Uses of Interface
com.genologics.ri.LimsLink

Packages that use LimsLink

Package	Description
com.genologics.ri	The root package of the classes generated (originally) from the Clarity schemas.
com.genologics.ri.artifact
com.genologics.ri.artifactgroup
com.genologics.ri.automation
com.genologics.ri.configuration
com.genologics.ri.container
com.genologics.ri.containertype
com.genologics.ri.controltype
com.genologics.ri.file
com.genologics.ri.instrument
com.genologics.ri.instrumenttype
com.genologics.ri.lab
com.genologics.ri.permission
com.genologics.ri.process
com.genologics.ri.processexecution
com.genologics.ri.processtemplate
com.genologics.ri.processtype
com.genologics.ri.project
com.genologics.ri.protocolconfiguration
com.genologics.ri.queue
com.genologics.ri.reagentkit
com.genologics.ri.reagentlot
com.genologics.ri.reagenttype
com.genologics.ri.researcher
com.genologics.ri.role
com.genologics.ri.routing
com.genologics.ri.sample
com.genologics.ri.stage
com.genologics.ri.step
com.genologics.ri.stepconfiguration
com.genologics.ri.workflowconfiguration
org.cruk.clarity.api	The main public package of the Clarity API.
org.cruk.clarity.api.impl	Concrete implementation classes of the Clarity API.

Uses of LimsLink in com.genologics.ri

Subinterfaces of LimsLink in com.genologics.ri

Modifier and Type	Interface	Description
interface	LimsEntityLink<E extends LimsEntity<E>>	Interface for links to LimsEntity objects.

Classes in com.genologics.ri that implement LimsLink

Modifier and Type	Class	Description
class	ContainerLink	Container is a child element of location and provides a URI linking to the detailed representation of the Container for the location.
class	Location	Location provides a URI linking to the detailed representation of a Container along with the well location within that Container.

Uses of LimsLink in com.genologics.ri.artifact

Classes in com.genologics.ri.artifact that implement LimsLink

Modifier and Type	Class	Description
class	ArtifactGroupLink	Artifact group is a child element of Artifact and provides a URI linking to the detailed representation of the artifact group that the Artifact belongs to.
class	ArtifactLink	Artifact-link is a child element type of artifacts and provides a URI linking to the detailed representation of an artifact.
class	ControlTypeLink	Provide a URI linking to the control type if this artifact is a control sample.
class	DemuxArtifactSample	The details of a sample that is part of a pooled artifact.
class	DemuxLink	Identifies the resource that will demultiplex this artifact.
class	DemuxSourceArtifact
class	ParentProcessLink	Parent-process is a child element of Artifact and provides a URI linking to the detailed representation of the process that produced the Artifact.
class	PoolStep	The details of the pooling step that created the pooled sample(s).
class	SampleLink	Sample is a child element of Artifact and provides a URI linking to the detailed representation of a submitted Sample for the Artifact.
class	WorkflowStage	Provides links to workflow stages, stage names and their respective statuses.

Uses of LimsLink in com.genologics.ri.artifactgroup

Classes in com.genologics.ri.artifactgroup that implement LimsLink

Modifier and Type	Class	Description
class	ArtifactGroupLink	artifactGroup-link is a child element type of artifactGroup and provides a URI linking to the detailed representation of a artifactGroup.

Uses of LimsLink in com.genologics.ri.automation

Classes in com.genologics.ri.automation that implement LimsLink

Modifier and Type	Class	Description
class	AutomationLink
class	ProcessTypeLink	Provides links to process types the automation is enabled on.

Uses of LimsLink in com.genologics.ri.configuration

Classes in com.genologics.ri.configuration that implement LimsLink

Modifier and Type	Class	Description
class	FieldLink	Field definition represents a user-defined field configured in the parent entity.
class	TypeDefinition	Type-definition provides a URI linking to the user defined type associated with the user-defined field, if applicable.
class	UdfConfigLink	Udfconfig-link is a child element type of udfs and provides a URI linking to the detailed representation of the configuration for a user defined field.
class	UdtConfigLink	Udtconfig-link is a child element type of udts and provides a URI linking to the detailed representation of the configuration for a user defined type.

Uses of LimsLink in com.genologics.ri.container

Classes in com.genologics.ri.container that implement LimsLink

Modifier and Type	Class	Description
class	ContainerLink	Container-link is a child element type of containers and provides a URI linking to the detailed representation of a container.
class	ContainerTypeLink	Container-type is a child element of container and provides a URI linking to the detailed representation of the container type that the container is associated with.
class	Placement	Placement is a child element of container and provides a URI linking to the detailed representation of the artifact that is located in a specific well of the container.

Uses of LimsLink in com.genologics.ri.containertype

Classes in com.genologics.ri.containertype that implement LimsLink

Modifier and Type	Class	Description
class	ContainerTypeLink	Container-type-link is a child element type of containers and provides a URI linking to the detailed representation of a container type.

Uses of LimsLink in com.genologics.ri.controltype

Classes in com.genologics.ri.controltype that implement LimsLink

Modifier and Type	Class	Description
class	ControlTypeLink	Control-type-link is a child element type of controlTypes and provides a URI linking to the detailed representation of a ControlType.

Uses of LimsLink in com.genologics.ri.file

Classes in com.genologics.ri.file that implement LimsLink

Modifier and Type	Class	Description
class	ClarityFile	The file element contains information about a file in the system.
class	FileLink	The file-link type provides a URI that links to information about a file in the system.

Uses of LimsLink in com.genologics.ri.instrument

Classes in com.genologics.ri.instrument that implement LimsLink

Modifier and Type	Class	Description
class	InstrumentLink	Instrument-link is a child element type of instruments and provides a URI linking to the detailed representation of an instrument.

Uses of LimsLink in com.genologics.ri.instrumenttype

Classes in com.genologics.ri.instrumenttype that implement LimsLink

Modifier and Type	Class	Description
class	InstrumentTypeLink
class	InstrumentTypeProcessType

Uses of LimsLink in com.genologics.ri.lab

Classes in com.genologics.ri.lab that implement LimsLink

Modifier and Type	Class	Description
class	LabLink	Lab-link is a child element type of labs and provides a URI linking to the detailed representation of a lab.

Uses of LimsLink in com.genologics.ri.permission

Classes in com.genologics.ri.permission that implement LimsLink

Modifier and Type	Class	Description
class	PermissionLink

Uses of LimsLink in com.genologics.ri.process

Classes in com.genologics.ri.process that implement LimsLink

Modifier and Type	Class	Description
class	ArtifactLink	Artifact is a child element of input-output-map and provides a link to an Artifact that was either an input or output of the Process for the input-output-map.
class	InstrumentLink	The instrument element provides a URI to the instrument that is responsible for running the process.
class	ParentProcessLink	Parent-process is a child element of Artifact and provides a URI linking to the Process that created the Artifact.
class	ProcessLink	Process-link is a child element type of process and provides a URI linking to the detailed representation of a process.
class	ProcessTypeLink	Process-type is a child element of process that identifies and provides a URI linking to the detailed representation of the process type that the process is associated with.
class	Technician	Technician is a child element of Process and provides a URI linking to the detailed representation of the technician that ran the Process.

Uses of LimsLink in com.genologics.ri.processexecution

Classes in com.genologics.ri.processexecution that implement LimsLink

Modifier and Type	Class	Description
class	Input	The input element provides URIs to one or more Artifacts that will be used by the Process.
class	InstrumentLink	The instrument element provides a URI to the instrument that is responsible for running the process.
class	Technician	The technician element provides a URI to the user that is responsible for the Process.

Uses of LimsLink in com.genologics.ri.processtemplate

Classes in com.genologics.ri.processtemplate that implement LimsLink

Modifier and Type	Class	Description
class	InstrumentLink	The instrument is a child element of process-template that provides a URI to the instrument that is responsible for running a Process created using this Process Template.
class	ProcessTemplateLink	process-template-link is a child element type of Process Templates and provides a URI linking to the detailed representation of a Process Template.
class	ProcessTypeLink	Process-type is a child element of process-template that identifies and provides a URI linking to the detailed representation of the Process Type that the Process Template is associated with.
class	Technician	Technician is a child element of process-template and provides a URI linking to the detailed representation of the technician that is configured to run a Process created using this Process Template.

Uses of LimsLink in com.genologics.ri.processtype

Classes in com.genologics.ri.processtype that implement LimsLink

Modifier and Type	Class	Description
class	ContainerTypeLink
class	ControlTypeLink
class	ProcessTypeLink	Process-type-link is a child element type of process types and provides a URI linking to the detailed representation of a process type.
class	ReagentKitLink	Reagent-kit-link is a child element type of reagentKits and provides a URI linking to the detailed representation of a ReagentKit.
class	TypeDefinition	Type-definition is a child element of process type providing a URI linking to the configuration of a user-defined type for the process type.

Uses of LimsLink in com.genologics.ri.project

Classes in com.genologics.ri.project that implement LimsLink

Modifier and Type	Class	Description
class	ProjectLink	Project-link is a child element type of projects and provides a URI linking to the detailed representation of a project.
class	ResearcherLink	Researcher is a child element of Project and provides a URI linking to the detailed representation of the Researcher for the Project.

Uses of LimsLink in com.genologics.ri.protocolconfiguration

Classes in com.genologics.ri.protocolconfiguration that implement LimsLink

Modifier and Type	Class	Description
class	ProtocolLink

Uses of LimsLink in com.genologics.ri.queue

Classes in com.genologics.ri.queue that implement LimsLink

Modifier and Type	Class	Description
class	ArtifactLink

Uses of LimsLink in com.genologics.ri.reagentkit

Classes in com.genologics.ri.reagentkit that implement LimsLink

Modifier and Type	Class	Description
class	ReagentKitLink	Reagent-Kit-Link is a child element type of reagent kits and provides a URI linking to the detailed representation of a reagent kit.

Uses of LimsLink in com.genologics.ri.reagentlot

Classes in com.genologics.ri.reagentlot that implement LimsLink

Modifier and Type	Class	Description
class	ReagentKitLink	Reagent-Kit-Link is an element providing a URI linking to the detailed representation of a reagent kit.
class	ReagentLotLink	Reagent-lot-link is a child element type of Reagent Lots and provides a URI linking to the detailed representation of a Reagent Lot.
class	ResearcherLink	Researcher is a child element of the reagent lot.

Uses of LimsLink in com.genologics.ri.reagenttype

Classes in com.genologics.ri.reagenttype that implement LimsLink

Modifier and Type	Class	Description
class	ReagentTypeLink	Reagent-type-link is a child element type of reagent types and provides a URI linking to the detailed representation of a reagent type.

Uses of LimsLink in com.genologics.ri.researcher

Classes in com.genologics.ri.researcher that implement LimsLink

Modifier and Type	Class	Description
class	LabLink	Lab is a child element of researcher and provides a URI linking to the detailed representation of the lab for the researcher.
class	ResearcherLink	Researcher-link is a child element type of researchers and provides a URI linking to the detailed representation of a researcher.
class	Role	The role element defines a researcher's level of access in the system.

Uses of LimsLink in com.genologics.ri.role

Classes in com.genologics.ri.role that implement LimsLink

Modifier and Type	Class	Description
class	PermissionLink	Permission-link is a child element type of permissions and provides a URI linking to the detailed representation of a Permission.
class	ResearcherLink	Researcher-link is a child element type of researchers and provides a URI linking to the detailed representation of a researcher.
class	RoleLink	Role-link is a child element type of roles and provides a URI linking to the detailed representation of a Role.

Uses of LimsLink in com.genologics.ri.routing

Classes in com.genologics.ri.routing that implement LimsLink

Modifier and Type	Class	Description
class	ArtifactLink

Uses of LimsLink in com.genologics.ri.sample

Classes in com.genologics.ri.sample that implement LimsLink

Modifier and Type	Class	Description
class	ArtifactLink	Artifact is a child element of Sample and provides a URI linking to the detailed representation of the artifact for the Sample.
class	ControlTypeLink	Control Type provides a name and a URI linking to the detailed representation of the Control Type associated with the Sample.
class	ProjectLink	Project is a child element of Sample and provides a URI linking to the detailed representation of the Project for the Sample.
class	SampleLink	Sample-link is a child element type of samples and provides a URI linking to the detailed representation of a sample.
class	Submitter	Submitter is a child element of Sample and provides a URI linking to the detailed representation of the submitter for the Sample.

Uses of LimsLink in com.genologics.ri.stage

Classes in com.genologics.ri.stage that implement LimsLink

Modifier and Type	Class	Description
class	ProtocolLink	Protocol link for the stage.
class	ProtocolStepLink	Protocol Step link for the stage.
class	WorkflowLink	Workflow link for the stage.

Uses of LimsLink in com.genologics.ri.step

Classes in com.genologics.ri.step that implement LimsLink

Modifier and Type	Class	Description
class	ActionsLink	Identifies the resource that represents the actions applied or to be applied by the step.
class	ArtifactLink	Artifact is a child element of input-output-map and provides a link to an Artifact that was either an input or output of the Step for the input-output-map.
class	AutomaticNextStepLink	Identifies the resource that represents the step that was automatically begun when the "Automatically start Next Step" option is enabled in a step's configuration.
class	ContainerLink	Provides a URI linking to a selected container to be used for placement.
class	CreationInput	Typically, provides a URI linking to the input artifact.
class	EscalatedArtifact	Sample next action or step.
class	Input	Provides input URI links.
class	InstrumentLink	The instrument element provides a URI to the selected instrument for the step.
class	NextAction	Sample next action or step.
class	Output	Provides a URI linking to the output artifact and reagent label.
class	OutputPlacement	Provides a URI linking to the output artifact and container placement.
class	PlacementsLink	Identifies the resource that represents the output placements for the step.
class	PoolsLink	Identifies the resource that represents the pools added by the step.
class	ProgramStatusLink	Identifies the resource that represents the program status for the step.
class	ReagentLotLink	Provides a URI linking to the reagent lot details.
class	ReagentLotsLink	Identifies the resource that represents the reagent lots for the step.
class	ReagentsLink	Identifies the resource that represents the reagents added by the step.
class	SharedResultFile	The file element describes a shared result file output that will be displayed in the step-setup view.
class	StepConfiguration	Identifies the configuration information for the step run.
class	StepDetailsLink	Identifies the resource that represents the details for the step.
class	StepSetupLink	Identifies the resource that represents the setup for the step.
class	UserLink	Describes a user as required in the context of step escalations.

Uses of LimsLink in com.genologics.ri.stepconfiguration

Classes in com.genologics.ri.stepconfiguration that implement LimsLink

Modifier and Type	Class	Description
class	ControlTypeLink	Control-type-link is a child element type of controlTypes and provides a URI linking to the detailed representation of a ControlType.
class	NextStep	List of step transitions including the URI allowing access to the specific next step
class	ProcessTypeLink	Process-type is a child element that provides a URI linking to the detailed representation of the process type that the step is associated with.
class	ReagentKitLink	Reagent-Kit-Link is an element providing a URI linking to the detailed representation of a reagent kit.

Uses of LimsLink in com.genologics.ri.workflowconfiguration

Classes in com.genologics.ri.workflowconfiguration that implement LimsLink

Modifier and Type	Class	Description
class	ProtocolLink	Protocol-link is a child element type of workflow and provides a URI linking to the detailed representation of a protocol.
class	StageLink	The detailed representation of a Stage (the portion of a workflow to which samples can be associated in order to be queued)
class	WorkflowLink	Workflow-link is a child element type of workflows and provides a URI linking to the detailed representation of a workflow.

Uses of LimsLink in org.cruk.clarity.api

Methods in org.cruk.clarity.api that return types with arguments of type LimsLink

Modifier and Type	Method	Description
<E extends Locatable> List<LimsLink<E>>	ClarityAPI.find(Map<String,?> searchTerms, Class<E> entityClass)	Search for entities of the given type based on name value pairs.
<E extends Locatable> List<LimsLink<E>>	ClarityAPI.listAll(Class<E> entityClass)	List all the objects of the given entity class.
<E extends Locatable> List<LimsLink<E>>	ClarityAPI.listSome(Class<E> entityClass, int startIndex, int number)	List an arbitrary number of objects of the given entity class.

Methods in org.cruk.clarity.api with parameters of type LimsLink

Modifier and Type	Method	Description
<E extends Locatable> E	ClarityAPI.load(LimsLink<E> link)	Load an entity using a link to that entity.

Method parameters in org.cruk.clarity.api with type arguments of type LimsLink

Modifier and Type	Method	Description
<E extends Locatable> List<E>	ClarityAPI.loadAll(Collection<? extends LimsLink<E>> links)	Fetch a collection of LIMS entities given in the collection.

Uses of LimsLink in org.cruk.clarity.api.impl

Methods in org.cruk.clarity.api.impl with type parameters of type LimsLink

Modifier and Type	Method	Description
protected <E extends Locatable, L extends LimsLink<E>> Class<E>	ClarityAPIImpl.checkLinkCollectionHomogeneousAndUnique(Collection<L> links)	Check that the given collection of links contains no nulls, that each link has a URI, that all links in the collection are links to the same entity class, and that there are no repeated URIs in the collection (ignoring state).
<E extends Locatable, BH extends Batch<? extends LimsLink<E>>> Class<BH>	ClarityAPIImpl.getQueryResultsClassForEntity(Class<E> entityClass)	Get the class that holds a list of links for the given entity when returned from a list or search operation.
<E extends Locatable, BH extends Batch<? extends LimsLink<E>>> Class<BH>	ClarityAPIInternal.getQueryResultsClassForEntity(Class<E> entityClass)	Get the class that holds a list of links for the given entity when returned from a list or search operation.

Methods in org.cruk.clarity.api.impl that return types with arguments of type LimsLink

Modifier and Type	Method	Description
<E extends Locatable> List<LimsLink<E>>	ClarityAPIImpl.find(Map<String,?> searchTerms, Class<E> entityClass)	Search for entities of the given type based on name value pairs.
<E extends Locatable> List<LimsLink<E>>	ClarityAPIImpl.listAll(Class<E> entityClass)	List all the objects of the given entity class.
<E extends Locatable> List<LimsLink<E>>	ClarityAPIImpl.listSome(Class<E> entityClass, int startIndex, int number)	List an arbitrary number of objects of the given entity class.

Methods in org.cruk.clarity.api.impl with parameters of type LimsLink

Modifier and Type	Method	Description
<E extends Locatable> E	ClarityAPIImpl.load(LimsLink<E> link)	Load an entity using a link to that entity.

Method parameters in org.cruk.clarity.api.impl with type arguments of type LimsLink

Modifier and Type	Method	Description
<E extends Locatable> List<E>	ClarityAPIImpl.loadAll(Collection<? extends LimsLink<E>> links)	Fetch a collection of LIMS entities given in the collection.