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

A

AccessionService - Class in org.molgenis.service

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

AccountController - Class in org.molgenis.omx.auth.controller

AccountController() - Constructor for class org.molgenis.omx.auth.controller.AccountController

AccountService - Class in org.molgenis.omx.auth.service

AccountService() - Constructor for class org.molgenis.omx.auth.service.AccountService

activateUser(String) - Method in class org.molgenis.omx.auth.controller.AccountController

activateUser(String) - Method in class org.molgenis.omx.auth.service.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.decorators.MolgenisUserDecorator

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

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

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

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

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

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

AFFILIATION_NAME - Static variable in class org.molgenis.omx.auth.Person

Authorizable - Interface in org.molgenis.omx.auth

Authorizable: Interface for row level security.

AuthtestGenerate - Class in org.molgenis.omx.auth

Generates the MOLGENIS application from the *db.xml and *ui.xml as set in molgenis.properties

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

B

BoolValueService - Class in org.molgenis.service

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

C

canRead(Class<? extends Entity>) - Method in class org.molgenis.omx.auth.DatabaseLogin

canRead(Entity) - Method in class org.molgenis.omx.auth.DatabaseLogin

Indicates whether the user has permissions to read data from this entity.

canRead(ScreenController<?>) - Method in class org.molgenis.omx.auth.DatabaseLogin

canReadScreenController(Class<? extends ScreenController<?>>) - Method in class org.molgenis.omx.auth.DatabaseLogin

canWrite(Class<? extends Entity>) - Method in class org.molgenis.omx.auth.DatabaseLogin

canWrite(Entity) - Method in class org.molgenis.omx.auth.DatabaseLogin

Indicates whether the user has permissions to write (and read) data from this entity.

CaptchaController - Class in org.molgenis.omx.auth.controller

CaptchaController() - Constructor for class org.molgenis.omx.auth.controller.CaptchaController

CaptchaRequest - Class in org.molgenis.omx.auth.vo

CaptchaRequest() - Constructor for class org.molgenis.omx.auth.vo.CaptchaRequest

CaptchaService - Class in org.molgenis.omx.auth.service

CaptchaService() - Constructor for class org.molgenis.omx.auth.service.CaptchaService

CaptchaService.CaptchaException - Exception in org.molgenis.omx.auth.service

CaptchaService.CaptchaException(String) - Constructor for exception org.molgenis.omx.auth.service.CaptchaService.CaptchaException

CategoricalValueService - Class in org.molgenis.service

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

CategoryService - Class in org.molgenis.service

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

CharacteristicService - Class in org.molgenis.service

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

checkPassword(String, String, String, String) - Method in class org.molgenis.omx.auth.service.MolgenisUserService

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

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

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

Contact - Interface in org.molgenis.omx.auth

Contact: A contact is either a person or an organization.

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

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

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

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

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.InstituteJpaMapper

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(MolgenisPermission) - Method in class org.molgenis.omx.auth.db.MolgenisPermissionJpaMapper

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.MolgenisPermissionJpaMapper

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

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.MolgenisRoleGroupLinkJpaMapper

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

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.MolgenisRoleJpaMapper

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(Person) - Method in class org.molgenis.omx.auth.db.PersonJpaMapper

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.PersonJpaMapper

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

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.PersonRoleJpaMapper

create(Tuple) - Method in class org.molgenis.omx.auth.Institute

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

create(Tuple) - Method in class org.molgenis.omx.auth.MolgenisPermission

create(Tuple) - Method in class org.molgenis.omx.auth.MolgenisRole

create(Tuple) - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

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

create(Tuple) - Method in class org.molgenis.omx.auth.Person

create(Tuple) - Method in class org.molgenis.omx.auth.PersonRole

create(Accession) - Method in class org.molgenis.service.AccessionService

create(BoolValue) - Method in class org.molgenis.service.BoolValueService

create(CategoricalValue) - Method in class org.molgenis.service.CategoricalValueService

create(Category) - Method in class org.molgenis.service.CategoryService

create(Characteristic) - Method in class org.molgenis.service.CharacteristicService

create(DataSet) - Method in class org.molgenis.service.DataSetService

create(DateTimeValue) - Method in class org.molgenis.service.DateTimeValueService

create(DateValue) - Method in class org.molgenis.service.DateValueService

create(DecimalValue) - Method in class org.molgenis.service.DecimalValueService

create(EmailValue) - Method in class org.molgenis.service.EmailValueService

create(HtmlValue) - Method in class org.molgenis.service.HtmlValueService

create(HyperlinkValue) - Method in class org.molgenis.service.HyperlinkValueService

create(Individual) - Method in class org.molgenis.service.IndividualService

create(Institute) - Method in class org.molgenis.service.InstituteService

create(IntValue) - Method in class org.molgenis.service.IntValueService

create(LongValue) - Method in class org.molgenis.service.LongValueService

create(MolgenisFile) - Method in class org.molgenis.service.MolgenisFileService

create(MrefValue) - Method in class org.molgenis.service.MrefValueService

create(ObservableFeature) - Method in class org.molgenis.service.ObservableFeatureService

create(ObservationSet) - Method in class org.molgenis.service.ObservationSetService

create(ObservationTarget) - Method in class org.molgenis.service.ObservationTargetService

create(ObservedValue) - Method in class org.molgenis.service.ObservedValueService

create(Ontology) - Method in class org.molgenis.service.OntologyService

create(OntologyTerm) - Method in class org.molgenis.service.OntologyTermService

create(Panel) - Method in class org.molgenis.service.PanelService

create(PanelSource) - Method in class org.molgenis.service.PanelSourceService

create(PersonRole) - Method in class org.molgenis.service.PersonRoleService

create(Person) - Method in class org.molgenis.service.PersonService

create(Protocol) - Method in class org.molgenis.service.ProtocolService

create(RuntimeProperty) - Method in class org.molgenis.service.RuntimePropertyService

create(Species) - Method in class org.molgenis.service.SpeciesService

create(StringValue) - Method in class org.molgenis.service.StringValueService

create(TextValue) - Method in class org.molgenis.service.TextValueService

create(Value) - Method in class org.molgenis.service.ValueService

create(XrefValue) - Method in class org.molgenis.service.XrefValueService

createCaptcha(int, int) - Method in class org.molgenis.omx.auth.service.CaptchaService

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

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

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

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

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

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

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

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

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

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.MolgenisPermissionJpaMapper

Return EMPTY list of given allocated size

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

Return EMPTY list of given allocated size

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

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.PersonJpaMapper

Return EMPTY list of given allocated size

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

Return EMPTY list of given allocated size

createUser(MolgenisUser, URI) - Method in class org.molgenis.omx.auth.service.AccountService

D

DatabaseLogin - Class in org.molgenis.omx.auth

DatabaseLogin(TokenFactory) - Constructor for class org.molgenis.omx.auth.DatabaseLogin

DatabaseLogin(Database, TokenFactory) - Constructor for class org.molgenis.omx.auth.DatabaseLogin

Constructor used to login anonymous

DatabaseLogin(Database, String, TokenFactory) - Constructor for class org.molgenis.omx.auth.DatabaseLogin

DataSetService - Class in org.molgenis.service

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

DateTimeValueService - Class in org.molgenis.service

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

DateValueService - Class in org.molgenis.service

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

DecimalValueService - Class in org.molgenis.service

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

destroy(Institute) - Method in class org.molgenis.omx.auth.db.InstituteJpaMapper

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

destroy(MolgenisPermission) - Method in class org.molgenis.omx.auth.db.MolgenisPermissionJpaMapper

destroy(MolgenisRoleGroupLink) - Method in class org.molgenis.omx.auth.db.MolgenisRoleGroupLinkJpaMapper

destroy(MolgenisRole) - Method in class org.molgenis.omx.auth.db.MolgenisRoleJpaMapper

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

destroy(Person) - Method in class org.molgenis.omx.auth.db.PersonJpaMapper

destroy(PersonRole) - Method in class org.molgenis.omx.auth.db.PersonRoleJpaMapper

E

edit(Institute) - Method in class org.molgenis.omx.auth.db.InstituteJpaMapper

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

edit(MolgenisPermission) - Method in class org.molgenis.omx.auth.db.MolgenisPermissionJpaMapper

edit(MolgenisRoleGroupLink) - Method in class org.molgenis.omx.auth.db.MolgenisRoleGroupLinkJpaMapper

edit(MolgenisRole) - Method in class org.molgenis.omx.auth.db.MolgenisRoleJpaMapper

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

edit(Person) - Method in class org.molgenis.omx.auth.db.PersonJpaMapper

edit(PersonRole) - Method in class org.molgenis.omx.auth.db.PersonRoleJpaMapper

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

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

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

EmailValueService - Class in org.molgenis.service

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

ENTITY - Static variable in class org.molgenis.omx.auth.MolgenisPermission

ENTITY_CLASSNAME - Static variable in class org.molgenis.omx.auth.MolgenisPermission

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

F

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

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

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

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

Shorthand for db.find(Institute.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.MolgenisPermission

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

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

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

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

Shorthand for db.find(MolgenisRoleGroupLink.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.Person

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

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

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

find(MolgenisUserSearchCriteriaVO) - Method in class org.molgenis.omx.auth.service.MolgenisUserService

findAdminEmail() - Method in class org.molgenis.omx.auth.service.MolgenisUserService

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

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

findByGroupRole(Database, Integer, Integer) - Static method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

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

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

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

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

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

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

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

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

findById(Integer) - Method in class org.molgenis.omx.auth.service.MolgenisUserService

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.auth.Institute

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.auth.MolgenisGroup

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.auth.MolgenisPermission

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.auth.MolgenisRole

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

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

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.auth.Person

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.auth.PersonRole

findByName(Database, String) - Static method in class org.molgenis.omx.auth.Institute

findByName(Database, String) - Static method in class org.molgenis.omx.auth.MolgenisGroup

findByName(Database, String) - Static method in class org.molgenis.omx.auth.MolgenisRole

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

findByOntologyTermAccession(Database, Integer, String) - Static method in class org.molgenis.omx.auth.PersonRole

findByRoleEntityPermission(Database, Integer, Integer, String) - Static method in class org.molgenis.omx.auth.MolgenisPermission

findGroupIds(MolgenisRole) - Method in class org.molgenis.omx.auth.service.MolgenisUserService

Get a list of group ids for the groups a user is member of

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

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

G

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

Generic getter.

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

Generic getter.

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

Generic getter.

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

Generic getter.

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

Generic getter.

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

Generic getter.

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

Generic getter.

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

Generic getter.

get__Type() - Method in class org.molgenis.omx.auth.MolgenisRole

Get the Subtypes have to be set to allow searching.

get__Type(Database) - Method in class org.molgenis.omx.auth.MolgenisRole

Deprecated.

get__TypeLabel() - Method in class org.molgenis.omx.auth.MolgenisRole

Get tha label for enum __Type.

get__TypeOptions() - Method in class org.molgenis.omx.auth.MolgenisRole

__Type is enum.

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.

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

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 interface org.molgenis.omx.auth.Contact

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

Get the The address of the Contact..

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

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.

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

Get the The address of the Contact..

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

Deprecated.

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

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

Get the Affiliation.

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

Deprecated.

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

Get the Affiliation.

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

Deprecated.

getAffiliation() - Method in interface org.molgenis.omx.auth.PersonContact

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

getAffiliation_Id() - Method in class org.molgenis.omx.auth.Person

getAffiliation_Id() - Method in interface org.molgenis.omx.auth.PersonContact

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

Get a pretty label Name for cross reference Affiliation to Institute.Id.

getAffiliation_Name() - Method in class org.molgenis.omx.auth.Person

Get a pretty label Name for cross reference Affiliation to Institute.Id.

getAffiliation_Name() - Method in interface org.molgenis.omx.auth.PersonContact

getCanRead() - Method in interface org.molgenis.omx.auth.Authorizable

getCanRead_Id() - Method in interface org.molgenis.omx.auth.Authorizable

getCanRead_Name() - Method in interface org.molgenis.omx.auth.Authorizable

getCanWrite() - Method in interface org.molgenis.omx.auth.Authorizable

getCanWrite_Id() - Method in interface org.molgenis.omx.auth.Authorizable

getCanWrite_Name() - Method in interface org.molgenis.omx.auth.Authorizable

getCaptcha() - Method in class org.molgenis.omx.auth.controller.CaptchaController

getCaptcha() - Method in class org.molgenis.omx.auth.vo.CaptchaRequest

getCity() - Method in interface org.molgenis.omx.auth.Contact

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

Get the Added from the old definition of MolgenisUser.

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

Deprecated.

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.

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

Get the Added from the old definition of MolgenisUser.

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

Deprecated.

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

getConfirmPassword() - Method in class org.molgenis.omx.auth.vo.RegisterRequest

getCountry() - Method in interface org.molgenis.omx.auth.Contact

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

Get the Added from the old definition of MolgenisUser.

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

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.

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

Get the Added from the old definition of MolgenisUser.

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

Deprecated.

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

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.

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

Get the Added from the old definition of MolgenisUser.

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

Deprecated.

getDepartment() - Method in interface org.molgenis.omx.auth.PersonContact

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

getEmail() - Method in interface org.molgenis.omx.auth.Contact

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

Get the The email address of the Contact..

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

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.

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

Get the The email address of the Contact..

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

Deprecated.

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

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

getEntity() - Method in class org.molgenis.omx.auth.MolgenisPermission

Get the entity.

getEntity(Database) - Method in class org.molgenis.omx.auth.MolgenisPermission

Deprecated.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

getEntity_ClassName() - Method in class org.molgenis.omx.auth.MolgenisPermission

Get a pretty label className for cross reference Entity to MolgenisEntity.Id.

getEntity_Id() - Method in class org.molgenis.omx.auth.MolgenisPermission

getFax() - Method in interface org.molgenis.omx.auth.Contact

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

Get the The fax number of the Contact..

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

Deprecated.

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.

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

Get the The fax number of the Contact..

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

Deprecated.

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

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

Get the names of all public properties of Institute.

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

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

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.MolgenisPermission

Get the names of all public properties of MolgenisPermission.

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

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

Deprecated.

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

Get the names of all public properties of MolgenisRole.

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

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

Deprecated.

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

Get the names of all public properties of MolgenisRoleGroupLink.

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

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

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.Person

Get the names of all public properties of Person.

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

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

Deprecated.

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

Get the names of all public properties of PersonRole.

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

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

Deprecated.

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

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

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

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

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

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

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

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

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

Get the First Name.

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

Deprecated.

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

Get the First Name.

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

Deprecated.

getFirstName() - Method in interface org.molgenis.omx.auth.PersonContact

getFirstname() - Method in class org.molgenis.omx.auth.vo.RegisterRequest

getFullUserName() - Method in class org.molgenis.omx.auth.DatabaseLogin

getGroup() - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

Get the group_.

getGroup(Database) - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

Deprecated.

getGroup_Id() - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

getGroup_Name() - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

Get a pretty label Name for cross reference Group to MolgenisGroup.Id.

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

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

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

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

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

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

getIdentifier() - Method in class org.molgenis.omx.auth.MolgenisPermission

Get the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.

getIdentifier(Database) - Method in class org.molgenis.omx.auth.MolgenisPermission

Deprecated.

getIdentifier() - Method in class org.molgenis.omx.auth.MolgenisRole

Get the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.

getIdentifier(Database) - Method in class org.molgenis.omx.auth.MolgenisRole

Deprecated.

getIdentifier() - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

Get the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.

getIdentifier(Database) - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

Deprecated.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

getInstance(Database) - Static method in class org.molgenis.omx.auth.service.MolgenisUserService

Get an instance of MolgenisUserService

getInstitute() - Method in class org.molgenis.omx.auth.vo.RegisterRequest

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

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

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

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

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

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

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

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

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

Get the Last Name.

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

Deprecated.

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

Get the Last Name.

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

Deprecated.

getLastName() - Method in interface org.molgenis.omx.auth.PersonContact

getLastname() - Method in class org.molgenis.omx.auth.vo.RegisterRequest

getLoginForm() - Method in class org.molgenis.omx.auth.controller.AccountController

getMessage() - Method in exception org.molgenis.omx.auth.service.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.

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

Get the Mid Initials.

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

Deprecated.

getMidInitials() - Method in interface org.molgenis.omx.auth.PersonContact

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

Get the Name.

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

Deprecated.

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

Get the human readible name, not necessary unique..

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

Deprecated.

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

Get the Name.

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

Deprecated.

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

Get the human readible name, not necessary unique..

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

Deprecated.

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

getOwns() - Method in interface org.molgenis.omx.auth.Authorizable

getOwns_Id() - Method in interface org.molgenis.omx.auth.Authorizable

getOwns_Name() - Method in interface org.molgenis.omx.auth.Authorizable

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.

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

getPasswordResetForm() - Method in class org.molgenis.omx.auth.controller.AccountController

getPermission() - Method in class org.molgenis.omx.auth.MolgenisPermission

Get the permission.

getPermission(Database) - Method in class org.molgenis.omx.auth.MolgenisPermission

Deprecated.

getPermissionLabel() - Method in class org.molgenis.omx.auth.MolgenisPermission

Get tha label for enum Permission.

getPermissionOptions() - Method in class org.molgenis.omx.auth.MolgenisPermission

Permission is enum.

getPhone() - Method in interface org.molgenis.omx.auth.Contact

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

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

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

Deprecated.

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.

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

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

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

Deprecated.

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

getPosition() - Method in class org.molgenis.omx.auth.vo.RegisterRequest

getRedirect() - Method in class org.molgenis.omx.auth.DatabaseLogin

getRegisterForm() - Method in class org.molgenis.omx.auth.controller.AccountController

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

Get the role_.

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

Deprecated.

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

Get the role_.

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

Deprecated.

getRole_Id() - Method in class org.molgenis.omx.auth.MolgenisPermission

getRole_Id() - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

getRole_Name() - Method in class org.molgenis.omx.auth.MolgenisPermission

Get a pretty label Name for cross reference Role to MolgenisRole.Id.

getRole_Name() - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

Get a pretty label Name for cross reference Role to MolgenisRole.Id.

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

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

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

Deprecated.

getRoles() - Method in class org.molgenis.omx.auth.Person

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

getRoles(Database) - Method in class org.molgenis.omx.auth.Person

Deprecated.

getRoles() - Method in interface org.molgenis.omx.auth.PersonContact

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

getRoles_Id() - Method in class org.molgenis.omx.auth.Person

getRoles_Id() - Method in interface org.molgenis.omx.auth.PersonContact

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

Get a pretty label Identifier for cross reference Roles to PersonRole.Id.

getRoles_Identifier() - Method in class org.molgenis.omx.auth.Person

Get a pretty label Identifier for cross reference Roles to PersonRole.Id.

getRoles_Identifier() - Method in interface org.molgenis.omx.auth.PersonContact

getRowlevelSecurityFilters(Class<? extends Entity>) - Method in class org.molgenis.omx.auth.DatabaseLogin

Deprecated.

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.InstituteJpaMapper

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

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

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

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

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

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

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

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.

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

Get the An academic title, e.g.

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

Deprecated.

getTitle() - Method in interface org.molgenis.omx.auth.PersonContact

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

getTollFreePhone() - Method in interface org.molgenis.omx.auth.Contact

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

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

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

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.

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

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

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

Deprecated.

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

getUserId() - Method in class org.molgenis.omx.auth.DatabaseLogin

getUserName() - Method in class org.molgenis.omx.auth.DatabaseLogin

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

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

Deprecated.

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

Deprecated.

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

Deprecated.

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

Deprecated.

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

Deprecated.

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

Deprecated.

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

Deprecated.

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

Deprecated.

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

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

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

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

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

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

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

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

GROUP_ - Static variable in class org.molgenis.omx.auth.MolgenisRoleGroupLink

GROUP__NAME - Static variable in class org.molgenis.omx.auth.MolgenisRoleGroupLink

H

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

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

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

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

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

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

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

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

hasPermissionOnEntity(String, MolgenisPermissionService.Permission) - Method in class org.molgenis.omx.auth.OmxPermissionService

hasPermissionOnEntity(Class<? extends Entity>, MolgenisPermissionService.Permission) - Method in class org.molgenis.omx.auth.OmxPermissionService

hasPermissionOnPlugin(String, MolgenisPermissionService.Permission) - Method in class org.molgenis.omx.auth.OmxPermissionService

hasPermissionOnPlugin(Class<? extends MolgenisPlugin>, MolgenisPermissionService.Permission) - Method in class org.molgenis.omx.auth.OmxPermissionService

HtmlValueService - Class in org.molgenis.service

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

HyperlinkValueService - Class in org.molgenis.service

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

I

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

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

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

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

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

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

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

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

IDENTIFIER - Static variable in class org.molgenis.omx.auth.MolgenisPermission

IDENTIFIER - Static variable in class org.molgenis.omx.auth.MolgenisRole

IDENTIFIER - Static variable in class org.molgenis.omx.auth.MolgenisRoleGroupLink

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.auth.db.InstituteEntityImporter

Imports Institute from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.auth.db.MolgenisGroupEntityImporter

Imports MolgenisGroup from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.auth.db.MolgenisPermissionEntityImporter

Imports MolgenisPermission from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.auth.db.MolgenisRoleEntityImporter

Imports MolgenisRole from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.auth.db.MolgenisRoleGroupLinkEntityImporter

Imports MolgenisRoleGroupLink from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.auth.db.MolgenisUserEntityImporter

Imports MolgenisUser from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.auth.db.PersonEntityImporter

Imports Person from tab/comma delimited File

importEntity(TupleReader, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.auth.db.PersonRoleEntityImporter

Imports PersonRole from tab/comma delimited File

IndividualService - Class in org.molgenis.service

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

insert(MolgenisUser) - Method in class org.molgenis.omx.auth.service.MolgenisUserService

Institute - Class in org.molgenis.omx.auth

Institute: A contact is either a person or an organization.

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

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

copy constructor

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

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

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

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

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

InstituteService - Class in org.molgenis.service

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

IntValueService - Class in org.molgenis.service

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

isAuthenticated() - Method in class org.molgenis.omx.auth.DatabaseLogin

Note: Anonymous is automatically logged in but does not count as being authenticated

isLoginRequired() - Method in class org.molgenis.omx.auth.DatabaseLogin

K

KEY_PLUGIN_AUTH_ACTIVATIONMODE - Static variable in class org.molgenis.omx.auth.service.AccountService

L

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

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

login(Database, String, String) - Method in class org.molgenis.omx.auth.DatabaseLogin

loginUser(String, String) - Method in class org.molgenis.omx.auth.controller.AccountController

logout(Database) - Method in class org.molgenis.omx.auth.DatabaseLogin

logoutUser() - Method in class org.molgenis.omx.auth.controller.AccountController

LongValueService - Class in org.molgenis.service

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

M

main(String[]) - Static method in class org.molgenis.omx.auth.AuthtestGenerate

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

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

MolgenisFileService - Class in org.molgenis.service

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

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

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

MolgenisPermission - Class in org.molgenis.omx.auth

MolgenisPermission: .

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

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

copy constructor

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

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

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

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

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

MolgenisRole - Class in org.molgenis.omx.auth

MolgenisRole: .

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

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

copy constructor

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

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

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

MolgenisRoleGroupLink - Class in org.molgenis.omx.auth

MolgenisRoleGroupLink: .

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

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

copy constructor

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

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

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

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

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

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

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

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

MolgenisUserDecorator<E extends MolgenisUser> - Class in org.molgenis.omx.auth.decorators

MolgenisUserDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.auth.decorators.MolgenisUserDecorator

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.omx.auth.service

MolgenisUserException(String) - Constructor for exception org.molgenis.omx.auth.service.MolgenisUserException

MolgenisUserException(Exception) - Constructor for exception org.molgenis.omx.auth.service.MolgenisUserException

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

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

MolgenisUserSearchCriteriaVO - Class in org.molgenis.omx.auth.vo

MolgenisUserSearchCriteriaVO() - Constructor for class org.molgenis.omx.auth.vo.MolgenisUserSearchCriteriaVO

MolgenisUserService - Class in org.molgenis.omx.auth.service

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

MolgenisUserService(Database) - Constructor for class org.molgenis.omx.auth.service.MolgenisUserService

MrefValueService - Class in org.molgenis.service

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

N

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

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

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

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

O

ObservableFeatureService - Class in org.molgenis.service

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

ObservationSetService - Class in org.molgenis.service

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

ObservationTargetService - Class in org.molgenis.service

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

ObservedValueService - Class in org.molgenis.service

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

OmxPermissionService - Class in org.molgenis.omx.auth

Permission service based on the OMX model

OmxPermissionService(Database, Login) - Constructor for class org.molgenis.omx.auth.OmxPermissionService

OntologyService - Class in org.molgenis.service

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

OntologyTermService - Class in org.molgenis.service

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

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

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

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

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

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

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

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

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

owns(Class<? extends Entity>) - Method in class org.molgenis.omx.auth.DatabaseLogin

owns(Entity) - Method in class org.molgenis.omx.auth.DatabaseLogin

P

PanelService - Class in org.molgenis.service

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

PanelSourceService - Class in org.molgenis.service

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

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

PasswordHasher - Class in org.molgenis.omx.auth.util

PasswordHasher() - Constructor for class org.molgenis.omx.auth.util.PasswordHasher

PasswordResetRequest - Class in org.molgenis.omx.auth.vo

PasswordResetRequest() - Constructor for class org.molgenis.omx.auth.vo.PasswordResetRequest

PERMISSION - Static variable in class org.molgenis.omx.auth.MolgenisPermission

Person - Class in org.molgenis.omx.auth

Person: Person represents one or more people involved with an Investigation.

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

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

copy constructor

PersonContact - Interface in org.molgenis.omx.auth

PersonContact: .

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

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

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

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

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

PersonRole - Class in org.molgenis.omx.auth

PersonRole: Seperate type of ontologyTerm to administrate roles..

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

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

copy constructor

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

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

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

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

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

PersonRoleService - Class in org.molgenis.service

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

PersonService - Class in org.molgenis.service

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

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

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

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

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

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

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

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

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

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

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

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

ProtocolService - Class in org.molgenis.service

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

Q

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

Shorthand for db.query(Institute.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.MolgenisPermission

Shorthand for db.query(MolgenisPermission.class).

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

Shorthand for db.query(MolgenisRole.class).

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

Shorthand for db.query(MolgenisRoleGroupLink.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.Person

Shorthand for db.query(Person.class).

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

Shorthand for db.query(PersonRole.class).

R

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

redirect - Variable in class org.molgenis.omx.auth.DatabaseLogin

RegisterRequest - Class in org.molgenis.omx.auth.vo

RegisterRequest() - Constructor for class org.molgenis.omx.auth.vo.RegisterRequest

registerUser(RegisterRequest, CaptchaRequest) - Method in class org.molgenis.omx.auth.controller.AccountController

reload(Database) - Method in class org.molgenis.omx.auth.DatabaseLogin

Reloads all permission settings for this user from database.

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

resetPassword(PasswordResetRequest) - Method in class org.molgenis.omx.auth.controller.AccountController

resetPassword(MolgenisUser) - Method in class org.molgenis.omx.auth.service.AccountService

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

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

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

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

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

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

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

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

ROLE_ - Static variable in class org.molgenis.omx.auth.MolgenisPermission

ROLE_ - Static variable in class org.molgenis.omx.auth.MolgenisRoleGroupLink

ROLE__NAME - Static variable in class org.molgenis.omx.auth.MolgenisPermission

ROLE__NAME - Static variable in class org.molgenis.omx.auth.MolgenisRoleGroupLink

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

ROLES - Static variable in class org.molgenis.omx.auth.Person

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

ROLES_IDENTIFIER - Static variable in class org.molgenis.omx.auth.Person

RuntimePropertyService - Class in org.molgenis.service

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

S

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

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

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

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

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

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

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

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

set(Tuple, boolean) - Method in class org.molgenis.omx.auth.Institute

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

set(Tuple, boolean) - Method in class org.molgenis.omx.auth.MolgenisPermission

set(Tuple, boolean) - Method in class org.molgenis.omx.auth.MolgenisRole

set(Tuple, boolean) - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

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

set(Tuple, boolean) - Method in class org.molgenis.omx.auth.Person

set(Tuple, boolean) - Method in class org.molgenis.omx.auth.PersonRole

set__Type(String) - Method in class org.molgenis.omx.auth.MolgenisRole

Set the Subtypes have to be set to allow searching.

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..

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

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 interface org.molgenis.omx.auth.Contact

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

Set the The address of the Contact..

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

Set the The address of the Contact..

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

Set the The address of the Contact..

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

setAdmin(List<? extends Entity>, Database) - Method in class org.molgenis.omx.auth.DatabaseLogin

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

Set the Affiliation.

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

setAffiliation(Institute) - Method in class org.molgenis.omx.auth.Person

Set the Affiliation.

setAffiliation(Integer) - Method in class org.molgenis.omx.auth.Person

setAffiliation(Institute) - Method in interface org.molgenis.omx.auth.PersonContact

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

Set foreign key for field affiliation.

setAffiliation_Id(Integer) - Method in class org.molgenis.omx.auth.Person

Set foreign key for field affiliation.

setAffiliation_Id(Integer) - Method in interface org.molgenis.omx.auth.PersonContact

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

Set a pretty label for cross reference Affiliation to Institute.Id.

setAffiliation_Name(String) - Method in class org.molgenis.omx.auth.Person

Set a pretty label for cross reference Affiliation to Institute.Id.

setAffiliation_Name(String) - Method in interface org.molgenis.omx.auth.PersonContact

setCanRead(MolgenisRole) - Method in interface org.molgenis.omx.auth.Authorizable

setCanRead_Id(Integer) - Method in interface org.molgenis.omx.auth.Authorizable

setCanRead_Name(String) - Method in interface org.molgenis.omx.auth.Authorizable

setCanWrite(MolgenisRole) - Method in interface org.molgenis.omx.auth.Authorizable

setCanWrite_Id(Integer) - Method in interface org.molgenis.omx.auth.Authorizable

setCanWrite_Name(String) - Method in interface org.molgenis.omx.auth.Authorizable

setCaptcha(String) - Method in class org.molgenis.omx.auth.vo.CaptchaRequest

setCity(String) - Method in interface org.molgenis.omx.auth.Contact

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

Set the Added from the old definition of MolgenisUser.

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

Set the Added from the old definition of MolgenisUser.

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

Set the Added from the old definition of MolgenisUser.

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

setConfirmPassword(String) - Method in class org.molgenis.omx.auth.vo.RegisterRequest

setCountry(String) - Method in interface org.molgenis.omx.auth.Contact

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

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.

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

Set the Added from the old definition of MolgenisUser.

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

setDatabase(Database) - Method in class org.molgenis.omx.auth.service.MolgenisUserService

setDepartment(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.Person

Set the Added from the old definition of MolgenisUser.

setDepartment(String) - Method in interface org.molgenis.omx.auth.PersonContact

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

setEmail(String) - Method in interface org.molgenis.omx.auth.Contact

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

Set the The email address of the Contact..

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

Set the The email address of the Contact..

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

Set the The email address of the Contact..

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

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

setEntity(MolgenisEntity) - Method in class org.molgenis.omx.auth.MolgenisPermission

Set the entity.

setEntity(Integer) - Method in class org.molgenis.omx.auth.MolgenisPermission

setEntity_ClassName(String) - Method in class org.molgenis.omx.auth.MolgenisPermission

Set a pretty label for cross reference Entity to MolgenisEntity.Id.

setEntity_Id(Integer) - Method in class org.molgenis.omx.auth.MolgenisPermission

Set foreign key for field entity.

setFax(String) - Method in interface org.molgenis.omx.auth.Contact

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

Set the The fax number of the Contact..

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

Set the The fax number of the Contact..

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

Set the The fax number of the Contact..

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

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

Set the First Name.

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

Set the First Name.

setFirstName(String) - Method in interface org.molgenis.omx.auth.PersonContact

setFirstname(String) - Method in class org.molgenis.omx.auth.vo.RegisterRequest

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

Set the group_.

setGroup(Integer) - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

setGroup_Id(Integer) - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

Set foreign key for field group_.

setGroup_Name(String) - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

Set a pretty label for cross reference Group to MolgenisGroup.Id.

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

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

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

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

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

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

setIdentifier(String) - Method in class org.molgenis.omx.auth.MolgenisPermission

Set the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.

setIdentifier(String) - Method in class org.molgenis.omx.auth.MolgenisRole

Set the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.

setIdentifier(String) - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

Set the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.

setInstitute(Integer) - Method in class org.molgenis.omx.auth.vo.RegisterRequest

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

Set the Last Name.

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

Set the Last Name.

setLastName(String) - Method in interface org.molgenis.omx.auth.PersonContact

setLastname(String) - Method in class org.molgenis.omx.auth.vo.RegisterRequest

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

Set the Mid Initials.

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

Set the Mid Initials.

setMidInitials(String) - Method in interface org.molgenis.omx.auth.PersonContact

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

Set the Name.

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

Set the human readible name, not necessary unique..

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

Set the Name.

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

Set the human readible name, not necessary unique..

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

setOwns(MolgenisRole) - Method in interface org.molgenis.omx.auth.Authorizable

setOwns_Id(Integer) - Method in interface org.molgenis.omx.auth.Authorizable

setOwns_Name(String) - Method in interface org.molgenis.omx.auth.Authorizable

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

Set the big fixme: password type.

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

setPermission(String) - Method in class org.molgenis.omx.auth.MolgenisPermission

Set the permission.

setPermissionOnEntity(String, Integer, MolgenisPermissionService.Permission) - Method in class org.molgenis.omx.auth.OmxPermissionService

setPermissionOnEntity(Class<? extends Entity>, Integer, MolgenisPermissionService.Permission) - Method in class org.molgenis.omx.auth.OmxPermissionService

setPermissionOnPlugin(String, Integer, MolgenisPermissionService.Permission) - Method in class org.molgenis.omx.auth.OmxPermissionService

setPermissionOnPlugin(Class<? extends MolgenisPlugin>, Integer, MolgenisPermissionService.Permission) - Method in class org.molgenis.omx.auth.OmxPermissionService

setPhone(String) - Method in interface org.molgenis.omx.auth.Contact

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

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

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

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

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

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

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

setPosition(Integer) - Method in class org.molgenis.omx.auth.vo.RegisterRequest

setRedirect(String) - Method in class org.molgenis.omx.auth.DatabaseLogin

setRole(MolgenisRole) - Method in class org.molgenis.omx.auth.MolgenisPermission

Set the role_.

setRole(Integer) - Method in class org.molgenis.omx.auth.MolgenisPermission

setRole(MolgenisRole) - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

Set the role_.

setRole(Integer) - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

setRole_Id(Integer) - Method in class org.molgenis.omx.auth.MolgenisPermission

Set foreign key for field role_.

setRole_Id(Integer) - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

Set foreign key for field role_.

setRole_Name(String) - Method in class org.molgenis.omx.auth.MolgenisPermission

Set a pretty label for cross reference Role to MolgenisRole.Id.

setRole_Name(String) - Method in class org.molgenis.omx.auth.MolgenisRoleGroupLink

Set a pretty label for cross reference Role to MolgenisRole.Id.

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

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

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

setRoles(PersonRole) - Method in class org.molgenis.omx.auth.Person

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

setRoles(Integer) - Method in class org.molgenis.omx.auth.Person

setRoles(PersonRole) - Method in interface org.molgenis.omx.auth.PersonContact

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

Set foreign key for field roles.

setRoles_Id(Integer) - Method in class org.molgenis.omx.auth.Person

Set foreign key for field roles.

setRoles_Id(Integer) - Method in interface org.molgenis.omx.auth.PersonContact

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

Set a pretty label for cross reference Roles to PersonRole.Id.

setRoles_Identifier(String) - Method in class org.molgenis.omx.auth.Person

Set a pretty label for cross reference Roles to PersonRole.Id.

setRoles_Identifier(String) - Method in interface org.molgenis.omx.auth.PersonContact

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.

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

Set the An academic title, e.g.

setTitle(String) - Method in interface org.molgenis.omx.auth.PersonContact

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

setTollFreePhone(String) - Method in interface org.molgenis.omx.auth.Contact

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

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

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

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

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

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

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

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

showAccount(Model) - Method in class org.molgenis.omx.auth.controller.UserAccountController

SpeciesService - Class in org.molgenis.service

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

StringValueService - Class in org.molgenis.service

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

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

T

TextValueService - Class in org.molgenis.service

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

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

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

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

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

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

toMD5(String) - Method in class org.molgenis.omx.auth.util.PasswordHasher

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

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

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

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.MolgenisPermission

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

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

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

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

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

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.Person

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

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

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

U

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

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

update(Accession) - Method in class org.molgenis.service.AccessionService

update(BoolValue) - Method in class org.molgenis.service.BoolValueService

update(CategoricalValue) - Method in class org.molgenis.service.CategoricalValueService

update(Category) - Method in class org.molgenis.service.CategoryService

update(Characteristic) - Method in class org.molgenis.service.CharacteristicService

update(DataSet) - Method in class org.molgenis.service.DataSetService

update(DateTimeValue) - Method in class org.molgenis.service.DateTimeValueService

update(DateValue) - Method in class org.molgenis.service.DateValueService

update(DecimalValue) - Method in class org.molgenis.service.DecimalValueService

update(EmailValue) - Method in class org.molgenis.service.EmailValueService

update(HtmlValue) - Method in class org.molgenis.service.HtmlValueService

update(HyperlinkValue) - Method in class org.molgenis.service.HyperlinkValueService

update(Individual) - Method in class org.molgenis.service.IndividualService

update(Institute) - Method in class org.molgenis.service.InstituteService

update(IntValue) - Method in class org.molgenis.service.IntValueService

update(LongValue) - Method in class org.molgenis.service.LongValueService

update(MolgenisFile) - Method in class org.molgenis.service.MolgenisFileService

update(MrefValue) - Method in class org.molgenis.service.MrefValueService

update(ObservableFeature) - Method in class org.molgenis.service.ObservableFeatureService

update(ObservationSet) - Method in class org.molgenis.service.ObservationSetService

update(ObservationTarget) - Method in class org.molgenis.service.ObservationTargetService

update(ObservedValue) - Method in class org.molgenis.service.ObservedValueService

update(Ontology) - Method in class org.molgenis.service.OntologyService

update(OntologyTerm) - Method in class org.molgenis.service.OntologyTermService

update(Panel) - Method in class org.molgenis.service.PanelService

update(PanelSource) - Method in class org.molgenis.service.PanelSourceService

update(PersonRole) - Method in class org.molgenis.service.PersonRoleService

update(Person) - Method in class org.molgenis.service.PersonService

update(Protocol) - Method in class org.molgenis.service.ProtocolService

update(RuntimeProperty) - Method in class org.molgenis.service.RuntimePropertyService

update(Species) - Method in class org.molgenis.service.SpeciesService

update(StringValue) - Method in class org.molgenis.service.StringValueService

update(TextValue) - Method in class org.molgenis.service.TextValueService

update(Value) - Method in class org.molgenis.service.ValueService

update(XrefValue) - Method in class org.molgenis.service.XrefValueService

updateAccount(HttpServletRequest) - Method in class org.molgenis.omx.auth.controller.UserAccountController

URI - Static variable in class org.molgenis.omx.auth.controller.UserAccountController

UserAccountController - Class in org.molgenis.omx.auth.controller

UserAccountController() - Constructor for class org.molgenis.omx.auth.controller.UserAccountController

V

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

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

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

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

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

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

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

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

validateCaptcha(CaptchaRequest) - Method in class org.molgenis.omx.auth.controller.CaptchaController

validateCaptcha(String) - Method in class org.molgenis.omx.auth.service.CaptchaService

validateCaptchaFromForm(CaptchaRequest) - Method in class org.molgenis.omx.auth.controller.CaptchaController

ValueService - Class in org.molgenis.service

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

X

XrefValueService - Class in org.molgenis.service

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

_

__TYPE - Static variable in class org.molgenis.omx.auth.MolgenisRole

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