Uses of Interface
com.genologics.ri.LimsEntityLinkable

Packages that use LimsEntityLinkable

Package	Description
com.genologics.ri	The root package of the classes generated (originally) from the Clarity schemas.
com.genologics.ri.artifact	Provides JAXB bindings for artifacts in the Genologics REST API.
com.genologics.ri.container	Container entity and support classes for the Clarity REST API.
com.genologics.ri.file	Entities for file resources in the Clarity system.
com.genologics.ri.instrument	Entities for instrument resources in the Clarity system.
com.genologics.ri.lab	Provides classes for representing and managing laboratory entities in the Clarity LIMS system.
com.genologics.ri.process	Entities for processes executed in the Clarity system.
com.genologics.ri.processexecution	Entities for process execution in the Clarity system.
com.genologics.ri.processtemplate	Entities for process templates in the Clarity system.
com.genologics.ri.project	Project entity and supporting classes for the Clarity REST API.
com.genologics.ri.queue	Entities for work queues in the Clarity system.
com.genologics.ri.reagentlot
com.genologics.ri.reagenttype	Entities for reagent type definitions in the Clarity system.
com.genologics.ri.researcher	Provides classes for representing researchers in the Clarity LIMS system.
com.genologics.ri.role	Provides JAXB binding classes for the Clarity REST API role entity and its related components.
com.genologics.ri.sample	Provides classes for sample entities in the Clarity LIMS API.
com.genologics.ri.step	Entities for workflow steps in the Clarity system.
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 LimsEntityLinkable in com.genologics.ri

Subinterfaces of LimsEntityLinkable in com.genologics.ri

Modifier and Type	Interface	Description
interface	LimsEntity<E extends LimsEntity<E>>	Interface for all objects that are real LIMS entities (i.e. not links or other references).
interface	LimsEntityLink<E extends LimsEntity<E>>	Interface for links to LimsEntity objects.

Classes in com.genologics.ri that implement LimsEntityLinkable

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	LimsEntityLinkBase<E extends LimsEntity<E>>	Helper base class for LimsEntityLink implementations extending from LimsLinkBase.
class	Location	Location provides a URI linking to the detailed representation of a Container along with the well location within that Container.

Methods in com.genologics.ri with parameters of type LimsEntityLinkable

Modifier and Type	Method	Description
ContainerLink	Location.setContainer(LimsEntityLinkable<Container> link)	Sets the container from a LIMS entity linkable.

Constructors in com.genologics.ri with parameters of type LimsEntityLinkable

Modifier	Constructor	Description
	ContainerLink(LimsEntityLinkable<Container> link)	Constructor from a LIMS entity linkable container.
	Location(LimsEntityLinkable<Container> container, String position)	Constructor with container and position.

Uses of LimsEntityLinkable in com.genologics.ri.artifact

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

Modifier and Type	Class	Description
class	Artifact	The detailed representation of an Artifact.
class	ArtifactLink	Artifact-link is a child element type of artifacts and provides a URI linking to the detailed representation of an artifact.
class	DemuxArtifactSample	The details of a sample that is part of a pooled artifact.
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	SampleLink	Sample is a child element of Artifact and provides a URI linking to the detailed representation of a submitted Sample for the Artifact.

Methods in com.genologics.ri.artifact with parameters of type LimsEntityLinkable

Modifier and Type	Method	Description
SampleLink	Artifact.addSample(LimsEntityLinkable<Sample> linkable)	Adds a sample to this artifact.
ParentProcessLink	Artifact.setParentProcess(LimsEntityLinkable<ClarityProcess> link)	Sets the parent process that produced this artifact.

Method parameters in com.genologics.ri.artifact with type arguments of type LimsEntityLinkable

Modifier and Type	Method	Description
void	Artifact.setSamples(Collection<? extends LimsEntityLinkable<Sample>> links)	Sets the list of samples associated with this artifact.

Constructors in com.genologics.ri.artifact with parameters of type LimsEntityLinkable

Modifier	Constructor	Description
	ArtifactLink(LimsEntityLinkable<Artifact> link)	Constructor from a LimsEntityLinkable.
	DemuxArtifactSample(LimsEntityLinkable<Sample> link)	Constructor from a LimsEntityLinkable.
	ParentProcessLink(LimsEntityLinkable<ClarityProcess> link)	Constructor from a LimsEntityLinkable.
	SampleLink(LimsEntityLinkable<Sample> link)	Constructor from a LimsEntityLinkable.

Uses of LimsEntityLinkable in com.genologics.ri.container

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

Modifier and Type	Class	Description
class	Container	Container entity representing a physical container in the Clarity LIMS.
class	ContainerLink	Container-link is a child element type of containers and provides a URI linking to the detailed representation of a container.
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.

Methods in com.genologics.ri.container with parameters of type LimsEntityLinkable

Modifier and Type	Method	Description
Placement	Container.addPlacement(LimsEntityLinkable<Artifact> artifact, String wellPosition)	Adds a placement to the container with an artifact and well position.

Method parameters in com.genologics.ri.container with type arguments of type LimsEntityLinkable

Modifier and Type	Method	Description
void	Container.setPlacements(Collection<? extends LimsEntityLinkable<Artifact>> links)	Sets the placements from a collection of artifact links.

Constructors in com.genologics.ri.container with parameters of type LimsEntityLinkable

Modifier	Constructor	Description
	ContainerLink(LimsEntityLinkable<Container> link)	Constructor from a LIMS entity linkable container.
	Placement(LimsEntityLinkable<Artifact> artifact)	Constructor from a LIMS entity linkable artifact.
	Placement(LimsEntityLinkable<Artifact> artifact, String wellPosition)	Constructor from a LIMS entity linkable artifact with well position.

Uses of LimsEntityLinkable in com.genologics.ri.file

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

Modifier and Type	Class	Description
class	ClarityFile	The file element contains information about a file in the system.

Constructors in com.genologics.ri.file with parameters of type LimsEntityLinkable

Modifier	Constructor	Description
	FileLink(LimsEntityLinkable<ClarityFile> link)	Creates a new FileLink from a linkable entity that references a ClarityFile, copying its URI and LIMS id.

Uses of LimsEntityLinkable in com.genologics.ri.instrument

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

Modifier and Type	Class	Description
class	Instrument	The detailed representation of an instrument.
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 LimsEntityLinkable in com.genologics.ri.lab

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

Modifier and Type	Class	Description
class	Lab	The detailed representation of a lab.
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 LimsEntityLinkable in com.genologics.ri.process

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

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	ClarityProcess	The detailed representation of a process.
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.

Methods in com.genologics.ri.process with parameters of type LimsEntityLinkable

Modifier and Type	Method	Description
void	InputOutputMap.setInput(LimsEntityLinkable<Artifact> link)	Sets the input from a LIMS entity linkable artifact.
void	InputOutputMap.setOutput(LimsEntityLinkable<Artifact> link)	Sets the output from a LIMS entity linkable artifact.
ParentProcessLink	ArtifactLink.setParentProcess(LimsEntityLinkable<ClarityProcess> parentProcess)	Sets the parent process from a LIMS entity linkable object.

Constructors in com.genologics.ri.process with parameters of type LimsEntityLinkable

Modifier	Constructor	Description
	ArtifactLink(LimsEntityLinkable<Artifact> link)	Constructor from a LIMS entity linkable object.
	InputOutputMap(LimsEntityLinkable<Artifact> input, LimsEntityLinkable<Artifact> output)	Constructor with input and output LIMS entity linkable artifacts.
	ParentProcessLink(LimsEntityLinkable<ClarityProcess> link)	Constructor from a LIMS entity linkable object.
	ProcessLink(LimsEntityLinkable<ClarityProcess> link)	Constructor from a LIMS entity linkable object.

Uses of LimsEntityLinkable in com.genologics.ri.processexecution

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

Modifier and Type	Class	Description
class	InstrumentLink	The instrument element provides a URI to the instrument that is responsible for running the process.

Methods in com.genologics.ri.processexecution with parameters of type LimsEntityLinkable

Modifier and Type	Method	Description
Location	Output.setLocation(LimsEntityLinkable<Container> container, String position)	Sets the location of the output artifact with container and position.
Output	ExecutableInputOutputMap.setOutput(OutputType type, LimsEntityLinkable<Container> container, String position)	Sets the output artifact with type, container, and position.

Constructors in com.genologics.ri.processexecution with parameters of type LimsEntityLinkable

Modifier	Constructor	Description
	Output(OutputType type, LimsEntityLinkable<Container> container, String position)	Constructor with output type, container, and position.

Uses of LimsEntityLinkable in com.genologics.ri.processtemplate

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

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.

Uses of LimsEntityLinkable in com.genologics.ri.project

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

Modifier and Type	Class	Description
class	Project	The detailed representation of a Project.
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.

Constructors in com.genologics.ri.project with parameters of type LimsEntityLinkable

Modifier	Constructor	Description
	ProjectLink(LimsEntityLinkable<Project> link)	Constructor for ProjectLink from a LimsEntityLinkable.

Uses of LimsEntityLinkable in com.genologics.ri.queue

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

Modifier and Type	Class	Description
class	ArtifactLink	Artifact-Link provides a URI linking to the detailed representation of an artifact in a queue.

Constructors in com.genologics.ri.queue with parameters of type LimsEntityLinkable

Modifier	Constructor	Description
	ArtifactLink(LimsEntityLinkable<Artifact> link)	Constructor from a LimsEntityLinkable.

Uses of LimsEntityLinkable in com.genologics.ri.reagentlot

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

Modifier and Type	Class	Description
class	ReagentLot	Represents a reagent lot in the Clarity LIMS system.
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.

Constructors in com.genologics.ri.reagentlot with parameters of type LimsEntityLinkable

Modifier	Constructor	Description
	ReagentLot(LimsEntityLinkable<ReagentLot> link)	Constructor from a linkable reagent lot.
	ReagentLotLink(LimsEntityLinkable<ReagentLot> link)	Constructor from a LIMS entity linkable reagent lot.

Uses of LimsEntityLinkable in com.genologics.ri.reagenttype

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

Modifier and Type	Class	Description
class	ReagentType	The detailed representation of a reagent type.
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 LimsEntityLinkable in com.genologics.ri.researcher

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

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	Researcher	The detailed representation of a researcher.
class	ResearcherLink	Researcher-link is a child element type of researchers and provides a URI linking to the detailed representation of a researcher.

Uses of LimsEntityLinkable in com.genologics.ri.role

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

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

Uses of LimsEntityLinkable in com.genologics.ri.sample

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

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	ProjectLink	Project is a child element of Sample and provides a URI linking to the detailed representation of the Project for the Sample.
class	Sample	The detailed representation of a sample.
class	SampleLink	Sample-link is a child element type of samples and provides a URI linking to the detailed representation of a sample.

Methods in com.genologics.ri.sample with parameters of type LimsEntityLinkable

Modifier and Type	Method	Description
void	SampleBase.setArtifact(LimsEntityLinkable<Artifact> artifact)	Sets the artifact for this sample.
void	Sample.setCreationLocation(LimsEntityLinkable<Container> container, String position)	Set the location of this sample for creation.
void	SampleBase.setProject(LimsEntityLinkable<Project> project)	Sets the project for this sample.

Constructors in com.genologics.ri.sample with parameters of type LimsEntityLinkable

Modifier	Constructor	Description
	ArtifactLink(LimsEntityLinkable<Artifact> link)	Constructor for an artifact link from a LIMS entity linkable artifact.
	ProjectLink(LimsEntityLinkable<Project> link)	Constructor for a project link from a LIMS entity linkable project.
	SampleLink(LimsEntityLinkable<Sample> link)	Constructor for a sample link from a LIMS entity linkable sample.

Uses of LimsEntityLinkable in com.genologics.ri.step

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

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 Step for the input-output-map.
class	InstrumentLink	The instrument element provides a URI to the selected instrument for the step.
class	ProcessStep	The detailed representation of a step.
class	ReagentLotLink	Provides a URI linking to the reagent lot details.
class	SharedResultFile	The file element describes a shared result file output that will be displayed in the step-setup view.

Methods in com.genologics.ri.step with parameters of type LimsEntityLinkable

Modifier and Type	Method	Description
InputOutputMap	StepDetails.addInputOutputMap(LimsEntityLinkable<Artifact> input, LimsEntityLinkable<Artifact> output)	Creates and adds an input/output mapping to the step.
ReagentLotLink	ReagentLots.addReagentLot(LimsEntityLinkable<ReagentLot> lot)	Adds a reagent lot to the list by creating a link from the linkable object.
void	InputOutputMap.setInput(LimsEntityLinkable<Artifact> link)	Sets the input from a LIMS entity linkable artifact.
void	OutputPlacement.setLocation(LimsEntityLinkable<Container> container, String wellPosition)	Sets the location from a container and well position.
void	InputOutputMap.setOutput(LimsEntityLinkable<Artifact> link)	Sets the output from a LIMS entity linkable artifact.

Constructors in com.genologics.ri.step with parameters of type LimsEntityLinkable

Modifier	Constructor	Description
	ArtifactLink(LimsEntityLinkable<Artifact> link)	Constructor from a LIMS entity linkable object.
	InputOutputMap(LimsEntityLinkable<Artifact> input, LimsEntityLinkable<Artifact> output)	Constructor with LIMS entity linkable input and output artifacts.
	OutputPlacement(Linkable<Artifact> artifact, LimsEntityLinkable<Container> container, String wellPosition)	Constructor with artifact, container and well position.
	ReagentLotLink(LimsEntityLinkable<ReagentLot> link)	Constructs a new ReagentLotLink from a LIMS entity linkable reagent lot.
	SharedResultFile(LimsEntityLinkable<Artifact> link)	Creates a shared result file from a LIMS entity linkable artifact.

Uses of LimsEntityLinkable in org.cruk.clarity.api

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

Modifier and Type	Method	Description
<E extends LimsEntity<E>, L extends LimsEntityLinkable<E>> void	ClarityAPI.setFieldDynamicPresets(Field field, L target, FieldDynamicPresetDetails presets)	Set dynamic presets for a field on an entity (certainly process, haven't tested artifacts).
default <E extends LimsEntity<E>, L extends LimsEntityLinkable<E>> void	ClarityAPI.setFieldDynamicPresets(Field field, L target, String... presets)	Convenience version of ClarityAPI.setFieldDynamicPresets(Field, LimsEntityLinkable, FieldDynamicPresetDetails) to set the presets with variable string arguments.
default <E extends LimsEntity<E>, L extends LimsEntityLinkable<E>> void	ClarityAPI.setFieldDynamicPresets(Field field, L target, Collection<String> presets)	Convenience version of ClarityAPI.setFieldDynamicPresets(Field, LimsEntityLinkable, FieldDynamicPresetDetails) to set the presets with variable string arguments.

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

Modifier and Type	Method	Description
<E extends LimsEntity<E>> ClarityFile	ClarityAPI.uploadFile(LimsEntityLinkable<E> entity, URL fileURL, boolean publishInLablink)	Attach a file to an entity and upload that file to the file store.

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

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

Modifier and Type	Method	Description
<E extends LimsEntity<E>, L extends LimsEntityLinkable<E>> void	ClarityAPIImpl.setFieldDynamicPresets(Field field, L target, FieldDynamicPresetDetails presets)	Set dynamic presets for a field on an entity (certainly process, haven't tested artifacts).

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

Modifier and Type	Method	Description
<E extends LimsEntity<E>> ClarityFile	ClarityAPIImpl.uploadFile(LimsEntityLinkable<E> entity, URL fileURL, boolean publishInLablink)	Attach a file to an entity and upload that file to the file store.