the request parameters (following lines below):
+          resetRoles = true;
+          // check if a teamproject parameter is found in the request:
+          String teamProjectRole = extractTeamProjectFromRequestParameters(request);
+          // if found, add teamproject as a role in the newUserRoles list:
+          if (teamProjectRole != null) {
+            newUserRoles.add(teamProjectRole);
+            // double check with Arborist if this role has really been granted to the user....
+            // TODO
+          }
+        }
+        this.authorizer.registerUser(login, name, defaultRoles, newUserRoles, resetRoles);
+
       } catch (Exception e) {
         WebUtils.toHttp(response).setHeader("x-auth-error", e.getMessage());
         throw new Exception(e);
@@ -174,4 +201,61 @@ private Date getExpirationDate(final int expirationIntervalInSeconds) {
     calendar.add(Calendar.SECOND, expirationIntervalInSeconds);
     return calendar.getTime();
   }
+
+  private String extractTeamProjectFromRequestParameters(ServletRequest request) {
+    // Get the url
+    HttpServletRequest httpRequest = (HttpServletRequest) request;
+    String url = httpRequest.getRequestURL().toString();
+
+    // try to find it in the redirectUrl parameter:
+    logger.debug("Looking for redirectUrl in request: {}....", url);
+    String[] redirectUrlParams = getParameterValues(request, "redirectUrl");
+    if (redirectUrlParams != null) {
+      logger.debug("Parameter redirectUrl found. Checking if it contains teamproject....");
+      // teamProject will be in first one in this case...as only parameter:
+      String firstParameter = redirectUrlParams[0].toLowerCase();
+      if (firstParameter.contains("teamproject=")) {
+        String teamProject = firstParameter.split("teamproject=")[1];
+        logger.debug("Found teamproject: {}", teamProject);
+        return teamProject;
+      }
+    }
+
+    // try to find "teamproject" param in url itself (there will be no redirectUrl if user session is still valid):
+    logger.debug("Fallback1: Looking for teamproject in request: {}....", url);
+    String[] teamProjectParams = getParameterValues(request, "teamproject");
+    if (teamProjectParams != null) {
+      logger.debug("Parameter teamproject found. Parsing....");
+      String teamProject = teamProjectParams[0].toLowerCase();
+      logger.debug("Found teamproject: {}", teamProject);
+      return teamProject;
+    }
+
+    logger.debug("Fallback2: Looking for teamproject in Action-Location header of request: {}....", url);
+    String actionLocationUrl = httpRequest.getHeader("Action-Location");
+    if (actionLocationUrl != null && actionLocationUrl.contains("teamproject=")) {
+      String teamProject = actionLocationUrl.split("teamproject=")[1];
+      logger.debug("Found teamproject: {}", teamProject);
+      return teamProject;
+    }
+
+    logger.debug("Found NO teamproject.");
+    return null;
+  }
+
+  private String[] getParameterValues(ServletRequest request, String parameterName) {
+    // Get the parameters
+    logger.debug("Looking for parameter with name: {} ...", parameterName);
+    Enumeration<String> paramNames = request.getParameterNames();
+    while(paramNames.hasMoreElements()) {
+        String paramName = paramNames.nextElement();
+        logger.debug("Parameter name: {}", paramName);
+        if (paramName.equals(parameterName)) {
+          String[] paramValues = request.getParameterValues(paramName);
+          return paramValues;
+        }
+    }
+    logger.debug("Found NO parameter with name: {}", parameterName);
+    return null;
+  }
 }

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

@@ -253,6 +253,9 @@ public class AtlasRegularSecurity extends AtlasSecurity {
     @Value("${security.auth.google.enabled}")
     private boolean googleAuthEnabled;
 
+    @Value("${security.ohdsi.custom.authorization.mode}")
+    private String authorizationMode;
+
     private RestTemplate restTemplate = new RestTemplate();
 
     @Autowired
@@ -269,8 +272,9 @@ public Map<FilterTemplates, Filter> getFilters() {
         Map<FilterTemplates, Filter> filters = super.getFilters();
 
         filters.put(LOGOUT, new LogoutFilter(eventPublisher));
+        logger.debug("Initializing UpdateAccessTokenFilter with AUTHORIZATION_MODE === '{}'", this.authorizationMode);
         filters.put(UPDATE_TOKEN, new UpdateAccessTokenFilter(this.authorizer, this.defaultRoles, this.tokenExpirationIntervalInSeconds,
-                this.redirectUrl));
+                this.redirectUrl, this.authorizationMode));
 
         filters.put(ACCESS_AUTHC, new GoogleAccessTokenFilter(restTemplate, permissionManager, Collections.emptySet()));
         filters.put(JWT_AUTHC, new AtlasJwtAuthFilter());

src/main/resources/application.properties

@@ -199,6 +199,9 @@ security.auth.ldap.enabled=${security.auth.ldap.enabled}
 security.auth.ad.enabled=${security.auth.ad.enabled}
 security.auth.cas.enabled=${security.auth.cas.enabled}
 
+#Authorization config
+security.ohdsi.custom.authorization.mode=${security.ohdsi.custom.authorization.mode}
+
 #Execution engine
 executionengine.updateStatusCallback=${executionengine.updateStatusCallback}
 executionengine.resultCallback=${executionengine.resultCallback}