Index

A B C D E F G H I J K L M N O P Q R S T U V W
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

AbstractDateAdapter - Class in com.genologics.ri.jaxb

Base for date adapters.

AbstractDateAdapter() - Constructor for class com.genologics.ri.jaxb.AbstractDateAdapter

Default constructor.

accountLocked - Variable in class com.genologics.ri.researcher.Credentials

Whether the researcher's account is locked.

action - Variable in class com.genologics.ri.permission.Permission

The permission action.

action - Variable in class com.genologics.ri.permission.PermissionLink

The permission action.

action - Variable in class com.genologics.ri.role.PermissionLink

The action associated with the permission.

action - Variable in class com.genologics.ri.step.NextAction

The action type.

actions - Variable in class com.genologics.ri.step.ProcessStep

Link to the actions associated with this step.

Actions - Class in com.genologics.ri.step

Represents actions applied or to be applied by a step in the workflow.

Actions() - Constructor for class com.genologics.ri.step.Actions

Default constructor.

Actions(URI) - Constructor for class com.genologics.ri.step.Actions

Constructor with URI.

ActionsLink - Class in com.genologics.ri.step

Identifies the resource that represents the actions applied or to be applied by the step.

ActionsLink() - Constructor for class com.genologics.ri.step.ActionsLink

Default constructor.

ActionsLink(Linkable<Actions>) - Constructor for class com.genologics.ri.step.ActionsLink

Constructor from a linkable object.

ActionsLink(URI) - Constructor for class com.genologics.ri.step.ActionsLink

Constructor with URI.

ActionType - Enum Class in com.genologics.ri.step

Enumeration of action types that can be performed on artifacts in a step.

ACTIVE - Enum constant in enum class com.genologics.ri.reagentlot.Status

The reagent lot is active.

ACTIVE - Enum constant in enum class com.genologics.ri.workflowconfiguration.Status

Workflow is currently active.

add(Link) - Method in class com.genologics.ri.Links

Adds a link to this collection.

add(Linkable<?>) - Method in class com.genologics.ri.Links

Adds a linkable object as a link to this collection.

ADD_REAGENT - Enum constant in enum class com.genologics.ri.processtype.TriggerStatus

The step is in the add reagent phase.

ADD_REAGENT - Enum constant in enum class com.genologics.ri.step.ProcessState

The step state when the step is in the stage where barcodes are attached to the samples.

ADD_REAGENT - Enum constant in enum class com.genologics.ri.stepconfiguration.TriggerStatus

Trigger executes when adding reagents.

addAll(Links) - Method in class com.genologics.ri.Links

Adds all links from another Links object.

addAll(Collection<? extends Linkable<Artifact>>) - Method in class com.genologics.ri.routing.ExtArtifactAssignments

Adds all artifacts from a collection to the list.

addAll(Collection<Link>) - Method in class com.genologics.ri.Links

Adds all links from a collection.

addArtifact(Linkable<Artifact>) - Method in class com.genologics.ri.routing.ExtArtifactAssignments

Adds an artifact to the list.

addArtifactGroup(Linkable<ArtifactGroup>) - Method in class com.genologics.ri.artifact.Artifact

Adds an artifact group to this artifact.

addAttribute(Attribute) - Method in class com.genologics.ri.reagenttype.SpecialType

Adds an attribute to this special type.

addAttribute(String, String) - Method in class com.genologics.ri.reagenttype.SpecialType

Adds an attribute to this special type using name and value.

addAvailableInput(Linkable<Artifact>) - Method in class com.genologics.ri.step.Pools

Creates and adds an available input from an artifact.

addAvailableInput(Input) - Method in class com.genologics.ri.step.Pools

Adds an available input artifact.

addAvailableProgram(AvailableProgram) - Method in class com.genologics.ri.step.ProcessStep

Adds an available program to the list of programs for this step.

addEppTriggers(EppTrigger) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Adds an EPP trigger.

addEscalatedArtifact(Linkable<Artifact>) - Method in class com.genologics.ri.step.Escalation

Adds an escalated artifact to the list from a linkable artifact.

addEscalatedArtifact(EscalatedArtifact) - Method in class com.genologics.ri.step.Escalation

Adds an escalated artifact to the list.

addField(UDF) - Method in class com.genologics.ri.userdefined.UDT

Adds a UDF to this user-defined type.

addField(String, FieldType, String) - Method in class com.genologics.ri.userdefined.UDT

Adds a UDF to this user-defined type.

addFile(ClarityFile) - Method in class com.genologics.ri.process.ClarityProcess

Adds a file to the process.

addFile(ClarityFile) - Method in class com.genologics.ri.project.Project

Add a file to the project.

addFile(ClarityFile) - Method in class com.genologics.ri.sample.SampleBase

Adds a file to this sample.

addFile(SharedResultFile) - Method in class com.genologics.ri.step.StepSetup

Adds a shared result file to the step.

addFile(SharedResultFile) - Method in class com.genologics.ri.stepconfiguration.StepSetup

Adds a shared result file to the step setup view.

addForCreate(Collection<Artifact>) - Method in class com.genologics.ri.artifact.ArtifactBatchFetchResult

Adds artifacts to be created.

addForCreate(Collection<Container>) - Method in class com.genologics.ri.container.ContainerBatchFetchResult

Adds containers for batch creation.

addForCreate(Collection<ClarityFile>) - Method in class com.genologics.ri.file.ClarityFileBatchFetchResult

Adds a collection of file entities to this batch for creation.

addForCreate(Collection<Sample>) - Method in class com.genologics.ri.sample.SampleBatchFetchResult

Add samples to this object ready for creation.

addForCreate(Collection<E>) - Method in interface com.genologics.ri.BatchUpdate

Add entities for creation operations.

addForUpdate(Collection<Artifact>) - Method in class com.genologics.ri.artifact.ArtifactBatchFetchResult

Adds artifacts to be updated.

addForUpdate(Collection<Container>) - Method in class com.genologics.ri.container.ContainerBatchFetchResult

Adds containers for batch update.

addForUpdate(Collection<ClarityFile>) - Method in class com.genologics.ri.file.ClarityFileBatchFetchResult

Adds a collection of file entities to this batch for update.

addForUpdate(Collection<Sample>) - Method in class com.genologics.ri.sample.SampleBatchFetchResult

Adds samples to this object for update.

addForUpdate(Collection<E>) - Method in interface com.genologics.ri.BatchUpdate

Add entities for update operations.

addIceBucketField(IceBucketField) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Adds an ice bucket field.

addInput(Linkable<Artifact>) - Method in class com.genologics.ri.step.PooledInputs

Creates and adds an input from an artifact.

addInput(Linkable<Artifact>, Linkable<ControlType>, Long) - Method in class com.genologics.ri.step.StepCreation

Creates and adds an input to the step.

addInput(Linkable<Artifact>, QCFlag) - Method in class com.genologics.ri.processexecution.ExecutableInputOutputMap

Adds an input with a QC flag to the input list.

addInput(Input) - Method in class com.genologics.ri.processexecution.ExecutableInputOutputMap

Adds an input to the input list.

addInput(CreationInput) - Method in class com.genologics.ri.step.StepCreation

Adds an input to the step.

addInput(Input) - Method in class com.genologics.ri.step.PooledInputs

Adds an input to this pool.

addInputOutputMap(LimsEntityLinkable<Artifact>, LimsEntityLinkable<Artifact>) - Method in class com.genologics.ri.step.StepDetails

Creates and adds an input/output mapping to the step.

addInputOutputMap(InputOutputMap) - Method in class com.genologics.ri.process.ClarityProcess

Adds an input-output mapping.

addInputOutputMap(ExecutableInputOutputMap) - Method in class com.genologics.ri.processexecution.ExecutableProcess

Adds an input-output map to the list.

addInputOutputMap(InputOutputMap) - Method in class com.genologics.ri.step.StepDetails

Adds an input/output mapping to the step.

addOutputPlacement(Linkable<Artifact>, Linkable<Container>, String) - Method in class com.genologics.ri.step.Placements

Creates and adds an output placement.

addOutputPlacement(OutputPlacement) - Method in class com.genologics.ri.step.Placements

Adds an output placement.

addOutputReagent(Output) - Method in class com.genologics.ri.step.Reagents

Adds an output reagent to the list.

addPermittedContainer(ContainerType) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Adds a permitted container type from a ContainerType entity.

addPermittedContainer(String) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Adds a permitted container type by name.

addPermittedControlType(Linkable<ControlType>) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Adds a permitted control type.

addPermittedReagentCategory(ReagentType) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Adds a permitted reagent category from a ReagentType entity.

addPermittedReagentCategory(String) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Adds a permitted reagent category by name.

addPlacement(Placement) - Method in class com.genologics.ri.container.Container

Adds a placement to the container.

addPlacement(LimsEntityLinkable<Artifact>, String) - Method in class com.genologics.ri.container.Container

Adds a placement to the container with an artifact and well position.

addPooledInputs(PooledInputs) - Method in class com.genologics.ri.step.Pools

Adds a pooled input group.

addPooledInputs(Collection<? extends Linkable<Artifact>>, String, Linkable<Artifact>) - Method in class com.genologics.ri.step.Pools

Creates and adds a pooled input group.

addPreset(FieldDynamicPreset) - Method in class com.genologics.ri.configuration.FieldDynamicPresetDetails

Adds a preset to the list.

addPreset(String) - Method in class com.genologics.ri.configuration.FieldDynamicPresetDetails

Adds a preset value to the list, creating a new FieldDynamicPreset.

addProtocol(Linkable<Protocol>) - Method in class com.genologics.ri.workflowconfiguration.Workflow

Adds a protocol to this workflow.

addQueueField(QueueField) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Adds a queue field.

addReagentLabel(ReagentLabel) - Method in class com.genologics.ri.artifact.Artifact

Adds a reagent label to this artifact.

addReagentLabel(String) - Method in class com.genologics.ri.artifact.Artifact

Adds a reagent label to this artifact.

addReagentLot(LimsEntityLinkable<ReagentLot>) - Method in class com.genologics.ri.step.ReagentLots

Adds a reagent lot to the list by creating a link from the linkable object.

addReagentLot(ReagentLotLink) - Method in class com.genologics.ri.step.ReagentLots

Adds a reagent lot link to the list.

addRequiredReagentKit(Linkable<ReagentKit>) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Adds a required reagent kit.

Address - Class in com.genologics.ri

Address contains the related fields of a mailing address.

Address() - Constructor for class com.genologics.ri.Address

addRole(Role) - Method in class com.genologics.ri.researcher.Credentials

Adds a role to the researcher's credentials.

addRole(String) - Method in class com.genologics.ri.researcher.Credentials

Adds a role to the researcher's credentials.

addSample(LimsEntityLinkable<Sample>) - Method in class com.genologics.ri.artifact.Artifact

Adds a sample to this artifact.

addSample(Linkable<Sample>) - Method in class com.genologics.ri.artifact.Artifact

Adds a sample to this artifact.

addSelectedContainer(Linkable<Container>) - Method in class com.genologics.ri.step.Placements

Adds a selected container.

addStage(Linkable<Stage>) - Method in class com.genologics.ri.workflowconfiguration.Workflow

Adds a stage to this workflow.

addStepField(Field) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Adds a step field.

addStepProperty(StepProperty) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Adds a step property.

addStepProperty(String, String) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Adds a step property with name and value.

addTransition(NextStep) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Adds a transition to a next step.

addTypeDefinition(Linkable<Field>) - Method in class com.genologics.ri.processtype.ProcessType

Adds a type definition for the specified field.

addWorkflowStage(WorkflowStage) - Method in class com.genologics.ri.artifact.Artifact

Adds a workflow stage to this artifact.

ADMIN_ROLE - Static variable in class com.genologics.ri.researcher.Role

The name for the facility administrator role.

advanceProcessStep(ProcessStep) - Method in interface org.cruk.clarity.api.ClarityAPI

Move the process step to its next stage.

advanceProcessStep(ProcessStep) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Move the process step to its next stage.

advanceStep(ProcessStep) - Method in interface org.cruk.clarity.api.automation.ClarityProcessAutomation

Move a process step on to the next stage.

advanceStep(ProcessStep) - Method in class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Move a process step on to the next stage.

AFTER - Enum constant in enum class com.genologics.ri.processtype.TriggerPoint

The trigger executes after the step.

AFTER - Enum constant in enum class com.genologics.ri.stepconfiguration.TriggerPoint

Trigger executes after the step action.

afterInitialisation() - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

When this bean has finished Spring set up (all properties set), the configuration that may have been supplied during start up needs to be applied correctly to this bean and some objects it depends on.

allowNonPresetValues - Variable in class com.genologics.ri.configuration.Field

Whether values other than preset values are allowed.

alpha - Variable in class com.genologics.ri.containertype.Dimension

Whether numbering in this dimension is using letters (true) or numbers (false).

ANALYTE - Enum constant in enum class com.genologics.ri.artifact.OutputType

Analyte output type.

ANY - Enum constant in enum class org.cruk.clarity.api.cache.CacheStatefulBehaviour

Only fetch entities if they are not in the cache.

api - Variable in class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Clarity API.

api - Variable in class org.cruk.clarity.api.cache.ClarityAPICache

The API this aspect will call through to.

api - Variable in class org.cruk.clarity.api.impl.LatestVersionsResetAspect

The API instance through its internal access methods.

API_PATH_BASE - Static variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

The first part of the path for API calls.

apiCredentials - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

User name and password credentials for accessing the Clarity API.

apiRoot - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

The root path for all API calls to Clarity server.

archived - Variable in class com.genologics.ri.controltype.ControlType

Flag indicating if the control type is archived.

archived - Variable in class com.genologics.ri.instrument.Instrument

Whether the instrument has been archived.

archived - Variable in class com.genologics.ri.reagentkit.ReagentKit

Whether the reagent kit is archived.

ARCHIVED - Enum constant in enum class com.genologics.ri.reagentlot.Status

The reagent lot is archived.

ARCHIVED - Enum constant in enum class com.genologics.ri.workflowconfiguration.Status

Workflow has been archived.

arrangements - Variable in class com.genologics.ri.step.ProcessStep

Link to the arrangements associated with this step.

Arrangements - Class in com.genologics.ri.step

The detailed representation of a step's output container Tube Rack arrangements only for an Add Label Step.

Arrangements() - Constructor for class com.genologics.ri.step.Arrangements

Default constructor.

ArrangementsLink - Class in com.genologics.ri.step

Identifies the resource that represents the arrangements (if any) for the step.

ArrangementsLink() - Constructor for class com.genologics.ri.step.ArrangementsLink

Default constructor.

ArrangementsLink(Linkable<Arrangements>) - Constructor for class com.genologics.ri.step.ArrangementsLink

Constructor from a linkable object.

ArrangementsLink(URI) - Constructor for class com.genologics.ri.step.ArrangementsLink

Constructor with URI.

artifact - Variable in class com.genologics.ri.artifact.Demux

The source artifact being demultiplexed.

artifact - Variable in class com.genologics.ri.sample.SampleBase

The artifact associated with this sample.

Artifact - Class in com.genologics.ri.artifact

The detailed representation of an Artifact.

Artifact() - Constructor for class com.genologics.ri.artifact.Artifact

Default constructor.

Artifact(URI) - Constructor for class com.genologics.ri.artifact.Artifact

Constructor with a URI.

Artifact(URI, String) - Constructor for class com.genologics.ri.artifact.Artifact

Constructor with URI and id.

ARTIFACT_GROUP_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The artifact group namespace.

ARTIFACT_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The artifact namespace.

ArtifactBase - Class in com.genologics.ri.processexecution

The base representation of an Artifact in the context of Process execution, defining common elements for both input and output Artifacts.

ArtifactBase() - Constructor for class com.genologics.ri.processexecution.ArtifactBase

ArtifactBatchFetchResult - Class in com.genologics.ri.artifact

The representation of a batch fetch result for artifacts.

ArtifactBatchFetchResult() - Constructor for class com.genologics.ri.artifact.ArtifactBatchFetchResult

Constructor.

ArtifactBatchFetchResult(Collection<Artifact>) - Constructor for class com.genologics.ri.artifact.ArtifactBatchFetchResult

Constructor taking a collection of artifacts.

ArtifactGroup - Class in com.genologics.ri.artifactgroup

ArtifactGroups are created by the Lab Scientist interface for each workflow.

ArtifactGroup() - Constructor for class com.genologics.ri.artifactgroup.ArtifactGroup

ArtifactGroupLink - Class in com.genologics.ri.artifact

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.

ArtifactGroupLink - Class in com.genologics.ri.artifactgroup

artifactGroup-link is a child element type of artifactGroup and provides a URI linking to the detailed representation of a artifactGroup.

ArtifactGroupLink() - Constructor for class com.genologics.ri.artifact.ArtifactGroupLink

Default constructor.

ArtifactGroupLink() - Constructor for class com.genologics.ri.artifactgroup.ArtifactGroupLink

Default constructor.

ArtifactGroupLink(Linkable<ArtifactGroup>) - Constructor for class com.genologics.ri.artifact.ArtifactGroupLink

Constructor from a Linkable.

ArtifactGroupLink(Linkable<ArtifactGroup>) - Constructor for class com.genologics.ri.artifactgroup.ArtifactGroupLink

Constructs a link from a Linkable object.

ArtifactGroupLink(URI) - Constructor for class com.genologics.ri.artifact.ArtifactGroupLink

Constructor taking a URI.

ArtifactGroupLink(URI) - Constructor for class com.genologics.ri.artifactgroup.ArtifactGroupLink

Constructs a link with the given URI.

ArtifactGroupLink(URI, String) - Constructor for class com.genologics.ri.artifact.ArtifactGroupLink

Constructor taking a URI and name.

ArtifactGroupLink(URI, String) - Constructor for class com.genologics.ri.artifactgroup.ArtifactGroupLink

Constructs a link with the given URI and name.

artifactGroups - Variable in class com.genologics.ri.artifact.Artifact

The list of artifact groups this artifact belongs to.

artifactGroups - Variable in class com.genologics.ri.artifactgroup.ArtifactGroups

The list of artifact group links.

ArtifactGroups - Class in com.genologics.ri.artifactgroup

The representation of a list of artifactGroup links.

ArtifactGroups() - Constructor for class com.genologics.ri.artifactgroup.ArtifactGroups

Default constructor.

ArtifactLink - Class in com.genologics.ri.artifact

Artifact-link is a child element type of artifacts and provides a URI linking to the detailed representation of an artifact.

ArtifactLink - Class in com.genologics.ri.process

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.

ArtifactLink - Class in com.genologics.ri.queue

Artifact-Link provides a URI linking to the detailed representation of an artifact in a queue.

ArtifactLink - Class in com.genologics.ri.routing

Link to an artifact for routing purposes.

ArtifactLink - Class in com.genologics.ri.sample

Artifact is a child element of Sample and provides a URI linking to the detailed representation of the artifact for the Sample.

ArtifactLink - Class in com.genologics.ri.step

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.

ArtifactLink() - Constructor for class com.genologics.ri.artifact.ArtifactLink

Default constructor.

ArtifactLink() - Constructor for class com.genologics.ri.process.ArtifactLink

Default constructor.

ArtifactLink() - Constructor for class com.genologics.ri.queue.ArtifactLink

Default constructor.

ArtifactLink() - Constructor for class com.genologics.ri.routing.ArtifactLink

Default constructor.

ArtifactLink() - Constructor for class com.genologics.ri.sample.ArtifactLink

Constructor for an empty artifact link.

ArtifactLink() - Constructor for class com.genologics.ri.step.ArtifactLink

Default constructor.

ArtifactLink(Artifact) - Constructor for class com.genologics.ri.process.ArtifactLink

Constructor from an artifact.

ArtifactLink(Artifact) - Constructor for class com.genologics.ri.queue.ArtifactLink

Constructor from an Artifact.

ArtifactLink(Artifact) - Constructor for class com.genologics.ri.step.ArtifactLink

Constructor from an artifact.

ArtifactLink(LimsEntityLinkable<Artifact>) - Constructor for class com.genologics.ri.artifact.ArtifactLink

Constructor from a LimsEntityLinkable.

ArtifactLink(LimsEntityLinkable<Artifact>) - Constructor for class com.genologics.ri.process.ArtifactLink

Constructor from a LIMS entity linkable object.

ArtifactLink(LimsEntityLinkable<Artifact>) - Constructor for class com.genologics.ri.queue.ArtifactLink

Constructor from a LimsEntityLinkable.

ArtifactLink(LimsEntityLinkable<Artifact>) - Constructor for class com.genologics.ri.sample.ArtifactLink

Constructor for an artifact link from a LIMS entity linkable artifact.

ArtifactLink(LimsEntityLinkable<Artifact>) - Constructor for class com.genologics.ri.step.ArtifactLink

Constructor from a LIMS entity linkable object.

ArtifactLink(Linkable<Artifact>) - Constructor for class com.genologics.ri.artifact.ArtifactLink

Constructor from a Linkable.

ArtifactLink(Linkable<Artifact>) - Constructor for class com.genologics.ri.process.ArtifactLink

Constructor from a linkable object.

ArtifactLink(Linkable<Artifact>) - Constructor for class com.genologics.ri.queue.ArtifactLink

Constructor from a Linkable.

ArtifactLink(Linkable<Artifact>) - Constructor for class com.genologics.ri.routing.ArtifactLink

Constructor from a Linkable.

ArtifactLink(Linkable<Artifact>) - Constructor for class com.genologics.ri.sample.ArtifactLink

Constructor for an artifact link from a linkable artifact.

ArtifactLink(Linkable<Artifact>) - Constructor for class com.genologics.ri.step.ArtifactLink

Constructor from a linkable object.

ArtifactLink(URI) - Constructor for class com.genologics.ri.artifact.ArtifactLink

Constructor taking a URI.

ArtifactLink(URI) - Constructor for class com.genologics.ri.process.ArtifactLink

Constructor with URI.

ArtifactLink(URI) - Constructor for class com.genologics.ri.queue.ArtifactLink

Constructor with URI.

ArtifactLink(URI) - Constructor for class com.genologics.ri.routing.ArtifactLink

Constructor with URI.

ArtifactLink(URI) - Constructor for class com.genologics.ri.sample.ArtifactLink

Constructor for an artifact link with a URI.

ArtifactLink(URI) - Constructor for class com.genologics.ri.step.ArtifactLink

Constructor with URI.

ArtifactLink(URI, String) - Constructor for class com.genologics.ri.artifact.ArtifactLink

Constructor taking a URI and LIMS id.

ArtifactLink(URI, String) - Constructor for class com.genologics.ri.process.ArtifactLink

Constructor with URI and LIMS id.

ArtifactLink(URI, String) - Constructor for class com.genologics.ri.queue.ArtifactLink

Constructor with URI and LIMS id.

ArtifactLink(URI, String) - Constructor for class com.genologics.ri.sample.ArtifactLink

Constructor for an artifact link with a URI and LIMS id.

ArtifactLink(URI, String) - Constructor for class com.genologics.ri.step.ArtifactLink

Constructor with URI and LIMS id.

artifacts - Variable in class com.genologics.ri.artifact.ArtifactBatchFetchResult

The list of artifacts in this batch.

artifacts - Variable in class com.genologics.ri.artifact.Artifacts

The list of artifact links.

artifacts - Variable in class com.genologics.ri.artifact.DemuxDetails

The artifacts in this demux details.

artifacts - Variable in class com.genologics.ri.artifactgroup.ArtifactGroup

Link to the artifacts contained in this group.

artifacts - Variable in class com.genologics.ri.queue.Queue

The list of artifacts in the queue.

artifacts - Variable in class com.genologics.ri.routing.ExtArtifactAssignments

The list of artifact links.

Artifacts - Class in com.genologics.ri.artifact

The representation of a list of artifact links.

Artifacts - Class in com.genologics.ri.artifactgroup

Artifacts is a link to 1...n child artifacts, that belong to the artifactGroup The link to an artifactList, filtered on artifactgroupID

Artifacts() - Constructor for class com.genologics.ri.artifact.Artifacts

Constructor.

Artifacts() - Constructor for class com.genologics.ri.artifactgroup.Artifacts

artifactType - Variable in class com.genologics.ri.processtype.ProcessInput

The artifact type for the input.

artifactType - Variable in class com.genologics.ri.processtype.ProcessOutput

The artifact type for the output.

artifactUri - Variable in class com.genologics.ri.step.NextAction

URI of the artifact.

artifactUri - Variable in class com.genologics.ri.step.Output

URI of the output artifact.

artifactUri - Variable in class com.genologics.ri.step.SharedResultFile

The URI of the artifact representing the shared result file.

assignedRoutes - Variable in class com.genologics.ri.routing.Routing

The list of artifact assignments to assign to workflows/stages.

assignWorkingFlag - Variable in class com.genologics.ri.processtype.ProcessOutput

Deprecated.

This property is no longer supported.

attachedTo - Variable in class com.genologics.ri.file.ClarityFile

The URI of the resource that this file is attached to (e.g., a project, sample, process, or artifact).

attachTo - Variable in class com.genologics.ri.processtype.Field

The entity to which this field is attached.

attachTo - Variable in class com.genologics.ri.stepconfiguration.Field

Defines what entity this field is attached to.

attachToCategory - Variable in class com.genologics.ri.configuration.Field

The category this field is attached to.

attachToCategory - Variable in class com.genologics.ri.configuration.Type

The category this user defined type is attached to.

attachToCategory - Variable in class com.genologics.ri.configuration.UdfConfigLink

The category this field is attached to.

attachToCategory - Variable in class com.genologics.ri.configuration.UdtConfigLink

The category this user defined type is attached to.

attachToName - Variable in class com.genologics.ri.configuration.Field

The name of the entity type this field is attached to.

attachToName - Variable in class com.genologics.ri.configuration.Type

The name of the entity type this user defined type is attached to.

attachToName - Variable in class com.genologics.ri.configuration.UdfConfigLink

The name of the entity type this field is attached to.

attachToName - Variable in class com.genologics.ri.configuration.UdtConfigLink

The name of the entity type this user defined type is attached to.

Attribute - Class in com.genologics.ri.reagenttype

Attribute is a child element of special type and provides a name-value pair of the special type.

Attribute() - Constructor for class com.genologics.ri.reagenttype.Attribute

Default constructor.

Attribute(String) - Constructor for class com.genologics.ri.reagenttype.Attribute

Constructor with name.

Attribute(String, String) - Constructor for class com.genologics.ri.reagenttype.Attribute

Constructor with name and value.

attributes - Variable in class com.genologics.ri.reagenttype.SpecialType

The list of attributes for this special type.

AuthenticatingClientHttpRequestFactory - Interface in org.cruk.clarity.api.http

Extension of the ClientHttpRequestFactory interface to allow authentication to be used with the REST client.

author - Variable in class com.genologics.ri.step.EscalationRequest

The author of the escalation request.

author - Variable in class com.genologics.ri.step.EscalationReview

The author of the escalation review.

AUTOMATIC - Enum constant in enum class com.genologics.ri.processtype.TriggerType

The trigger is invoked automatically.

AUTOMATIC - Enum constant in enum class com.genologics.ri.stepconfiguration.TriggerType

Automatic trigger that executes automatically.

automaticNextStep - Variable in class com.genologics.ri.step.ProcessStep

Link to the next step that will be automatically triggered after this step.

AutomaticNextStepLink - Class in com.genologics.ri.step

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.

AutomaticNextStepLink() - Constructor for class com.genologics.ri.step.AutomaticNextStepLink

Default constructor.

AutomaticNextStepLink(Linkable<ProcessStep>) - Constructor for class com.genologics.ri.step.AutomaticNextStepLink

Constructor from a linkable object.

AutomaticNextStepLink(URI) - Constructor for class com.genologics.ri.step.AutomaticNextStepLink

Constructor with URI.

Automation - Class in com.genologics.ri.automation

The automation element integrates the process with the Automation Worker (previously called External Program Plugin or EPP).

Automation() - Constructor for class com.genologics.ri.automation.Automation

Default constructor.

AUTOMATION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The automation namespace.

AutomationLink - Class in com.genologics.ri.automation

A link to an Automation entity.

AutomationLink() - Constructor for class com.genologics.ri.automation.AutomationLink

Default constructor.

AutomationLink(Automation) - Constructor for class com.genologics.ri.automation.AutomationLink

Constructor from an Automation entity.

AutomationLink(Linkable<Automation>) - Constructor for class com.genologics.ri.automation.AutomationLink

Constructor from a Linkable.

AutomationLink(URI) - Constructor for class com.genologics.ri.automation.AutomationLink

Constructor with URI.

AutomationLink(URI, String) - Constructor for class com.genologics.ri.automation.AutomationLink

Constructor with URI and name.

automations - Variable in class com.genologics.ri.automation.Automations

The list of automation links.

Automations - Class in com.genologics.ri.automation

A list of automation links returned from a query.

Automations() - Constructor for class com.genologics.ri.automation.Automations

Default constructor.

autoRevertToSFTP - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

Whether the SFTP mechanism can be used as a fall back for uploading files if a file exceeds the HTTP upload size limit.

availableInputs - Variable in class com.genologics.ri.step.Pools

The list of available input artifacts that can be pooled.

AvailableProgram - Class in com.genologics.ri.step

Identifies a program that is available for a step.

AvailableProgram() - Constructor for class com.genologics.ri.step.AvailableProgram

Default constructor.

AvailableProgram(URI) - Constructor for class com.genologics.ri.step.AvailableProgram

Constructor with URI.

AvailableProgram(URI, String) - Constructor for class com.genologics.ri.step.AvailableProgram

Constructor with URI and name.

availablePrograms - Variable in class com.genologics.ri.step.ProcessStep

The list of programs available for this step.

B

Batch<L> - Interface in com.genologics.ri

Interface for objects that hold batches of linkable items (links or entities).

batchCreate() - Element in annotation interface com.genologics.ri.ClarityBatchRetrieveResult

Flag indicating that the annotated entity can be created using a batch creation call.

batchUpdate() - Element in annotation interface com.genologics.ri.ClarityBatchRetrieveResult

Flag indicating that the annotated entity can be updated using a batch update call.

BatchUpdate<E> - Interface in com.genologics.ri

Extension of the Batch interface for classes that support bulk create or update operations for entities.

BEFORE - Enum constant in enum class com.genologics.ri.processtype.TriggerPoint

The trigger executes before the step.

BEFORE - Enum constant in enum class com.genologics.ri.stepconfiguration.TriggerPoint

Trigger executes before the step action.

beginProcessStep(StepCreation) - Method in interface org.cruk.clarity.api.automation.ClarityProcessAutomation

Start a protocol step as if running through Clarity.

beginProcessStep(StepCreation) - Method in class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Start a protocol step as if running through Clarity.

beginProcessStep(StepCreation) - Method in interface org.cruk.clarity.api.ClarityAPI

Start a protocol step as if running through Clarity.

beginProcessStep(StepCreation) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Start a protocol step as if running through Clarity.

behaviour - Variable in class org.cruk.clarity.api.cache.ClarityAPICache

The behaviour for dealing with stateful entities.

billingAddress - Variable in class com.genologics.ri.lab.Lab

The billing address for the lab.

bioSource - Variable in class com.genologics.ri.sample.SampleBase

Deprecated.

Biosource is not supported in Clarity.

BioSource - Class in com.genologics.ri.sample

Deprecated.

Biosource is not supported in Clarity.

BioSource() - Constructor for class com.genologics.ri.sample.BioSource

Deprecated.

Constructor for an empty biosource.

BioSource(String) - Constructor for class com.genologics.ri.sample.BioSource

Deprecated.

Constructor for a biosource with a name.

blockWrite(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Join point around methods that would cause a change in Clarity (create, update, delete, upload).

BOOLEAN - Enum constant in enum class com.genologics.ri.configuration.FieldType

Boolean field type.

BUILT_IN - Enum constant in enum class com.genologics.ri.processtype.Style

Built-in field.

BUILT_IN - Enum constant in enum class com.genologics.ri.stepconfiguration.Style

Built-in field style.

builtIn - Variable in class com.genologics.ri.role.Role

Whether this is a built-in system role.

C

cacheable() - Element in annotation interface com.genologics.ri.ClarityEntity

Whether entities of the class can be cached.

cacheConfig(int, int) - Method in class org.cruk.clarity.api.cache.spring.ClarityClientCacheConfiguration

Creates a cache configuration with the specified heap size and time-to-idle expiry.

cacheManager - Variable in class org.cruk.clarity.api.cache.ClarityAPICache

The cache manager.

CacheStatefulBehaviour - Enum Class in org.cruk.clarity.api.cache

Options for how the API cache handles entities that are stateful.

CalibrantWell - Class in com.genologics.ri.containertype

Deprecated.

This type is no longer supported.

CalibrantWell() - Constructor for class com.genologics.ri.containertype.CalibrantWell

Deprecated.

Default constructor for creating a new calibrant well.

CalibrantWell(String) - Constructor for class com.genologics.ri.containertype.CalibrantWell

Deprecated.

Constructor for creating a calibrant well with a specified name.

CalibrantWell(String, String) - Constructor for class com.genologics.ri.containertype.CalibrantWell

Deprecated.

Constructor for creating a calibrant well with a specified name and value.

calibrantWells - Variable in class com.genologics.ri.containertype.ContainerType

Deprecated.

This property is no longer supported and will be ignored if provided.

cancelStatefulOverride(String) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Undoes the effects of ClarityAPI.overrideStateful(StatefulOverride) after a call to ensure subsequent calls will respect the state parameter for stateful entities.

cancelStatefulOverride(String) - Method in interface org.cruk.clarity.api.impl.ClarityAPIInternal

Undoes the effects of ClarityAPI.overrideStateful(StatefulOverride) after a call to ensure subsequent calls will respect the state parameter for stateful entities.

cancelStatefulOverride(JoinPoint) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Makes sure the effects of ClarityAPI.overrideStateful() is reset after a call.

cancelStatefulOverride(JoinPoint) - Method in class org.cruk.clarity.api.impl.LatestVersionsResetAspect

Method invoked after any call on the API to not fetch the latest versions of stateful entities on the next call.

catalogueNumber - Variable in class com.genologics.ri.controltype.ControlType

The catalogue number of the control type.

catalogueNumber - Variable in class com.genologics.ri.reagentkit.ReagentKit

The catalogue number of the reagent kit.

category - Variable in class com.genologics.ri.exception.Exception

The category of the exception.

category - Variable in exception org.cruk.clarity.api.ClarityException

The category of the error.

channel - Variable in class com.genologics.ri.automation.Automation

The channel for this automation.

channel - Variable in class com.genologics.ri.processtype.Parameter

The channel on which the EPP runs.

checkCollectionHomogeneousAndUnique(Collection<E>, boolean) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Check that the given collection contains no nulls, that each item either has a URI or does not have a URI (depending on requireUri, that all objects in the collection are of the same class, and that, if requireUri is true, there are no repeated URIs in the collection (ignoring state).

checkDelete(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.debugging.RestClientSnoopingAspect

Join point for the rest template's exchange operations.

checkEntityAnnotated(Class<?>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Check that the class given as an entity class is annotated with the ClarityEntity annotation.

checkExchange(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.debugging.RestClientSnoopingAspect

Join point for the rest template's exchange operations.

checkFilestoreSet() - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Check the file store's host name and credentials have been set.

checkGet(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.debugging.RestClientSnoopingAspect

Join point for the rest template's get operations.

checkLinkCollectionHomogeneousAndUnique(Collection<L>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

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).

checkPutOrPost(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.debugging.RestClientSnoopingAspect

Join point for the rest template's put and post operations.

checkServerSet() - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Check the server's URL has been set.

childUris - Variable in class com.genologics.ri.configuration.Field

The URIs of child fields for hierarchical fields.

city - Variable in class com.genologics.ri.Address

The city.

CLARITY_ROLE - Static variable in class com.genologics.ri.researcher.Role

The name for the researcher role.

ClarityAPI - Interface in org.cruk.clarity.api

Interface to the Clarity API version 2 via REST.

ClarityAPICache - Class in org.cruk.clarity.api.cache

A cache optionally deployed around a ClarityAPI bean as an aspect.

ClarityAPICache() - Constructor for class org.cruk.clarity.api.cache.ClarityAPICache

Empty constructor.

ClarityAPIImpl - Class in org.cruk.clarity.api.impl

Implementation of ClarityAPI using the Clarity REST operations.

ClarityAPIImpl() - Constructor for class org.cruk.clarity.api.impl.ClarityAPIImpl

Standard constructor.

ClarityAPIImpl(Properties) - Constructor for class org.cruk.clarity.api.impl.ClarityAPIImpl

Initialise with an initial configuration from a properties file.

ClarityAPIInternal - Interface in org.cruk.clarity.api.impl

Interface to the Clarity API for internal use, mostly by the cache.

ClarityAPIPlaybackAspect - Class in org.cruk.clarity.api.playback

Aspect for replaying server exchanges from a directory containing XML representations of entities as would be returned from a real Clarity server.

ClarityAPIPlaybackAspect() - Constructor for class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Constructor.

ClarityAPIPlaybackAspect(File) - Constructor for class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Constructor.

ClarityAPIRecordingAspect - Class in org.cruk.clarity.api.record

Aspect for recording server exchanges with a real Clarity server as XML files to a directory on disk.

ClarityAPIRecordingAspect() - Constructor for class org.cruk.clarity.api.record.ClarityAPIRecordingAspect

Constructor.

ClarityAPIRecordingAspect(File) - Constructor for class org.cruk.clarity.api.record.ClarityAPIRecordingAspect

Constructor.

ClarityAutomationException - Exception in org.cruk.clarity.api.automation

Runtime exception when there is a failure in automating a Clarity process.

ClarityAutomationException() - Constructor for exception org.cruk.clarity.api.automation.ClarityAutomationException

Initialise with no details.

ClarityAutomationException(String) - Constructor for exception org.cruk.clarity.api.automation.ClarityAutomationException

Initialise with an error message.

ClarityAutomationException(String, Throwable) - Constructor for exception org.cruk.clarity.api.automation.ClarityAutomationException

Initialise with an error message and a cause.

ClarityAutomationException(Throwable) - Constructor for exception org.cruk.clarity.api.automation.ClarityAutomationException

Initialise with a cause.

ClarityBatchRetrieveResult - Annotation Interface in com.genologics.ri

Annotation for classes that contain lists of entities fetched from the API's batch retrieve mechanism.

clarityCacheManager() - Method in class org.cruk.clarity.api.cache.spring.ClarityClientCacheConfiguration

Creates and configures the EhCache cache manager for Clarity API entities.

ClarityClientCacheConfiguration - Class in org.cruk.clarity.api.cache.spring

Spring configuration class for the Clarity API cache.

ClarityClientCacheConfiguration() - Constructor for class org.cruk.clarity.api.cache.spring.ClarityClientCacheConfiguration

Constructor.

ClarityClientConfiguration - Class in org.cruk.clarity.api.spring

Main Spring configuration for the Clarity Client.

ClarityClientConfiguration() - Constructor for class org.cruk.clarity.api.spring.ClarityClientConfiguration

Constructor with just the standard packages.

ClarityClientConfiguration(Class<?>...) - Constructor for class org.cruk.clarity.api.spring.ClarityClientConfiguration

Constructor allowing additional package classes to be given for the JAXB context.

clarityClientHttpRequestFactory() - Method in class org.cruk.clarity.api.spring.ClarityClientConfiguration

HTTP client request factory.

ClarityClientPlaybackConfiguration - Class in org.cruk.clarity.api.playback.spring

Spring configuration for playback.

ClarityClientPlaybackConfiguration() - Constructor for class org.cruk.clarity.api.playback.spring.ClarityClientPlaybackConfiguration

Constructor.

ClarityClientRecordConfiguration - Class in org.cruk.clarity.api.record.spring

Spring configuration for recording.

ClarityClientRecordConfiguration() - Constructor for class org.cruk.clarity.api.record.spring.ClarityClientRecordConfiguration

Constructor.

ClarityClientSearchConfiguration - Class in org.cruk.clarity.api.search

Spring configuration for the Clarity Client with searches.

ClarityClientSearchConfiguration() - Constructor for class org.cruk.clarity.api.search.ClarityClientSearchConfiguration

Constructor.

ClarityEntity - Annotation Interface in com.genologics.ri

Annotation to put on classes that are entities in the Clarity LIMS.

ClarityException - Exception in org.cruk.clarity.api

Exception decoded when a response from an API call gives an exception object.

ClarityException(Exception) - Constructor for exception org.cruk.clarity.api.ClarityException

Initialise from the given API exception.

ClarityException(Exception, HttpStatusCode) - Constructor for exception org.cruk.clarity.api.ClarityException

Initialise from the given API exception with an HTTP status code.

clarityExceptionErrorHandler() - Method in class org.cruk.clarity.api.spring.ClarityClientConfiguration

Clarity client response handler.

ClarityFailureResponseErrorHandler - Class in org.cruk.clarity.api.http

REST client error handler that looks at the response body when there is a failure code (an HTTP 400 or 500 code) and sees if the body contains a Clarity exception message.

ClarityFailureResponseErrorHandler() - Constructor for class org.cruk.clarity.api.http.ClarityFailureResponseErrorHandler

Empty constructor.

ClarityFailureResponseErrorHandler(Unmarshaller) - Constructor for class org.cruk.clarity.api.http.ClarityFailureResponseErrorHandler

Constructor with the unmarshaller.

ClarityFile - Class in com.genologics.ri.file

The file element contains information about a file in the system.

ClarityFile() - Constructor for class com.genologics.ri.file.ClarityFile

Creates a new, empty ClarityFile.

ClarityFile(ClarityFile) - Constructor for class com.genologics.ri.file.ClarityFile

Creates a new ClarityFile as a copy of another ClarityFile, copying its URI and LIMS id.

ClarityFile(URI) - Constructor for class com.genologics.ri.file.ClarityFile

Creates a new ClarityFile with the specified URI.

ClarityFile(URI, String) - Constructor for class com.genologics.ri.file.ClarityFile

Creates a new ClarityFile with the specified URI and LIMS id.

ClarityFileBatchFetchResult - Class in com.genologics.ri.file

The representation of a batch of file resources.

ClarityFileBatchFetchResult() - Constructor for class com.genologics.ri.file.ClarityFileBatchFetchResult

Creates a new, empty ClarityFileBatchFetchResult.

ClarityFiles - Class in com.genologics.ri.file

The representation for a list of file links.

ClarityFiles() - Constructor for class com.genologics.ri.file.ClarityFiles

Creates a new, empty ClarityFiles instance.

clarityFileUploadTemplate() - Method in class org.cruk.clarity.api.spring.ClarityClientConfiguration

REST template for HTTP file uploads.

clarityHttpClient() - Method in class org.cruk.clarity.api.spring.ClarityClientConfiguration

Clarity HTTP client.

clarityJaxbClasses() - Method in class org.cruk.clarity.api.spring.ClarityClientConfiguration

Access to the list of classes managed by the Clarity client JAXB context.

clarityJaxbMarshaller() - Method in class org.cruk.clarity.api.spring.ClarityClientConfiguration

JAXB marshaller.

clarityJaxbUnmarshaller() - Method in class org.cruk.clarity.api.spring.ClarityClientConfiguration

JAXB unmarshaller.

ClarityProcess - Class in com.genologics.ri.process

The detailed representation of a process.

ClarityProcess() - Constructor for class com.genologics.ri.process.ClarityProcess

Default constructor.

ClarityProcess(URI) - Constructor for class com.genologics.ri.process.ClarityProcess

Constructor with URI.

ClarityProcess(URI, String) - Constructor for class com.genologics.ri.process.ClarityProcess

Constructor with URI and LIMS id.

ClarityProcessAutomation - Interface in org.cruk.clarity.api.automation

Helper for moving Clarity processes through their stages using the "click through" newer methods rather than the API's ExecutableProcess end point.

ClarityProcessAutomationImpl - Class in org.cruk.clarity.api.automation.impl

Helper for moving Clarity processes through their stages using the "click through" newer methods rather than the API's ExecutableProcess end point.

ClarityProcessAutomationImpl() - Constructor for class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Constructor.

ClarityProcessAutomationImpl(ClarityAPI) - Constructor for class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Constructor.

ClarityProcesses - Class in com.genologics.ri.process

The representation of a list of process links.

ClarityProcesses() - Constructor for class com.genologics.ri.process.ClarityProcesses

Default constructor.

ClarityQueryResult - Annotation Interface in com.genologics.ri

Annotation to put on classes that are the results of querying the API for entities.

clarityRestTemplate() - Method in class org.cruk.clarity.api.spring.ClarityClientConfiguration

REST template for the main Clarity client.

ClaritySFTPUploader - Interface in org.cruk.clarity.api.filestore

Interface for SFTP file store upload and delete implementations to adhere to.

ClarityUpdateException - Exception in org.cruk.clarity.api

Exception thrown when an attempt is made to change an object that cannot be altered in such a manner through the Clarity API.

ClarityUpdateException() - Constructor for exception org.cruk.clarity.api.ClarityUpdateException

Initialise with no details.

ClarityUpdateException(String) - Constructor for exception org.cruk.clarity.api.ClarityUpdateException

Initialise with an error message.

clear() - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Clears the cache of all cached entities.

clearDetailFields() - Method in class com.genologics.ri.file.ClarityFile

Helper method to clear the detail fields (attachedTo, contentLocation, originalLocation and published).

close() - Method in class org.cruk.clarity.api.impl.URLInputStreamResource

Close the resource's input stream and disconnect the URL connection.

closeDate - Variable in class com.genologics.ri.project.Project

The date the project was closed.

code - Variable in class com.genologics.ri.exception.Exception

The HTTP response code corresponding to the error (e.g., 400 for bad request, 500 for internal server error).

code - Variable in exception org.cruk.clarity.api.ClarityException

The error code.

columns - Variable in class com.genologics.ri.containertype.ContainerType

The x-dimension (horizontal/columns) of the container's coordinate system.

com.genologics.ri - module com.genologics.ri

The Clarity model classes for Clarity 6+.

com.genologics.ri - package com.genologics.ri

The root package of the classes generated (originally) from the Clarity schemas.

com.genologics.ri.artifact - package com.genologics.ri.artifact

Provides JAXB bindings for artifacts in the Genologics REST API.

com.genologics.ri.artifactgroup - package com.genologics.ri.artifactgroup

Entities for artifact groups in the Clarity system.

com.genologics.ri.automation - package com.genologics.ri.automation

Entities for automation resources in the Clarity system.

com.genologics.ri.configuration - package com.genologics.ri.configuration

Entities for system configuration in the Clarity system.

com.genologics.ri.container - package com.genologics.ri.container

Container entity and support classes for the Clarity REST API.

com.genologics.ri.containertype - package com.genologics.ri.containertype

Entities for container type definitions in the Clarity system.

com.genologics.ri.controltype - package com.genologics.ri.controltype

Entities for control types in the Clarity LIMS system.

com.genologics.ri.exception - package com.genologics.ri.exception

Entities for exception handling in the Clarity system.

com.genologics.ri.file - package com.genologics.ri.file

Entities for file resources in the Clarity system.

com.genologics.ri.globaltoken - package com.genologics.ri.globaltoken

Illumina have said that the types in this package are not actually released, and there's nothing in Clarity that uses them.

com.genologics.ri.instrument - package com.genologics.ri.instrument

Entities for instrument resources in the Clarity system.

com.genologics.ri.instrumenttype - package com.genologics.ri.instrumenttype

Entities for instrument type definitions in the Clarity system.

com.genologics.ri.jaxb - package com.genologics.ri.jaxb

Classes to aid the JAXB object mapping process.

com.genologics.ri.lab - package com.genologics.ri.lab

Provides classes for representing and managing laboratory entities in the Clarity LIMS system.

com.genologics.ri.permission - package com.genologics.ri.permission

Entities for user permissions in the Clarity system.

com.genologics.ri.process - package com.genologics.ri.process

Entities for processes executed in the Clarity system.

com.genologics.ri.processexecution - package com.genologics.ri.processexecution

Entities for process execution in the Clarity system.

com.genologics.ri.processtemplate - package com.genologics.ri.processtemplate

Entities for process templates in the Clarity system.

com.genologics.ri.processtype - package com.genologics.ri.processtype

Entities for process type definitions in the Clarity system.

com.genologics.ri.project - package com.genologics.ri.project

Project entity and supporting classes for the Clarity REST API.

com.genologics.ri.property - package com.genologics.ri.property

Entities for system properties in the Clarity system.

com.genologics.ri.protocolconfiguration - package com.genologics.ri.protocolconfiguration

Provides JAXB bindings for the protocol configuration domain model.

com.genologics.ri.queue - package com.genologics.ri.queue

Entities for work queues in the Clarity system.

com.genologics.ri.reagentkit - package com.genologics.ri.reagentkit

Provides JAXB binding classes for the Clarity REST API reagent kit entity and its related components.

com.genologics.ri.reagentlot - package com.genologics.ri.reagentlot

com.genologics.ri.reagenttype - package com.genologics.ri.reagenttype

Entities for reagent type definitions in the Clarity system.

com.genologics.ri.researcher - package com.genologics.ri.researcher

Provides classes for representing researchers in the Clarity LIMS system.

com.genologics.ri.role - package com.genologics.ri.role

Provides JAXB binding classes for the Clarity REST API role entity and its related components.

com.genologics.ri.routing - package com.genologics.ri.routing

Provides JAXB binding classes for the Clarity REST API routing entity and its related components.

com.genologics.ri.sample - package com.genologics.ri.sample

Provides classes for sample entities in the Clarity LIMS API.

com.genologics.ri.savedquery - package com.genologics.ri.savedquery

Entities for saved queries in the Clarity system.

com.genologics.ri.stage - package com.genologics.ri.stage

Entities for workflow stages in the Clarity system.

com.genologics.ri.step - package com.genologics.ri.step

Entities for workflow steps in the Clarity system.

com.genologics.ri.stepconfiguration - package com.genologics.ri.stepconfiguration

Entities for step configuration in the Clarity system.

com.genologics.ri.userdefined - package com.genologics.ri.userdefined

Entities for user-defined fields (UDFs) in the Clarity system.

com.genologics.ri.version - package com.genologics.ri.version

Entities for API version information in the Clarity system.

com.genologics.ri.workflowconfiguration - package com.genologics.ri.workflowconfiguration

Entities for workflow configuration in the Clarity system.

comment - Variable in class com.genologics.ri.step.EscalationRequest

Comment for the escalation request.

comment - Variable in class com.genologics.ri.step.EscalationReview

Comment for the escalation review.

compareTo(Placement) - Method in class com.genologics.ri.container.Placement

Compares this placement to another based on well position.

compareTo(Location) - Method in class com.genologics.ri.Location

Compares this location with another location.

COMPLETE - Enum constant in enum class com.genologics.ri.artifact.Status

Complete status.

COMPLETE - Enum constant in enum class com.genologics.ri.processtype.TriggerStatus

The step has been completed.

COMPLETE - Enum constant in enum class com.genologics.ri.step.ActionType

Complete the action.

COMPLETE - Enum constant in enum class com.genologics.ri.stepconfiguration.TriggerStatus

Trigger executes when the step is completed.

COMPLETE_REPEAT - Enum constant in enum class com.genologics.ri.step.ActionType

Complete and repeat.

COMPLETED - Enum constant in enum class com.genologics.ri.step.ProcessState

The step state when the step is complete.

concentration - Variable in class com.genologics.ri.controltype.ControlType

The concentration of the control type.

configuration - Variable in class com.genologics.ri.step.Actions

Configuration of the step.

configuration - Variable in class com.genologics.ri.step.Arrangements

Configuration of the step.

configuration - Variable in class com.genologics.ri.step.Placements

The configuration for this step.

configuration - Variable in class com.genologics.ri.step.Pools

The configuration for this step.

configuration - Variable in class com.genologics.ri.step.ProcessStep

The configuration of the step.

configuration - Variable in class com.genologics.ri.step.ProgramStatus

The configuration of the step.

configuration - Variable in class com.genologics.ri.step.ReagentLots

Provides a URI linking to the configuration resource that identifies the protocol step.

configuration - Variable in class com.genologics.ri.step.Reagents

Configuration of the step.

configuration - Variable in class com.genologics.ri.step.StepCreation

The configuration for the step.

configuration - Variable in class com.genologics.ri.step.StepDetails

The configuration of the step.

configuration - Variable in class com.genologics.ri.step.StepSetup

The configuration of the step.

CONFIGURATION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The configuration namespace.

Container - Class in com.genologics.ri.container

Container entity representing a physical container in the Clarity LIMS.

Container() - Constructor for class com.genologics.ri.container.Container

Default constructor.

Container(ContainerType) - Constructor for class com.genologics.ri.container.Container

Constructor with container type.

Container(ContainerType, String) - Constructor for class com.genologics.ri.container.Container

Constructor with container type and name.

Container(Linkable<ContainerType>) - Constructor for class com.genologics.ri.container.Container

Constructor with container type link.

Container(Linkable<ContainerType>, String) - Constructor for class com.genologics.ri.container.Container

Constructor with container type link and name.

Container(URI) - Constructor for class com.genologics.ri.container.Container

Constructor for Container with a URI.

Container(URI, String) - Constructor for class com.genologics.ri.container.Container

Constructor for Container with a URI and LIMS id.

CONTAINER_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The container namespace.

CONTAINER_TYPE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The container type namespace.

ContainerBatchFetchResult - Class in com.genologics.ri.container

The representation of a list of resource details for batch operations on containers.

ContainerBatchFetchResult() - Constructor for class com.genologics.ri.container.ContainerBatchFetchResult

Default constructor.

ContainerBatchFetchResult(Collection<Container>) - Constructor for class com.genologics.ri.container.ContainerBatchFetchResult

Constructor with a collection of containers.

ContainerLink - Class in com.genologics.ri.container

Container-link is a child element type of containers and provides a URI linking to the detailed representation of a container.

ContainerLink - Class in com.genologics.ri

Container is a child element of location and provides a URI linking to the detailed representation of the Container for the location.

ContainerLink - Class in com.genologics.ri.step

Provides a URI linking to a selected container to be used for placement.

ContainerLink() - Constructor for class com.genologics.ri.container.ContainerLink

Default constructor.

ContainerLink() - Constructor for class com.genologics.ri.ContainerLink

Default constructor.

ContainerLink() - Constructor for class com.genologics.ri.step.ContainerLink

Default constructor.

ContainerLink(Container) - Constructor for class com.genologics.ri.container.ContainerLink

Constructor from a container.

ContainerLink(LimsEntityLinkable<Container>) - Constructor for class com.genologics.ri.container.ContainerLink

Constructor from a LIMS entity linkable container.

ContainerLink(LimsEntityLinkable<Container>) - Constructor for class com.genologics.ri.ContainerLink

Constructor from a LIMS entity linkable container.

ContainerLink(Linkable<Container>) - Constructor for class com.genologics.ri.container.ContainerLink

Constructor from a linkable container.

ContainerLink(Linkable<Container>) - Constructor for class com.genologics.ri.ContainerLink

Constructor from a linkable container.

ContainerLink(Linkable<Container>) - Constructor for class com.genologics.ri.step.ContainerLink

Constructor from a linkable object.

ContainerLink(URI) - Constructor for class com.genologics.ri.container.ContainerLink

Constructor with URI.

ContainerLink(URI) - Constructor for class com.genologics.ri.ContainerLink

Constructor with URI.

ContainerLink(URI) - Constructor for class com.genologics.ri.step.ContainerLink

Constructor with URI.

ContainerLink(URI, String) - Constructor for class com.genologics.ri.container.ContainerLink

Constructor with URI and LIMS id.

ContainerLink(URI, String) - Constructor for class com.genologics.ri.ContainerLink

Constructor with URI and LIMS id.

ContainerLink(URI, String, String) - Constructor for class com.genologics.ri.container.ContainerLink

Constructor with URI, LIMS id, and name.

containers - Variable in class com.genologics.ri.container.ContainerBatchFetchResult

The list of containers.

containers - Variable in class com.genologics.ri.container.Containers

The list of container links.

Containers - Class in com.genologics.ri.container

The representation for a list of container links.

Containers() - Constructor for class com.genologics.ri.container.Containers

Default constructor.

ContainerState - Enum Class in com.genologics.ri.container

An enumeration of the values possible in the Container.state attribute.

containerType - Variable in class com.genologics.ri.container.Container

Link to the container type.

containerType - Variable in class com.genologics.ri.step.StepCreation

The name of the container type to be used for outputs.

ContainerType - Class in com.genologics.ri.containertype

The detailed representation of a container type.

ContainerType() - Constructor for class com.genologics.ri.containertype.ContainerType

ContainerTypeLink - Class in com.genologics.ri.container

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.

ContainerTypeLink - Class in com.genologics.ri.containertype

Container-type-link is a child element type of containers and provides a URI linking to the detailed representation of a container type.

ContainerTypeLink - Class in com.genologics.ri.processtype

Link to a container type within a process type configuration.

ContainerTypeLink() - Constructor for class com.genologics.ri.container.ContainerTypeLink

Default constructor.

ContainerTypeLink() - Constructor for class com.genologics.ri.containertype.ContainerTypeLink

Default constructor for creating a new container type link.

ContainerTypeLink() - Constructor for class com.genologics.ri.processtype.ContainerTypeLink

Constructs a new container type link.

ContainerTypeLink(ContainerType) - Constructor for class com.genologics.ri.container.ContainerTypeLink

Constructor from a container type.

ContainerTypeLink(ContainerType) - Constructor for class com.genologics.ri.containertype.ContainerTypeLink

Constructor for creating a container type link from a container type object.

ContainerTypeLink(ContainerType) - Constructor for class com.genologics.ri.processtype.ContainerTypeLink

Constructs a new container type link from a container type entity.

ContainerTypeLink(Linkable<ContainerType>) - Constructor for class com.genologics.ri.container.ContainerTypeLink

Constructor from a linkable container type.

ContainerTypeLink(Linkable<ContainerType>) - Constructor for class com.genologics.ri.containertype.ContainerTypeLink

Constructor for creating a container type link from a linkable object.

ContainerTypeLink(Linkable<ContainerType>) - Constructor for class com.genologics.ri.processtype.ContainerTypeLink

Constructs a new container type link from a linkable object.

ContainerTypeLink(URI) - Constructor for class com.genologics.ri.container.ContainerTypeLink

Constructor with URI.

ContainerTypeLink(URI) - Constructor for class com.genologics.ri.containertype.ContainerTypeLink

Constructor for creating a container type link with a specified URI.

ContainerTypeLink(URI) - Constructor for class com.genologics.ri.processtype.ContainerTypeLink

Constructs a new container type link with the specified URI.

ContainerTypeLink(URI, String) - Constructor for class com.genologics.ri.container.ContainerTypeLink

Constructor with URI and name.

ContainerTypeLink(URI, String) - Constructor for class com.genologics.ri.containertype.ContainerTypeLink

Constructor for creating a container type link with a specified URI and name.

ContainerTypeLink(URI, String) - Constructor for class com.genologics.ri.processtype.ContainerTypeLink

Constructs a new container type link with the specified URI and name.

containerTypes - Variable in class com.genologics.ri.containertype.ContainerTypes

The list of container type links.

ContainerTypes - Class in com.genologics.ri.containertype

The representation for a list of container type links.

ContainerTypes() - Constructor for class com.genologics.ri.containertype.ContainerTypes

Default constructor for creating a new container types list.

contentLength() - Method in class org.cruk.clarity.api.impl.URLInputStreamResource

Get the size of the resource.

contentLocation - Variable in class com.genologics.ri.file.ClarityFile

The network location URI where the file content can be retrieved.

context - Variable in class com.genologics.ri.automation.Automation

The context in which this automation runs.

Context - Enum Class in com.genologics.ri.automation

The available options for the automation context.

CONTINUE - Enum constant in enum class com.genologics.ri.artifact.QCFlag

Continue despite quality control status.

CONTINUE - Enum constant in enum class com.genologics.ri.processexecution.QCFlag

Continue processing despite QC concerns.

CONTROL_TYPE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The control type namespace.

controlledVocabulary - Variable in class com.genologics.ri.configuration.Field

Whether this field uses a controlled vocabulary.

controlType - Variable in class com.genologics.ri.artifact.Artifact

The control type if this artifact is a control sample.

controlType - Variable in class com.genologics.ri.sample.SampleBase

The control type associated with this sample.

ControlType - Class in com.genologics.ri.controltype

Represents a control type in the Clarity LIMS system.

ControlType() - Constructor for class com.genologics.ri.controltype.ControlType

Default constructor.

ControlType(URI) - Constructor for class com.genologics.ri.controltype.ControlType

Constructor with a URI.

ControlTypeLink - Class in com.genologics.ri.artifact

Provide a URI linking to the control type if this artifact is a control sample.

ControlTypeLink - Class in com.genologics.ri.controltype

Control-type-link is a child element type of controlTypes and provides a URI linking to the detailed representation of a ControlType.

ControlTypeLink - Class in com.genologics.ri.processtype

Link to a control type within a process type configuration.

ControlTypeLink - Class in com.genologics.ri.sample

Control Type provides a name and a URI linking to the detailed representation of the Control Type associated with the Sample.

ControlTypeLink - Class in com.genologics.ri.stepconfiguration

Control-type-link is a child element type of controlTypes and provides a URI linking to the detailed representation of a ControlType.

ControlTypeLink() - Constructor for class com.genologics.ri.artifact.ControlTypeLink

Default constructor.

ControlTypeLink() - Constructor for class com.genologics.ri.controltype.ControlTypeLink

Default constructor.

ControlTypeLink() - Constructor for class com.genologics.ri.processtype.ControlTypeLink

Constructs a new control type link.

ControlTypeLink() - Constructor for class com.genologics.ri.sample.ControlTypeLink

Constructor for an empty control type link.

ControlTypeLink() - Constructor for class com.genologics.ri.stepconfiguration.ControlTypeLink

Default constructor.

ControlTypeLink(ControlType) - Constructor for class com.genologics.ri.controltype.ControlTypeLink

Constructs a control type link from a control type object.

ControlTypeLink(ControlType) - Constructor for class com.genologics.ri.processtype.ControlTypeLink

Constructs a new control type link from a control type entity.

ControlTypeLink(ControlType) - Constructor for class com.genologics.ri.sample.ControlTypeLink

Constructor for a control type link from a control type entity.

ControlTypeLink(ControlType) - Constructor for class com.genologics.ri.stepconfiguration.ControlTypeLink

Constructor from a control type entity.

ControlTypeLink(Linkable<ControlType>) - Constructor for class com.genologics.ri.artifact.ControlTypeLink

Constructor from a Linkable.

ControlTypeLink(Linkable<ControlType>) - Constructor for class com.genologics.ri.controltype.ControlTypeLink

Constructs a control type link from a linkable object.

ControlTypeLink(Linkable<ControlType>) - Constructor for class com.genologics.ri.processtype.ControlTypeLink

Constructs a new control type link from a linkable object.

ControlTypeLink(Linkable<ControlType>) - Constructor for class com.genologics.ri.sample.ControlTypeLink

Constructor for a control type link from a linkable control type.

ControlTypeLink(Linkable<ControlType>) - Constructor for class com.genologics.ri.stepconfiguration.ControlTypeLink

Constructor from a linkable control type.

ControlTypeLink(URI) - Constructor for class com.genologics.ri.artifact.ControlTypeLink

Constructor taking a URI.

ControlTypeLink(URI) - Constructor for class com.genologics.ri.controltype.ControlTypeLink

Constructs a control type link with the specified URI.

ControlTypeLink(URI) - Constructor for class com.genologics.ri.processtype.ControlTypeLink

Constructs a new control type link with the specified URI.

ControlTypeLink(URI) - Constructor for class com.genologics.ri.sample.ControlTypeLink

Constructor for a control type link with a URI.

ControlTypeLink(URI) - Constructor for class com.genologics.ri.stepconfiguration.ControlTypeLink

Constructor with URI.

ControlTypeLink(URI, String) - Constructor for class com.genologics.ri.controltype.ControlTypeLink

Constructs a control type link with the specified URI and name.

ControlTypeLink(URI, String) - Constructor for class com.genologics.ri.processtype.ControlTypeLink

Constructs a new control type link with the specified URI and name.

ControlTypeLink(URI, String) - Constructor for class com.genologics.ri.sample.ControlTypeLink

Constructor for a control type link with a URI and name.

ControlTypeLink(URI, String) - Constructor for class com.genologics.ri.stepconfiguration.ControlTypeLink

Constructor with URI and name.

controlTypes - Variable in class com.genologics.ri.controltype.ControlTypes

The list of control type links.

ControlTypes - Class in com.genologics.ri.controltype

The representation of a list of control types in the Clarity LIMS system.

ControlTypes() - Constructor for class com.genologics.ri.controltype.ControlTypes

Default constructor.

controlTypeUri - Variable in class com.genologics.ri.step.CreationInput

URI of the control type.

country - Variable in class com.genologics.ri.Address

The country.

creatable() - Element in annotation interface com.genologics.ri.ClarityEntity

If true, the flag indicates that entities of the annotated type can be created with a POST.

create(E) - Method in interface org.cruk.clarity.api.ClarityAPI

Create an instance of the given entity on the server.

create(E) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Create an instance of the given entity on the server.

create(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Join point for the ClarityAPI.create method.

createActions() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of Actions.

createActions(Actions) - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of JAXBElement<Actions>.

createActionsLink() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of ActionsLink.

createAddress() - Method in class com.genologics.ri.ObjectFactory

Creates a new Address instance.

createAll(Collection<E>) - Method in interface org.cruk.clarity.api.ClarityAPI

Create a batch of entities on the server.

createAll(Collection<E>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Create a batch of entities on the server.

createAll(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Join point for the ClarityAPI.createAll method.

createArtifact() - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a new Artifact instance.

createArtifact() - Method in class com.genologics.ri.process.ObjectFactory

Creates a new ArtifactLink instance.

createArtifact() - Method in class com.genologics.ri.routing.ObjectFactory

Creates a new ArtifactLink instance.

createArtifact() - Method in class com.genologics.ri.sample.ObjectFactory

Create an instance of ArtifactLink.

createArtifact() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of ArtifactLink.

createArtifact(Artifact) - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a JAXBElement for Artifact.

createArtifactgroup() - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a new ArtifactGroupLink instance.

createArtifactgroup() - Method in class com.genologics.ri.artifactgroup.ObjectFactory

Create an instance of ArtifactGroup.

createArtifactgroup(ArtifactGroup) - Method in class com.genologics.ri.artifactgroup.ObjectFactory

Create an instance of JAXBElement<ArtifactGroup>.

createArtifactgroupLink() - Method in class com.genologics.ri.artifactgroup.ObjectFactory

Create an instance of ArtifactGroupLink.

createArtifactgroups() - Method in class com.genologics.ri.artifactgroup.ObjectFactory

Create an instance of ArtifactGroups.

createArtifactgroups(ArtifactGroups) - Method in class com.genologics.ri.artifactgroup.ObjectFactory

Create an instance of JAXBElement<ArtifactGroups>.

createArtifactLink() - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a new ArtifactLink instance.

createArtifactLink() - Method in class com.genologics.ri.queue.ObjectFactory

Creates a new ArtifactLink instance.

createArtifacts() - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a new Artifacts instance.

createArtifacts() - Method in class com.genologics.ri.artifactgroup.ObjectFactory

Create an instance of Artifacts.

createArtifacts(Artifacts) - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a JAXBElement for Artifacts.

createAttribute() - Method in class com.genologics.ri.reagenttype.ObjectFactory

Create an instance of Attribute.

createAutomaticNextStepLink() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of AutomaticNextStepLink.

createAutomation() - Method in class com.genologics.ri.automation.ObjectFactory

Creates a new Automation instance.

createAutomation(Automation) - Method in class com.genologics.ri.automation.ObjectFactory

Creates a JAXBElement for Automation.

createAutomationLink() - Method in class com.genologics.ri.automation.ObjectFactory

Creates a new AutomationLink instance.

createAutomations() - Method in class com.genologics.ri.automation.ObjectFactory

Creates a new Automations instance.

createAutomations(Automations) - Method in class com.genologics.ri.automation.ObjectFactory

Creates a JAXBElement for Automations.

createAvailableProgram() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of AvailableProgram.

createBiosource() - Method in class com.genologics.ri.sample.ObjectFactory

Deprecated.

Biosource is not supported in Clarity.

createCalibrantWell() - Method in class com.genologics.ri.containertype.ObjectFactory

Deprecated.

This method is no longer supported as CalibrantWell is deprecated.

createContainer() - Method in class com.genologics.ri.container.ObjectFactory

Creates a new Container instance.

createContainer() - Method in class com.genologics.ri.ObjectFactory

Creates a new ContainerLink instance.

createContainer() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of ContainerLink.

createContainer(Container) - Method in class com.genologics.ri.container.ObjectFactory

Creates a JAXBElement for Container.

createContainerLink() - Method in class com.genologics.ri.container.ObjectFactory

Creates a new ContainerLink instance.

createContainerName(String) - Method in class com.genologics.ri.container.ObjectFactory

Creates a JAXBElement for name in Container scope.

createContainerOccupiedWells(Long) - Method in class com.genologics.ri.container.ObjectFactory

Creates a JAXBElement for occupied-wells in Container scope.

createContainerPlacement(Placement) - Method in class com.genologics.ri.container.ObjectFactory

Creates a JAXBElement for Placement in Container scope.

createContainers() - Method in class com.genologics.ri.container.ObjectFactory

Creates a new Containers instance.

createContainers(Containers) - Method in class com.genologics.ri.container.ObjectFactory

Creates a JAXBElement for Containers.

createContainerState(String) - Method in class com.genologics.ri.container.ObjectFactory

Creates a JAXBElement for state in Container scope.

createContainerType() - Method in class com.genologics.ri.container.ObjectFactory

Creates a new ContainerTypeLink instance.

createContainerType() - Method in class com.genologics.ri.containertype.ObjectFactory

Creates a new instance of ContainerType.

createContainerType(ContainerTypeLink) - Method in class com.genologics.ri.container.ObjectFactory

Creates a JAXBElement for type in Container scope.

createContainerType(ContainerType) - Method in class com.genologics.ri.containertype.ObjectFactory

Creates a JAXBElement for marshalling a ContainerType object.

createContainerTypeLink() - Method in class com.genologics.ri.containertype.ObjectFactory

Creates a new instance of ContainerTypeLink.

createContainerTypeLink() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new ContainerTypeLink instance.

createContainerTypes() - Method in class com.genologics.ri.containertype.ObjectFactory

Creates a new instance of ContainerTypes.

createContainerTypes(ContainerTypes) - Method in class com.genologics.ri.containertype.ObjectFactory

Creates a JAXBElement for marshalling a ContainerTypes object.

createControlType() - Method in class com.genologics.ri.controltype.ObjectFactory

Creates a new instance of ControlType.

createControlType(ControlType) - Method in class com.genologics.ri.controltype.ObjectFactory

Creates a JAXBElement wrapping a ControlType instance.

createControlTypeLink() - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a new ControlTypeLink instance.

createControlTypeLink() - Method in class com.genologics.ri.controltype.ObjectFactory

Creates a new instance of ControlTypeLink.

createControlTypeLink() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new ControlTypeLink instance.

createControlTypeLink() - Method in class com.genologics.ri.sample.ObjectFactory

Create an instance of ControlTypeLink.

createControlTypeLink() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory

Creates a new ControlTypeLink instance.

createControlTypes() - Method in class com.genologics.ri.controltype.ObjectFactory

Creates a new instance of ControlTypes.

createControlTypes(ControlTypes) - Method in class com.genologics.ri.controltype.ObjectFactory

Creates a JAXBElement wrapping a ControlTypes instance.

createCreationInput() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of CreationInput.

createCredentials() - Method in class com.genologics.ri.researcher.ObjectFactory

Creates a new Credentials instance.

createdBy - Variable in class com.genologics.ri.reagentlot.ReagentLot

Link to the researcher who created this reagent lot.

createdDate - Variable in class com.genologics.ri.reagentlot.ReagentLot

The date when this reagent lot was created in the system.

createDemux() - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a new Demux instance.

createDemux(Demux) - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a JAXBElement for Demux.

createDemuxArtifact() - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a new DemuxArtifact instance.

createDemuxArtifactSample() - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a new DemuxArtifactSample instance.

createDemuxDetails() - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a new DemuxDetails instance.

createDemuxDetails(DemuxDetails) - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a JAXBElement for DemuxDetails.

createDemuxLink() - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a new DemuxLink instance.

createDemuxSourceArtifact() - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a new DemuxSourceArtifact instance.

createDetails() - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a new ArtifactBatchFetchResult instance.

createDetails() - Method in class com.genologics.ri.container.ObjectFactory

Creates a new ContainerBatchFetchResult instance.

createDetails() - Method in class com.genologics.ri.file.ObjectFactory

Creates a new instance of ClarityFileBatchFetchResult.

createDetails() - Method in class com.genologics.ri.sample.ObjectFactory

Create an instance of SampleBatchFetchResult.

createDetails() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of StepDetails.

createDetails(ArtifactBatchFetchResult) - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a JAXBElement for ArtifactBatchFetchResult.

createDetails(ContainerBatchFetchResult) - Method in class com.genologics.ri.container.ObjectFactory

Creates a JAXBElement for ContainerBatchFetchResult.

createDetails(ClarityFileBatchFetchResult) - Method in class com.genologics.ri.file.ObjectFactory

Creates a JAXBElement wrapping a ClarityFileBatchFetchResult instance.

createDetails(SampleBatchFetchResult) - Method in class com.genologics.ri.sample.ObjectFactory

Create an instance of JAXBElement<SampleBatchFetchResult>.

createDetails(StepDetails) - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of JAXBElement<StepDetails>.

createDetailsLink() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of StepDetailsLink.

createDimension() - Method in class com.genologics.ri.containertype.ObjectFactory

Creates a new instance of Dimension.

createEppTrigger() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new EppTrigger instance.

createEppTrigger() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory

Creates a new EppTrigger instance.

createEscalatedArtifact() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of EscalatedArtifact.

createEscalation() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of Escalation.

createEscalationRequest() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of EscalationRequest.

createEscalationReview() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of EscalationReview.

createException() - Method in class com.genologics.ri.exception.ObjectFactory

Creates an instance of Exception.

createException(Exception) - Method in class com.genologics.ri.exception.ObjectFactory

Creates an instance of JAXBElement<Exception> for use in marshalling the exception element.

createExternalArtifactAssignments() - Method in class com.genologics.ri.routing.ObjectFactory

Creates a new ExtArtifactAssignments instance.

createExternalid() - Method in class com.genologics.ri.ObjectFactory

Creates a new ExternalId instance.

createExternalid(ExternalId) - Method in class com.genologics.ri.ObjectFactory

Creates a JAXBElement for ExternalId.

createField() - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a new Field instance.

createField() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new Field instance.

createField() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory

Creates a new Field instance.

createField() - Method in class com.genologics.ri.userdefined.ObjectFactory

Create an instance of UDF

createField(Field) - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a JAXBElement for a Field.

createField(UDF) - Method in class com.genologics.ri.userdefined.ObjectFactory

Create an instance of JAXBElement<UDF>

createFieldDynamicPreset() - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a new FieldDynamicPreset instance.

createFieldDynamicPreset(FieldDynamicPreset) - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a JAXBElement for a FieldDynamicPreset.

createFieldDynamicPresetDetails() - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a new FieldDynamicPresetDetails instance.

createFieldDynamicPresetDetails(FieldDynamicPresetDetails) - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a JAXBElement for FieldDynamicPresetDetails.

createFieldLink() - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a new FieldLink instance.

createFile() - Method in class com.genologics.ri.file.ObjectFactory

Creates a new instance of ClarityFile.

createFile() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of SharedResultFile.

createFile(ClarityFile) - Method in class com.genologics.ri.file.ObjectFactory

Creates a JAXBElement wrapping a ClarityFile instance.

createFileLink() - Method in class com.genologics.ri.file.ObjectFactory

Creates a new instance of FileLink.

createFiles() - Method in class com.genologics.ri.file.ObjectFactory

Creates a new instance of ClarityFiles.

createFiles(ClarityFiles) - Method in class com.genologics.ri.file.ObjectFactory

Creates a JAXBElement wrapping a ClarityFiles instance.

createFormatter() - Method in class com.genologics.ri.jaxb.AbstractDateAdapter

Create the correct date format object for the type of dates expected.

createFormatter() - Method in class com.genologics.ri.jaxb.LongTimestampAdapter

Create a date formatter for the long timestamp format.

createFormatter() - Method in class com.genologics.ri.jaxb.ShortDateAdapter

Create a date formatter for the short date format.

createGenericTypeLink() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory

Creates a new GenericTypeLink instance.

createGlobalToken() - Method in class com.genologics.ri.globaltoken.ObjectFactory

Create an instance of GlobalToken.

createGlobalToken(GlobalToken) - Method in class com.genologics.ri.globaltoken.ObjectFactory

Create an instance of JAXBElement<GlobalToken>.

createGlobalTokenLink() - Method in class com.genologics.ri.globaltoken.ObjectFactory

Create an instance of GlobalTokenLink.

createGlobalTokens() - Method in class com.genologics.ri.globaltoken.ObjectFactory

Create an instance of GlobalTokens.

createGlobalTokens(GlobalTokens) - Method in class com.genologics.ri.globaltoken.ObjectFactory

Create an instance of JAXBElement<GlobalTokens>.

createHttpContext(HttpMethod, URI) - Method in class org.cruk.clarity.api.http.HttpComponentsClientHttpRequestFactoryBasicAuth

Provide the HTTP context set up for basic authentication by this factory.

createIceBucketField() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new IceBucketField instance.

createIceBucketField() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory

Creates a new IceBucketField instance.

createIndex() - Method in class com.genologics.ri.ObjectFactory

Creates a new Index instance.

createIndex(Index) - Method in class com.genologics.ri.ObjectFactory

Creates a JAXBElement for Index.

createInput() - Method in class com.genologics.ri.processexecution.ObjectFactory

Create an instance of Input.

createInput() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of Input.

createInputOutputMap() - Method in class com.genologics.ri.process.ObjectFactory

Creates a new InputOutputMap instance.

createInputOutputMap() - Method in class com.genologics.ri.processexecution.ObjectFactory

Create an instance of ExecutableInputOutputMap.

createInputOutputMap() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of InputOutputMap.

createInstrument() - Method in class com.genologics.ri.instrument.ObjectFactory

Create an instance of Instrument.

createInstrument() - Method in class com.genologics.ri.process.ObjectFactory

Creates a new InstrumentLink instance.

createInstrument() - Method in class com.genologics.ri.processexecution.ObjectFactory

Create an instance of InstrumentLink.

createInstrument() - Method in class com.genologics.ri.processtemplate.ObjectFactory

Creates a new InstrumentLink instance.

createInstrument() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of InstrumentLink.

createInstrument(Instrument) - Method in class com.genologics.ri.instrument.ObjectFactory

Create a JAXBElement for Instrument.

createInstrumentLink() - Method in class com.genologics.ri.instrument.ObjectFactory

Create an instance of InstrumentLink.

createInstruments() - Method in class com.genologics.ri.instrument.ObjectFactory

Create an instance of Instruments.

createInstruments(Instruments) - Method in class com.genologics.ri.instrument.ObjectFactory

Create a JAXBElement for Instruments.

createInstrumentType() - Method in class com.genologics.ri.instrumenttype.ObjectFactory

Create an instance of InstrumentType.

createInstrumentType(InstrumentType) - Method in class com.genologics.ri.instrumenttype.ObjectFactory

Create a JAXBElement for InstrumentType.

createInstrumentTypeLink() - Method in class com.genologics.ri.instrumenttype.ObjectFactory

Create an instance of InstrumentTypeLink.

createInstrumentTypeProcessType() - Method in class com.genologics.ri.instrumenttype.ObjectFactory

Create an instance of InstrumentTypeProcessType.

createInstrumentTypes() - Method in class com.genologics.ri.instrumenttype.ObjectFactory

Create an instance of InstrumentTypes.

createInstrumentTypes(InstrumentTypes) - Method in class com.genologics.ri.instrumenttype.ObjectFactory

Create a JAXBElement for InstrumentTypes.

createLab() - Method in class com.genologics.ri.lab.ObjectFactory

Creates a new Lab instance.

createLab() - Method in class com.genologics.ri.researcher.ObjectFactory

Creates a new LabLink instance.

createLab(Lab) - Method in class com.genologics.ri.lab.ObjectFactory

Creates a JAXBElement for the lab element.

createLabLink() - Method in class com.genologics.ri.lab.ObjectFactory

Creates a new LabLink instance.

createLabs() - Method in class com.genologics.ri.lab.ObjectFactory

Creates a new Labs instance.

createLabs(Labs) - Method in class com.genologics.ri.lab.ObjectFactory

Creates a JAXBElement for the labs element.

createLink() - Method in class com.genologics.ri.ObjectFactory

Creates a new Link instance.

createLinks() - Method in class com.genologics.ri.ObjectFactory

Creates a new Links instance.

createLinks(Links) - Method in class com.genologics.ri.ObjectFactory

Creates a JAXBElement for Links.

createLocation() - Method in class com.genologics.ri.ObjectFactory

Creates a new Location instance.

createLockableSetting() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory

Creates a new LockableSetting instance.

createLots(ReagentLots) - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of JAXBElement<ReagentLots>.

createNextAction() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of NextAction.

createNextStep() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory

Creates a new NextStep instance.

createOutput() - Method in class com.genologics.ri.processexecution.ObjectFactory

Create an instance of Output.

createOutput() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of Output.

createOutputPlacement() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of OutputPlacement.

createPage() - Method in class com.genologics.ri.ObjectFactory

Creates a new Page instance.

createParameter() - Method in class com.genologics.ri.process.ObjectFactory

Creates a new Parameter instance.

createParameter() - Method in class com.genologics.ri.processexecution.ObjectFactory

Create an instance of Parameter.

createParameter() - Method in class com.genologics.ri.processtemplate.ObjectFactory

Creates a new Parameter instance.

createParameter() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new Parameter instance.

createParentProcess() - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a new ParentProcessLink instance.

createParentProcess() - Method in class com.genologics.ri.process.ObjectFactory

Creates a new ParentProcessLink instance.

createPermission() - Method in class com.genologics.ri.permission.ObjectFactory

Create an instance of Permission.

createPermission(Permission) - Method in class com.genologics.ri.permission.ObjectFactory

Create a JAXBElement for Permission.

createPermissionLink() - Method in class com.genologics.ri.permission.ObjectFactory

Create an instance of PermissionLink.

createPermissionLink() - Method in class com.genologics.ri.role.ObjectFactory

Creates a new PermissionLink instance.

createPermissions() - Method in class com.genologics.ri.permission.ObjectFactory

Create an instance of Permissions.

createPermissions(Permissions) - Method in class com.genologics.ri.permission.ObjectFactory

Create a JAXBElement for Permissions.

createPlacement() - Method in class com.genologics.ri.container.ObjectFactory

Creates a new Placement instance.

createPlacements() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of Placements.

createPlacements(Placements) - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of JAXBElement<Placements>.

createPlacementsLink() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of PlacementsLink.

createPooledInputs() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of PooledInputs.

createPools() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of Pools.

createPools(Pools) - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of JAXBElement<Pools>.

createPoolsLink() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of PoolsLink.

createPoolStep() - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a new PoolStep instance.

createProcess() - Method in class com.genologics.ri.process.ObjectFactory

Creates a new ClarityProcess instance.

createProcess() - Method in class com.genologics.ri.processexecution.ObjectFactory

Create an instance of ExecutableProcess.

createProcess(ClarityProcess) - Method in class com.genologics.ri.process.ObjectFactory

Creates a JAXBElement for ClarityProcess.

createProcess(ExecutableProcess) - Method in class com.genologics.ri.processexecution.ObjectFactory

Create an instance of JAXBElement<ExecutableProcess>.

createProcessDateRun(String) - Method in class com.genologics.ri.process.ObjectFactory

Creates a JAXBElement for the process date run.

createProcessDateRun(String) - Method in class com.genologics.ri.processexecution.ObjectFactory

Create an instance of JAXBElement<String> for date run.

createProcesses() - Method in class com.genologics.ri.process.ObjectFactory

Creates a new ClarityProcesses instance.

createProcesses(ClarityProcesses) - Method in class com.genologics.ri.process.ObjectFactory

Creates a JAXBElement for ClarityProcesses.

createProcessInput() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new ProcessInput instance.

createProcessInputOutputMap(InputOutputMap) - Method in class com.genologics.ri.process.ObjectFactory

Creates a JAXBElement for the process input-output map.

createProcessInputOutputMap(ExecutableInputOutputMap) - Method in class com.genologics.ri.processexecution.ObjectFactory

Create an instance of JAXBElement<ExecutableInputOutputMap>.

createProcessInstrument(InstrumentLink) - Method in class com.genologics.ri.process.ObjectFactory

Creates a JAXBElement for the process instrument.

createProcessInstrument(InstrumentLink) - Method in class com.genologics.ri.processexecution.ObjectFactory

Create an instance of JAXBElement<InstrumentLink>.

createProcessLink() - Method in class com.genologics.ri.process.ObjectFactory

Creates a new ProcessLink instance.

createProcessOutput() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new ProcessOutput instance.

createProcessProcessParameter(Parameter) - Method in class com.genologics.ri.process.ObjectFactory

Creates a JAXBElement for the process parameter.

createProcessProcessParameter(Parameter) - Method in class com.genologics.ri.processexecution.ObjectFactory

Create an instance of JAXBElement<Parameter>.

createProcessProtocolName(String) - Method in class com.genologics.ri.process.ObjectFactory

Creates a JAXBElement for the process protocol name.

createProcessTechnician(Technician) - Method in class com.genologics.ri.process.ObjectFactory

Creates a JAXBElement for the process technician.

createProcessTechnician(Technician) - Method in class com.genologics.ri.processexecution.ObjectFactory

Create an instance of JAXBElement<Technician>.

createProcessTemplate() - Method in class com.genologics.ri.processtemplate.ObjectFactory

Creates a new ProcessTemplate instance.

createProcessTemplate(ProcessTemplate) - Method in class com.genologics.ri.processtemplate.ObjectFactory

Creates a JAXBElement for ProcessTemplate.

createProcessTemplateInstrument(InstrumentLink) - Method in class com.genologics.ri.processtemplate.ObjectFactory

Creates a JAXBElement for process template instrument.

createProcessTemplateIsDefault(Boolean) - Method in class com.genologics.ri.processtemplate.ObjectFactory

Creates a JAXBElement for process template default flag.

createProcessTemplateLink() - Method in class com.genologics.ri.processtemplate.ObjectFactory

Creates a new ProcessTemplateLink instance.

createProcessTemplateName(String) - Method in class com.genologics.ri.processtemplate.ObjectFactory

Creates a JAXBElement for process template name.

createProcessTemplateProcessParameter(Parameter) - Method in class com.genologics.ri.processtemplate.ObjectFactory

Creates a JAXBElement for process template parameter.

createProcessTemplates() - Method in class com.genologics.ri.processtemplate.ObjectFactory

Creates a new ProcessTemplates instance.

createProcessTemplates(ProcessTemplates) - Method in class com.genologics.ri.processtemplate.ObjectFactory

Creates a JAXBElement for ProcessTemplates.

createProcessTemplateTechnician(Technician) - Method in class com.genologics.ri.processtemplate.ObjectFactory

Creates a JAXBElement for process template technician.

createProcessTemplateType(ProcessTypeLink) - Method in class com.genologics.ri.processtemplate.ObjectFactory

Creates a JAXBElement for process template type.

createProcessType() - Method in class com.genologics.ri.process.ObjectFactory

Creates a new ProcessTypeLink instance.

createProcessType() - Method in class com.genologics.ri.processtemplate.ObjectFactory

Creates a new ProcessTypeLink instance.

createProcessType() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new ProcessType instance.

createProcessType(ProcessTypeLink) - Method in class com.genologics.ri.process.ObjectFactory

Creates a JAXBElement for the process type.

createProcessType(ProcessType) - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a JAXB element wrapping ProcessType.

createProcessType(String) - Method in class com.genologics.ri.processexecution.ObjectFactory

Create an instance of JAXBElement<String> for process type.

createProcessTypeAttribute() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new ProcessTypeAttribute instance.

createProcessTypeLink() - Method in class com.genologics.ri.automation.ObjectFactory

Creates a new ProcessTypeLink instance.

createProcessTypeLink() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new ProcessTypeLink instance.

createProcessTypeLink() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory

Creates a new ProcessTypeLink instance.

createProcessTypes() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new ProcessTypes instance.

createProcessTypes(ProcessTypes) - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a JAXB element wrapping ProcessTypes.

createProgramStatus() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of ProgramStatus.

createProgramStatus(ProgramStatus) - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of JAXBElement<ProgramStatus>.

createProgramStatusLink() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of ProgramStatusLink.

createProject() - Method in class com.genologics.ri.project.ObjectFactory

Create an instance of Project.

createProject() - Method in class com.genologics.ri.sample.ObjectFactory

Create an instance of ProjectLink.

createProject(Project) - Method in class com.genologics.ri.project.ObjectFactory

Create an instance of JAXBElement<Project>.

createProjectLink() - Method in class com.genologics.ri.project.ObjectFactory

Create an instance of ProjectLink.

createProjects() - Method in class com.genologics.ri.project.ObjectFactory

Create an instance of Projects.

createProjects(Projects) - Method in class com.genologics.ri.project.ObjectFactory

Create an instance of JAXBElement<Projects>.

createProperties() - Method in class com.genologics.ri.property.ObjectFactory

Creates a new Properties instance.

createProperties(Properties) - Method in class com.genologics.ri.property.ObjectFactory

Creates a JAXBElement for Properties.

createPropertyLink() - Method in class com.genologics.ri.property.ObjectFactory

Creates a new PropertyLink instance.

createProtocol() - Method in class com.genologics.ri.protocolconfiguration.ObjectFactory

Creates a new Protocol instance.

createProtocol(Protocol) - Method in class com.genologics.ri.protocolconfiguration.ObjectFactory

Creates a JAXBElement for a Protocol.

createProtocolLink() - Method in class com.genologics.ri.protocolconfiguration.ObjectFactory

Creates a new ProtocolLink instance.

createProtocolLink() - Method in class com.genologics.ri.stage.ObjectFactory

Creates an instance of ProtocolLink.

createProtocolLink() - Method in class com.genologics.ri.workflowconfiguration.ObjectFactory

Create an instance of ProtocolLink.

createProtocolProperty() - Method in class com.genologics.ri.protocolconfiguration.ObjectFactory

Creates a new ProtocolProperty instance.

createProtocols() - Method in class com.genologics.ri.protocolconfiguration.ObjectFactory

Creates a new Protocols instance.

createProtocols(Protocols) - Method in class com.genologics.ri.protocolconfiguration.ObjectFactory

Creates a JAXBElement for Protocols.

createProtocolStep() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory

Creates a new ProtocolStep instance.

createProtocolStepLink() - Method in class com.genologics.ri.stage.ObjectFactory

Creates an instance of ProtocolStepLink.

createQueue() - Method in class com.genologics.ri.queue.ObjectFactory

Creates a new Queue instance.

createQueue(Queue) - Method in class com.genologics.ri.queue.ObjectFactory

Creates a JAXBElement for a Queue.

createQueueField() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new QueueField instance.

createQueueField() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory

Creates a new QueueField instance.

createReagentKit() - Method in class com.genologics.ri.reagentkit.ObjectFactory

Creates a new ReagentKit instance.

createReagentKit(ReagentKit) - Method in class com.genologics.ri.reagentkit.ObjectFactory

Creates a JAXBElement for a ReagentKit.

createReagentKitLink() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new ReagentKitLink instance.

createReagentKitLink() - Method in class com.genologics.ri.reagentkit.ObjectFactory

Creates a new ReagentKitLink instance.

createReagentKitLink() - Method in class com.genologics.ri.reagentlot.ObjectFactory

Create an instance of ReagentKitLink.

createReagentKitLink() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory

Creates a new ReagentKitLink instance.

createReagentKits() - Method in class com.genologics.ri.reagentkit.ObjectFactory

Creates a new ReagentKits instance.

createReagentKits(ReagentKits) - Method in class com.genologics.ri.reagentkit.ObjectFactory

Creates a JAXBElement for ReagentKits.

createReagentLabel() - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a new ReagentLabel instance.

createReagentLabel() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of ReagentLabel.

createReagentLot() - Method in class com.genologics.ri.reagentlot.ObjectFactory

Create an instance of ReagentLot.

createReagentLot(ReagentLot) - Method in class com.genologics.ri.reagentlot.ObjectFactory

Create an instance of JAXBElement<ReagentLot>.

createReagentLotLink() - Method in class com.genologics.ri.reagentlot.ObjectFactory

Create an instance of ReagentLotLink.

createReagentLotLink() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of ReagentLotLink.

createReagentLots() - Method in class com.genologics.ri.reagentlot.ObjectFactory

Create an instance of ReagentLots.

createReagentLots(ReagentLots) - Method in class com.genologics.ri.reagentlot.ObjectFactory

Create an instance of JAXBElement<ReagentLots>.

createReagentLotsLink() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of ReagentLotsLink.

createReagents() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of Reagents.

createReagents(Reagents) - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of JAXBElement<Reagents>.

createReagentsLink() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of ReagentsLink.

createReagentsLots() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of ReagentLots.

createReagentType() - Method in class com.genologics.ri.reagenttype.ObjectFactory

Create an instance of ReagentType.

createReagentType(ReagentType) - Method in class com.genologics.ri.reagenttype.ObjectFactory

Create an instance of JAXBElement<ReagentType>.

createReagentTypeLink() - Method in class com.genologics.ri.reagenttype.ObjectFactory

Create an instance of ReagentTypeLink.

createReagentTypes() - Method in class com.genologics.ri.reagenttype.ObjectFactory

Create an instance of ReagentTypes.

createReagentTypes(ReagentTypes) - Method in class com.genologics.ri.reagenttype.ObjectFactory

Create an instance of JAXBElement<ReagentTypes>.

createResearcher() - Method in class com.genologics.ri.project.ObjectFactory

Create an instance of ResearcherLink.

createResearcher() - Method in class com.genologics.ri.reagentlot.ObjectFactory

Create an instance of ResearcherLink.

createResearcher() - Method in class com.genologics.ri.researcher.ObjectFactory

Creates a new Researcher instance.

createResearcher(Researcher) - Method in class com.genologics.ri.researcher.ObjectFactory

Creates a JAXBElement wrapper for a Researcher.

createResearcherLink() - Method in class com.genologics.ri.researcher.ObjectFactory

Creates a new ResearcherLink instance.

createResearcherLink() - Method in class com.genologics.ri.role.ObjectFactory

Creates a new ResearcherLink instance.

createResearchers() - Method in class com.genologics.ri.researcher.ObjectFactory

Creates a new Researchers instance.

createResearchers(Researchers) - Method in class com.genologics.ri.researcher.ObjectFactory

Creates a JAXBElement wrapper for Researchers.

createRestTemplate() - Method in class org.cruk.clarity.api.spring.ClarityClientConfiguration

Helper method to create REST templates based on the JAXB context and HTTP client request factory.

createRole() - Method in class com.genologics.ri.researcher.ObjectFactory

Creates a new Role instance.

createRole() - Method in class com.genologics.ri.role.ObjectFactory

Creates a new Role instance.

createRole(Role) - Method in class com.genologics.ri.role.ObjectFactory

Creates a JAXBElement for a Role.

createRoleLink() - Method in class com.genologics.ri.role.ObjectFactory

Creates a new RoleLink instance.

createRoles() - Method in class com.genologics.ri.role.ObjectFactory

Creates a new Roles instance.

createRoles(Roles) - Method in class com.genologics.ri.role.ObjectFactory

Creates a JAXBElement for Roles.

createRouting() - Method in class com.genologics.ri.routing.ObjectFactory

Creates a new Routing instance.

createRouting(Routing) - Method in class com.genologics.ri.routing.ObjectFactory

Creates a JAXBElement for Routing.

createSample() - Method in class com.genologics.ri.artifact.ObjectFactory

Creates a new SampleLink instance.

createSample() - Method in class com.genologics.ri.sample.ObjectFactory

Create an instance of Sample.

createSample(Sample) - Method in class com.genologics.ri.sample.ObjectFactory

Create an instance of JAXBElement<Sample>.

createSamplebase() - Method in class com.genologics.ri.sample.ObjectFactory

Create an instance of SampleBase.

createSamplecreation() - Method in class com.genologics.ri.sample.ObjectFactory

Create an instance of SampleCreation.

createSamplecreation(SampleCreation) - Method in class com.genologics.ri.sample.ObjectFactory

Create an instance of JAXBElement<SampleCreation>.

createSampleLink() - Method in class com.genologics.ri.sample.ObjectFactory

Create an instance of SampleLink.

createSamples() - Method in class com.genologics.ri.sample.ObjectFactory

Create an instance of Samples.

createSamples(Samples) - Method in class com.genologics.ri.sample.ObjectFactory

Create an instance of JAXBElement<Samples>.

createSavedQueries() - Method in class com.genologics.ri.savedquery.ObjectFactory

Create an instance of SavedQueries.

createSavedQueries(SavedQueries) - Method in class com.genologics.ri.savedquery.ObjectFactory

Create an instance of JAXBElement<SavedQueries>

createSavedQuery() - Method in class com.genologics.ri.savedquery.ObjectFactory

Create an instance of SavedQuery.

createSavedQuery(SavedQuery) - Method in class com.genologics.ri.savedquery.ObjectFactory

Create an instance of JAXBElement<SavedQuery>

createSavedQueryLink() - Method in class com.genologics.ri.savedquery.ObjectFactory

Create an instance of SavedQueryLink.

createSetup() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of StepSetup.

createSetup(StepSetup) - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of JAXBElement<StepSetup>.

createSetupLink() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of StepSetupLink.

createSharedResultFile() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new SharedResultFile instance.

createSharedResultFile() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory

Creates a new SharedResultFile instance.

createSpecialType() - Method in class com.genologics.ri.reagenttype.ObjectFactory

Create an instance of SpecialType.

createStage() - Method in class com.genologics.ri.stage.ObjectFactory

Creates an instance of Stage.

createStage(Stage) - Method in class com.genologics.ri.stage.ObjectFactory

Creates an instance of JAXBElement<Stage>.

createStageLink() - Method in class com.genologics.ri.workflowconfiguration.ObjectFactory

Create an instance of StageLink.

createStep() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of ProcessStep.

createStep(ProcessStep) - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of JAXBElement<ProcessStep>.

createStep(ProtocolStep) - Method in class com.genologics.ri.stepconfiguration.ObjectFactory

Creates a JAXBElement wrapping a ProtocolStep.

createStepConfiguration() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of StepConfiguration.

createStepCreation() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of StepCreation.

createStepCreation(StepCreation) - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of JAXBElement<StepCreation>.

createStepProperty() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new StepProperty instance.

createStepProperty() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory

Creates a new StepProperty instance.

createStepSetup() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new StepSetup instance.

createStepSetup() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory

Creates a new StepSetup instance.

createSubmitter() - Method in class com.genologics.ri.sample.ObjectFactory

Create an instance of Submitter.

createTechnician() - Method in class com.genologics.ri.process.ObjectFactory

Creates a new Technician instance.

createTechnician() - Method in class com.genologics.ri.processexecution.ObjectFactory

Create an instance of Technician.

createTechnician() - Method in class com.genologics.ri.processtemplate.ObjectFactory

Creates a new Technician instance.

createType() - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a new Type instance.

createType() - Method in class com.genologics.ri.userdefined.ObjectFactory

Create an instance of UDT

createType(Type) - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a JAXBElement for a Type.

createType(UDT) - Method in class com.genologics.ri.userdefined.ObjectFactory

Create an instance of JAXBElement<UDT>

createTypeDefinition() - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a new TypeDefinition instance.

createTypeDefinition() - Method in class com.genologics.ri.processtype.ObjectFactory

Creates a new TypeDefinition instance.

createUdfconfigLink() - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a new UdfConfigLink instance.

createUdfconfigLink(UdfConfigLink) - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a JAXBElement for a UdfConfigLink.

createUdfs() - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a new Udfs instance.

createUdfs(Udfs) - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a JAXBElement for Udfs.

createUdtconfigLink() - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a new UdtConfigLink instance.

createUdtconfigLink(UdtConfigLink) - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a JAXBElement for a UdtConfigLink.

createUdts() - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a new Udts instance.

createUdts(Udts) - Method in class com.genologics.ri.configuration.ObjectFactory

Creates a JAXBElement for Udts.

createUser() - Method in class com.genologics.ri.step.ObjectFactory

Create an instance of UserLink.

createVersion() - Method in class com.genologics.ri.version.ObjectFactory

Create an instance of Version

createVersion(Version) - Method in class com.genologics.ri.version.ObjectFactory

Create an instance of JAXBElement<Version>

createVersions() - Method in class com.genologics.ri.version.ObjectFactory

Create an instance of Versions

createVersions(Versions) - Method in class com.genologics.ri.version.ObjectFactory

Create an instance of JAXBElement<Versions>

createWorkflow() - Method in class com.genologics.ri.workflowconfiguration.ObjectFactory

Create an instance of Workflow.

createWorkflow(Workflow) - Method in class com.genologics.ri.workflowconfiguration.ObjectFactory

Create a JAXBElement for Workflow.

createWorkflowLink() - Method in class com.genologics.ri.stage.ObjectFactory

Creates an instance of WorkflowLink.

createWorkflowLink() - Method in class com.genologics.ri.workflowconfiguration.ObjectFactory

Create an instance of WorkflowLink.

createWorkflows() - Method in class com.genologics.ri.workflowconfiguration.ObjectFactory

Create an instance of Workflows.

createWorkflows(Workflows) - Method in class com.genologics.ri.workflowconfiguration.ObjectFactory

Create a JAXBElement for Workflows.

creationClass() - Element in annotation interface com.genologics.ri.ClarityEntity

For some awkward classes that have a similar alternative class for the creation process, this attribute allows that class used in creation to be specified.

CreationInput - Class in com.genologics.ri.step

Typically, provides a URI linking to the input artifact.

CreationInput() - Constructor for class com.genologics.ri.step.CreationInput

Default constructor.

CreationInput(Linkable<Artifact>) - Constructor for class com.genologics.ri.step.CreationInput

Constructor from a linkable artifact.

CreationInput(Linkable<Artifact>, Linkable<ControlType>) - Constructor for class com.genologics.ri.step.CreationInput

Constructor from a linkable artifact and control type.

CreationInput(Linkable<Artifact>, Linkable<ControlType>, Long) - Constructor for class com.genologics.ri.step.CreationInput

Constructor from a linkable artifact, control type, and replicates.

CreationInput(URI) - Constructor for class com.genologics.ri.step.CreationInput

Constructor with URI.

CreationInput(URI, URI) - Constructor for class com.genologics.ri.step.CreationInput

Constructor with URI and control type URI.

CreationInput(URI, URI, Long) - Constructor for class com.genologics.ri.step.CreationInput

Constructor with URI, control type URI, and replicates.

credentials - Variable in class com.genologics.ri.researcher.Researcher

The researcher's credentials.

Credentials - Class in com.genologics.ri.researcher

The credentials element contains information about a researcher's access to the client software interface.

Credentials() - Constructor for class com.genologics.ri.researcher.Credentials

currentState - Variable in class com.genologics.ri.step.ProcessStep

The current state of the step.

currentStatus(ProgramStatus) - Method in interface org.cruk.clarity.api.ClarityAPI

Get an updated program status from Clarity.

currentStatus(ProgramStatus) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Get an updated program status from Clarity.

D

date - Variable in class com.genologics.ri.step.EscalationRequest

The date of the escalation request.

date - Variable in class com.genologics.ri.step.EscalationReview

The date of the escalation review.

DATE - Enum constant in enum class com.genologics.ri.configuration.FieldType

Date field type.

dateCompleted - Variable in class com.genologics.ri.sample.SampleBase

The date the sample was completed.

dateCompleted - Variable in class com.genologics.ri.step.ProcessStep

The date and time the step was completed.

dateReceived - Variable in class com.genologics.ri.sample.SampleBase

The date the sample was received.

dateRun - Variable in class com.genologics.ri.process.ClarityProcess

The date the process was run.

dateRun - Variable in class com.genologics.ri.processexecution.ExecutableProcess

The date the process was run.

dateStarted - Variable in class com.genologics.ri.step.ProcessStep

The date and time the step was started.

defaultGrouping - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

Deprecated.

Please use "<milestone>DefaultGrouping" in a StepProperty field instead.

defaultTemplate - Variable in class com.genologics.ri.processtemplate.ProcessTemplate

Indicates whether this is the default template for the associated process type.

delete(ClarityFile) - Method in interface org.cruk.clarity.api.filestore.ClaritySFTPUploader

Delete a file from the Clarity file store.

delete(E) - Method in interface org.cruk.clarity.api.ClarityAPI

Deletes an entity from the server.

delete(E) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Deletes an entity from the server.

delete(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Join point for the ClarityAPI.delete method.

deleteAll(Collection<E>) - Method in interface org.cruk.clarity.api.ClarityAPI

Deletes a batch of entities from the server.

deleteAll(Collection<E>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Deletes a batch of entities from the server.

deleteAll(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Join point for the ClarityAPI.deleteAll method.

deleteAndRemoveFile(Linkable<ClarityFile>) - Method in interface org.cruk.clarity.api.ClarityAPI

Delete a file from the file store and remove its record from the LIMS.

deleteAndRemoveFile(Linkable<ClarityFile>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Delete a file from the file store and remove its record from the LIMS.

deleteAndRemoveFile(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Join point for the ClarityAPI.deleteAndRemoveFile method.

demux - Variable in class com.genologics.ri.artifact.Artifact

The demultiplexing information for this artifact if it is a pool.

demux - Variable in class com.genologics.ri.artifact.DemuxArtifact

The demux details of this demux artifact.

Demux - Class in com.genologics.ri.artifact

The detailed representation of the demultiplexing of a pooled artifact.

Demux() - Constructor for class com.genologics.ri.artifact.Demux

Default constructor.

Demux(URI) - Constructor for class com.genologics.ri.artifact.Demux

Constructor with a URI.

DemuxArtifact - Class in com.genologics.ri.artifact

Details of an individual artifact that is part of a pooled artifact.

DemuxArtifact() - Constructor for class com.genologics.ri.artifact.DemuxArtifact

Default constructor.

DemuxArtifactSample - Class in com.genologics.ri.artifact

The details of a sample that is part of a pooled artifact.

DemuxArtifactSample() - Constructor for class com.genologics.ri.artifact.DemuxArtifactSample

Default constructor.

DemuxArtifactSample(LimsEntityLinkable<Sample>) - Constructor for class com.genologics.ri.artifact.DemuxArtifactSample

Constructor from a LimsEntityLinkable.

DemuxArtifactSample(Linkable<Sample>) - Constructor for class com.genologics.ri.artifact.DemuxArtifactSample

Constructor from a Linkable.

DemuxArtifactSample(URI) - Constructor for class com.genologics.ri.artifact.DemuxArtifactSample

Constructor taking a URI.

DemuxArtifactSample(URI, String) - Constructor for class com.genologics.ri.artifact.DemuxArtifactSample

Constructor taking a URI and LIMS id.

demuxDetails - Variable in class com.genologics.ri.artifact.Demux

The demux details of this demux.

DemuxDetails - Class in com.genologics.ri.artifact

Demultiplexing of the Artifact showing all pooling steps that this artifact has been part of.

DemuxDetails() - Constructor for class com.genologics.ri.artifact.DemuxDetails

Default constructor.

DemuxLink - Class in com.genologics.ri.artifact

Identifies the resource that will demultiplex this artifact.

DemuxLink() - Constructor for class com.genologics.ri.artifact.DemuxLink

Default constructor.

DemuxLink(Linkable<DemuxArtifact>) - Constructor for class com.genologics.ri.artifact.DemuxLink

Constructor from a Linkable.

DemuxLink(URI) - Constructor for class com.genologics.ri.artifact.DemuxLink

Constructor taking a URI.

DemuxSourceArtifact - Class in com.genologics.ri.artifact

Link to a source artifact for demultiplexing.

DemuxSourceArtifact() - Constructor for class com.genologics.ri.artifact.DemuxSourceArtifact

Default constructor.

DemuxSourceArtifact(Artifact) - Constructor for class com.genologics.ri.artifact.DemuxSourceArtifact

Constructor from an Artifact.

DemuxSourceArtifact(Linkable<Artifact>) - Constructor for class com.genologics.ri.artifact.DemuxSourceArtifact

Constructor from a Linkable.

DemuxSourceArtifact(URI) - Constructor for class com.genologics.ri.artifact.DemuxSourceArtifact

Constructor taking a URI.

DemuxSourceArtifact(URI, String) - Constructor for class com.genologics.ri.artifact.DemuxSourceArtifact

Constructor taking a URI and name.

department - Variable in class com.genologics.ri.Address

The department.

DEPLETED - Enum constant in enum class com.genologics.ri.container.ContainerState

The container state when the container is depleted.

DERIVED_SAMPLE - Enum constant in enum class com.genologics.ri.automation.Context

Derived sample context.

description - Variable in class com.genologics.ri.globaltoken.GlobalToken

The token description.

description - Variable in class com.genologics.ri.permission.Permission

The permission description.

description - Variable in class com.genologics.ri.sample.BioSource

Deprecated.

The description of the biosource.

detail - Variable in class com.genologics.ri.processtype.IceBucketField

Indicates whether this field shows in the detail view.

detail - Variable in class com.genologics.ri.processtype.QueueField

Indicates whether this field shows in the detail view.

detail - Variable in class com.genologics.ri.stepconfiguration.IceBucketField

Indicates whether this ice bucket field should be shown in detail view.

detail - Variable in class com.genologics.ri.stepconfiguration.QueueField

Indicates whether this queue field should be shown in detail view.

details - Variable in class com.genologics.ri.step.ProcessStep

Link to the details associated with this step.

deviation - Variable in class com.genologics.ri.configuration.Field

Whether this field represents a deviation.

Dimension - Class in com.genologics.ri.containertype

Dimension is a child element of container type and describes the size and identification method of the horizontal and vertical dimensions of the coordinate system of the container type.

Dimension() - Constructor for class com.genologics.ri.containertype.Dimension

Default constructor for creating a new dimension.

Dimension(Integer) - Constructor for class com.genologics.ri.containertype.Dimension

Constructor for creating a dimension with a specified size.

DISCARDED - Enum constant in enum class com.genologics.ri.container.ContainerState

The container state when the container has been discarded.

displayName - Variable in enum class com.genologics.ri.container.ContainerState

The display name of the state.

displayName - Variable in class com.genologics.ri.processtype.ProcessInput

The display name for the input.

displayName - Variable in class com.genologics.ri.processtype.ProcessOutput

The display name for the output.

displayName - Variable in enum class com.genologics.ri.step.ProcessState

The display name of the state.

doFind(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Join point around the Clarity client's find() method.

doFind(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.record.ClarityAPIRecordingAspect

Join point around the Clarity client's find() method.

doGet(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Join point around the Spring REST client's getForObject() methods.

doGetEntity(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Join point around the Spring REST client's getForEntity() methods.

doList(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Join point around the listAll and listSome methods load the list of links from a serialised Batch object in XML file in the messages directory.

doList(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.record.ClarityAPIRecordingAspect

Join point around the listAll and listSome methods that recreate the Batch object that holds the list of links to the real things and writes that list to an XML file in the messages directory.

doLoad(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.record.ClarityAPIRecordingAspect

Join point around the Clarity client's load() and retrieve() methods.

doLoadAll(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Join point around calls to the API's loadAll method.

doLoadAll(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.record.ClarityAPIRecordingAspect

Join point around the Clarity client's loadAll() method.

doUpdate(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Join point around the Clarity client's update() method.

doUpdateAll(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Join point around the Clarity client's updateAll() method.

downloadDirectFromHttpStore - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

Whether to download files that have an HTTP URL directly from their store, or whether to download via the files/id/download API end point.

downloadFile(Linkable<ClarityFile>, OutputStream) - Method in interface org.cruk.clarity.api.ClarityAPI

Download the given file from its source.

downloadFile(Linkable<ClarityFile>, OutputStream) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Download the given file from its source.

dynamicPresets - Variable in class com.genologics.ri.configuration.Field

Whether this field uses dynamic presets.

E

editable - Variable in class com.genologics.ri.configuration.Field

Whether this field is editable.

email - Variable in class com.genologics.ri.researcher.Researcher

The researcher's email address.

EMPTY - Enum constant in enum class com.genologics.ri.container.ContainerState

The container state when the container is empty.

EMPTY_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The empty namespace.

enabled - Variable in class com.genologics.ri.processtype.StepSetup

Whether the step setup view is enabled for this process type.

enabled - Variable in class com.genologics.ri.stepconfiguration.StepSetup

Indicates whether the step setup view is enabled.

entityClass() - Element in annotation interface com.genologics.ri.ClarityBatchRetrieveResult

The class of entity indicated by the links returned in the annotated object.

entityClass() - Element in annotation interface com.genologics.ri.ClarityQueryResult

The class of entity indicated by the links returned in the annotated object.

entityToBatchRetrieveClassMap - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

Map of Locatable class to the class that provides the mass fetch or update operation.

entityToListClassMap - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

Map of Locatable class to the class that provides the list of links returned from listing or searching for objects of that type.

EppTrigger - Class in com.genologics.ri.processtype

EPP trigger configuration for the Master Step.

EppTrigger - Class in com.genologics.ri.stepconfiguration

EPP trigger configuration for the Protocol Step.

EppTrigger() - Constructor for class com.genologics.ri.processtype.EppTrigger

Constructs a new EPP trigger.

EppTrigger() - Constructor for class com.genologics.ri.stepconfiguration.EppTrigger

EppTrigger(String) - Constructor for class com.genologics.ri.processtype.EppTrigger

Constructs a new EPP trigger with the specified name.

eppTriggers - Variable in class com.genologics.ri.processtype.ProcessType

EPP triggers for this process type.

eppTriggers - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

List of EPP triggers for this step.

equals(LimsLink<?>, Object) - Static method in interface com.genologics.ri.LimsLink

Test a LimsLink against another object for equivalence.

equals(Object) - Method in class com.genologics.ri.instrumenttype.InstrumentTypeProcessType

equals(Object) - Method in class com.genologics.ri.LimsLinkBase

equals(Object) - Method in class com.genologics.ri.Location

Compares this location with another object for equality.

equals(Object) - Method in class com.genologics.ri.process.ProcessTypeLink

equals(Object) - Method in class com.genologics.ri.processexecution.Input

equals(Object) - Method in class com.genologics.ri.processtemplate.ProcessTypeLink

equals(Object) - Method in class com.genologics.ri.step.InstrumentLink

equals(Object) - Method in class com.genologics.ri.step.StepConfiguration

equals(Object) - Method in class com.genologics.ri.stepconfiguration.ControlTypeLink

equals(Object) - Method in class com.genologics.ri.stepconfiguration.ProcessTypeLink

equals(Object) - Method in class com.genologics.ri.stepconfiguration.ReagentKitLink

equals(Object) - Method in class org.cruk.clarity.api.impl.URLInputStreamResource

Test for equality.

equals(Object) - Method in class org.cruk.clarity.api.search.SearchTerm

Test whether the given object is equal to this SearchTerm.

equals(Object) - Method in class org.cruk.clarity.api.search.SearchTerms

Test whether the given object is equal to these SearchTerms.

ERROR - Enum constant in enum class com.genologics.ri.step.Status

The step completed with errors.

errorHandler - Variable in class org.cruk.clarity.api.impl.SavedQueryRunner

The error handler.

EscalatedArtifact - Class in com.genologics.ri.step

Sample next action or step.

EscalatedArtifact() - Constructor for class com.genologics.ri.step.EscalatedArtifact

Default constructor.

EscalatedArtifact(Linkable<Artifact>) - Constructor for class com.genologics.ri.step.EscalatedArtifact

Constructor from a linkable object.

EscalatedArtifact(URI) - Constructor for class com.genologics.ri.step.EscalatedArtifact

Constructor with URI.

escalatedArtifacts - Variable in class com.genologics.ri.step.Escalation

List of escalated artifacts.

escalation - Variable in class com.genologics.ri.step.Actions

Escalation information for the step.

Escalation - Class in com.genologics.ri.step

Escalation details.

Escalation() - Constructor for class com.genologics.ri.step.Escalation

EscalationRequest - Class in com.genologics.ri.step

Represents an escalation request in a step.

EscalationRequest() - Constructor for class com.genologics.ri.step.EscalationRequest

EscalationReview - Class in com.genologics.ri.step

Represents an escalation review in a step.

EscalationReview() - Constructor for class com.genologics.ri.step.EscalationReview

EXACT - Enum constant in enum class org.cruk.clarity.api.cache.CacheStatefulBehaviour

The version of the entity in the cache must match exactly, otherwise it is fetched from the server.

EXACT - Enum constant in enum class org.cruk.clarity.api.StatefulOverride

Fetch the exact version of a stateful entity, the version as specified by its state parameter.

Exception - Class in com.genologics.ri.exception

Exception is a descriptive error message that is returned instead of the standard response for any request that the system was unable to process.

Exception() - Constructor for class com.genologics.ri.exception.Exception

Creates a new Exception instance.

EXCEPTION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The exception namespace.

ExecutableInputOutputMap - Class in com.genologics.ri.processexecution

Processes link inputs to outputs and this relationship is called an input-output map.

ExecutableInputOutputMap() - Constructor for class com.genologics.ri.processexecution.ExecutableInputOutputMap

Default constructor.

ExecutableInputOutputMap(Boolean) - Constructor for class com.genologics.ri.processexecution.ExecutableInputOutputMap

Constructor with shared flag.

ExecutableProcess - Class in com.genologics.ri.processexecution

The process element defines the XML needed to run a process.

ExecutableProcess() - Constructor for class com.genologics.ri.processexecution.ExecutableProcess

Default constructor.

ExecutableProcess(String) - Constructor for class com.genologics.ri.processexecution.ExecutableProcess

Constructor with process type.

ExecutableProcess(String, Linkable<Researcher>) - Constructor for class com.genologics.ri.processexecution.ExecutableProcess

Constructor with process type and technician.

executeProcess(ExecutableProcess) - Method in interface org.cruk.clarity.api.ClarityAPI

Execute a process within the LIMS.

executeProcess(ExecutableProcess) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Execute a process within the LIMS.

exists() - Method in class org.cruk.clarity.api.impl.URLInputStreamResource

Check whether the resource exists.

expandSearchTerms(Map<String, ?>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Expand a map of search terms into a query string suitable for a URI.

expiryDate - Variable in class com.genologics.ri.instrument.Instrument

The instrument expiry date.

expiryDate - Variable in class com.genologics.ri.reagentlot.ReagentLot

The expiry date of this reagent lot.

ExtArtifactAssignments - Class in com.genologics.ri.routing

External artifact assignments for routing to workflows and stages.

ExtArtifactAssignments() - Constructor for class com.genologics.ri.routing.ExtArtifactAssignments

ExternalId - Class in com.genologics.ri

An external id is a reference to an identifier in an external system that contains additional information about a representation within the API.

ExternalId() - Constructor for class com.genologics.ri.ExternalId

Default constructor.

ExternalId(URI) - Constructor for class com.genologics.ri.ExternalId

Constructor with id.

ExternalId(URI, URI) - Constructor for class com.genologics.ri.ExternalId

Constructor with id and URI.

externalIds - Variable in class com.genologics.ri.lab.Lab

The list of external identifiers for the lab.

externalIds - Variable in class com.genologics.ri.project.Project

The external identifiers for the project.

externalIds - Variable in class com.genologics.ri.researcher.Researcher

The external identifiers for the researcher.

externalIds - Variable in class com.genologics.ri.sample.SampleBase

The external identifiers for this sample.

F

FAILED - Enum constant in enum class com.genologics.ri.artifact.QCFlag

Failed quality control.

FAILED - Enum constant in enum class com.genologics.ri.processexecution.QCFlag

QC check failed.

fax - Variable in class com.genologics.ri.researcher.Researcher

The researcher's fax number.

Field - Class in com.genologics.ri.configuration

The detailed representation of the configuration of a user-defined field.

Field - Class in com.genologics.ri.processtype

A field has a name and an attach to value, these fields are used to keep track of all the User Defined and Built In values for samples in queue and work view as well as those on the actual step

Field - Class in com.genologics.ri.stepconfiguration

A field has a name and an attach to value, these fields are used to keep track of all the User Defined and Built In values for samples in queue and work view as well as those on the actual step.

Field() - Constructor for class com.genologics.ri.configuration.Field

Constructor for creating an empty Field object.

Field() - Constructor for class com.genologics.ri.processtype.Field

Constructs a new field.

Field() - Constructor for class com.genologics.ri.stepconfiguration.Field

Default constructor.

Field(String) - Constructor for class com.genologics.ri.processtype.Field

Constructs a new field with the specified name.

Field(String) - Constructor for class com.genologics.ri.stepconfiguration.Field

Constructor with field name.

Field(String, String) - Constructor for class com.genologics.ri.stepconfiguration.Field

Constructor with field name and attach-to value.

fieldDefinitions - Variable in class com.genologics.ri.configuration.Type

The list of field definitions for this type.

fieldDefinitions - Variable in class com.genologics.ri.processtype.ProcessOutput

Deprecated.

These field definitions are ignored as of Clarity LIMS 5.0.

fieldDefinitions - Variable in class com.genologics.ri.processtype.ProcessType

Field definitions for user-defined fields.

FieldDynamicPreset - Class in com.genologics.ri.configuration

The detailed representation of a field dynamic UDF preset.

FieldDynamicPreset() - Constructor for class com.genologics.ri.configuration.FieldDynamicPreset

Constructor for creating an empty FieldDynamicPreset object.

FieldDynamicPreset(String) - Constructor for class com.genologics.ri.configuration.FieldDynamicPreset

Constructor for creating a FieldDynamicPreset with a specific value.

FieldDynamicPresetDetails - Class in com.genologics.ri.configuration

The representation of a list of field dynamic UDF preset.

FieldDynamicPresetDetails() - Constructor for class com.genologics.ri.configuration.FieldDynamicPresetDetails

Constructor for creating an empty FieldDynamicPresetDetails object.

FieldDynamicPresetDetails(String...) - Constructor for class com.genologics.ri.configuration.FieldDynamicPresetDetails

Constructor for creating a FieldDynamicPresetDetails with preset value strings.

FieldDynamicPresetDetails(URI) - Constructor for class com.genologics.ri.configuration.FieldDynamicPresetDetails

Constructor for creating a FieldDynamicPresetDetails with a URI.

FieldDynamicPresetDetails(URI, String...) - Constructor for class com.genologics.ri.configuration.FieldDynamicPresetDetails

Constructor for creating a FieldDynamicPresetDetails with a URI and preset value strings.

FieldDynamicPresetDetails(URI, Collection<String>) - Constructor for class com.genologics.ri.configuration.FieldDynamicPresetDetails

Constructor for creating a FieldDynamicPresetDetails with a URI and preset values.

FieldDynamicPresetDetails(Collection<String>) - Constructor for class com.genologics.ri.configuration.FieldDynamicPresetDetails

Constructor for creating a FieldDynamicPresetDetails with preset values.

FieldLink - Class in com.genologics.ri.configuration

Field definition represents a user-defined field configured in the parent entity.

FieldLink() - Constructor for class com.genologics.ri.configuration.FieldLink

Constructor for creating an empty FieldLink object.

FieldLink(Field) - Constructor for class com.genologics.ri.configuration.FieldLink

Constructor for creating a FieldLink from a Field object.

FieldLink(Linkable<Field>) - Constructor for class com.genologics.ri.configuration.FieldLink

Constructor for creating a FieldLink from a Linkable object.

FieldLink(URI) - Constructor for class com.genologics.ri.configuration.FieldLink

Constructor for creating a FieldLink with a URI.

FieldLink(URI, String) - Constructor for class com.genologics.ri.configuration.FieldLink

Constructor for creating a FieldLink with a URI and name.

fields - Variable in class com.genologics.ri.artifact.Artifact

The list of user-defined fields for this artifact.

fields - Variable in class com.genologics.ri.container.Container

The list of user-defined fields for the container.

fields - Variable in class com.genologics.ri.lab.Lab

The list of user-defined fields for the lab.

fields - Variable in class com.genologics.ri.process.ClarityProcess

The user defined fields.

fields - Variable in class com.genologics.ri.processexecution.ExecutableProcess

The user-defined fields.

fields - Variable in class com.genologics.ri.processtemplate.ProcessTemplate

The user-defined fields.

fields - Variable in class com.genologics.ri.project.Project

The user-defined fields for the project.

fields - Variable in class com.genologics.ri.researcher.Researcher

The user-defined fields for the researcher.

fields - Variable in class com.genologics.ri.sample.BioSource

Deprecated.

The user-defined fields for the biosource.

fields - Variable in class com.genologics.ri.sample.SampleBase

The user-defined fields for this sample.

fields - Variable in class com.genologics.ri.step.StepDetails

The user-defined fields for the step.

fields - Variable in class com.genologics.ri.userdefined.UDT

The list of user-defined fields in this type.

FieldType - Enum Class in com.genologics.ri.configuration

UDF field types.

file - Variable in class com.genologics.ri.artifact.Artifact

The file associated with this artifact, if any.

file - Variable in class com.genologics.ri.processtype.Parameter

Deprecated.

This property is no longer supported.

FILE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The file namespace.

FileLink - Class in com.genologics.ri.file

The file-link type provides a URI that links to information about a file in the system.

FileLink() - Constructor for class com.genologics.ri.file.FileLink

Creates a new, empty FileLink.

FileLink(LimsEntityLinkable<ClarityFile>) - Constructor for class com.genologics.ri.file.FileLink

Creates a new FileLink from a linkable entity that references a ClarityFile, copying its URI and LIMS id.

FileLink(URI) - Constructor for class com.genologics.ri.file.FileLink

Creates a new FileLink with the specified URI.

FileLink(URI, String) - Constructor for class com.genologics.ri.file.FileLink

Creates a new FileLink with the specified URI and LIMS id.

FILENAME_PATTERN - Static variable in class org.cruk.clarity.api.record.ClarityAPIRecordingAspect

Template for the file name pattern.

files - Variable in class com.genologics.ri.automation.Automation

The files associated with this automation.

files - Variable in class com.genologics.ri.file.ClarityFileBatchFetchResult

The list of file resources in this batch.

files - Variable in class com.genologics.ri.file.ClarityFiles

The list of file links.

files - Variable in class com.genologics.ri.process.ClarityProcess

The files associated with the process.

files - Variable in class com.genologics.ri.processtype.Parameter

Files associated with this parameter.

files - Variable in class com.genologics.ri.processtype.StepSetup

The list of shared result file configurations.

files - Variable in class com.genologics.ri.project.Project

The files attached to the project.

files - Variable in class com.genologics.ri.sample.SampleBase

The files associated with this sample.

files - Variable in class com.genologics.ri.step.StepSetup

The list of shared result files for the step.

files - Variable in class com.genologics.ri.stepconfiguration.StepSetup

List of shared result files for the step setup view.

filestoreCredentials - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

User name and password credentials for accessing the file store.

filestoreServer - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

Host for the file store.

fileUploadClient - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

Adapted REST client for uploading files through the HTTP mechanism.

find(Map<String, ?>, Class<E>) - Method in interface org.cruk.clarity.api.ClarityAPI

Search for entities of the given type based on name value pairs.

find(Map<String, ?>, Class<E>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Search for entities of the given type based on name value pairs.

findProtocol(String) - Method in interface org.cruk.clarity.api.automation.ClarityProcessAutomation

Find a protocol by name.

findProtocol(String) - Method in class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Find a protocol by name.

findStage(Workflow, String) - Method in interface org.cruk.clarity.api.automation.ClarityProcessAutomation

Find a stage in a work flow by name.

findStage(Workflow, String) - Method in class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Find a stage in a work flow by name.

findStep(Protocol, String) - Method in interface org.cruk.clarity.api.automation.ClarityProcessAutomation

Find a step in a protocol by name.

findStep(Protocol, String) - Method in class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Find a step in a protocol by name.

findWorkflow(String) - Method in interface org.cruk.clarity.api.automation.ClarityProcessAutomation

Find a work flow by name.

findWorkflow(String) - Method in class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Find a work flow by name.

firstName - Variable in class com.genologics.ri.process.Technician

The first name of the technician.

firstName - Variable in class com.genologics.ri.processtemplate.Technician

The first name of the technician.

firstName - Variable in class com.genologics.ri.researcher.Researcher

The researcher's first name.

firstName - Variable in class com.genologics.ri.researcher.ResearcherLink

The researcher's first name.

firstName - Variable in class com.genologics.ri.role.ResearcherLink

The first name of the researcher.

firstName - Variable in class com.genologics.ri.sample.Submitter

The first name of the submitter.

firstName - Variable in class com.genologics.ri.step.Technician

The first name of the technician.

firstName - Variable in class com.genologics.ri.step.UserLink

The first name of the user.

firstPresetIsDefaultValue - Variable in class com.genologics.ri.configuration.Field

Whether the first preset value is the default.

FIXED - Enum constant in enum class com.genologics.ri.processtype.VariabilityType

A fixed number of outputs is generated.

fromValue(String) - Static method in enum class com.genologics.ri.artifact.OutputType

Gets the OutputType from a string value.

fromValue(String) - Static method in enum class com.genologics.ri.artifact.QCFlag

Gets the QCFlag from a string value.

fromValue(String) - Static method in enum class com.genologics.ri.artifact.Status

Gets the Status from a string value.

fromValue(String) - Static method in enum class com.genologics.ri.automation.Context

Creates a Context from a string value.

fromValue(String) - Static method in enum class com.genologics.ri.configuration.FieldType

Gets the FieldType enum value from its string representation.

fromValue(String) - Static method in enum class com.genologics.ri.container.ContainerState

Get the container state that has the given display name.

fromValue(String) - Static method in enum class com.genologics.ri.process.OutputGenerationType

Converts from an XML value to an enum constant.

fromValue(String) - Static method in enum class com.genologics.ri.processexecution.QCFlag

Converts a string value to a QCFlag enum constant.

fromValue(String) - Static method in enum class com.genologics.ri.processtype.InvocationType

Gets the invocation type corresponding to the specified XML value.

fromValue(String) - Static method in enum class com.genologics.ri.processtype.OutputGenerationType

Gets the output generation type corresponding to the specified XML value.

fromValue(String) - Static method in enum class com.genologics.ri.processtype.Style

Gets the style corresponding to the specified XML value.

fromValue(String) - Static method in enum class com.genologics.ri.processtype.TriggerPoint

Gets the trigger point corresponding to the specified XML value.

fromValue(String) - Static method in enum class com.genologics.ri.processtype.TriggerStatus

Gets the trigger status corresponding to the specified XML value.

fromValue(String) - Static method in enum class com.genologics.ri.processtype.TriggerType

Gets the trigger type corresponding to the specified XML value.

fromValue(String) - Static method in enum class com.genologics.ri.processtype.VariabilityType

Gets the variability type corresponding to the specified XML value.

fromValue(String) - Static method in enum class com.genologics.ri.reagentlot.Status

Returns the Status enum constant for the given string value.

fromValue(String) - Static method in enum class com.genologics.ri.step.ActionType

Converts a string value to an ActionType.

fromValue(String) - Static method in enum class com.genologics.ri.step.OutputGenerationType

Converts a string value to an OutputGenerationType.

fromValue(String) - Static method in enum class com.genologics.ri.step.ProcessState

Get the process state that has the given display name.

fromValue(String) - Static method in enum class com.genologics.ri.step.Status

Creates a status from a string value.

fromValue(String) - Static method in enum class com.genologics.ri.stepconfiguration.Style

Converts a string value to a Style enum constant.

fromValue(String) - Static method in enum class com.genologics.ri.stepconfiguration.TriggerPoint

Converts a string value to a TriggerPoint enum constant.

fromValue(String) - Static method in enum class com.genologics.ri.stepconfiguration.TriggerStatus

Converts a string value to a TriggerStatus enum constant.

fromValue(String) - Static method in enum class com.genologics.ri.stepconfiguration.TriggerType

Converts a string value to a TriggerType enum constant.

fromValue(String) - Static method in enum class com.genologics.ri.workflowconfiguration.Status

Creates a Status from a string value.

G

GenericTypeLink - Class in com.genologics.ri.stepconfiguration

Generic-type is a lockable child element that provides a name linking an entity to the step.

GenericTypeLink() - Constructor for class com.genologics.ri.stepconfiguration.GenericTypeLink

Default constructor.

GenericTypeLink(String) - Constructor for class com.genologics.ri.stepconfiguration.GenericTypeLink

Constructor with value.

getAction() - Method in class com.genologics.ri.permission.Permission

Get the permission action.

getAction() - Method in class com.genologics.ri.permission.PermissionLink

Get the permission action.

getAction() - Method in class com.genologics.ri.role.PermissionLink

Gets the action associated with the permission.

getAction() - Method in class com.genologics.ri.step.NextAction

Gets the action type.

getActions() - Method in class com.genologics.ri.step.ProcessStep

Gets the link to the actions associated with this step.

getArchived() - Method in class com.genologics.ri.controltype.ControlType

Gets the archived flag.

getArchived() - Method in class com.genologics.ri.instrument.Instrument

Get whether the instrument has been archived.

getArchived() - Method in class com.genologics.ri.reagentkit.ReagentKit

Gets whether the reagent kit is archived.

getArrangements() - Method in class com.genologics.ri.step.ProcessStep

Gets the link to the arrangements associated with this step.

getArtifact() - Method in class com.genologics.ri.artifact.Demux

Gets the artifact.

getArtifact() - Method in class com.genologics.ri.sample.SampleBase

Gets the artifact link for this sample.

getArtifactGroups() - Method in class com.genologics.ri.artifact.Artifact

Gets the list of artifact groups this artifact belongs to.

getArtifactGroups() - Method in class com.genologics.ri.artifactgroup.ArtifactGroups

Gets the list of artifact groups.

getArtifacts() - Method in class com.genologics.ri.artifact.ArtifactBatchFetchResult

Gets the list of artifacts in this batch.

getArtifacts() - Method in class com.genologics.ri.artifact.Artifacts

Gets the list of artifact links.

getArtifacts() - Method in class com.genologics.ri.artifact.DemuxDetails

Gets the list of artifacts.

getArtifacts() - Method in class com.genologics.ri.artifactgroup.ArtifactGroup

Gets the link to the artifacts in this group.

getArtifacts() - Method in class com.genologics.ri.queue.Queue

Gets the list of artifacts in the queue.

getArtifacts() - Method in class com.genologics.ri.routing.ExtArtifactAssignments

Gets the list of artifact links.

getArtifactType() - Method in class com.genologics.ri.processtype.ProcessInput

Gets the artifact type for the input.

getArtifactType() - Method in class com.genologics.ri.processtype.ProcessOutput

Artifact type for this output.

getArtifactUri() - Method in class com.genologics.ri.step.NextAction

Gets the artifact URI.

getAssign() - Method in class com.genologics.ri.routing.Routing

Gets the list of assigned routes.

getAttachedTo() - Method in class com.genologics.ri.file.ClarityFile

This element contains a URI that identifies and links to further information about the resource that the file is attached to, such as a project, sample, process, or file-based artifact.

getAttachTo() - Method in class com.genologics.ri.processtype.Field

Gets the entity to which this field is attached.

getAttachTo() - Method in class com.genologics.ri.stepconfiguration.Field

Gets the attach-to value indicating what entity this field is attached to.

getAttachToCategory() - Method in class com.genologics.ri.configuration.Field

Gets the category this field is attached to.

getAttachToCategory() - Method in class com.genologics.ri.configuration.Type

Gets the category this user defined type is attached to.

getAttachToCategory() - Method in class com.genologics.ri.configuration.UdfConfigLink

Gets the category this field is attached to.

getAttachToCategory() - Method in class com.genologics.ri.configuration.UdtConfigLink

Gets the category this user defined type is attached to.

getAttachToName() - Method in class com.genologics.ri.configuration.Field

Gets the name of the entity type this field is attached to.

getAttachToName() - Method in class com.genologics.ri.configuration.Type

Gets the name of the entity type this user defined type is attached to.

getAttachToName() - Method in class com.genologics.ri.configuration.UdfConfigLink

Gets the name of the entity type this field is attached to.

getAttachToName() - Method in class com.genologics.ri.configuration.UdtConfigLink

Gets the name of the entity type this user defined type is attached to.

getAttributes() - Method in class com.genologics.ri.reagenttype.SpecialType

Gets the list of attributes for this special type.

getAuthor() - Method in class com.genologics.ri.step.EscalationRequest

Gets the author.

getAuthor() - Method in class com.genologics.ri.step.EscalationReview

Gets the author.

getAutomaticNextStep() - Method in class com.genologics.ri.step.ProcessStep

Gets the link to the next step that will be automatically triggered after this step.

getAutomations() - Method in class com.genologics.ri.automation.Automations

Gets the list of automations.

getAvailableInputs() - Method in class com.genologics.ri.step.Pools

Gets the list of available input artifacts.

getAvailablePrograms() - Method in class com.genologics.ri.step.ProcessStep

Gets the list of programs available for this step.

getBatchRetrieveClassForEntity(Class<E>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Get the class that allow mass retrieve or update operations for the given entity class.

getBehaviourForCall() - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Get the type of stateful behaviour to use for the current call.

getBillingAddress() - Method in class com.genologics.ri.lab.Lab

Gets the billing address of the lab.

getBioSource() - Method in class com.genologics.ri.sample.SampleBase

Deprecated.

Biosource is not supported in Clarity.

getBuiltIn() - Method in class com.genologics.ri.role.Role

Gets whether this is a built-in system role.

getBulkOperationBatchSize() - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Get the size of each batch of objects fetched, updated or created in a bulk operation.

getCalibrantWells() - Method in class com.genologics.ri.containertype.ContainerType

Deprecated.

This property is no longer supported and will be ignored if provided.

getCapacity() - Method in class com.genologics.ri.containertype.ContainerType

Get the capacity of a container of this type, i.e. the columns * rows.

getCatalogueNumber() - Method in class com.genologics.ri.controltype.ControlType

Gets the catalogue number of the control type.

getCatalogueNumber() - Method in class com.genologics.ri.reagentkit.ReagentKit

Gets the catalogue number of the reagent kit.

getCategory() - Method in class com.genologics.ri.exception.Exception

Gets the category of the exception.

getCategory() - Method in exception org.cruk.clarity.api.ClarityException

Get the error category.

getChannel() - Method in class com.genologics.ri.automation.Automation

Gets the channel for this automation.

getChannel() - Method in class com.genologics.ri.processtype.Parameter

Gets the channel on which the EPP runs.

getChildUris() - Method in class com.genologics.ri.configuration.Field

Gets the list of child URIs for hierarchical fields.

getCity() - Method in class com.genologics.ri.Address

Gets the city.

getCloseDate() - Method in class com.genologics.ri.project.Project

Get the close date of the project.

getCode() - Method in class com.genologics.ri.exception.Exception

Gets the HTTP response code of the error.

getCode() - Method in exception org.cruk.clarity.api.ClarityException

Get the error code.

getColumns() - Method in class com.genologics.ri.containertype.ContainerType

Gets the x-dimension (horizontal/columns) of the container's coordinate system.

getComment() - Method in class com.genologics.ri.step.EscalationRequest

Gets the comment.

getComment() - Method in class com.genologics.ri.step.EscalationReview

Gets the comment.

getConcentration() - Method in class com.genologics.ri.controltype.ControlType

Gets the concentration of the control type.

getConfiguration() - Method in class com.genologics.ri.step.Actions

Gets the step configuration.

getConfiguration() - Method in class com.genologics.ri.step.Arrangements

Gets the step configuration.

getConfiguration() - Method in class com.genologics.ri.step.Placements

Gets the step configuration.

getConfiguration() - Method in class com.genologics.ri.step.Pools

Gets the step configuration.

getConfiguration() - Method in class com.genologics.ri.step.ProcessStep

Gets the configuration of the step.

getConfiguration() - Method in class com.genologics.ri.step.ProgramStatus

Gets the configuration of the step.

getConfiguration() - Method in class com.genologics.ri.step.ReagentLots

Gets the step configuration.

getConfiguration() - Method in class com.genologics.ri.step.Reagents

Gets the step configuration.

getConfiguration() - Method in class com.genologics.ri.step.StepCreation

Gets the step configuration.

getConfiguration() - Method in class com.genologics.ri.step.StepDetails

Gets the step configuration.

getConfiguration() - Method in class com.genologics.ri.step.StepSetup

Gets the step configuration.

getContainer() - Method in class com.genologics.ri.Location

Gets the container link.

getContainers() - Method in class com.genologics.ri.container.ContainerBatchFetchResult

Gets the list of containers.

getContainers() - Method in class com.genologics.ri.container.Containers

Gets the list of container links.

getContainerType() - Method in class com.genologics.ri.container.Container

Gets the container type link.

getContainerType() - Method in class com.genologics.ri.step.StepCreation

Gets the container type name.

getContainerTypes() - Method in class com.genologics.ri.containertype.ContainerTypes

Gets the list of container type links.

getContentLocation() - Method in class com.genologics.ri.file.ClarityFile

This element contains a URI that identifies and links to the network location of the file, which can be used to retrieve the file and process its contents.

getContext() - Method in class com.genologics.ri.automation.Automation

Gets the context in which this automation runs.

getControlType() - Method in class com.genologics.ri.artifact.Artifact

Gets the control type if this artifact is a control sample.

getControlType() - Method in class com.genologics.ri.sample.SampleBase

Gets the control type link for this sample.

getControlTypes() - Method in class com.genologics.ri.controltype.ControlTypes

Gets the list of control types.

getControlTypeUri() - Method in class com.genologics.ri.step.CreationInput

Gets the control type URI.

getCountry() - Method in class com.genologics.ri.Address

Gets the country.

getCreatedBy() - Method in class com.genologics.ri.reagentlot.ReagentLot

Gets the link to the researcher who created this lot.

getCreatedDate() - Method in class com.genologics.ri.reagentlot.ReagentLot

Gets the creation date.

getCreationLocation() - Method in class com.genologics.ri.sample.Sample

Get the initial creation location for this sample.

getCredentials() - Method in class com.genologics.ri.researcher.Researcher

Gets the researcher's credentials.

getCredentials() - Method in interface org.cruk.clarity.api.http.AuthenticatingClientHttpRequestFactory

Get the credentials currently in use.

getCredentials() - Method in class org.cruk.clarity.api.http.HttpComponentsClientHttpRequestFactoryBasicAuth

Get the credentials currently in use.

getCredentialsProvider() - Method in class org.cruk.clarity.api.http.HttpComponentsClientHttpRequestFactoryBasicAuth

Get the credentials provider used by this factory.

getCurrentState() - Method in class com.genologics.ri.step.ProcessStep

Gets the current state of the step.

getDate() - Method in class com.genologics.ri.step.EscalationRequest

Gets the date.

getDate() - Method in class com.genologics.ri.step.EscalationReview

Gets the date.

getDateCompleted() - Method in class com.genologics.ri.sample.SampleBase

Gets the date the sample was completed.

getDateCompleted() - Method in class com.genologics.ri.step.ProcessStep

Gets the date and time the step was completed.

getDateReceived() - Method in class com.genologics.ri.sample.SampleBase

Gets the date the sample was received.

getDateRun() - Method in class com.genologics.ri.process.ClarityProcess

Gets the date the process was run.

getDateRun() - Method in class com.genologics.ri.processexecution.ExecutableProcess

Gets the date the process was run.

getDateStarted() - Method in class com.genologics.ri.step.ProcessStep

Gets the date and time the step was started.

getDefaultGrouping() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Deprecated.

Please use "<milestone>DefaultGrouping" (for example, "queueDefaultGrouping") in a StepProperty field instead.

getDemux() - Method in class com.genologics.ri.artifact.Artifact

Gets the demultiplexing information for this artifact.

getDemux() - Method in class com.genologics.ri.artifact.DemuxArtifact

Gets the demux details.

getDemuxDetails() - Method in class com.genologics.ri.artifact.Demux

Gets the demux details.

getDepartment() - Method in class com.genologics.ri.Address

Gets the department.

getDescription() - Method in class com.genologics.ri.globaltoken.GlobalToken

Get the token description.

getDescription() - Method in class com.genologics.ri.permission.Permission

Get the permission description.

getDescription() - Method in class com.genologics.ri.sample.BioSource

Deprecated.

Gets the description of the biosource.

getDescription() - Method in class org.cruk.clarity.api.impl.URLInputStreamResource

Get a description of the resource.

getDetail() - Method in class com.genologics.ri.processtype.IceBucketField

Gets whether this field shows in the detail view.

getDetail() - Method in class com.genologics.ri.processtype.QueueField

Gets whether this field shows in the detail view.

getDetail() - Method in class com.genologics.ri.stepconfiguration.IceBucketField

Gets whether this field should be shown in detail view.

getDetail() - Method in class com.genologics.ri.stepconfiguration.QueueField

Gets whether this field should be shown in detail view.

getDisplayName() - Method in class com.genologics.ri.processtype.ProcessInput

Gets the display name for the input.

getDisplayName() - Method in class com.genologics.ri.processtype.ProcessOutput

The display name for the output.

getDisplayPrecision() - Method in class com.genologics.ri.configuration.Field

Gets the display precision for numeric fields.

getEmail() - Method in class com.genologics.ri.researcher.Researcher

The researcher's e-mail address.

getEnabled() - Method in class com.genologics.ri.processtype.StepSetup

Gets whether the step setup view is enabled for this process type.

getEntityClass() - Method in class com.genologics.ri.artifact.ArtifactGroupLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.artifact.ArtifactLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.artifact.ControlTypeLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.artifact.DemuxArtifact

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.artifact.DemuxArtifactSample

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.artifact.DemuxLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.artifact.DemuxSourceArtifact

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.artifact.ParentProcessLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.artifact.PoolStep

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.artifact.SampleLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.artifact.WorkflowStage

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.artifactgroup.ArtifactGroupLink

Gets the entity class this link refers to.

getEntityClass() - Method in class com.genologics.ri.automation.AutomationLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.automation.ProcessTypeLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.configuration.FieldLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.configuration.TypeDefinition

Gets the entity class for this type definition.

getEntityClass() - Method in class com.genologics.ri.configuration.UdfConfigLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.configuration.UdtConfigLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.container.ContainerLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.container.ContainerTypeLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.container.Placement

Gets the entity class for this placement.

getEntityClass() - Method in class com.genologics.ri.ContainerLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.containertype.ContainerTypeLink

Get the class of the true, full LIMS entity this object links to.

getEntityClass() - Method in class com.genologics.ri.controltype.ControlTypeLink

Gets the entity class that this link refers to.

getEntityClass() - Method in class com.genologics.ri.file.ClarityFile

Gets the entity class for this file.

getEntityClass() - Method in class com.genologics.ri.file.FileLink

Gets the entity class that this link references.

getEntityClass() - Method in class com.genologics.ri.globaltoken.GlobalTokenLink

Get the class of the true, full LIMS entity this object links to.

getEntityClass() - Method in class com.genologics.ri.instrument.InstrumentLink

Get the class of the true, full LIMS entity this object links to.

getEntityClass() - Method in class com.genologics.ri.instrumenttype.InstrumentTypeLink

Get the class of the true, full LIMS entity this object links to.

getEntityClass() - Method in class com.genologics.ri.instrumenttype.InstrumentTypeProcessType

Get the class of the true, full LIMS entity this object links to.

getEntityClass() - Method in class com.genologics.ri.lab.LabLink

Gets the entity class for this link.

getEntityClass() - Method in interface com.genologics.ri.LimsLink

Get the class of the true, full LIMS entity this object links to.

getEntityClass() - Method in class com.genologics.ri.Location

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.permission.PermissionLink

Get the class of the true, full LIMS entity this object links to.

getEntityClass() - Method in class com.genologics.ri.process.ArtifactLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.process.InstrumentLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.process.ParentProcessLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.process.ProcessLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.process.ProcessTypeLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.process.Technician

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.processexecution.Input

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.processexecution.InstrumentLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.processexecution.Technician

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.processtemplate.InstrumentLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.processtemplate.ProcessTemplateLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.processtemplate.ProcessTypeLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.processtemplate.Technician

Gets the entity class that this link references.

getEntityClass() - Method in class com.genologics.ri.processtype.ContainerTypeLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.processtype.ControlTypeLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.processtype.ProcessTypeLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.processtype.ReagentKitLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.processtype.TypeDefinition

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.project.ProjectLink

Get the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.project.ResearcherLink

Get the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.protocolconfiguration.ProtocolLink

Gets the entity class this link refers to.

getEntityClass() - Method in class com.genologics.ri.queue.ArtifactLink

Get the class of the true, full LIMS entity this object links to.

getEntityClass() - Method in class com.genologics.ri.reagentkit.ReagentKitLink

Get the class of the true, full LIMS entity this object links to.

getEntityClass() - Method in class com.genologics.ri.reagentlot.ReagentKitLink

Get the class of the true, full LIMS entity this object links to.

getEntityClass() - Method in class com.genologics.ri.reagentlot.ReagentLotLink

Get the class of the true, full LIMS entity this object links to.

getEntityClass() - Method in class com.genologics.ri.reagentlot.ResearcherLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.reagenttype.ReagentTypeLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.researcher.LabLink

Gets the entity class this link refers to.

getEntityClass() - Method in class com.genologics.ri.researcher.ResearcherLink

Gets the entity class this link refers to.

getEntityClass() - Method in class com.genologics.ri.researcher.Role

Gets the entity class this link refers to.

getEntityClass() - Method in class com.genologics.ri.role.PermissionLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.role.ResearcherLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.role.RoleLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.routing.ArtifactLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.sample.ArtifactLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.sample.ControlTypeLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.sample.ProjectLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.sample.SampleLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.sample.Submitter

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.savedquery.SavedQueryLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.stage.ProtocolLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.stage.ProtocolStepLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.stage.WorkflowLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.step.ActionsLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.step.ArrangementsLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.step.ArtifactLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.step.AutomaticNextStepLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.step.ContainerLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.step.CreationInput

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.step.EscalatedArtifact

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.step.Input

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.step.InstrumentLink

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.step.NextAction

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.step.Output

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.step.OutputArrangement

Gets the entity class.

getEntityClass() - Method in class com.genologics.ri.step.OutputPlacement

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.step.PlacementsLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.step.PoolsLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.step.ProgramStatusLink

Get the class of the true, full LIMS entity this object links to.

getEntityClass() - Method in class com.genologics.ri.step.ReagentLotLink

Get the class of the true, full LIMS entity this object links to.

getEntityClass() - Method in class com.genologics.ri.step.ReagentLotsLink

Get the class of the true, full LIMS entity this object links to.

getEntityClass() - Method in class com.genologics.ri.step.ReagentsLink

Get the class of the true, full LIMS entity this object links to.

getEntityClass() - Method in class com.genologics.ri.step.SharedResultFile

Get the class of the true, full LIMS entity this object links to.

getEntityClass() - Method in class com.genologics.ri.step.StepConfiguration

Get the class of the true, full LIMS entity this object links to.

getEntityClass() - Method in class com.genologics.ri.step.StepDetailsLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.step.StepSetupLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.step.Technician

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.step.UserLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.stepconfiguration.ControlTypeLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.stepconfiguration.NextStep

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.stepconfiguration.ProcessTypeLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.stepconfiguration.ReagentKitLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.workflowconfiguration.ProtocolLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.workflowconfiguration.StageLink

Gets the entity class for this link.

getEntityClass() - Method in class com.genologics.ri.workflowconfiguration.WorkflowLink

Gets the entity class for this link.

getEntityClass() - Method in class org.cruk.clarity.api.search.SearchTerms

Get the class being searched for.

getEppTriggers() - Method in class com.genologics.ri.processtype.ProcessType

Gets the EPP triggers for this process type.

getEppTriggers() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the list of EPP triggers for this step.

getEscalatedArtifacts() - Method in class com.genologics.ri.step.Escalation

Gets the list of escalated artifacts, creating it if it doesn't exist.

getEscalation() - Method in class com.genologics.ri.step.Actions

Gets the escalation information.

getExpiryDate() - Method in class com.genologics.ri.instrument.Instrument

Get the instrument expiry date.

getExpiryDate() - Method in class com.genologics.ri.reagentlot.ReagentLot

Gets the expiry date.

getExternalid() - Method in class com.genologics.ri.lab.Lab

Gets the list of external identifiers for the lab.

getExternalIds() - Method in class com.genologics.ri.project.Project

Get the external identifiers for the project.

getExternalIds() - Method in class com.genologics.ri.researcher.Researcher

Gets the list of external identifiers for the researcher.

getExternalIds() - Method in class com.genologics.ri.sample.SampleBase

Gets the list of external identifiers for this sample.

getFax() - Method in class com.genologics.ri.researcher.Researcher

Gets the researcher's fax number.

getFieldDefinitions() - Method in class com.genologics.ri.configuration.Type

Gets the list of field definitions for this type.

getFieldDefinitions() - Method in class com.genologics.ri.processtype.ProcessOutput

Deprecated.

These field definitions are ignored as of Clarity LIMS 5.0.

getFieldDefinitions() - Method in class com.genologics.ri.processtype.ProcessType

Each field definition provides a URI linking to the configuration of a user-defined field for the output type.

getFieldName() - Method in exception com.genologics.ri.userdefined.MissingUDFException

Gets the name of the missing field.

getFields() - Method in class com.genologics.ri.sample.BioSource

Deprecated.

Gets the list of user-defined fields for the biosource.

getFields() - Method in class com.genologics.ri.userdefined.UDT

Gets the list of fields in this user-defined type.

getFile() - Method in class com.genologics.ri.artifact.Artifact

File provides a URI linking to the detailed representation of the File associated with the Artifact.

getFile() - Method in class com.genologics.ri.processtype.Parameter

Deprecated.

This property is no longer supported.

getFile() - Method in class org.cruk.clarity.api.impl.URLInputStreamResource

Get a file object for the URL.

getFilename() - Method in class org.cruk.clarity.api.impl.URLInputStreamResource

Get the file name of the resource.

getFiles() - Method in class com.genologics.ri.automation.Automation

Gets the list of files associated with this automation.

getFiles() - Method in class com.genologics.ri.file.ClarityFileBatchFetchResult

Gets the list of files in this batch.

getFiles() - Method in class com.genologics.ri.file.ClarityFiles

Gets the list of file links.

getFiles() - Method in class com.genologics.ri.process.ClarityProcess

Gets the files associated with the process.

getFiles() - Method in class com.genologics.ri.processtype.Parameter

Each File provides a URI linking to the detailed representation of a File associated with the Process Parameter.

getFiles() - Method in class com.genologics.ri.processtype.StepSetup

Gets the list of shared result file configurations.

getFiles() - Method in class com.genologics.ri.project.Project

Get the files attached to the project.

getFiles() - Method in class com.genologics.ri.sample.SampleBase

Gets the list of files associated with this sample.

getFiles() - Method in class com.genologics.ri.step.StepSetup

Gets the list of shared result files.

getFiles() - Method in class com.genologics.ri.stepconfiguration.StepSetup

Gets the list of shared result files for the step setup view.

getFirstName() - Method in class com.genologics.ri.process.Technician

Gets the first name.

getFirstName() - Method in class com.genologics.ri.processtemplate.Technician

Gets the first name of the technician.

getFirstName() - Method in class com.genologics.ri.researcher.Researcher

Gets the researcher's first name.

getFirstName() - Method in class com.genologics.ri.researcher.ResearcherLink

Gets the researcher's first name.

getFirstName() - Method in class com.genologics.ri.role.ResearcherLink

Gets the first name of the researcher.

getFirstName() - Method in class com.genologics.ri.sample.Submitter

Gets the first name of the submitter.

getFirstName() - Method in class com.genologics.ri.step.Technician

Gets the first name of the technician.

getFirstName() - Method in class com.genologics.ri.step.UserLink

Gets the first name of the user.

getFromWrapper(CacheElementWrapper) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Get the object from its cache wrapper.

getFullName() - Method in class com.genologics.ri.process.Technician

Convenience method for returning the full name of the technician.

getFullName() - Method in class com.genologics.ri.processtemplate.Technician

Convenience method for returning the full name of the technician.

getFullName() - Method in class com.genologics.ri.researcher.Researcher

Convenience method for returning the full name of the researcher.

getFullName() - Method in class com.genologics.ri.researcher.ResearcherLink

Convenience method for returning the full name of the researcher.

getFullName() - Method in class com.genologics.ri.role.ResearcherLink

Convenience method for returning the full name of the researcher.

getFullName() - Method in class com.genologics.ri.sample.Submitter

Convenience method for returning the full name of the submitter.

getFullName() - Method in class com.genologics.ri.step.Technician

Convenience method for returning the full name of the technician.

getGlobalTokens() - Method in class com.genologics.ri.globaltoken.GlobalTokens

Get the list of global token links.

getHost() - Method in interface org.cruk.clarity.api.http.AuthenticatingClientHttpRequestFactory

Get the host to which the credentials will be applied.

getHost() - Method in class org.cruk.clarity.api.http.HttpComponentsClientHttpRequestFactoryBasicAuth

Get the host to which the credentials will be applied.

getHttpStatus() - Method in exception org.cruk.clarity.api.ClarityException

Get the HTTP status code.

getHttpUploadSizeLimit() - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Get the maximum size of file that can be uploaded using HTTP.

getIceBucketFields() - Method in class com.genologics.ri.processtype.ProcessType

Gets the fields displayed in the ice bucket view.

getIceBucketFields() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the list of ice bucket fields for this step.

getId() - Method in class com.genologics.ri.artifact.WorkflowStage

Get the numeric identifier for this workflow stage from its URI.

getId() - Method in class com.genologics.ri.configuration.Field

Convenience method for getting the field's id from its URI.

getId() - Method in class com.genologics.ri.ExternalId

Gets the external id.

getId() - Method in class com.genologics.ri.protocolconfiguration.Protocol

Get the numeric identifier for this protocol from its URI.

getId() - Method in class com.genologics.ri.savedquery.SavedQuery

Gets the unique identifier of the saved query.

getId() - Method in class com.genologics.ri.savedquery.SavedQueryLink

Gets the unique identifier of the saved query.

getId() - Method in class com.genologics.ri.stage.Stage

Gets the numeric identifier for this workflow stage from its URI.

getId() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Get the numeric identifier for this protocol step from its URI.

getId() - Method in class com.genologics.ri.workflowconfiguration.Workflow

Get the numeric identifier for this workflow from its URI.

getIndex() - Method in class com.genologics.ri.protocolconfiguration.Protocol

Gets the index of the protocol.

getIndex() - Method in class com.genologics.ri.stage.Stage

Gets the index of the stage in the workflow.

getInitials() - Method in class com.genologics.ri.researcher.Researcher

Gets the researcher's initials.

getInput() - Method in class com.genologics.ri.process.InputOutputMap

Gets the input artifact link.

getInput() - Method in class com.genologics.ri.step.InputOutputMap

Gets the input artifact link.

getInputOutputMaps() - Method in class com.genologics.ri.process.ClarityProcess

Gets the input-output mappings.

getInputOutputMaps() - Method in class com.genologics.ri.processexecution.ExecutableProcess

Gets the input-output mappings.

getInputOutputMaps() - Method in class com.genologics.ri.step.StepDetails

Gets the list of input to output artifact mappings.

getInputs() - Method in class com.genologics.ri.processexecution.ExecutableInputOutputMap

Gets the list of inputs.

getInputs() - Method in class com.genologics.ri.step.PooledInputs

Gets the list of input artifacts.

getInputs() - Method in class com.genologics.ri.step.StepCreation

Gets the list of input artifacts for the step.

getInputStream() - Method in class org.cruk.clarity.api.impl.URLInputStreamResource

Get the input stream to read the resource content.

getInstitution() - Method in class com.genologics.ri.Address

Gets the institution.

getInstrument() - Method in class com.genologics.ri.process.ClarityProcess

Gets the instrument link.

getInstrument() - Method in class com.genologics.ri.processexecution.ExecutableProcess

Gets the instrument used for the process.

getInstrument() - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Gets the instrument link.

getInstrument() - Method in class com.genologics.ri.step.StepDetails

Gets the link to the instrument.

getInstruments() - Method in class com.genologics.ri.instrument.Instruments

Get the list of instrument links.

getInvocationType() - Method in class com.genologics.ri.processtype.Parameter

Deprecated.

This property is no longer supported.

getInvoiceDate() - Method in class com.genologics.ri.project.Project

Get the invoice date of the project.

getLab() - Method in class com.genologics.ri.researcher.Researcher

Gets the link to the researcher's lab.

getLabs() - Method in class com.genologics.ri.lab.Labs

Gets the list of lab links.

getLastModifiedBy() - Method in class com.genologics.ri.reagentlot.ReagentLot

Gets the link to the researcher who last modified this lot.

getLastModifiedDate() - Method in class com.genologics.ri.reagentlot.ReagentLot

Gets the last modification date.

getLastName() - Method in class com.genologics.ri.process.Technician

Gets the last name.

getLastName() - Method in class com.genologics.ri.processtemplate.Technician

Gets the last name of the technician.

getLastName() - Method in class com.genologics.ri.researcher.Researcher

Gets the researcher's last name.

getLastName() - Method in class com.genologics.ri.researcher.ResearcherLink

Gets the researcher's last name.

getLastName() - Method in class com.genologics.ri.role.ResearcherLink

Gets the last name of the researcher.

getLastName() - Method in class com.genologics.ri.sample.Submitter

Gets the last name of the submitter.

getLastName() - Method in class com.genologics.ri.step.Technician

Gets the last name of the technician.

getLastName() - Method in class com.genologics.ri.step.UserLink

Gets the last name of the user.

getLength() - Method in class org.cruk.clarity.api.SavedQuerySummary

Get the length in bytes of the response.

getLimsid() - Method in class com.genologics.ri.artifact.Artifact

Gets the LIMS id of this artifact.

getLimsid() - Method in class com.genologics.ri.artifact.ArtifactLink

Gets the LIMS id.

getLimsid() - Method in class com.genologics.ri.artifact.DemuxArtifactSample

Gets the LIMS id.

getLimsid() - Method in class com.genologics.ri.artifact.ParentProcessLink

Gets the LIMS id.

getLimsid() - Method in class com.genologics.ri.artifact.SampleLink

Gets the LIMS id.

getLimsid() - Method in class com.genologics.ri.container.Container

Gets the LIMS id.

getLimsid() - Method in class com.genologics.ri.container.ContainerLink

Gets the LIMS id.

getLimsid() - Method in class com.genologics.ri.container.Placement

Gets the LIMS id of the artifact.

getLimsid() - Method in class com.genologics.ri.ContainerLink

Gets the LIMS id of the container.

getLimsid() - Method in class com.genologics.ri.file.ClarityFile

Gets the LIMS id of this file.

getLimsid() - Method in class com.genologics.ri.file.FileLink

Gets the LIMS id of the file.

getLimsid() - Method in class com.genologics.ri.instrument.Instrument

Get the LIMS id of this instrument.

getLimsid() - Method in class com.genologics.ri.instrument.InstrumentLink

Get the LIMS id for this object.

getLimsid() - Method in class com.genologics.ri.lab.Lab

Gets the LIMS id extracted from the URI.

getLimsid() - Method in class com.genologics.ri.lab.LabLink

Gets the LIMS id extracted from the URI.

getLimsid() - Method in interface com.genologics.ri.LimsEntityLinkable

Get the LIMS id for this object.

getLimsid() - Method in class com.genologics.ri.Location

Gets the LIMS id of the container.

getLimsid() - Method in class com.genologics.ri.process.ArtifactLink

Gets the LIMS id.

getLimsid() - Method in class com.genologics.ri.process.ClarityProcess

Gets the LIMS id.

getLimsid() - Method in class com.genologics.ri.process.InstrumentLink

Gets the LIMS id extracted from the URI.

getLimsid() - Method in class com.genologics.ri.process.ParentProcessLink

Gets the LIMS id.

getLimsid() - Method in class com.genologics.ri.process.ProcessLink

Gets the LIMS id.

getLimsid() - Method in class com.genologics.ri.processexecution.InstrumentLink

Gets the LIMS id from the URI.

getLimsid() - Method in class com.genologics.ri.processtemplate.InstrumentLink

Gets the LIMS id extracted from the URI.

getLimsid() - Method in class com.genologics.ri.project.Project

Get the LIMS id of the project.

getLimsid() - Method in class com.genologics.ri.project.ProjectLink

Get the LIMS id of the project.

getLimsid() - Method in class com.genologics.ri.project.ResearcherLink

Get the LIMS id of the researcher.

getLimsid() - Method in class com.genologics.ri.queue.ArtifactLink

Get the LIMS id for this object.

getLimsid() - Method in class com.genologics.ri.reagentlot.ReagentLot

getLimsid() - Method in class com.genologics.ri.reagentlot.ReagentLotLink

Get the LIMS id for this object.

getLimsid() - Method in class com.genologics.ri.reagentlot.ResearcherLink

Gets the LIMS id from the URI.

getLimsid() - Method in class com.genologics.ri.reagenttype.ReagentType

Gets the LIMS id.

getLimsid() - Method in class com.genologics.ri.reagenttype.ReagentTypeLink

Gets the LIMS id from the URI.

getLimsid() - Method in class com.genologics.ri.researcher.LabLink

Gets the LIMS id from the URI.

getLimsid() - Method in class com.genologics.ri.researcher.Researcher

Gets the LIMS id from the URI.

getLimsid() - Method in class com.genologics.ri.researcher.ResearcherLink

Gets the LIMS id from the URI.

getLimsid() - Method in class com.genologics.ri.role.ResearcherLink

Gets the LIMS id from the URI.

getLimsid() - Method in class com.genologics.ri.sample.ArtifactLink

Gets the LIMS id of the artifact.

getLimsid() - Method in class com.genologics.ri.sample.ProjectLink

Gets the LIMS id of the project.

getLimsid() - Method in class com.genologics.ri.sample.SampleBase

Gets the LIMS id of this sample.

getLimsid() - Method in class com.genologics.ri.sample.SampleLink

Gets the LIMS id of the sample.

getLimsid() - Method in class com.genologics.ri.step.ArtifactLink

Gets the LIMS id.

getLimsid() - Method in class com.genologics.ri.step.InstrumentLink

Gets the LIMS id from the URI.

getLimsid() - Method in class com.genologics.ri.step.ProcessStep

Gets the LIMS id of the step.

getLimsid() - Method in class com.genologics.ri.step.ReagentLotLink

Get the LIMS id for this object.

getLimsid() - Method in class com.genologics.ri.step.SharedResultFile

Gets the LIMS id of the artifact.

getLimsId() - Method in interface com.genologics.ri.LimsEntityLinkable

Same as getLimsid() but written in a more pleasing form for camel case.

getLink() - Method in class com.genologics.ri.artifact.Artifact

Get a concrete link object to this LimsEntityLinkable entity.

getLink() - Method in class com.genologics.ri.automation.Automation

Gets a link to this automation.

getLink() - Method in class com.genologics.ri.configuration.Field

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.configuration.Type

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.container.Container

Gets a link to this container.

getLink() - Method in class com.genologics.ri.containertype.ContainerType

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.controltype.ControlType

Gets a link representation of this control type.

getLink() - Method in class com.genologics.ri.globaltoken.GlobalToken

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.instrument.Instrument

Get a concrete link object to this LimsEntityLinkable entity.

getLink() - Method in class com.genologics.ri.instrumenttype.InstrumentType

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.lab.Lab

Get a concrete link object to this LimsEntityLinkable entity.

getLink() - Method in interface com.genologics.ri.LimsEntityLink

Since anything implementing this interface is already an entity link, this default implementation will just return itself.

getLink() - Method in interface com.genologics.ri.LimsEntityLinkable

Get a concrete link object to this LimsEntityLinkable entity.

getLink() - Method in interface com.genologics.ri.LimsLink

Since anything implementing this interface is already a link, this default implementation will just return itself.

getLink() - Method in interface com.genologics.ri.Linkable

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.permission.Permission

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.process.ClarityProcess

Get a concrete link object to this LimsEntityLinkable entity.

getLink() - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.processtype.ProcessType

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.project.Project

Get a concrete link object to this LimsEntityLinkable entity.

getLink() - Method in class com.genologics.ri.protocolconfiguration.Protocol

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.reagentkit.ReagentKit

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.reagentlot.ReagentLot

Get a concrete link object to this LimsEntityLinkable entity.

getLink() - Method in class com.genologics.ri.reagenttype.ReagentType

Get a concrete link object to this LimsEntityLinkable entity.

getLink() - Method in class com.genologics.ri.researcher.Researcher

Get a concrete link object to this LimsEntityLinkable entity.

getLink() - Method in class com.genologics.ri.role.Role

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.sample.Sample

Get a concrete link object to this LimsEntityLinkable entity.

getLink() - Method in class com.genologics.ri.savedquery.SavedQuery

Gets a link to this saved query.

getLink() - Method in class com.genologics.ri.stage.Stage

Gets a link to this stage entity.

getLink() - Method in class com.genologics.ri.step.Actions

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.step.Arrangements

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.step.Placements

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.step.Pools

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.step.ProcessStep

Get a concrete link object to this LimsEntityLinkable entity.

getLink() - Method in class com.genologics.ri.step.ProgramStatus

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.step.ReagentLots

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.step.Reagents

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.step.StepDetails

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.step.StepSetup

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Get a concrete link object to this Linkable thing.

getLink() - Method in class com.genologics.ri.workflowconfiguration.Workflow

Get a concrete link object to this Linkable thing.

getLinks() - Method in class com.genologics.ri.configuration.Udfs

Gets the list of UDF configuration links.

getLinks() - Method in class com.genologics.ri.configuration.Udts

Gets the list of UDT configuration links.

getLinks() - Method in class com.genologics.ri.Index

Gets the list of links in this index.

getLinks() - Method in class com.genologics.ri.Links

Gets the list of links.

getList() - Method in class com.genologics.ri.artifact.ArtifactBatchFetchResult

Gets the list of artifacts in this batch.

getList() - Method in class com.genologics.ri.artifact.Artifacts

Gets the list of artifact links.

getList() - Method in class com.genologics.ri.artifactgroup.ArtifactGroups

Gets the list of artifact group links.

getList() - Method in class com.genologics.ri.automation.Automations

Gets the list of automation links.

getList() - Method in interface com.genologics.ri.Batch

Gets the list of items in this batch.

getList() - Method in class com.genologics.ri.configuration.Type

Gets the list of field definitions as required by the Batch interface.

getList() - Method in class com.genologics.ri.configuration.Udfs

Gets the list of links as required by the PaginatedBatch interface.

getList() - Method in class com.genologics.ri.configuration.Udts

Gets the list of links as required by the PaginatedBatch interface.

getList() - Method in class com.genologics.ri.container.ContainerBatchFetchResult

Gets the list of containers.

getList() - Method in class com.genologics.ri.container.Containers

Gets the list of container links as required by the PaginatedBatch interface.

getList() - Method in class com.genologics.ri.containertype.ContainerTypes

Gets the list of items in this batch.

getList() - Method in class com.genologics.ri.controltype.ControlTypes

Gets the list of control type links.

getList() - Method in class com.genologics.ri.file.ClarityFileBatchFetchResult

Gets the list of files in this batch.

getList() - Method in class com.genologics.ri.file.ClarityFiles

Gets the list of file links.

getList() - Method in class com.genologics.ri.globaltoken.GlobalTokens

Gets the list of items in this batch.

getList() - Method in class com.genologics.ri.Index

Gets the list of links for the Batch interface.

getList() - Method in class com.genologics.ri.instrument.Instruments

Gets the list of items in this batch.

getList() - Method in class com.genologics.ri.instrumenttype.InstrumentTypes

Gets the list of items in this batch.

getList() - Method in class com.genologics.ri.lab.Labs

Gets the list of lab links (implements PaginatedBatch interface).

getList() - Method in class com.genologics.ri.Links

Gets the list of links for the Batch interface.

getList() - Method in class com.genologics.ri.permission.Permissions

Gets the list of items in this batch.

getList() - Method in class com.genologics.ri.process.ClarityProcesses

Gets the list of process links.

getList() - Method in class com.genologics.ri.processtemplate.ProcessTemplates

Gets the list of process template links.

getList() - Method in class com.genologics.ri.processtype.ProcessTypes

Gets the list of process type links.

getList() - Method in class com.genologics.ri.project.Projects

Get the list of project links.

getList() - Method in class com.genologics.ri.property.Properties

Gets the list of items in this batch.

getList() - Method in class com.genologics.ri.protocolconfiguration.Protocols

Gets the list of items in this batch.

getList() - Method in class com.genologics.ri.queue.Queue

Gets the list of items in this batch.

getList() - Method in class com.genologics.ri.reagentkit.ReagentKits

Gets the list of items in this batch.

getList() - Method in class com.genologics.ri.reagentlot.ReagentLots

getList() - Method in class com.genologics.ri.reagenttype.ReagentTypes

Gets the list of reagent type links for batch processing.

getList() - Method in class com.genologics.ri.researcher.Researchers

Gets the list of researcher links.

getList() - Method in class com.genologics.ri.role.Roles

Gets the list of role links for batch processing.

getList() - Method in class com.genologics.ri.sample.SampleBatchFetchResult

Gets the list of samples for batch operations.

getList() - Method in class com.genologics.ri.sample.Samples

Gets the list of sample links for batch operations.

getList() - Method in class com.genologics.ri.savedquery.SavedQueries

Gets the list of saved query links.

getList() - Method in class com.genologics.ri.version.Versions

Gets the list of versions.

getList() - Method in class com.genologics.ri.workflowconfiguration.Workflows

Gets the list of workflows.

getLocation() - Method in class com.genologics.ri.artifact.Artifact

Gets the location of the artifact.

getLocation() - Method in class com.genologics.ri.processexecution.Output

Gets the location of the output artifact.

getLocation() - Method in class com.genologics.ri.queue.ArtifactLink

Gets the location of the artifact.

getLocation() - Method in class com.genologics.ri.sample.SampleCreation

Gets the location where the sample will be created.

getLocation() - Method in class com.genologics.ri.step.OutputPlacement

Gets the location of the output artifact.

getLocked() - Method in class com.genologics.ri.stepconfiguration.GenericTypeLink

Gets whether this generic type link is locked.

getLotNumber() - Method in class com.genologics.ri.reagentlot.ReagentLot

Gets the lot number.

getMajor() - Method in class com.genologics.ri.version.Version

Gets the major version number.

getMaxValue() - Method in class com.genologics.ri.configuration.Field

Gets the maximum value for numeric fields.

getMediaType() - Method in class org.cruk.clarity.api.SavedQuerySummary

Get the media type and character set returned from the server.

getMessage() - Method in class com.genologics.ri.exception.Exception

Gets the error message.

getMessage() - Method in class com.genologics.ri.processtype.SharedResultFile

Gets the message associated with this shared result file.

getMessage() - Method in class com.genologics.ri.step.ProgramStatus

Gets the message associated with the program status.

getMessage() - Method in class com.genologics.ri.step.SharedResultFile

Gets the error message.

getMessage() - Method in class com.genologics.ri.stepconfiguration.SharedResultFile

Gets the message associated with this shared result file.

getMessageDirectory() - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Get the directory the messages are being read from.

getMessageDirectory() - Method in class org.cruk.clarity.api.record.ClarityAPIRecordingAspect

Get the directory the messages are being written to.

getMinor() - Method in class com.genologics.ri.version.Version

Gets the minor version number.

getMinValue() - Method in class com.genologics.ri.configuration.Field

Gets the minimum value for numeric fields.

getName() - Method in class com.genologics.ri.artifact.Artifact

Gets the name of the artifact.

getName() - Method in class com.genologics.ri.artifact.ArtifactGroupLink

Gets the name.

getName() - Method in class com.genologics.ri.artifact.DemuxArtifact

Gets the name.

getName() - Method in class com.genologics.ri.artifact.DemuxSourceArtifact

Gets the name.

getName() - Method in class com.genologics.ri.artifact.PoolStep

Gets the name.

getName() - Method in class com.genologics.ri.artifact.ReagentLabel

Gets the name.

getName() - Method in class com.genologics.ri.artifact.WorkflowStage

Gets the name.

getName() - Method in class com.genologics.ri.artifactgroup.ArtifactGroup

Gets the name of the artifact group.

getName() - Method in class com.genologics.ri.artifactgroup.ArtifactGroupLink

Gets the name of the artifact group.

getName() - Method in class com.genologics.ri.automation.Automation

Gets the name of this automation.

getName() - Method in class com.genologics.ri.automation.AutomationLink

Gets the name of the automation.

getName() - Method in class com.genologics.ri.automation.ProcessTypeLink

Gets the name of the process type.

getName() - Method in class com.genologics.ri.configuration.Field

Gets the name of this field.

getName() - Method in class com.genologics.ri.configuration.FieldLink

Gets the name of the field.

getName() - Method in class com.genologics.ri.configuration.Type

Gets the name of this type.

getName() - Method in class com.genologics.ri.configuration.TypeDefinition

Gets the name of the type.

getName() - Method in class com.genologics.ri.configuration.UdfConfigLink

Gets the name of the field.

getName() - Method in class com.genologics.ri.configuration.UdtConfigLink

Gets the name of the type.

getName() - Method in class com.genologics.ri.container.Container

Gets the name.

getName() - Method in class com.genologics.ri.container.ContainerLink

Gets the name.

getName() - Method in class com.genologics.ri.container.ContainerTypeLink

Gets the name of the container type.

getName() - Method in class com.genologics.ri.containertype.CalibrantWell

Deprecated.

Gets the name of the calibrant well.

getName() - Method in class com.genologics.ri.containertype.ContainerType

Gets the name of the container type.

getName() - Method in class com.genologics.ri.containertype.ContainerTypeLink

Gets the name of the container type.

getName() - Method in class com.genologics.ri.controltype.ControlType

Gets the name of the control type.

getName() - Method in class com.genologics.ri.controltype.ControlTypeLink

Gets the name of the control type.

getName() - Method in class com.genologics.ri.globaltoken.GlobalToken

Get the token name.

getName() - Method in class com.genologics.ri.globaltoken.GlobalTokenLink

Get the token name.

getName() - Method in class com.genologics.ri.instrument.Instrument

Get the instrument name.

getName() - Method in class com.genologics.ri.instrument.InstrumentLink

Get the instrument name.

getName() - Method in class com.genologics.ri.instrumenttype.InstrumentType

Get the instrument type name.

getName() - Method in class com.genologics.ri.instrumenttype.InstrumentTypeLink

Get the instrument type name.

getName() - Method in class com.genologics.ri.instrumenttype.InstrumentTypeProcessType

Get the process type name.

getName() - Method in class com.genologics.ri.lab.Lab

Gets the name of the lab.

getName() - Method in class com.genologics.ri.lab.LabLink

Gets the name of the lab.

getName() - Method in class com.genologics.ri.permission.Permission

Get the permission name.

getName() - Method in class com.genologics.ri.permission.PermissionLink

Get the permission name.

getName() - Method in class com.genologics.ri.process.Parameter

Gets the name of the parameter.

getName() - Method in class com.genologics.ri.process.ProcessTypeLink

Gets the name of the process type.

getName() - Method in class com.genologics.ri.processexecution.Parameter

Gets the parameter name.

getName() - Method in class com.genologics.ri.processtemplate.Parameter

Gets the name.

getName() - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Gets the name.

getName() - Method in class com.genologics.ri.processtemplate.ProcessTemplateLink

Gets the name.

getName() - Method in class com.genologics.ri.processtemplate.ProcessTypeLink

Gets the name.

getName() - Method in class com.genologics.ri.processtype.ContainerTypeLink

Gets the name of the container type.

getName() - Method in class com.genologics.ri.processtype.ControlTypeLink

Gets the name of the control type.

getName() - Method in class com.genologics.ri.processtype.EppTrigger

Gets the name of the EPP trigger.

getName() - Method in class com.genologics.ri.processtype.Field

Gets the name of the field.

getName() - Method in class com.genologics.ri.processtype.Parameter

Gets the name of the parameter.

getName() - Method in class com.genologics.ri.processtype.ProcessType

Gets the name of the process type.

getName() - Method in class com.genologics.ri.processtype.ProcessTypeAttribute

Gets the name of the attribute.

getName() - Method in class com.genologics.ri.processtype.ProcessTypeLink

Gets the name of the process type.

getName() - Method in class com.genologics.ri.processtype.ReagentKitLink

Gets the name of the reagent kit.

getName() - Method in class com.genologics.ri.processtype.StepProperty

Gets the name of the step property.

getName() - Method in class com.genologics.ri.processtype.TypeDefinition

Gets the name of the field.

getName() - Method in class com.genologics.ri.project.Project

Get the name of the project.

getName() - Method in class com.genologics.ri.project.ProjectLink

Get the name of the project.

getName() - Method in class com.genologics.ri.property.PropertyLink

Gets the name of the property.

getName() - Method in class com.genologics.ri.protocolconfiguration.Protocol

Gets the name of the protocol.

getName() - Method in class com.genologics.ri.protocolconfiguration.ProtocolLink

Gets the name of the protocol.

getName() - Method in class com.genologics.ri.protocolconfiguration.ProtocolProperty

Gets the name of the protocol property.

getName() - Method in class com.genologics.ri.queue.Queue

Gets the name of the queue.

getName() - Method in class com.genologics.ri.reagentkit.ReagentKit

Gets the name of the reagent kit.

getName() - Method in class com.genologics.ri.reagentkit.ReagentKitLink

Gets the name of the reagent kit.

getName() - Method in class com.genologics.ri.reagentlot.ReagentKitLink

Gets the name of the reagent kit.

getName() - Method in class com.genologics.ri.reagentlot.ReagentLot

Gets the name of the reagent lot.

getName() - Method in class com.genologics.ri.reagentlot.ReagentLotLink

Gets the name of the reagent lot.

getName() - Method in class com.genologics.ri.reagenttype.Attribute

Gets the name of the attribute.

getName() - Method in class com.genologics.ri.reagenttype.ReagentType

Gets the name.

getName() - Method in class com.genologics.ri.reagenttype.ReagentTypeLink

Gets the name of the reagent type.

getName() - Method in class com.genologics.ri.reagenttype.SpecialType

Gets the name of the special type.

getName() - Method in class com.genologics.ri.researcher.Role

The user-facing name of the security role assigned to the researcher.

getName() - Method in class com.genologics.ri.role.PermissionLink

Gets the name of the permission.

getName() - Method in class com.genologics.ri.role.Role

Gets the name of the role.

getName() - Method in class com.genologics.ri.role.RoleLink

Gets the name of the role.

getName() - Method in class com.genologics.ri.sample.BioSource

Deprecated.

Gets the name of the biosource.

getName() - Method in class com.genologics.ri.sample.ControlTypeLink

Gets the name of the control type.

getName() - Method in class com.genologics.ri.sample.SampleBase

Gets the name of the sample.

getName() - Method in class com.genologics.ri.savedquery.SavedQuery

Gets the name of the saved query.

getName() - Method in class com.genologics.ri.savedquery.SavedQueryLink

Gets the name of the saved query.

getName() - Method in class com.genologics.ri.stage.Stage

Gets the name of the stage.

getName() - Method in class com.genologics.ri.step.AvailableProgram

Gets the name.

getName() - Method in class com.genologics.ri.step.InstrumentLink

Gets the name.

getName() - Method in class com.genologics.ri.step.PooledInputs

Gets the name of this pool.

getName() - Method in class com.genologics.ri.step.ReagentLabel

Gets the name of the reagent label.

getName() - Method in class com.genologics.ri.step.SharedResultFile

Gets the name of the artifact.

getName() - Method in class com.genologics.ri.stepconfiguration.ControlTypeLink

Gets the name of the control type.

getName() - Method in class com.genologics.ri.stepconfiguration.EppTrigger

Gets the name of the EPP trigger.

getName() - Method in class com.genologics.ri.stepconfiguration.Field

Gets the name of the field.

getName() - Method in class com.genologics.ri.stepconfiguration.NextStep

Gets the name of the next step.

getName() - Method in class com.genologics.ri.stepconfiguration.ProcessTypeLink

Gets the name of the process type.

getName() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the name of the protocol step.

getName() - Method in class com.genologics.ri.stepconfiguration.ReagentKitLink

Gets the name of the reagent kit.

getName() - Method in class com.genologics.ri.stepconfiguration.StepProperty

Gets the name of the step property.

getName() - Method in class com.genologics.ri.userdefined.UDF

Gets the name of the UDF.

getName() - Method in class com.genologics.ri.userdefined.UDT

Gets the name of the user-defined type.

getName() - Method in class com.genologics.ri.workflowconfiguration.ProtocolLink

Gets the name of the protocol.

getName() - Method in class com.genologics.ri.workflowconfiguration.StageLink

Gets the name of the stage.

getName() - Method in class com.genologics.ri.workflowconfiguration.Workflow

Gets the name of the workflow.

getName() - Method in class com.genologics.ri.workflowconfiguration.WorkflowLink

Gets the name of the workflow.

getNextActions() - Method in class com.genologics.ri.step.Actions

Gets the list of next actions, creating it if it doesn't exist.

getNextPage() - Method in class com.genologics.ri.artifact.Artifacts

Gets the next page of results.

getNextPage() - Method in class com.genologics.ri.artifactgroup.ArtifactGroups

Gets the link to the next page.

getNextPage() - Method in class com.genologics.ri.automation.Automations

Gets the next page of results.

getNextPage() - Method in class com.genologics.ri.configuration.Udfs

Gets the link to the next page of results.

getNextPage() - Method in class com.genologics.ri.configuration.Udts

Gets the link to the next page of results.

getNextPage() - Method in class com.genologics.ri.container.Containers

Gets the link to the next page of results.

getNextPage() - Method in class com.genologics.ri.containertype.ContainerTypes

Gets the next page of results.

getNextPage() - Method in class com.genologics.ri.file.ClarityFiles

Gets the link to the next page of results.

getNextPage() - Method in class com.genologics.ri.globaltoken.GlobalTokens

Get the next page of results.

getNextPage() - Method in class com.genologics.ri.instrument.Instruments

Gets the next page of results.

getNextPage() - Method in class com.genologics.ri.instrumenttype.InstrumentTypes

Gets the next page of results.

getNextPage() - Method in class com.genologics.ri.lab.Labs

Gets the next page of results.

getNextPage() - Method in interface com.genologics.ri.PaginatedBatch

Gets the next page of results.

getNextPage() - Method in class com.genologics.ri.process.ClarityProcesses

Gets the next page link.

getNextPage() - Method in class com.genologics.ri.processtemplate.ProcessTemplates

Gets the next page link.

getNextPage() - Method in class com.genologics.ri.processtype.ProcessTypes

Gets the link to the next page of results.

getNextPage() - Method in class com.genologics.ri.project.Projects

Get the next page of results.

getNextPage() - Method in class com.genologics.ri.property.Properties

Gets the next page link.

getNextPage() - Method in class com.genologics.ri.queue.Queue

Gets the next page of results.

getNextPage() - Method in class com.genologics.ri.reagentkit.ReagentKits

Gets the next page link.

getNextPage() - Method in class com.genologics.ri.reagentlot.ReagentLots

getNextPage() - Method in class com.genologics.ri.reagenttype.ReagentTypes

Gets the link to the next page of results.

getNextPage() - Method in class com.genologics.ri.researcher.Researchers

Gets the link to the next page of results.

getNextPage() - Method in class com.genologics.ri.sample.Samples

Gets the next page link.

getNextPage() - Method in class com.genologics.ri.savedquery.SavedQueries

Gets the next page of results.

getNextStepUri() - Method in class com.genologics.ri.stepconfiguration.NextStep

Gets the URI of the next step.

getNotes() - Method in class com.genologics.ri.reagentlot.ReagentLot

Gets the notes.

getNumberOfOutputs() - Method in class com.genologics.ri.processtype.ProcessOutput

Number of outputs to generate (only applies if variabilityType is FIXED).

getOccupiedWells() - Method in class com.genologics.ri.container.Container

Gets the number of occupied wells.

getOffset() - Method in class com.genologics.ri.containertype.Dimension

Gets the offset applied to the first element in this dimension.

getOpenDate() - Method in class com.genologics.ri.project.Project

Get the open date of the project.

getOriginalLocation() - Method in class com.genologics.ri.file.ClarityFile

This element provides the original name and location of the file before it was imported into the system.

getOriginalName() - Method in class com.genologics.ri.file.ClarityFile

This element provides the original name of the file before it was imported into the system.

getOutput() - Method in class com.genologics.ri.process.InputOutputMap

Gets the output artifact link.

getOutput() - Method in class com.genologics.ri.processexecution.ExecutableInputOutputMap

Gets the output artifact.

getOutput() - Method in class com.genologics.ri.step.InputOutputMap

Gets the output artifact link.

getOutputArrangements() - Method in class com.genologics.ri.step.Arrangements

Gets the list of output arrangements, creating it if it doesn't exist.

getOutputGenerationType() - Method in class com.genologics.ri.process.ArtifactLink

Gets the output generation type.

getOutputGenerationType() - Method in class com.genologics.ri.processtype.ProcessOutput

Specifies how the outputs are generated in relation to the inputs (COMPOUND, PER_REAGENT_LABEL, or PER_INPUT).

getOutputGenerationType() - Method in class com.genologics.ri.step.ArtifactLink

Gets the output generation type.

getOutputName() - Method in class com.genologics.ri.processtype.ProcessOutput

Pattern for specifying how the output name is generated.

getOutputPlacements() - Method in class com.genologics.ri.step.Placements

Gets the list of output placements.

getOutputReagents() - Method in class com.genologics.ri.step.Reagents

Gets the list of output reagents, creating it if it doesn't exist.

getOutputType() - Method in class com.genologics.ri.artifact.Artifact

Gets the output type of the artifact.

getOutputType() - Method in class com.genologics.ri.process.ArtifactLink

Gets the output type.

getOutputUri() - Method in class com.genologics.ri.step.PooledInputs

Gets the URI of the output artifact.

getParam() - Method in class org.cruk.clarity.api.search.SearchTerm

Get the parameter name.

getParameter() - Method in class com.genologics.ri.process.ClarityProcess

Gets the parameter.

getParameter() - Method in class com.genologics.ri.processexecution.ExecutableProcess

Gets the process parameter.

getParameter() - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Gets the parameter.

getParameters() - Method in class com.genologics.ri.processtype.ProcessType

Gets the EPP parameters for this process type.

getParentProcess() - Method in class com.genologics.ri.artifact.Artifact

Gets the parent process that produced this artifact.

getParentProcess() - Method in class com.genologics.ri.process.ArtifactLink

Gets the parent process link.

getParentUri() - Method in class com.genologics.ri.configuration.Field

Gets the URI of the parent field for hierarchical fields.

getPassword() - Method in class com.genologics.ri.researcher.Credentials

Gets the password.

getPermissions() - Method in class com.genologics.ri.permission.Permissions

Get the list of permission links.

getPermissions() - Method in class com.genologics.ri.role.Role

Gets the list of permissions assigned to this role.

getPermittedContainers() - Method in class com.genologics.ri.processtype.ProcessType

Gets the permitted container types for this process.

getPermittedContainerTypes() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the list of permitted container types for this step.

getPermittedControlTypes() - Method in class com.genologics.ri.processtype.ProcessType

Gets the permitted control types for this process.

getPermittedControlTypes() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the list of permitted control types for this step.

getPermittedInstrumentTypes() - Method in class com.genologics.ri.processtype.ProcessType

Gets the permitted instrument types for this process.

getPermittedInstrumentTypes() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the list of permitted instrument types for this step.

getPermittedReagentCategories() - Method in class com.genologics.ri.processtype.ProcessType

Gets the permitted reagent categories for this process.

getPermittedReagentCategories() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the list of permitted reagent categories for this step.

getPhone() - Method in class com.genologics.ri.researcher.Researcher

Gets the researcher's phone number.

getPlacements() - Method in class com.genologics.ri.container.Container

Gets the list of placements.

getPlacements() - Method in class com.genologics.ri.step.ProcessStep

Gets the link to the placements associated with this step.

getPoint() - Method in class com.genologics.ri.processtype.EppTrigger

Gets the point at which the trigger executes.

getPoint() - Method in class com.genologics.ri.stepconfiguration.EppTrigger

Gets the point when the EPP trigger executes.

getPooledInputs() - Method in class com.genologics.ri.step.Pools

Gets the list of pooled input groups.

getPools() - Method in class com.genologics.ri.step.ProcessStep

Gets the link to the pools associated with this step.

getPoolStep() - Method in class com.genologics.ri.artifact.DemuxDetails

Gets the pool step.

getPostalCode() - Method in class com.genologics.ri.Address

Gets the postal or zip code.

getPostProcessUri() - Method in class com.genologics.ri.process.ArtifactLink

Gets the post-process URI.

getPreset() - Method in class com.genologics.ri.step.StepDetails

Gets the preset name.

getPresets() - Method in class com.genologics.ri.configuration.Field

Gets the list of preset values for this field.

getPresets() - Method in class com.genologics.ri.configuration.FieldDynamicPresetDetails

Gets the list of field dynamic presets.

getPreviousPage() - Method in class com.genologics.ri.artifact.Artifacts

Gets the previous page of results.

getPreviousPage() - Method in class com.genologics.ri.artifactgroup.ArtifactGroups

Gets the link to the previous page.

getPreviousPage() - Method in class com.genologics.ri.automation.Automations

Gets the previous page of results.

getPreviousPage() - Method in class com.genologics.ri.configuration.Udfs

Gets the link to the previous page of results.

getPreviousPage() - Method in class com.genologics.ri.configuration.Udts

Gets the link to the previous page of results.

getPreviousPage() - Method in class com.genologics.ri.container.Containers

Gets the link to the previous page of results.

getPreviousPage() - Method in class com.genologics.ri.containertype.ContainerTypes

Gets the previous page of results.

getPreviousPage() - Method in class com.genologics.ri.file.ClarityFiles

Gets the link to the previous page of results.

getPreviousPage() - Method in class com.genologics.ri.globaltoken.GlobalTokens

Get the previous page of results.

getPreviousPage() - Method in class com.genologics.ri.instrument.Instruments

Gets the previous page of results.

getPreviousPage() - Method in class com.genologics.ri.instrumenttype.InstrumentTypes

Gets the previous page of results.

getPreviousPage() - Method in class com.genologics.ri.lab.Labs

Gets the previous page of results.

getPreviousPage() - Method in interface com.genologics.ri.PaginatedBatch

Gets the previous page of results.

getPreviousPage() - Method in class com.genologics.ri.process.ClarityProcesses

Gets the previous page link.

getPreviousPage() - Method in class com.genologics.ri.processtemplate.ProcessTemplates

Gets the previous page link.

getPreviousPage() - Method in class com.genologics.ri.processtype.ProcessTypes

Gets the link to the previous page of results.

getPreviousPage() - Method in class com.genologics.ri.project.Projects

Get the previous page of results.

getPreviousPage() - Method in class com.genologics.ri.property.Properties

Gets the previous page link.

getPreviousPage() - Method in class com.genologics.ri.queue.Queue

Gets the previous page of results.

getPreviousPage() - Method in class com.genologics.ri.reagentkit.ReagentKits

Gets the previous page link.

getPreviousPage() - Method in class com.genologics.ri.reagentlot.ReagentLots

getPreviousPage() - Method in class com.genologics.ri.reagenttype.ReagentTypes

Gets the link to the previous page of results.

getPreviousPage() - Method in class com.genologics.ri.researcher.Researchers

Gets the link to the previous page of results.

getPreviousPage() - Method in class com.genologics.ri.sample.Samples

Gets the previous page link.

getPreviousPage() - Method in class com.genologics.ri.savedquery.SavedQueries

Gets the previous page of results.

getPriority() - Method in class com.genologics.ri.project.Project

Get the priority of the project.

getProcesses() - Method in class com.genologics.ri.process.ClarityProcesses

Gets the list of processes.

getProcessInputs() - Method in class com.genologics.ri.processtype.ProcessType

Gets the process input configurations.

getProcessOutputs() - Method in class com.genologics.ri.processtype.ProcessType

Gets the process output configurations.

getProcessTemplates() - Method in class com.genologics.ri.processtemplate.ProcessTemplates

Gets the list of process template links.

getProcessType() - Method in class com.genologics.ri.process.ClarityProcess

Gets the process type link.

getProcessType() - Method in class com.genologics.ri.processexecution.ExecutableProcess

Gets the process type name.

getProcessType() - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Gets the process type link.

getProcessType() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the process type for this step.

getProcessTypeAttributes() - Method in class com.genologics.ri.processtype.ProcessType

Gets the process type attributes.

getProcessTypes() - Method in class com.genologics.ri.automation.Automation

Gets the list of process types associated with this automation.

getProcessTypes() - Method in class com.genologics.ri.instrumenttype.InstrumentType

Get the list of process types associated with this instrument type.

getProcessTypes() - Method in class com.genologics.ri.processtype.ProcessTypes

Gets the list of process type links.

getProgramStatus() - Method in class com.genologics.ri.step.ProcessStep

Gets the link to the program status associated with this step.

getProject() - Method in class com.genologics.ri.sample.SampleBase

Gets the project link for this sample.

getProjects() - Method in class com.genologics.ri.project.Projects

Get the list of project links.

getProperties() - Method in class com.genologics.ri.property.Properties

Gets the list of property links.

getProtocol() - Method in class com.genologics.ri.stage.Stage

Gets the protocol link for this stage.

getProtocolId() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Get the numeric identifier for this step's protocol from its URI.

getProtocolName() - Method in class com.genologics.ri.process.ClarityProcess

Gets the protocol name.

getProtocolProperties() - Method in class com.genologics.ri.protocolconfiguration.Protocol

Gets the list of protocol properties.

getProtocols() - Method in class com.genologics.ri.protocolconfiguration.Protocols

Gets the list of protocol links.

getProtocols() - Method in class com.genologics.ri.workflowconfiguration.Workflow

Gets the list of protocols associated with this workflow.

getProtocolStepIndex() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the protocol step index.

getProtocolStepUri() - Method in class com.genologics.ri.queue.Queue

Gets the protocol step URI.

getProtocolStepUri() - Method in class com.genologics.ri.step.StepConfiguration

Gets the protocol step URI.

getProtocolUri() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the URI of the protocol this step belongs to.

getQCFlag() - Method in class com.genologics.ri.artifact.Artifact

Gets the quality control flag for this artifact.

getQCFlag() - Method in class com.genologics.ri.processexecution.ArtifactBase

Gets the quality control flag for this artifact.

getQueryResultsClassForEntity(Class<E>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Get the class that holds a list of links for the given entity when returned from a list or search operation.

getQueryResultsClassForEntity(Class<E>) - Method in interface org.cruk.clarity.api.impl.ClarityAPIInternal

Get the class that holds a list of links for the given entity when returned from a list or search operation.

getQueueFields() - Method in class com.genologics.ri.processtype.ProcessType

Gets the fields displayed in the queue view.

getQueueFields() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the list of queue fields for this step.

getQueueTime() - Method in class com.genologics.ri.queue.ArtifactLink

Gets the time when the artifact was queued.

getRackColumn() - Method in class com.genologics.ri.step.RackLocation

Gets the column position within the rack.

getRackIndex() - Method in class com.genologics.ri.step.RackLocation

Gets the index of the rack.

getRackLocation() - Method in class com.genologics.ri.step.OutputArrangement

Gets the rack location.

getRackRow() - Method in class com.genologics.ri.step.RackLocation

Gets the row position within the rack.

getReagentCategory() - Method in class com.genologics.ri.reagenttype.ReagentType

Gets the reagent category.

getReagentCategory() - Method in class com.genologics.ri.step.Reagents

The permitted reagent category of the step.

getReagentCategory() - Method in class com.genologics.ri.step.StepCreation

Gets the reagent category name.

getReagentKit() - Method in class com.genologics.ri.reagentlot.ReagentLot

Gets the link to the reagent kit.

getReagentKits() - Method in class com.genologics.ri.reagentkit.ReagentKits

Gets the list of reagent kit links.

getReagentLabels() - Method in class com.genologics.ri.artifact.Artifact

Gets the list of reagent labels applied to this artifact.

getReagentLabels() - Method in class com.genologics.ri.artifact.DemuxArtifact

Gets the list of reagent labels.

getReagentLabels() - Method in class com.genologics.ri.step.Output

Gets the list of reagent labels, creating it if it doesn't exist.

getReagentLots() - Method in class com.genologics.ri.reagentlot.ReagentLots

Gets the list of reagent lot links in this batch.

getReagentLots() - Method in class com.genologics.ri.step.ProcessStep

Gets the link to the reagent lots associated with this step.

getReagentLots() - Method in class com.genologics.ri.step.ReagentLots

Gets the list of reagent lot links.

getReagents() - Method in class com.genologics.ri.step.ProcessStep

Gets the link to the reagents associated with this step.

getReagentTypes() - Method in class com.genologics.ri.reagenttype.ReagentTypes

Gets the list of reagent type links.

getRelative() - Method in class com.genologics.ri.Link

Gets the relative part of the link.

getReplicates() - Method in class com.genologics.ri.step.CreationInput

Gets the number of replicates.

getReplicates() - Method in class com.genologics.ri.step.Input

Gets the number of replicates.

getReportFile() - Method in class org.cruk.clarity.api.SavedQuerySummary

Get the file the report was saved as.

getRequest() - Method in class com.genologics.ri.step.Escalation

Gets the escalation request.

getRequiredReagentKits() - Method in class com.genologics.ri.processtype.ProcessType

Gets the required reagent kits for this process.

getRequiredReagentKits() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the list of required reagent kits for this step.

getResearcher() - Method in class com.genologics.ri.project.Project

Get the researcher associated with the project.

getResearchers() - Method in class com.genologics.ri.researcher.Researchers

Gets the list of researcher links.

getResearchers() - Method in class com.genologics.ri.role.Role

Gets the list of researchers assigned to this role.

getResults() - Method in class org.cruk.clarity.api.search.Search

Get the results of the search.

getReview() - Method in class com.genologics.ri.step.Escalation

Gets the escalation review.

getReviewer() - Method in class com.genologics.ri.step.EscalationRequest

Gets the reviewer.

getReworkStepUri() - Method in class com.genologics.ri.step.NextAction

Gets the rework step URI.

getRoleName() - Method in class com.genologics.ri.researcher.Role

Deprecated.

Deprecated from version 2.19.

getRoles() - Method in class com.genologics.ri.researcher.Credentials

Gets the list of roles assigned to the researcher.

getRoles() - Method in class com.genologics.ri.role.Roles

Gets the list of role links.

getRows() - Method in class com.genologics.ri.containertype.ContainerType

Gets the y-dimension (vertical/rows) of the container's coordinate system.

getSampleCreations() - Method in class com.genologics.ri.sample.SampleBatchFetchResult

Gets the list of sample creations.

getSampleFields() - Method in class com.genologics.ri.processtype.ProcessType

Gets the fields displayed for samples in the step view.

getSampleFields() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the list of sample fields.

getSamples() - Method in class com.genologics.ri.artifact.Artifact

Gets the list of samples associated with this artifact.

getSamples() - Method in class com.genologics.ri.artifact.DemuxArtifact

Gets the list of samples.

getSamples() - Method in class com.genologics.ri.sample.SampleBatchFetchResult

Gets the list of samples.

getSamples() - Method in class com.genologics.ri.sample.Samples

Gets the list of sample links.

getSavedQueries() - Method in class com.genologics.ri.savedquery.SavedQueries

Gets the list of saved query links.

getScript() - Method in class com.genologics.ri.automation.Automation

Gets the script content for this automation.

getScript() - Method in class com.genologics.ri.processtype.Parameter

Gets the EPP script text that will actually run.

getSearchFileName() - Method in class org.cruk.clarity.api.search.Search

Get the name of the file that will store the result of this search.

getSearchFileName(SearchTerms<?>) - Static method in class org.cruk.clarity.api.search.Search

Get the name of the file that will store the result of the given search.

getSearchTerm() - Method in exception org.cruk.clarity.api.IllegalSearchTermException

Get the search term that caused the error.

getSearchTerms() - Method in class org.cruk.clarity.api.search.Search

Get the parameters of this search.

getSearchTerms() - Method in class org.cruk.clarity.api.search.SearchTerms

Get the parameters of the search.

getSelectedContainers() - Method in class com.genologics.ri.step.Placements

Gets the list of selected containers.

getSequence() - Method in class com.genologics.ri.stepconfiguration.NextStep

Gets the sequence index of the next step.

getSerialNumber() - Method in class com.genologics.ri.instrument.Instrument

Get the instrument serial number.

getServer() - Method in interface org.cruk.clarity.api.ClarityAPI

Deprecated.

Use ClarityAPI.getServerURI() to get the URI instead.

getServer() - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Deprecated.

getServerApiAddress() - Method in interface org.cruk.clarity.api.ClarityAPI

Get the base address of the REST API.

getServerApiAddress() - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Get the base address of the REST API.

getServerURI() - Method in interface org.cruk.clarity.api.ClarityAPI

Get the base URI of the Clarity server.

getServerURI() - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Get the base URI of the Clarity server.

getSetup() - Method in class com.genologics.ri.step.ProcessStep

Gets the link to the setup associated with this step.

getSharedResultFileIndex() - Method in class com.genologics.ri.processtype.SharedResultFile

Gets the index of this shared result file.

getSharedResultFileIndex() - Method in class com.genologics.ri.step.SharedResultFile

Gets the shared result file index.

getSharedResultFileIndex() - Method in class com.genologics.ri.stepconfiguration.SharedResultFile

Gets the index of this shared result file.

getShippingAddress() - Method in class com.genologics.ri.lab.Lab

Gets the shipping address of the lab.

getSingleStep() - Method in class com.genologics.ri.controltype.ControlType

Gets the single step flag.

getSize() - Method in class com.genologics.ri.artifact.ArtifactBatchFetchResult

Gets the size of the artifact list.

getSize() - Method in class com.genologics.ri.artifact.Artifacts

Gets the size of the artifact list.

getSize() - Method in class com.genologics.ri.artifactgroup.ArtifactGroups

Gets the size of the artifact groups list.

getSize() - Method in class com.genologics.ri.automation.Automations

Gets the size of the automation list.

getSize() - Method in interface com.genologics.ri.Batch

Gets the number of items in this batch.

getSize() - Method in class com.genologics.ri.configuration.Type

Gets the number of field definitions.

getSize() - Method in class com.genologics.ri.configuration.Udfs

Gets the number of UDF configuration links.

getSize() - Method in class com.genologics.ri.configuration.Udts

Gets the number of UDT configuration links.

getSize() - Method in class com.genologics.ri.container.ContainerBatchFetchResult

Gets the size of the container list.

getSize() - Method in class com.genologics.ri.container.Containers

Gets the number of container links.

getSize() - Method in class com.genologics.ri.containertype.ContainerTypes

Gets the number of items in this batch.

getSize() - Method in class com.genologics.ri.containertype.Dimension

Gets the size (number of elements) in this dimension.

getSize() - Method in class com.genologics.ri.controltype.ControlTypes

Gets the size of the control types list.

getSize() - Method in class com.genologics.ri.file.ClarityFileBatchFetchResult

Gets the number of files in this batch.

getSize() - Method in class com.genologics.ri.file.ClarityFiles

Gets the number of file links in this collection.

getSize() - Method in class com.genologics.ri.globaltoken.GlobalTokens

Gets the number of items in this batch.

getSize() - Method in class com.genologics.ri.Index

Gets the number of links in this index.

getSize() - Method in class com.genologics.ri.instrument.Instruments

Gets the number of items in this batch.

getSize() - Method in class com.genologics.ri.instrumenttype.InstrumentTypes

Gets the number of items in this batch.

getSize() - Method in class com.genologics.ri.lab.Labs

Gets the size of the lab links list.

getSize() - Method in class com.genologics.ri.Links

Gets the number of links in this collection.

getSize() - Method in class com.genologics.ri.permission.Permissions

Gets the number of items in this batch.

getSize() - Method in class com.genologics.ri.process.ClarityProcesses

Gets the size of the list.

getSize() - Method in class com.genologics.ri.processtemplate.ProcessTemplates

Gets the number of process template links.

getSize() - Method in class com.genologics.ri.processtype.ProcessTypes

Gets the size of the process types list.

getSize() - Method in class com.genologics.ri.project.Projects

Get the number of project links.

getSize() - Method in class com.genologics.ri.property.Properties

Gets the number of items in this batch.

getSize() - Method in class com.genologics.ri.protocolconfiguration.Protocols

Gets the number of items in this batch.

getSize() - Method in class com.genologics.ri.queue.Queue

Gets the number of items in this batch.

getSize() - Method in class com.genologics.ri.reagentkit.ReagentKits

Gets the number of items in this batch.

getSize() - Method in class com.genologics.ri.reagentlot.ReagentLots

getSize() - Method in class com.genologics.ri.reagenttype.ReagentTypes

Gets the size of the reagent types list.

getSize() - Method in class com.genologics.ri.researcher.Researchers

Gets the size of the researcher list.

getSize() - Method in class com.genologics.ri.role.Roles

Gets the size of the roles list.

getSize() - Method in class com.genologics.ri.sample.SampleBatchFetchResult

Gets the size of the sample list.

getSize() - Method in class com.genologics.ri.sample.Samples

Gets the size of the sample links list.

getSize() - Method in class com.genologics.ri.savedquery.SavedQueries

Gets the size of the saved query list.

getSize() - Method in class com.genologics.ri.version.Versions

Gets the size of the versions list.

getSize() - Method in class com.genologics.ri.workflowconfiguration.Workflows

Gets the number of workflows in the list.

getSpecialType() - Method in class com.genologics.ri.reagenttype.ReagentType

Gets the special type.

getStages() - Method in class com.genologics.ri.workflowconfiguration.Workflow

Gets the list of stages associated with this workflow.

getStageUri() - Method in class com.genologics.ri.routing.ExtArtifactAssignments

Gets the stage URI.

getState() - Method in class com.genologics.ri.Address

Gets the state or province.

getState() - Method in class com.genologics.ri.container.Container

Gets the container state.

getStatefulOverride() - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Helper method for the cache, this method returns whether the next call on the current thread will need to fetch stateful entities in a special way or not.

getStatefulOverride() - Method in interface org.cruk.clarity.api.impl.ClarityAPIInternal

Helper method for the cache, this method returns whether the next call on the current thread will need to fetch stateful entities in a special way or not.

getStatus() - Method in class com.genologics.ri.artifact.WorkflowStage

Gets the status.

getStatus() - Method in class com.genologics.ri.processtype.EppTrigger

Gets the status at which the trigger executes.

getStatus() - Method in class com.genologics.ri.reagentlot.ReagentLot

Gets the status of the reagent lot.

getStatus() - Method in class com.genologics.ri.step.ProgramStatus

Gets the current status of the program.

getStatus() - Method in class com.genologics.ri.stepconfiguration.EppTrigger

Gets the status at which the EPP trigger executes.

getStatus() - Method in class com.genologics.ri.workflowconfiguration.Workflow

Gets the status of the workflow.

getStatus() - Method in class com.genologics.ri.workflowconfiguration.WorkflowLink

Gets the status of the workflow.

getStep() - Method in class com.genologics.ri.stage.Stage

Gets the protocol step link for this stage.

getStep() - Method in class com.genologics.ri.step.Actions

Gets the step link.

getStep() - Method in class com.genologics.ri.step.Arrangements

Gets the step link.

getStep() - Method in class com.genologics.ri.step.Placements

Gets the link to the step.

getStep() - Method in class com.genologics.ri.step.Pools

Gets the link to the step.

getStep() - Method in class com.genologics.ri.step.ProgramStatus

Gets the link to the step associated with this program status.

getStep() - Method in class com.genologics.ri.step.ReagentLots

Gets the step link.

getStep() - Method in class com.genologics.ri.step.Reagents

Gets the step link.

getStep() - Method in class com.genologics.ri.step.StepDetails

Gets the link to the step.

getStep() - Method in class com.genologics.ri.step.StepSetup

Gets the link to the step.

getStepDetails() - Method in class com.genologics.ri.step.ProcessStep

Gets the link to the details associated with this step.

getStepFields() - Method in class com.genologics.ri.processtype.ProcessType

Gets the fields displayed in the step view.

getStepFields() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the list of step fields.

getStepName() - Method in class com.genologics.ri.step.StepConfiguration

Gets the name of the protocol step.

getStepProperties() - Method in class com.genologics.ri.processtype.ProcessType

Gets the step properties for this process type.

getStepProperties() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the list of step properties.

getSteps() - Method in class com.genologics.ri.protocolconfiguration.Protocol

Gets the list of steps in this protocol.

getStepSetup() - Method in class com.genologics.ri.processtype.ProcessType

Gets the step setup configuration.

getStepSetup() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the step setup configuration.

getStepUri() - Method in class com.genologics.ri.step.NextAction

Gets the step URI.

getStorageLocation() - Method in class com.genologics.ri.reagentlot.ReagentLot

Gets the storage location.

getStreet() - Method in class com.genologics.ri.Address

Gets the street address.

getStyle() - Method in class com.genologics.ri.processtype.Field

Gets the style of the field.

getStyle() - Method in class com.genologics.ri.stepconfiguration.Field

Gets the style of the field.

getSubmitter() - Method in class com.genologics.ri.sample.SampleBase

Gets the submitter of this sample.

getSuggestedActions() - Method in class com.genologics.ri.exception.Exception

Gets the suggested actions to correct the error.

getSuggestedActions() - Method in exception org.cruk.clarity.api.ClarityException

Get the "suggested actions" text.

getSupplier() - Method in class com.genologics.ri.controltype.ControlType

Gets the supplier of the control type.

getSupplier() - Method in class com.genologics.ri.reagentkit.ReagentKit

Gets the supplier of the reagent kit.

getTechnician() - Method in class com.genologics.ri.process.ClarityProcess

Gets the technician.

getTechnician() - Method in class com.genologics.ri.processexecution.ExecutableProcess

Gets the technician who ran the process.

getTechnician() - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Gets the technician.

getTechnician() - Method in class com.genologics.ri.step.ProcessStep

Gets the technician assigned to this step.

getTransitions() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the list of transitions to next steps.

getType() - Method in class com.genologics.ri.artifact.Artifact

Gets the type of the artifact.

getType() - Method in class com.genologics.ri.configuration.Field

Gets the type of this field.

getType() - Method in class com.genologics.ri.instrument.Instrument

Get the instrument type.

getType() - Method in class com.genologics.ri.processexecution.Output

Gets the output type.

getType() - Method in class com.genologics.ri.processtype.EppTrigger

Gets the type of the trigger.

getType() - Method in class com.genologics.ri.step.ArtifactLink

Gets the output type.

getType() - Method in class com.genologics.ri.stepconfiguration.EppTrigger

Gets the type of the EPP trigger.

getType() - Method in class com.genologics.ri.userdefined.UDF

Gets the type of the UDF.

getTypeDefinition() - Method in class com.genologics.ri.configuration.Field

Gets the type definition for complex types.

getTypeDefinitions() - Method in class com.genologics.ri.processtype.ProcessType

Gets the type definitions for this process type.

getUDF(UDFHolder, String) - Static method in class com.genologics.ri.userdefined.UDF

Finds a UDF by name in the UDFs of the given object.

getUDF(UDFHolder, String, boolean) - Static method in class com.genologics.ri.userdefined.UDF

Finds a UDF by name in the UDFs of the given object.

getUDF(UDFHolder, String, boolean, String) - Static method in class com.genologics.ri.userdefined.UDF

Finds a UDF by name in the UDFs of the given object.

getUDF(String) - Method in interface com.genologics.ri.userdefined.UDFHolder

Finds a UDF by name.

getUDF(String, boolean) - Method in interface com.genologics.ri.userdefined.UDFHolder

Finds a UDF by name.

getUDF(String, boolean, String) - Method in interface com.genologics.ri.userdefined.UDFHolder

Finds a UDF by name.

getUDF(Collection<UDF>, String) - Static method in class com.genologics.ri.userdefined.UDF

Finds a UDF by name in a collection of UDF objects.

getUDF(Collection<UDF>, String, boolean) - Static method in class com.genologics.ri.userdefined.UDF

Finds a UDF by name in a collection of UDF objects.

getUDF(Collection<UDF>, String, boolean, String) - Static method in class com.genologics.ri.userdefined.UDF

Finds a UDF by name in a collection of UDF objects.

getUdfs() - Method in interface com.genologics.ri.userdefined.UDFHolder

Another alternative for getUserDefinedFields that is more pleasant on the eye when used in Groovy or other scripting systems where the property is accessed as if it were a field.

getUDFs() - Method in interface com.genologics.ri.userdefined.UDFHolder

Alternative method used as a shorthand for getUserDefinedFields.

getUDFValue(UDFHolder, String) - Static method in class com.genologics.ri.userdefined.UDF

Finds a UDF by name in the UDFs of the given object and, if found, returns its value.

getUDFValue(UDFHolder, String, boolean) - Static method in class com.genologics.ri.userdefined.UDF

Finds a UDF by name in the UDFs of the given object and returns its value.

getUDFValue(UDFHolder, String, boolean, String) - Static method in class com.genologics.ri.userdefined.UDF

Finds a UDF by name in the UDFs of the given object and returns its value.

getUDFValue(UDFHolder, String, String) - Static method in class com.genologics.ri.userdefined.UDF

Finds a UDF by name in the UDFs of the given object and, if found, returns its value.

getUDFValue(String) - Method in interface com.genologics.ri.userdefined.UDFHolder

Finds a UDF by name and, if found, returns its value.

getUDFValue(String, boolean) - Method in interface com.genologics.ri.userdefined.UDFHolder

Finds a UDF by name and returns its value.

getUDFValue(String, boolean, String) - Method in interface com.genologics.ri.userdefined.UDFHolder

Finds a UDF by name and return its value.

getUDFValue(String, String) - Method in interface com.genologics.ri.userdefined.UDFHolder

Finds a UDF by name and, if found, returns its value.

getUDFValue(Collection<UDF>, String) - Static method in class com.genologics.ri.userdefined.UDF

Finds a UDF by name in a collection of UDF objects and, if found, returns its value.

getUDFValue(Collection<UDF>, String, boolean) - Static method in class com.genologics.ri.userdefined.UDF

Finds a UDF by name in a collection of UDF objects and returns its value.

getUDFValue(Collection<UDF>, String, boolean, String) - Static method in class com.genologics.ri.userdefined.UDF

Finds a UDF by name in a collection of UDF objects and returns its value.

getUDFValue(Collection<UDF>, String, String) - Static method in class com.genologics.ri.userdefined.UDF

Finds a UDF by name in a collection of UDF objects and, if found, returns its value.

getUnassign() - Method in class com.genologics.ri.routing.Routing

Gets the list of unassigned routes.

getUnavailableWells() - Method in class com.genologics.ri.containertype.ContainerType

Gets the list of unavailable wells for this container type.

getUnit() - Method in class com.genologics.ri.userdefined.UDF

Gets the unit of the UDF.

getUnitLabel() - Method in class com.genologics.ri.configuration.Field

Gets the unit label for numeric fields.

getUpdatesDirectory() - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Get the directory the updated entities are being written to.

getUri() - Method in class com.genologics.ri.artifact.Artifact

Gets the URI of this artifact.

getUri() - Method in class com.genologics.ri.artifact.ArtifactGroupLink

Gets the URI.

getUri() - Method in class com.genologics.ri.artifact.ArtifactLink

Gets the URI.

getUri() - Method in class com.genologics.ri.artifact.ControlTypeLink

Gets the URI.

getUri() - Method in class com.genologics.ri.artifact.Demux

Gets the URI.

getUri() - Method in class com.genologics.ri.artifact.DemuxArtifact

Gets the URI.

getUri() - Method in class com.genologics.ri.artifact.DemuxArtifactSample

Gets the URI.

getUri() - Method in class com.genologics.ri.artifact.DemuxLink

Gets the URI.

getUri() - Method in class com.genologics.ri.artifact.DemuxSourceArtifact

Gets the URI.

getUri() - Method in class com.genologics.ri.artifact.ParentProcessLink

Gets the URI.

getUri() - Method in class com.genologics.ri.artifact.PoolStep

Gets the URI.

getUri() - Method in class com.genologics.ri.artifact.SampleLink

Gets the URI.

getUri() - Method in class com.genologics.ri.artifact.WorkflowStage

Gets the URI.

getUri() - Method in class com.genologics.ri.artifactgroup.ArtifactGroup

Gets the URI of this artifact group.

getUri() - Method in class com.genologics.ri.artifactgroup.ArtifactGroupLink

Gets the URI of the artifact group.

getUri() - Method in class com.genologics.ri.artifactgroup.Artifacts

Gets the URI of the artifacts in this group.

getUri() - Method in class com.genologics.ri.automation.Automation

Gets the URI of this automation.

getUri() - Method in class com.genologics.ri.automation.AutomationLink

Gets the URI of the automation.

getUri() - Method in class com.genologics.ri.automation.Automations

Gets the URI of this automations resource.

getUri() - Method in class com.genologics.ri.automation.ProcessTypeLink

Gets the URI of the process type.

getUri() - Method in class com.genologics.ri.configuration.Field

Gets the URI of this field configuration.

getUri() - Method in class com.genologics.ri.configuration.FieldDynamicPresetDetails

Gets the URI of this preset details resource.

getUri() - Method in class com.genologics.ri.configuration.FieldLink

Gets the URI of the field configuration.

getUri() - Method in class com.genologics.ri.configuration.Type

Gets the URI of this type configuration.

getUri() - Method in class com.genologics.ri.configuration.TypeDefinition

Gets the URI of the type definition.

getUri() - Method in class com.genologics.ri.configuration.UdfConfigLink

Gets the URI of the field configuration.

getUri() - Method in class com.genologics.ri.configuration.UdtConfigLink

Gets the URI of the type configuration.

getUri() - Method in class com.genologics.ri.container.Container

Gets the URI.

getUri() - Method in class com.genologics.ri.container.ContainerLink

Gets the URI.

getUri() - Method in class com.genologics.ri.container.ContainerTypeLink

Gets the URI of the container type.

getUri() - Method in class com.genologics.ri.container.Placement

Gets the URI of the artifact.

getUri() - Method in class com.genologics.ri.ContainerLink

Gets the URI of the container.

getUri() - Method in class com.genologics.ri.containertype.ContainerType

Gets the URI for accessing this container type resource.

getUri() - Method in class com.genologics.ri.containertype.ContainerTypeLink

Gets the URI for accessing the container type resource.

getUri() - Method in class com.genologics.ri.controltype.ControlType

Gets the URI of the control type.

getUri() - Method in class com.genologics.ri.controltype.ControlTypeLink

Gets the URI of the control type.

getUri() - Method in class com.genologics.ri.controltype.ControlTypes

Gets the URI of the control types collection.

getUri() - Method in class com.genologics.ri.ExternalId

Gets the URI within the external system.

getUri() - Method in class com.genologics.ri.file.ClarityFile

Gets the URI of this file resource.

getUri() - Method in class com.genologics.ri.file.FileLink

Gets the URI of the file resource.

getUri() - Method in class com.genologics.ri.globaltoken.GlobalToken

Get the URI of this global token.

getUri() - Method in class com.genologics.ri.globaltoken.GlobalTokenLink

Get the URI of this global token.

getUri() - Method in class com.genologics.ri.instrument.Instrument

Get the URI of this object.

getUri() - Method in class com.genologics.ri.instrument.InstrumentLink

Get the URI of the object we are linking to.

getUri() - Method in class com.genologics.ri.instrumenttype.InstrumentType

Get the URI of this object.

getUri() - Method in class com.genologics.ri.instrumenttype.InstrumentTypeLink

Get the URI of the object we are linking to.

getUri() - Method in class com.genologics.ri.instrumenttype.InstrumentTypeProcessType

Get the URI of the object we are linking to.

getUri() - Method in class com.genologics.ri.lab.Lab

Gets the URI of the lab resource.

getUri() - Method in class com.genologics.ri.lab.LabLink

Gets the URI of the lab resource.

getUri() - Method in interface com.genologics.ri.LimsLink

Get the URI of the object we are linking to.

getUri() - Method in class com.genologics.ri.Link

Gets the URI of the link.

getUri() - Method in interface com.genologics.ri.Locatable

Get the URI of this object.

getUri() - Method in class com.genologics.ri.Location

Gets the URI of the container.

getUri() - Method in class com.genologics.ri.Page

Gets the URI to the page.

getUri() - Method in class com.genologics.ri.permission.Permission

Get the URI of this object.

getUri() - Method in class com.genologics.ri.permission.PermissionLink

Get the URI of the object we are linking to.

getUri() - Method in class com.genologics.ri.permission.Permissions

Get the URI.

getUri() - Method in class com.genologics.ri.process.ArtifactLink

Gets the URI.

getUri() - Method in class com.genologics.ri.process.ClarityProcess

Gets the URI.

getUri() - Method in class com.genologics.ri.process.InstrumentLink

Gets the URI.

getUri() - Method in class com.genologics.ri.process.ParentProcessLink

Gets the URI.

getUri() - Method in class com.genologics.ri.process.ProcessLink

Gets the URI.

getUri() - Method in class com.genologics.ri.process.ProcessTypeLink

Gets the URI.

getUri() - Method in class com.genologics.ri.process.Technician

Gets the URI.

getUri() - Method in class com.genologics.ri.processexecution.Input

Gets the URI of the input artifact.

getUri() - Method in class com.genologics.ri.processexecution.InstrumentLink

Gets the URI of the instrument.

getUri() - Method in class com.genologics.ri.processexecution.Technician

Gets the URI of the researcher.

getUri() - Method in class com.genologics.ri.processtemplate.InstrumentLink

Gets the URI.

getUri() - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Gets the URI.

getUri() - Method in class com.genologics.ri.processtemplate.ProcessTemplateLink

Gets the URI.

getUri() - Method in class com.genologics.ri.processtemplate.ProcessTypeLink

Gets the URI.

getUri() - Method in class com.genologics.ri.processtemplate.Technician

Gets the URI of this technician resource.

getUri() - Method in class com.genologics.ri.processtype.ContainerTypeLink

Gets the URI of the container type.

getUri() - Method in class com.genologics.ri.processtype.ControlTypeLink

Gets the URI of the control type.

getUri() - Method in class com.genologics.ri.processtype.ProcessType

Gets the URI of the process type.

getUri() - Method in class com.genologics.ri.processtype.ProcessTypeLink

Gets the URI of the process type.

getUri() - Method in class com.genologics.ri.processtype.ReagentKitLink

Gets the URI of the reagent kit.

getUri() - Method in class com.genologics.ri.processtype.TypeDefinition

Gets the URI of the field.

getUri() - Method in class com.genologics.ri.project.Project

Get the URI of the project.

getUri() - Method in class com.genologics.ri.project.ProjectLink

Get the URI of the project.

getUri() - Method in class com.genologics.ri.project.ResearcherLink

Get the URI of the researcher.

getUri() - Method in class com.genologics.ri.property.PropertyLink

Gets the URI of the property.

getUri() - Method in class com.genologics.ri.protocolconfiguration.Protocol

Gets the URI of the protocol.

getUri() - Method in class com.genologics.ri.protocolconfiguration.ProtocolLink

Gets the URI to the protocol.

getUri() - Method in class com.genologics.ri.queue.ArtifactLink

Get the URI of the object we are linking to.

getUri() - Method in class com.genologics.ri.queue.Queue

Gets the URI of the queue.

getUri() - Method in class com.genologics.ri.reagentkit.ReagentKit

Gets the URI of the reagent kit.

getUri() - Method in class com.genologics.ri.reagentkit.ReagentKitLink

Gets the URI of the reagent kit.

getUri() - Method in class com.genologics.ri.reagentkit.ReagentKits

Gets the URI of the reagent kits list.

getUri() - Method in class com.genologics.ri.reagentlot.ReagentKitLink

Gets the URI of the reagent kit.

getUri() - Method in class com.genologics.ri.reagentlot.ReagentLot

getUri() - Method in class com.genologics.ri.reagentlot.ReagentLotLink

Get the URI of the object we are linking to.

getUri() - Method in class com.genologics.ri.reagentlot.ReagentLots

Gets the URI of this reagent lots collection.

getUri() - Method in class com.genologics.ri.reagentlot.ResearcherLink

Gets the URI of the researcher.

getUri() - Method in class com.genologics.ri.reagenttype.ReagentType

Gets the URI.

getUri() - Method in class com.genologics.ri.reagenttype.ReagentTypeLink

Gets the URI of the reagent type.

getUri() - Method in class com.genologics.ri.researcher.LabLink

Gets the URI to the lab.

getUri() - Method in class com.genologics.ri.researcher.Researcher

Gets the URI to the researcher.

getUri() - Method in class com.genologics.ri.researcher.ResearcherLink

Gets the URI to the researcher.

getUri() - Method in class com.genologics.ri.researcher.Role

Get the URI to the role.

getUri() - Method in class com.genologics.ri.role.PermissionLink

Gets the URI of the permission.

getUri() - Method in class com.genologics.ri.role.ResearcherLink

Gets the URI of the researcher.

getUri() - Method in class com.genologics.ri.role.Role

Gets the URI of the role.

getUri() - Method in class com.genologics.ri.role.RoleLink

Gets the URI of the role.

getUri() - Method in class com.genologics.ri.role.Roles

Gets the URI of the roles list.

getUri() - Method in class com.genologics.ri.routing.ArtifactLink

Gets the URI of the artifact.

getUri() - Method in class com.genologics.ri.sample.ArtifactLink

Gets the URI of the artifact.

getUri() - Method in class com.genologics.ri.sample.ControlTypeLink

Gets the URI of the control type.

getUri() - Method in class com.genologics.ri.sample.ProjectLink

Gets the URI of the project.

getUri() - Method in class com.genologics.ri.sample.SampleBase

Gets the URI of this sample.

getUri() - Method in class com.genologics.ri.sample.SampleLink

Gets the URI of the sample.

getUri() - Method in class com.genologics.ri.sample.Submitter

Gets the URI of the submitter.

getUri() - Method in class com.genologics.ri.savedquery.SavedQuery

Gets the URI of the saved query.

getUri() - Method in class com.genologics.ri.savedquery.SavedQueryLink

Gets the URI of the saved query.

getUri() - Method in class com.genologics.ri.stage.ProtocolLink

Gets the URI of the protocol.

getUri() - Method in class com.genologics.ri.stage.ProtocolStepLink

Gets the URI of the protocol step.

getUri() - Method in class com.genologics.ri.stage.Stage

Gets the URI of the stage.

getUri() - Method in class com.genologics.ri.stage.WorkflowLink

Gets the URI of the workflow.

getUri() - Method in class com.genologics.ri.step.Actions

Gets the URI.

getUri() - Method in class com.genologics.ri.step.ActionsLink

Gets the URI.

getUri() - Method in class com.genologics.ri.step.Arrangements

Gets the URI.

getUri() - Method in class com.genologics.ri.step.ArrangementsLink

Gets the URI.

getUri() - Method in class com.genologics.ri.step.ArtifactLink

Gets the URI.

getUri() - Method in class com.genologics.ri.step.AutomaticNextStepLink

Gets the URI.

getUri() - Method in class com.genologics.ri.step.AvailableProgram

Gets the URI.

getUri() - Method in class com.genologics.ri.step.ContainerLink

Gets the URI.

getUri() - Method in class com.genologics.ri.step.CreationInput

Gets the URI.

getUri() - Method in class com.genologics.ri.step.EscalatedArtifact

Gets the URI.

getUri() - Method in class com.genologics.ri.step.Input

Gets the URI.

getUri() - Method in class com.genologics.ri.step.InstrumentLink

Gets the URI.

getUri() - Method in class com.genologics.ri.step.NextAction

Gets the URI (artifact URI).

getUri() - Method in class com.genologics.ri.step.Output

Gets the URI.

getUri() - Method in class com.genologics.ri.step.OutputArrangement

Gets the URI.

getUri() - Method in class com.genologics.ri.step.OutputPlacement

Gets the URI of the output artifact.

getUri() - Method in class com.genologics.ri.step.Placements

Gets the URI of this placements resource.

getUri() - Method in class com.genologics.ri.step.PlacementsLink

Gets the URI of the placements resource.

getUri() - Method in class com.genologics.ri.step.Pools

Gets the URI of this pools resource.

getUri() - Method in class com.genologics.ri.step.PoolsLink

Gets the URI of the pools resource.

getUri() - Method in class com.genologics.ri.step.ProcessStep

Gets the URI of the step.

getUri() - Method in class com.genologics.ri.step.ProgramStatus

Gets the URI of the program status.

getUri() - Method in class com.genologics.ri.step.ProgramStatusLink

Gets the URI of the program status.

getUri() - Method in class com.genologics.ri.step.ReagentLotLink

Get the URI of the object we are linking to.

getUri() - Method in class com.genologics.ri.step.ReagentLots

Gets the URI of this reagent lots resource.

getUri() - Method in class com.genologics.ri.step.ReagentLotsLink

Gets the URI of the reagent lots resource.

getUri() - Method in class com.genologics.ri.step.Reagents

Gets the URI.

getUri() - Method in class com.genologics.ri.step.ReagentsLink

Gets the URI of the reagents resource.

getUri() - Method in class com.genologics.ri.step.SharedResultFile

Gets the URI of the artifact.

getUri() - Method in class com.genologics.ri.step.StepConfiguration

Get the URI of the object we are linking to.

getUri() - Method in class com.genologics.ri.step.StepDetails

Gets the URI of this step details resource.

getUri() - Method in class com.genologics.ri.step.StepDetailsLink

Gets the URI of the step details resource.

getUri() - Method in class com.genologics.ri.step.StepSetup

Gets the URI of this step setup resource.

getUri() - Method in class com.genologics.ri.step.StepSetupLink

Gets the URI of the step setup resource.

getUri() - Method in class com.genologics.ri.step.Technician

Gets the URI of the researcher resource.

getUri() - Method in class com.genologics.ri.step.UserLink

Gets the URI of the researcher resource.

getUri() - Method in class com.genologics.ri.stepconfiguration.ControlTypeLink

Gets the URI of the control type.

getUri() - Method in class com.genologics.ri.stepconfiguration.NextStep

Gets the URI of the next step (alias for getNextStepUri).

getUri() - Method in class com.genologics.ri.stepconfiguration.ProcessTypeLink

Gets the URI of the process type.

getUri() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Gets the URI of the protocol step.

getUri() - Method in class com.genologics.ri.stepconfiguration.ReagentKitLink

Gets the URI of the reagent kit.

getUri() - Method in class com.genologics.ri.version.Version

Gets the URI of the version.

getUri() - Method in class com.genologics.ri.workflowconfiguration.ProtocolLink

Gets the URI of the protocol.

getUri() - Method in class com.genologics.ri.workflowconfiguration.StageLink

Gets the URI of the stage.

getUri() - Method in class com.genologics.ri.workflowconfiguration.Workflow

Gets the URI of the workflow.

getUri() - Method in class com.genologics.ri.workflowconfiguration.WorkflowLink

Gets the URI of the workflow.

getURI() - Method in class org.cruk.clarity.api.impl.URLInputStreamResource

Get the URI of the resource.

getURL() - Method in class org.cruk.clarity.api.impl.URLInputStreamResource

Get the URL of the resource.

getUsageCount() - Method in class com.genologics.ri.reagentlot.ReagentLot

Gets the usage count.

getUserDefinedFields() - Method in class com.genologics.ri.artifact.Artifact

getUserDefinedFields() - Method in class com.genologics.ri.container.Container

Gets the list of user-defined fields.

getUserDefinedFields() - Method in class com.genologics.ri.lab.Lab

getUserDefinedFields() - Method in class com.genologics.ri.process.ClarityProcess

Gets the user defined fields.

getUserDefinedFields() - Method in class com.genologics.ri.processexecution.ExecutableProcess

Gets the user-defined fields.

getUserDefinedFields() - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Gets the user-defined fields.

getUserDefinedFields() - Method in class com.genologics.ri.project.Project

Get the user-defined fields for the project.

getUserDefinedFields() - Method in class com.genologics.ri.researcher.Researcher

Gets the list of user-defined fields for the researcher.

getUserDefinedFields() - Method in class com.genologics.ri.sample.SampleBase

Gets the list of user-defined fields for this sample.

getUserDefinedFields() - Method in class com.genologics.ri.step.StepDetails

Gets the list of user-defined fields for the step.

getUserDefinedFields() - Method in interface com.genologics.ri.userdefined.UDFHolder

Get a list of user defined fields held by the entity.

getUserDefinedFields() - Method in class com.genologics.ri.userdefined.UDT

Replicates getFields but allows the UDT to be used by the UDF static helper methods.

getUserDefinedType() - Method in class com.genologics.ri.container.Container

Gets the user-defined type.

getUserDefinedType() - Method in class com.genologics.ri.lab.Lab

Gets the user-defined type of the lab.

getUserDefinedType() - Method in class com.genologics.ri.process.ClarityProcess

Gets the user defined type.

getUserDefinedType() - Method in class com.genologics.ri.processexecution.ExecutableProcess

Gets the user-defined type.

getUserDefinedType() - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Gets the user-defined type.

getUserDefinedType() - Method in class com.genologics.ri.project.Project

Get the user-defined type of the project.

getUserDefinedType() - Method in class com.genologics.ri.researcher.Researcher

Gets the user-defined type for the researcher.

getUserDefinedType() - Method in class com.genologics.ri.sample.SampleBase

Gets the user-defined type of this sample.

getUsername() - Method in class com.genologics.ri.researcher.Credentials

Gets the username.

getUsername() - Method in interface org.cruk.clarity.api.ClarityAPI

Get the user name of the researcher currently connecting to the server.

getUsername() - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Get the user name of the researcher currently connecting to the server.

getValue() - Method in class com.genologics.ri.configuration.FieldDynamicPreset

Gets the preset value.

getValue() - Method in class com.genologics.ri.containertype.CalibrantWell

Deprecated.

Gets the value or content of the calibrant well.

getValue() - Method in class com.genologics.ri.globaltoken.GlobalToken

Get the token value.

getValue() - Method in class com.genologics.ri.processtype.ProcessTypeAttribute

Gets the value of the attribute.

getValue() - Method in class com.genologics.ri.processtype.StepProperty

Gets the value of the step property.

getValue() - Method in class com.genologics.ri.property.PropertyLink

Gets the value of the property.

getValue() - Method in class com.genologics.ri.protocolconfiguration.ProtocolProperty

Gets the value of the protocol property.

getValue() - Method in class com.genologics.ri.reagenttype.Attribute

Gets the value of the attribute.

getValue() - Method in class com.genologics.ri.stepconfiguration.GenericTypeLink

Gets the value of the generic type link.

getValue() - Method in class com.genologics.ri.stepconfiguration.StepProperty

Gets the value of the step property.

getValue() - Method in class com.genologics.ri.userdefined.UDF

Gets the value of the UDF.

getValues() - Method in class org.cruk.clarity.api.search.SearchTerm

Get the values to search for for this parameter.

getVariabilityType() - Method in class com.genologics.ri.processtype.ProcessOutput

Specifies how the process determines the number of outputs to generated (FIXED, VARIABLE, or VARIABLE_BY_INPUT).

getVendor() - Method in class com.genologics.ri.instrumenttype.InstrumentType

Get the instrument vendor.

getVendor() - Method in class com.genologics.ri.instrumenttype.InstrumentTypeLink

Get the instrument vendor.

getVersions() - Method in class com.genologics.ri.version.Versions

Gets the list of versions.

getWait() - Method in interface org.cruk.clarity.api.automation.ClarityProcessAutomation

Get the time to wait between polls.

getWait() - Method in class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Get the time to wait between polls.

getWaitAttempts() - Method in interface org.cruk.clarity.api.automation.ClarityProcessAutomation

Get the number of times to ask for a state change before stopping.

getWaitAttempts() - Method in class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Get the number of times to ask for a state change before stopping.

getWebsite() - Method in class com.genologics.ri.controltype.ControlType

Gets the website URL for the control type.

getWebsite() - Method in class com.genologics.ri.lab.Lab

Gets the website URL of the lab.

getWebsite() - Method in class com.genologics.ri.reagentkit.ReagentKit

Gets the website of the reagent kit.

getWellPosition() - Method in class com.genologics.ri.container.Placement

Gets the well position in the container.

getWellPosition() - Method in class com.genologics.ri.Location

Gets the well position.

getWorkflow() - Method in class com.genologics.ri.stage.Stage

Gets the workflow link for this stage.

getWorkflowId() - Method in class com.genologics.ri.artifact.WorkflowStage

Get the numeric identifier for this stage's workflow from its URI.

getWorkflowId() - Method in class com.genologics.ri.stage.Stage

Gets the numeric identifier for this stage's workflow from its URI.

getWorkflows() - Method in class com.genologics.ri.workflowconfiguration.Workflows

Gets the list of workflows.

getWorkflowStages() - Method in class com.genologics.ri.artifact.Artifact

Gets the workflow stages this artifact is associated with.

getWorkflowUri() - Method in class com.genologics.ri.routing.ExtArtifactAssignments

Gets the workflow URI.

GLOBAL_TOKEN_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The global token namespace.

GlobalToken - Class in com.genologics.ri.globaltoken

Clarity global token.

GlobalToken() - Constructor for class com.genologics.ri.globaltoken.GlobalToken

Default constructor.

GlobalToken(URI) - Constructor for class com.genologics.ri.globaltoken.GlobalToken

Constructor with URI.

GlobalToken(URI, String) - Constructor for class com.genologics.ri.globaltoken.GlobalToken

Constructor with URI and name.

GlobalTokenLink - Class in com.genologics.ri.globaltoken

global-token-link is a child element type of global tokens and provides a URI linking to the detailed representation of a global token.

GlobalTokenLink() - Constructor for class com.genologics.ri.globaltoken.GlobalTokenLink

Default constructor.

GlobalTokenLink(URI) - Constructor for class com.genologics.ri.globaltoken.GlobalTokenLink

Constructor with URI.

GlobalTokenLink(URI, String) - Constructor for class com.genologics.ri.globaltoken.GlobalTokenLink

Constructor with URI and name.

globalTokens - Variable in class com.genologics.ri.globaltoken.GlobalTokens

The list of global token links.

GlobalTokens - Class in com.genologics.ri.globaltoken

List of global token links.

GlobalTokens() - Constructor for class com.genologics.ri.globaltoken.GlobalTokens

Default constructor.

H

handleError(ClientHttpResponse) - Method in class org.cruk.clarity.api.http.ClarityFailureResponseErrorHandler

See if the response indicates an error and, if the body of the response is a Clarity error reply, create a throwable ClarityException from it and throw that.

hasError(HttpStatusCode) - Method in class org.cruk.clarity.api.http.ClarityFailureResponseErrorHandler

Refinement of the default implementation, as we want anything that's not a successful error code (in the 200 series) to be classed as a failure.

hashCode() - Method in class com.genologics.ri.instrumenttype.InstrumentTypeProcessType

hashCode() - Method in class com.genologics.ri.LimsLinkBase

hashCode() - Method in class com.genologics.ri.Location

Computes a hash code for this location.

hashCode() - Method in class com.genologics.ri.process.ProcessTypeLink

hashCode() - Method in class com.genologics.ri.processexecution.Input

hashCode() - Method in class com.genologics.ri.processtemplate.ProcessTypeLink

hashCode() - Method in class com.genologics.ri.step.InstrumentLink

hashCode() - Method in class com.genologics.ri.step.StepConfiguration

hashCode() - Method in class com.genologics.ri.stepconfiguration.ControlTypeLink

hashCode() - Method in class com.genologics.ri.stepconfiguration.ProcessTypeLink

hashCode() - Method in class com.genologics.ri.stepconfiguration.ReagentKitLink

hashCode() - Method in class org.cruk.clarity.api.impl.URLInputStreamResource

Get a hash code for this URLInputStreamResource.

hashCode() - Method in class org.cruk.clarity.api.search.SearchTerm

Override of hash code.

hashCode() - Method in class org.cruk.clarity.api.search.SearchTerms

Override of hash code.

hashCode(LimsLink<?>) - Static method in interface com.genologics.ri.LimsLink

Calculate a hash code for the given link.

httpClient - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

The HTTP client.

HttpClientTimingAspect - Class in org.cruk.clarity.api.debugging

Testing aspect that reports on the calls being made by the HTTP client talking to the Clarity API.

HttpClientTimingAspect() - Constructor for class org.cruk.clarity.api.debugging.HttpClientTimingAspect

HttpComponentsClientHttpRequestFactoryBasicAuth - Class in org.cruk.clarity.api.http

Client HTTP request factory adding basic authentication to the request.

HttpComponentsClientHttpRequestFactoryBasicAuth() - Constructor for class org.cruk.clarity.api.http.HttpComponentsClientHttpRequestFactoryBasicAuth

Constructor.

HttpComponentsClientHttpRequestFactoryBasicAuth(HttpClient) - Constructor for class org.cruk.clarity.api.http.HttpComponentsClientHttpRequestFactoryBasicAuth

Constructor with an HTTP client.

HttpComponentsClientHttpRequestFactoryBasicAuth(HttpClient, CredentialsProvider) - Constructor for class org.cruk.clarity.api.http.HttpComponentsClientHttpRequestFactoryBasicAuth

Constructor with an HTTP client and credentials provider.

httpRequestFactory - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

The request factory for direct communication with the HTTP client.

httpRequestFactory - Variable in class org.cruk.clarity.api.impl.SavedQueryRunner

Client request factory.

httpStatus - Variable in exception org.cruk.clarity.api.ClarityException

The HTTP status code returned from the server.

httpUploadSizeLimit - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

The maximum size of file that can be uploaded using HTTP.

HYBRIDIZED - Enum constant in enum class com.genologics.ri.container.ContainerState

The container state when the container's contents have been hybridized.

I

IceBucketField - Class in com.genologics.ri.processtype

A field has a name and an attach to value, these fields are used to keep track of all the UDF values for samples in ice bucket view.

IceBucketField - Class in com.genologics.ri.stepconfiguration

A field has a name and an attach to value, these fields are used to keep track of all the UDF values for samples in ice bucket view

IceBucketField() - Constructor for class com.genologics.ri.processtype.IceBucketField

Constructs a new ice bucket field.

IceBucketField() - Constructor for class com.genologics.ri.stepconfiguration.IceBucketField

Default constructor.

IceBucketField(String) - Constructor for class com.genologics.ri.stepconfiguration.IceBucketField

Constructor with field name.

IceBucketField(String, String) - Constructor for class com.genologics.ri.stepconfiguration.IceBucketField

Constructor with field name and attach-to value.

iceBucketFields - Variable in class com.genologics.ri.processtype.ProcessType

Fields displayed in the ice bucket view.

iceBucketFields - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

List of fields to display in the ice bucket view.

id - Variable in class com.genologics.ri.ExternalId

The id referencing the external system.

id - Variable in class com.genologics.ri.savedquery.SavedQuery

The unique identifier of the saved query.

id - Variable in class com.genologics.ri.savedquery.SavedQueryLink

The unique identifier of the saved query.

ID_EXTRACTOR_PATTERN - Static variable in class com.genologics.ri.artifact.WorkflowStage

Regular expression to extract workflow id and workflow stage id from a workflow stage URI.

ID_EXTRACTOR_PATTERN - Static variable in class com.genologics.ri.protocolconfiguration.Protocol

Regular expression to extract protocol id from a protocol URI.

ID_EXTRACTOR_PATTERN - Static variable in class com.genologics.ri.stage.Stage

Regular expression pattern to extract workflow id and workflow stage id from a workflow stage URI.

ID_EXTRACTOR_PATTERN - Static variable in class com.genologics.ri.stepconfiguration.ProtocolStep

Regular expression to extract protocol id and protocol step id from a protocol step URI.

ID_EXTRACTOR_PATTERN - Static variable in class com.genologics.ri.workflowconfiguration.Workflow

Regular expression to extract workflow id from a workflow URI.

idFromUri(Locatable) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Get an identifier for a locatable object from its URI.

IllegalSearchTermException - Exception in org.cruk.clarity.api

Exception raised when a search for entities is provided with search terms that are illegal.

IllegalSearchTermException(String, String) - Constructor for exception org.cruk.clarity.api.IllegalSearchTermException

Construct a new IllegalSearchTermException.

IN_PROGRESS - Enum constant in enum class com.genologics.ri.artifact.Status

In progress status.

index - Variable in class com.genologics.ri.protocolconfiguration.Protocol

The index of the protocol.

index - Variable in class com.genologics.ri.stage.Stage

The index of the stage in the workflow.

Index - Class in com.genologics.ri

Index is the entry point to a supported version of the API, providing a list of links to the available resources in that version in the system.

Index() - Constructor for class com.genologics.ri.Index

Default constructor.

initials - Variable in class com.genologics.ri.researcher.Researcher

The researcher's initials.

input - Variable in class com.genologics.ri.process.InputOutputMap

The input artifact link.

input - Variable in class com.genologics.ri.step.InputOutputMap

The input artifact link.

Input - Class in com.genologics.ri.processexecution

The input element provides URIs to one or more Artifacts that will be used by the Process.

Input - Class in com.genologics.ri.step

Provides input URI links.

Input() - Constructor for class com.genologics.ri.processexecution.Input

Default constructor.

Input() - Constructor for class com.genologics.ri.step.Input

Default constructor.

Input(Linkable<Artifact>) - Constructor for class com.genologics.ri.processexecution.Input

Constructor from a linkable artifact.

Input(Linkable<Artifact>) - Constructor for class com.genologics.ri.step.Input

Constructor from a linkable object.

Input(URI) - Constructor for class com.genologics.ri.processexecution.Input

Constructor with URI.

Input(URI) - Constructor for class com.genologics.ri.step.Input

Constructor with URI.

Input(URI, QCFlag) - Constructor for class com.genologics.ri.processexecution.Input

Constructor with URI and QC flag.

InputOutputMap - Class in com.genologics.ri.process

Input-output-map is a child element of Process and relates one of the Process inputs to one of the outputs that was produced for that input.

InputOutputMap - Class in com.genologics.ri.step

Input-output-map is a child element of Step and relates one of the Step inputs to one of the outputs that was produced for that input.

InputOutputMap() - Constructor for class com.genologics.ri.process.InputOutputMap

Default constructor.

InputOutputMap() - Constructor for class com.genologics.ri.step.InputOutputMap

Default constructor.

InputOutputMap(LimsEntityLinkable<Artifact>, LimsEntityLinkable<Artifact>) - Constructor for class com.genologics.ri.process.InputOutputMap

Constructor with input and output LIMS entity linkable artifacts.

InputOutputMap(LimsEntityLinkable<Artifact>, LimsEntityLinkable<Artifact>) - Constructor for class com.genologics.ri.step.InputOutputMap

Constructor with LIMS entity linkable input and output artifacts.

InputOutputMap(Linkable<Artifact>, Linkable<Artifact>) - Constructor for class com.genologics.ri.process.InputOutputMap

Constructor with input and output linkable artifacts.

InputOutputMap(Linkable<Artifact>, Linkable<Artifact>) - Constructor for class com.genologics.ri.step.InputOutputMap

Constructor with linkable input and output artifacts.

InputOutputMap(ArtifactLink, ArtifactLink) - Constructor for class com.genologics.ri.process.InputOutputMap

Constructor with input and output artifact links.

InputOutputMap(ArtifactLink, ArtifactLink) - Constructor for class com.genologics.ri.step.InputOutputMap

Constructor with input and output artifact links.

inputOutputMaps - Variable in class com.genologics.ri.process.ClarityProcess

The input-output mappings for the process.

inputOutputMaps - Variable in class com.genologics.ri.processexecution.ExecutableProcess

The input-output mappings for the process.

inputOutputMaps - Variable in class com.genologics.ri.step.StepDetails

The list of input to output artifact mappings for the step.

inputs - Variable in class com.genologics.ri.processexecution.ExecutableInputOutputMap

List of input artifacts.

inputs - Variable in class com.genologics.ri.step.PooledInputs

The list of input artifacts in this pool.

inputs - Variable in class com.genologics.ri.step.StepCreation

The list of input artifacts for the step.

institution - Variable in class com.genologics.ri.Address

The institution.

instrument - Variable in class com.genologics.ri.process.ClarityProcess

The instrument used to run the process.

instrument - Variable in class com.genologics.ri.processexecution.ExecutableProcess

The instrument used for the process.

instrument - Variable in class com.genologics.ri.processtemplate.ProcessTemplate

The instrument configured to run processes created from this template.

instrument - Variable in class com.genologics.ri.step.StepDetails

Link to the instrument used for the step.

Instrument - Class in com.genologics.ri.instrument

The detailed representation of an instrument.

Instrument() - Constructor for class com.genologics.ri.instrument.Instrument

Default constructor.

Instrument(String) - Constructor for class com.genologics.ri.instrument.Instrument

Constructor with instrument name.

Instrument(String, String) - Constructor for class com.genologics.ri.instrument.Instrument

Constructor with instrument name and type.

INSTRUMENT_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The instrument namespace.

INSTRUMENT_TYPE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The instrument type namespace.

InstrumentLink - Class in com.genologics.ri.instrument

Instrument-link is a child element type of instruments and provides a URI linking to the detailed representation of an instrument.

InstrumentLink - Class in com.genologics.ri.process

The instrument element provides a URI to the instrument that is responsible for running the process.

InstrumentLink - Class in com.genologics.ri.processexecution

The instrument element provides a URI to the instrument that is responsible for running the process.

InstrumentLink - Class in com.genologics.ri.processtemplate

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.

InstrumentLink - Class in com.genologics.ri.step

The instrument element provides a URI to the selected instrument for the step.

InstrumentLink() - Constructor for class com.genologics.ri.instrument.InstrumentLink

Default constructor.

InstrumentLink() - Constructor for class com.genologics.ri.process.InstrumentLink

Default constructor.

InstrumentLink() - Constructor for class com.genologics.ri.processexecution.InstrumentLink

Default constructor.

InstrumentLink() - Constructor for class com.genologics.ri.processtemplate.InstrumentLink

Default constructor.

InstrumentLink() - Constructor for class com.genologics.ri.step.InstrumentLink

Default constructor.

InstrumentLink(Instrument) - Constructor for class com.genologics.ri.instrument.InstrumentLink

Constructor from an instrument.

InstrumentLink(Instrument) - Constructor for class com.genologics.ri.step.InstrumentLink

Constructor from an instrument.

InstrumentLink(Linkable<Instrument>) - Constructor for class com.genologics.ri.instrument.InstrumentLink

Constructor from a linkable instrument.

InstrumentLink(Linkable<Instrument>) - Constructor for class com.genologics.ri.process.InstrumentLink

Constructor from a linkable object.

InstrumentLink(Linkable<Instrument>) - Constructor for class com.genologics.ri.processexecution.InstrumentLink

Constructor from a linkable instrument.

InstrumentLink(Linkable<Instrument>) - Constructor for class com.genologics.ri.processtemplate.InstrumentLink

Constructor from a linkable instrument.

InstrumentLink(Linkable<Instrument>) - Constructor for class com.genologics.ri.step.InstrumentLink

Constructor from a linkable object.

InstrumentLink(URI) - Constructor for class com.genologics.ri.instrument.InstrumentLink

Constructor with URI.

InstrumentLink(URI) - Constructor for class com.genologics.ri.process.InstrumentLink

Constructor with URI.

InstrumentLink(URI) - Constructor for class com.genologics.ri.processexecution.InstrumentLink

Constructor with URI.

InstrumentLink(URI) - Constructor for class com.genologics.ri.processtemplate.InstrumentLink

Constructor with URI.

InstrumentLink(URI) - Constructor for class com.genologics.ri.step.InstrumentLink

Constructor with URI.

InstrumentLink(URI, String) - Constructor for class com.genologics.ri.instrument.InstrumentLink

Constructor with URI and name.

InstrumentLink(URI, String) - Constructor for class com.genologics.ri.step.InstrumentLink

Constructor with URI and name.

instruments - Variable in class com.genologics.ri.instrument.Instruments

The list of instrument links.

Instruments - Class in com.genologics.ri.instrument

The representation of a list of instrument links.

Instruments() - Constructor for class com.genologics.ri.instrument.Instruments

Default constructor.

InstrumentType - Class in com.genologics.ri.instrumenttype

An instrument describes properties common to all instruments of that type.

InstrumentType() - Constructor for class com.genologics.ri.instrumenttype.InstrumentType

Default constructor.

InstrumentType(URI) - Constructor for class com.genologics.ri.instrumenttype.InstrumentType

Constructor with URI.

InstrumentType(URI, String) - Constructor for class com.genologics.ri.instrumenttype.InstrumentType

Constructor with URI and name.

InstrumentTypeLink - Class in com.genologics.ri.instrumenttype

Instrument-type-link provides a URI linking to the detailed representation of an instrument type.

InstrumentTypeLink() - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypeLink

Default constructor.

InstrumentTypeLink(InstrumentType) - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypeLink

Constructor from an instrument type.

InstrumentTypeLink(Linkable<InstrumentType>) - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypeLink

Constructor from a linkable instrument type.

InstrumentTypeLink(URI) - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypeLink

Constructor with URI.

InstrumentTypeLink(URI, String) - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypeLink

Constructor with URI and name.

InstrumentTypeLink(URI, String, String) - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypeLink

Constructor with URI, name and vendor.

InstrumentTypeProcessType - Class in com.genologics.ri.instrumenttype

Process type link for instrument types.

InstrumentTypeProcessType() - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypeProcessType

Default constructor.

InstrumentTypeProcessType(Linkable<ProcessType>) - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypeProcessType

Constructor from a linkable process type.

InstrumentTypeProcessType(ProcessType) - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypeProcessType

Constructor from a process type.

InstrumentTypeProcessType(URI) - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypeProcessType

Constructor with URI.

InstrumentTypeProcessType(URI, String) - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypeProcessType

Constructor with URI and name.

instrumentTypes - Variable in class com.genologics.ri.instrumenttype.InstrumentTypes

The list of instrument type links.

InstrumentTypes - Class in com.genologics.ri.instrumenttype

The representation of a list of instrument type links.

InstrumentTypes() - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypes

Default constructor.

InvalidURIException - Exception in org.cruk.clarity.api

Exception raised when a URI or URL object is created from a string but the string isn't a valid URI or URL.

InvalidURIException(String, MalformedURLException) - Constructor for exception org.cruk.clarity.api.InvalidURIException

Construct a new InvalidURIException from a MalformedURLException.

InvalidURIException(String, URISyntaxException) - Constructor for exception org.cruk.clarity.api.InvalidURIException

Construct a new InvalidURIException from a URISyntaxException.

InvalidURIException(MalformedURLException) - Constructor for exception org.cruk.clarity.api.InvalidURIException

Construct a new InvalidURIException from a MalformedURLException.

InvalidURIException(URISyntaxException) - Constructor for exception org.cruk.clarity.api.InvalidURIException

Construct a new InvalidURIException from a URISyntaxException.

invocationType - Variable in class com.genologics.ri.processtype.Parameter

Deprecated.

This property is no longer supported.

InvocationType - Enum Class in com.genologics.ri.processtype

Enumeration of EPP invocation types.

invoiceDate - Variable in class com.genologics.ri.project.Project

The date the project was invoiced.

isAccountLocked() - Method in class com.genologics.ri.researcher.Credentials

Checks whether the account is locked.

isAllowNonPresetValues() - Method in class com.genologics.ri.configuration.Field

Checks if values other than preset values are allowed.

isAlpha() - Method in class com.genologics.ri.containertype.Dimension

Checks if numbering in this dimension is alphabetic.

isAssignWorkingFlag() - Method in class com.genologics.ri.processtype.ProcessOutput

Deprecated.

This property is no longer supported.

isCacheable(Class<?>) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Test whether entities of a class are cacheable.

isCacheable(Object) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Test whether an entity is cacheable.

isCacheable(Collection<?>) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Test whether a collection of entities is cacheable.

isControlledVocabulary() - Method in class com.genologics.ri.configuration.Field

Checks if this field uses a controlled vocabulary.

isControlSample() - Method in class com.genologics.ri.sample.SampleBase

Checks if this sample is a control sample.

isCustom - Variable in class com.genologics.ri.globaltoken.GlobalToken

Flag indicating whether this is a custom token.

isCustom() - Method in class com.genologics.ri.globaltoken.GlobalToken

Check whether this is a custom token.

isDefault() - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Checks if this is the default template.

isDeviation() - Method in class com.genologics.ri.configuration.Field

Checks if this field represents a deviation.

isDynamicPresets() - Method in class com.genologics.ri.configuration.Field

Checks if this field uses dynamic presets.

isEditable() - Method in class com.genologics.ri.configuration.Field

Checks if this field is editable.

isEmpty() - Method in interface com.genologics.ri.Batch

Checks if this batch is empty.

isEmpty() - Method in class com.genologics.ri.configuration.FieldDynamicPresetDetails

Checks if the preset list is empty.

isEnabled() - Method in class com.genologics.ri.stepconfiguration.StepSetup

Gets whether the step setup view is enabled.

isFailOnMissingSearch() - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Whether to fail if there is no result recorded for a search, or whether to simply return no results.

isFetchLatestVersions() - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Convenience method to test whether the latest version of stateful entities is required.

isFirstPresetDefaultValue() - Method in class com.genologics.ri.configuration.Field

Checks if the first preset value is the default.

isLocked() - Method in class com.genologics.ri.stepconfiguration.LockableSetting

Gets whether this setting is locked by the master step.

isNotFound() - Method in exception org.cruk.clarity.api.ClarityException

Convenience method to test whether this exception is because something is not found.

isPublished() - Method in class com.genologics.ri.file.ClarityFile

This element specifies whether the file is displayed in LabLink.

isRecordSearchesWithoutResults() - Method in class org.cruk.clarity.api.record.ClarityAPIRecordingAspect

Whether to record a search that returns no results.

isRemoveWorkingFlag() - Method in class com.genologics.ri.processtype.ProcessInput

Deprecated.

This property is no longer supported.

isRequired() - Method in class com.genologics.ri.configuration.Field

Checks if this field is required.

isRunProgramPerEvent() - Method in class com.genologics.ri.automation.Automation

Checks if the program should run per event.

isRunProgramPerEvent() - Method in class com.genologics.ri.processtype.Parameter

Deprecated.

This property is no longer supported.

isShared() - Method in class com.genologics.ri.processexecution.ExecutableInputOutputMap

Checks if the output is shared among multiple inputs.

isShowInLablink() - Method in class com.genologics.ri.configuration.Field

Checks if this field should be shown in Lablink.

isShowInTables() - Method in class com.genologics.ri.configuration.Field

Checks if this field should be shown in tables.

isStateful(Class<?>) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Test whether entities of a class are stateful.

isStateful(Object) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Test whether an entity is stateful.

isStateful(Collection<?>) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Test whether a collection of entities is stateful.

isTube() - Method in class com.genologics.ri.containertype.ContainerType

Checks if this container type represents a tube (single well container).

isWorkingFlag() - Method in class com.genologics.ri.artifact.Artifact

Checks if this artifact is in a working state.

iterator() - Method in interface com.genologics.ri.Batch

Returns an iterator over the items in this batch.

J

JaxbMarshallingTool - Class in org.cruk.clarity.api.jaxb

Tool to help debugging: a short cut for marshalling an object to a string.

JaxbMarshallingTool() - Constructor for class org.cruk.clarity.api.jaxb.JaxbMarshallingTool

Constructor.

JaxbMarshallingTool(Marshaller) - Constructor for class org.cruk.clarity.api.jaxb.JaxbMarshallingTool

Constructor with marshaller.

JaxbUnmarshallingAspect - Class in org.cruk.clarity.api.jaxb

Aspect that wraps the unmarshalling of responses from the Clarity API.

JaxbUnmarshallingAspect() - Constructor for class org.cruk.clarity.api.jaxb.JaxbUnmarshallingAspect

K

keyFromLocatable(Locatable) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Extract the cache key value from the given object's URI.

keyFromUri(String) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Extract the cache key value from the given URI string.

keyFromUri(URI) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Extract the cache key value from the given URI.

L

lab - Variable in class com.genologics.ri.researcher.Researcher

Link to the researcher's lab.

Lab - Class in com.genologics.ri.lab

The detailed representation of a lab.

Lab() - Constructor for class com.genologics.ri.lab.Lab

Constructs a new Lab instance.

Lab(URI) - Constructor for class com.genologics.ri.lab.Lab

Constructs a new Lab instance with the specified URI.

Lab(URI, String) - Constructor for class com.genologics.ri.lab.Lab

Constructs a new Lab instance with the specified URI and name.

LAB_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The lab namespace.

LabLink - Class in com.genologics.ri.lab

Lab-link is a child element type of labs and provides a URI linking to the detailed representation of a lab.

LabLink - Class in com.genologics.ri.researcher

Lab is a child element of researcher and provides a URI linking to the detailed representation of the lab for the researcher.

LabLink() - Constructor for class com.genologics.ri.lab.LabLink

Constructs a new LabLink instance.

LabLink() - Constructor for class com.genologics.ri.researcher.LabLink

Default constructor.

LabLink(Lab) - Constructor for class com.genologics.ri.lab.LabLink

Constructs a new LabLink instance from a Lab object.

LabLink(Linkable<Lab>) - Constructor for class com.genologics.ri.lab.LabLink

Constructs a new LabLink instance from a linkable object.

LabLink(Linkable<Lab>) - Constructor for class com.genologics.ri.researcher.LabLink

Constructor from a linkable object.

LabLink(URI) - Constructor for class com.genologics.ri.lab.LabLink

Constructs a new LabLink instance with the specified URI.

LabLink(URI) - Constructor for class com.genologics.ri.researcher.LabLink

Constructor with URI.

LabLink(URI, String) - Constructor for class com.genologics.ri.lab.LabLink

Constructs a new LabLink instance with the specified URI and name.

LABLINK_ROLE - Static variable in class com.genologics.ri.researcher.Role

The name for the collaborator role.

labs - Variable in class com.genologics.ri.lab.Labs

The list of lab links.

Labs - Class in com.genologics.ri.lab

The representation of a list of lab links.

Labs() - Constructor for class com.genologics.ri.lab.Labs

Constructs a new Labs instance.

largeShort - Variable in class org.cruk.clarity.api.cache.spring.ClarityClientCacheConfiguration

Cache configuration for large heap (1800 entries) with short expiry (5 minutes).

lastModified() - Method in class org.cruk.clarity.api.impl.URLInputStreamResource

Get the last modified time of the resource.

lastModifiedBy - Variable in class com.genologics.ri.reagentlot.ReagentLot

Link to the researcher who last modified this reagent lot.

lastModifiedDate - Variable in class com.genologics.ri.reagentlot.ReagentLot

The date when this reagent lot was last modified.

lastName - Variable in class com.genologics.ri.process.Technician

The last name of the technician.

lastName - Variable in class com.genologics.ri.processtemplate.Technician

The last name of the technician.

lastName - Variable in class com.genologics.ri.researcher.Researcher

The researcher's last name.

lastName - Variable in class com.genologics.ri.researcher.ResearcherLink

The researcher's last name.

lastName - Variable in class com.genologics.ri.role.ResearcherLink

The last name of the researcher.

lastName - Variable in class com.genologics.ri.sample.Submitter

The last name of the submitter.

lastName - Variable in class com.genologics.ri.step.Technician

The last name of the technician.

lastName - Variable in class com.genologics.ri.step.UserLink

The last name of the user.

LATEST - Enum constant in enum class org.cruk.clarity.api.cache.CacheStatefulBehaviour

The entity is fetched if the version in the cache is older than the version in the URI.

LATEST - Enum constant in enum class org.cruk.clarity.api.StatefulOverride

Fetch the latest version of the stateful entity.

latestVersionsResetAspect - Variable in class org.cruk.clarity.api.cache.ClarityAPICache

The aspect that resets API version behaviour.

LatestVersionsResetAspect - Class in org.cruk.clarity.api.impl

Aspect to ensure that the API will not fetch the latest versions of stateful entities on the next call.

LatestVersionsResetAspect() - Constructor for class org.cruk.clarity.api.impl.LatestVersionsResetAspect

Constructor.

LatestVersionsResetAspect(ClarityAPIInternal) - Constructor for class org.cruk.clarity.api.impl.LatestVersionsResetAspect

Constructor with API reference.

LEAVE - Enum constant in enum class com.genologics.ri.step.ActionType

Leave the artifact as is.

LimsEntity<E extends LimsEntity<E>> - Interface in com.genologics.ri

Interface for all objects that are real LIMS entities (i.e. not links or other references).

LimsEntityLink<E extends LimsEntity<E>> - Interface in com.genologics.ri

Interface for links to LimsEntity objects.

LimsEntityLinkable<E extends LimsEntity<E>> - Interface in com.genologics.ri

Interface for entities and links to entities that are identifiable in the system (i.e. have a LIMS id).

LimsEntityLinkBase<E extends LimsEntity<E>> - Class in com.genologics.ri

Helper base class for LimsEntityLink implementations extending from LimsLinkBase.

LimsEntityLinkBase() - Constructor for class com.genologics.ri.LimsEntityLinkBase

Protected constructor.

limsid - Variable in class com.genologics.ri.artifact.Artifact

The LIMS id of the artifact.

limsid - Variable in class com.genologics.ri.artifact.ArtifactLink

The LIMS id of this artifact.

limsid - Variable in class com.genologics.ri.artifact.DemuxArtifactSample

The LIMS id of this demux artifact sample.

limsid - Variable in class com.genologics.ri.artifact.ParentProcessLink

The LIMS id of this parent process.

limsid - Variable in class com.genologics.ri.artifact.SampleLink

The LIMS id of this sample.

limsid - Variable in class com.genologics.ri.container.Container

The LIMS id of the container.

limsid - Variable in class com.genologics.ri.container.ContainerLink

The LIMS id of the container.

limsid - Variable in class com.genologics.ri.container.Placement

The LIMS id of the artifact.

limsid - Variable in class com.genologics.ri.ContainerLink

The LIMS id of the container.

limsid - Variable in class com.genologics.ri.file.ClarityFile

The LIMS id of the file.

limsid - Variable in class com.genologics.ri.file.FileLink

The LIMS id of the file.

limsid - Variable in class com.genologics.ri.instrument.Instrument

The LIMS id of this instrument as provided by the server.

limsid - Variable in class com.genologics.ri.process.ArtifactLink

The LIMS id of the artifact.

limsid - Variable in class com.genologics.ri.process.ClarityProcess

The LIMS id of the process.

limsid - Variable in class com.genologics.ri.process.ParentProcessLink

The LIMS id of the parent process.

limsid - Variable in class com.genologics.ri.process.ProcessLink

The LIMS id of the process.

limsid - Variable in class com.genologics.ri.project.Project

The LIMS id of the project.

limsid - Variable in class com.genologics.ri.project.ProjectLink

The LIMS id of the project.

limsid - Variable in class com.genologics.ri.queue.ArtifactLink

The LIMS id of the artifact.

limsid - Variable in class com.genologics.ri.reagentlot.ReagentLot

The LIMS id of this reagent lot.

limsid - Variable in class com.genologics.ri.reagentlot.ReagentLotLink

The LIMS id of the reagent lot.

limsid - Variable in class com.genologics.ri.sample.ArtifactLink

The LIMS id of the artifact.

limsid - Variable in class com.genologics.ri.sample.ProjectLink

The LIMS id of the project.

limsid - Variable in class com.genologics.ri.sample.SampleBase

The LIMS id of this sample.

limsid - Variable in class com.genologics.ri.sample.SampleLink

The LIMS id of the sample.

limsid - Variable in class com.genologics.ri.step.ArtifactLink

LIMS id of the artifact.

limsid - Variable in class com.genologics.ri.step.ProcessStep

The LIMS id of the step.

limsid - Variable in class com.genologics.ri.step.ReagentLotLink

The LIMS id of the reagent lot.

limsid - Variable in class com.genologics.ri.step.SharedResultFile

The LIMS id of the artifact.

limsIdFromObject(Object) - Static method in class org.cruk.clarity.api.record.ClarityAPIRecordingAspect

Shared method to get the LIMS id from an object, which must at least implement Locatable.

limsIdFromUri(Locatable) - Static method in class com.genologics.ri.Link

Extract the LIMS identifier from the URI of a Locatable object.

limsIdFromUri(Class<?>, String) - Static method in class org.cruk.clarity.api.record.ClarityAPIRecordingAspect

Shared method to get the LIMS id out of a URI, public to let the playback aspect use it.

limsIdFromUri(URI) - Static method in class com.genologics.ri.Link

Extract the LIMS identifier from a URI.

limsIdToUri(String, Class<E>) - Method in interface org.cruk.clarity.api.ClarityAPI

Convert the given LIMS id to a full URI for that entity.

limsIdToUri(String, Class<E>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Convert the given LIMS id to a full URI for that entity.

limsIdToUri(String, String, Class<E>) - Method in interface org.cruk.clarity.api.ClarityAPI

Convert the given LIMS ids to a full URI for that entity.

limsIdToUri(String, String, Class<E>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Convert the given LIMS ids to a full URI for that entity.

LimsLink<E extends Locatable> - Interface in com.genologics.ri

Interface for classes that are links to real LIMS objects.

LimsLinkAdapter - Class in org.cruk.clarity.api.search.internal

JAXB adapter for dealing with LimsLink objects.

LimsLinkAdapter() - Constructor for class org.cruk.clarity.api.search.internal.LimsLinkAdapter

Constructor.

LimsLinkBase<E extends Locatable> - Class in com.genologics.ri

Helper base class for LimsLink implementations that implements LimsLinkBase.hashCode() and LimsLinkBase.equals(Object) to consider links that point to the same entities as equivalent.

LimsLinkBase() - Constructor for class com.genologics.ri.LimsLinkBase

Protected constructor.

Link - Class in com.genologics.ri

A link provides a URI linking to an additional resource.

Link() - Constructor for class com.genologics.ri.Link

Default constructor.

Link(Linkable<?>) - Constructor for class com.genologics.ri.Link

Constructor from a linkable object.

Link(String) - Constructor for class com.genologics.ri.Link

Constructor with relative part.

Link(String, URI) - Constructor for class com.genologics.ri.Link

Constructor with relative part and URI.

Linkable<E extends Locatable> - Interface in com.genologics.ri

Marker interface that indicates a locatable object can be linked to.

linkList - Variable in class com.genologics.ri.Links

The list of links.

links - Variable in class com.genologics.ri.Index

The list of links in this index.

Links - Class in com.genologics.ri

The representation of a list of resource links.

Links() - Constructor for class com.genologics.ri.Links

Default constructor.

Links(int) - Constructor for class com.genologics.ri.Links

Constructor with initial capacity.

Links(Links) - Constructor for class com.genologics.ri.Links

Copy constructor.

Links(Collection<Link>) - Constructor for class com.genologics.ri.Links

Constructor from a collection of links.

listAll(Class<E>) - Method in interface org.cruk.clarity.api.ClarityAPI

List all the objects of the given entity class.

listAll(Class<E>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

List all the objects of the given entity class.

listQueue(Linkable<ProtocolStep>) - Method in interface org.cruk.clarity.api.ClarityAPI

List the artifacts in the queue for the given protocol step.

listQueue(Linkable<ProtocolStep>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

List the artifacts in the queue for the given protocol step.

listQueue(Linkable<ProtocolStep>, Map<String, ?>) - Method in interface org.cruk.clarity.api.ClarityAPI

List the artifacts in the queue for the given protocol step, additionally filtering using the parameters available for the "queues" end point.

listQueue(Linkable<ProtocolStep>, Map<String, ?>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

List the artifacts in the queue for the given protocol step, additionally filtering using the parameters available for the "queues" end point.

listSome(Class<E>, int, int) - Method in interface org.cruk.clarity.api.ClarityAPI

List an arbitrary number of objects of the given entity class.

listSome(Class<E>, int, int) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

List an arbitrary number of objects of the given entity class.

load(LimsLink<E>) - Method in interface org.cruk.clarity.api.ClarityAPI

Load an entity using a link to that entity.

load(LimsLink<E>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Load an entity using a link to that entity.

load(String, Class<E>) - Method in interface org.cruk.clarity.api.ClarityAPI

Load an entity by its LIMS id.

load(String, Class<E>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Load an entity by its LIMS id.

load(String, String, Class<E>) - Method in interface org.cruk.clarity.api.ClarityAPI

Load an entity by its two required LIMS ids.

load(String, String, Class<E>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Load an entity by its two required LIMS ids.

loadAll(Collection<? extends LimsLink<E>>) - Method in interface org.cruk.clarity.api.ClarityAPI

Fetch a collection of LIMS entities given in the collection.

loadAll(Collection<? extends LimsLink<E>>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Fetch a collection of LIMS entities given in the collection.

loadAll(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Join point for the ClarityAPI.loadAll method.

loadById(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Join point for the ClarityAPI.load methods taking an id and a class.

loadByLink(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Join point for the ClarityAPI.load methods taking a LimsLink.

loadOrRetrieve(ProceedingJoinPoint, String, Class<?>) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Fetch an object from the cache or, if it's not yet been seen, from the API and store the result in the cache for future use.

Locatable - Interface in com.genologics.ri

Interface for LIMS objects that can be located via a URI.

location - Variable in class com.genologics.ri.artifact.Artifact

The location of the artifact.

location - Variable in class com.genologics.ri.processexecution.Output

The location of the output artifact.

location - Variable in class com.genologics.ri.queue.ArtifactLink

The location of the artifact.

location - Variable in class com.genologics.ri.sample.SampleCreation

The location where the sample will be created.

location - Variable in class com.genologics.ri.step.OutputPlacement

The location of the output artifact in a container.

Location - Class in com.genologics.ri

Location provides a URI linking to the detailed representation of a Container along with the well location within that Container.

Location() - Constructor for class com.genologics.ri.Location

Default constructor.

Location(LimsEntityLinkable<Container>, String) - Constructor for class com.genologics.ri.Location

Constructor with container and position.

Location(Linkable<Container>, String) - Constructor for class com.genologics.ri.Location

Constructor with container and position.

LockableSetting - Class in com.genologics.ri.stepconfiguration

A protocol step setting is considered locked if the Master Step has defined that setting.

LockableSetting() - Constructor for class com.genologics.ri.stepconfiguration.LockableSetting

Default constructor.

locked - Variable in class com.genologics.ri.stepconfiguration.GenericTypeLink

Indicates whether this generic type link is locked.

locked - Variable in class com.genologics.ri.stepconfiguration.LockableSetting

Indicates whether this setting is locked by the master step.

logger - Variable in class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Logger.

logger - Variable in class org.cruk.clarity.api.cache.ClarityAPICache

Logger.

logger - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

Logger.

logger - Variable in class org.cruk.clarity.api.impl.SavedQueryRunner

Logger.

LongTimestampAdapter - Class in com.genologics.ri.jaxb

Adapter for those dates that are exchanged with the API in the long timestamp format.

LongTimestampAdapter() - Constructor for class com.genologics.ri.jaxb.LongTimestampAdapter

Default constructor.

lotNumber - Variable in class com.genologics.ri.reagentlot.ReagentLot

The lot number identifier for this reagent lot.

M

major - Variable in class com.genologics.ri.version.Version

The major version number.

makeFullName(String, String) - Static method in class com.genologics.ri.researcher.Researcher

Convenience method for making the full name of the researcher.

makeUri(String, Class<E>, String) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Convert the given LIMS id to a full URI for that entity without creating a URI object.

makeUri(String, String, Class<E>, String) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Convert the given LIMS ids to a full URI for that entity without creating a URI object.

MANUAL - Enum constant in enum class com.genologics.ri.processtype.TriggerType

The trigger must be invoked manually.

MANUAL - Enum constant in enum class com.genologics.ri.stepconfiguration.TriggerType

Manual trigger that must be invoked by a user.

marshal(LimsLink<?>) - Method in class org.cruk.clarity.api.search.internal.LimsLinkAdapter

Converts a LimsLink object to an XML-compatible object during marshalling.

marshal(Object) - Method in class org.cruk.clarity.api.jaxb.JaxbMarshallingTool

Marshals the object into a string of XML.

marshal(URI) - Method in class com.genologics.ri.jaxb.URIAdapter

Convert the given URI into its string format.

marshal(Date) - Method in class com.genologics.ri.jaxb.AbstractDateAdapter

Convert the given date into the expected date format.

maxValue - Variable in class com.genologics.ri.configuration.Field

The maximum value for numeric fields.

mediumMedium - Variable in class org.cruk.clarity.api.cache.spring.ClarityClientCacheConfiguration

Cache configuration for medium heap (250 entries) with medium expiry (10 minutes).

mediumShort - Variable in class org.cruk.clarity.api.cache.spring.ClarityClientCacheConfiguration

Cache configuration for medium heap (250 entries) with short expiry (5 minutes).

merge(Search<E>) - Method in class org.cruk.clarity.api.search.Search

Merge the results of another search into this search's results.

message - Variable in class com.genologics.ri.exception.Exception

A textual summary of the error that occurred.

message - Variable in class com.genologics.ri.processtype.SharedResultFile

The message associated with this shared result file.

message - Variable in class com.genologics.ri.step.ProgramStatus

The message associated with the program status.

message - Variable in class com.genologics.ri.step.SharedResultFile

Error message associated with the shared result file.

message - Variable in class com.genologics.ri.stepconfiguration.SharedResultFile

The message associated with this shared result file.

minor - Variable in class com.genologics.ri.version.Version

The minor version number.

minValue - Variable in class com.genologics.ri.configuration.Field

The minimum value for numeric fields.

MissingUDFException - Exception in com.genologics.ri.userdefined

Exception thrown when a required user-defined field is not found.

MissingUDFException(String) - Constructor for exception com.genologics.ri.userdefined.MissingUDFException

Constructor with field name.

MissingUDFException(String, String) - Constructor for exception com.genologics.ri.userdefined.MissingUDFException

Constructor with field name and message.

N

name - Variable in class com.genologics.ri.artifact.Artifact

The name of the artifact.

name - Variable in class com.genologics.ri.artifact.ArtifactGroupLink

The name of this artifact group.

name - Variable in class com.genologics.ri.artifact.DemuxArtifact

The name of this demux artifact.

name - Variable in class com.genologics.ri.artifact.DemuxSourceArtifact

The name of this demux source artifact.

name - Variable in class com.genologics.ri.artifact.PoolStep

The name of this pool step.

name - Variable in class com.genologics.ri.artifact.ReagentLabel

The name of this reagent label.

name - Variable in class com.genologics.ri.artifact.WorkflowStage

The name of this workflow stage.

name - Variable in class com.genologics.ri.artifactgroup.ArtifactGroup

The name of the artifact group.

name - Variable in class com.genologics.ri.artifactgroup.ArtifactGroupLink

The name of the artifact group.

name - Variable in class com.genologics.ri.automation.Automation

The name of this automation.

name - Variable in class com.genologics.ri.automation.AutomationLink

The name of the automation.

name - Variable in class com.genologics.ri.automation.ProcessTypeLink

The name of the process type.

name - Variable in class com.genologics.ri.configuration.Field

The name of the field.

name - Variable in class com.genologics.ri.configuration.FieldLink

The name of the field.

name - Variable in class com.genologics.ri.configuration.Type

The name of this type.

name - Variable in class com.genologics.ri.configuration.TypeDefinition

The name of the type.

name - Variable in class com.genologics.ri.configuration.UdfConfigLink

The name of the field.

name - Variable in class com.genologics.ri.configuration.UdtConfigLink

The name of the type.

name - Variable in class com.genologics.ri.container.Container

The name of the container.

name - Variable in class com.genologics.ri.container.ContainerLink

The name of the container.

name - Variable in class com.genologics.ri.container.ContainerTypeLink

The name of the container type.

name - Variable in class com.genologics.ri.containertype.CalibrantWell

Deprecated.

The name of the calibrant well.

name - Variable in class com.genologics.ri.containertype.ContainerType

The name of the container type.

name - Variable in class com.genologics.ri.containertype.ContainerTypeLink

The name of the container type.

name - Variable in class com.genologics.ri.controltype.ControlType

The name of the control type.

name - Variable in class com.genologics.ri.controltype.ControlTypeLink

The name of the control type.

name - Variable in class com.genologics.ri.globaltoken.GlobalToken

The token name.

name - Variable in class com.genologics.ri.globaltoken.GlobalTokenLink

The token name.

name - Variable in class com.genologics.ri.instrument.Instrument

The instrument name.

name - Variable in class com.genologics.ri.instrument.InstrumentLink

The instrument name.

name - Variable in class com.genologics.ri.instrumenttype.InstrumentType

The instrument type name.

name - Variable in class com.genologics.ri.instrumenttype.InstrumentTypeLink

The instrument type name.

name - Variable in class com.genologics.ri.instrumenttype.InstrumentTypeProcessType

The process type name.

name - Variable in class com.genologics.ri.lab.Lab

The name of the lab.

name - Variable in class com.genologics.ri.lab.LabLink

The name of the lab.

name - Variable in class com.genologics.ri.permission.Permission

The permission name.

name - Variable in class com.genologics.ri.permission.PermissionLink

The permission name.

name - Variable in class com.genologics.ri.process.Parameter

The name of the parameter.

name - Variable in class com.genologics.ri.process.ProcessTypeLink

The name of the process type.

name - Variable in class com.genologics.ri.processexecution.Parameter

The name of the parameter.

name - Variable in class com.genologics.ri.processtemplate.Parameter

The name of the parameter.

name - Variable in class com.genologics.ri.processtemplate.ProcessTemplate

The name of this process template.

name - Variable in class com.genologics.ri.processtemplate.ProcessTemplateLink

The name of the process template.

name - Variable in class com.genologics.ri.processtemplate.ProcessTypeLink

The name of the process type.

name - Variable in class com.genologics.ri.processtype.ContainerTypeLink

The name of the container type.

name - Variable in class com.genologics.ri.processtype.ControlTypeLink

The name of the control type.

name - Variable in class com.genologics.ri.processtype.EppTrigger

The name of the EPP trigger.

name - Variable in class com.genologics.ri.processtype.Field

The name of the field.

name - Variable in class com.genologics.ri.processtype.Parameter

The name of the parameter.

name - Variable in class com.genologics.ri.processtype.ProcessType

The name of the process type.

name - Variable in class com.genologics.ri.processtype.ProcessTypeAttribute

The name of the attribute.

name - Variable in class com.genologics.ri.processtype.ProcessTypeLink

The name of the process type.

name - Variable in class com.genologics.ri.processtype.ReagentKitLink

The name of the reagent kit.

name - Variable in class com.genologics.ri.processtype.StepProperty

The name of the step property.

name - Variable in class com.genologics.ri.processtype.TypeDefinition

The name of the field.

name - Variable in class com.genologics.ri.project.Project

The name of the project.

name - Variable in class com.genologics.ri.project.ProjectLink

The name of the project.

name - Variable in class com.genologics.ri.property.PropertyLink

The name of the property.

name - Variable in class com.genologics.ri.protocolconfiguration.Protocol

The name of the protocol.

name - Variable in class com.genologics.ri.protocolconfiguration.ProtocolLink

The name of the protocol.

name - Variable in class com.genologics.ri.protocolconfiguration.ProtocolProperty

The name of the protocol property.

name - Variable in class com.genologics.ri.queue.Queue

The name of the queue.

name - Variable in class com.genologics.ri.reagentkit.ReagentKit

The name of the reagent kit.

name - Variable in class com.genologics.ri.reagentkit.ReagentKitLink

The name of the reagent kit.

name - Variable in class com.genologics.ri.reagentlot.ReagentKitLink

The name of the reagent kit.

name - Variable in class com.genologics.ri.reagentlot.ReagentLot

The name of this reagent lot.

name - Variable in class com.genologics.ri.reagentlot.ReagentLotLink

The name of the Reagent Lot.

name - Variable in class com.genologics.ri.reagenttype.Attribute

The name of the attribute.

name - Variable in class com.genologics.ri.reagenttype.ReagentType

The name of the reagent type.

name - Variable in class com.genologics.ri.reagenttype.ReagentTypeLink

The name of the reagent type.

name - Variable in class com.genologics.ri.reagenttype.SpecialType

The name of the special type.

name - Variable in class com.genologics.ri.researcher.Role

The user-facing name of the security role.

name - Variable in class com.genologics.ri.role.PermissionLink

The name of the permission.

name - Variable in class com.genologics.ri.role.Role

The name of the role.

name - Variable in class com.genologics.ri.role.RoleLink

The name of the role.

name - Variable in class com.genologics.ri.sample.BioSource

Deprecated.

The name of the biosource.

name - Variable in class com.genologics.ri.sample.ControlTypeLink

The name of the control type.

name - Variable in class com.genologics.ri.sample.SampleBase

The name of the sample.

name - Variable in class com.genologics.ri.savedquery.SavedQuery

The name of the saved query.

name - Variable in class com.genologics.ri.savedquery.SavedQueryLink

The name of the saved query.

name - Variable in class com.genologics.ri.stage.Stage

The name of the stage.

name - Variable in class com.genologics.ri.step.AvailableProgram

Name of the available program.

name - Variable in class com.genologics.ri.step.InstrumentLink

Name of the instrument.

name - Variable in class com.genologics.ri.step.PooledInputs

The name of this pool.

name - Variable in class com.genologics.ri.step.ReagentLabel

The name of the reagent label.

name - Variable in class com.genologics.ri.step.SharedResultFile

The name of the artifact.

name - Variable in class com.genologics.ri.stepconfiguration.ControlTypeLink

The name of the control type.

name - Variable in class com.genologics.ri.stepconfiguration.EppTrigger

The name of the EPP trigger.

name - Variable in class com.genologics.ri.stepconfiguration.Field

The name of the field.

name - Variable in class com.genologics.ri.stepconfiguration.NextStep

The name of the next step.

name - Variable in class com.genologics.ri.stepconfiguration.ProcessTypeLink

The name of the process type.

name - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

The name of the protocol step.

name - Variable in class com.genologics.ri.stepconfiguration.ReagentKitLink

The name of the reagent kit.

name - Variable in class com.genologics.ri.stepconfiguration.StepProperty

The name of the step property.

name - Variable in class com.genologics.ri.userdefined.UDF

The name of the user-defined field.

name - Variable in class com.genologics.ri.userdefined.UDT

The name of the user-defined type.

name - Variable in class com.genologics.ri.workflowconfiguration.ProtocolLink

The name of the protocol.

name - Variable in class com.genologics.ri.workflowconfiguration.StageLink

The name of the stage.

name - Variable in class com.genologics.ri.workflowconfiguration.Workflow

The name of the workflow.

name - Variable in class com.genologics.ri.workflowconfiguration.WorkflowLink

The name of the workflow.

Namespaces - Class in com.genologics.ri

Static list of all the namespaces in the Genologics API.

NEW - Enum constant in enum class com.genologics.ri.container.ContainerState

The container state when the container is newly created.

newInputOutputMap() - Method in class com.genologics.ri.processexecution.ExecutableProcess

Creates and adds a new input-output map.

NEXT_STEPS - Enum constant in enum class com.genologics.ri.step.ProcessState

The step state when the step is in the next steps stage.

NextAction - Class in com.genologics.ri.step

Sample next action or step.

NextAction() - Constructor for class com.genologics.ri.step.NextAction

Default constructor.

NextAction(Linkable<Artifact>) - Constructor for class com.genologics.ri.step.NextAction

Constructor from a linkable artifact.

NextAction(Linkable<Artifact>, ActionType) - Constructor for class com.genologics.ri.step.NextAction

Constructor from a linkable artifact and action.

NextAction(Linkable<Artifact>, ActionType, Linkable<ProtocolStep>) - Constructor for class com.genologics.ri.step.NextAction

Constructor from a linkable artifact, action, and next step.

NextAction(URI) - Constructor for class com.genologics.ri.step.NextAction

Constructor with artifact URI.

NextAction(URI, ActionType) - Constructor for class com.genologics.ri.step.NextAction

Constructor with artifact URI and action.

NextAction(URI, ActionType, Linkable<ProtocolStep>) - Constructor for class com.genologics.ri.step.NextAction

Constructor with artifact URI, action, and next step.

nextActions - Variable in class com.genologics.ri.step.Actions

List of next actions to be performed.

nextPage - Variable in class com.genologics.ri.artifact.Artifacts

The next page of results.

nextPage - Variable in class com.genologics.ri.artifactgroup.ArtifactGroups

Link to the next page of results.

nextPage - Variable in class com.genologics.ri.automation.Automations

The link to the next page of results.

nextPage - Variable in class com.genologics.ri.configuration.Udfs

The link to the next page of results.

nextPage - Variable in class com.genologics.ri.configuration.Udts

The link to the next page of results.

nextPage - Variable in class com.genologics.ri.container.Containers

The link to the next page of results.

nextPage - Variable in class com.genologics.ri.containertype.ContainerTypes

The link to the next page of results.

nextPage - Variable in class com.genologics.ri.file.ClarityFiles

A link to the next page of results, if available.

nextPage - Variable in class com.genologics.ri.globaltoken.GlobalTokens

The next page of results.

nextPage - Variable in class com.genologics.ri.instrument.Instruments

The next page reference.

nextPage - Variable in class com.genologics.ri.instrumenttype.InstrumentTypes

The next page reference.

nextPage - Variable in class com.genologics.ri.lab.Labs

The next page of results.

nextPage - Variable in class com.genologics.ri.process.ClarityProcesses

The link to the next page of results.

nextPage - Variable in class com.genologics.ri.processtemplate.ProcessTemplates

The link to the next page of results.

nextPage - Variable in class com.genologics.ri.processtype.ProcessTypes

Link to the next page of results.

nextPage - Variable in class com.genologics.ri.project.Projects

The next page of results.

nextPage - Variable in class com.genologics.ri.property.Properties

The link to the next page of results.

nextPage - Variable in class com.genologics.ri.queue.Queue

The link to the next page of results.

nextPage - Variable in class com.genologics.ri.reagentkit.ReagentKits

The link to the next page of results.

nextPage - Variable in class com.genologics.ri.reagentlot.ReagentLots

Link to the next page of results, if available.

nextPage - Variable in class com.genologics.ri.reagenttype.ReagentTypes

Link to the next page of results.

nextPage - Variable in class com.genologics.ri.researcher.Researchers

Link to the next page of results.

nextPage - Variable in class com.genologics.ri.sample.Samples

The next page link for pagination.

nextPage - Variable in class com.genologics.ri.savedquery.SavedQueries

The link to the next page of results.

NextStep - Class in com.genologics.ri.stepconfiguration

List of step transitions including the URI allowing access to the specific next step

NextStep() - Constructor for class com.genologics.ri.stepconfiguration.NextStep

Default constructor.

NextStep(ProtocolStep) - Constructor for class com.genologics.ri.stepconfiguration.NextStep

Constructor from a protocol step entity.

NextStep(URI) - Constructor for class com.genologics.ri.stepconfiguration.NextStep

Constructor with next step URI.

NextStep(URI, String) - Constructor for class com.genologics.ri.stepconfiguration.NextStep

Constructor with next step URI and name.

NextStep(URI, String, Integer) - Constructor for class com.genologics.ri.stepconfiguration.NextStep

Constructor with next step URI, name, and sequence.

NEXTSTEP - Enum constant in enum class com.genologics.ri.step.ActionType

Move to the next step.

nextStepUri - Variable in class com.genologics.ri.stepconfiguration.NextStep

The URI of the next step.

NO_STATE_VALUE - Static variable in class org.cruk.clarity.api.cache.ClarityAPICache

The version to use for objects and requests that give no state.

NoRecordingException - Exception in org.cruk.clarity.api.playback

Exception thrown when an entity or search is requested that has no recording in the playback message directory.

NoRecordingException(String) - Constructor for exception org.cruk.clarity.api.playback.NoRecordingException

Constructor.

notes - Variable in class com.genologics.ri.reagentlot.ReagentLot

Additional notes about this reagent lot.

numberOfOutputs - Variable in class com.genologics.ri.processtype.ProcessOutput

The number of outputs to generate (only applies if variabilityType is FIXED).

NUMERIC - Enum constant in enum class com.genologics.ri.configuration.FieldType

Numeric field type.

O

ObjectFactory - Class in com.genologics.ri.artifact

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.artifact package.

ObjectFactory - Class in com.genologics.ri.artifactgroup

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.artifactgroup package.

ObjectFactory - Class in com.genologics.ri.automation

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.automation package.

ObjectFactory - Class in com.genologics.ri.configuration

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.configuration package.

ObjectFactory - Class in com.genologics.ri.container

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.container package.

ObjectFactory - Class in com.genologics.ri.containertype

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.containertype package.

ObjectFactory - Class in com.genologics.ri.controltype

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.controltype package.

ObjectFactory - Class in com.genologics.ri.exception

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.exception package.

ObjectFactory - Class in com.genologics.ri.file

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.file package.

ObjectFactory - Class in com.genologics.ri.globaltoken

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.globaltoken package.

ObjectFactory - Class in com.genologics.ri.instrument

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.instrument package.

ObjectFactory - Class in com.genologics.ri.instrumenttype

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.instrumenttype package.

ObjectFactory - Class in com.genologics.ri.lab

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.lab package.

ObjectFactory - Class in com.genologics.ri

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri package.

ObjectFactory - Class in com.genologics.ri.permission

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.permission package.

ObjectFactory - Class in com.genologics.ri.process

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.process package.

ObjectFactory - Class in com.genologics.ri.processexecution

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.processexecution package.

ObjectFactory - Class in com.genologics.ri.processtemplate

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.processtemplate package.

ObjectFactory - Class in com.genologics.ri.processtype

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.processtype package.

ObjectFactory - Class in com.genologics.ri.project

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.project package.

ObjectFactory - Class in com.genologics.ri.property

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.property package.

ObjectFactory - Class in com.genologics.ri.protocolconfiguration

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.protocolconfiguration package.

ObjectFactory - Class in com.genologics.ri.queue

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.queue package.

ObjectFactory - Class in com.genologics.ri.reagentkit

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.reagentkit package.

ObjectFactory - Class in com.genologics.ri.reagentlot

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.reagentlot package.

ObjectFactory - Class in com.genologics.ri.reagenttype

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.reagenttype package.

ObjectFactory - Class in com.genologics.ri.researcher

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.researcher package.

ObjectFactory - Class in com.genologics.ri.role

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.role package.

ObjectFactory - Class in com.genologics.ri.routing

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.routing package.

ObjectFactory - Class in com.genologics.ri.sample

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.sample package.

ObjectFactory - Class in com.genologics.ri.savedquery

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.savedquery package.

ObjectFactory - Class in com.genologics.ri.stage

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.stage package.

ObjectFactory - Class in com.genologics.ri.step

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.step package.

ObjectFactory - Class in com.genologics.ri.stepconfiguration

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.stepconfiguration package.

ObjectFactory - Class in com.genologics.ri.userdefined

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.userdefined package.

ObjectFactory - Class in com.genologics.ri.version

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.version package.

ObjectFactory - Class in com.genologics.ri.workflowconfiguration

Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.workflowconfiguration package.

ObjectFactory() - Constructor for class com.genologics.ri.artifact.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.artifact

ObjectFactory() - Constructor for class com.genologics.ri.artifactgroup.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.artifactgroup

ObjectFactory() - Constructor for class com.genologics.ri.automation.ObjectFactory

Default constructor.

ObjectFactory() - Constructor for class com.genologics.ri.configuration.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.configuration.

ObjectFactory() - Constructor for class com.genologics.ri.container.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.container.

ObjectFactory() - Constructor for class com.genologics.ri.containertype.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.containertype

ObjectFactory() - Constructor for class com.genologics.ri.controltype.ObjectFactory

Creates a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.controltype

ObjectFactory() - Constructor for class com.genologics.ri.exception.ObjectFactory

Creates a new ObjectFactory that can be used to create new instances of schema-derived classes for package: com.genologics.ri.exception.

ObjectFactory() - Constructor for class com.genologics.ri.file.ObjectFactory

Creates a new ObjectFactory that can be used to create new instances of schema-derived classes for package: com.genologics.ri.file.

ObjectFactory() - Constructor for class com.genologics.ri.globaltoken.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.globaltoken

ObjectFactory() - Constructor for class com.genologics.ri.instrument.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.instrument

ObjectFactory() - Constructor for class com.genologics.ri.instrumenttype.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.instrumenttype

ObjectFactory() - Constructor for class com.genologics.ri.lab.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.lab

ObjectFactory() - Constructor for class com.genologics.ri.ObjectFactory

Constructor.

ObjectFactory() - Constructor for class com.genologics.ri.permission.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.permission

ObjectFactory() - Constructor for class com.genologics.ri.process.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.process

ObjectFactory() - Constructor for class com.genologics.ri.processexecution.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.processexecution

ObjectFactory() - Constructor for class com.genologics.ri.processtemplate.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.processtemplate

ObjectFactory() - Constructor for class com.genologics.ri.processtype.ObjectFactory

Creates a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.processtype.

ObjectFactory() - Constructor for class com.genologics.ri.project.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.project

ObjectFactory() - Constructor for class com.genologics.ri.property.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.property

ObjectFactory() - Constructor for class com.genologics.ri.protocolconfiguration.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.protocolconfiguration

ObjectFactory() - Constructor for class com.genologics.ri.queue.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.queue

ObjectFactory() - Constructor for class com.genologics.ri.reagentkit.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.reagentkit

ObjectFactory() - Constructor for class com.genologics.ri.reagentlot.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.reagentlot

ObjectFactory() - Constructor for class com.genologics.ri.reagenttype.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.reagenttype

ObjectFactory() - Constructor for class com.genologics.ri.researcher.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.researcher

ObjectFactory() - Constructor for class com.genologics.ri.role.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.role

ObjectFactory() - Constructor for class com.genologics.ri.routing.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.routing

ObjectFactory() - Constructor for class com.genologics.ri.sample.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.sample

ObjectFactory() - Constructor for class com.genologics.ri.savedquery.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.savedquery

ObjectFactory() - Constructor for class com.genologics.ri.stage.ObjectFactory

Creates a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.stage.

ObjectFactory() - Constructor for class com.genologics.ri.step.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.step

ObjectFactory() - Constructor for class com.genologics.ri.stepconfiguration.ObjectFactory

Creates a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.stepconfiguration.

ObjectFactory() - Constructor for class com.genologics.ri.userdefined.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.userdefined

ObjectFactory() - Constructor for class com.genologics.ri.version.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.version

ObjectFactory() - Constructor for class com.genologics.ri.workflowconfiguration.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri.workflowconfiguration

objectUnmarshalled(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.jaxb.JaxbUnmarshallingAspect

Join point that replaces the JAXBElement object with the real object it contains, then tests whether the reply object is an error and, if so, throws a Java exception.

occupiedWells - Variable in class com.genologics.ri.container.Container

The number of occupied wells in the container.

offset - Variable in class com.genologics.ri.containertype.Dimension

The offset applied to the first element in this dimension.

OK - Enum constant in enum class com.genologics.ri.step.Status

The step completed successfully.

openDate - Variable in class com.genologics.ri.project.Project

The date the project was opened.

org.cruk.clarity.api - module org.cruk.clarity.api

The Clarity Java client for Clarity 6+.

org.cruk.clarity.api - package org.cruk.clarity.api

The main public package of the Clarity API.

org.cruk.clarity.api.automation - package org.cruk.clarity.api.automation

Tools to help move steps through Clarity using the API that allows processes to be run as if they are done through the browser, rather than the ExecutableProcess mechanism.

org.cruk.clarity.api.automation.impl - package org.cruk.clarity.api.automation.impl

Implementation of the automation service.

org.cruk.clarity.api.cache - module org.cruk.clarity.api.cache

The Clarity Java client cache for Clarity 6+.

org.cruk.clarity.api.cache - package org.cruk.clarity.api.cache

Package supporting caching of Clarity entities in memory (or, if so configured, on disk) to reduce the amount of traffic being sent to and from the REST API.

org.cruk.clarity.api.cache.spring - package org.cruk.clarity.api.cache.spring

Spring configuration for the Clarity API Client cache.

org.cruk.clarity.api.debugging - package org.cruk.clarity.api.debugging

Aspects and beans to aid with tracking the exchanges with the Clarity API for debugging purposes.

org.cruk.clarity.api.filestore - package org.cruk.clarity.api.filestore

Top level package for SFTP file store providers for the API.

org.cruk.clarity.api.http - package org.cruk.clarity.api.http

Classes specific to the REST template operation.

org.cruk.clarity.api.impl - package org.cruk.clarity.api.impl

Concrete implementation classes of the Clarity API.

org.cruk.clarity.api.jaxb - package org.cruk.clarity.api.jaxb

Classes to aid the JAXB object mapping process.

org.cruk.clarity.api.playback - package org.cruk.clarity.api.playback

The classes necessary to replay server calls from entity XML files on disk.

org.cruk.clarity.api.playback.spring - package org.cruk.clarity.api.playback.spring

Spring configuration for Clarity API playback.

org.cruk.clarity.api.record - package org.cruk.clarity.api.record

The classes necessary to record entities returned from a Clarity server to XML files on disk.

org.cruk.clarity.api.record.spring - package org.cruk.clarity.api.record.spring

Spring configuration for Clarity API recording.

org.cruk.clarity.api.recorder - module org.cruk.clarity.api.recorder

The Clarity Java client recorder for Clarity 6+.

org.cruk.clarity.api.search - package org.cruk.clarity.api.search

Classes supporting the recording of searches for record and playback.

org.cruk.clarity.api.search.internal - package org.cruk.clarity.api.search.internal

Internal classes for the implementation of storing and retrieving searches.

org.cruk.clarity.api.spring - package org.cruk.clarity.api.spring

Spring configuration for the Clarity API Client.

originalLocation - Variable in class com.genologics.ri.file.ClarityFile

The original name and location of the file before it was imported into the system.

originalName - Variable in class com.genologics.ri.file.ClarityFile

The original name of the file before it was imported into the system.

output - Variable in class com.genologics.ri.process.InputOutputMap

The output artifact link.

output - Variable in class com.genologics.ri.processexecution.ExecutableInputOutputMap

The output artifact.

output - Variable in class com.genologics.ri.step.InputOutputMap

The output artifact link.

Output - Class in com.genologics.ri.processexecution

The output element provides information about the Artifacts that will be created by the Process.

Output - Class in com.genologics.ri.step

Provides a URI linking to the output artifact and reagent label.

Output() - Constructor for class com.genologics.ri.processexecution.Output

Default constructor.

Output() - Constructor for class com.genologics.ri.step.Output

Default constructor.

Output(OutputType) - Constructor for class com.genologics.ri.processexecution.Output

Constructor with output type.

Output(OutputType, LimsEntityLinkable<Container>, String) - Constructor for class com.genologics.ri.processexecution.Output

Constructor with output type, container, and position.

Output(LimsLink<Artifact>) - Constructor for class com.genologics.ri.step.Output

Constructor from a LIMS link.

Output(URI) - Constructor for class com.genologics.ri.step.Output

Constructor with artifact URI.

OutputArrangement - Class in com.genologics.ri.step

Provides a URI linking to the output container and Tube Rack arrangement.

OutputArrangement() - Constructor for class com.genologics.ri.step.OutputArrangement

Default constructor.

OutputArrangement(URI) - Constructor for class com.genologics.ri.step.OutputArrangement

Constructor with URI.

outputArrangements - Variable in class com.genologics.ri.step.Arrangements

List of output arrangements.

outputGenerationType - Variable in class com.genologics.ri.process.ArtifactLink

The output generation type of the artifact.

outputGenerationType - Variable in class com.genologics.ri.processtype.ProcessOutput

Specifies how the outputs are generated in relation to the inputs.

outputGenerationType - Variable in class com.genologics.ri.step.ArtifactLink

The output generation type.

OutputGenerationType - Enum Class in com.genologics.ri.process

The output generation type enumeration.

OutputGenerationType - Enum Class in com.genologics.ri.processtype

Enumeration of output generation types for process outputs.

OutputGenerationType - Enum Class in com.genologics.ri.step

Enumeration of output generation types for step artifacts.

outputName - Variable in class com.genologics.ri.processtype.ProcessOutput

Pattern for specifying how the output name is generated.

OutputPlacement - Class in com.genologics.ri.step

Provides a URI linking to the output artifact and container placement.

OutputPlacement() - Constructor for class com.genologics.ri.step.OutputPlacement

Default constructor.

OutputPlacement(Linkable<Artifact>) - Constructor for class com.genologics.ri.step.OutputPlacement

Constructor with artifact.

OutputPlacement(Linkable<Artifact>, LimsEntityLinkable<Container>, String) - Constructor for class com.genologics.ri.step.OutputPlacement

Constructor with artifact, container and well position.

OutputPlacement(Linkable<Artifact>, Linkable<Container>, String) - Constructor for class com.genologics.ri.step.OutputPlacement

Constructor with artifact, container and well position.

outputPlacements - Variable in class com.genologics.ri.step.Placements

The list of output placements.

outputReagents - Variable in class com.genologics.ri.step.Reagents

List of output reagents.

outputType - Variable in class com.genologics.ri.artifact.Artifact

The output type of the artifact.

outputType - Variable in class com.genologics.ri.process.ArtifactLink

The output type of the artifact.

OutputType - Enum Class in com.genologics.ri.artifact

Enumeration of artifact output types.

outputUri - Variable in class com.genologics.ri.step.PooledInputs

The URI of the output artifact created from this pool.

overrideStateful(StatefulOverride) - Method in interface org.cruk.clarity.api.ClarityAPI

Forces the API to fetch stateful entities according to the rule given for the next API call only.

overrideStateful(StatefulOverride) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Forces the API to fetch stateful entities according to the rule given for the next API call only.

P

Page - Class in com.genologics.ri

The link to a page of additional content.

Page() - Constructor for class com.genologics.ri.Page

Default constructor.

PaginatedBatch<L> - Interface in com.genologics.ri

Interface for objects that hold paginated batches of links to entities.

parameter - Variable in class com.genologics.ri.process.ClarityProcess

The process parameter for external program integration.

parameter - Variable in class com.genologics.ri.processexecution.ExecutableProcess

The process parameter for external program integration.

parameter - Variable in class com.genologics.ri.processtemplate.ProcessTemplate

The process parameter for external program integration.

Parameter - Class in com.genologics.ri.process

The parameter is a child element of process that integrates the Process with the External Program Integration plug-in (EPP).

Parameter - Class in com.genologics.ri.processexecution

The parameter is a child element of process execution that integrates the Process with the External Program Integration plug-in (EPP).

Parameter - Class in com.genologics.ri.processtemplate

The parameter is a child element of process-template that integrates the Process this Process Template represents, with the External Program Integration plug-in (EPP).

Parameter - Class in com.genologics.ri.processtype

The parameter element integrates the process with the External Program Integration plug-in (EPP).

Parameter() - Constructor for class com.genologics.ri.process.Parameter

Default constructor.

Parameter() - Constructor for class com.genologics.ri.processexecution.Parameter

Default constructor.

Parameter() - Constructor for class com.genologics.ri.processtemplate.Parameter

Default constructor.

Parameter() - Constructor for class com.genologics.ri.processtype.Parameter

Parameter(String) - Constructor for class com.genologics.ri.process.Parameter

Constructor with name.

Parameter(String) - Constructor for class com.genologics.ri.processexecution.Parameter

Constructor with parameter name.

Parameter(String) - Constructor for class com.genologics.ri.processtemplate.Parameter

Constructor with name.

parameters - Variable in class com.genologics.ri.processtype.ProcessType

EPP parameters for this process type.

parentProcess - Variable in class com.genologics.ri.artifact.Artifact

The parent process that produced this artifact.

parentProcess - Variable in class com.genologics.ri.process.ArtifactLink

The parent process link.

ParentProcessLink - Class in com.genologics.ri.artifact

Parent-process is a child element of Artifact and provides a URI linking to the detailed representation of the process that produced the Artifact.

ParentProcessLink - Class in com.genologics.ri.process

Parent-process is a child element of Artifact and provides a URI linking to the Process that created the Artifact.

ParentProcessLink() - Constructor for class com.genologics.ri.artifact.ParentProcessLink

Default constructor.

ParentProcessLink() - Constructor for class com.genologics.ri.process.ParentProcessLink

Default constructor.

ParentProcessLink(LimsEntityLinkable<ClarityProcess>) - Constructor for class com.genologics.ri.artifact.ParentProcessLink

Constructor from a LimsEntityLinkable.

ParentProcessLink(LimsEntityLinkable<ClarityProcess>) - Constructor for class com.genologics.ri.process.ParentProcessLink

Constructor from a LIMS entity linkable object.

ParentProcessLink(Linkable<ClarityProcess>) - Constructor for class com.genologics.ri.artifact.ParentProcessLink

Constructor from a Linkable.

ParentProcessLink(Linkable<ClarityProcess>) - Constructor for class com.genologics.ri.process.ParentProcessLink

Constructor from a linkable object.

ParentProcessLink(URI) - Constructor for class com.genologics.ri.artifact.ParentProcessLink

Constructor taking a URI.

ParentProcessLink(URI) - Constructor for class com.genologics.ri.process.ParentProcessLink

Constructor with URI.

ParentProcessLink(URI, String) - Constructor for class com.genologics.ri.artifact.ParentProcessLink

Constructor taking a URI and LIMS id.

ParentProcessLink(URI, String) - Constructor for class com.genologics.ri.process.ParentProcessLink

Constructor with URI and LIMS id.

parentUri - Variable in class com.genologics.ri.configuration.Field

The URI of the parent field for hierarchical fields.

PASSED - Enum constant in enum class com.genologics.ri.artifact.QCFlag

Passed quality control.

PASSED - Enum constant in enum class com.genologics.ri.processexecution.QCFlag

QC check passed.

password - Variable in class com.genologics.ri.researcher.Credentials

The researcher's password.

PENDING - Enum constant in enum class com.genologics.ri.reagentlot.Status

The reagent lot is pending.

PENDING - Enum constant in enum class com.genologics.ri.workflowconfiguration.Status

Workflow is pending activation.

PER_ALL_INPUTS - Enum constant in enum class com.genologics.ri.process.OutputGenerationType

One output for all inputs.

PER_ALL_INPUTS - Enum constant in enum class com.genologics.ri.processtype.OutputGenerationType

One output is generated for all inputs combined.

PER_ALL_INPUTS - Enum constant in enum class com.genologics.ri.step.OutputGenerationType

Generate one output per all inputs.

PER_INPUT - Enum constant in enum class com.genologics.ri.process.OutputGenerationType

One output per input.

PER_INPUT - Enum constant in enum class com.genologics.ri.processtype.OutputGenerationType

One output is generated per input.

PER_INPUT - Enum constant in enum class com.genologics.ri.step.OutputGenerationType

Generate one output per input.

PER_REAGENT_LABEL - Enum constant in enum class com.genologics.ri.process.OutputGenerationType

One output per reagent label.

PER_REAGENT_LABEL - Enum constant in enum class com.genologics.ri.processtype.OutputGenerationType

Outputs are generated based on reagent labels.

PER_REAGENT_LABEL - Enum constant in enum class com.genologics.ri.step.OutputGenerationType

Generate one output per reagent label.

Permission - Class in com.genologics.ri.permission

The detailed representation of a permission.

Permission() - Constructor for class com.genologics.ri.permission.Permission

Default constructor.

Permission(URI) - Constructor for class com.genologics.ri.permission.Permission

Constructor with URI.

Permission(URI, String) - Constructor for class com.genologics.ri.permission.Permission

Constructor with URI and name.

PERMISSION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The permission namespace.

PermissionLink - Class in com.genologics.ri.permission

Permission-link provides a URI linking to the detailed representation of a permission.

PermissionLink - Class in com.genologics.ri.role

Permission-link is a child element type of permissions and provides a URI linking to the detailed representation of a Permission.

PermissionLink() - Constructor for class com.genologics.ri.permission.PermissionLink

Default constructor.

PermissionLink() - Constructor for class com.genologics.ri.role.PermissionLink

Default constructor.

PermissionLink(Permission) - Constructor for class com.genologics.ri.permission.PermissionLink

Constructor from a permission.

PermissionLink(Permission) - Constructor for class com.genologics.ri.role.PermissionLink

Constructor from a Permission entity.

PermissionLink(URI) - Constructor for class com.genologics.ri.permission.PermissionLink

Constructor with URI.

PermissionLink(URI) - Constructor for class com.genologics.ri.role.PermissionLink

Constructor with URI.

PermissionLink(URI, String) - Constructor for class com.genologics.ri.role.PermissionLink

Constructor with URI and name.

PermissionLink(URI, String, String) - Constructor for class com.genologics.ri.permission.PermissionLink

Constructor with URI, name and action.

PermissionLink(URI, String, String) - Constructor for class com.genologics.ri.role.PermissionLink

Constructor with URI, name, and action.

permissions - Variable in class com.genologics.ri.permission.Permissions

The list of permission links.

permissions - Variable in class com.genologics.ri.role.Role

The list of permissions assigned to this role.

Permissions - Class in com.genologics.ri.permission

The representation of a list of permission links.

Permissions() - Constructor for class com.genologics.ri.permission.Permissions

Default constructor.

Permissions(String) - Constructor for class com.genologics.ri.permission.Permissions

Constructor with URI.

permittedContainers - Variable in class com.genologics.ri.processtype.ProcessType

Permitted container types for this process.

permittedContainerTypes - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

List of permitted container types for this step.

permittedControlTypes - Variable in class com.genologics.ri.processtype.ProcessType

Permitted control types for this process.

permittedControlTypes - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

List of permitted control types for this step.

permittedInstrumentTypes - Variable in class com.genologics.ri.processtype.ProcessType

Permitted instrument types for this process.

permittedInstrumentTypes - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

List of permitted instrument types for this step.

permittedReagentCategories - Variable in class com.genologics.ri.processtype.ProcessType

Permitted reagent categories for this process.

permittedReagentCategories - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

List of permitted reagent categories for this step.

phone - Variable in class com.genologics.ri.researcher.Researcher

The researcher's phone number.

Placement - Class in com.genologics.ri.container

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.

Placement() - Constructor for class com.genologics.ri.container.Placement

Default constructor.

Placement(Artifact) - Constructor for class com.genologics.ri.container.Placement

Constructor from an artifact.

Placement(LimsEntityLinkable<Artifact>) - Constructor for class com.genologics.ri.container.Placement

Constructor from a LIMS entity linkable artifact.

Placement(LimsEntityLinkable<Artifact>, String) - Constructor for class com.genologics.ri.container.Placement

Constructor from a LIMS entity linkable artifact with well position.

Placement(URI) - Constructor for class com.genologics.ri.container.Placement

Constructor with URI.

Placement(URI, String) - Constructor for class com.genologics.ri.container.Placement

Constructor with URI and well position.

Placement(URI, String, String) - Constructor for class com.genologics.ri.container.Placement

Constructor with URI, LIMS id, and well position.

PLACEMENT - Enum constant in enum class com.genologics.ri.processtype.TriggerStatus

The step is in the placement phase.

PLACEMENT - Enum constant in enum class com.genologics.ri.step.ProcessState

The step state when the step is in the sample placement stage.

PLACEMENT - Enum constant in enum class com.genologics.ri.stepconfiguration.TriggerStatus

Trigger executes during placement.

placements - Variable in class com.genologics.ri.container.Container

The list of placements in the container.

placements - Variable in class com.genologics.ri.step.ProcessStep

Link to the placements associated with this step.

Placements - Class in com.genologics.ri.step

The detailed representation of a step's output artifact container placements

Placements() - Constructor for class com.genologics.ri.step.Placements

Default constructor.

Placements(URI) - Constructor for class com.genologics.ri.step.Placements

Constructor with URI.

PlacementsLink - Class in com.genologics.ri.step

Identifies the resource that represents the output placements for the step.

PlacementsLink() - Constructor for class com.genologics.ri.step.PlacementsLink

Default constructor.

PlacementsLink(Linkable<Placements>) - Constructor for class com.genologics.ri.step.PlacementsLink

Constructor with placements object.

PlacementsLink(URI) - Constructor for class com.genologics.ri.step.PlacementsLink

Constructor with URI.

point - Variable in class com.genologics.ri.processtype.EppTrigger

The point at which the trigger executes (before or after).

point - Variable in class com.genologics.ri.stepconfiguration.EppTrigger

The point when the EPP trigger executes.

pooledInputs - Variable in class com.genologics.ri.step.Pools

The list of pooled input groups.

PooledInputs - Class in com.genologics.ri.step

Provides pooled input groups.

PooledInputs() - Constructor for class com.genologics.ri.step.PooledInputs

Default constructor.

PooledInputs(Collection<? extends Linkable<Artifact>>, String) - Constructor for class com.genologics.ri.step.PooledInputs

Constructor with input artifacts and pool name.

PooledInputs(Collection<? extends Linkable<Artifact>>, String, Linkable<Artifact>) - Constructor for class com.genologics.ri.step.PooledInputs

Constructor with input artifacts, pool name and output artifact.

POOLING - Enum constant in enum class com.genologics.ri.processtype.TriggerStatus

The step is in the pooling phase.

POOLING - Enum constant in enum class com.genologics.ri.step.ProcessState

The step state when the step is in the pooling stage.

POOLING - Enum constant in enum class com.genologics.ri.stepconfiguration.TriggerStatus

Trigger executes during pooling.

pools - Variable in class com.genologics.ri.step.ProcessStep

Link to the pools associated with this step.

Pools - Class in com.genologics.ri.step

The detailed representation of a step's pooled inputs.

Pools() - Constructor for class com.genologics.ri.step.Pools

Default constructor.

Pools(URI) - Constructor for class com.genologics.ri.step.Pools

Constructor with URI.

PoolsLink - Class in com.genologics.ri.step

Identifies the resource that represents the pools added by the step.

PoolsLink() - Constructor for class com.genologics.ri.step.PoolsLink

Default constructor.

PoolsLink(Linkable<Pools>) - Constructor for class com.genologics.ri.step.PoolsLink

Constructor with pools object.

PoolsLink(URI) - Constructor for class com.genologics.ri.step.PoolsLink

Constructor with URI.

poolStep - Variable in class com.genologics.ri.artifact.DemuxDetails

The pool step of this demux details.

PoolStep - Class in com.genologics.ri.artifact

The details of the pooling step that created the pooled sample(s).

PoolStep() - Constructor for class com.genologics.ri.artifact.PoolStep

Default constructor.

PoolStep(Linkable<ProcessStep>) - Constructor for class com.genologics.ri.artifact.PoolStep

Constructor from a Linkable.

PoolStep(URI) - Constructor for class com.genologics.ri.artifact.PoolStep

Constructor taking a URI.

PoolStep(URI, String) - Constructor for class com.genologics.ri.artifact.PoolStep

Constructor taking a URI and name.

POPULATED - Enum constant in enum class com.genologics.ri.container.ContainerState

The container state when the container has something in it.

POST_PROCESS - Enum constant in enum class com.genologics.ri.processtype.InvocationType

EPP runs after the process.

postalCode - Variable in class com.genologics.ri.Address

The postal or zip code.

postProcessUri - Variable in class com.genologics.ri.process.ArtifactLink

The post-process URI of the artifact.

PRE_PROCESS - Enum constant in enum class com.genologics.ri.processtype.InvocationType

EPP runs before the process.

precision - Variable in class com.genologics.ri.configuration.Field

The display precision for numeric fields.

preset - Variable in class com.genologics.ri.step.StepDetails

The name of the preset configuration used for the step.

presets - Variable in class com.genologics.ri.configuration.Field

The list of preset values for this field.

presets - Variable in class com.genologics.ri.configuration.FieldDynamicPresetDetails

The list of field dynamic presets.

previousPage - Variable in class com.genologics.ri.artifact.Artifacts

The previous page of results.

previousPage - Variable in class com.genologics.ri.artifactgroup.ArtifactGroups

Link to the previous page of results.

previousPage - Variable in class com.genologics.ri.automation.Automations

The link to the previous page of results.

previousPage - Variable in class com.genologics.ri.configuration.Udfs

The link to the previous page of results.

previousPage - Variable in class com.genologics.ri.configuration.Udts

The link to the previous page of results.

previousPage - Variable in class com.genologics.ri.container.Containers

The link to the previous page of results.

previousPage - Variable in class com.genologics.ri.containertype.ContainerTypes

The link to the previous page of results.

previousPage - Variable in class com.genologics.ri.file.ClarityFiles

A link to the previous page of results, if available.

previousPage - Variable in class com.genologics.ri.globaltoken.GlobalTokens

The previous page of results.

previousPage - Variable in class com.genologics.ri.instrument.Instruments

The previous page reference.

previousPage - Variable in class com.genologics.ri.instrumenttype.InstrumentTypes

The previous page reference.

previousPage - Variable in class com.genologics.ri.lab.Labs

The previous page of results.

previousPage - Variable in class com.genologics.ri.process.ClarityProcesses

The link to the previous page of results.

previousPage - Variable in class com.genologics.ri.processtemplate.ProcessTemplates

The link to the previous page of results.

previousPage - Variable in class com.genologics.ri.processtype.ProcessTypes

Link to the previous page of results.

previousPage - Variable in class com.genologics.ri.project.Projects

The previous page of results.

previousPage - Variable in class com.genologics.ri.property.Properties

The link to the previous page of results.

previousPage - Variable in class com.genologics.ri.queue.Queue

The link to the previous page of results.

previousPage - Variable in class com.genologics.ri.reagentkit.ReagentKits

The link to the previous page of results.

previousPage - Variable in class com.genologics.ri.reagentlot.ReagentLots

Link to the previous page of results, if available.

previousPage - Variable in class com.genologics.ri.reagenttype.ReagentTypes

Link to the previous page of results.

previousPage - Variable in class com.genologics.ri.researcher.Researchers

Link to the previous page of results.

previousPage - Variable in class com.genologics.ri.sample.Samples

The previous page link for pagination.

previousPage - Variable in class com.genologics.ri.savedquery.SavedQueries

The link to the previous page of results.

primaryEntity() - Element in annotation interface com.genologics.ri.ClarityEntity

Specifies the outer entity of the API for which the annotated class is the inner entity.

priority - Variable in class com.genologics.ri.project.Project

The priority of the project.

PROCESS_EXECUTION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The process execution namespace.

PROCESS_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The process namespace.

PROCESS_TEMPLATE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The process template namespace.

PROCESS_TYPE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The process type namespace.

processes - Variable in class com.genologics.ri.process.ClarityProcesses

The list of process links.

ProcessInput - Class in com.genologics.ri.processtype

Process-input is a child element of process type specifying the available input types for the process

ProcessInput() - Constructor for class com.genologics.ri.processtype.ProcessInput

processInputs - Variable in class com.genologics.ri.processtype.ProcessType

Process input configurations.

ProcessLink - Class in com.genologics.ri.process

Process-link is a child element type of process and provides a URI linking to the detailed representation of a process.

ProcessLink() - Constructor for class com.genologics.ri.process.ProcessLink

Default constructor.

ProcessLink(LimsEntityLinkable<ClarityProcess>) - Constructor for class com.genologics.ri.process.ProcessLink

Constructor from a LIMS entity linkable object.

ProcessLink(Linkable<ClarityProcess>) - Constructor for class com.genologics.ri.process.ProcessLink

Constructor from a linkable object.

ProcessLink(URI) - Constructor for class com.genologics.ri.process.ProcessLink

Constructor with URI.

ProcessLink(URI, String) - Constructor for class com.genologics.ri.process.ProcessLink

Constructor with URI and LIMS id.

ProcessOutput - Class in com.genologics.ri.processtype

Process-output is a child element of process type specifying the configured output generation types for the process

ProcessOutput() - Constructor for class com.genologics.ri.processtype.ProcessOutput

processOutputs - Variable in class com.genologics.ri.processtype.ProcessType

Process output configurations.

ProcessState - Enum Class in com.genologics.ri.step

An enumeration of the values possible in the ProcessStep.currentState attribute.

ProcessStep - Class in com.genologics.ri.step

The detailed representation of a step.

ProcessStep() - Constructor for class com.genologics.ri.step.ProcessStep

Constructs a new empty ProcessStep.

ProcessStep(URI) - Constructor for class com.genologics.ri.step.ProcessStep

Constructs a new ProcessStep with the given URI.

ProcessStep(URI, String) - Constructor for class com.genologics.ri.step.ProcessStep

Constructs a new ProcessStep with the given URI and LIMS id.

ProcessTemplate - Class in com.genologics.ri.processtemplate

The detailed representation of a Process Template.

ProcessTemplate() - Constructor for class com.genologics.ri.processtemplate.ProcessTemplate

Default constructor.

ProcessTemplate(URI) - Constructor for class com.genologics.ri.processtemplate.ProcessTemplate

Constructor with URI.

ProcessTemplate(URI, String) - Constructor for class com.genologics.ri.processtemplate.ProcessTemplate

Constructor with URI and name.

ProcessTemplateLink - Class in com.genologics.ri.processtemplate

process-template-link is a child element type of Process Templates and provides a URI linking to the detailed representation of a Process Template.

ProcessTemplateLink() - Constructor for class com.genologics.ri.processtemplate.ProcessTemplateLink

Default constructor.

ProcessTemplateLink(Linkable<ProcessTemplate>) - Constructor for class com.genologics.ri.processtemplate.ProcessTemplateLink

Constructor from a linkable process template.

ProcessTemplateLink(ProcessTemplate) - Constructor for class com.genologics.ri.processtemplate.ProcessTemplateLink

Constructor from a ProcessTemplate object.

ProcessTemplateLink(URI) - Constructor for class com.genologics.ri.processtemplate.ProcessTemplateLink

Constructor with URI.

ProcessTemplateLink(URI, String) - Constructor for class com.genologics.ri.processtemplate.ProcessTemplateLink

Constructor with URI and name.

processTemplates - Variable in class com.genologics.ri.processtemplate.ProcessTemplates

The list of process template links.

ProcessTemplates - Class in com.genologics.ri.processtemplate

The representation of a list of Process Template links.

ProcessTemplates() - Constructor for class com.genologics.ri.processtemplate.ProcessTemplates

Default constructor.

processType - Variable in class com.genologics.ri.process.ClarityProcess

The type of the process.

processType - Variable in class com.genologics.ri.processexecution.ExecutableProcess

The process type name.

processType - Variable in class com.genologics.ri.processtemplate.ProcessTemplate

The process type this template is associated with.

processType - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

The process type associated with this step.

ProcessType - Class in com.genologics.ri.processtype

The process-type element contains the XML representation of a type of process configured in the system.

ProcessType() - Constructor for class com.genologics.ri.processtype.ProcessType

Constructs a new process type.

ProcessType(URI) - Constructor for class com.genologics.ri.processtype.ProcessType

Constructs a new process type with the specified URI.

ProcessType(URI, String) - Constructor for class com.genologics.ri.processtype.ProcessType

Constructs a new process type with the specified URI and name.

ProcessTypeAttribute - Class in com.genologics.ri.processtype

Process-type-attributes is a child element of process type containing key/value pairs for setting specific attributes that can be set for process types.

ProcessTypeAttribute() - Constructor for class com.genologics.ri.processtype.ProcessTypeAttribute

Constructs a new process type attribute.

ProcessTypeAttribute(String) - Constructor for class com.genologics.ri.processtype.ProcessTypeAttribute

Constructs a new process type attribute with the specified name.

ProcessTypeAttribute(String, String) - Constructor for class com.genologics.ri.processtype.ProcessTypeAttribute

Constructs a new process type attribute with the specified name and value.

processTypeAttributes - Variable in class com.genologics.ri.processtype.ProcessType

Internal process type attributes.

ProcessTypeLink - Class in com.genologics.ri.automation

Provides links to process types the automation is enabled on.

ProcessTypeLink - Class in com.genologics.ri.process

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.

ProcessTypeLink - Class in com.genologics.ri.processtemplate

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.

ProcessTypeLink - Class in com.genologics.ri.processtype

Process-type-link is a child element type of process types and provides a URI linking to the detailed representation of a process type.

ProcessTypeLink - Class in com.genologics.ri.stepconfiguration

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.

ProcessTypeLink() - Constructor for class com.genologics.ri.automation.ProcessTypeLink

Default constructor.

ProcessTypeLink() - Constructor for class com.genologics.ri.process.ProcessTypeLink

Default constructor.

ProcessTypeLink() - Constructor for class com.genologics.ri.processtemplate.ProcessTypeLink

Default constructor.

ProcessTypeLink() - Constructor for class com.genologics.ri.processtype.ProcessTypeLink

Constructs a new process type link.

ProcessTypeLink() - Constructor for class com.genologics.ri.stepconfiguration.ProcessTypeLink

Default constructor.

ProcessTypeLink(Linkable<ProcessType>) - Constructor for class com.genologics.ri.automation.ProcessTypeLink

Constructor from a Linkable.

ProcessTypeLink(Linkable<ProcessType>) - Constructor for class com.genologics.ri.process.ProcessTypeLink

Constructor from a linkable object.

ProcessTypeLink(Linkable<ProcessType>) - Constructor for class com.genologics.ri.processtemplate.ProcessTypeLink

Constructor from a linkable process type.

ProcessTypeLink(Linkable<ProcessType>) - Constructor for class com.genologics.ri.processtype.ProcessTypeLink

Constructs a new process type link from a linkable object.

ProcessTypeLink(Linkable<ProcessType>) - Constructor for class com.genologics.ri.stepconfiguration.ProcessTypeLink

Constructor from a linkable process type.

ProcessTypeLink(ProcessType) - Constructor for class com.genologics.ri.automation.ProcessTypeLink

Constructor from a ProcessType entity.

ProcessTypeLink(ProcessType) - Constructor for class com.genologics.ri.process.ProcessTypeLink

Constructor from a process type.

ProcessTypeLink(ProcessType) - Constructor for class com.genologics.ri.processtemplate.ProcessTypeLink

Constructor from a ProcessType object.

ProcessTypeLink(ProcessType) - Constructor for class com.genologics.ri.processtype.ProcessTypeLink

Constructs a new process type link from a process type entity.

ProcessTypeLink(ProcessType) - Constructor for class com.genologics.ri.stepconfiguration.ProcessTypeLink

Constructor from a process type entity.

ProcessTypeLink(URI) - Constructor for class com.genologics.ri.automation.ProcessTypeLink

Constructor with URI.

ProcessTypeLink(URI) - Constructor for class com.genologics.ri.process.ProcessTypeLink

Constructor with URI.

ProcessTypeLink(URI) - Constructor for class com.genologics.ri.processtemplate.ProcessTypeLink

Constructor with URI.

ProcessTypeLink(URI) - Constructor for class com.genologics.ri.processtype.ProcessTypeLink

Constructs a new process type link with the specified URI.

ProcessTypeLink(URI) - Constructor for class com.genologics.ri.stepconfiguration.ProcessTypeLink

Constructor with URI.

ProcessTypeLink(URI, String) - Constructor for class com.genologics.ri.automation.ProcessTypeLink

Constructor with URI and name.

ProcessTypeLink(URI, String) - Constructor for class com.genologics.ri.process.ProcessTypeLink

Constructor with URI and name.

ProcessTypeLink(URI, String) - Constructor for class com.genologics.ri.processtemplate.ProcessTypeLink

Constructor with URI and name.

ProcessTypeLink(URI, String) - Constructor for class com.genologics.ri.processtype.ProcessTypeLink

Constructs a new process type link with the specified URI and name.

ProcessTypeLink(URI, String) - Constructor for class com.genologics.ri.stepconfiguration.ProcessTypeLink

Constructor with URI and name.

processTypes - Variable in class com.genologics.ri.automation.Automation

The process types associated with this automation.

processTypes - Variable in class com.genologics.ri.instrumenttype.InstrumentType

The list of process types associated with this instrument type.

processTypes - Variable in class com.genologics.ri.processtype.ProcessTypes

The list of process type links.

ProcessTypes - Class in com.genologics.ri.processtype

The representation for a list of process type links.

ProcessTypes() - Constructor for class com.genologics.ri.processtype.ProcessTypes

Constructs a new process types batch.

programStatus - Variable in class com.genologics.ri.step.ProcessStep

Link to the program status associated with this step.

ProgramStatus - Class in com.genologics.ri.step

The current EPP status for a step (supports automatically triggered programs only).

ProgramStatus() - Constructor for class com.genologics.ri.step.ProgramStatus

Constructs a new empty ProgramStatus.

ProgramStatus(URI) - Constructor for class com.genologics.ri.step.ProgramStatus

Constructs a new ProgramStatus with the given URI.

ProgramStatusLink - Class in com.genologics.ri.step

Identifies the resource that represents the program status for the step.

ProgramStatusLink() - Constructor for class com.genologics.ri.step.ProgramStatusLink

Constructs a new empty ProgramStatusLink.

ProgramStatusLink(Linkable<ProgramStatus>) - Constructor for class com.genologics.ri.step.ProgramStatusLink

Constructs a new ProgramStatusLink from a linkable program status.

ProgramStatusLink(URI) - Constructor for class com.genologics.ri.step.ProgramStatusLink

Constructs a new ProgramStatusLink with the given URI.

project - Variable in class com.genologics.ri.sample.SampleBase

The project associated with this sample.

Project - Class in com.genologics.ri.project

The detailed representation of a Project.

Project() - Constructor for class com.genologics.ri.project.Project

Constructor for Project.

Project(URI) - Constructor for class com.genologics.ri.project.Project

Constructor for Project with a URI.

Project(URI, String) - Constructor for class com.genologics.ri.project.Project

Constructor for Project with a URI and LIMS id.

PROJECT - Enum constant in enum class com.genologics.ri.automation.Context

Project context.

PROJECT_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The project namespace.

ProjectLink - Class in com.genologics.ri.project

Project-link is a child element type of projects and provides a URI linking to the detailed representation of a project.

ProjectLink - Class in com.genologics.ri.sample

Project is a child element of Sample and provides a URI linking to the detailed representation of the Project for the Sample.

ProjectLink() - Constructor for class com.genologics.ri.project.ProjectLink

Constructor for ProjectLink.

ProjectLink() - Constructor for class com.genologics.ri.sample.ProjectLink

Constructor for an empty project link.

ProjectLink(LimsEntityLinkable<Project>) - Constructor for class com.genologics.ri.project.ProjectLink

Constructor for ProjectLink from a LimsEntityLinkable.

ProjectLink(LimsEntityLinkable<Project>) - Constructor for class com.genologics.ri.sample.ProjectLink

Constructor for a project link from a LIMS entity linkable project.

ProjectLink(Linkable<Project>) - Constructor for class com.genologics.ri.project.ProjectLink

Constructor for ProjectLink from a Linkable.

ProjectLink(Linkable<Project>) - Constructor for class com.genologics.ri.sample.ProjectLink

Constructor for a project link from a linkable project.

ProjectLink(Project) - Constructor for class com.genologics.ri.project.ProjectLink

Constructor for ProjectLink from a Project.

ProjectLink(URI) - Constructor for class com.genologics.ri.project.ProjectLink

Constructor for ProjectLink with a URI.

ProjectLink(URI) - Constructor for class com.genologics.ri.sample.ProjectLink

Constructor for a project link with a URI.

ProjectLink(URI, String) - Constructor for class com.genologics.ri.project.ProjectLink

Constructor for ProjectLink with a URI and LIMS id.

ProjectLink(URI, String) - Constructor for class com.genologics.ri.sample.ProjectLink

Constructor for a project link with a URI and LIMS id.

ProjectLink(URI, String, String) - Constructor for class com.genologics.ri.project.ProjectLink

Constructor for ProjectLink with a URI, LIMS id, and name.

projects - Variable in class com.genologics.ri.project.Projects

The list of project links.

Projects - Class in com.genologics.ri.project

The representation of a list of project links.

Projects() - Constructor for class com.genologics.ri.project.Projects

Constructor for Projects.

properties - Variable in class com.genologics.ri.property.Properties

The list of property links.

Properties - Class in com.genologics.ri.property

The representation for a list of property links.

Properties() - Constructor for class com.genologics.ri.property.Properties

Default constructor.

PROPERTY_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The property namespace.

PropertyLink - Class in com.genologics.ri.property

property-link is a child element type of property and provides a URI linking to the detailed representation of a property.

PropertyLink() - Constructor for class com.genologics.ri.property.PropertyLink

Default constructor.

PropertyLink(URI) - Constructor for class com.genologics.ri.property.PropertyLink

Constructor with URI.

PropertyLink(URI, String, String) - Constructor for class com.genologics.ri.property.PropertyLink

Constructor with URI, name, and value.

protocol - Variable in class com.genologics.ri.stage.Stage

Link to the protocol for this stage.

Protocol - Class in com.genologics.ri.protocolconfiguration

Detailed representation of a protocol.

Protocol() - Constructor for class com.genologics.ri.protocolconfiguration.Protocol

Default constructor.

Protocol(URI) - Constructor for class com.genologics.ri.protocolconfiguration.Protocol

Constructor with URI.

Protocol(URI, String) - Constructor for class com.genologics.ri.protocolconfiguration.Protocol

Constructor with URI and name.

Protocol(URI, String, Integer) - Constructor for class com.genologics.ri.protocolconfiguration.Protocol

Constructor with URI, name, and index.

PROTOCOL_CONFIGURATION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The protocol configuration namespace.

ProtocolLink - Class in com.genologics.ri.protocolconfiguration

Link to a protocol configuration.

ProtocolLink - Class in com.genologics.ri.stage

Protocol link for a stage in a workflow.

ProtocolLink - Class in com.genologics.ri.workflowconfiguration

Protocol-link is a child element type of workflow and provides a URI linking to the detailed representation of a protocol.

ProtocolLink() - Constructor for class com.genologics.ri.protocolconfiguration.ProtocolLink

Default constructor.

ProtocolLink() - Constructor for class com.genologics.ri.stage.ProtocolLink

Default constructor.

ProtocolLink() - Constructor for class com.genologics.ri.workflowconfiguration.ProtocolLink

Default constructor.

ProtocolLink(Linkable<Protocol>) - Constructor for class com.genologics.ri.protocolconfiguration.ProtocolLink

Constructor from a linkable object.

ProtocolLink(Linkable<Protocol>) - Constructor for class com.genologics.ri.stage.ProtocolLink

Constructor from a linkable protocol object.

ProtocolLink(Linkable<Protocol>) - Constructor for class com.genologics.ri.workflowconfiguration.ProtocolLink

Constructor accepting a Linkable object.

ProtocolLink(Protocol) - Constructor for class com.genologics.ri.protocolconfiguration.ProtocolLink

Constructor from a protocol.

ProtocolLink(Protocol) - Constructor for class com.genologics.ri.workflowconfiguration.ProtocolLink

Constructor accepting a Protocol object.

ProtocolLink(URI) - Constructor for class com.genologics.ri.protocolconfiguration.ProtocolLink

Constructor with URI.

ProtocolLink(URI) - Constructor for class com.genologics.ri.stage.ProtocolLink

Constructor with URI.

ProtocolLink(URI) - Constructor for class com.genologics.ri.workflowconfiguration.ProtocolLink

Constructor accepting a URI.

ProtocolLink(URI, String) - Constructor for class com.genologics.ri.protocolconfiguration.ProtocolLink

Constructor with URI and name.

ProtocolLink(URI, String) - Constructor for class com.genologics.ri.workflowconfiguration.ProtocolLink

Constructor accepting a URI and name.

protocolName - Variable in class com.genologics.ri.process.ClarityProcess

The protocol name.

protocolProperties - Variable in class com.genologics.ri.protocolconfiguration.Protocol

The list of protocol properties.

ProtocolProperty - Class in com.genologics.ri.protocolconfiguration

Protocol-property is a child element of protocol containing key/value pairs for setting specific attributes of protocols.

ProtocolProperty() - Constructor for class com.genologics.ri.protocolconfiguration.ProtocolProperty

Default constructor.

ProtocolProperty(String, String) - Constructor for class com.genologics.ri.protocolconfiguration.ProtocolProperty

Constructor with name and value.

protocols - Variable in class com.genologics.ri.protocolconfiguration.Protocols

The list of protocol links.

protocols - Variable in class com.genologics.ri.workflowconfiguration.Workflow

The list of protocols associated with this workflow.

Protocols - Class in com.genologics.ri.protocolconfiguration

Returns the representation of a list of protocols

Protocols() - Constructor for class com.genologics.ri.protocolconfiguration.Protocols

Default constructor.

ProtocolStep - Class in com.genologics.ri.stepconfiguration

Detailed representation of a Step

ProtocolStep() - Constructor for class com.genologics.ri.stepconfiguration.ProtocolStep

Default constructor.

ProtocolStep(URI) - Constructor for class com.genologics.ri.stepconfiguration.ProtocolStep

Constructor with URI.

ProtocolStep(URI, String) - Constructor for class com.genologics.ri.stepconfiguration.ProtocolStep

Constructor with URI and name.

protocolStepIndex - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

The index of this step within the protocol.

ProtocolStepLink - Class in com.genologics.ri.stage

Protocol step link for a stage in a workflow.

ProtocolStepLink() - Constructor for class com.genologics.ri.stage.ProtocolStepLink

Default constructor.

ProtocolStepLink(Linkable<ProtocolStep>) - Constructor for class com.genologics.ri.stage.ProtocolStepLink

Constructor from a linkable protocol step object.

ProtocolStepLink(URI) - Constructor for class com.genologics.ri.stage.ProtocolStepLink

Constructor with URI.

protocolStepUri - Variable in class com.genologics.ri.queue.Queue

The URI of the protocol step for this queue.

protocolStepUri - Variable in class com.genologics.ri.step.StepConfiguration

The URI of the protocol step configuration.

protocolUri - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

The URI of the protocol this step belongs to.

published - Variable in class com.genologics.ri.file.ClarityFile

Indicates whether the file is displayed in LabLink.

Q

qcFlag - Variable in class com.genologics.ri.artifact.Artifact

The quality control flag for this artifact.

qcFlag - Variable in class com.genologics.ri.processexecution.ArtifactBase

The quality control flag for this artifact.

QCFlag - Enum Class in com.genologics.ri.artifact

Enumeration of quality control flag values.

QCFlag - Enum Class in com.genologics.ri.processexecution

Quality control flag enumeration for artifacts in process execution.

Queue - Class in com.genologics.ri.queue

The representation of a queue.

Queue() - Constructor for class com.genologics.ri.queue.Queue

Default constructor.

Queue(URI) - Constructor for class com.genologics.ri.queue.Queue

Constructor with URI.

Queue(URI, String) - Constructor for class com.genologics.ri.queue.Queue

Constructor with URI and name.

QUEUE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The queue namespace.

QUEUED - Enum constant in enum class com.genologics.ri.artifact.Status

Queued status.

QUEUED - Enum constant in enum class com.genologics.ri.step.Status

The step is queued for execution.

QueueField - Class in com.genologics.ri.processtype

A field has a name and an attach to value, these fields are used to keep track of all the UDF values for samples in queue and work view as well as those on the actual step

QueueField - Class in com.genologics.ri.stepconfiguration

A field has a name and an attach to value, these fields are used to keep track of all the UDF values for samples in queue and work view as well as those on the actual step

QueueField() - Constructor for class com.genologics.ri.processtype.QueueField

Constructs a new queue field.

QueueField() - Constructor for class com.genologics.ri.stepconfiguration.QueueField

Default constructor.

QueueField(String) - Constructor for class com.genologics.ri.stepconfiguration.QueueField

Constructor with field name.

QueueField(String, String) - Constructor for class com.genologics.ri.stepconfiguration.QueueField

Constructor with field name and attach-to value.

QueueField(String, String, Boolean) - Constructor for class com.genologics.ri.stepconfiguration.QueueField

Constructor with field name, attach-to value, and detail flag.

queueFields - Variable in class com.genologics.ri.processtype.ProcessType

Fields displayed in the queue view.

queueFields - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

List of fields to display in the queue view.

queueTime - Variable in class com.genologics.ri.queue.ArtifactLink

The time when the artifact was queued.

R

rackColumn - Variable in class com.genologics.ri.step.RackLocation

The column position within the rack.

rackIndex - Variable in class com.genologics.ri.step.RackLocation

The index of the rack.

rackLocation - Variable in class com.genologics.ri.step.OutputArrangement

The rack location for the output arrangement.

RackLocation - Class in com.genologics.ri.step

Provides the row and column location within a Tube Rack.

RackLocation() - Constructor for class com.genologics.ri.step.RackLocation

Constructs a new empty RackLocation.

rackRow - Variable in class com.genologics.ri.step.RackLocation

The row position within the rack.

REAGENT_KIT_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The reagent kit namespace.

REAGENT_LOT_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The reagent lot namespace.

REAGENT_ONLY - Enum constant in enum class com.genologics.ri.container.ContainerState

The container state when the container only container reagents.

REAGENT_TYPE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The reagent type namespace.

reagentCategory - Variable in class com.genologics.ri.reagenttype.ReagentType

The category of this reagent.

reagentCategory - Variable in class com.genologics.ri.step.Reagents

The reagent category for the step.

reagentCategory - Variable in class com.genologics.ri.step.StepCreation

The reagent category name.

reagentKit - Variable in class com.genologics.ri.reagentlot.ReagentLot

Link to the reagent kit that this lot belongs to.

ReagentKit - Class in com.genologics.ri.reagentkit

The detailed representation of a reagent kit.

ReagentKit() - Constructor for class com.genologics.ri.reagentkit.ReagentKit

Default constructor.

ReagentKit(URI) - Constructor for class com.genologics.ri.reagentkit.ReagentKit

Constructor with URI.

ReagentKit(URI, String) - Constructor for class com.genologics.ri.reagentkit.ReagentKit

Constructor with URI and name.

ReagentKitLink - Class in com.genologics.ri.processtype

Reagent-kit-link is a child element type of reagentKits and provides a URI linking to the detailed representation of a ReagentKit.

ReagentKitLink - Class in com.genologics.ri.reagentkit

Reagent-Kit-Link is a child element type of reagent kits and provides a URI linking to the detailed representation of a reagent kit.

ReagentKitLink - Class in com.genologics.ri.reagentlot

Reagent-Kit-Link is an element providing a URI linking to the detailed representation of a reagent kit.

ReagentKitLink - Class in com.genologics.ri.stepconfiguration

Reagent-Kit-Link is an element providing a URI linking to the detailed representation of a reagent kit.

ReagentKitLink() - Constructor for class com.genologics.ri.processtype.ReagentKitLink

Constructs a new reagent kit link.

ReagentKitLink() - Constructor for class com.genologics.ri.reagentkit.ReagentKitLink

Default constructor.

ReagentKitLink() - Constructor for class com.genologics.ri.reagentlot.ReagentKitLink

Default constructor.

ReagentKitLink() - Constructor for class com.genologics.ri.stepconfiguration.ReagentKitLink

Default constructor.

ReagentKitLink(Linkable<ReagentKit>) - Constructor for class com.genologics.ri.processtype.ReagentKitLink

Constructs a new reagent kit link from a linkable object.

ReagentKitLink(Linkable<ReagentKit>) - Constructor for class com.genologics.ri.reagentkit.ReagentKitLink

Constructor from a Linkable.

ReagentKitLink(Linkable<ReagentKit>) - Constructor for class com.genologics.ri.reagentlot.ReagentKitLink

Constructor from a linkable reagent kit.

ReagentKitLink(Linkable<ReagentKit>) - Constructor for class com.genologics.ri.stepconfiguration.ReagentKitLink

Constructor from a linkable reagent kit.

ReagentKitLink(ReagentKit) - Constructor for class com.genologics.ri.processtype.ReagentKitLink

Constructs a new reagent kit link from a reagent kit entity.

ReagentKitLink(ReagentKit) - Constructor for class com.genologics.ri.reagentkit.ReagentKitLink

Constructor from a ReagentKit.

ReagentKitLink(ReagentKit) - Constructor for class com.genologics.ri.reagentlot.ReagentKitLink

Constructor from a reagent kit entity.

ReagentKitLink(ReagentKit) - Constructor for class com.genologics.ri.stepconfiguration.ReagentKitLink

Constructor from a reagent kit entity.

ReagentKitLink(String) - Constructor for class com.genologics.ri.processtype.ReagentKitLink

Constructs a new reagent kit link with the specified name.

ReagentKitLink(URI) - Constructor for class com.genologics.ri.reagentkit.ReagentKitLink

Constructor with URI.

ReagentKitLink(URI) - Constructor for class com.genologics.ri.reagentlot.ReagentKitLink

Constructor with URI.

ReagentKitLink(URI) - Constructor for class com.genologics.ri.stepconfiguration.ReagentKitLink

Constructor with URI.

ReagentKitLink(URI, String) - Constructor for class com.genologics.ri.reagentkit.ReagentKitLink

Constructor with URI and name.

ReagentKitLink(URI, String) - Constructor for class com.genologics.ri.reagentlot.ReagentKitLink

Constructor with URI and name.

ReagentKitLink(URI, String) - Constructor for class com.genologics.ri.stepconfiguration.ReagentKitLink

Constructor with URI and name.

reagentKits - Variable in class com.genologics.ri.reagentkit.ReagentKits

The list of reagent kit links.

ReagentKits - Class in com.genologics.ri.reagentkit

The representation for a list of reagent type links.

ReagentKits() - Constructor for class com.genologics.ri.reagentkit.ReagentKits

Default constructor.

ReagentLabel - Class in com.genologics.ri.artifact

Reagent-label is a child element of Artifact and provides the name of a label or reagent that has been added to the Artifact.

ReagentLabel - Class in com.genologics.ri.step

Reagent-label is a child element of ExtStepReagentListElement and provides the name of a label or reagent that has been added to the Artifact.

ReagentLabel() - Constructor for class com.genologics.ri.artifact.ReagentLabel

Default constructor.

ReagentLabel() - Constructor for class com.genologics.ri.step.ReagentLabel

Constructs a new empty ReagentLabel.

ReagentLabel(String) - Constructor for class com.genologics.ri.artifact.ReagentLabel

Constructor taking a name.

ReagentLabel(String) - Constructor for class com.genologics.ri.step.ReagentLabel

Constructs a new ReagentLabel with the given name.

reagentLabels - Variable in class com.genologics.ri.artifact.Artifact

The list of reagent labels applied to this artifact.

reagentLabels - Variable in class com.genologics.ri.artifact.DemuxArtifact

The reagent labels in this demux artifact.

reagentLabels - Variable in class com.genologics.ri.step.Output

List of reagent labels for the output.

ReagentLot - Class in com.genologics.ri.reagentlot

Represents a reagent lot in the Clarity LIMS system.

ReagentLot() - Constructor for class com.genologics.ri.reagentlot.ReagentLot

Default constructor.

ReagentLot(LimsEntityLinkable<ReagentLot>) - Constructor for class com.genologics.ri.reagentlot.ReagentLot

Constructor from a linkable reagent lot.

ReagentLot(URI) - Constructor for class com.genologics.ri.reagentlot.ReagentLot

Constructor with URI.

ReagentLot(URI, String) - Constructor for class com.genologics.ri.reagentlot.ReagentLot

Constructor with URI and LIMS id.

ReagentLotLink - Class in com.genologics.ri.reagentlot

Reagent-lot-link is a child element type of Reagent Lots and provides a URI linking to the detailed representation of a Reagent Lot.

ReagentLotLink - Class in com.genologics.ri.step

Provides a URI linking to the reagent lot details.

ReagentLotLink() - Constructor for class com.genologics.ri.reagentlot.ReagentLotLink

Default constructor.

ReagentLotLink() - Constructor for class com.genologics.ri.step.ReagentLotLink

Constructs a new empty ReagentLotLink.

ReagentLotLink(LimsEntityLinkable<ReagentLot>) - Constructor for class com.genologics.ri.reagentlot.ReagentLotLink

Constructor from a LIMS entity linkable reagent lot.

ReagentLotLink(LimsEntityLinkable<ReagentLot>) - Constructor for class com.genologics.ri.step.ReagentLotLink

Constructs a new ReagentLotLink from a LIMS entity linkable reagent lot.

ReagentLotLink(Linkable<ReagentLot>) - Constructor for class com.genologics.ri.reagentlot.ReagentLotLink

Constructor from a linkable reagent lot.

ReagentLotLink(Linkable<ReagentLot>) - Constructor for class com.genologics.ri.step.ReagentLotLink

Constructs a new ReagentLotLink from a linkable reagent lot.

ReagentLotLink(ReagentLot) - Constructor for class com.genologics.ri.reagentlot.ReagentLotLink

Constructor from a reagent lot entity.

ReagentLotLink(URI) - Constructor for class com.genologics.ri.reagentlot.ReagentLotLink

Constructor with URI.

ReagentLotLink(URI) - Constructor for class com.genologics.ri.step.ReagentLotLink

Constructs a new ReagentLotLink with the given URI.

ReagentLotLink(URI, String) - Constructor for class com.genologics.ri.reagentlot.ReagentLotLink

Constructor with URI and LIMS id.

ReagentLotLink(URI, String) - Constructor for class com.genologics.ri.step.ReagentLotLink

Constructs a new ReagentLotLink with the given URI and LIMS id.

ReagentLotLink(URI, String, String) - Constructor for class com.genologics.ri.reagentlot.ReagentLotLink

Constructor with URI, LIMS id, and name.

reagentLots - Variable in class com.genologics.ri.reagentlot.ReagentLots

The list of reagent lot links.

reagentLots - Variable in class com.genologics.ri.step.ProcessStep

Link to the reagent lots associated with this step.

reagentLots - Variable in class com.genologics.ri.step.ReagentLots

The list of reagent lots associated with the step.

ReagentLots - Class in com.genologics.ri.reagentlot

Represents a paginated collection of reagent lot links returned by the API.

ReagentLots - Class in com.genologics.ri.step

The list representation of a step's reagent lots.

ReagentLots() - Constructor for class com.genologics.ri.reagentlot.ReagentLots

Default constructor.

ReagentLots() - Constructor for class com.genologics.ri.step.ReagentLots

ReagentLotsLink - Class in com.genologics.ri.step

Identifies the resource that represents the reagent lots for the step.

ReagentLotsLink() - Constructor for class com.genologics.ri.step.ReagentLotsLink

Creates an empty reagent lots link.

ReagentLotsLink(Linkable<ReagentLots>) - Constructor for class com.genologics.ri.step.ReagentLotsLink

Creates a reagent lots link from a linkable object.

ReagentLotsLink(URI) - Constructor for class com.genologics.ri.step.ReagentLotsLink

Creates a reagent lots link with the given URI.

reagents - Variable in class com.genologics.ri.step.ProcessStep

Link to the reagents associated with this step.

Reagents - Class in com.genologics.ri.step

The detailed representation of a step's output artifact reagents.

Reagents() - Constructor for class com.genologics.ri.step.Reagents

Default constructor.

Reagents(URI) - Constructor for class com.genologics.ri.step.Reagents

Constructor with URI.

ReagentsLink - Class in com.genologics.ri.step

Identifies the resource that represents the reagents added by the step.

ReagentsLink() - Constructor for class com.genologics.ri.step.ReagentsLink

Creates an empty reagents link.

ReagentsLink(Linkable<Reagents>) - Constructor for class com.genologics.ri.step.ReagentsLink

Creates a reagents link from a linkable object.

ReagentsLink(URI) - Constructor for class com.genologics.ri.step.ReagentsLink

Creates a reagents link with the given URI.

ReagentType - Class in com.genologics.ri.reagenttype

The detailed representation of a reagent type.

ReagentType() - Constructor for class com.genologics.ri.reagenttype.ReagentType

Default constructor.

ReagentType(URI) - Constructor for class com.genologics.ri.reagenttype.ReagentType

Constructor with URI.

ReagentType(URI, String) - Constructor for class com.genologics.ri.reagenttype.ReagentType

Constructor with URI and name.

ReagentTypeLink - Class in com.genologics.ri.reagenttype

Reagent-type-link is a child element type of reagent types and provides a URI linking to the detailed representation of a reagent type.

ReagentTypeLink() - Constructor for class com.genologics.ri.reagenttype.ReagentTypeLink

Default constructor.

ReagentTypeLink(Linkable<ReagentType>) - Constructor for class com.genologics.ri.reagenttype.ReagentTypeLink

Constructor from a Linkable object.

ReagentTypeLink(ReagentType) - Constructor for class com.genologics.ri.reagenttype.ReagentTypeLink

Constructor from a ReagentType entity.

ReagentTypeLink(URI) - Constructor for class com.genologics.ri.reagenttype.ReagentTypeLink

Constructor with URI.

ReagentTypeLink(URI, String) - Constructor for class com.genologics.ri.reagenttype.ReagentTypeLink

Constructor with URI and name.

reagentTypes - Variable in class com.genologics.ri.reagenttype.ReagentTypes

The list of reagent type links.

ReagentTypes - Class in com.genologics.ri.reagenttype

The representation for a list of reagent type links.

ReagentTypes() - Constructor for class com.genologics.ri.reagenttype.ReagentTypes

Default constructor.

RECORD_DETAILS - Enum constant in enum class com.genologics.ri.processtype.TriggerStatus

The step is in the record details phase.

RECORD_DETAILS - Enum constant in enum class com.genologics.ri.step.ProcessState

The step state when the step is in the record details stage.

RECORD_DETAILS - Enum constant in enum class com.genologics.ri.stepconfiguration.TriggerStatus

Trigger executes when recording details.

reflectiveCollectionUpdate(Collection<E>, List<E>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Update a collection of original entities with the fields from an equivalent list of freshly retrieved versions of the same entities.

reflectiveUpdate(Object, Object) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Reflectively set all the attributes in original to the values given by updated.

relative - Variable in class com.genologics.ri.Link

The relative part of the link.

reload(E) - Method in interface org.cruk.clarity.api.ClarityAPI

Reload an entity in-situ.

reload(E) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Reload an entity in-situ.

reload(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Join point for the ClarityAPI.reload method.

removable() - Element in annotation interface com.genologics.ri.ClarityEntity

If true, the flag indicates that entities of the annotated type can be removed with DELETE.

REMOVE - Enum constant in enum class com.genologics.ri.step.ActionType

Remove the artifact.

REMOVED - Enum constant in enum class com.genologics.ri.artifact.Status

Removed status.

removeStateParameter(String) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Strip the state parameter from a URI in string form.

removeStateParameter(URI) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Strip the state parameter from a URI.

removeWorkingFlag - Variable in class com.genologics.ri.processtype.ProcessInput

Deprecated.

This property is no longer supported.

reorderBatchFetchList(Collection<? extends Locatable>, List<E>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Reorder a collection of entities into the same order given by their request objects.

REPEAT - Enum constant in enum class com.genologics.ri.step.ActionType

Repeat the action on the artifact.

replicates - Variable in class com.genologics.ri.step.CreationInput

Number of replicates.

replicates - Variable in class com.genologics.ri.step.Input

Number of replicates for the input.

request - Variable in class com.genologics.ri.step.Escalation

The escalation request.

required - Variable in class com.genologics.ri.configuration.Field

Whether this field is required.

requiredReagentKits - Variable in class com.genologics.ri.processtype.ProcessType

Required reagent kits for this process.

requiredReagentKits - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

List of required reagent kits for this step.

researcher - Variable in class com.genologics.ri.project.Project

The researcher associated with the project.

Researcher - Class in com.genologics.ri.researcher

The detailed representation of a researcher.

Researcher() - Constructor for class com.genologics.ri.researcher.Researcher

Default constructor.

Researcher(URI) - Constructor for class com.genologics.ri.researcher.Researcher

Constructor with URI.

RESEARCHER_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The researcher namespace.

ResearcherLink - Class in com.genologics.ri.project

Researcher is a child element of Project and provides a URI linking to the detailed representation of the Researcher for the Project.

ResearcherLink - Class in com.genologics.ri.reagentlot

Researcher is a child element of the reagent lot.

ResearcherLink - Class in com.genologics.ri.researcher

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

ResearcherLink - Class in com.genologics.ri.role

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

ResearcherLink() - Constructor for class com.genologics.ri.project.ResearcherLink

Constructor for ResearcherLink.

ResearcherLink() - Constructor for class com.genologics.ri.reagentlot.ResearcherLink

Default constructor.

ResearcherLink() - Constructor for class com.genologics.ri.researcher.ResearcherLink

Default constructor.

ResearcherLink() - Constructor for class com.genologics.ri.role.ResearcherLink

Default constructor.

ResearcherLink(Linkable<Researcher>) - Constructor for class com.genologics.ri.project.ResearcherLink

Constructor for ResearcherLink from a Linkable.

ResearcherLink(Linkable<Researcher>) - Constructor for class com.genologics.ri.reagentlot.ResearcherLink

Constructor from a linkable researcher.

ResearcherLink(Linkable<Researcher>) - Constructor for class com.genologics.ri.researcher.ResearcherLink

Constructor from a linkable object.

ResearcherLink(Linkable<Researcher>) - Constructor for class com.genologics.ri.role.ResearcherLink

Constructor from a Linkable.

ResearcherLink(Researcher) - Constructor for class com.genologics.ri.researcher.ResearcherLink

Constructor from a researcher object.

ResearcherLink(Researcher) - Constructor for class com.genologics.ri.role.ResearcherLink

Constructor from a Researcher entity.

ResearcherLink(URI) - Constructor for class com.genologics.ri.project.ResearcherLink

Constructor for ResearcherLink with a URI.

ResearcherLink(URI) - Constructor for class com.genologics.ri.reagentlot.ResearcherLink

Constructor with URI.

ResearcherLink(URI) - Constructor for class com.genologics.ri.researcher.ResearcherLink

Constructor with URI.

ResearcherLink(URI) - Constructor for class com.genologics.ri.role.ResearcherLink

Constructor with URI.

ResearcherLink(URI, String, String) - Constructor for class com.genologics.ri.researcher.ResearcherLink

Constructor with URI and names.

researchers - Variable in class com.genologics.ri.researcher.Researchers

The list of researcher links.

researchers - Variable in class com.genologics.ri.role.Role

The list of researchers assigned to this role.

Researchers - Class in com.genologics.ri.researcher

The representation of a list of researcher links.

Researchers() - Constructor for class com.genologics.ri.researcher.Researchers

Default constructor.

restClient - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

The Spring REST client.

RestClientSnoopingAspect - Class in org.cruk.clarity.api.debugging

Aspect used to examine calls from the REST template to the Clarity API.

RestClientSnoopingAspect() - Constructor for class org.cruk.clarity.api.debugging.RestClientSnoopingAspect

Constructor.

RestClientSnoopingAspect(JaxbMarshallingTool) - Constructor for class org.cruk.clarity.api.debugging.RestClientSnoopingAspect

Constructor with marshalling tool.

RESULT_FILE - Enum constant in enum class com.genologics.ri.artifact.OutputType

Result file output type.

retrieve(String, Class<E>) - Method in interface org.cruk.clarity.api.ClarityAPI

Retrieve an entity using a String form of its URI.

retrieve(String, Class<E>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Retrieve an entity using a String form of its URI.

retrieve(URI, Class<E>) - Method in interface org.cruk.clarity.api.ClarityAPI

Retrieve an entity by its URI.

retrieve(URI, Class<E>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Retrieve an entity by its URI.

retrieve(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Join point for the ClarityAPI.retrieve methods.

review - Variable in class com.genologics.ri.step.Escalation

The escalation review.

REVIEW - Enum constant in enum class com.genologics.ri.step.ActionType

Review the artifact.

reviewer - Variable in class com.genologics.ri.step.EscalationRequest

The reviewer of the escalation request.

REWORK - Enum constant in enum class com.genologics.ri.step.ActionType

Rework the artifact.

REWORKED - Enum constant in enum class com.genologics.ri.artifact.Status

Reworked status.

reworkStepUri - Variable in class com.genologics.ri.step.NextAction

URI of the rework step.

Role - Class in com.genologics.ri.researcher

The role element defines a researcher's level of access in the system.

Role - Class in com.genologics.ri.role

The detailed representation of a Role

Role() - Constructor for class com.genologics.ri.researcher.Role

Default constructor.

Role() - Constructor for class com.genologics.ri.role.Role

Default constructor.

Role(Linkable<Role>) - Constructor for class com.genologics.ri.researcher.Role

Constructor from a linkable object.

Role(Role) - Constructor for class com.genologics.ri.researcher.Role

Constructor from another role object.

Role(URI) - Constructor for class com.genologics.ri.researcher.Role

Constructor with URI.

Role(URI) - Constructor for class com.genologics.ri.role.Role

Constructor with URI.

Role(URI, String) - Constructor for class com.genologics.ri.researcher.Role

Constructor with URI and name.

Role(URI, String) - Constructor for class com.genologics.ri.role.Role

Constructor with URI and name.

ROLE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The role namespace.

RoleLink - Class in com.genologics.ri.role

Role-link is a child element type of roles and provides a URI linking to the detailed representation of a Role.

RoleLink() - Constructor for class com.genologics.ri.role.RoleLink

Default constructor.

RoleLink(Role) - Constructor for class com.genologics.ri.role.RoleLink

Constructor from a Role entity.

RoleLink(URI) - Constructor for class com.genologics.ri.role.RoleLink

Constructor with URI.

RoleLink(URI, String) - Constructor for class com.genologics.ri.role.RoleLink

Constructor with URI and name.

roleName - Variable in class com.genologics.ri.researcher.Role

Deprecated.

Deprecated from version 2.19.

roles - Variable in class com.genologics.ri.researcher.Credentials

The roles assigned to the researcher.

roles - Variable in class com.genologics.ri.role.Roles

The list of role links.

Roles - Class in com.genologics.ri.role

The representation for a list of role links.

Roles() - Constructor for class com.genologics.ri.role.Roles

Default constructor.

Roles(URI) - Constructor for class com.genologics.ri.role.Roles

Constructor with URI.

ROOT_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The root namespace.

routeArtifacts(Routing) - Method in interface org.cruk.clarity.api.ClarityAPI

Issue a routing request for artifacts into workflows.

routeArtifacts(Routing) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Issue a routing request for artifacts into workflows.

Routing - Class in com.genologics.ri.routing

The root element for a routing API call.

Routing() - Constructor for class com.genologics.ri.routing.Routing

ROUTING_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The routing namespace.

rows - Variable in class com.genologics.ri.containertype.ContainerType

The y-dimension (vertical/rows) of the container's coordinate system.

RUNNING - Enum constant in enum class com.genologics.ri.step.Status

The step is currently running.

runProgramPerEvent - Variable in class com.genologics.ri.automation.Automation

Flag indicating whether the program should run per event.

runProgramPerEvent - Variable in class com.genologics.ri.processtype.Parameter

Deprecated.

This property is no longer supported.

runSavedQuery(Linkable<SavedQuery>, OutputStream) - Method in interface org.cruk.clarity.api.ClarityAPI

Run a saved query and write the result to the given output stream.

runSavedQuery(Linkable<SavedQuery>, OutputStream, long) - Method in interface org.cruk.clarity.api.ClarityAPI

Run a saved query and write the result to the given output stream.

runSavedQuery(Linkable<SavedQuery>, OutputStream, long) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Run a saved query and write the result to the given output stream.

runSavedQuery(Linkable<SavedQuery>, OutputStream, long) - Method in class org.cruk.clarity.api.impl.SavedQueryRunner

Run a saved query and write the result to the given output stream.

runSomething(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Join point for the methods that take an object in to perform an operation and return an object as a result (not necessarily object passed in).

S

Sample - Class in com.genologics.ri.sample

The detailed representation of a sample.

Sample() - Constructor for class com.genologics.ri.sample.Sample

Default constructor.

Sample(URI) - Constructor for class com.genologics.ri.sample.Sample

Constructor with a URI.

Sample(URI, String) - Constructor for class com.genologics.ri.sample.Sample

Constructor with URI and id.

SAMPLE - Enum constant in enum class com.genologics.ri.artifact.OutputType

Sample output type.

SAMPLE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The sample namespace.

SampleBase - Class in com.genologics.ri.sample

The base representation of a Sample, defining common elements for both Sample and Sample creation.

SampleBase() - Constructor for class com.genologics.ri.sample.SampleBase

Constructor for an empty sample base.

SampleBase(SampleBase) - Constructor for class com.genologics.ri.sample.SampleBase

Copy constructor for a sample base.

SampleBatchFetchResult - Class in com.genologics.ri.sample

Batch fetch and update holder for samples.

SampleBatchFetchResult() - Constructor for class com.genologics.ri.sample.SampleBatchFetchResult

Constructor for an empty sample batch fetch result.

SampleCreation - Class in com.genologics.ri.sample

Sample creation is the detailed representation required when creating a new Sample in the system.

SampleCreation() - Constructor for class com.genologics.ri.sample.SampleCreation

Constructor for an empty sample creation.

SampleCreation(Sample) - Constructor for class com.genologics.ri.sample.SampleCreation

Construct a new object for sample creation via the API.

sampleCreations - Variable in class com.genologics.ri.sample.SampleBatchFetchResult

The list of sample creations.

sampleFields - Variable in class com.genologics.ri.processtype.ProcessType

Fields displayed for samples in the step view.

sampleFields - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

List of fields to display for samples.

SampleLink - Class in com.genologics.ri.artifact

Sample is a child element of Artifact and provides a URI linking to the detailed representation of a submitted Sample for the Artifact.

SampleLink - Class in com.genologics.ri.sample

Sample-link is a child element type of samples and provides a URI linking to the detailed representation of a sample.

SampleLink() - Constructor for class com.genologics.ri.artifact.SampleLink

Default constructor.

SampleLink() - Constructor for class com.genologics.ri.sample.SampleLink

Constructor for an empty sample link.

SampleLink(LimsEntityLinkable<Sample>) - Constructor for class com.genologics.ri.artifact.SampleLink

Constructor from a LimsEntityLinkable.

SampleLink(LimsEntityLinkable<Sample>) - Constructor for class com.genologics.ri.sample.SampleLink

Constructor for a sample link from a LIMS entity linkable sample.

SampleLink(Linkable<Sample>) - Constructor for class com.genologics.ri.artifact.SampleLink

Constructor from a Linkable.

SampleLink(Linkable<Sample>) - Constructor for class com.genologics.ri.sample.SampleLink

Constructor for a sample link from a linkable sample.

SampleLink(URI) - Constructor for class com.genologics.ri.artifact.SampleLink

Constructor taking a URI.

SampleLink(URI) - Constructor for class com.genologics.ri.sample.SampleLink

Constructor for a sample link with a URI.

SampleLink(URI, String) - Constructor for class com.genologics.ri.artifact.SampleLink

Constructor taking a URI and LIMS id.

SampleLink(URI, String) - Constructor for class com.genologics.ri.sample.SampleLink

Constructor for a sample link with a URI and LIMS id.

samples - Variable in class com.genologics.ri.artifact.Artifact

The list of samples associated with this artifact.

samples - Variable in class com.genologics.ri.artifact.DemuxArtifact

The samples in this demux artifact.

samples - Variable in class com.genologics.ri.sample.SampleBatchFetchResult

The list of samples.

samples - Variable in class com.genologics.ri.sample.Samples

The list of sample links.

Samples - Class in com.genologics.ri.sample

The representation for a list of sample links.

Samples() - Constructor for class com.genologics.ri.sample.Samples

Constructor for an empty samples list.

SAVED_QUERY_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The saved query namespace.

savedQueries - Variable in class com.genologics.ri.savedquery.SavedQueries

The list of saved query links.

SavedQueries - Class in com.genologics.ri.savedquery

Represents a paginated list of saved queries.

SavedQueries() - Constructor for class com.genologics.ri.savedquery.SavedQueries

Default constructor.

SavedQuery - Class in com.genologics.ri.savedquery

Represents a saved query in the Clarity LIMS system.

SavedQuery() - Constructor for class com.genologics.ri.savedquery.SavedQuery

Default constructor.

SavedQuery(URI) - Constructor for class com.genologics.ri.savedquery.SavedQuery

Constructor with URI.

SavedQueryLink - Class in com.genologics.ri.savedquery

Link to a saved query entity.

SavedQueryLink() - Constructor for class com.genologics.ri.savedquery.SavedQueryLink

Default constructor.

SavedQueryLink(URI) - Constructor for class com.genologics.ri.savedquery.SavedQueryLink

Constructor with URI.

savedQueryRunner - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

Runner for saved queries.

SavedQueryRunner - Class in org.cruk.clarity.api.impl

Extraction of code to run a saved query to simplify ClarityAPIImpl.

SavedQueryRunner() - Constructor for class org.cruk.clarity.api.impl.SavedQueryRunner

Constructor.

SavedQuerySummary - Class in org.cruk.clarity.api

The summary of a result of running a saved query.

SavedQuerySummary(Linkable<SavedQuery>, MediaType, long) - Constructor for class org.cruk.clarity.api.SavedQuerySummary

Constructor.

SCANNED - Enum constant in enum class com.genologics.ri.container.ContainerState

The container state when the container's contents have been scanned.

script - Variable in class com.genologics.ri.automation.Automation

The script content for this automation.

script - Variable in class com.genologics.ri.processtype.Parameter

The EPP script text that will actually run.

Search<E extends Locatable> - Class in org.cruk.clarity.api.search

A class holding both the parameters of a search and the links returned from that search.

Search(Map<String, ?>, Class<E>) - Constructor for class org.cruk.clarity.api.search.Search

Constructor that takes the parameters from a call to the API's find method.

Search(SearchTerms<E>) - Constructor for class org.cruk.clarity.api.search.Search

Constructor that accepts an already created SearchTerms object.

SEARCH_FILE_PATTERN - Static variable in class org.cruk.clarity.api.search.Search

The default name for search files.

SEARCH_RESULT_FILE - Enum constant in enum class com.genologics.ri.artifact.OutputType

Search result file output type.

SearchTerm - Class in org.cruk.clarity.api.search

Class recording an individual parameter and its value or values of a call to the API's find method.

SearchTerm(String) - Constructor for class org.cruk.clarity.api.search.SearchTerm

Create a search term with no values.

SearchTerm(String, Collection<? extends Object>) - Constructor for class org.cruk.clarity.api.search.SearchTerm

Create a search term with the given values.

SearchTerms<E extends Locatable> - Class in org.cruk.clarity.api.search

Class recording the parameters and entity class of a call to the API's find method.

SearchTerms(Map<String, ?>, Class<E>) - Constructor for class org.cruk.clarity.api.search.SearchTerms

Creates a new SearchTerms object with the given values (as have been passed to find).

selectedContainers - Variable in class com.genologics.ri.step.Placements

The list of selected containers.

sequence - Variable in class com.genologics.ri.stepconfiguration.NextStep

The sequence index of the next step.

serialNumber - Variable in class com.genologics.ri.instrument.Instrument

The instrument serial number.

serverAddress - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

The root URI to the Clarity server.

setAccountLocked(Boolean) - Method in class com.genologics.ri.researcher.Credentials

Sets whether the account is locked.

setAction(ActionType) - Method in class com.genologics.ri.step.NextAction

Sets the action type.

setAction(String) - Method in class com.genologics.ri.permission.Permission

Set the permission action.

setAction(String) - Method in class com.genologics.ri.permission.PermissionLink

Set the permission action.

setAction(String) - Method in class com.genologics.ri.role.PermissionLink

Sets the action associated with the permission.

setActions(ActionsLink) - Method in class com.genologics.ri.step.ProcessStep

Sets the link to the actions associated with this step.

setAllowNonPresetValues(Boolean) - Method in class com.genologics.ri.configuration.Field

Sets whether values other than preset values are allowed.

setAlpha(Boolean) - Method in class com.genologics.ri.containertype.Dimension

Sets whether numbering in this dimension is alphabetic.

setArchived(Boolean) - Method in class com.genologics.ri.controltype.ControlType

Sets the archived flag.

setArchived(Boolean) - Method in class com.genologics.ri.instrument.Instrument

Set whether the instrument has been archived.

setArchived(Boolean) - Method in class com.genologics.ri.reagentkit.ReagentKit

Sets whether the reagent kit is archived.

setArrangements(Linkable<Arrangements>) - Method in class com.genologics.ri.step.ProcessStep

Sets the link to the arrangements associated with this step.

setArtifact(DemuxSourceArtifact) - Method in class com.genologics.ri.artifact.Demux

Sets the artifact.

setArtifact(LimsEntityLinkable<Artifact>) - Method in class com.genologics.ri.sample.SampleBase

Sets the artifact for this sample.

setArtifact(Linkable<Artifact>) - Method in class com.genologics.ri.artifact.DemuxSourceArtifact

Sets the artifact from a Linkable.

setArtifact(Linkable<Artifact>) - Method in class com.genologics.ri.step.CreationInput

Sets the artifact.

setArtifact(Linkable<Artifact>) - Method in class com.genologics.ri.step.NextAction

Sets the artifact.

setArtifact(Linkable<Artifact>) - Method in class com.genologics.ri.step.Output

Sets the artifact.

setArtifact(Linkable<Artifact>) - Method in class com.genologics.ri.step.OutputPlacement

Sets the artifact for this output placement.

setArtifact(Linkable<DemuxArtifact>) - Method in class com.genologics.ri.artifact.DemuxLink

Sets the artifact from a Linkable.

setArtifactGroups(Collection<? extends Linkable<ArtifactGroup>>) - Method in class com.genologics.ri.artifact.Artifact

Sets the artifact groups this artifact belongs to.

setArtifacts(Artifacts) - Method in class com.genologics.ri.artifactgroup.ArtifactGroup

Sets the link to the artifacts in this group.

setArtifactType(String) - Method in class com.genologics.ri.processtype.ProcessInput

Sets the artifact type for the input.

setArtifactType(String) - Method in class com.genologics.ri.processtype.ProcessOutput

Sets the artifact type for this output.

setArtifactUri(URI) - Method in class com.genologics.ri.step.NextAction

Sets the artifact URI.

setAssignWorkingFlag(Boolean) - Method in class com.genologics.ri.processtype.ProcessOutput

Deprecated.

This property is no longer supported.

setAttachedTo(Linkable<?>) - Method in class com.genologics.ri.file.ClarityFile

Sets the resource that this file is attached to.

setAttachTo(String) - Method in class com.genologics.ri.processtype.Field

Sets the entity to which this field is attached.

setAttachTo(String) - Method in class com.genologics.ri.stepconfiguration.Field

Sets the attach-to value indicating what entity this field is attached to.

setAttachToCategory(String) - Method in class com.genologics.ri.configuration.Field

Sets the category this field is attached to.

setAttachToCategory(String) - Method in class com.genologics.ri.configuration.Type

Sets the category this user defined type is attached to.

setAttachToCategory(String) - Method in class com.genologics.ri.configuration.UdfConfigLink

Sets the category this field is attached to.

setAttachToCategory(String) - Method in class com.genologics.ri.configuration.UdtConfigLink

Sets the category this user defined type is attached to.

setAttachToName(String) - Method in class com.genologics.ri.configuration.Field

Sets the name of the entity type this field is attached to.

setAttachToName(String) - Method in class com.genologics.ri.configuration.Type

Sets the name of the entity type this user defined type is attached to.

setAttachToName(String) - Method in class com.genologics.ri.configuration.UdfConfigLink

Sets the name of the entity type this field is attached to.

setAttachToName(String) - Method in class com.genologics.ri.configuration.UdtConfigLink

Sets the name of the entity type this user defined type is attached to.

setAuthor(Linkable<Researcher>) - Method in class com.genologics.ri.step.EscalationRequest

Sets the author.

setAuthor(Linkable<Researcher>) - Method in class com.genologics.ri.step.EscalationReview

Sets the author.

setAutomaticNextStep(Linkable<ProcessStep>) - Method in class com.genologics.ri.step.ProcessStep

Sets the link to the next step that will be automatically triggered after this step.

setAutoRevertToSFTPUploads(boolean) - Method in interface org.cruk.clarity.api.ClarityAPI

Set whether the SFTP mechanism can be used as a fall back for uploading files if a file exceeds the HTTP upload size limit.

setAutoRevertToSFTPUploads(boolean) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set whether the SFTP mechanism can be used as a fall back for uploading files if a file exceeds the HTTP upload size limit.

setBillingAddress(Address) - Method in class com.genologics.ri.lab.Lab

Sets the billing address of the lab.

setBioSource(BioSource) - Method in class com.genologics.ri.sample.SampleBase

Deprecated.

Biosource is not supported in Clarity.

setBuiltIn(Boolean) - Method in class com.genologics.ri.role.Role

Sets whether this is a built-in system role.

setBulkOperationBatchSize(int) - Method in interface org.cruk.clarity.api.ClarityAPI

Set the number of objects that will be fetched, updated or created in each call the Clarity API for the bulk operations (those that use a collection of links or objects).

setBulkOperationBatchSize(int) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set the number of objects that will be fetched, updated or created in each call the Clarity API for the bulk operations (those that use a collection of links or objects).

setCacheManager(CacheManager) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Set the Ehcache cache manager.

setCatalogueNumber(String) - Method in class com.genologics.ri.controltype.ControlType

Sets the catalogue number of the control type.

setCatalogueNumber(String) - Method in class com.genologics.ri.reagentkit.ReagentKit

Sets the catalogue number of the reagent kit.

setCategory(String) - Method in class com.genologics.ri.exception.Exception

Sets the category of the exception.

setChannel(String) - Method in class com.genologics.ri.automation.Automation

Sets the channel for this automation.

setChannel(String) - Method in class com.genologics.ri.processtype.Parameter

Sets the channel on which the EPP runs.

setCity(String) - Method in class com.genologics.ri.Address

Sets the city.

setClarityAPI(ClarityAPI) - Method in class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Set the API.

setClarityAPI(ClarityAPI) - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Set the public interface access to the API.

setClarityAPI(ClarityAPIInternal) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Sets the API being used.

setClarityAPI(ClarityAPIInternal) - Method in class org.cruk.clarity.api.impl.LatestVersionsResetAspect

Sets the API being used.

setClarityMarshaller(Marshaller) - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Inject the JAXB marshaller.

setClarityMarshaller(Marshaller) - Method in class org.cruk.clarity.api.record.ClarityAPIRecordingAspect

Inject the JAXB marshaller.

setClarityUnmarshaller(Unmarshaller) - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Inject the JAXB unmarshaller.

setClarityUnmarshaller(Unmarshaller) - Method in class org.cruk.clarity.api.record.ClarityAPIRecordingAspect

Inject the JAXB unmarshaller.

setCloseDate(Date) - Method in class com.genologics.ri.project.Project

Set the close date of the project.

setCode(String) - Method in class com.genologics.ri.exception.Exception

Sets the HTTP response code of the error.

setColumns(Dimension) - Method in class com.genologics.ri.containertype.ContainerType

Sets the x-dimension (horizontal/columns) of the container's coordinate system.

setComment(String) - Method in class com.genologics.ri.step.EscalationRequest

Sets the comment.

setComment(String) - Method in class com.genologics.ri.step.EscalationReview

Sets the comment.

setConcentration(String) - Method in class com.genologics.ri.controltype.ControlType

Sets the concentration of the control type.

setConfiguration(Linkable<ProtocolStep>) - Method in class com.genologics.ri.step.StepCreation

Sets the step configuration from a protocol step link.

setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.Actions

Sets the step configuration.

setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.Arrangements

Sets the step configuration.

setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.Placements

Sets the step configuration.

setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.Pools

Sets the step configuration.

setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.ProcessStep

Sets the configuration of the step.

setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.ProgramStatus

Sets the configuration of the step.

setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.ReagentLots

Sets the step configuration.

setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.Reagents

Sets the step configuration.

setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.StepCreation

Sets the step configuration.

setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.StepDetails

Sets the step configuration.

setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.StepSetup

Sets the step configuration.

setConfiguration(ProtocolStep) - Method in class com.genologics.ri.step.StepCreation

Sets the step configuration from a protocol step.

setConfiguration(Properties) - Method in interface org.cruk.clarity.api.ClarityAPI

Set configuration from a properties file.

setConfiguration(Properties) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set configuration from a properties file.

setContainer(LimsEntityLinkable<Container>) - Method in class com.genologics.ri.Location

Sets the container from a LIMS entity linkable.

setContainerType(ContainerType) - Method in class com.genologics.ri.container.Container

Sets the container type.

setContainerType(ContainerType) - Method in class com.genologics.ri.step.StepCreation

Sets the container type from a container type object.

setContainerType(Linkable<ContainerType>) - Method in class com.genologics.ri.container.Container

Sets the container type from a linkable.

setContainerType(String) - Method in class com.genologics.ri.step.StepCreation

Sets the container type name.

setContentLocation(URI) - Method in class com.genologics.ri.file.ClarityFile

Sets the network location URI where the file content can be retrieved.

setContext(Context) - Method in class com.genologics.ri.automation.Automation

Sets the context in which this automation runs.

setControlledVocabulary(Boolean) - Method in class com.genologics.ri.configuration.Field

Sets whether this field uses a controlled vocabulary.

setControlType(Linkable<ControlType>) - Method in class com.genologics.ri.artifact.Artifact

Sets the control type for this artifact.

setControlType(Linkable<ControlType>) - Method in class com.genologics.ri.sample.SampleBase

Sets the control type for this sample.

setControlType(Linkable<ControlType>) - Method in class com.genologics.ri.step.CreationInput

Sets the control type.

setControlTypeUri(URI) - Method in class com.genologics.ri.step.CreationInput

Sets the control type URI.

setCountry(String) - Method in class com.genologics.ri.Address

Sets the country.

setCreatedBy(Linkable<Researcher>) - Method in class com.genologics.ri.reagentlot.ReagentLot

Sets the researcher who created this lot.

setCreatedDate(Date) - Method in class com.genologics.ri.reagentlot.ReagentLot

Sets the creation date.

setCreationLocation(LimsEntityLinkable<Container>, String) - Method in class com.genologics.ri.sample.Sample

Set the location of this sample for creation.

setCreationLocation(Location) - Method in class com.genologics.ri.sample.Sample

Set the location of this sample for creation.

setCredentials(Credentials) - Method in class com.genologics.ri.researcher.Researcher

Sets the researcher's credentials.

setCredentials(String, String) - Method in interface org.cruk.clarity.api.ClarityAPI

Set the credentials to use to connect to the REST API.

setCredentials(String, String) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set the credentials to use to connect to the REST API.

setCredentials(URI, Credentials) - Method in interface org.cruk.clarity.api.http.AuthenticatingClientHttpRequestFactory

Set the credentials based on the protocol, host and port in the URL.

setCredentials(URI, Credentials) - Method in class org.cruk.clarity.api.http.HttpComponentsClientHttpRequestFactoryBasicAuth

Set the credentials based on the protocol, host and port in the URL.

setCredentials(Credentials) - Method in interface org.cruk.clarity.api.ClarityAPI

Set the credentials to use to connect to the REST API.

setCredentials(Credentials) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set the credentials to use to connect to the REST API.

setCredentials(HttpHost, Credentials) - Method in interface org.cruk.clarity.api.http.AuthenticatingClientHttpRequestFactory

Set the credentials based on the HTTP host specification.

setCredentials(HttpHost, Credentials) - Method in class org.cruk.clarity.api.http.HttpComponentsClientHttpRequestFactoryBasicAuth

Set the credentials based on the HTTP host specification.

setCredentialsProvider(CredentialsProvider) - Method in class org.cruk.clarity.api.http.HttpComponentsClientHttpRequestFactoryBasicAuth

Set the credentials provider to use.

setCurrentState(ProcessState) - Method in class com.genologics.ri.step.ProcessStep

Sets the current state of the step.

setCustom(Boolean) - Method in class com.genologics.ri.globaltoken.GlobalToken

Set whether this is a custom token.

setDate(Date) - Method in class com.genologics.ri.step.EscalationRequest

Sets the date.

setDate(Date) - Method in class com.genologics.ri.step.EscalationReview

Sets the date.

setDateCompleted(Date) - Method in class com.genologics.ri.sample.SampleBase

Sets the date the sample was completed.

setDateCompleted(Date) - Method in class com.genologics.ri.step.ProcessStep

Sets the date and time the step was completed.

setDateReceived(Date) - Method in class com.genologics.ri.sample.SampleBase

Sets the date the sample was received.

setDateRun(Date) - Method in class com.genologics.ri.process.ClarityProcess

Sets the date the process was run.

setDateRun(Date) - Method in class com.genologics.ri.processexecution.ExecutableProcess

Sets the date the process was run.

setDateStarted(Date) - Method in class com.genologics.ri.step.ProcessStep

Sets the date and time the step was started.

setDefault(Boolean) - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Sets whether this is the default template.

setDefaultGrouping(GenericTypeLink) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Deprecated.

Please use "<milestone>DefaultGrouping" (for example, "queueDefaultGrouping") in a StepProperty field instead.

setDemux(DemuxDetails) - Method in class com.genologics.ri.artifact.DemuxArtifact

Sets the demux details.

setDemux(Linkable<Demux>) - Method in class com.genologics.ri.artifact.Artifact

Sets the demultiplexing information for this artifact.

setDemuxDetails(DemuxDetails) - Method in class com.genologics.ri.artifact.Demux

Sets the demux details.

setDepartment(String) - Method in class com.genologics.ri.Address

Sets the department.

setDescription(String) - Method in class com.genologics.ri.globaltoken.GlobalToken

Set the token description.

setDescription(String) - Method in class com.genologics.ri.permission.Permission

Set the permission description.

setDescription(String) - Method in class com.genologics.ri.sample.BioSource

Deprecated.

Sets the description of the biosource.

setDetail(Boolean) - Method in class com.genologics.ri.processtype.IceBucketField

Sets whether this field shows in the detail view.

setDetail(Boolean) - Method in class com.genologics.ri.processtype.QueueField

Sets whether this field shows in the detail view.

setDetail(Boolean) - Method in class com.genologics.ri.stepconfiguration.IceBucketField

Sets whether this field should be shown in detail view.

setDetail(Boolean) - Method in class com.genologics.ri.stepconfiguration.QueueField

Sets whether this field should be shown in detail view.

setDetails(Linkable<StepDetails>) - Method in class com.genologics.ri.step.ProcessStep

Sets the link to the details associated with this step.

setDeviation(Boolean) - Method in class com.genologics.ri.configuration.Field

Sets whether this field represents a deviation.

setDisplayName(String) - Method in class com.genologics.ri.processtype.ProcessInput

Sets the display name for the input.

setDisplayName(String) - Method in class com.genologics.ri.processtype.ProcessOutput

Sets the display name for the output.

setDisplayPrecision(Integer) - Method in class com.genologics.ri.configuration.Field

Sets the display precision for numeric fields.

setDownloadDirectFromHttpStore(boolean) - Method in interface org.cruk.clarity.api.ClarityAPI

For files stored in a HTTP file store, set whether to download these files directly from their HTTP server or whether to fetch them via the API's files/id/download end point (i.e. the same as files in the regular file store).

setDownloadDirectFromHttpStore(boolean) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

For files stored in a HTTP file store, set whether to download these files directly from their HTTP server or whether to fetch them via the API's files/id/download end point (i.e. the same as files in the regular file store).

setDynamicPresets(Boolean) - Method in class com.genologics.ri.configuration.Field

Sets whether this field uses dynamic presets.

setEditable(Boolean) - Method in class com.genologics.ri.configuration.Field

Sets whether this field is editable.

setEmail(String) - Method in class com.genologics.ri.researcher.Researcher

Sets the researcher's email address.

setEnabled(boolean) - Method in class com.genologics.ri.stepconfiguration.StepSetup

Sets whether the step setup view is enabled.

setEnabled(Boolean) - Method in class com.genologics.ri.processtype.StepSetup

Sets whether the step setup view is enabled for this process type.

setErrorHandler(ResponseErrorHandler) - Method in class org.cruk.clarity.api.impl.SavedQueryRunner

Set the error handler.

setEscalation(Escalation) - Method in class com.genologics.ri.step.Actions

Sets the escalation information.

setExpiryDate(String) - Method in class com.genologics.ri.instrument.Instrument

Set the instrument expiry date.

setExpiryDate(Date) - Method in class com.genologics.ri.reagentlot.ReagentLot

Sets the expiry date.

setFailOnMissingSearch(boolean) - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Get whether this aspect should fail if a search doesn't have a recording.

setFax(String) - Method in class com.genologics.ri.researcher.Researcher

Sets the researcher's fax number.

setFieldDynamicPresets(Field, L, FieldDynamicPresetDetails) - Method in interface org.cruk.clarity.api.ClarityAPI

Set dynamic presets for a field on an entity (certainly process, haven't tested artifacts).

setFieldDynamicPresets(Field, L, FieldDynamicPresetDetails) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set dynamic presets for a field on an entity (certainly process, haven't tested artifacts).

setFieldDynamicPresets(Field, L, String...) - Method in interface org.cruk.clarity.api.ClarityAPI

Convenience version of ClarityAPI.setFieldDynamicPresets(Field, LimsEntityLinkable, FieldDynamicPresetDetails) to set the presets with variable string arguments.

setFieldDynamicPresets(Field, L, Collection<String>) - Method in interface org.cruk.clarity.api.ClarityAPI

Convenience version of ClarityAPI.setFieldDynamicPresets(Field, LimsEntityLinkable, FieldDynamicPresetDetails) to set the presets with variable string arguments.

setFile(ClarityFile) - Method in class com.genologics.ri.artifact.Artifact

Sets the file associated with this artifact.

setFile(String) - Method in class com.genologics.ri.processtype.Parameter

Deprecated.

This property is no longer supported.

setFilestoreCredentials(String, String) - Method in interface org.cruk.clarity.api.ClarityAPI

Set the credentials used to connect to the file store.

setFilestoreCredentials(String, String) - Method in interface org.cruk.clarity.api.filestore.ClaritySFTPUploader

Set the credentials used to connect to the file store.

setFilestoreCredentials(String, String) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set the credentials used to connect to the file store.

setFilestoreServer(String) - Method in interface org.cruk.clarity.api.ClarityAPI

Set the name of the file store host.

setFilestoreServer(String) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set the name of the file store host.

setFilestoreSFTPUploader(ClaritySFTPUploader) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set the file store SFTP upload implementation.

setFileUploadClient(RestOperations) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set the REST client used for file uploads over HTTP.

setFirstName(String) - Method in class com.genologics.ri.process.Technician

Sets the first name.

setFirstName(String) - Method in class com.genologics.ri.processtemplate.Technician

Sets the first name of the technician.

setFirstName(String) - Method in class com.genologics.ri.researcher.Researcher

Sets the researcher's first name.

setFirstName(String) - Method in class com.genologics.ri.researcher.ResearcherLink

Sets the researcher's first name.

setFirstName(String) - Method in class com.genologics.ri.role.ResearcherLink

Sets the first name of the researcher.

setFirstName(String) - Method in class com.genologics.ri.sample.Submitter

Sets the first name of the submitter.

setFirstName(String) - Method in class com.genologics.ri.step.Technician

Sets the first name of the technician.

setFirstName(String) - Method in class com.genologics.ri.step.UserLink

Sets the first name of the user.

setFirstPresetDefaultValue(Boolean) - Method in class com.genologics.ri.configuration.Field

Sets whether the first preset value is the default.

setHttpClient(HttpClient) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set the HTTP client.

setHttpRequestFactory(AuthenticatingClientHttpRequestFactory) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set the factory used for obtaining HTTP requests.

setHttpRequestFactory(ClientHttpRequestFactory) - Method in class org.cruk.clarity.api.impl.SavedQueryRunner

Set the request factory.

setHttpStatus(HttpStatusCode) - Method in exception org.cruk.clarity.api.ClarityException

Set the HTTP status code.

setHttpUploadSizeLimit(long) - Method in interface org.cruk.clarity.api.ClarityAPI

Set the maximum size of file that can be uploaded using HTTP.

setHttpUploadSizeLimit(long) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set the maximum size of file that can be uploaded using HTTP.

setId(String) - Method in class com.genologics.ri.savedquery.SavedQuery

Sets the unique identifier of the saved query.

setId(String) - Method in class com.genologics.ri.savedquery.SavedQueryLink

Sets the unique identifier of the saved query.

setId(URI) - Method in class com.genologics.ri.ExternalId

Sets the external id.

setIndex(Integer) - Method in class com.genologics.ri.protocolconfiguration.Protocol

Sets the index of the protocol.

setIndex(Integer) - Method in class com.genologics.ri.stage.Stage

Sets the index of the stage in the workflow.

setInitials(String) - Method in class com.genologics.ri.researcher.Researcher

Sets the researcher's initials.

setInput(LimsEntityLinkable<Artifact>) - Method in class com.genologics.ri.process.InputOutputMap

Sets the input from a LIMS entity linkable artifact.

setInput(LimsEntityLinkable<Artifact>) - Method in class com.genologics.ri.step.InputOutputMap

Sets the input from a LIMS entity linkable artifact.

setInput(Linkable<Artifact>) - Method in class com.genologics.ri.process.InputOutputMap

Sets the input from a linkable artifact.

setInput(Linkable<Artifact>) - Method in class com.genologics.ri.step.InputOutputMap

Sets the input from a linkable artifact.

setInput(ArtifactLink) - Method in class com.genologics.ri.process.InputOutputMap

Sets the input artifact link.

setInput(ArtifactLink) - Method in class com.genologics.ri.step.InputOutputMap

Sets the input artifact link.

setInputArtifacts(Collection<? extends Linkable<Artifact>>) - Method in class com.genologics.ri.step.PooledInputs

Sets the input artifacts, replacing any existing inputs.

setInputs(Collection<? extends Linkable<Artifact>>) - Method in class com.genologics.ri.processexecution.ExecutableInputOutputMap

Sets the inputs from a collection of artifact links.

setInstitution(String) - Method in class com.genologics.ri.Address

Sets the institution.

setInstrument(Instrument) - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Sets the instrument from an Instrument object.

setInstrument(Instrument) - Method in class com.genologics.ri.step.StepDetails

Sets the instrument from an instrument object.

setInstrument(Linkable<Instrument>) - Method in class com.genologics.ri.process.ClarityProcess

Sets the instrument from a linkable object.

setInstrument(Linkable<Instrument>) - Method in class com.genologics.ri.processexecution.ExecutableProcess

Sets the instrument from an instrument link.

setInstrument(Linkable<Instrument>) - Method in class com.genologics.ri.step.StepDetails

Sets the instrument from a link.

setInstrument(InstrumentLink) - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Sets the instrument.

setInternalClarityAPI(ClarityAPIInternal) - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Set the internal interface access to the API.

setInternalClarityAPI(ClarityAPIInternal) - Method in class org.cruk.clarity.api.record.ClarityAPIRecordingAspect

Set the internal interface access to the API.

setInvocationType(InvocationType) - Method in class com.genologics.ri.processtype.Parameter

Deprecated.

This property is no longer supported.

setInvoiceDate(Date) - Method in class com.genologics.ri.project.Project

Set the invoice date of the project.

setJaxbConfig(List<Class<?>>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set the list of classes that are managed by the Clarity JAXB context.

setLab(Linkable<Lab>) - Method in class com.genologics.ri.researcher.Researcher

Sets the link to the researcher's lab.

setLastModifiedBy(Linkable<Researcher>) - Method in class com.genologics.ri.reagentlot.ReagentLot

Sets the researcher who last modified this lot.

setLastModifiedDate(Date) - Method in class com.genologics.ri.reagentlot.ReagentLot

Sets the last modification date.

setLastName(String) - Method in class com.genologics.ri.process.Technician

Sets the last name.

setLastName(String) - Method in class com.genologics.ri.processtemplate.Technician

Sets the last name of the technician.

setLastName(String) - Method in class com.genologics.ri.researcher.Researcher

Sets the researcher's last name.

setLastName(String) - Method in class com.genologics.ri.researcher.ResearcherLink

Sets the researcher's last name.

setLastName(String) - Method in class com.genologics.ri.role.ResearcherLink

Sets the last name of the researcher.

setLastName(String) - Method in class com.genologics.ri.sample.Submitter

Sets the last name of the submitter.

setLastName(String) - Method in class com.genologics.ri.step.Technician

Sets the last name of the technician.

setLastName(String) - Method in class com.genologics.ri.step.UserLink

Sets the last name of the user.

setLatestVersionsResetAspect(LatestVersionsResetAspect) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Set a reference to the aspect that resets the API's behaviour around stateful entities.

setLimsid(String) - Method in class com.genologics.ri.artifact.Artifact

Sets the LIMS id of this artifact.

setLimsid(String) - Method in class com.genologics.ri.artifact.ArtifactLink

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.artifact.DemuxArtifactSample

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.artifact.ParentProcessLink

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.artifact.SampleLink

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.container.Container

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.container.ContainerLink

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.container.Placement

Sets the LIMS id of the artifact.

setLimsid(String) - Method in class com.genologics.ri.ContainerLink

Sets the LIMS id of the container.

setLimsid(String) - Method in class com.genologics.ri.file.ClarityFile

Sets the LIMS id of this file.

setLimsid(String) - Method in class com.genologics.ri.file.FileLink

Sets the LIMS id of the file.

setLimsid(String) - Method in class com.genologics.ri.instrument.Instrument

Set the LIMS id for this object.

setLimsid(String) - Method in class com.genologics.ri.instrument.InstrumentLink

Set the LIMS id for this object.

setLimsid(String) - Method in class com.genologics.ri.lab.Lab

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.lab.LabLink

Sets the LIMS id.

setLimsid(String) - Method in interface com.genologics.ri.LimsEntityLinkable

Set the LIMS id for this object.

setLimsid(String) - Method in class com.genologics.ri.Location

Sets the LIMS id of the container.

setLimsid(String) - Method in class com.genologics.ri.process.ArtifactLink

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.process.ClarityProcess

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.process.InstrumentLink

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.process.ParentProcessLink

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.process.ProcessLink

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.processexecution.InstrumentLink

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.processtemplate.InstrumentLink

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.project.Project

Set the LIMS id of the project.

setLimsid(String) - Method in class com.genologics.ri.project.ProjectLink

Set the LIMS id of the project.

setLimsid(String) - Method in class com.genologics.ri.project.ResearcherLink

Set the LIMS id of the researcher.

setLimsid(String) - Method in class com.genologics.ri.queue.ArtifactLink

Sets the LIMS id of the artifact.

setLimsid(String) - Method in class com.genologics.ri.reagentlot.ReagentLot

setLimsid(String) - Method in class com.genologics.ri.reagentlot.ReagentLotLink

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.reagentlot.ResearcherLink

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.reagenttype.ReagentType

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.reagenttype.ReagentTypeLink

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.researcher.LabLink

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.researcher.Researcher

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.researcher.ResearcherLink

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.role.ResearcherLink

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.sample.ArtifactLink

Sets the LIMS id of the artifact.

setLimsid(String) - Method in class com.genologics.ri.sample.ProjectLink

Sets the LIMS id of the project.

setLimsid(String) - Method in class com.genologics.ri.sample.SampleBase

Sets the LIMS id for this sample.

setLimsid(String) - Method in class com.genologics.ri.sample.SampleLink

Sets the LIMS id of the sample.

setLimsid(String) - Method in class com.genologics.ri.step.ArtifactLink

Sets the LIMS id.

setLimsid(String) - Method in class com.genologics.ri.step.InstrumentLink

Sets the LIMS id (does nothing for this implementation).

setLimsid(String) - Method in class com.genologics.ri.step.ProcessStep

Sets the LIMS id of the step.

setLimsid(String) - Method in class com.genologics.ri.step.ReagentLotLink

Sets the LIMS id of the reagent lot.

setLimsid(String) - Method in class com.genologics.ri.step.SharedResultFile

Sets the LIMS id of the artifact.

setLimsId(String) - Method in interface com.genologics.ri.LimsEntityLinkable

Same as setLimsid(String) but written in a more pleasing form for camel case.

setLocation(LimsEntityLinkable<Container>, String) - Method in class com.genologics.ri.processexecution.Output

Sets the location of the output artifact with container and position.

setLocation(LimsEntityLinkable<Container>, String) - Method in class com.genologics.ri.step.OutputPlacement

Sets the location from a container and well position.

setLocation(Linkable<Container>, String) - Method in class com.genologics.ri.step.OutputPlacement

Sets the location from a container and well position.

setLocation(Location) - Method in class com.genologics.ri.artifact.Artifact

Sets the location of the artifact.

setLocation(Location) - Method in class com.genologics.ri.processexecution.Output

Sets the location of the output artifact.

setLocation(Location) - Method in class com.genologics.ri.queue.ArtifactLink

Sets the location of the artifact.

setLocation(Location) - Method in class com.genologics.ri.sample.SampleCreation

Sets the location where the sample will be created.

setLocation(Location) - Method in class com.genologics.ri.step.OutputPlacement

Sets the location of the output artifact.

setLocked(Boolean) - Method in class com.genologics.ri.stepconfiguration.GenericTypeLink

Sets whether this generic type link is locked.

setLocked(Boolean) - Method in class com.genologics.ri.stepconfiguration.LockableSetting

Sets whether this setting is locked by the master step.

setLotNumber(String) - Method in class com.genologics.ri.reagentlot.ReagentLot

Sets the lot number.

setMajor(String) - Method in class com.genologics.ri.version.Version

Sets the major version number.

setMarshaller(JaxbMarshallingTool) - Method in class org.cruk.clarity.api.debugging.RestClientSnoopingAspect

Set the tool to convert an object back into XML for printing.

setMarshaller(Marshaller) - Method in class org.cruk.clarity.api.jaxb.JaxbMarshallingTool

Set the marshaller used to create the XML.

setMaxValue(Double) - Method in class com.genologics.ri.configuration.Field

Sets the maximum value for numeric fields.

setMessage(String) - Method in class com.genologics.ri.exception.Exception

Sets the error message.

setMessage(String) - Method in class com.genologics.ri.processtype.SharedResultFile

Sets the message associated with this shared result file.

setMessage(String) - Method in class com.genologics.ri.step.ProgramStatus

Sets the message associated with the program status.

setMessage(String) - Method in class com.genologics.ri.step.SharedResultFile

Sets the error message.

setMessage(String) - Method in class com.genologics.ri.stepconfiguration.SharedResultFile

Sets the message associated with this shared result file.

setMessageDirectory(File) - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Set the directory the messages are being written to.

setMessageDirectory(File) - Method in class org.cruk.clarity.api.record.ClarityAPIRecordingAspect

Set the directory the messages are being written to.

setMinor(String) - Method in class com.genologics.ri.version.Version

Sets the minor version number.

setMinValue(Double) - Method in class com.genologics.ri.configuration.Field

Sets the minimum value for numeric fields.

setName(String) - Method in class com.genologics.ri.artifact.Artifact

Sets the name of the artifact.

setName(String) - Method in class com.genologics.ri.artifact.ArtifactGroupLink

Sets the name.

setName(String) - Method in class com.genologics.ri.artifact.DemuxArtifact

Sets the name.

setName(String) - Method in class com.genologics.ri.artifact.DemuxSourceArtifact

Sets the name.

setName(String) - Method in class com.genologics.ri.artifact.PoolStep

Sets the name.

setName(String) - Method in class com.genologics.ri.artifact.ReagentLabel

Sets the name.

setName(String) - Method in class com.genologics.ri.artifact.WorkflowStage

Sets the name.

setName(String) - Method in class com.genologics.ri.artifactgroup.ArtifactGroup

Sets the name of the artifact group.

setName(String) - Method in class com.genologics.ri.artifactgroup.ArtifactGroupLink

Sets the name of the artifact group.

setName(String) - Method in class com.genologics.ri.automation.Automation

Sets the name of this automation.

setName(String) - Method in class com.genologics.ri.automation.AutomationLink

Sets the name of the automation.

setName(String) - Method in class com.genologics.ri.automation.ProcessTypeLink

Sets the name of the process type.

setName(String) - Method in class com.genologics.ri.configuration.Field

Sets the name of this field.

setName(String) - Method in class com.genologics.ri.configuration.FieldLink

Sets the name of the field.

setName(String) - Method in class com.genologics.ri.configuration.Type

Sets the name of this type.

setName(String) - Method in class com.genologics.ri.configuration.TypeDefinition

Sets the name of the type.

setName(String) - Method in class com.genologics.ri.configuration.UdfConfigLink

Sets the name of the field.

setName(String) - Method in class com.genologics.ri.configuration.UdtConfigLink

Sets the name of the type.

setName(String) - Method in class com.genologics.ri.container.Container

Sets the name.

setName(String) - Method in class com.genologics.ri.container.ContainerLink

Sets the name.

setName(String) - Method in class com.genologics.ri.container.ContainerTypeLink

Sets the name of the container type.

setName(String) - Method in class com.genologics.ri.containertype.CalibrantWell

Deprecated.

Sets the name of the calibrant well.

setName(String) - Method in class com.genologics.ri.containertype.ContainerType

Sets the name of the container type.

setName(String) - Method in class com.genologics.ri.containertype.ContainerTypeLink

Sets the name of the container type.

setName(String) - Method in class com.genologics.ri.controltype.ControlType

Sets the name of the control type.

setName(String) - Method in class com.genologics.ri.controltype.ControlTypeLink

Sets the name of the control type.

setName(String) - Method in class com.genologics.ri.globaltoken.GlobalToken

Set the token name.

setName(String) - Method in class com.genologics.ri.globaltoken.GlobalTokenLink

Set the token name.

setName(String) - Method in class com.genologics.ri.instrument.Instrument

Set the instrument name.

setName(String) - Method in class com.genologics.ri.instrument.InstrumentLink

Set the instrument name.

setName(String) - Method in class com.genologics.ri.instrumenttype.InstrumentType

Set the instrument type name.

setName(String) - Method in class com.genologics.ri.instrumenttype.InstrumentTypeLink

Set the instrument type name.

setName(String) - Method in class com.genologics.ri.instrumenttype.InstrumentTypeProcessType

Set the process type name.

setName(String) - Method in class com.genologics.ri.lab.Lab

Sets the name of the lab.

setName(String) - Method in class com.genologics.ri.lab.LabLink

Sets the name of the lab.

setName(String) - Method in class com.genologics.ri.permission.Permission

Set the permission name.

setName(String) - Method in class com.genologics.ri.permission.PermissionLink

Set the permission name.

setName(String) - Method in class com.genologics.ri.process.Parameter

Sets the name of the parameter.

setName(String) - Method in class com.genologics.ri.process.ProcessTypeLink

Sets the name of the process type.

setName(String) - Method in class com.genologics.ri.processexecution.Parameter

Sets the parameter name.

setName(String) - Method in class com.genologics.ri.processtemplate.Parameter

Sets the name.

setName(String) - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Sets the name.

setName(String) - Method in class com.genologics.ri.processtemplate.ProcessTemplateLink

Sets the name.

setName(String) - Method in class com.genologics.ri.processtemplate.ProcessTypeLink

Sets the name.

setName(String) - Method in class com.genologics.ri.processtype.ContainerTypeLink

Sets the name of the container type.

setName(String) - Method in class com.genologics.ri.processtype.ControlTypeLink

Sets the name of the control type.

setName(String) - Method in class com.genologics.ri.processtype.EppTrigger

Sets the name of the EPP trigger.

setName(String) - Method in class com.genologics.ri.processtype.Field

Sets the name of the field.

setName(String) - Method in class com.genologics.ri.processtype.Parameter

Sets the name of the parameter.

setName(String) - Method in class com.genologics.ri.processtype.ProcessType

Sets the name of the process type.

setName(String) - Method in class com.genologics.ri.processtype.ProcessTypeAttribute

Sets the name of the attribute.

setName(String) - Method in class com.genologics.ri.processtype.ProcessTypeLink

Sets the name of the process type.

setName(String) - Method in class com.genologics.ri.processtype.ReagentKitLink

Sets the name of the reagent kit.

setName(String) - Method in class com.genologics.ri.processtype.StepProperty

Sets the name of the step property.

setName(String) - Method in class com.genologics.ri.processtype.TypeDefinition

Sets the name of the field.

setName(String) - Method in class com.genologics.ri.project.Project

Set the name of the project.

setName(String) - Method in class com.genologics.ri.project.ProjectLink

Set the name of the project.

setName(String) - Method in class com.genologics.ri.property.PropertyLink

Sets the name of the property.

setName(String) - Method in class com.genologics.ri.protocolconfiguration.Protocol

Sets the name of the protocol.

setName(String) - Method in class com.genologics.ri.protocolconfiguration.ProtocolLink

Sets the name of the protocol.

setName(String) - Method in class com.genologics.ri.protocolconfiguration.ProtocolProperty

Sets the name of the protocol property.

setName(String) - Method in class com.genologics.ri.queue.Queue

Sets the name of the queue.

setName(String) - Method in class com.genologics.ri.reagentkit.ReagentKit

Sets the name of the reagent kit.

setName(String) - Method in class com.genologics.ri.reagentkit.ReagentKitLink

Sets the name of the reagent kit.

setName(String) - Method in class com.genologics.ri.reagentlot.ReagentKitLink

Sets the name of the reagent kit.

setName(String) - Method in class com.genologics.ri.reagentlot.ReagentLot

Sets the name of the reagent lot.

setName(String) - Method in class com.genologics.ri.reagentlot.ReagentLotLink

Sets the name of the reagent lot.

setName(String) - Method in class com.genologics.ri.reagenttype.Attribute

Sets the name of the attribute.

setName(String) - Method in class com.genologics.ri.reagenttype.ReagentType

Sets the name.

setName(String) - Method in class com.genologics.ri.reagenttype.ReagentTypeLink

Sets the name of the reagent type.

setName(String) - Method in class com.genologics.ri.reagenttype.SpecialType

Sets the name of the special type.

setName(String) - Method in class com.genologics.ri.researcher.Role

Set the role name.

setName(String) - Method in class com.genologics.ri.role.PermissionLink

Sets the name of the permission.

setName(String) - Method in class com.genologics.ri.role.Role

Sets the name of the role.

setName(String) - Method in class com.genologics.ri.role.RoleLink

Sets the name of the role.

setName(String) - Method in class com.genologics.ri.sample.BioSource

Deprecated.

Sets the name of the biosource.

setName(String) - Method in class com.genologics.ri.sample.ControlTypeLink

Sets the name of the control type.

setName(String) - Method in class com.genologics.ri.sample.SampleBase

Sets the name of the sample.

setName(String) - Method in class com.genologics.ri.savedquery.SavedQuery

Sets the name of the saved query.

setName(String) - Method in class com.genologics.ri.savedquery.SavedQueryLink

Sets the name of the saved query.

setName(String) - Method in class com.genologics.ri.stage.Stage

Sets the name of the stage.

setName(String) - Method in class com.genologics.ri.step.AvailableProgram

Sets the name.

setName(String) - Method in class com.genologics.ri.step.InstrumentLink

Sets the name.

setName(String) - Method in class com.genologics.ri.step.PooledInputs

Sets the name of this pool.

setName(String) - Method in class com.genologics.ri.step.ReagentLabel

Sets the name of the reagent label.

setName(String) - Method in class com.genologics.ri.step.SharedResultFile

Sets the name of the artifact.

setName(String) - Method in class com.genologics.ri.stepconfiguration.ControlTypeLink

Sets the name of the control type.

setName(String) - Method in class com.genologics.ri.stepconfiguration.EppTrigger

Sets the name of the EPP trigger.

setName(String) - Method in class com.genologics.ri.stepconfiguration.Field

Sets the name of the field.

setName(String) - Method in class com.genologics.ri.stepconfiguration.NextStep

Sets the name of the next step.

setName(String) - Method in class com.genologics.ri.stepconfiguration.ProcessTypeLink

Sets the name of the process type.

setName(String) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Sets the name of the protocol step.

setName(String) - Method in class com.genologics.ri.stepconfiguration.ReagentKitLink

Sets the name of the reagent kit.

setName(String) - Method in class com.genologics.ri.stepconfiguration.StepProperty

Sets the name of the step property.

setName(String) - Method in class com.genologics.ri.userdefined.UDF

Sets the name of the UDF.

setName(String) - Method in class com.genologics.ri.userdefined.UDT

Sets the name of the user-defined type.

setName(String) - Method in class com.genologics.ri.workflowconfiguration.ProtocolLink

Sets the name of the protocol.

setName(String) - Method in class com.genologics.ri.workflowconfiguration.StageLink

Sets the name of the stage.

setName(String) - Method in class com.genologics.ri.workflowconfiguration.Workflow

Sets the name of the workflow.

setName(String) - Method in class com.genologics.ri.workflowconfiguration.WorkflowLink

Sets the name of the workflow.

setNextPage(Page) - Method in class com.genologics.ri.artifact.Artifacts

Sets the next page of results.

setNextPage(Page) - Method in class com.genologics.ri.artifactgroup.ArtifactGroups

Sets the link to the next page.

setNextPage(Page) - Method in class com.genologics.ri.automation.Automations

Sets the next page of results.

setNextPage(Page) - Method in class com.genologics.ri.configuration.Udfs

Sets the link to the next page of results.

setNextPage(Page) - Method in class com.genologics.ri.configuration.Udts

Sets the link to the next page of results.

setNextPage(Page) - Method in class com.genologics.ri.container.Containers

Sets the link to the next page of results.

setNextPage(Page) - Method in class com.genologics.ri.containertype.ContainerTypes

Sets the next page of results.

setNextPage(Page) - Method in class com.genologics.ri.file.ClarityFiles

Sets the link to the next page of results.

setNextPage(Page) - Method in class com.genologics.ri.globaltoken.GlobalTokens

Set the next page of results.

setNextPage(Page) - Method in class com.genologics.ri.instrument.Instruments

Sets the next page of results.

setNextPage(Page) - Method in class com.genologics.ri.instrumenttype.InstrumentTypes

Sets the next page of results.

setNextPage(Page) - Method in class com.genologics.ri.lab.Labs

Sets the next page of results.

setNextPage(Page) - Method in interface com.genologics.ri.PaginatedBatch

Sets the next page of results.

setNextPage(Page) - Method in class com.genologics.ri.process.ClarityProcesses

Sets the next page link.

setNextPage(Page) - Method in class com.genologics.ri.processtemplate.ProcessTemplates

Sets the next page link.

setNextPage(Page) - Method in class com.genologics.ri.processtype.ProcessTypes

Sets the link to the next page of results.

setNextPage(Page) - Method in class com.genologics.ri.project.Projects

Set the next page of results.

setNextPage(Page) - Method in class com.genologics.ri.property.Properties

Sets the next page link.

setNextPage(Page) - Method in class com.genologics.ri.queue.Queue

Sets the next page of results.

setNextPage(Page) - Method in class com.genologics.ri.reagentkit.ReagentKits

Sets the next page link.

setNextPage(Page) - Method in class com.genologics.ri.reagentlot.ReagentLots

setNextPage(Page) - Method in class com.genologics.ri.reagenttype.ReagentTypes

Sets the link to the next page of results.

setNextPage(Page) - Method in class com.genologics.ri.researcher.Researchers

Sets the link to the next page of results.

setNextPage(Page) - Method in class com.genologics.ri.sample.Samples

Sets the next page link.

setNextPage(Page) - Method in class com.genologics.ri.savedquery.SavedQueries

Sets the next page of results.

setNextStep(Linkable<ProtocolStep>) - Method in class com.genologics.ri.stepconfiguration.NextStep

Sets the next step from a linkable protocol step.

setNextStepUri(URI) - Method in class com.genologics.ri.stepconfiguration.NextStep

Sets the URI of the next step.

setNotes(String) - Method in class com.genologics.ri.reagentlot.ReagentLot

Sets the notes.

setNumberOfOutputs(Integer) - Method in class com.genologics.ri.processtype.ProcessOutput

Sets the number of outputs to generate.

setOccupiedWells(Long) - Method in class com.genologics.ri.container.Container

Sets the number of occupied wells.

setOffset(Integer) - Method in class com.genologics.ri.containertype.Dimension

Sets the offset applied to the first element in this dimension.

setOpenDate(Date) - Method in class com.genologics.ri.project.Project

Set the open date of the project.

setOriginalLocation(String) - Method in class com.genologics.ri.file.ClarityFile

Sets the original name and location of the file before it was imported into the system.

setOriginalName(String) - Method in class com.genologics.ri.file.ClarityFile

Sets the original name of the file before it was imported into the system.

setOutput(OutputType, LimsEntityLinkable<Container>, String) - Method in class com.genologics.ri.processexecution.ExecutableInputOutputMap

Sets the output artifact with type, container, and position.

setOutput(LimsEntityLinkable<Artifact>) - Method in class com.genologics.ri.process.InputOutputMap

Sets the output from a LIMS entity linkable artifact.

setOutput(LimsEntityLinkable<Artifact>) - Method in class com.genologics.ri.step.InputOutputMap

Sets the output from a LIMS entity linkable artifact.

setOutput(Linkable<Artifact>) - Method in class com.genologics.ri.process.InputOutputMap

Sets the output from a linkable artifact.

setOutput(Linkable<Artifact>) - Method in class com.genologics.ri.step.InputOutputMap

Sets the output from a linkable artifact.

setOutput(ArtifactLink) - Method in class com.genologics.ri.process.InputOutputMap

Sets the output artifact link.

setOutput(Output) - Method in class com.genologics.ri.processexecution.ExecutableInputOutputMap

Sets the output artifact.

setOutput(ArtifactLink) - Method in class com.genologics.ri.step.InputOutputMap

Sets the output artifact link.

setOutput(Output) - Method in class com.genologics.ri.step.PooledInputs

Sets the output from an Output object.

setOutputArtifact(Linkable<Artifact>) - Method in class com.genologics.ri.step.PooledInputs

Sets the output artifact.

setOutputGenerationType(OutputGenerationType) - Method in class com.genologics.ri.process.ArtifactLink

Sets the output generation type.

setOutputGenerationType(OutputGenerationType) - Method in class com.genologics.ri.processtype.ProcessOutput

Sets the output generation type.

setOutputGenerationType(OutputGenerationType) - Method in class com.genologics.ri.step.ArtifactLink

Sets the output generation type.

setOutputName(String) - Method in class com.genologics.ri.processtype.ProcessOutput

Sets the output name pattern.

setOutputType(OutputType) - Method in class com.genologics.ri.artifact.Artifact

Sets the output type of the artifact.

setOutputType(OutputType) - Method in class com.genologics.ri.process.ArtifactLink

Sets the output type.

setOutputUri(URI) - Method in class com.genologics.ri.step.PooledInputs

Sets the URI of the output artifact.

setOverrideStateful(StatefulOverride) - Method in interface org.cruk.clarity.api.ClarityAPI

Pseudonym for ClarityAPI.overrideStateful(StatefulOverride) that follows the setter pattern and will aid using this as a property in Groovy and the like.

setParam(String) - Method in class org.cruk.clarity.api.search.SearchTerm

Set the parameter name.

setParameter(Parameter) - Method in class com.genologics.ri.process.ClarityProcess

Sets the parameter.

setParameter(Parameter) - Method in class com.genologics.ri.processexecution.ExecutableProcess

Sets the process parameter.

setParameter(Parameter) - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Sets the parameter.

setParentProcess(LimsEntityLinkable<ClarityProcess>) - Method in class com.genologics.ri.artifact.Artifact

Sets the parent process that produced this artifact.

setParentProcess(LimsEntityLinkable<ClarityProcess>) - Method in class com.genologics.ri.process.ArtifactLink

Sets the parent process from a LIMS entity linkable object.

setParentUri(URI) - Method in class com.genologics.ri.configuration.Field

Sets the URI of the parent field for hierarchical fields.

setPassword(String) - Method in class com.genologics.ri.researcher.Credentials

Sets the password.

setPhone(String) - Method in class com.genologics.ri.researcher.Researcher

Sets the researcher's phone number.

setPlacements(Linkable<Placements>) - Method in class com.genologics.ri.step.ProcessStep

Sets the link to the placements associated with this step.

setPlacements(Collection<? extends LimsEntityLinkable<Artifact>>) - Method in class com.genologics.ri.container.Container

Sets the placements from a collection of artifact links.

setPoint(TriggerPoint) - Method in class com.genologics.ri.processtype.EppTrigger

Sets the point at which the trigger executes.

setPoint(TriggerPoint) - Method in class com.genologics.ri.stepconfiguration.EppTrigger

Sets the point when the EPP trigger executes.

setPools(Linkable<Pools>) - Method in class com.genologics.ri.step.ProcessStep

Sets the link to the pools associated with this step.

setPoolStep(PoolStep) - Method in class com.genologics.ri.artifact.DemuxDetails

Sets the pool step.

setPoolStep(Linkable<ProcessStep>) - Method in class com.genologics.ri.artifact.DemuxDetails

Sets the pool step from a Linkable.

setPostalCode(String) - Method in class com.genologics.ri.Address

Sets the postal or zip code.

setPostProcessUri(URI) - Method in class com.genologics.ri.process.ArtifactLink

Sets the post-process URI.

setPreset(String) - Method in class com.genologics.ri.step.StepDetails

Sets the preset name.

setPresets(String...) - Method in class com.genologics.ri.configuration.FieldDynamicPresetDetails

Sets the presets from an array of strings.

setPresets(Collection<String>) - Method in class com.genologics.ri.configuration.FieldDynamicPresetDetails

Sets the presets from a collection of strings.

setPreviousPage(Page) - Method in class com.genologics.ri.artifact.Artifacts

Sets the previous page of results.

setPreviousPage(Page) - Method in class com.genologics.ri.artifactgroup.ArtifactGroups

Sets the link to the previous page.

setPreviousPage(Page) - Method in class com.genologics.ri.automation.Automations

Sets the previous page of results.

setPreviousPage(Page) - Method in class com.genologics.ri.configuration.Udfs

Sets the link to the previous page of results.

setPreviousPage(Page) - Method in class com.genologics.ri.configuration.Udts

Sets the link to the previous page of results.

setPreviousPage(Page) - Method in class com.genologics.ri.container.Containers

Sets the link to the previous page of results.

setPreviousPage(Page) - Method in class com.genologics.ri.containertype.ContainerTypes

Sets the previous page of results.

setPreviousPage(Page) - Method in class com.genologics.ri.file.ClarityFiles

Sets the link to the previous page of results.

setPreviousPage(Page) - Method in class com.genologics.ri.globaltoken.GlobalTokens

Set the previous page of results.

setPreviousPage(Page) - Method in class com.genologics.ri.instrument.Instruments

Sets the previous page of results.

setPreviousPage(Page) - Method in class com.genologics.ri.instrumenttype.InstrumentTypes

Sets the previous page of results.

setPreviousPage(Page) - Method in class com.genologics.ri.lab.Labs

Sets the previous page of results.

setPreviousPage(Page) - Method in interface com.genologics.ri.PaginatedBatch

Sets the previous page of results.

setPreviousPage(Page) - Method in class com.genologics.ri.process.ClarityProcesses

Sets the previous page link.

setPreviousPage(Page) - Method in class com.genologics.ri.processtemplate.ProcessTemplates

Sets the previous page link.

setPreviousPage(Page) - Method in class com.genologics.ri.processtype.ProcessTypes

Sets the link to the previous page of results.

setPreviousPage(Page) - Method in class com.genologics.ri.project.Projects

Set the previous page of results.

setPreviousPage(Page) - Method in class com.genologics.ri.property.Properties

Sets the previous page link.

setPreviousPage(Page) - Method in class com.genologics.ri.queue.Queue

Sets the previous page of results.

setPreviousPage(Page) - Method in class com.genologics.ri.reagentkit.ReagentKits

Sets the previous page link.

setPreviousPage(Page) - Method in class com.genologics.ri.reagentlot.ReagentLots

setPreviousPage(Page) - Method in class com.genologics.ri.reagenttype.ReagentTypes

Sets the link to the previous page of results.

setPreviousPage(Page) - Method in class com.genologics.ri.researcher.Researchers

Sets the link to the previous page of results.

setPreviousPage(Page) - Method in class com.genologics.ri.sample.Samples

Sets the previous page link.

setPreviousPage(Page) - Method in class com.genologics.ri.savedquery.SavedQueries

Sets the previous page of results.

setPriority(String) - Method in class com.genologics.ri.project.Project

Set the priority of the project.

setProcessType(Linkable<ProcessType>) - Method in class com.genologics.ri.automation.ProcessTypeLink

Sets the process type from a linkable.

setProcessType(Linkable<ProcessType>) - Method in class com.genologics.ri.process.ClarityProcess

Sets the process type from a linkable object.

setProcessType(Linkable<ProcessType>) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Sets the process type for this step.

setProcessType(ProcessTypeLink) - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Sets the process type.

setProcessType(ProcessType) - Method in class com.genologics.ri.process.ClarityProcess

Sets the process type.

setProcessType(ProcessType) - Method in class com.genologics.ri.processexecution.ExecutableProcess

Sets the process type from a ProcessType object.

setProcessType(ProcessType) - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Sets the process type from a ProcessType object.

setProcessType(String) - Method in class com.genologics.ri.processexecution.ExecutableProcess

Sets the process type name.

setProgramStatus(Linkable<ProgramStatus>) - Method in class com.genologics.ri.step.ProcessStep

Sets the link to the program status associated with this step.

setProject(LimsEntityLinkable<Project>) - Method in class com.genologics.ri.sample.SampleBase

Sets the project for this sample.

setProtocol(Linkable<Protocol>) - Method in class com.genologics.ri.stage.Stage

Sets the protocol for this stage.

setProtocolName(String) - Method in class com.genologics.ri.process.ClarityProcess

Sets the protocol name.

setProtocolStep(Linkable<ProtocolStep>) - Method in class com.genologics.ri.step.StepConfiguration

Sets the protocol step from a linkable object.

setProtocolStepIndex(Integer) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Sets the protocol step index.

setProtocolStepUri(URI) - Method in class com.genologics.ri.queue.Queue

Sets the protocol step URI.

setProtocolStepUri(URI) - Method in class com.genologics.ri.step.StepConfiguration

Sets the protocol step URI.

setProtocolUri(URI) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Sets the URI of the protocol this step belongs to.

setPublished(Boolean) - Method in class com.genologics.ri.file.ClarityFile

Sets whether the file should be displayed in LabLink.

setQCFlag(QCFlag) - Method in class com.genologics.ri.artifact.Artifact

Sets the quality control flag for this artifact.

setQCFlag(QCFlag) - Method in class com.genologics.ri.processexecution.ArtifactBase

Sets the quality control flag for this artifact.

setQueueTime(Date) - Method in class com.genologics.ri.queue.ArtifactLink

Sets the time when the artifact was queued.

setRackColumn(Integer) - Method in class com.genologics.ri.step.RackLocation

Sets the column position within the rack.

setRackIndex(Integer) - Method in class com.genologics.ri.step.RackLocation

Sets the index of the rack.

setRackLocation(RackLocation) - Method in class com.genologics.ri.step.OutputArrangement

Sets the rack location.

setRackRow(Integer) - Method in class com.genologics.ri.step.RackLocation

Sets the row position within the rack.

setReagentCategory(String) - Method in class com.genologics.ri.reagenttype.ReagentType

Sets the reagent category.

setReagentCategory(String) - Method in class com.genologics.ri.step.Reagents

Sets the reagent category.

setReagentCategory(String) - Method in class com.genologics.ri.step.StepCreation

Sets the reagent category name.

setReagentKit(Linkable<ReagentKit>) - Method in class com.genologics.ri.reagentlot.ReagentLot

Sets the reagent kit for this lot.

setReagentLots(Linkable<ReagentLots>) - Method in class com.genologics.ri.step.ProcessStep

Sets the link to the reagent lots associated with this step.

setReagents(Linkable<Reagents>) - Method in class com.genologics.ri.step.ProcessStep

Sets the link to the reagents associated with this step.

setRecordSearchesWithoutResults(boolean) - Method in class org.cruk.clarity.api.record.ClarityAPIRecordingAspect

Set whether to record a search with zero results or not.

setRelative(String) - Method in class com.genologics.ri.Link

Sets the relative part of the link.

setRemoveWorkingFlag(Boolean) - Method in class com.genologics.ri.processtype.ProcessInput

Deprecated.

This property is no longer supported.

setReplicates(Long) - Method in class com.genologics.ri.step.CreationInput

Sets the number of replicates.

setReplicates(Long) - Method in class com.genologics.ri.step.Input

Sets the number of replicates.

setReportFile(File) - Method in class org.cruk.clarity.api.SavedQuerySummary

Set the file the report was saved as.

setRequest(EscalationRequest) - Method in class com.genologics.ri.step.Escalation

Sets the escalation request.

setRequired(Boolean) - Method in class com.genologics.ri.configuration.Field

Sets whether this field is required.

setResearcher(Linkable<Researcher>) - Method in class com.genologics.ri.project.Project

Set the researcher associated with the project.

setRestClient(RestOperations) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set the REST client.

setResults(List<LimsLink<E>>) - Method in class org.cruk.clarity.api.search.Search

Set the results of the search.

setReview(EscalationReview) - Method in class com.genologics.ri.step.Escalation

Sets the escalation review.

setReviewer(Linkable<Researcher>) - Method in class com.genologics.ri.step.EscalationRequest

Sets the reviewer.

setReworkStep(Linkable<ProtocolStep>) - Method in class com.genologics.ri.step.NextAction

Sets the rework step.

setReworkStepUri(URI) - Method in class com.genologics.ri.step.NextAction

Sets the rework step URI.

setRoleName(String) - Method in class com.genologics.ri.researcher.Role

Deprecated.

Deprecated from version 2.19.

setRows(Dimension) - Method in class com.genologics.ri.containertype.ContainerType

Sets the y-dimension (vertical/rows) of the container's coordinate system.

setRunProgramPerEvent(Boolean) - Method in class com.genologics.ri.automation.Automation

Sets whether the program should run per event.

setRunProgramPerEvent(Boolean) - Method in class com.genologics.ri.processtype.Parameter

Deprecated.

This property is no longer supported.

setSampleFields(Field) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Adds a sample field.

setSamples(Collection<? extends LimsEntityLinkable<Sample>>) - Method in class com.genologics.ri.artifact.Artifact

Sets the list of samples associated with this artifact.

setSavedQueryRunner(SavedQueryRunner) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set the runner for saved queries.

setScript(String) - Method in class com.genologics.ri.automation.Automation

Sets the script content for this automation.

setScript(String) - Method in class com.genologics.ri.processtype.Parameter

Sets the EPP script text that will actually run.

setSequence(Integer) - Method in class com.genologics.ri.stepconfiguration.NextStep

Sets the sequence index of the next step.

setSerialNumber(String) - Method in class com.genologics.ri.instrument.Instrument

Set the instrument serial number.

setServer(URL) - Method in interface org.cruk.clarity.api.ClarityAPI

Deprecated.

Use ClarityAPI.setServerURI(URI) to set the URI instead.

setServer(URL) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Deprecated.

setServerURI(URI) - Method in interface org.cruk.clarity.api.ClarityAPI

Set the base URI to the Clarity server.

setServerURI(URI) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set the base URI to the Clarity server.

setSetup(Linkable<StepSetup>) - Method in class com.genologics.ri.step.ProcessStep

Sets the link to the setup associated with this step.

setShared(Boolean) - Method in class com.genologics.ri.processexecution.ExecutableInputOutputMap

Sets whether the output is shared.

setSharedResultFileIndex(String) - Method in class com.genologics.ri.processtype.SharedResultFile

Sets the index of this shared result file.

setSharedResultFileIndex(String) - Method in class com.genologics.ri.step.SharedResultFile

Sets the shared result file index.

setSharedResultFileIndex(String) - Method in class com.genologics.ri.stepconfiguration.SharedResultFile

Sets the index of this shared result file.

setShippingAddress(Address) - Method in class com.genologics.ri.lab.Lab

Sets the shipping address of the lab.

setShowInLablink(Boolean) - Method in class com.genologics.ri.configuration.Field

Sets whether this field should be shown in Lablink.

setShowInTables(Boolean) - Method in class com.genologics.ri.configuration.Field

Sets whether this field should be shown in tables.

setSingleStep(Boolean) - Method in class com.genologics.ri.controltype.ControlType

Sets the single step flag.

setSize(Integer) - Method in class com.genologics.ri.containertype.Dimension

Sets the size (number of elements) in this dimension.

setSpecialType(SpecialType) - Method in class com.genologics.ri.reagenttype.ReagentType

Sets the special type.

setStage(Linkable<Stage>) - Method in class com.genologics.ri.routing.ExtArtifactAssignments

Sets the stage from a Linkable.

setStageUri(URI) - Method in class com.genologics.ri.routing.ExtArtifactAssignments

Sets the stage URI.

setState(ContainerState) - Method in class com.genologics.ri.container.Container

Sets the container state.

setState(String) - Method in class com.genologics.ri.Address

Sets the state or province.

setStatefulBehaviour(CacheStatefulBehaviour) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Set the behaviour for dealing with stateful objects.

setStatus(Status) - Method in class com.genologics.ri.artifact.WorkflowStage

Sets the status.

setStatus(TriggerStatus) - Method in class com.genologics.ri.processtype.EppTrigger

Sets the status at which the trigger executes.

setStatus(Status) - Method in class com.genologics.ri.reagentlot.ReagentLot

Sets the status of the reagent lot.

setStatus(Status) - Method in class com.genologics.ri.step.ProgramStatus

Sets the current status of the program.

setStatus(TriggerStatus) - Method in class com.genologics.ri.stepconfiguration.EppTrigger

Sets the status at which the EPP trigger executes.

setStatus(Status) - Method in class com.genologics.ri.workflowconfiguration.Workflow

Sets the status of the workflow.

setStatus(Status) - Method in class com.genologics.ri.workflowconfiguration.WorkflowLink

Sets the status of the workflow.

setStep(Link) - Method in class com.genologics.ri.step.Actions

Sets the step link.

setStep(Link) - Method in class com.genologics.ri.step.Arrangements

Sets the step link.

setStep(Link) - Method in class com.genologics.ri.step.Placements

Sets the link to the step.

setStep(Link) - Method in class com.genologics.ri.step.Pools

Sets the link to the step.

setStep(Link) - Method in class com.genologics.ri.step.ProgramStatus

Sets the link to the step associated with this program status.

setStep(Link) - Method in class com.genologics.ri.step.ReagentLots

Sets the step link.

setStep(Link) - Method in class com.genologics.ri.step.Reagents

Sets the step link.

setStep(Link) - Method in class com.genologics.ri.step.StepDetails

Sets the link to the step.

setStep(Link) - Method in class com.genologics.ri.step.StepSetup

Sets the link to the step.

setStep(Linkable<ProcessStep>) - Method in class com.genologics.ri.step.Placements

Sets the step from a linkable process step.

setStep(Linkable<ProtocolStep>) - Method in class com.genologics.ri.stage.Stage

Sets the protocol step for this stage.

setStep(Linkable<ProtocolStep>) - Method in class com.genologics.ri.step.NextAction

Sets the next step.

setStepName(String) - Method in class com.genologics.ri.step.StepConfiguration

Sets the name of the protocol step.

setStepSetup(StepSetup) - Method in class com.genologics.ri.processtype.ProcessType

Sets the step setup configuration.

setStepSetup(StepSetup) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Sets the step setup configuration.

setStepUri(URI) - Method in class com.genologics.ri.step.NextAction

Sets the step URI.

setStorageLocation(String) - Method in class com.genologics.ri.reagentlot.ReagentLot

Sets the storage location.

setStreet(String) - Method in class com.genologics.ri.Address

Sets the street address.

setStyle(Style) - Method in class com.genologics.ri.processtype.Field

Sets the style of the field.

setStyle(Style) - Method in class com.genologics.ri.stepconfiguration.Field

Sets the style of the field.

setSubmitter(Linkable<Researcher>) - Method in class com.genologics.ri.sample.SampleBase

Sets the submitter for this sample.

setSuggestedActions(String) - Method in class com.genologics.ri.exception.Exception

Sets the suggested actions to correct the error.

setSupplier(String) - Method in class com.genologics.ri.controltype.ControlType

Sets the supplier of the control type.

setSupplier(String) - Method in class com.genologics.ri.reagentkit.ReagentKit

Sets the supplier of the reagent kit.

setTechnician(Linkable<Researcher>) - Method in class com.genologics.ri.process.ClarityProcess

Sets the technician from a linkable researcher.

setTechnician(Linkable<Researcher>) - Method in class com.genologics.ri.processexecution.ExecutableProcess

Sets the technician from a researcher link.

setTechnician(Linkable<Researcher>) - Method in class com.genologics.ri.step.ProcessStep

Sets the technician assigned to this step from a linkable researcher.

setTechnician(Technician) - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Sets the technician.

setTechnician(Researcher) - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Sets the technician from a Researcher object.

setTechnician(Researcher) - Method in class com.genologics.ri.step.ProcessStep

Sets the technician assigned to this step from a researcher.

setTechnician(Technician) - Method in class com.genologics.ri.step.ProcessStep

Sets the technician assigned to this step.

setTimeout(int) - Method in interface org.cruk.clarity.api.filestore.ClaritySFTPUploader

Set how long an SSH connection will take to time out (in milliseconds).

setTimeoutOnUploader() - Method in class org.cruk.clarity.api.spring.ClarityClientConfiguration

Set the timeout on the SFTP file uploader to the same as the HTTP connection timeout.

setTube(Boolean) - Method in class com.genologics.ri.containertype.ContainerType

Sets whether this container type represents a tube.

setType(OutputType) - Method in class com.genologics.ri.processexecution.Output

Sets the output type.

setType(OutputType) - Method in class com.genologics.ri.step.ArtifactLink

Sets the output type.

setType(FieldType) - Method in class com.genologics.ri.configuration.Field

Sets the type of this field.

setType(FieldType) - Method in class com.genologics.ri.userdefined.UDF

Sets the type of the UDF.

setType(TriggerType) - Method in class com.genologics.ri.processtype.EppTrigger

Sets the type of the trigger.

setType(TriggerType) - Method in class com.genologics.ri.stepconfiguration.EppTrigger

Sets the type of the EPP trigger.

setType(String) - Method in class com.genologics.ri.artifact.Artifact

Sets the type of the artifact.

setType(String) - Method in class com.genologics.ri.instrument.Instrument

Set the instrument type.

setTypeDefinition(TypeDefinition) - Method in class com.genologics.ri.configuration.Field

Sets the type definition for complex types.

setUDF(UDFHolder, String, Object) - Static method in class com.genologics.ri.userdefined.UDF

Adds, sets or removes a UDF from the collection of fields on the given object.

setUDF(String, Object) - Method in interface com.genologics.ri.userdefined.UDFHolder

Adds, sets or removes a UDF.

setUDF(Collection<UDF>, String, Object) - Static method in class com.genologics.ri.userdefined.UDF

Adds, sets or removes a UDF from the given collection of fields.

setUnitLabel(String) - Method in class com.genologics.ri.configuration.Field

Sets the unit label for numeric fields.

setUnmarshaller(Unmarshaller) - Method in class org.cruk.clarity.api.http.ClarityFailureResponseErrorHandler

Set the unmarshaller used to create the XML.

setup - Variable in class com.genologics.ri.step.ProcessStep

Link to the setup associated with this step.

setUpdatesDirectory(File) - Method in class org.cruk.clarity.api.playback.ClarityAPIPlaybackAspect

Set the directory the updated entities are being written to.

setUploadOverHttp(boolean) - Method in interface org.cruk.clarity.api.ClarityAPI

Set whether uploads over HTTP are permitted using the files/id/upload API end point, or whether only SFTP uploads are allowed.

setUploadOverHttp(boolean) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Set whether uploads over HTTP are permitted using the files/id/upload API end point, or whether only SFTP uploads are allowed.

setUri(String) - Method in class com.genologics.ri.permission.Permissions

Set the URI.

setUri(String) - Method in class com.genologics.ri.reagentlot.ReagentLots

Sets the URI of this reagent lots collection.

setUri(URI) - Method in class com.genologics.ri.artifact.Artifact

Sets the URI of this artifact.

setUri(URI) - Method in class com.genologics.ri.artifact.ArtifactGroupLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.artifact.ArtifactLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.artifact.ControlTypeLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.artifact.Demux

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.artifact.DemuxArtifact

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.artifact.DemuxArtifactSample

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.artifact.DemuxLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.artifact.DemuxSourceArtifact

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.artifact.ParentProcessLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.artifact.PoolStep

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.artifact.SampleLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.artifact.WorkflowStage

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.artifactgroup.ArtifactGroup

Sets the URI of this artifact group.

setUri(URI) - Method in class com.genologics.ri.artifactgroup.ArtifactGroupLink

Sets the URI of the artifact group.

setUri(URI) - Method in class com.genologics.ri.artifactgroup.Artifacts

Sets the URI of the artifacts in this group.

setUri(URI) - Method in class com.genologics.ri.automation.Automation

Sets the URI of this automation.

setUri(URI) - Method in class com.genologics.ri.automation.AutomationLink

Sets the URI of the automation.

setUri(URI) - Method in class com.genologics.ri.automation.Automations

Sets the URI of this automations resource.

setUri(URI) - Method in class com.genologics.ri.automation.ProcessTypeLink

Sets the URI of the process type.

setUri(URI) - Method in class com.genologics.ri.configuration.Field

Sets the URI of this field configuration.

setUri(URI) - Method in class com.genologics.ri.configuration.FieldDynamicPresetDetails

Sets the URI of this preset details resource.

setUri(URI) - Method in class com.genologics.ri.configuration.FieldLink

Sets the URI of the field configuration.

setUri(URI) - Method in class com.genologics.ri.configuration.Type

Sets the URI of this type configuration.

setUri(URI) - Method in class com.genologics.ri.configuration.TypeDefinition

Sets the URI of the type definition.

setUri(URI) - Method in class com.genologics.ri.configuration.UdfConfigLink

Sets the URI of the field configuration.

setUri(URI) - Method in class com.genologics.ri.configuration.UdtConfigLink

Sets the URI of the type configuration.

setUri(URI) - Method in class com.genologics.ri.container.Container

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.container.ContainerLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.container.ContainerTypeLink

Sets the URI of the container type.

setUri(URI) - Method in class com.genologics.ri.container.Placement

Sets the URI of the artifact.

setUri(URI) - Method in class com.genologics.ri.ContainerLink

Sets the URI of the container.

setUri(URI) - Method in class com.genologics.ri.containertype.ContainerType

Sets the URI for this container type.

setUri(URI) - Method in class com.genologics.ri.containertype.ContainerTypeLink

Sets the URI for the container type resource.

setUri(URI) - Method in class com.genologics.ri.controltype.ControlType

Sets the URI of the control type.

setUri(URI) - Method in class com.genologics.ri.controltype.ControlTypeLink

Sets the URI of the control type.

setUri(URI) - Method in class com.genologics.ri.controltype.ControlTypes

Sets the URI of the control types collection.

setUri(URI) - Method in class com.genologics.ri.ExternalId

Sets the URI within the external system.

setUri(URI) - Method in class com.genologics.ri.file.ClarityFile

Sets the URI of this file resource.

setUri(URI) - Method in class com.genologics.ri.file.FileLink

Sets the URI of the file resource.

setUri(URI) - Method in class com.genologics.ri.globaltoken.GlobalToken

Set the URI of this global token.

setUri(URI) - Method in class com.genologics.ri.globaltoken.GlobalTokenLink

Set the URI of this global token.

setUri(URI) - Method in class com.genologics.ri.instrument.Instrument

Set the URI of this object.

setUri(URI) - Method in class com.genologics.ri.instrument.InstrumentLink

Set the URI of this object.

setUri(URI) - Method in class com.genologics.ri.instrumenttype.InstrumentType

Set the URI of this object.

setUri(URI) - Method in class com.genologics.ri.instrumenttype.InstrumentTypeLink

Set the URI of this object.

setUri(URI) - Method in class com.genologics.ri.instrumenttype.InstrumentTypeProcessType

Set the URI of this object.

setUri(URI) - Method in class com.genologics.ri.lab.Lab

Sets the URI of the lab resource.

setUri(URI) - Method in class com.genologics.ri.lab.LabLink

Sets the URI of the lab resource.

setUri(URI) - Method in class com.genologics.ri.Link

Sets the URI of the link.

setUri(URI) - Method in interface com.genologics.ri.Locatable

Set the URI of this object.

setUri(URI) - Method in class com.genologics.ri.Location

Sets the URI of the container.

setUri(URI) - Method in class com.genologics.ri.Page

Sets the URI to the page.

setUri(URI) - Method in class com.genologics.ri.permission.Permission

Set the URI of this object.

setUri(URI) - Method in class com.genologics.ri.permission.PermissionLink

Set the URI of this object.

setUri(URI) - Method in class com.genologics.ri.process.ArtifactLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.process.ClarityProcess

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.process.InstrumentLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.process.ParentProcessLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.process.ProcessLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.process.ProcessTypeLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.process.Technician

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.processexecution.Input

Sets the URI of the input artifact.

setUri(URI) - Method in class com.genologics.ri.processexecution.InstrumentLink

Sets the URI of the instrument.

setUri(URI) - Method in class com.genologics.ri.processexecution.Technician

Sets the URI of the researcher.

setUri(URI) - Method in class com.genologics.ri.processtemplate.InstrumentLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.processtemplate.ProcessTemplateLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.processtemplate.ProcessTypeLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.processtemplate.Technician

Sets the URI of this technician resource.

setUri(URI) - Method in class com.genologics.ri.processtype.ContainerTypeLink

Sets the URI of the container type.

setUri(URI) - Method in class com.genologics.ri.processtype.ControlTypeLink

Sets the URI of the control type.

setUri(URI) - Method in class com.genologics.ri.processtype.ProcessType

Sets the URI of the process type.

setUri(URI) - Method in class com.genologics.ri.processtype.ProcessTypeLink

Sets the URI of the process type.

setUri(URI) - Method in class com.genologics.ri.processtype.ReagentKitLink

Sets the URI of the reagent kit.

setUri(URI) - Method in class com.genologics.ri.processtype.TypeDefinition

Sets the URI of the field.

setUri(URI) - Method in class com.genologics.ri.project.Project

Set the URI of the project.

setUri(URI) - Method in class com.genologics.ri.project.ProjectLink

Set the URI of the project.

setUri(URI) - Method in class com.genologics.ri.project.ResearcherLink

Set the URI of the researcher.

setUri(URI) - Method in class com.genologics.ri.property.PropertyLink

Sets the URI of the property.

setUri(URI) - Method in class com.genologics.ri.protocolconfiguration.Protocol

Sets the URI of the protocol.

setUri(URI) - Method in class com.genologics.ri.protocolconfiguration.ProtocolLink

Sets the URI to the protocol.

setUri(URI) - Method in class com.genologics.ri.queue.ArtifactLink

Set the URI of this object.

setUri(URI) - Method in class com.genologics.ri.queue.Queue

Sets the URI of the queue.

setUri(URI) - Method in class com.genologics.ri.reagentkit.ReagentKit

Sets the URI of the reagent kit.

setUri(URI) - Method in class com.genologics.ri.reagentkit.ReagentKitLink

Sets the URI of the reagent kit.

setUri(URI) - Method in class com.genologics.ri.reagentkit.ReagentKits

Sets the URI of the reagent kits list.

setUri(URI) - Method in class com.genologics.ri.reagentlot.ReagentKitLink

Sets the URI of the reagent kit.

setUri(URI) - Method in class com.genologics.ri.reagentlot.ReagentLot

setUri(URI) - Method in class com.genologics.ri.reagentlot.ReagentLotLink

Set the URI of this object.

setUri(URI) - Method in class com.genologics.ri.reagentlot.ResearcherLink

Sets the URI of the researcher.

setUri(URI) - Method in class com.genologics.ri.reagenttype.ReagentType

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.reagenttype.ReagentTypeLink

Sets the URI of the reagent type.

setUri(URI) - Method in class com.genologics.ri.researcher.LabLink

Sets the URI to the lab.

setUri(URI) - Method in class com.genologics.ri.researcher.Researcher

Sets the URI to the researcher.

setUri(URI) - Method in class com.genologics.ri.researcher.ResearcherLink

Sets the URI to the researcher.

setUri(URI) - Method in class com.genologics.ri.researcher.Role

Set the URI to the role.

setUri(URI) - Method in class com.genologics.ri.role.PermissionLink

Sets the URI of the permission.

setUri(URI) - Method in class com.genologics.ri.role.ResearcherLink

Sets the URI of the researcher.

setUri(URI) - Method in class com.genologics.ri.role.Role

Sets the URI of the role.

setUri(URI) - Method in class com.genologics.ri.role.RoleLink

Sets the URI of the role.

setUri(URI) - Method in class com.genologics.ri.role.Roles

Sets the URI of the roles list.

setUri(URI) - Method in class com.genologics.ri.routing.ArtifactLink

Sets the URI of the artifact.

setUri(URI) - Method in class com.genologics.ri.sample.ArtifactLink

Sets the URI of the artifact.

setUri(URI) - Method in class com.genologics.ri.sample.ControlTypeLink

Sets the URI of the control type.

setUri(URI) - Method in class com.genologics.ri.sample.ProjectLink

Sets the URI of the project.

setUri(URI) - Method in class com.genologics.ri.sample.SampleBase

Sets the URI for this sample.

setUri(URI) - Method in class com.genologics.ri.sample.SampleLink

Sets the URI of the sample.

setUri(URI) - Method in class com.genologics.ri.sample.Submitter

Sets the URI of the submitter.

setUri(URI) - Method in class com.genologics.ri.savedquery.SavedQuery

Sets the URI of the saved query.

setUri(URI) - Method in class com.genologics.ri.savedquery.SavedQueryLink

Sets the URI of the saved query.

setUri(URI) - Method in class com.genologics.ri.stage.ProtocolLink

Sets the URI of the protocol.

setUri(URI) - Method in class com.genologics.ri.stage.ProtocolStepLink

Sets the URI of the protocol step.

setUri(URI) - Method in class com.genologics.ri.stage.Stage

Sets the URI of the stage.

setUri(URI) - Method in class com.genologics.ri.stage.WorkflowLink

Sets the URI of the workflow.

setUri(URI) - Method in class com.genologics.ri.step.Actions

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.step.ActionsLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.step.Arrangements

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.step.ArrangementsLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.step.ArtifactLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.step.AutomaticNextStepLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.step.AvailableProgram

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.step.ContainerLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.step.CreationInput

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.step.EscalatedArtifact

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.step.Input

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.step.InstrumentLink

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.step.NextAction

Sets the URI (artifact URI).

setUri(URI) - Method in class com.genologics.ri.step.Output

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.step.OutputArrangement

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.step.OutputPlacement

Sets the URI of the output artifact.

setUri(URI) - Method in class com.genologics.ri.step.Placements

Sets the URI of this placements resource.

setUri(URI) - Method in class com.genologics.ri.step.PlacementsLink

Sets the URI of the placements resource.

setUri(URI) - Method in class com.genologics.ri.step.Pools

Sets the URI of this pools resource.

setUri(URI) - Method in class com.genologics.ri.step.PoolsLink

Sets the URI of the pools resource.

setUri(URI) - Method in class com.genologics.ri.step.ProcessStep

Sets the URI of the step.

setUri(URI) - Method in class com.genologics.ri.step.ProgramStatus

Sets the URI of the program status.

setUri(URI) - Method in class com.genologics.ri.step.ProgramStatusLink

Sets the URI of the program status.

setUri(URI) - Method in class com.genologics.ri.step.ReagentLotLink

Set the URI of this object.

setUri(URI) - Method in class com.genologics.ri.step.ReagentLots

Sets the URI of this reagent lots resource.

setUri(URI) - Method in class com.genologics.ri.step.ReagentLotsLink

Sets the URI of the reagent lots resource.

setUri(URI) - Method in class com.genologics.ri.step.Reagents

Sets the URI.

setUri(URI) - Method in class com.genologics.ri.step.ReagentsLink

Sets the URI of the reagents resource.

setUri(URI) - Method in class com.genologics.ri.step.SharedResultFile

Sets the URI of the artifact.

setUri(URI) - Method in class com.genologics.ri.step.StepConfiguration

Set the URI of this object.

setUri(URI) - Method in class com.genologics.ri.step.StepDetails

Sets the URI of this step details resource.

setUri(URI) - Method in class com.genologics.ri.step.StepDetailsLink

Sets the URI of the step details resource.

setUri(URI) - Method in class com.genologics.ri.step.StepSetup

Sets the URI of this step setup resource.

setUri(URI) - Method in class com.genologics.ri.step.StepSetupLink

Sets the URI of the step setup resource.

setUri(URI) - Method in class com.genologics.ri.step.Technician

Sets the URI of the researcher resource.

setUri(URI) - Method in class com.genologics.ri.step.UserLink

Sets the URI of the researcher resource.

setUri(URI) - Method in class com.genologics.ri.stepconfiguration.ControlTypeLink

Sets the URI of the control type.

setUri(URI) - Method in class com.genologics.ri.stepconfiguration.NextStep

Sets the URI of the next step (alias for setNextStepUri).

setUri(URI) - Method in class com.genologics.ri.stepconfiguration.ProcessTypeLink

Sets the URI of the process type.

setUri(URI) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep

Sets the URI of the protocol step.

setUri(URI) - Method in class com.genologics.ri.stepconfiguration.ReagentKitLink

Sets the URI of the reagent kit.

setUri(URI) - Method in class com.genologics.ri.version.Version

Sets the URI of the version.

setUri(URI) - Method in class com.genologics.ri.workflowconfiguration.ProtocolLink

Sets the URI of the protocol.

setUri(URI) - Method in class com.genologics.ri.workflowconfiguration.StageLink

Sets the URI of the stage.

setUri(URI) - Method in class com.genologics.ri.workflowconfiguration.Workflow

Sets the URI of the workflow.

setUri(URI) - Method in class com.genologics.ri.workflowconfiguration.WorkflowLink

Sets the URI of the workflow.

setUsageCount(Long) - Method in class com.genologics.ri.reagentlot.ReagentLot

Sets the usage count.

setUserDefinedType(UDT) - Method in class com.genologics.ri.container.Container

Sets the user-defined type.

setUserDefinedType(UDT) - Method in class com.genologics.ri.lab.Lab

Sets the user-defined type of the lab.

setUserDefinedType(UDT) - Method in class com.genologics.ri.process.ClarityProcess

Sets the user defined type.

setUserDefinedType(UDT) - Method in class com.genologics.ri.processexecution.ExecutableProcess

Sets the user-defined type.

setUserDefinedType(UDT) - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Sets the user-defined type.

setUserDefinedType(UDT) - Method in class com.genologics.ri.project.Project

Set the user-defined type of the project.

setUserDefinedType(UDT) - Method in class com.genologics.ri.researcher.Researcher

Sets the user-defined type for the researcher.

setUserDefinedType(UDT) - Method in class com.genologics.ri.sample.SampleBase

Sets the user-defined type for this sample.

setUserDefinedType(String) - Method in class com.genologics.ri.container.Container

Sets the user-defined type from a string.

setUserDefinedType(String) - Method in class com.genologics.ri.lab.Lab

Sets the user-defined type of the lab using a type name.

setUserDefinedType(String) - Method in class com.genologics.ri.process.ClarityProcess

Sets the user defined type by name.

setUserDefinedType(String) - Method in class com.genologics.ri.processexecution.ExecutableProcess

Sets the user-defined type by name.

setUserDefinedType(String) - Method in class com.genologics.ri.processtemplate.ProcessTemplate

Sets the user-defined type by name.

setUserDefinedType(String) - Method in class com.genologics.ri.project.Project

Set the user-defined type of the project by name.

setUserDefinedType(String) - Method in class com.genologics.ri.researcher.Researcher

Sets the user-defined type for the researcher.

setUserDefinedType(String) - Method in class com.genologics.ri.sample.SampleBase

Sets the user-defined type for this sample by type name.

setUsername(String) - Method in class com.genologics.ri.researcher.Credentials

Sets the username.

setValue(Object) - Method in class com.genologics.ri.userdefined.UDF

Sets the value of the UDF.

setValue(Object) - Method in class org.cruk.clarity.api.search.SearchTerm

Set the single value to search for.

setValue(String) - Method in class com.genologics.ri.configuration.FieldDynamicPreset

Sets the preset value.

setValue(String) - Method in class com.genologics.ri.containertype.CalibrantWell

Deprecated.

Sets the value or content of the calibrant well.

setValue(String) - Method in class com.genologics.ri.globaltoken.GlobalToken

Set the token value.

setValue(String) - Method in class com.genologics.ri.processtype.ProcessTypeAttribute

Sets the value of the attribute.

setValue(String) - Method in class com.genologics.ri.processtype.StepProperty

Sets the value of the step property.

setValue(String) - Method in class com.genologics.ri.property.PropertyLink

Sets the value of the property.

setValue(String) - Method in class com.genologics.ri.protocolconfiguration.ProtocolProperty

Sets the value of the protocol property.

setValue(String) - Method in class com.genologics.ri.reagenttype.Attribute

Sets the value of the attribute.

setValue(String) - Method in class com.genologics.ri.stepconfiguration.GenericTypeLink

Sets the value of the generic type link.

setValue(String) - Method in class com.genologics.ri.stepconfiguration.StepProperty

Sets the value of the step property.

setValues(Object[]) - Method in class org.cruk.clarity.api.search.SearchTerm

Set the values to search for from an array.

setValues(Collection<? extends Object>) - Method in class org.cruk.clarity.api.search.SearchTerm

Set the values to search for from a collection.

setValues(Stream<? extends Object>) - Method in class org.cruk.clarity.api.search.SearchTerm

Set the values to search for from a stream.

setVariabilityType(VariabilityType) - Method in class com.genologics.ri.processtype.ProcessOutput

Sets the variability type.

setVendor(String) - Method in class com.genologics.ri.instrumenttype.InstrumentType

Set the instrument vendor.

setVendor(String) - Method in class com.genologics.ri.instrumenttype.InstrumentTypeLink

Set the instrument vendor.

setWait(int) - Method in interface org.cruk.clarity.api.automation.ClarityProcessAutomation

Set the wait time between polls.

setWait(int) - Method in class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Set the wait time between polls.

setWaitAttempts(int) - Method in interface org.cruk.clarity.api.automation.ClarityProcessAutomation

Set the number of times to ask for a state change before stopping.

setWaitAttempts(int) - Method in class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Set the number of times to ask for a state change before stopping.

setWebsite(String) - Method in class com.genologics.ri.controltype.ControlType

Sets the website URL for the control type.

setWebsite(String) - Method in class com.genologics.ri.lab.Lab

Sets the website URL of the lab.

setWebsite(String) - Method in class com.genologics.ri.reagentkit.ReagentKit

Sets the website of the reagent kit.

setWellPosition(String) - Method in class com.genologics.ri.container.Placement

Sets the well position in the container.

setWellPosition(String) - Method in class com.genologics.ri.Location

Sets the well position.

setWorkflow(Linkable<Workflow>) - Method in class com.genologics.ri.routing.ExtArtifactAssignments

Sets the workflow from a Linkable.

setWorkflow(Linkable<Workflow>) - Method in class com.genologics.ri.stage.Stage

Sets the workflow for this stage.

setWorkflowStages(Collection<WorkflowStage>) - Method in class com.genologics.ri.artifact.Artifact

Sets the workflow stages this artifact is associated with.

setWorkflowUri(URI) - Method in class com.genologics.ri.routing.ExtArtifactAssignments

Sets the workflow URI.

setWorkingFlag(Boolean) - Method in class com.genologics.ri.artifact.Artifact

Sets the working flag for this artifact.

sftpUploader - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

Session factory for SSH connections to the file store over SFTP.

shared - Variable in class com.genologics.ri.processexecution.ExecutableInputOutputMap

Indicates whether the output is shared among multiple inputs.

SHARED_RESULT_FILE - Enum constant in enum class com.genologics.ri.artifact.OutputType

Shared result file output type.

SharedResultFile - Class in com.genologics.ri.processtype

The file element describes a shared result file output that will be displayed in the step-setup view.

SharedResultFile - Class in com.genologics.ri.step

The file element describes a shared result file output that will be displayed in the step-setup view.

SharedResultFile - Class in com.genologics.ri.stepconfiguration

The file element describes a shared result file output that will be displayed in the step-setup view.

SharedResultFile() - Constructor for class com.genologics.ri.processtype.SharedResultFile

Constructs a new shared result file.

SharedResultFile() - Constructor for class com.genologics.ri.step.SharedResultFile

Creates an empty shared result file.

SharedResultFile() - Constructor for class com.genologics.ri.stepconfiguration.SharedResultFile

SharedResultFile(Artifact) - Constructor for class com.genologics.ri.step.SharedResultFile

Creates a shared result file from an artifact.

SharedResultFile(LimsEntityLinkable<Artifact>) - Constructor for class com.genologics.ri.step.SharedResultFile

Creates a shared result file from a LIMS entity linkable artifact.

SharedResultFile(Linkable<Artifact>) - Constructor for class com.genologics.ri.step.SharedResultFile

Creates a shared result file from a linkable artifact.

SharedResultFile(URI) - Constructor for class com.genologics.ri.step.SharedResultFile

Creates a shared result file with the given artifact URI.

SharedResultFile(URI, String) - Constructor for class com.genologics.ri.step.SharedResultFile

Creates a shared result file with the given artifact URI and LIMS id.

sharedResultFileIndex - Variable in class com.genologics.ri.processtype.SharedResultFile

The index of this shared result file.

sharedResultFileIndex - Variable in class com.genologics.ri.step.SharedResultFile

Index of the shared result file in the configuration.

sharedResultFileIndex - Variable in class com.genologics.ri.stepconfiguration.SharedResultFile

The index of this shared result file.

shippingAddress - Variable in class com.genologics.ri.lab.Lab

The shipping address for the lab.

ShortDateAdapter - Class in com.genologics.ri.jaxb

Adapter for those dates that are exchanged with the API in the short date only format.

ShortDateAdapter() - Constructor for class com.genologics.ri.jaxb.ShortDateAdapter

Default constructor.

showInLablink - Variable in class com.genologics.ri.configuration.Field

Whether this field should be shown in Lablink.

showInTables - Variable in class com.genologics.ri.configuration.Field

Whether this field should be shown in tables.

singleStep - Variable in class com.genologics.ri.controltype.ControlType

Flag indicating if the control type is for single step.

size - Variable in class com.genologics.ri.containertype.Dimension

The size (number of elements) in this dimension.

SKIPPED - Enum constant in enum class com.genologics.ri.artifact.Status

Skipped status.

smallLong - Variable in class org.cruk.clarity.api.cache.spring.ClarityClientCacheConfiguration

Cache configuration for small heap (100 entries) with long expiry (30 minutes).

smallMedium - Variable in class org.cruk.clarity.api.cache.spring.ClarityClientCacheConfiguration

Cache configuration for small heap (100 entries) with medium expiry (10 minutes).

specialType - Variable in class com.genologics.ri.reagenttype.ReagentType

The special type of this reagent type.

SpecialType - Class in com.genologics.ri.reagenttype

Special-type is a child element of reagent type and provides a name and attributes describing a special type of reagent type.

SpecialType() - Constructor for class com.genologics.ri.reagenttype.SpecialType

Default constructor.

SpecialType(String) - Constructor for class com.genologics.ri.reagenttype.SpecialType

Constructor with name.

SPOT_LIST - Enum constant in enum class com.genologics.ri.artifact.OutputType

Spot list output type.

Stage - Class in com.genologics.ri.stage

The detailed representation of a workflow stage.

Stage() - Constructor for class com.genologics.ri.stage.Stage

Default constructor.

Stage(URI) - Constructor for class com.genologics.ri.stage.Stage

Constructor with URI.

Stage(URI, String) - Constructor for class com.genologics.ri.stage.Stage

Constructor with URI and name.

STAGE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The stage namespace.

StageLink - Class in com.genologics.ri.workflowconfiguration

The detailed representation of a Stage (the portion of a workflow to which samples can be associated in order to be queued)

StageLink() - Constructor for class com.genologics.ri.workflowconfiguration.StageLink

Default constructor.

StageLink(Linkable<Stage>) - Constructor for class com.genologics.ri.workflowconfiguration.StageLink

Constructor accepting a Linkable object.

StageLink(Stage) - Constructor for class com.genologics.ri.workflowconfiguration.StageLink

Constructor accepting a Stage object.

StageLink(URI) - Constructor for class com.genologics.ri.workflowconfiguration.StageLink

Constructor accepting a URI.

StageLink(URI, String) - Constructor for class com.genologics.ri.workflowconfiguration.StageLink

Constructor accepting a URI and name.

stages - Variable in class com.genologics.ri.workflowconfiguration.Workflow

The list of stages associated with this workflow.

stageUri - Variable in class com.genologics.ri.routing.ExtArtifactAssignments

The URI of the stage.

STARTED - Enum constant in enum class com.genologics.ri.processtype.TriggerStatus

The step has been started.

STARTED - Enum constant in enum class com.genologics.ri.step.ProcessState

The step state when the step is in the sample placement stage.

STARTED - Enum constant in enum class com.genologics.ri.stepconfiguration.TriggerStatus

Trigger executes when the step is started.

startProgram(AvailableProgram) - Method in interface org.cruk.clarity.api.automation.ClarityProcessAutomation

Start execution of an EPP as part of a process step moving through Clarity.

startProgram(AvailableProgram) - Method in class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Start execution of an EPP as part of a process step moving through Clarity.

startProgram(AvailableProgram) - Method in interface org.cruk.clarity.api.ClarityAPI

Start execution of an EPP as part of a process step moving through Clarity.

startProgram(AvailableProgram) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Start execution of an EPP as part of a process step moving through Clarity.

state - Variable in class com.genologics.ri.Address

The state or province.

state - Variable in class com.genologics.ri.container.Container

Container state.

stateful() - Element in annotation interface com.genologics.ri.ClarityEntity

Whether the class represents objects that have explicit states (versions) in the Clarity system.

statefulOverride - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

Thread local flag indicating whether the next call on the thread should fetch stateful entities according to a different rule to the normal.

StatefulOverride - Enum Class in org.cruk.clarity.api

Enumeration of the ways to override the normal behaviour of the API and the cache to get specific versions of stateful entities.

stateId - Variable in enum class com.genologics.ri.container.ContainerState

The numeric state id for the container state, as stored in the database.

status - Variable in class com.genologics.ri.artifact.WorkflowStage

The status of this workflow stage.

status - Variable in class com.genologics.ri.processtype.EppTrigger

The status at which the trigger executes.

status - Variable in class com.genologics.ri.reagentlot.ReagentLot

The current status of this reagent lot (e.g., ACTIVE, ARCHIVED).

status - Variable in class com.genologics.ri.step.ProgramStatus

The current status of the program.

status - Variable in class com.genologics.ri.stepconfiguration.EppTrigger

The status at which the EPP trigger executes.

status - Variable in class com.genologics.ri.workflowconfiguration.Workflow

The status of the workflow.

status - Variable in class com.genologics.ri.workflowconfiguration.WorkflowLink

The status of the workflow.

Status - Enum Class in com.genologics.ri.artifact

The workflow stage status for the artifact.

Status - Enum Class in com.genologics.ri.reagentlot

The status of a reagent lot.

Status - Enum Class in com.genologics.ri.step

Enumeration of status values for a step.

Status - Enum Class in com.genologics.ri.workflowconfiguration

Enumeration representing the status of a workflow.

step - Variable in class com.genologics.ri.stage.Stage

Link to the protocol step for this stage.

step - Variable in class com.genologics.ri.step.Actions

Link to the step.

step - Variable in class com.genologics.ri.step.Arrangements

Link to the step.

step - Variable in class com.genologics.ri.step.Placements

The link to the step.

step - Variable in class com.genologics.ri.step.Pools

The link to the step.

step - Variable in class com.genologics.ri.step.ProgramStatus

Link to the step associated with this program status.

step - Variable in class com.genologics.ri.step.ReagentLots

Provides a URI linking to the step resource.

step - Variable in class com.genologics.ri.step.Reagents

Link to the step.

step - Variable in class com.genologics.ri.step.StepDetails

Link to the step this details object describes.

step - Variable in class com.genologics.ri.step.StepSetup

Link to the step this setup is for.

STEP - Enum constant in enum class com.genologics.ri.automation.Context

Step context.

STEP_CONFIGURATION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The step configuration namespace.

STEP_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The step namespace.

STEP_SETUP - Enum constant in enum class com.genologics.ri.processtype.TriggerStatus

The step is in the setup phase.

STEP_SETUP - Enum constant in enum class com.genologics.ri.stepconfiguration.TriggerStatus

Trigger executes during step setup.

StepConfiguration - Class in com.genologics.ri.step

Identifies the configuration information for the step run.

StepConfiguration() - Constructor for class com.genologics.ri.step.StepConfiguration

Creates an empty step configuration.

StepConfiguration(Linkable<ProtocolStep>) - Constructor for class com.genologics.ri.step.StepConfiguration

Creates a step configuration from a linkable protocol step.

StepConfiguration(ProtocolStep) - Constructor for class com.genologics.ri.step.StepConfiguration

Creates a step configuration from a protocol step.

StepConfiguration(URI) - Constructor for class com.genologics.ri.step.StepConfiguration

Creates a step configuration with the given protocol step URI.

StepConfiguration(URI, String) - Constructor for class com.genologics.ri.step.StepConfiguration

Creates a step configuration with the given protocol step URI and name.

StepCreation - Class in com.genologics.ri.step

A request to create a step.

StepCreation() - Constructor for class com.genologics.ri.step.StepCreation

Default constructor.

StepCreation(Linkable<ProtocolStep>) - Constructor for class com.genologics.ri.step.StepCreation

Constructor taking a protocol step link.

StepCreation(StepConfiguration) - Constructor for class com.genologics.ri.step.StepCreation

Constructor taking the step configuration.

StepCreation(ProtocolStep) - Constructor for class com.genologics.ri.step.StepCreation

Constructor taking a protocol step.

StepDetails - Class in com.genologics.ri.step

Represents the detailed view of a step, including configuration, input/output mappings, user-defined fields, and associated resources.

StepDetails() - Constructor for class com.genologics.ri.step.StepDetails

Default constructor.

StepDetails(URI) - Constructor for class com.genologics.ri.step.StepDetails

Constructor taking the URI of the step details.

StepDetailsLink - Class in com.genologics.ri.step

Identifies the resource that represents the details for the step.

StepDetailsLink() - Constructor for class com.genologics.ri.step.StepDetailsLink

Default constructor.

StepDetailsLink(Linkable<StepDetails>) - Constructor for class com.genologics.ri.step.StepDetailsLink

Constructor taking a linkable object.

StepDetailsLink(URI) - Constructor for class com.genologics.ri.step.StepDetailsLink

Constructor taking a URI.

stepFields - Variable in class com.genologics.ri.processtype.ProcessType

Fields displayed in the step view.

stepFields - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

List of fields to display on the step.

stepName - Variable in class com.genologics.ri.step.StepConfiguration

The name of the protocol step.

stepProperties - Variable in class com.genologics.ri.processtype.ProcessType

Properties for the step configuration.

stepProperties - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

List of step properties.

StepProperty - Class in com.genologics.ri.processtype

Step-property is a child element of master step containing key/value pairs for setting specific attributes of master steps.

StepProperty - Class in com.genologics.ri.stepconfiguration

Step-property is a child element of protocol step containing key/value pairs for setting specific attributes of protocol steps.

StepProperty() - Constructor for class com.genologics.ri.processtype.StepProperty

Constructs a new step property.

StepProperty() - Constructor for class com.genologics.ri.stepconfiguration.StepProperty

Default constructor.

StepProperty(String) - Constructor for class com.genologics.ri.stepconfiguration.StepProperty

Constructor with property name.

StepProperty(String, String) - Constructor for class com.genologics.ri.stepconfiguration.StepProperty

Constructor with property name and value.

steps - Variable in class com.genologics.ri.protocolconfiguration.Protocol

The list of steps in this protocol.

stepSetup - Variable in class com.genologics.ri.processtype.ProcessType

Step setup configuration.

stepSetup - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

Configuration for the step setup view.

StepSetup - Class in com.genologics.ri.processtype

Step-setup is a child element that describes the shared result file placeholder information for the step-setup view.

StepSetup - Class in com.genologics.ri.step

Represents the setup configuration for a step, including files and configuration settings.

StepSetup - Class in com.genologics.ri.stepconfiguration

Step-setup is a child element that describes the shared result file placeholder information for the step-setup view.

StepSetup() - Constructor for class com.genologics.ri.processtype.StepSetup

Constructs a new step setup.

StepSetup() - Constructor for class com.genologics.ri.step.StepSetup

Default constructor.

StepSetup() - Constructor for class com.genologics.ri.stepconfiguration.StepSetup

StepSetup(URI) - Constructor for class com.genologics.ri.step.StepSetup

Constructor taking the URI of the step setup.

StepSetupLink - Class in com.genologics.ri.step

Identifies the resource that represents the setup for the step.

StepSetupLink() - Constructor for class com.genologics.ri.step.StepSetupLink

Default constructor.

StepSetupLink(Linkable<StepSetup>) - Constructor for class com.genologics.ri.step.StepSetupLink

Constructor taking a linkable object.

StepSetupLink(URI) - Constructor for class com.genologics.ri.step.StepSetupLink

Constructor taking a URI.

stepUri - Variable in class com.genologics.ri.step.NextAction

URI of the next step.

storageLocation - Variable in class com.genologics.ri.reagentlot.ReagentLot

The physical storage location of this reagent lot.

STORE - Enum constant in enum class com.genologics.ri.step.ActionType

Store the artifact.

street - Variable in class com.genologics.ri.Address

The street address.

STRING - Enum constant in enum class com.genologics.ri.configuration.FieldType

String field type.

style - Variable in class com.genologics.ri.processtype.Field

The style of the field (user-defined or built-in).

style - Variable in class com.genologics.ri.stepconfiguration.Field

The style of the field (user-defined or built-in).

Style - Enum Class in com.genologics.ri.processtype

The different styles of Fields.

Style - Enum Class in com.genologics.ri.stepconfiguration

Enumeration of field styles.

submitter - Variable in class com.genologics.ri.sample.SampleBase

The submitter of this sample.

Submitter - Class in com.genologics.ri.sample

Submitter is a child element of Sample and provides a URI linking to the detailed representation of the submitter for the Sample.

Submitter() - Constructor for class com.genologics.ri.sample.Submitter

Constructor for an empty submitter.

Submitter(Linkable<Researcher>) - Constructor for class com.genologics.ri.sample.Submitter

Constructor for a submitter from a linkable researcher.

Submitter(Researcher) - Constructor for class com.genologics.ri.sample.Submitter

Constructor for a submitter from a researcher entity.

Submitter(URI) - Constructor for class com.genologics.ri.sample.Submitter

Constructor for a submitter with a URI.

suggestedActions - Variable in class com.genologics.ri.exception.Exception

Details on how to correct the problem that caused the exception.

suggestedActions - Variable in exception org.cruk.clarity.api.ClarityException

Suggested actions to rectify the error, provided by the Clarity API.

supplier - Variable in class com.genologics.ri.controltype.ControlType

The supplier of the control type.

supplier - Variable in class com.genologics.ri.reagentkit.ReagentKit

The supplier of the reagent kit.

SYSTEM_ADMIN_ROLE - Static variable in class com.genologics.ri.researcher.Role

The name for the system administrator role.

T

technician - Variable in class com.genologics.ri.process.ClarityProcess

The technician who ran the process.

technician - Variable in class com.genologics.ri.processexecution.ExecutableProcess

The technician who ran the process.

technician - Variable in class com.genologics.ri.processtemplate.ProcessTemplate

The technician configured to run processes created from this template.

technician - Variable in class com.genologics.ri.step.ProcessStep

The technician assigned to this step.

Technician - Class in com.genologics.ri.process

Technician is a child element of Process and provides a URI linking to the detailed representation of the technician that ran the Process.

Technician - Class in com.genologics.ri.processexecution

The technician element provides a URI to the user that is responsible for the Process.

Technician - Class in com.genologics.ri.processtemplate

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.

Technician - Class in com.genologics.ri.step

Technician is a child element of Step and provides a URI linking to the detailed representation of the technician that ran the Step.

Technician() - Constructor for class com.genologics.ri.process.Technician

Default constructor.

Technician() - Constructor for class com.genologics.ri.processexecution.Technician

Default constructor.

Technician() - Constructor for class com.genologics.ri.processtemplate.Technician

Constructs a new Technician with default values.

Technician() - Constructor for class com.genologics.ri.step.Technician

Default constructor.

Technician(Linkable<Researcher>) - Constructor for class com.genologics.ri.process.Technician

Constructor from a linkable object.

Technician(Linkable<Researcher>) - Constructor for class com.genologics.ri.processexecution.Technician

Constructor from a linkable researcher.

Technician(Linkable<Researcher>) - Constructor for class com.genologics.ri.processtemplate.Technician

Constructs a new Technician from a linkable researcher object.

Technician(Linkable<Researcher>) - Constructor for class com.genologics.ri.step.Technician

Constructor taking a linkable researcher.

Technician(Researcher) - Constructor for class com.genologics.ri.process.Technician

Constructor from a researcher.

Technician(Researcher) - Constructor for class com.genologics.ri.processtemplate.Technician

Constructs a new Technician from a Researcher object, copying the URI, first name, and last name.

Technician(Researcher) - Constructor for class com.genologics.ri.step.Technician

Constructor taking a researcher.

Technician(URI) - Constructor for class com.genologics.ri.process.Technician

Constructor with URI.

Technician(URI) - Constructor for class com.genologics.ri.processexecution.Technician

Constructor with URI.

Technician(URI) - Constructor for class com.genologics.ri.processtemplate.Technician

Constructs a new Technician with the specified URI.

Technician(URI) - Constructor for class com.genologics.ri.step.Technician

Constructor taking a URI.

TEXT - Enum constant in enum class com.genologics.ri.configuration.FieldType

Text field type for longer text content.

throwUnlessNotFound() - Method in exception org.cruk.clarity.api.ClarityException

Convenience method absorb this exception if it is because something is not found, otherwise rethrow itself.

timeCall(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.debugging.HttpClientTimingAspect

Join point that, if the logging is set to DEBUG, will report on the call made with the HttpClient and the time taken to get a response.

toLinks(Collection<? extends Linkable<?>>, boolean) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Create a Links object containing the URIs of the link objects given.

toString() - Method in class com.genologics.ri.artifact.Artifact

Returns a string representation of this artifact.

toString() - Method in class com.genologics.ri.artifact.ArtifactGroupLink

Returns a string representation of this link.

toString() - Method in class com.genologics.ri.artifact.DemuxArtifact

Produces a string representation of this demux artifact.

toString() - Method in class com.genologics.ri.artifact.DemuxSourceArtifact

Produces a string representation of this demux source artifact.

toString() - Method in class com.genologics.ri.artifact.ReagentLabel

Returns a string representation of this reagent label.

toString() - Method in class com.genologics.ri.artifact.WorkflowStage

Returns a string representation of this workflow stage.

toString() - Method in class com.genologics.ri.artifactgroup.ArtifactGroupLink

Returns a string representation of this link.

toString() - Method in class com.genologics.ri.automation.AutomationLink

Returns a string representation of this link.

toString() - Method in class com.genologics.ri.automation.ProcessTypeLink

Returns a string representation of this process type link.

toString() - Method in class com.genologics.ri.configuration.FieldDynamicPreset

Returns the string representation of this preset, which is its value.

toString() - Method in class com.genologics.ri.configuration.FieldDynamicPresetDetails

Returns the string representation of this object, which is the URI as a string.

toString() - Method in class com.genologics.ri.configuration.FieldLink

Returns a string representation of this link.

toString() - Method in class com.genologics.ri.configuration.TypeDefinition

Returns a string representation of this type definition.

toString() - Method in class com.genologics.ri.configuration.UdfConfigLink

Returns a string representation of this UDF config link.

toString() - Method in class com.genologics.ri.configuration.UdtConfigLink

Returns a string representation of this UDF config link.

toString() - Method in class com.genologics.ri.container.Container

Returns a string representation of the container.

toString() - Method in class com.genologics.ri.container.ContainerLink

Returns a string representation of the container link.

toString() - Method in enum class com.genologics.ri.container.ContainerState

Returns a string representation of the container state.

toString() - Method in class com.genologics.ri.container.ContainerTypeLink

Returns a string representation of this link.

toString() - Method in class com.genologics.ri.container.Placement

Returns a string representation of the placement.

toString() - Method in class com.genologics.ri.containertype.ContainerType

Returns a string representation of this container type, which is its name.

toString() - Method in class com.genologics.ri.containertype.ContainerTypeLink

Returns a string representation of this link.

toString() - Method in class com.genologics.ri.controltype.ControlTypeLink

Returns a string representation of this link.

toString() - Method in class com.genologics.ri.globaltoken.GlobalToken

Returns a string representation of this global token.

toString() - Method in class com.genologics.ri.instrumenttype.InstrumentTypeLink

Returns a string representation of this link.

toString() - Method in class com.genologics.ri.instrumenttype.InstrumentTypeProcessType

toString() - Method in class com.genologics.ri.lab.Lab

Returns a string representation of the lab.

toString() - Method in class com.genologics.ri.LimsLinkBase

toString() - Method in class com.genologics.ri.Link

Gets a string representation of the link.

toString() - Method in class com.genologics.ri.Location

Returns a string representation of this location.

toString() - Method in class com.genologics.ri.Page

Gets a string representation of the page.

toString() - Method in class com.genologics.ri.permission.PermissionLink

Returns a string representation of this permission link.

toString() - Method in class com.genologics.ri.process.ClarityProcess

Returns a string representation of this process.

toString() - Method in class com.genologics.ri.process.ProcessTypeLink

Returns a string representation of this object.

toString() - Method in class com.genologics.ri.process.Technician

Returns a string representation of this technician.

toString() - Method in class com.genologics.ri.processexecution.Input

Returns a string representation of the input.

toString() - Method in class com.genologics.ri.processtemplate.ProcessTemplateLink

Returns a string representation of this process template link.

toString() - Method in class com.genologics.ri.processtemplate.ProcessTypeLink

Returns a string representation of this object.

toString() - Method in class com.genologics.ri.processtemplate.Technician

Returns a string representation of this technician.

toString() - Method in class com.genologics.ri.processtype.ContainerTypeLink

Returns a string representation of this link.

toString() - Method in class com.genologics.ri.processtype.ControlTypeLink

Returns a string representation of this link.

toString() - Method in class com.genologics.ri.processtype.Field

Returns a string representation of this field.

toString() - Method in class com.genologics.ri.processtype.ProcessTypeLink

Returns a string representation of this process type link.

toString() - Method in class com.genologics.ri.processtype.ReagentKitLink

Returns a string representation of this reagent kit link.

toString() - Method in class com.genologics.ri.processtype.TypeDefinition

Returns a string representation of this type definition.

toString() - Method in class com.genologics.ri.project.Project

Return a string representation of the project.

toString() - Method in class com.genologics.ri.protocolconfiguration.ProtocolLink

Returns a string representation of this protocol link.

toString() - Method in class com.genologics.ri.reagentkit.ReagentKitLink

Returns a string representation of this reagent kit link.

toString() - Method in class com.genologics.ri.reagentlot.ReagentKitLink

Returns a string representation of this reagent kit link.

toString() - Method in class com.genologics.ri.reagentlot.ReagentLot

Returns a string representation of this reagent lot.

toString() - Method in class com.genologics.ri.reagenttype.ReagentType

Returns a string representation of this reagent type.

toString() - Method in class com.genologics.ri.reagenttype.ReagentTypeLink

Returns a string representation of this link.

toString() - Method in class com.genologics.ri.researcher.Researcher

Gets a string representation of the researcher.

toString() - Method in class com.genologics.ri.researcher.ResearcherLink

Returns a string representation of this link.

toString() - Method in class com.genologics.ri.researcher.Role

Returns a string representation of this role link.

toString() - Method in class com.genologics.ri.role.PermissionLink

Returns a string representation of this permission link.

toString() - Method in class com.genologics.ri.role.ResearcherLink

Returns a string representation of this link.

toString() - Method in class com.genologics.ri.role.RoleLink

Returns a string representation of this role link.

toString() - Method in class com.genologics.ri.sample.ControlTypeLink

Returns a string representation of this link.

toString() - Method in class com.genologics.ri.sample.SampleBase

Returns a string representation of this sample.

toString() - Method in class com.genologics.ri.sample.Submitter

Returns a string representation of this submitter.

toString() - Method in class com.genologics.ri.savedquery.SavedQuery

Returns the string representation of the saved query.

toString() - Method in class com.genologics.ri.savedquery.SavedQueryLink

Returns a string representation of this saved query link.

toString() - Method in class com.genologics.ri.step.Actions

Produces a string representation of this actions object.

toString() - Method in class com.genologics.ri.step.InstrumentLink

Produces a string representation of this instrument link.

toString() - Method in class com.genologics.ri.step.NextAction

Produces a string representation of this next action.

toString() - Method in class com.genologics.ri.step.OutputPlacement

Returns a string representation of this output placement.

toString() - Method in enum class com.genologics.ri.step.ProcessState

Returns a string representation of the process state.

toString() - Method in class com.genologics.ri.step.ReagentLabel

Returns a string representation of the reagent label.

toString() - Method in class com.genologics.ri.step.StepConfiguration

toString() - Method in class com.genologics.ri.step.Technician

Returns a string representation of this technician.

toString() - Method in class com.genologics.ri.step.UserLink

Returns a string representation of this user link.

toString() - Method in class com.genologics.ri.stepconfiguration.ControlTypeLink

Returns a string representation of this control type link.

toString() - Method in class com.genologics.ri.stepconfiguration.GenericTypeLink

Returns a string representation of this generic type link.

toString() - Method in class com.genologics.ri.stepconfiguration.NextStep

Produces a string representation of this next action.

toString() - Method in class com.genologics.ri.stepconfiguration.ProcessTypeLink

Returns a string representation of this process type link.

toString() - Method in class com.genologics.ri.stepconfiguration.ReagentKitLink

Returns a string representation of this reagent kit link.

toString() - Method in class com.genologics.ri.userdefined.UDF

Returns the string representation of the UDF.

toString() - Method in class com.genologics.ri.workflowconfiguration.ProtocolLink

Returns a string representation of this protocol link.

toString() - Method in class com.genologics.ri.workflowconfiguration.StageLink

Returns a string representation of this stage link.

toString() - Method in class com.genologics.ri.workflowconfiguration.WorkflowLink

Returns a string representation of this workflow link.

toString() - Method in exception org.cruk.clarity.api.ClarityException

Provide a printable representation of this exception.

toString() - Method in class org.cruk.clarity.api.impl.URLInputStreamResource

Print this resource in a human readable manner.

toString() - Method in class org.cruk.clarity.api.SavedQuerySummary

Print the content type and length of the response.

toString() - Method in class org.cruk.clarity.api.search.Search

Get a human readable representation of this object.

toString() - Method in class org.cruk.clarity.api.search.SearchTerm

Get a human readable representation of this object.

toString() - Method in class org.cruk.clarity.api.search.SearchTerms

Get a human readable representation of this object.

toString(LimsLink<?>) - Static method in interface com.genologics.ri.LimsLink

An implementation of toString() for links.

toURI(CharSequence) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Convert a character sequence into a URI object.

toUriString(Class<?>, String...) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Assemble a URI for an object's id and class.

transitions - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

List of transitions to next steps in the protocol.

TriggerPoint - Enum Class in com.genologics.ri.processtype

The trigger-point enumeration lists the possible values of the EPP Trigger point attribute.

TriggerPoint - Enum Class in com.genologics.ri.stepconfiguration

Enumeration of EPP trigger execution points.

TriggerStatus - Enum Class in com.genologics.ri.processtype

The trigger-status enumeration lists the possible values of the EPP Trigger status attribute.

TriggerStatus - Enum Class in com.genologics.ri.stepconfiguration

Enumeration of step statuses at which EPP triggers can execute.

TriggerType - Enum Class in com.genologics.ri.processtype

The trigger-type enumeration lists the possible values of the EPP Trigger type attribute.

TriggerType - Enum Class in com.genologics.ri.stepconfiguration

Enumeration of EPP trigger types.

tube - Variable in class com.genologics.ri.containertype.ContainerType

Indicates whether this container type represents a tube (single well) or a multi-well container.

type - Variable in class com.genologics.ri.artifact.Artifact

The type of the artifact.

type - Variable in class com.genologics.ri.configuration.Field

The type of this field.

type - Variable in class com.genologics.ri.container.Container

The user-defined type for the container.

type - Variable in class com.genologics.ri.instrument.Instrument

The instrument type.

type - Variable in class com.genologics.ri.lab.Lab

The user-defined type for the lab.

type - Variable in class com.genologics.ri.process.ClarityProcess

The user defined type.

type - Variable in class com.genologics.ri.processexecution.ExecutableProcess

The user-defined type.

type - Variable in class com.genologics.ri.processexecution.Output

The output type.

type - Variable in class com.genologics.ri.processtemplate.ProcessTemplate

The user-defined type.

type - Variable in class com.genologics.ri.processtype.EppTrigger

The type of the trigger (manual, automatic, or unused).

type - Variable in class com.genologics.ri.project.Project

The user-defined type of the project.

type - Variable in class com.genologics.ri.researcher.Researcher

The user-defined type for the researcher.

type - Variable in class com.genologics.ri.sample.SampleBase

The user-defined type of this sample.

type - Variable in class com.genologics.ri.step.ArtifactLink

The type of the artifact output.

type - Variable in class com.genologics.ri.stepconfiguration.EppTrigger

The type of the EPP trigger.

type - Variable in class com.genologics.ri.userdefined.UDF

The data type of the user-defined field.

Type - Class in com.genologics.ri.configuration

The detailed representation of the configuration of a user defined type.

Type() - Constructor for class com.genologics.ri.configuration.Type

Constructor for creating an empty Type object.

Type(String) - Constructor for class com.genologics.ri.configuration.Type

Constructor for creating a Type with a name.

Type(String, URI) - Constructor for class com.genologics.ri.configuration.Type

Constructor for creating a Type with a name and URI.

typeDefinition - Variable in class com.genologics.ri.configuration.Field

The type definition for complex types.

TypeDefinition - Class in com.genologics.ri.configuration

Type-definition provides a URI linking to the user defined type associated with the user-defined field, if applicable.

TypeDefinition - Class in com.genologics.ri.processtype

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.

TypeDefinition() - Constructor for class com.genologics.ri.configuration.TypeDefinition

Constructor for creating an empty TypeDefinition object.

TypeDefinition() - Constructor for class com.genologics.ri.processtype.TypeDefinition

Constructs a new type definition.

TypeDefinition(Field) - Constructor for class com.genologics.ri.processtype.TypeDefinition

Constructs a new type definition from a field entity.

TypeDefinition(Type) - Constructor for class com.genologics.ri.configuration.TypeDefinition

Constructor for creating a TypeDefinition from a Type object.

TypeDefinition(Linkable<Field>) - Constructor for class com.genologics.ri.processtype.TypeDefinition

Constructs a new type definition from a linkable field.

TypeDefinition(Linkable<Type>) - Constructor for class com.genologics.ri.configuration.TypeDefinition

Constructor for creating a TypeDefinition from a Linkable object.

TypeDefinition(URI) - Constructor for class com.genologics.ri.configuration.TypeDefinition

Constructor for creating a TypeDefinition with a URI.

TypeDefinition(URI) - Constructor for class com.genologics.ri.processtype.TypeDefinition

Constructs a new type definition with the specified URI.

TypeDefinition(URI, String) - Constructor for class com.genologics.ri.configuration.TypeDefinition

Constructor for creating a TypeDefinition with a URI and name.

TypeDefinition(URI, String) - Constructor for class com.genologics.ri.processtype.TypeDefinition

Constructs a new type definition with the specified URI and name.

typeDefinitions - Variable in class com.genologics.ri.processtype.ProcessType

Type definitions for user-defined types.

U

UDF - Class in com.genologics.ri.userdefined

Field is the value and data type of a user-defined field.

UDF() - Constructor for class com.genologics.ri.userdefined.UDF

Default constructor.

UDF(String, FieldType) - Constructor for class com.genologics.ri.userdefined.UDF

Constructor with name and type.

UDF(String, FieldType, Object) - Constructor for class com.genologics.ri.userdefined.UDF

Constructor with name, type and value.

UDF(String, Object) - Constructor for class com.genologics.ri.userdefined.UDF

Constructor with name and value.

UDF_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The user-defined field (UDF) namespace.

UdfConfigLink - Class in com.genologics.ri.configuration

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.

UdfConfigLink() - Constructor for class com.genologics.ri.configuration.UdfConfigLink

Constructor for creating an empty UdfConfigLink object.

UdfConfigLink(Field) - Constructor for class com.genologics.ri.configuration.UdfConfigLink

Constructor for creating a UdfConfigLink from a Field object.

UdfConfigLink(URI) - Constructor for class com.genologics.ri.configuration.UdfConfigLink

Constructor for creating a UdfConfigLink with a URI.

udfConfigLinks - Variable in class com.genologics.ri.configuration.Udfs

The list of user defined field configuration links.

UDFHolder - Interface in com.genologics.ri.userdefined

Interface for any entity or other object that holds user defined fields (UDFs).

Udfs - Class in com.genologics.ri.configuration

The representation of a list of user defined field configuration links.

Udfs() - Constructor for class com.genologics.ri.configuration.Udfs

Constructor for creating an empty Udfs object.

UDT - Class in com.genologics.ri.userdefined

Type is the name and user-defined fields of a user-defined type.

UDT() - Constructor for class com.genologics.ri.userdefined.UDT

Default constructor.

UDT(String) - Constructor for class com.genologics.ri.userdefined.UDT

Constructor with name.

UdtConfigLink - Class in com.genologics.ri.configuration

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.

UdtConfigLink() - Constructor for class com.genologics.ri.configuration.UdtConfigLink

Constructor for creating an empty UdtConfigLink object.

UdtConfigLink(Type) - Constructor for class com.genologics.ri.configuration.UdtConfigLink

Constructor for creating a UdtConfigLink from a Type object.

UdtConfigLink(URI) - Constructor for class com.genologics.ri.configuration.UdtConfigLink

Constructor for creating a UdtConfigLink with a URI.

udtConfigLinks - Variable in class com.genologics.ri.configuration.Udts

The list of user defined type configuration links.

Udts - Class in com.genologics.ri.configuration

The representation of a list of user defined type configuration links.

Udts() - Constructor for class com.genologics.ri.configuration.Udts

Constructor for creating an empty Udts object.

unassignedRoutes - Variable in class com.genologics.ri.routing.Routing

The list of artifact assignments to unassign from workflows/stages.

unavailableWells - Variable in class com.genologics.ri.containertype.ContainerType

List of well locations that are not available for storing samples or reagents.

unit - Variable in class com.genologics.ri.userdefined.UDF

The unit of the user-defined field (if applicable).

unitLabel - Variable in class com.genologics.ri.configuration.Field

The unit label for numeric fields.

UNKNOWN - Enum constant in enum class com.genologics.ri.artifact.QCFlag

Unknown quality control status.

UNKNOWN - Enum constant in enum class com.genologics.ri.processexecution.QCFlag

QC status is unknown.

UNKNOWN - Enum constant in enum class com.genologics.ri.step.ActionType

Unknown action type.

unmarshal(Object) - Method in class org.cruk.clarity.api.search.internal.LimsLinkAdapter

Converts an XML object to a LimsLink object during unmarshalling.

unmarshal(String) - Method in class com.genologics.ri.jaxb.AbstractDateAdapter

Parse the string into a Date object.

unmarshal(String) - Method in class com.genologics.ri.jaxb.URIAdapter

Convert a string into a URI.

UNSET - Static variable in class com.genologics.ri.Link

Shared constant for use throughout this library to indicate a field is not set.

UNUSED - Enum constant in enum class com.genologics.ri.processtype.TriggerType

The trigger is not currently used.

UNUSED - Enum constant in enum class com.genologics.ri.stepconfiguration.TriggerType

Unused trigger.

update(E) - Method in interface org.cruk.clarity.api.ClarityAPI

Update the given entity on the server.

update(E) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Update the given entity on the server.

update(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Join point for the ClarityAPI.update method.

updateable() - Element in annotation interface com.genologics.ri.ClarityEntity

If true, the flag indicates that entities of the annotated type can be updated with PUT.

updateAll(Collection<E>) - Method in interface org.cruk.clarity.api.ClarityAPI

Updates a batch of entities.

updateAll(Collection<E>) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Updates a batch of entities.

updateAll(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Join point for the ClarityAPI.updateAll method.

updateQCFlag(Linkable<Artifact>) - Method in class com.genologics.ri.processexecution.ArtifactBase

Updates the QC flag from a linkable artifact.

updaterFields - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

Cache of fields to update by reflective examination of an updated object from the server.

upload(URLInputStreamResource, ClarityFile) - Method in interface org.cruk.clarity.api.filestore.ClaritySFTPUploader

Upload a file to the Clarity file store.

uploadFile(LimsEntityLinkable<E>, URL, boolean) - Method in interface org.cruk.clarity.api.ClarityAPI

Attach a file to an entity and upload that file to the file store.

uploadFile(LimsEntityLinkable<E>, URL, boolean) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Attach a file to an entity and upload that file to the file store.

uploadFile(ProceedingJoinPoint) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Join point for the ClarityAPI.uploadFile method.

uploadOverHttp - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl

Whether files can be uploaded using HTTP to the files/id/upload API end point.

uploadViaHTTP(URLInputStreamResource, ClarityFile) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Upload a file to the Clarity file store.

uploadViaSFTP(URLInputStreamResource, ClarityFile) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl

Upload a file to the Clarity file store.

uri - Variable in class com.genologics.ri.artifact.Artifact

The URI of the artifact.

uri - Variable in class com.genologics.ri.artifact.ArtifactGroupLink

The URI of this artifact group.

uri - Variable in class com.genologics.ri.artifact.ArtifactLink

The URI of this artifact.

uri - Variable in class com.genologics.ri.artifact.ControlTypeLink

The URI of this control type.

uri - Variable in class com.genologics.ri.artifact.Demux

The URI of this demux.

uri - Variable in class com.genologics.ri.artifact.DemuxArtifact

The URI of this demux artifact.

uri - Variable in class com.genologics.ri.artifact.DemuxArtifactSample

The URI of this demux artifact sample.

uri - Variable in class com.genologics.ri.artifact.DemuxLink

The URI of this demux artifact.

uri - Variable in class com.genologics.ri.artifact.DemuxSourceArtifact

The URI of this demux source artifact.

uri - Variable in class com.genologics.ri.artifact.ParentProcessLink

The URI of this parent process.

uri - Variable in class com.genologics.ri.artifact.PoolStep

The URI of this pool step.

uri - Variable in class com.genologics.ri.artifact.SampleLink

The URI of this sample.

uri - Variable in class com.genologics.ri.artifact.WorkflowStage

The URI of this workflow stage.

uri - Variable in class com.genologics.ri.artifactgroup.ArtifactGroup

The URI of this artifact group.

uri - Variable in class com.genologics.ri.artifactgroup.ArtifactGroupLink

The URI of the artifact group.

uri - Variable in class com.genologics.ri.artifactgroup.Artifacts

The URI of the artifacts in this group.

uri - Variable in class com.genologics.ri.automation.Automation

The URI of this automation.

uri - Variable in class com.genologics.ri.automation.AutomationLink

The URI of the automation.

uri - Variable in class com.genologics.ri.automation.Automations

The URI of this automations resource.

uri - Variable in class com.genologics.ri.automation.ProcessTypeLink

The URI of the process type.

uri - Variable in class com.genologics.ri.configuration.Field

The URI of this field configuration.

uri - Variable in class com.genologics.ri.configuration.FieldDynamicPresetDetails

The URI of this preset details resource.

uri - Variable in class com.genologics.ri.configuration.FieldLink

The URI of the field configuration.

uri - Variable in class com.genologics.ri.configuration.Type

The URI of this type configuration.

uri - Variable in class com.genologics.ri.configuration.TypeDefinition

The URI of the type definition.

uri - Variable in class com.genologics.ri.configuration.UdfConfigLink

The URI of the field configuration.

uri - Variable in class com.genologics.ri.configuration.UdtConfigLink

The URI of the type configuration.

uri - Variable in class com.genologics.ri.container.Container

The URI of the container.

uri - Variable in class com.genologics.ri.container.ContainerLink

The URI of the container.

uri - Variable in class com.genologics.ri.container.ContainerTypeLink

The URI of the container type.

uri - Variable in class com.genologics.ri.container.Placement

The URI of the artifact.

uri - Variable in class com.genologics.ri.ContainerLink

The URI of the container.

uri - Variable in class com.genologics.ri.containertype.ContainerType

The URI for accessing this container type resource.

uri - Variable in class com.genologics.ri.containertype.ContainerTypeLink

The URI for accessing the container type resource.

uri - Variable in class com.genologics.ri.controltype.ControlType

The URI of the control type.

uri - Variable in class com.genologics.ri.controltype.ControlTypeLink

The URI of the control type.

uri - Variable in class com.genologics.ri.controltype.ControlTypes

The URI of the control types collection.

uri - Variable in class com.genologics.ri.ExternalId

The URI within the external system.

uri - Variable in class com.genologics.ri.file.ClarityFile

The URI of the file resource.

uri - Variable in class com.genologics.ri.file.FileLink

The URI of the file resource.

uri - Variable in class com.genologics.ri.globaltoken.GlobalToken

The URI of this global token.

uri - Variable in class com.genologics.ri.globaltoken.GlobalTokenLink

The URI of the global token.

uri - Variable in class com.genologics.ri.instrument.Instrument

The URI of this instrument.

uri - Variable in class com.genologics.ri.instrument.InstrumentLink

The URI of the instrument.

uri - Variable in class com.genologics.ri.instrumenttype.InstrumentType

The URI of the instrument type.

uri - Variable in class com.genologics.ri.instrumenttype.InstrumentTypeLink

The URI of the instrument type.

uri - Variable in class com.genologics.ri.instrumenttype.InstrumentTypeProcessType

The process type URI.

uri - Variable in class com.genologics.ri.lab.Lab

The URI of the lab resource.

uri - Variable in class com.genologics.ri.lab.LabLink

The URI of the lab resource.

uri - Variable in class com.genologics.ri.Link

The URI of the link.

uri - Variable in class com.genologics.ri.Page

The URI to the page.

uri - Variable in class com.genologics.ri.permission.Permission

The URI of the permission.

uri - Variable in class com.genologics.ri.permission.PermissionLink

The URI of the permission.

uri - Variable in class com.genologics.ri.permission.Permissions

The URI of the permissions collection.

uri - Variable in class com.genologics.ri.process.ArtifactLink

The URI of the artifact.

uri - Variable in class com.genologics.ri.process.ClarityProcess

The URI of the process.

uri - Variable in class com.genologics.ri.process.InstrumentLink

The URI of the instrument.

uri - Variable in class com.genologics.ri.process.ParentProcessLink

The URI of the parent process.

uri - Variable in class com.genologics.ri.process.ProcessLink

The URI of the process.

uri - Variable in class com.genologics.ri.process.ProcessTypeLink

The URI of the process type.

uri - Variable in class com.genologics.ri.process.Technician

The URI of the technician.

uri - Variable in class com.genologics.ri.processexecution.Input

The URI of the input artifact.

uri - Variable in class com.genologics.ri.processexecution.InstrumentLink

The URI of the instrument.

uri - Variable in class com.genologics.ri.processexecution.Technician

The URI of the researcher acting as technician.

uri - Variable in class com.genologics.ri.processtemplate.InstrumentLink

The URI of the instrument.

uri - Variable in class com.genologics.ri.processtemplate.ProcessTemplate

The URI of this process template.

uri - Variable in class com.genologics.ri.processtemplate.ProcessTemplateLink

The URI of the process template.

uri - Variable in class com.genologics.ri.processtemplate.ProcessTypeLink

The URI of the process type.

uri - Variable in class com.genologics.ri.processtemplate.Technician

The URI linking to the detailed representation of this technician in the system.

uri - Variable in class com.genologics.ri.processtype.ContainerTypeLink

The URI of the container type.

uri - Variable in class com.genologics.ri.processtype.ControlTypeLink

The URI of the control type.

uri - Variable in class com.genologics.ri.processtype.ProcessType

The URI of the process type.

uri - Variable in class com.genologics.ri.processtype.ProcessTypeLink

The URI of the process type.

uri - Variable in class com.genologics.ri.processtype.ReagentKitLink

The URI of the reagent kit.

uri - Variable in class com.genologics.ri.processtype.TypeDefinition

The URI of the field.

uri - Variable in class com.genologics.ri.project.Project

The URI of the project.

uri - Variable in class com.genologics.ri.project.ProjectLink

The URI of the project.

uri - Variable in class com.genologics.ri.project.ResearcherLink

The URI of the researcher.

uri - Variable in class com.genologics.ri.property.PropertyLink

The URI of the property.

uri - Variable in class com.genologics.ri.protocolconfiguration.Protocol

The URI of the protocol.

uri - Variable in class com.genologics.ri.protocolconfiguration.ProtocolLink

The URI to the protocol.

uri - Variable in class com.genologics.ri.queue.ArtifactLink

The URI of the artifact.

uri - Variable in class com.genologics.ri.queue.Queue

The URI of the queue.

uri - Variable in class com.genologics.ri.reagentkit.ReagentKit

The URI of the reagent kit.

uri - Variable in class com.genologics.ri.reagentkit.ReagentKitLink

The URI of the reagent kit.

uri - Variable in class com.genologics.ri.reagentkit.ReagentKits

The URI of the reagent kits list.

uri - Variable in class com.genologics.ri.reagentlot.ReagentKitLink

The URI of the reagent kit.

uri - Variable in class com.genologics.ri.reagentlot.ReagentLot

The URI of this reagent lot resource.

uri - Variable in class com.genologics.ri.reagentlot.ReagentLotLink

The URI of the reagent lot.

uri - Variable in class com.genologics.ri.reagentlot.ReagentLots

The URI of this reagent lots collection.

uri - Variable in class com.genologics.ri.reagentlot.ResearcherLink

The URI of the researcher.

uri - Variable in class com.genologics.ri.reagenttype.ReagentType

The URI of the reagent type.

uri - Variable in class com.genologics.ri.reagenttype.ReagentTypeLink

The URI of the reagent type.

uri - Variable in class com.genologics.ri.researcher.LabLink

The URI to the lab.

uri - Variable in class com.genologics.ri.researcher.Researcher

The URI to the researcher.

uri - Variable in class com.genologics.ri.researcher.ResearcherLink

The URI to the researcher.

uri - Variable in class com.genologics.ri.researcher.Role

The URI to the role.

uri - Variable in class com.genologics.ri.role.PermissionLink

The URI of the permission.

uri - Variable in class com.genologics.ri.role.ResearcherLink

The URI of the researcher.

uri - Variable in class com.genologics.ri.role.Role

The URI of the role.

uri - Variable in class com.genologics.ri.role.RoleLink

The URI of the role.

uri - Variable in class com.genologics.ri.role.Roles

The URI of the roles list.

uri - Variable in class com.genologics.ri.routing.ArtifactLink

The URI of the artifact.

uri - Variable in class com.genologics.ri.sample.ArtifactLink

The URI of the artifact.

uri - Variable in class com.genologics.ri.sample.ControlTypeLink

The URI of the control type.

uri - Variable in class com.genologics.ri.sample.ProjectLink

The URI of the project.

uri - Variable in class com.genologics.ri.sample.SampleBase

The URI of this sample.

uri - Variable in class com.genologics.ri.sample.SampleLink

The URI of the sample.

uri - Variable in class com.genologics.ri.sample.Submitter

The URI of the submitter.

uri - Variable in class com.genologics.ri.savedquery.SavedQuery

The URI of the saved query.

uri - Variable in class com.genologics.ri.savedquery.SavedQueryLink

The URI of the saved query.

uri - Variable in class com.genologics.ri.stage.ProtocolLink

The URI of the protocol.

uri - Variable in class com.genologics.ri.stage.ProtocolStepLink

The URI of the protocol step.

uri - Variable in class com.genologics.ri.stage.Stage

The URI of the stage.

uri - Variable in class com.genologics.ri.stage.WorkflowLink

The URI of the workflow.

uri - Variable in class com.genologics.ri.step.Actions

URI of the actions resource.

uri - Variable in class com.genologics.ri.step.ActionsLink

URI of the actions resource.

uri - Variable in class com.genologics.ri.step.Arrangements

URI of the arrangements resource.

uri - Variable in class com.genologics.ri.step.ArrangementsLink

URI of the arrangements resource.

uri - Variable in class com.genologics.ri.step.ArtifactLink

URI of the artifact.

uri - Variable in class com.genologics.ri.step.AutomaticNextStepLink

URI of the automatic next step.

uri - Variable in class com.genologics.ri.step.AvailableProgram

URI of the available program.

uri - Variable in class com.genologics.ri.step.ContainerLink

URI of the container.

uri - Variable in class com.genologics.ri.step.CreationInput

URI of the input artifact.

uri - Variable in class com.genologics.ri.step.EscalatedArtifact

URI of the escalated artifact.

uri - Variable in class com.genologics.ri.step.Input

URI of the input artifact.

uri - Variable in class com.genologics.ri.step.InstrumentLink

URI of the instrument.

uri - Variable in class com.genologics.ri.step.OutputArrangement

URI of the output container.

uri - Variable in class com.genologics.ri.step.OutputPlacement

The URI of the output artifact.

uri - Variable in class com.genologics.ri.step.Placements

The URI of this placements resource.

uri - Variable in class com.genologics.ri.step.PlacementsLink

The URI of the placements resource.

uri - Variable in class com.genologics.ri.step.Pools

The URI of this pools resource.

uri - Variable in class com.genologics.ri.step.PoolsLink

The URI of the pools resource.

uri - Variable in class com.genologics.ri.step.ProcessStep

The URI of the step.

uri - Variable in class com.genologics.ri.step.ProgramStatus

The URI of the program status.

uri - Variable in class com.genologics.ri.step.ProgramStatusLink

The URI of the program status.

uri - Variable in class com.genologics.ri.step.ReagentLotLink

The URI of the reagent lot.

uri - Variable in class com.genologics.ri.step.ReagentLots

The URI of the reagent lots resource.

uri - Variable in class com.genologics.ri.step.ReagentLotsLink

The URI of the reagent lots resource.

uri - Variable in class com.genologics.ri.step.Reagents

URI of the reagents resource.

uri - Variable in class com.genologics.ri.step.ReagentsLink

The URI of the reagents resource.

uri - Variable in class com.genologics.ri.step.StepDetails

The URI of this step details resource.

uri - Variable in class com.genologics.ri.step.StepDetailsLink

The URI of the step details resource.

uri - Variable in class com.genologics.ri.step.StepSetup

The URI of this step setup resource.

uri - Variable in class com.genologics.ri.step.StepSetupLink

The URI of the step setup resource.

uri - Variable in class com.genologics.ri.step.Technician

The URI of the researcher resource representing the technician.

uri - Variable in class com.genologics.ri.step.UserLink

The URI of the researcher resource representing the user.

uri - Variable in class com.genologics.ri.stepconfiguration.ControlTypeLink

The URI of the control type.

uri - Variable in class com.genologics.ri.stepconfiguration.ProcessTypeLink

The URI of the process type.

uri - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep

The URI of the protocol step.

uri - Variable in class com.genologics.ri.stepconfiguration.ReagentKitLink

The URI of the reagent kit.

uri - Variable in class com.genologics.ri.version.Version

The URI of the version.

uri - Variable in class com.genologics.ri.workflowconfiguration.ProtocolLink

The URI of the protocol.

uri - Variable in class com.genologics.ri.workflowconfiguration.StageLink

The URI of the stage.

uri - Variable in class com.genologics.ri.workflowconfiguration.Workflow

The URI of the workflow.

uri - Variable in class com.genologics.ri.workflowconfiguration.WorkflowLink

The URI of the workflow.

URI - Enum constant in enum class com.genologics.ri.configuration.FieldType

URI field type.

URIAdapter - Class in com.genologics.ri.jaxb

Convert to and from URI objects, correctly encoding the query string.

URIAdapter() - Constructor for class com.genologics.ri.jaxb.URIAdapter

Default constructor.

uriSection() - Element in annotation interface com.genologics.ri.ClarityEntity

The part of the URL that specifies how to list or load entities of the annotated class.

uriSubsection() - Element in annotation interface com.genologics.ri.ClarityEntity

Whether the class is a subsection of a base end point.

URLInputStreamResource - Class in org.cruk.clarity.api.impl

Resource implementation based around a URL.

URLInputStreamResource(URL) - Constructor for class org.cruk.clarity.api.impl.URLInputStreamResource

Create a new resource around the given URL.

URLInputStreamResource(URL, int) - Constructor for class org.cruk.clarity.api.impl.URLInputStreamResource

Create a new resource around the given URL.

usageCount - Variable in class com.genologics.ri.reagentlot.ReagentLot

The number of times this reagent lot has been used.

USER_DEFINED - Enum constant in enum class com.genologics.ri.processtype.Style

User-defined field.

USER_DEFINED - Enum constant in enum class com.genologics.ri.stepconfiguration.Style

User-defined field style.

UserLink - Class in com.genologics.ri.step

Describes a user as required in the context of step escalations.

UserLink() - Constructor for class com.genologics.ri.step.UserLink

Default constructor.

UserLink(Linkable<Researcher>) - Constructor for class com.genologics.ri.step.UserLink

Constructor taking a linkable researcher.

UserLink(Researcher) - Constructor for class com.genologics.ri.step.UserLink

Constructor taking a researcher.

UserLink(URI) - Constructor for class com.genologics.ri.step.UserLink

Constructor taking a URI.

username - Variable in class com.genologics.ri.researcher.Credentials

The researcher's username.

V

value - Variable in class com.genologics.ri.configuration.FieldDynamicPreset

The preset value.

value - Variable in class com.genologics.ri.containertype.CalibrantWell

Deprecated.

The value or content of the calibrant well.

value - Variable in class com.genologics.ri.globaltoken.GlobalToken

The token value.

value - Variable in class com.genologics.ri.processtype.ProcessTypeAttribute

The value of the attribute.

value - Variable in class com.genologics.ri.processtype.StepProperty

The value of the step property.

value - Variable in class com.genologics.ri.property.PropertyLink

The value of the property.

value - Variable in class com.genologics.ri.protocolconfiguration.ProtocolProperty

The value of the protocol property.

value - Variable in class com.genologics.ri.reagenttype.Attribute

The value of the attribute.

value - Variable in class com.genologics.ri.stepconfiguration.GenericTypeLink

The value of the generic type link.

value - Variable in class com.genologics.ri.stepconfiguration.StepProperty

The value of the step property.

value - Variable in class com.genologics.ri.userdefined.UDF

The value of the user-defined field.

value() - Method in enum class com.genologics.ri.artifact.OutputType

Gets the string value.

value() - Method in enum class com.genologics.ri.artifact.QCFlag

Gets the string value.

value() - Method in enum class com.genologics.ri.artifact.Status

Gets the string value.

value() - Method in enum class com.genologics.ri.automation.Context

Gets the string value of this context.

value() - Method in enum class com.genologics.ri.configuration.FieldType

Gets the string value of this field type.

value() - Method in enum class com.genologics.ri.container.ContainerState

Gets the string value of this container state.

value() - Method in enum class com.genologics.ri.process.OutputGenerationType

Gets the XML value.

value() - Method in enum class com.genologics.ri.processexecution.QCFlag

Gets the string value of the enum constant.

value() - Method in enum class com.genologics.ri.processtype.InvocationType

Gets the XML value of this invocation type.

value() - Method in enum class com.genologics.ri.processtype.OutputGenerationType

Gets the XML value of this output generation type.

value() - Method in enum class com.genologics.ri.processtype.Style

Gets the XML value of this style.

value() - Method in enum class com.genologics.ri.processtype.TriggerPoint

Gets the XML value of this trigger point.

value() - Method in enum class com.genologics.ri.processtype.TriggerStatus

Gets the XML value of this trigger status.

value() - Method in enum class com.genologics.ri.processtype.TriggerType

Gets the XML value of this trigger type.

value() - Method in enum class com.genologics.ri.processtype.VariabilityType

Gets the XML value of this variability type.

value() - Method in enum class com.genologics.ri.step.ActionType

Gets the string value.

value() - Method in enum class com.genologics.ri.step.OutputGenerationType

Gets the string value.

value() - Method in enum class com.genologics.ri.step.ProcessState

Gets the string value of the process state.

value() - Method in enum class com.genologics.ri.step.Status

Gets the string value of the status.

value() - Method in enum class com.genologics.ri.stepconfiguration.Style

Gets the value of this enum constant.

value() - Method in enum class com.genologics.ri.stepconfiguration.TriggerPoint

Gets the value of this enum constant.

value() - Method in enum class com.genologics.ri.stepconfiguration.TriggerStatus

Gets the value of this enum constant.

value() - Method in enum class com.genologics.ri.stepconfiguration.TriggerType

Gets the value of this enum constant.

value() - Method in enum class com.genologics.ri.workflowconfiguration.Status

Gets the string value of this status.

valueOf(String) - Static method in enum class com.genologics.ri.artifact.OutputType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.artifact.QCFlag

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.artifact.Status

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.automation.Context

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.configuration.FieldType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.container.ContainerState

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.process.OutputGenerationType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.processexecution.QCFlag

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.processtype.InvocationType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.processtype.OutputGenerationType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.processtype.Style

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.processtype.TriggerPoint

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.processtype.TriggerStatus

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.processtype.TriggerType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.processtype.VariabilityType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.reagentlot.Status

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.step.ActionType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.step.OutputGenerationType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.step.ProcessState

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.step.Status

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.stepconfiguration.Style

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.stepconfiguration.TriggerPoint

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.stepconfiguration.TriggerStatus

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.stepconfiguration.TriggerType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class com.genologics.ri.workflowconfiguration.Status

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class org.cruk.clarity.api.cache.CacheStatefulBehaviour

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class org.cruk.clarity.api.StatefulOverride

Returns the enum constant of this class with the specified name.

values() - Static method in enum class com.genologics.ri.artifact.OutputType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.artifact.QCFlag

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.artifact.Status

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.automation.Context

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.configuration.FieldType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.container.ContainerState

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.process.OutputGenerationType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.processexecution.QCFlag

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.processtype.InvocationType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.processtype.OutputGenerationType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.processtype.Style

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.processtype.TriggerPoint

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.processtype.TriggerStatus

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.processtype.TriggerType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.processtype.VariabilityType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.reagentlot.Status

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.step.ActionType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.step.OutputGenerationType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.step.ProcessState

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.step.Status

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.stepconfiguration.Style

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.stepconfiguration.TriggerPoint

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.stepconfiguration.TriggerStatus

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.stepconfiguration.TriggerType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class com.genologics.ri.workflowconfiguration.Status

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class org.cruk.clarity.api.cache.CacheStatefulBehaviour

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class org.cruk.clarity.api.StatefulOverride

Returns an array containing the constants of this enum class, in the order they are declared.

variabilityType - Variable in class com.genologics.ri.processtype.ProcessOutput

Specifies how the process determines the number of outputs to generate.

VariabilityType - Enum Class in com.genologics.ri.processtype

Enumeration of variability types for process outputs.

VARIABLE - Enum constant in enum class com.genologics.ri.processtype.VariabilityType

A variable number of outputs is generated.

VARIABLE_BY_INPUT - Enum constant in enum class com.genologics.ri.processtype.VariabilityType

The number of outputs varies based on the input.

vendor - Variable in class com.genologics.ri.instrumenttype.InstrumentType

The instrument vendor.

vendor - Variable in class com.genologics.ri.instrumenttype.InstrumentTypeLink

The instrument vendor.

Version - Class in com.genologics.ri.version

Represents a Clarity LIMS API version.

Version() - Constructor for class com.genologics.ri.version.Version

VERSION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The version namespace.

versionFromLocatable(Locatable) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Extract the state value from the given object's URI, if such an entity can have a state value.

versionFromUri(String) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Extract the state value from a string version of a URI.

versionFromUri(URI) - Method in class org.cruk.clarity.api.cache.ClarityAPICache

Extract the state value from a URI.

versions - Variable in class com.genologics.ri.version.Versions

The list of versions.

Versions - Class in com.genologics.ri.version

Index is the base entry point to the API, providing a list of supported versions in the system.

Versions() - Constructor for class com.genologics.ri.version.Versions

Default constructor.

W

waitUntilProcessInState(ProcessStep, ProcessState) - Method in interface org.cruk.clarity.api.automation.ClarityProcessAutomation

Wait until a process has reached a certain state.

waitUntilProcessInState(ProcessStep, ProcessState) - Method in class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Wait until a process has reached a certain state.

waitUntilProgramCompletes(AvailableProgram, ProgramStatus) - Method in interface org.cruk.clarity.api.automation.ClarityProcessAutomation

Wait for an EPP to finish running.

waitUntilProgramCompletes(AvailableProgram, ProgramStatus) - Method in class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl

Wait for an EPP to finish running.

WARNING - Enum constant in enum class com.genologics.ri.step.Status

The step completed with warnings.

website - Variable in class com.genologics.ri.controltype.ControlType

The website URL for the control type.

website - Variable in class com.genologics.ri.lab.Lab

The website URL of the lab.

website - Variable in class com.genologics.ri.reagentkit.ReagentKit

The website of the reagent kit.

WELL_POSITION_SPLITTER - Static variable in class com.genologics.ri.Location

Pattern for splitting well position strings.

wellPosition - Variable in class com.genologics.ri.container.Placement

The well position in the container.

workflow - Variable in class com.genologics.ri.stage.Stage

Link to the workflow this stage belongs to.

Workflow - Class in com.genologics.ri.workflowconfiguration

The detailed representation of a Workflow.

Workflow() - Constructor for class com.genologics.ri.workflowconfiguration.Workflow

Default constructor.

Workflow(URI) - Constructor for class com.genologics.ri.workflowconfiguration.Workflow

Constructor accepting a URI.

Workflow(URI, String) - Constructor for class com.genologics.ri.workflowconfiguration.Workflow

Constructor accepting a URI and name.

WORKFLOW_CONFIGURATION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces

The workflow configuration namespace.

WorkflowLink - Class in com.genologics.ri.stage

Workflow link for a stage.

WorkflowLink - Class in com.genologics.ri.workflowconfiguration

Workflow-link is a child element type of workflows and provides a URI linking to the detailed representation of a workflow.

WorkflowLink() - Constructor for class com.genologics.ri.stage.WorkflowLink

Default constructor.

WorkflowLink() - Constructor for class com.genologics.ri.workflowconfiguration.WorkflowLink

Default constructor.

WorkflowLink(Linkable<Workflow>) - Constructor for class com.genologics.ri.stage.WorkflowLink

Constructor from a linkable workflow object.

WorkflowLink(Linkable<Workflow>) - Constructor for class com.genologics.ri.workflowconfiguration.WorkflowLink

Constructor accepting a Linkable object.

WorkflowLink(Workflow) - Constructor for class com.genologics.ri.workflowconfiguration.WorkflowLink

Constructor accepting a Workflow object.

WorkflowLink(URI) - Constructor for class com.genologics.ri.stage.WorkflowLink

Constructor with URI.

WorkflowLink(URI) - Constructor for class com.genologics.ri.workflowconfiguration.WorkflowLink

Constructor accepting a URI.

WorkflowLink(URI, String) - Constructor for class com.genologics.ri.workflowconfiguration.WorkflowLink

Constructor accepting a URI and name.

WorkflowLink(URI, String, Status) - Constructor for class com.genologics.ri.workflowconfiguration.WorkflowLink

Constructor accepting a URI, name, and status.

workflows - Variable in class com.genologics.ri.workflowconfiguration.Workflows

The list of workflow links.

Workflows - Class in com.genologics.ri.workflowconfiguration

The representation of a list of Workflow links.

Workflows() - Constructor for class com.genologics.ri.workflowconfiguration.Workflows

Default constructor.

WorkflowStage - Class in com.genologics.ri.artifact

Provides links to workflow stages, stage names and their respective statuses.

WorkflowStage() - Constructor for class com.genologics.ri.artifact.WorkflowStage

Default constructor.

WorkflowStage(Linkable<Stage>) - Constructor for class com.genologics.ri.artifact.WorkflowStage

Constructor from a Linkable.

WorkflowStage(Stage) - Constructor for class com.genologics.ri.artifact.WorkflowStage

Constructor from a Stage.

WorkflowStage(Stage, Status) - Constructor for class com.genologics.ri.artifact.WorkflowStage

Constructor from a Stage with status.

WorkflowStage(URI) - Constructor for class com.genologics.ri.artifact.WorkflowStage

Constructor taking a URI.

WorkflowStage(URI, String) - Constructor for class com.genologics.ri.artifact.WorkflowStage

Constructor taking a URI and name.

WorkflowStage(URI, String, Status) - Constructor for class com.genologics.ri.artifact.WorkflowStage

Constructor taking a URI, name and status.

workflowStages - Variable in class com.genologics.ri.artifact.Artifact

The workflow stages this artifact is associated with.

workflowUri - Variable in class com.genologics.ri.routing.ExtArtifactAssignments

The URI of the workflow.

workingFlag - Variable in class com.genologics.ri.artifact.Artifact

Flag indicating if this artifact is in a working state.

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