Uses of Interface
ubic.gemma.core.security.model.Securable

Packages that use Securable

Package	Description
ubic.gemma.core.security	Gsec is an attempt to generalise the security framework of Gemma to make it usable in other projects such as ASPIREdb.
ubic.gemma.core.security.acl
ubic.gemma.core.security.acl.domain
ubic.gemma.core.security.authorization.acl
ubic.gemma.core.security.model
ubic.gemma.model.analysis
ubic.gemma.model.analysis.expression
ubic.gemma.model.analysis.expression.coexpression
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.analysis.expression.pca
ubic.gemma.model.common.auditAndSecurity
ubic.gemma.model.common.auditAndSecurity.curation
ubic.gemma.model.common.description
ubic.gemma.model.common.protocol
ubic.gemma.model.expression.arrayDesign
ubic.gemma.model.expression.bioAssay
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.biomaterial
ubic.gemma.model.expression.experiment
ubic.gemma.model.genome.gene
ubic.gemma.model.pipeline
ubic.gemma.rest

Uses of Securable in ubic.gemma.core.security

Methods in ubic.gemma.core.security with type parameters of type Securable

Modifier and Type	Method	Description
<T extends Securable> Map<T,Boolean>	SecurityService.arePrivate(Collection<T> securables)	Check if the given securables are private.
<T extends Securable> Map<T,Boolean>	SecurityServiceImpl.arePrivate(Collection<T> securables)
<T extends Securable> Map<T,Boolean>	SecurityService.arePublic(Collection<T> securables)	Check if the given securables are public.
<T extends Securable> Map<T,Boolean>	SecurityServiceImpl.arePublic(Collection<T> securables)
<T extends Securable> Map<T,Boolean>	SecurityService.areShared(Collection<T> securables)	Check if the given securable are shared.
<T extends Securable> Map<T,Boolean>	SecurityServiceImpl.areShared(Collection<T> securables)
<T extends Securable> Collection<T>	SecurityService.choosePrivate(Collection<T> securables)	Pick private securables.
<T extends Securable> Collection<T>	SecurityServiceImpl.choosePrivate(Collection<T> securables)
<T extends Securable> Collection<T>	SecurityService.choosePublic(Collection<T> securables)	Pick public securables.
<T extends Securable> Collection<T>	SecurityServiceImpl.choosePublic(Collection<T> securables)
<T extends Securable> Map<T, Collection<String>>	SecurityService.getGroupsEditableBy(Collection<T> securables)
<T extends Securable> Map<T, Collection<String>>	SecurityServiceImpl.getGroupsEditableBy(Collection<T> securables)
<T extends Securable> Map<T, Collection<String>>	SecurityService.getGroupsReadableBy(Collection<T> securables)
<T extends Securable> Map<T, Collection<String>>	SecurityServiceImpl.getGroupsReadableBy(Collection<T> securables)
<T extends Securable> Map<T, org.springframework.security.acls.model.Sid>	SecurityService.getOwners(Collection<T> securables)	Obtain the owners of a collection of objects.
<T extends Securable> Map<T, org.springframework.security.acls.model.Sid>	SecurityServiceImpl.getOwners(Collection<T> securables)

Methods in ubic.gemma.core.security with parameters of type Securable

Modifier and Type	Method	Description
Collection<String>	SecurityService.editableBy(Securable s)	Retrieve a list of users allowed to edit a given securable.
Collection<String>	SecurityServiceImpl.editableBy(Securable s)
Collection<String>	SecurityService.getGroupsEditableBy(Securable s)
Collection<String>	SecurityServiceImpl.getGroupsEditableBy(Securable s)
Collection<String>	SecurityService.getGroupsReadableBy(Securable s)	Obtain all the groups whose members can read a given object.
Collection<String>	SecurityServiceImpl.getGroupsReadableBy(Securable s)
org.springframework.security.acls.model.Sid	SecurityService.getOwner(Securable s)	Obtain the owner of a given object.
org.springframework.security.acls.model.Sid	SecurityServiceImpl.getOwner(Securable s)
boolean	SecurityService.isEditableByCurrentUser(Securable s)	Determine if the current user can edit the securable.
boolean	SecurityServiceImpl.isEditableByCurrentUser(Securable s)
boolean	SecurityService.isEditableByGroup(Securable s, String groupName)	Determine if the given group is allowed to edit an object.
boolean	SecurityServiceImpl.isEditableByGroup(Securable s, String groupName)
boolean	SecurityService.isEditableByUser(Securable s, String userName)	Determine if the given user is allowed to edit an object.
boolean	SecurityServiceImpl.isEditableByUser(Securable s, String userName)
boolean	SecurityService.isOwnedByCurrentUser(Securable s)
boolean	SecurityServiceImpl.isOwnedByCurrentUser(Securable s)
boolean	SecurityService.isPrivate(Securable s)	Determine if a securable is private (i.e.
boolean	SecurityServiceImpl.isPrivate(Securable s)
boolean	SecurityService.isPublic(Securable s)	Determine if a securable is public (i.e.
boolean	SecurityServiceImpl.isPublic(Securable s)
boolean	SecurityService.isReadableByCurrentUser(Securable s)	Determine if the current user can read an object.
boolean	SecurityServiceImpl.isReadableByCurrentUser(Securable s)
boolean	SecurityService.isReadableByGroup(Securable s, String groupName)	Determine if members of a group is allowed to read an object.
boolean	SecurityServiceImpl.isReadableByGroup(Securable s, String groupName)
boolean	SecurityService.isReadableByUser(Securable s, String userName)
boolean	SecurityServiceImpl.isReadableByUser(Securable s, String userName)
boolean	SecurityService.isShared(Securable s)	Determine if a securable is shared (i.e.
boolean	SecurityServiceImpl.isShared(Securable s)
void	SecurityService.makeEditableByGroup(Securable s, String groupName)	Adds write (and read) permissions.
void	SecurityServiceImpl.makeEditableByGroup(Securable s, String groupName)
void	SecurityService.makeOwnedByUser(Securable s, String userName)	Administrative method to allow a user to get access to an object.
void	SecurityServiceImpl.makeOwnedByUser(Securable s, String userName)
void	SecurityService.makePrivate(Securable object)	Makes the object private.
void	SecurityServiceImpl.makePrivate(Securable object)
void	SecurityService.makePublic(Securable object)	Makes the object public
void	SecurityServiceImpl.makePublic(Securable object)
void	SecurityService.makeReadableByGroup(Securable s, String groupName)	Adds read permission for a given group.
void	SecurityServiceImpl.makeReadableByGroup(Securable s, String groupName)
void	SecurityService.makeUneditableByGroup(Securable s, String groupName)	Remove write permissions.
void	SecurityServiceImpl.makeUneditableByGroup(Securable s, String groupName)
void	SecurityService.makeUnreadableByGroup(Securable s, String groupName)	Remove read permissions; also removes write permissions.
void	SecurityServiceImpl.makeUnreadableByGroup(Securable s, String groupName)
Collection<String>	SecurityService.readableBy(Securable s)
Collection<String>	SecurityServiceImpl.readableBy(Securable s)
void	SecurityService.setOwner(Securable s, String userName)	Change the 'owner' of an object to a specific user.
void	SecurityServiceImpl.setOwner(Securable s, String userName)

Method parameters in ubic.gemma.core.security with type arguments of type Securable

Modifier and Type	Method	Description
void	SecurityService.makePrivate(Collection<? extends Securable> objs)	Make a collection of objects private.
void	SecurityServiceImpl.makePrivate(Collection<? extends Securable> objs)
void	SecurityService.makePublic(Collection<? extends Securable> objs)	Make a collection of objects public.
void	SecurityServiceImpl.makePublic(Collection<? extends Securable> objs)

Uses of Securable in ubic.gemma.core.security.acl

Methods in ubic.gemma.core.security.acl with parameters of type Securable

Modifier and Type	Method	Description
void	BaseAclAdvice.addOrUpdateAcl(org.springframework.security.acls.model.MutableAcl acl, Securable object, org.springframework.security.acls.model.Acl parentAcl)	Renovations Phase 3: visibility relaxed so AclEventListener (in the same package) can drive ACL maintenance directly off Hibernate insert events without going through the AOP advice's entity-graph walk.
protected void	BaseAclAdvice.createOrUpdateAclSpecialCases(org.springframework.security.acls.model.MutableAcl acl, org.springframework.security.acls.model.Acl parentAcl, org.springframework.security.acls.model.Sid sid, Securable object)	Subclasses can modify this to address special cases.
protected abstract org.springframework.security.core.GrantedAuthority	BaseAclAdvice.getUserGroupGrantedAuthority(Securable object)
protected abstract String	BaseAclAdvice.getUserName(Securable object)
protected final org.springframework.security.acls.model.ObjectIdentity	BaseAclAdvice.makeObjectIdentity(Securable object)	Forms the object identity to be inserted in acl_object_identity table.
protected abstract boolean	BaseAclAdvice.objectIsUser(Securable object)
protected abstract boolean	BaseAclAdvice.objectIsUserGroup(Securable object)
protected boolean	BaseAclAdvice.specialCaseToAllowRemovingAcesFromChild(Securable object, org.springframework.security.acls.model.Acl parentAcl)	For cases in which the object is not a SecuredChild, but we still want to erase ACEs on it when it has a parent.
protected boolean	BaseAclAdvice.specialCaseToKeepPrivateOnCreation(Securable object)	Indicate if the given object should not be made public immediately on creation by administrators.

Uses of Securable in ubic.gemma.core.security.acl.domain

Constructors in ubic.gemma.core.security.acl.domain with parameters of type Securable

Modifier	Constructor	Description
	AclObjectIdentity(Securable object)	If the object is a proxy, its superclass must be the correct one to give the OBJECT_CLASS (type) in the ACL tables.

Constructor parameters in ubic.gemma.core.security.acl.domain with type arguments of type Securable

Modifier	Constructor	Description
	AclObjectIdentity(Class<? extends Securable> javaType, Long identifier)

Uses of Securable in ubic.gemma.core.security.authorization.acl

Methods in ubic.gemma.core.security.authorization.acl with parameters of type Securable

Modifier and Type	Method	Description
protected void	AclAdvice.createOrUpdateAclSpecialCases(org.springframework.security.acls.model.MutableAcl acl, org.springframework.security.acls.model.Acl parentAcl, org.springframework.security.acls.model.Sid sid, Securable object)
protected org.springframework.security.core.GrantedAuthority	AclAdvice.getUserGroupGrantedAuthority(Securable object)
protected String	AclAdvice.getUserName(Securable user)
protected boolean	AclAdvice.objectIsUser(Securable object)
protected boolean	AclAdvice.objectIsUserGroup(Securable object)
protected boolean	AclAdvice.specialCaseToKeepPrivateOnCreation(Securable object)

Uses of Securable in ubic.gemma.core.security.model

Subinterfaces of Securable in ubic.gemma.core.security.model

Modifier and Type	Interface	Description
interface	SecuredChild	Indicates a securable that must have a parent that holds the permissons.
interface	SecuredNotChild	Interface to mark entities which are secured, and which should not have 'parent's, and therefore do not inherit permissions from other objects.
interface	SecureValueObject	Indicates that a value object represents a Securable so security filtering can be provided during reading.
interface	User	TODO Document Me
interface	UserGroup	Represents a group of users whom are conferred a set of GrantedAuthority.

Methods in ubic.gemma.core.security.model that return Securable

Modifier and Type	Method	Description
Securable	SecuredChild.getSecurityOwner()

Methods in ubic.gemma.core.security.model that return types with arguments of type Securable

Modifier and Type	Method	Description
Class<? extends Securable>	SecureValueObject.getSecurableClass()

Uses of Securable in ubic.gemma.model.analysis

Classes in ubic.gemma.model.analysis that implement Securable

Modifier and Type	Class	Description
class	Investigation	An abstract concept of a scientific study
class	SingleExperimentAnalysis<T extends BioAssaySet>	An analysis of a single experiment or subset.

Uses of Securable in ubic.gemma.model.analysis.expression

Classes in ubic.gemma.model.analysis.expression that implement Securable

Modifier and Type	Class	Description
class	ExpressionExperimentSet	A grouping of expression studies.

Uses of Securable in ubic.gemma.model.analysis.expression.coexpression

Classes in ubic.gemma.model.analysis.expression.coexpression that implement Securable

Modifier and Type	Class	Description
class	SampleCoexpressionAnalysis	The 'analysis' in the name is a bit of a stretch here, as this object servers purely as an aggregator of all the sample coexpression matrices.

Uses of Securable in ubic.gemma.model.analysis.expression.diff

Classes in ubic.gemma.model.analysis.expression.diff that implement Securable

Modifier and Type	Class	Description
class	DifferentialExpressionAnalysis	An analysis of changes in expression levels across experimental conditions
class	ExpressionAnalysisResultSet	A group of results for an ExpressionExperiment.
class	GeneDifferentialExpressionMetaAnalysis	Represents an analysis that combines the results of other analyses of differential expression.
class	GeneDifferentialExpressionMetaAnalysisSummaryValueObject

Uses of Securable in ubic.gemma.model.analysis.expression.pca

Classes in ubic.gemma.model.analysis.expression.pca that implement Securable

Modifier and Type	Class	Description
class	PrincipalComponentAnalysis

Uses of Securable in ubic.gemma.model.common.auditAndSecurity

Subinterfaces of Securable in ubic.gemma.model.common.auditAndSecurity

Modifier and Type	Interface	Description
interface	Auditable	Created by tesarst on 07/03/17.
interface	Securable
interface	SecuredChild<OT extends Securable>
interface	SecuredNotChild

Classes in ubic.gemma.model.common.auditAndSecurity that implement Securable

Modifier and Type	Class	Description
class	AbstractAuditable	An entity which can have an audit trail attached to it.
class	JobInfo
class	User	A user of the software system, who is authenticated.
class	UserGroup	An organized group of researchers with an identifiable leader and group members.

Uses of Securable in ubic.gemma.model.common.auditAndSecurity.curation

Subinterfaces of Securable in ubic.gemma.model.common.auditAndSecurity.curation

Modifier and Type	Interface	Description
interface	Curatable	Created by tesarst on 06/03/17.

Classes in ubic.gemma.model.common.auditAndSecurity.curation that implement Securable

Modifier and Type	Class	Description
class	Ticket	A curation ticket targeting one or more entities (initially TicketTargetType.EXPRESSION_EXPERIMENT and TicketTargetType.ARRAY_DESIGN).

Uses of Securable in ubic.gemma.model.common.description

Classes in ubic.gemma.model.common.description that implement Securable

Modifier and Type	Class	Description
class	ExternalDatabase

Uses of Securable in ubic.gemma.model.common.protocol

Classes in ubic.gemma.model.common.protocol that implement Securable

Modifier and Type	Class	Description
class	Protocol

Uses of Securable in ubic.gemma.model.expression.arrayDesign

Classes in ubic.gemma.model.expression.arrayDesign that implement Securable

Modifier and Type	Class	Description
class	ArrayDesign	Represents an assembly of design elements that are assayed all at once.

Uses of Securable in ubic.gemma.model.expression.bioAssay

Classes in ubic.gemma.model.expression.bioAssay that implement Securable

Modifier and Type	Class	Description
class	BioAssay	Represents the bringing together of a biomaterial with an assay of some sort (typically an expression assay).

Uses of Securable in ubic.gemma.model.expression.bioAssayData

Classes in ubic.gemma.model.expression.bioAssayData that implement Securable

Modifier and Type	Class	Description
class	MeanVarianceRelation

Uses of Securable in ubic.gemma.model.expression.biomaterial

Classes in ubic.gemma.model.expression.biomaterial that implement Securable

Modifier and Type	Class	Description
class	BioMaterial	In MAGE, BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc...

Uses of Securable in ubic.gemma.model.expression.experiment

Subinterfaces of Securable in ubic.gemma.model.expression.experiment

Modifier and Type	Interface	Description
interface	BioAssaySetValueObject	Interface for VOs deriving from BioAssaySet.

Classes in ubic.gemma.model.expression.experiment that implement Securable

Modifier and Type	Class	Description
class	BioAssaySet	Represents a set of BioAssays.
class	ExperimentalDesign	Hibernate Search 7 mapping: indexed root and embedded contributor to ExpressionExperiment.getExperimentalDesign().
class	ExperimentalFactor	ExperimentFactors are the dependent variables of an experiment (e.g., genotype, time, glucose concentration).
class	ExpressionExperiment	Hibernate Search 7 indexed root.
class	ExpressionExperimentDetailsValueObject
class	ExpressionExperimentSetValueObject
class	ExpressionExperimentSubSet	A subset of assays (or derived assays) from an ExpressionExperiment.
class	ExpressionExperimentSubsetValueObject
class	ExpressionExperimentValueObject
class	FactorValue	The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"
class	FreeTextExpressionExperimentResultsValueObject
class	PreboardedExperiment	Subclass of Investigation representing a proposed-but-not-yet-loaded dataset.
class	SessionBoundExpressionExperimentSetValueObject

Uses of Securable in ubic.gemma.model.genome.gene

Classes in ubic.gemma.model.genome.gene that implement Securable

Modifier and Type	Class	Description
class	DatabaseBackedGeneSetValueObject
class	FreeTextGeneResultsValueObject	*
class	GeneSet	A grouping of genes that share a common relationship.
class	GeneSetValueObject	Represents a Gene group gene set
class	GOGroupValueObject
class	SessionBoundGeneSetValueObject

Uses of Securable in ubic.gemma.model.pipeline

Classes in ubic.gemma.model.pipeline that implement Securable

Modifier and Type	Class	Description
class	PipelineJobBatch	One curator-initiated submission of a pipeline against a set of experiments.

Uses of Securable in ubic.gemma.rest

Classes in ubic.gemma.rest that implement Securable

Modifier and Type	Class	Description
static class	DatasetsWebService.ExpressionExperimentSubsetWithFactorValuesObject
static class	DatasetsWebService.ExpressionExperimentSubSetWithGroupsValueObject
static final class	DatasetsWebService.ExpressionExperimentWithSearchResultValueObject