A C D E F G H I K L M N O P Q R S T U V W

A

AccountController - Class in org.molgenis.security.account

AccountController() - Constructor for class org.molgenis.security.account.AccountController

AccountService - Class in org.molgenis.security.account

AccountService() - Constructor for class org.molgenis.security.account.AccountService

activateUser(String, Model) - Method in class org.molgenis.security.account.AccountController

activateUser(String) - Method in class org.molgenis.security.account.AccountService

Activate a registered user

ACTIVATIONCODE - Static variable in class org.molgenis.omx.auth.MolgenisUser

ACTIVE - Static variable in class org.molgenis.omx.auth.MolgenisUser

add(List<E>) - Method in class org.molgenis.omx.auth.db.GroupAuthoritySecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.auth.db.MolgenisUserSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.auth.db.UserAuthoritySecurityDecorator

addGroupPermission(String, Permission) - Method in class org.molgenis.security.permission.Permissions

addHierarchyPermission(String, Permission) - Method in class org.molgenis.security.permission.Permissions

ADDRESS - Static variable in class org.molgenis.omx.auth.MolgenisUser

addUserPermission(String, Permission) - Method in class org.molgenis.security.permission.Permissions

addUserToGroup(Integer) - Method in class org.molgenis.security.usermanager.UserManagerController

addUserToGroup(Integer, Integer) - Method in interface org.molgenis.security.usermanager.UserManagerService

addUserToGroup(Integer, Integer) - Method in class org.molgenis.security.usermanager.UserManagerServiceImpl

AFFILIATION - Static variable in class org.molgenis.omx.auth.MolgenisUser

ALL_USER_GROUP - Static variable in class org.molgenis.security.account.AccountService

ANONYMOUS_USERNAME - Static variable in class org.molgenis.security.SecurityUtils

anonymousAuthenticationProvider() - Method in class org.molgenis.security.MolgenisWebAppSecurityConfig

anonymousAuthFilter() - Method in class org.molgenis.security.MolgenisWebAppSecurityConfig

authenticationManagerBean() - Method in class org.molgenis.security.MolgenisWebAppSecurityConfig

Authority - Interface in org.molgenis.omx.auth

Authority: .

AUTHORITY_ENTITY_PREFIX - Static variable in class org.molgenis.security.SecurityUtils

AUTHORITY_ENTITY_READ_PREFIX - Static variable in class org.molgenis.security.SecurityUtils

AUTHORITY_ENTITY_WRITE_PREFIX - Static variable in class org.molgenis.security.SecurityUtils

AUTHORITY_PLUGIN_PREFIX - Static variable in class org.molgenis.security.SecurityUtils

AUTHORITY_PLUGIN_READ_PREFIX - Static variable in class org.molgenis.security.SecurityUtils

AUTHORITY_PLUGIN_WRITE_PREFIX - Static variable in class org.molgenis.security.SecurityUtils

AUTHORITY_SU - Static variable in class org.molgenis.security.SecurityUtils

C

CaptchaController - Class in org.molgenis.security.captcha

CaptchaController() - Constructor for class org.molgenis.security.captcha.CaptchaController

CaptchaException - Exception in org.molgenis.security.captcha

CaptchaException(String) - Constructor for exception org.molgenis.security.captcha.CaptchaException

CaptchaRequest - Class in org.molgenis.security.captcha

CaptchaRequest() - Constructor for class org.molgenis.security.captcha.CaptchaRequest

CaptchaService - Class in org.molgenis.security.captcha

CaptchaService() - Constructor for class org.molgenis.security.captcha.CaptchaService

check(UserDetails) - Method in class org.molgenis.security.user.MolgenisUserDetailsChecker

CITY - Static variable in class org.molgenis.omx.auth.MolgenisUser

configure(HttpSecurity) - Method in class org.molgenis.security.MolgenisWebAppSecurityConfig

configure(AuthenticationManagerBuilder) - Method in class org.molgenis.security.MolgenisWebAppSecurityConfig

configureUrlAuthorization(ExpressionUrlAuthorizationConfigurer<HttpSecurity>.ExpressionInterceptUrlRegistry) - Method in class org.molgenis.security.MolgenisWebAppSecurityConfig

count(QueryRule...) - Method in class org.molgenis.omx.auth.db.GroupAuthoritySecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.auth.db.MolgenisGroupSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.auth.db.MolgenisUserSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.auth.db.UserAuthoritySecurityDecorator

COUNTRY - Static variable in class org.molgenis.omx.auth.MolgenisUser

create(GroupAuthority) - Method in class org.molgenis.omx.auth.db.GroupAuthorityJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.auth.db.GroupAuthorityJpaMapper

create(MolgenisGroup) - Method in class org.molgenis.omx.auth.db.MolgenisGroupJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.auth.db.MolgenisGroupJpaMapper

create(MolgenisGroupMember) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberJpaMapper

create(MolgenisUser) - Method in class org.molgenis.omx.auth.db.MolgenisUserJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.auth.db.MolgenisUserJpaMapper

create(UserAuthority) - Method in class org.molgenis.omx.auth.db.UserAuthorityJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.auth.db.UserAuthorityJpaMapper

create(Entity) - Method in class org.molgenis.omx.auth.GroupAuthority

create(Entity) - Method in class org.molgenis.omx.auth.MolgenisGroup

create(Entity) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

create(Entity) - Method in class org.molgenis.omx.auth.MolgenisUser

create(Entity) - Method in class org.molgenis.omx.auth.UserAuthority

create(GroupAuthority) - Method in class org.molgenis.service.GroupAuthorityService

create(MolgenisGroupMember) - Method in class org.molgenis.service.MolgenisGroupMemberService

create(MolgenisGroup) - Method in class org.molgenis.service.MolgenisGroupService

create(MolgenisUser) - Method in class org.molgenis.service.MolgenisUserService

create(UserAuthority) - Method in class org.molgenis.service.UserAuthorityService

createAnonymousUserAuthorities() - Method in class org.molgenis.security.MolgenisWebAppSecurityConfig

createCaptcha(int, int) - Method in class org.molgenis.security.captcha.CaptchaService

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.auth.db.GroupAuthorityJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.auth.db.GroupAuthoritySecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.auth.db.MolgenisGroupJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.auth.db.MolgenisGroupSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.auth.db.MolgenisUserJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.auth.db.MolgenisUserSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.auth.db.UserAuthorityJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.auth.db.UserAuthoritySecurityDecorator

createList(int) - Method in class org.molgenis.omx.auth.db.GroupAuthorityJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.auth.db.MolgenisGroupJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.auth.db.MolgenisUserJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.auth.db.UserAuthorityJpaMapper

Return EMPTY list of given allocated size

createUser(MolgenisUser, URI) - Method in class org.molgenis.security.account.AccountService

currentUserHasRole(String...) - Static method in class org.molgenis.security.SecurityUtils

Returns whether the current user has at least one of the given roles

currentUserIsAuthenticated() - Static method in class org.molgenis.security.SecurityUtils

Returns whether the current user is authenticated and not the anonymous user

currentUserIsSu() - Static method in class org.molgenis.security.SecurityUtils

Returns whether the current user is a super user

D

defaultPluginAuthorities(String...) - Static method in class org.molgenis.security.SecurityUtils

Returns the default (su, read, write) roles related to a plugin

deleteById(Integer) - Method in class org.molgenis.service.GroupAuthorityService

deleteById(Integer) - Method in class org.molgenis.service.MolgenisGroupMemberService

deleteById(Integer) - Method in class org.molgenis.service.MolgenisGroupService

deleteById(Integer) - Method in class org.molgenis.service.MolgenisUserService

deleteById(Integer) - Method in class org.molgenis.service.UserAuthorityService

DEPARTMENT - Static variable in class org.molgenis.omx.auth.MolgenisUser

destroy(GroupAuthority) - Method in class org.molgenis.omx.auth.db.GroupAuthorityJpaMapper

destroy(MolgenisGroup) - Method in class org.molgenis.omx.auth.db.MolgenisGroupJpaMapper

destroy(MolgenisGroupMember) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberJpaMapper

destroy(MolgenisUser) - Method in class org.molgenis.omx.auth.db.MolgenisUserJpaMapper

destroy(UserAuthority) - Method in class org.molgenis.omx.auth.db.UserAuthorityJpaMapper

E

edit(GroupAuthority) - Method in class org.molgenis.omx.auth.db.GroupAuthorityJpaMapper

edit(MolgenisGroup) - Method in class org.molgenis.omx.auth.db.MolgenisGroupJpaMapper

edit(MolgenisGroupMember) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberJpaMapper

edit(MolgenisUser) - Method in class org.molgenis.omx.auth.db.MolgenisUserJpaMapper

edit(UserAuthority) - Method in class org.molgenis.omx.auth.db.UserAuthorityJpaMapper

EMAIL - Static variable in class org.molgenis.omx.auth.MolgenisUser

encode(CharSequence) - Method in class org.molgenis.security.MolgenisPasswordEncoder

equals(Object) - Method in class org.molgenis.omx.auth.GroupAuthority

equals(Object) - Method in class org.molgenis.omx.auth.MolgenisGroup

equals(Object) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

equals(Object) - Method in class org.molgenis.omx.auth.MolgenisUser

equals(Object) - Method in class org.molgenis.omx.auth.UserAuthority

equals(Object) - Method in class org.molgenis.security.permission.Permission

executeAdd(List<? extends GroupAuthority>) - Method in class org.molgenis.omx.auth.db.GroupAuthorityJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.auth.db.GroupAuthoritySecurityDecorator

executeAdd(List<? extends MolgenisGroup>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupJpaMapper

executeAdd(List<? extends MolgenisGroupMember>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupSecurityDecorator

executeAdd(List<? extends MolgenisUser>) - Method in class org.molgenis.omx.auth.db.MolgenisUserJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.auth.db.MolgenisUserSecurityDecorator

executeAdd(List<? extends UserAuthority>) - Method in class org.molgenis.omx.auth.db.UserAuthorityJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.auth.db.UserAuthoritySecurityDecorator

executeRemove(List<? extends GroupAuthority>) - Method in class org.molgenis.omx.auth.db.GroupAuthorityJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.auth.db.GroupAuthoritySecurityDecorator

executeRemove(List<? extends MolgenisGroup>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupJpaMapper

executeRemove(List<? extends MolgenisGroupMember>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupSecurityDecorator

executeRemove(List<? extends MolgenisUser>) - Method in class org.molgenis.omx.auth.db.MolgenisUserJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.auth.db.MolgenisUserSecurityDecorator

executeRemove(List<? extends UserAuthority>) - Method in class org.molgenis.omx.auth.db.UserAuthorityJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.auth.db.UserAuthoritySecurityDecorator

executeUpdate(List<? extends GroupAuthority>) - Method in class org.molgenis.omx.auth.db.GroupAuthorityJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.auth.db.GroupAuthoritySecurityDecorator

executeUpdate(List<? extends MolgenisGroup>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupJpaMapper

executeUpdate(List<? extends MolgenisGroupMember>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupSecurityDecorator

executeUpdate(List<? extends MolgenisUser>) - Method in class org.molgenis.omx.auth.db.MolgenisUserJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.auth.db.MolgenisUserSecurityDecorator

executeUpdate(List<? extends UserAuthority>) - Method in class org.molgenis.omx.auth.db.UserAuthorityJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.auth.db.UserAuthoritySecurityDecorator

F

FAX - Static variable in class org.molgenis.omx.auth.MolgenisUser

find(QueryRule...) - Method in class org.molgenis.omx.auth.db.GroupAuthoritySecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.auth.db.MolgenisGroupSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.auth.db.MolgenisUserSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.auth.db.UserAuthoritySecurityDecorator

find(Database, QueryRule...) - Static method in class org.molgenis.omx.auth.GroupAuthority

Shorthand for db.find(GroupAuthority.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.auth.MolgenisGroup

Shorthand for db.find(MolgenisGroup.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.auth.MolgenisGroupMember

Shorthand for db.find(MolgenisGroupMember.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.auth.MolgenisUser

Shorthand for db.find(MolgenisUser.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.auth.UserAuthority

Shorthand for db.find(UserAuthority.class, org.molgenis.framework.db.QueryRule ...

findByEmail(Database, String) - Static method in class org.molgenis.omx.auth.MolgenisUser

findById(Object) - Method in class org.molgenis.omx.auth.db.GroupAuthoritySecurityDecorator

findById(Object) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.auth.db.MolgenisGroupSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.auth.db.MolgenisUserSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.auth.db.UserAuthoritySecurityDecorator

findById(Database, Integer) - Static method in class org.molgenis.omx.auth.GroupAuthority

findById(Database, Integer) - Static method in class org.molgenis.omx.auth.MolgenisGroup

findById(Database, Integer) - Static method in class org.molgenis.omx.auth.MolgenisGroupMember

findById(Database, Integer) - Static method in class org.molgenis.omx.auth.MolgenisUser

findById(Database, Integer) - Static method in class org.molgenis.omx.auth.UserAuthority

findByUsername(Database, String) - Static method in class org.molgenis.omx.auth.MolgenisUser

FIRSTNAME - Static variable in class org.molgenis.omx.auth.MolgenisUser

G

get(String) - Method in class org.molgenis.omx.auth.GroupAuthority

Generic getter.

get(String) - Method in class org.molgenis.omx.auth.MolgenisGroup

Generic getter.

get(String) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

Generic getter.

get(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Generic getter.

get(String) - Method in class org.molgenis.omx.auth.UserAuthority

Generic getter.

getActivationCode() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the Used as alternative authentication mechanism to verify user email and/or if user has lost password..

getActivationCode(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getActive() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the Boolean to indicate if this account can be used to login.

getActive(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getAddress() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the The address of the Contact..

getAddress(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getAffiliation() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the Affiliation.

getAffiliation(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getAllMolgenisGroups() - Method in interface org.molgenis.security.usermanager.UserManagerService

getAllMolgenisGroups() - Method in class org.molgenis.security.usermanager.UserManagerServiceImpl

getAllMolgenisUsers() - Method in interface org.molgenis.security.usermanager.UserManagerService

getAllMolgenisUsers() - Method in class org.molgenis.security.usermanager.UserManagerServiceImpl

getCaptcha() - Method in class org.molgenis.security.captcha.CaptchaController

getCaptcha() - Method in class org.molgenis.security.captcha.CaptchaRequest

getCity() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the Added from the old definition of MolgenisUser.

getCity(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getCountry() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the Added from the old definition of MolgenisUser.

getCountry(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getCurrentUser() - Method in interface org.molgenis.security.user.MolgenisUserService

Returns the currently logged in user

getCurrentUser() - Method in class org.molgenis.security.user.MolgenisUserServiceImpl

getCurrentUser() - Method in interface org.molgenis.security.user.UserAccountService

Returns the currently logged in user

getCurrentUser() - Method in class org.molgenis.security.user.UserAccountServiceImpl

getCurrentUsername() - Static method in class org.molgenis.security.SecurityUtils

getDepartment() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the Added from the old definition of MolgenisUser.

getDepartment(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getEmail() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the The email address of the Contact..

getEmail(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getEntity() - Method in class org.molgenis.service.GroupAuthorityService

getEntity() - Method in class org.molgenis.service.MolgenisGroupMemberService

getEntity() - Method in class org.molgenis.service.MolgenisGroupService

getEntity() - Method in class org.molgenis.service.MolgenisUserService

getEntity() - Method in class org.molgenis.service.UserAuthorityService

getEntityClassIds() - Method in interface org.molgenis.security.permission.PermissionManagerService

getEntityClassIds() - Method in class org.molgenis.security.permission.PermissionManagerServiceImpl

getEntityIds() - Method in class org.molgenis.security.permission.Permissions

getFax() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the The fax number of the Contact..

getFax(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.auth.GroupAuthority

Get the names of all public properties of GroupAuthority.

getFields() - Method in class org.molgenis.omx.auth.GroupAuthority

getFields(String) - Method in class org.molgenis.omx.auth.GroupAuthority

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.auth.MolgenisGroup

Get the names of all public properties of MolgenisGroup.

getFields() - Method in class org.molgenis.omx.auth.MolgenisGroup

getFields(String) - Method in class org.molgenis.omx.auth.MolgenisGroup

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

Get the names of all public properties of MolgenisGroupMember.

getFields() - Method in class org.molgenis.omx.auth.MolgenisGroupMember

getFields(String) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.auth.MolgenisUser

Get the names of all public properties of MolgenisUser.

getFields() - Method in class org.molgenis.omx.auth.MolgenisUser

getFields(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.auth.UserAuthority

Get the names of all public properties of UserAuthority.

getFields() - Method in class org.molgenis.omx.auth.UserAuthority

getFields(String) - Method in class org.molgenis.omx.auth.UserAuthority

Deprecated.

getFieldType(String) - Method in class org.molgenis.omx.auth.db.GroupAuthorityJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.auth.db.MolgenisGroupJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.auth.db.MolgenisUserJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.auth.db.UserAuthorityJpaMapper

getFirstName() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the First Name.

getFirstName(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getGroup() - Method in class org.molgenis.security.permission.Permission

getGroupEntityClassPermissions(Integer) - Method in class org.molgenis.security.permission.PermissionManagerController

getGroupEntityClassPermissions(Integer) - Method in interface org.molgenis.security.permission.PermissionManagerService

getGroupEntityClassPermissions(Integer) - Method in class org.molgenis.security.permission.PermissionManagerServiceImpl

getGroupId() - Method in class org.molgenis.security.permission.Permissions

getGroupPermissions() - Method in class org.molgenis.security.permission.Permissions

getGroupPluginPermissions(Integer) - Method in class org.molgenis.security.permission.PermissionManagerController

getGroupPluginPermissions(Integer) - Method in interface org.molgenis.security.permission.PermissionManagerService

getGroupPluginPermissions(Integer) - Method in class org.molgenis.security.permission.PermissionManagerServiceImpl

getGroups() - Method in interface org.molgenis.security.permission.PermissionManagerService

getGroups() - Method in class org.molgenis.security.permission.PermissionManagerServiceImpl

getGroupsWhereUserIsMember(Integer) - Method in interface org.molgenis.security.usermanager.UserManagerService

getGroupsWhereUserIsMember(Integer) - Method in class org.molgenis.security.usermanager.UserManagerServiceImpl

getGroupsWhereUserIsNotMember(Integer) - Method in interface org.molgenis.security.usermanager.UserManagerService

getGroupsWhereUserIsNotMember(Integer) - Method in class org.molgenis.security.usermanager.UserManagerServiceImpl

getHierarchyPermissionMap() - Method in class org.molgenis.security.permission.Permissions

getId() - Method in class org.molgenis.omx.auth.GroupAuthority

Get the id.

getId() - Method in class org.molgenis.omx.auth.MolgenisGroup

Get the id.

getId() - Method in class org.molgenis.omx.auth.MolgenisGroupMember

Get the id.

getId() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the automatically generated internal id, only for internal use..

getId() - Method in class org.molgenis.omx.auth.UserAuthority

Get the id.

getId() - Method in class org.molgenis.security.usermanager.MolgenisUserViewData

getIdField() - Method in class org.molgenis.omx.auth.GroupAuthority

getIdField() - Method in class org.molgenis.omx.auth.MolgenisGroup

getIdField() - Method in class org.molgenis.omx.auth.MolgenisGroupMember

getIdField() - Method in class org.molgenis.omx.auth.MolgenisUser

getIdField() - Method in class org.molgenis.omx.auth.UserAuthority

getIdValue() - Method in class org.molgenis.omx.auth.GroupAuthority

getIdValue() - Method in class org.molgenis.omx.auth.MolgenisGroup

getIdValue() - Method in class org.molgenis.omx.auth.MolgenisGroupMember

getIdValue() - Method in class org.molgenis.omx.auth.MolgenisUser

getIdValue() - Method in class org.molgenis.omx.auth.UserAuthority

getLabelFields() - Method in class org.molgenis.omx.auth.GroupAuthority

getLabelFields() - Method in class org.molgenis.omx.auth.MolgenisGroup

getLabelFields() - Method in class org.molgenis.omx.auth.MolgenisGroupMember

getLabelFields() - Method in class org.molgenis.omx.auth.MolgenisUser

getLabelFields() - Method in class org.molgenis.omx.auth.UserAuthority

getLastName() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the Last Name.

getLastName(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getLoginErrorPage(Model) - Method in class org.molgenis.security.login.MolgenisLoginController

getLoginForm() - Method in class org.molgenis.security.account.AccountController

getLoginPage() - Method in class org.molgenis.security.login.MolgenisLoginController

getMessage() - Method in exception org.molgenis.security.user.MolgenisUserException

getMidInitials() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the Mid Initials.

getMidInitials(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getMolgenisGroup() - Method in class org.molgenis.omx.auth.GroupAuthority

Get the molgenisGroup.

getMolgenisGroup(Database) - Method in class org.molgenis.omx.auth.GroupAuthority

Deprecated.

getMolgenisGroup() - Method in class org.molgenis.omx.auth.MolgenisGroupMember

Get the molgenisGroup.

getMolgenisGroup(Database) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

Deprecated.

getMolgenisGroup_Id() - Method in class org.molgenis.omx.auth.GroupAuthority

getMolgenisGroup_Id() - Method in class org.molgenis.omx.auth.MolgenisGroupMember

getMolgenisUser() - Method in class org.molgenis.omx.auth.MolgenisGroupMember

Get the molgenisUser.

getMolgenisUser(Database) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

Deprecated.

getMolgenisUser() - Method in class org.molgenis.omx.auth.UserAuthority

Get the molgenisUser.

getMolgenisUser(Database) - Method in class org.molgenis.omx.auth.UserAuthority

Deprecated.

getMolgenisUser_Email() - Method in class org.molgenis.omx.auth.MolgenisGroupMember

Get a pretty label Email for cross reference MolgenisUser to MolgenisUser.Id.

getMolgenisUser_Email() - Method in class org.molgenis.omx.auth.UserAuthority

Get a pretty label Email for cross reference MolgenisUser to MolgenisUser.Id.

getMolgenisUser_Id() - Method in class org.molgenis.omx.auth.MolgenisGroupMember

getMolgenisUser_Id() - Method in class org.molgenis.omx.auth.UserAuthority

getName() - Method in class org.molgenis.omx.auth.MolgenisGroup

Get the name.

getName(Database) - Method in class org.molgenis.omx.auth.MolgenisGroup

Deprecated.

getPassword() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the big fixme: password type.

getPassword(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getPasswordResetForm() - Method in class org.molgenis.security.account.AccountController

getPhone() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the The telephone number of the Contact including the suitable area codes..

getPhone(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getPluginReadAuthority(String) - Static method in class org.molgenis.security.SecurityUtils

getPlugins() - Method in interface org.molgenis.security.permission.PermissionManagerService

getPlugins() - Method in class org.molgenis.security.permission.PermissionManagerServiceImpl

getPluginWriteAuthority(String) - Static method in class org.molgenis.security.SecurityUtils

getRegisterForm() - Method in class org.molgenis.security.account.AccountController

getRole() - Method in interface org.molgenis.omx.auth.Authority

getRole() - Method in class org.molgenis.omx.auth.GroupAuthority

Get the role.

getRole(Database) - Method in class org.molgenis.omx.auth.GroupAuthority

Deprecated.

getRole() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the Indicate role of the contact, e.g.

getRole(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getRole() - Method in class org.molgenis.omx.auth.UserAuthority

Get the role.

getRole(Database) - Method in class org.molgenis.omx.auth.UserAuthority

Deprecated.

getSuEmailAddresses() - Method in interface org.molgenis.security.user.MolgenisUserService

Returns e-mail addresses of super users

getSuEmailAddresses() - Method in class org.molgenis.security.user.MolgenisUserServiceImpl

getSuperuser() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the superuser.

getSuperuser(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getTableFieldName(String) - Method in class org.molgenis.omx.auth.db.GroupAuthorityJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.auth.db.MolgenisGroupJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.auth.db.MolgenisUserJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.auth.db.UserAuthorityJpaMapper

getTitle() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the An academic title, e.g.

getTitle(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getTollFreePhone() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the A toll free phone number for the Contact, including suitable area codes..

getTollFreePhone(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getType() - Method in class org.molgenis.security.permission.Permission

getUserEntityClassPermissions(Integer) - Method in class org.molgenis.security.permission.PermissionManagerController

getUserEntityClassPermissions(Integer) - Method in interface org.molgenis.security.permission.PermissionManagerService

getUserEntityClassPermissions(Integer) - Method in class org.molgenis.security.permission.PermissionManagerServiceImpl

getUserId() - Method in class org.molgenis.security.permission.Permissions

getUsername() - Method in class org.molgenis.omx.auth.MolgenisUser

Get the username.

getUsername(Database) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getUsername() - Method in class org.molgenis.security.usermanager.MolgenisUserViewData

getUserPermissions() - Method in class org.molgenis.security.permission.Permissions

getUserPluginPermissions(Integer) - Method in class org.molgenis.security.permission.PermissionManagerController

getUserPluginPermissions(Integer) - Method in interface org.molgenis.security.permission.PermissionManagerService

getUserPluginPermissions(Integer) - Method in class org.molgenis.security.permission.PermissionManagerServiceImpl

getUsers() - Method in interface org.molgenis.security.permission.PermissionManagerService

getUsers() - Method in class org.molgenis.security.permission.PermissionManagerServiceImpl

getUsersMemberInGroup(Integer, Model) - Method in class org.molgenis.security.usermanager.UserManagerController

getUsersMemberInGroup(Integer) - Method in interface org.molgenis.security.usermanager.UserManagerService

getUsersMemberInGroup(Integer) - Method in class org.molgenis.security.usermanager.UserManagerServiceImpl

getValues(String) - Method in class org.molgenis.omx.auth.GroupAuthority

Deprecated.

getValues(String) - Method in class org.molgenis.omx.auth.MolgenisGroup

Deprecated.

getValues(String) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

Deprecated.

getValues(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Deprecated.

getValues(String) - Method in class org.molgenis.omx.auth.UserAuthority

Deprecated.

getXrefIdFieldName(String) - Method in class org.molgenis.omx.auth.GroupAuthority

getXrefIdFieldName(String) - Method in class org.molgenis.omx.auth.MolgenisGroup

getXrefIdFieldName(String) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

getXrefIdFieldName(String) - Method in class org.molgenis.omx.auth.MolgenisUser

getXrefIdFieldName(String) - Method in class org.molgenis.omx.auth.UserAuthority

GroupAuthority - Class in org.molgenis.omx.auth

GroupAuthority: .

GroupAuthority() - Constructor for class org.molgenis.omx.auth.GroupAuthority

GroupAuthority(GroupAuthority) - Constructor for class org.molgenis.omx.auth.GroupAuthority

copy constructor

GroupAuthorityEntityImporter - Class in org.molgenis.omx.auth.db

Reads GroupAuthority from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

GroupAuthorityEntityImporter() - Constructor for class org.molgenis.omx.auth.db.GroupAuthorityEntityImporter

GroupAuthorityJpaMapper - Class in org.molgenis.omx.auth.db

GroupAuthorityJpaMapper(Database) - Constructor for class org.molgenis.omx.auth.db.GroupAuthorityJpaMapper

GroupAuthoritySecurityDecorator<E extends GroupAuthority> - Class in org.molgenis.omx.auth.db

TODO add column level security filters

GroupAuthoritySecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.auth.db.GroupAuthoritySecurityDecorator

GroupAuthorityService - Class in org.molgenis.service

GroupAuthorityService() - Constructor for class org.molgenis.service.GroupAuthorityService

H

handleDatabaseException(DatabaseException) - Method in class org.molgenis.security.account.AccountController

handleMolgenisUserException(MolgenisUserException) - Method in class org.molgenis.security.account.AccountController

handleRuntimeException(RuntimeException) - Method in class org.molgenis.security.account.AccountController

handleRuntimeException(RuntimeException) - Method in class org.molgenis.security.permission.PermissionManagerController

hashCode() - Method in class org.molgenis.omx.auth.GroupAuthority

hashCode() - Method in class org.molgenis.omx.auth.MolgenisGroup

hashCode() - Method in class org.molgenis.omx.auth.MolgenisGroupMember

hashCode() - Method in class org.molgenis.omx.auth.MolgenisUser

hashCode() - Method in class org.molgenis.omx.auth.UserAuthority

hashCode() - Method in class org.molgenis.security.permission.Permission

hasPermissionOnEntity(String, MolgenisPermissionService.Permission) - Method in class org.molgenis.security.permission.MolgenisPermissionServiceImpl

hasPermissionOnPlugin(String, MolgenisPermissionService.Permission) - Method in class org.molgenis.security.permission.MolgenisPermissionServiceImpl

I

ID - Static variable in class org.molgenis.omx.auth.GroupAuthority

ID - Static variable in class org.molgenis.omx.auth.MolgenisGroup

ID - Static variable in class org.molgenis.omx.auth.MolgenisGroupMember

ID - Static variable in class org.molgenis.omx.auth.MolgenisUser

ID - Static variable in class org.molgenis.omx.auth.UserAuthority

ID - Static variable in class org.molgenis.security.user.UserAccountController

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.auth.db.GroupAuthorityEntityImporter

Imports GroupAuthority from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.auth.db.MolgenisGroupEntityImporter

Imports MolgenisGroup from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberEntityImporter

Imports MolgenisGroupMember from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.auth.db.MolgenisUserEntityImporter

Imports MolgenisUser from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.auth.db.UserAuthorityEntityImporter

Imports UserAuthority from tab/comma delimited File

init(Model) - Method in class org.molgenis.security.permission.PermissionManagerController

init(Model) - Method in class org.molgenis.security.usermanager.UserManagerController

K

KEY_PLUGIN_AUTH_ACTIVATIONMODE - Static variable in class org.molgenis.security.account.AccountService

L

LASTNAME - Static variable in class org.molgenis.omx.auth.MolgenisUser

loadUserByUsername(String) - Method in class org.molgenis.security.user.MolgenisUserDetailsService

M

matches(CharSequence, String) - Method in class org.molgenis.security.MolgenisPasswordEncoder

messages - Variable in class org.molgenis.security.user.MolgenisUserDetailsChecker

MIDINITIALS - Static variable in class org.molgenis.omx.auth.MolgenisUser

MIN_PASSWORD_LENGTH - Static variable in class org.molgenis.security.user.UserAccountController

MOLGENISGROUP - Static variable in class org.molgenis.omx.auth.GroupAuthority

MolgenisGroup - Class in org.molgenis.omx.auth

MolgenisGroup: .

MolgenisGroup() - Constructor for class org.molgenis.omx.auth.MolgenisGroup

MolgenisGroup(MolgenisGroup) - Constructor for class org.molgenis.omx.auth.MolgenisGroup

copy constructor

MOLGENISGROUP - Static variable in class org.molgenis.omx.auth.MolgenisGroupMember

MOLGENISGROUP_ID - Static variable in class org.molgenis.omx.auth.GroupAuthority

MOLGENISGROUP_ID - Static variable in class org.molgenis.omx.auth.MolgenisGroupMember

MolgenisGroupEntityImporter - Class in org.molgenis.omx.auth.db

Reads MolgenisGroup from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

MolgenisGroupEntityImporter() - Constructor for class org.molgenis.omx.auth.db.MolgenisGroupEntityImporter

MolgenisGroupJpaMapper - Class in org.molgenis.omx.auth.db

MolgenisGroupJpaMapper(Database) - Constructor for class org.molgenis.omx.auth.db.MolgenisGroupJpaMapper

MolgenisGroupMember - Class in org.molgenis.omx.auth

MolgenisGroupMember: .

MolgenisGroupMember() - Constructor for class org.molgenis.omx.auth.MolgenisGroupMember

MolgenisGroupMember(MolgenisGroupMember) - Constructor for class org.molgenis.omx.auth.MolgenisGroupMember

copy constructor

MolgenisGroupMemberEntityImporter - Class in org.molgenis.omx.auth.db

Reads MolgenisGroupMember from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

MolgenisGroupMemberEntityImporter() - Constructor for class org.molgenis.omx.auth.db.MolgenisGroupMemberEntityImporter

MolgenisGroupMemberJpaMapper - Class in org.molgenis.omx.auth.db

MolgenisGroupMemberJpaMapper(Database) - Constructor for class org.molgenis.omx.auth.db.MolgenisGroupMemberJpaMapper

MolgenisGroupMemberSecurityDecorator<E extends MolgenisGroupMember> - Class in org.molgenis.omx.auth.db

TODO add column level security filters

MolgenisGroupMemberSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.auth.db.MolgenisGroupMemberSecurityDecorator

MolgenisGroupMemberService - Class in org.molgenis.service

MolgenisGroupMemberService() - Constructor for class org.molgenis.service.MolgenisGroupMemberService

MolgenisGroupSecurityDecorator<E extends MolgenisGroup> - Class in org.molgenis.omx.auth.db

TODO add column level security filters

MolgenisGroupSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.auth.db.MolgenisGroupSecurityDecorator

MolgenisGroupService - Class in org.molgenis.service

MolgenisGroupService() - Constructor for class org.molgenis.service.MolgenisGroupService

MolgenisLoginController - Class in org.molgenis.security.login

MolgenisLoginController() - Constructor for class org.molgenis.security.login.MolgenisLoginController

MolgenisPasswordEncoder - Class in org.molgenis.security

MolgenisPasswordEncoder(BCryptPasswordEncoder) - Constructor for class org.molgenis.security.MolgenisPasswordEncoder

molgenisPermissionService() - Method in class org.molgenis.security.MolgenisWebAppSecurityConfig

MolgenisPermissionServiceImpl - Class in org.molgenis.security.permission

MolgenisPermissionServiceImpl() - Constructor for class org.molgenis.security.permission.MolgenisPermissionServiceImpl

MOLGENISUSER - Static variable in class org.molgenis.omx.auth.MolgenisGroupMember

MolgenisUser - Class in org.molgenis.omx.auth

MolgenisUser: Anyone who can login.

MolgenisUser() - Constructor for class org.molgenis.omx.auth.MolgenisUser

MolgenisUser(MolgenisUser) - Constructor for class org.molgenis.omx.auth.MolgenisUser

copy constructor

MOLGENISUSER - Static variable in class org.molgenis.omx.auth.UserAuthority

MOLGENISUSER_EMAIL - Static variable in class org.molgenis.omx.auth.MolgenisGroupMember

MOLGENISUSER_EMAIL - Static variable in class org.molgenis.omx.auth.UserAuthority

MolgenisUserDetailsChecker - Class in org.molgenis.security.user

Checks user details during the authentication process

MolgenisUserDetailsChecker() - Constructor for class org.molgenis.security.user.MolgenisUserDetailsChecker

MolgenisUserDetailsService - Class in org.molgenis.security.user

MolgenisUserDetailsService(Database, GrantedAuthoritiesMapper) - Constructor for class org.molgenis.security.user.MolgenisUserDetailsService

MolgenisUserEntityImporter - Class in org.molgenis.omx.auth.db

Reads MolgenisUser from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

MolgenisUserEntityImporter() - Constructor for class org.molgenis.omx.auth.db.MolgenisUserEntityImporter

MolgenisUserException - Exception in org.molgenis.security.user

MolgenisUserException(String) - Constructor for exception org.molgenis.security.user.MolgenisUserException

MolgenisUserException(Exception) - Constructor for exception org.molgenis.security.user.MolgenisUserException

MolgenisUserJpaMapper - Class in org.molgenis.omx.auth.db

MolgenisUserJpaMapper(Database) - Constructor for class org.molgenis.omx.auth.db.MolgenisUserJpaMapper

MolgenisUserSecurityDecorator<E extends MolgenisUser> - Class in org.molgenis.omx.auth.db

TODO add column level security filters

MolgenisUserSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.auth.db.MolgenisUserSecurityDecorator

MolgenisUserService - Interface in org.molgenis.security.user

MolgenisUserService - Class in org.molgenis.service

MolgenisUserService() - Constructor for class org.molgenis.service.MolgenisUserService

MolgenisUserServiceImpl - Class in org.molgenis.security.user

MolgenisUserServiceImpl(Database) - Constructor for class org.molgenis.security.user.MolgenisUserServiceImpl

MolgenisUserViewData - Class in org.molgenis.security.usermanager

MolgenisWebAppSecurityConfig - Class in org.molgenis.security

MolgenisWebAppSecurityConfig() - Constructor for class org.molgenis.security.MolgenisWebAppSecurityConfig

N

NAME - Static variable in class org.molgenis.omx.auth.MolgenisGroup

O

org.molgenis.omx.auth - package org.molgenis.omx.auth

org.molgenis.omx.auth.db - package org.molgenis.omx.auth.db

org.molgenis.security - package org.molgenis.security

org.molgenis.security.account - package org.molgenis.security.account

org.molgenis.security.captcha - package org.molgenis.security.captcha

org.molgenis.security.login - package org.molgenis.security.login

org.molgenis.security.permission - package org.molgenis.security.permission

org.molgenis.security.user - package org.molgenis.security.user

org.molgenis.security.usermanager - package org.molgenis.security.usermanager

org.molgenis.service - package org.molgenis.service

P

PASSWORD_ - Static variable in class org.molgenis.omx.auth.MolgenisUser

passwordEncoder() - Method in class org.molgenis.security.MolgenisWebAppSecurityConfig

Permission - Class in org.molgenis.security.permission

Permission() - Constructor for class org.molgenis.security.permission.Permission

PermissionManagerController - Class in org.molgenis.security.permission

PermissionManagerController(PermissionManagerService) - Constructor for class org.molgenis.security.permission.PermissionManagerController

PermissionManagerService - Interface in org.molgenis.security.permission

Manage user and group permissions for plugins and entity classes

PermissionManagerServiceImpl - Class in org.molgenis.security.permission

PermissionManagerServiceImpl(Database, MolgenisPluginRegistry, GrantedAuthoritiesMapper) - Constructor for class org.molgenis.security.permission.PermissionManagerServiceImpl

Permissions - Class in org.molgenis.security.permission

Permissions() - Constructor for class org.molgenis.security.permission.Permissions

PHONE - Static variable in class org.molgenis.omx.auth.MolgenisUser

prepareFileAttachements(List<GroupAuthority>, File) - Method in class org.molgenis.omx.auth.db.GroupAuthorityJpaMapper

prepareFileAttachements(List<MolgenisGroup>, File) - Method in class org.molgenis.omx.auth.db.MolgenisGroupJpaMapper

prepareFileAttachements(List<MolgenisGroupMember>, File) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberJpaMapper

prepareFileAttachements(List<MolgenisUser>, File) - Method in class org.molgenis.omx.auth.db.MolgenisUserJpaMapper

prepareFileAttachements(List<UserAuthority>, File) - Method in class org.molgenis.omx.auth.db.UserAuthorityJpaMapper

Q

query(Database) - Static method in class org.molgenis.omx.auth.GroupAuthority

Shorthand for db.query(GroupAuthority.class).

query(Database) - Static method in class org.molgenis.omx.auth.MolgenisGroup

Shorthand for db.query(MolgenisGroup.class).

query(Database) - Static method in class org.molgenis.omx.auth.MolgenisGroupMember

Shorthand for db.query(MolgenisGroupMember.class).

query(Database) - Static method in class org.molgenis.omx.auth.MolgenisUser

Shorthand for db.query(MolgenisUser.class).

query(Database) - Static method in class org.molgenis.omx.auth.UserAuthority

Shorthand for db.query(UserAuthority.class).

R

read(Integer) - Method in class org.molgenis.service.GroupAuthorityService

read(Integer) - Method in class org.molgenis.service.MolgenisGroupMemberService

read(Integer) - Method in class org.molgenis.service.MolgenisGroupService

read(Integer) - Method in class org.molgenis.service.MolgenisUserService

read(Integer) - Method in class org.molgenis.service.UserAuthorityService

readAll() - Method in class org.molgenis.service.GroupAuthorityService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.GroupAuthorityService

readAll() - Method in class org.molgenis.service.MolgenisGroupMemberService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.MolgenisGroupMemberService

readAll() - Method in class org.molgenis.service.MolgenisGroupService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.MolgenisGroupService

readAll() - Method in class org.molgenis.service.MolgenisUserService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.MolgenisUserService

readAll() - Method in class org.molgenis.service.UserAuthorityService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.UserAuthorityService

registerUser(RegisterRequest, CaptchaRequest) - Method in class org.molgenis.security.account.AccountController

remove(List<E>) - Method in class org.molgenis.omx.auth.db.GroupAuthoritySecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.auth.db.MolgenisUserSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.auth.db.UserAuthoritySecurityDecorator

removeUserFromGroup(Integer) - Method in class org.molgenis.security.usermanager.UserManagerController

removeUserFromGroup(Integer, Integer) - Method in interface org.molgenis.security.usermanager.UserManagerService

removeUserFromGroup(Integer, Integer) - Method in class org.molgenis.security.usermanager.UserManagerServiceImpl

replaceGroupEntityClassPermissions(List<GroupAuthority>, Integer) - Method in interface org.molgenis.security.permission.PermissionManagerService

replaceGroupEntityClassPermissions(List<GroupAuthority>, Integer) - Method in class org.molgenis.security.permission.PermissionManagerServiceImpl

replaceGroupPluginPermissions(List<GroupAuthority>, Integer) - Method in interface org.molgenis.security.permission.PermissionManagerService

replaceGroupPluginPermissions(List<GroupAuthority>, Integer) - Method in class org.molgenis.security.permission.PermissionManagerServiceImpl

replaceUserEntityClassPermissions(List<UserAuthority>, Integer) - Method in interface org.molgenis.security.permission.PermissionManagerService

replaceUserEntityClassPermissions(List<UserAuthority>, Integer) - Method in class org.molgenis.security.permission.PermissionManagerServiceImpl

replaceUserPluginPermissions(List<UserAuthority>, Integer) - Method in interface org.molgenis.security.permission.PermissionManagerService

replaceUserPluginPermissions(List<UserAuthority>, Integer) - Method in class org.molgenis.security.permission.PermissionManagerServiceImpl

resetPassword(PasswordResetRequest) - Method in class org.molgenis.security.account.AccountController

resetPassword(String) - Method in class org.molgenis.security.account.AccountService

resolveForeignKeys(List<GroupAuthority>) - Method in class org.molgenis.omx.auth.db.GroupAuthorityJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.auth.db.GroupAuthoritySecurityDecorator

resolveForeignKeys(List<MolgenisGroup>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupJpaMapper

resolveForeignKeys(List<MolgenisGroupMember>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupSecurityDecorator

resolveForeignKeys(List<MolgenisUser>) - Method in class org.molgenis.omx.auth.db.MolgenisUserJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.auth.db.MolgenisUserSecurityDecorator

resolveForeignKeys(List<UserAuthority>) - Method in class org.molgenis.omx.auth.db.UserAuthorityJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.auth.db.UserAuthoritySecurityDecorator

ROLE - Static variable in class org.molgenis.omx.auth.GroupAuthority

ROLE - Static variable in class org.molgenis.omx.auth.MolgenisUser

ROLE - Static variable in class org.molgenis.omx.auth.UserAuthority

roleHierarchy() - Method in class org.molgenis.security.MolgenisWebAppSecurityConfig

roleHierarchyAuthoritiesMapper() - Method in class org.molgenis.security.MolgenisWebAppSecurityConfig

roleHierarchyBean() - Method in class org.molgenis.security.MolgenisWebAppSecurityConfig

roleVoter() - Method in class org.molgenis.security.MolgenisWebAppSecurityConfig

S

saveFileAttachements(List<GroupAuthority>, File) - Method in class org.molgenis.omx.auth.db.GroupAuthorityJpaMapper

saveFileAttachements(List<MolgenisGroup>, File) - Method in class org.molgenis.omx.auth.db.MolgenisGroupJpaMapper

saveFileAttachements(List<MolgenisGroupMember>, File) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberJpaMapper

saveFileAttachements(List<MolgenisUser>, File) - Method in class org.molgenis.omx.auth.db.MolgenisUserJpaMapper

saveFileAttachements(List<UserAuthority>, File) - Method in class org.molgenis.omx.auth.db.UserAuthorityJpaMapper

SecurityUtils - Class in org.molgenis.security

SecurityUtils() - Constructor for class org.molgenis.security.SecurityUtils

set(Entity, boolean) - Method in class org.molgenis.omx.auth.GroupAuthority

set(Entity, boolean) - Method in class org.molgenis.omx.auth.MolgenisGroup

set(Entity, boolean) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

set(Entity, boolean) - Method in class org.molgenis.omx.auth.MolgenisUser

set(Entity, boolean) - Method in class org.molgenis.omx.auth.UserAuthority

setActivationCode(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the Used as alternative authentication mechanism to verify user email and/or if user has lost password..

setActive(Boolean) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the Boolean to indicate if this account can be used to login.

setAddress(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the The address of the Contact..

setAffiliation(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the Affiliation.

setCaptcha(String) - Method in class org.molgenis.security.captcha.CaptchaRequest

setCity(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the Added from the old definition of MolgenisUser.

setCountry(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the Added from the old definition of MolgenisUser.

setDepartment(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the Added from the old definition of MolgenisUser.

setEmail(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the The email address of the Contact..

setEntityIds(Map<String, String>) - Method in class org.molgenis.security.permission.Permissions

setFax(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the The fax number of the Contact..

setFirstName(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the First Name.

setGroup(String) - Method in class org.molgenis.security.permission.Permission

setGroupId(Integer) - Method in class org.molgenis.security.permission.Permissions

setId(Integer) - Method in class org.molgenis.omx.auth.GroupAuthority

Set the id.

setId(Integer) - Method in class org.molgenis.omx.auth.MolgenisGroup

Set the id.

setId(Integer) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

Set the id.

setId(Integer) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the automatically generated internal id, only for internal use..

setId(Integer) - Method in class org.molgenis.omx.auth.UserAuthority

Set the id.

setLastName(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the Last Name.

setMidInitials(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the Mid Initials.

setMolgenisGroup(MolgenisGroup) - Method in class org.molgenis.omx.auth.GroupAuthority

Set the molgenisGroup.

setMolgenisGroup(Integer) - Method in class org.molgenis.omx.auth.GroupAuthority

setMolgenisGroup(MolgenisGroup) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

Set the molgenisGroup.

setMolgenisGroup(Integer) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

setMolgenisGroup_Id(Integer) - Method in class org.molgenis.omx.auth.GroupAuthority

Set foreign key for field molgenisGroup.

setMolgenisGroup_Id(Integer) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

Set foreign key for field molgenisGroup.

setMolgenisUser(MolgenisUser) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

Set the molgenisUser.

setMolgenisUser(Integer) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

setMolgenisUser(MolgenisUser) - Method in class org.molgenis.omx.auth.UserAuthority

Set the molgenisUser.

setMolgenisUser(Integer) - Method in class org.molgenis.omx.auth.UserAuthority

setMolgenisUser_Email(String) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

Set a pretty label for cross reference MolgenisUser to MolgenisUser.Id.

setMolgenisUser_Email(String) - Method in class org.molgenis.omx.auth.UserAuthority

Set a pretty label for cross reference MolgenisUser to MolgenisUser.Id.

setMolgenisUser_Id(Integer) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

Set foreign key for field molgenisUser.

setMolgenisUser_Id(Integer) - Method in class org.molgenis.omx.auth.UserAuthority

Set foreign key for field molgenisUser.

setName(String) - Method in class org.molgenis.omx.auth.MolgenisGroup

Set the name.

setPassword(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the big fixme: password type.

setPhone(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the The telephone number of the Contact including the suitable area codes..

setRole(String) - Method in interface org.molgenis.omx.auth.Authority

setRole(String) - Method in class org.molgenis.omx.auth.GroupAuthority

Set the role.

setRole(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the Indicate role of the contact, e.g.

setRole(String) - Method in class org.molgenis.omx.auth.UserAuthority

Set the role.

setSuperuser(Boolean) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the superuser.

setTitle(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the An academic title, e.g.

setTollFreePhone(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the A toll free phone number for the Contact, including suitable area codes..

setType(String) - Method in class org.molgenis.security.permission.Permission

setUserId(Integer) - Method in class org.molgenis.security.permission.Permissions

setUsername(String) - Method in class org.molgenis.omx.auth.MolgenisUser

Set the username.

showAccount(Model) - Method in class org.molgenis.security.user.UserAccountController

sort() - Method in class org.molgenis.security.permission.Permissions

SUPERUSER - Static variable in class org.molgenis.omx.auth.MolgenisUser

T

TITLE - Static variable in class org.molgenis.omx.auth.MolgenisUser

TOLLFREEPHONE - Static variable in class org.molgenis.omx.auth.MolgenisUser

toString() - Method in class org.molgenis.omx.auth.GroupAuthority

toString(boolean) - Method in class org.molgenis.omx.auth.GroupAuthority

toString() - Method in class org.molgenis.omx.auth.MolgenisGroup

toString(boolean) - Method in class org.molgenis.omx.auth.MolgenisGroup

toString() - Method in class org.molgenis.omx.auth.MolgenisGroupMember

toString(boolean) - Method in class org.molgenis.omx.auth.MolgenisGroupMember

toString() - Method in class org.molgenis.omx.auth.MolgenisUser

toString(boolean) - Method in class org.molgenis.omx.auth.MolgenisUser

toString() - Method in class org.molgenis.omx.auth.UserAuthority

toString(boolean) - Method in class org.molgenis.omx.auth.UserAuthority

toString() - Method in class org.molgenis.security.permission.Permission

U

update(List<E>) - Method in class org.molgenis.omx.auth.db.GroupAuthoritySecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupMemberSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.auth.db.MolgenisGroupSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.auth.db.MolgenisUserSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.auth.db.UserAuthoritySecurityDecorator

update(GroupAuthority) - Method in class org.molgenis.service.GroupAuthorityService

update(MolgenisGroupMember) - Method in class org.molgenis.service.MolgenisGroupMemberService

update(MolgenisGroup) - Method in class org.molgenis.service.MolgenisGroupService

update(MolgenisUser) - Method in class org.molgenis.service.MolgenisUserService

update(UserAuthority) - Method in class org.molgenis.service.UserAuthorityService

updateAccount(UserAccountController.AccountUpdateRequest) - Method in class org.molgenis.security.user.UserAccountController

updateCurrentUser(MolgenisUser) - Method in interface org.molgenis.security.user.UserAccountService

Update the currently logged in user

updateCurrentUser(MolgenisUser) - Method in class org.molgenis.security.user.UserAccountServiceImpl

updateGroupEntityClassPermissions(Integer, WebRequest) - Method in class org.molgenis.security.permission.PermissionManagerController

updateGroupPluginPermissions(Integer, WebRequest) - Method in class org.molgenis.security.permission.PermissionManagerController

updateUserEntityClassPermissions(Integer, WebRequest) - Method in class org.molgenis.security.permission.PermissionManagerController

updateUserPluginPermissions(Integer, WebRequest) - Method in class org.molgenis.security.permission.PermissionManagerController

updateView(Integer, Integer, Model) - Method in class org.molgenis.security.usermanager.UserManagerController

URI - Static variable in class org.molgenis.security.permission.PermissionManagerController

URI - Static variable in class org.molgenis.security.user.UserAccountController

URI - Static variable in class org.molgenis.security.usermanager.UserManagerController

UserAccountController - Class in org.molgenis.security.user

UserAccountController(UserAccountService) - Constructor for class org.molgenis.security.user.UserAccountController

UserAccountService - Interface in org.molgenis.security.user

Manage account of the current user

UserAccountServiceImpl - Class in org.molgenis.security.user

UserAccountServiceImpl() - Constructor for class org.molgenis.security.user.UserAccountServiceImpl

UserAuthority - Class in org.molgenis.omx.auth

UserAuthority: .

UserAuthority() - Constructor for class org.molgenis.omx.auth.UserAuthority

UserAuthority(UserAuthority) - Constructor for class org.molgenis.omx.auth.UserAuthority

copy constructor

UserAuthorityEntityImporter - Class in org.molgenis.omx.auth.db

Reads UserAuthority from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

UserAuthorityEntityImporter() - Constructor for class org.molgenis.omx.auth.db.UserAuthorityEntityImporter

UserAuthorityJpaMapper - Class in org.molgenis.omx.auth.db

UserAuthorityJpaMapper(Database) - Constructor for class org.molgenis.omx.auth.db.UserAuthorityJpaMapper

UserAuthoritySecurityDecorator<E extends UserAuthority> - Class in org.molgenis.omx.auth.db

TODO add column level security filters

UserAuthoritySecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.auth.db.UserAuthoritySecurityDecorator

UserAuthorityService - Class in org.molgenis.service

UserAuthorityService() - Constructor for class org.molgenis.service.UserAuthorityService

userDetailsChecker() - Method in class org.molgenis.security.MolgenisWebAppSecurityConfig

userDetailsService() - Method in class org.molgenis.security.MolgenisWebAppSecurityConfig

userDetailsServiceBean() - Method in class org.molgenis.security.MolgenisWebAppSecurityConfig

UserManagerController - Class in org.molgenis.security.usermanager

UserManagerController(UserManagerService) - Constructor for class org.molgenis.security.usermanager.UserManagerController

UserManagerService - Interface in org.molgenis.security.usermanager

UserManagerServiceImpl - Class in org.molgenis.security.usermanager

Manage user in groups

UserManagerServiceImpl(Database) - Constructor for class org.molgenis.security.usermanager.UserManagerServiceImpl

USERNAME - Static variable in class org.molgenis.omx.auth.MolgenisUser

V

validate() - Method in class org.molgenis.omx.auth.GroupAuthority

validate() - Method in class org.molgenis.omx.auth.MolgenisGroup

validate() - Method in class org.molgenis.omx.auth.MolgenisGroupMember

validate() - Method in class org.molgenis.omx.auth.MolgenisUser

validate() - Method in class org.molgenis.omx.auth.UserAuthority

validateCaptcha(CaptchaRequest) - Method in class org.molgenis.security.captcha.CaptchaController

validateCaptcha(String) - Method in class org.molgenis.security.captcha.CaptchaService

validateCaptchaFromForm(CaptchaRequest) - Method in class org.molgenis.security.captcha.CaptchaController

validateCurrentUserPassword(String) - Method in interface org.molgenis.security.user.UserAccountService

Validates the password of the current logged in user

validateCurrentUserPassword(String) - Method in class org.molgenis.security.user.UserAccountServiceImpl

W

WebAppSecurityInitializer - Class in org.molgenis.security

WebAppSecurityInitializer() - Constructor for class org.molgenis.security.WebAppSecurityInitializer

A C D E F G H I K L M N O P Q R S T U V W