Index (CRUK-CI Clarity API Client 2.31.7 API)

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 org.cruk.clarity.api.jaxb: Base for date adapters.
AbstractDateAdapter() - Constructor for class org.cruk.clarity.api.jaxb.AbstractDateAdapter: Empty constructor.
accountLocked - Variable in class com.genologics.ri.researcher.Credentials
action - Variable in class com.genologics.ri.permission.Permission
action - Variable in class com.genologics.ri.permission.PermissionLink
action - Variable in class com.genologics.ri.role.PermissionLink
action - Variable in class com.genologics.ri.step.NextAction
actions - Variable in class com.genologics.ri.step.ProcessStep
Actions - Class in com.genologics.ri.step
Actions() - Constructor for class com.genologics.ri.step.Actions
Actions(URI) - Constructor for class com.genologics.ri.step.Actions
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
ActionsLink(Linkable<Actions>) - Constructor for class com.genologics.ri.step.ActionsLink
ActionsLink(URI) - Constructor for class com.genologics.ri.step.ActionsLink
ActionType - Enum in com.genologics.ri.step
ACTIVE - Enum constant in enum com.genologics.ri.reagentlot.Status
ACTIVE - Enum constant in enum com.genologics.ri.workflowconfiguration.Status
add(Link) - Method in class com.genologics.ri.Links
add(Linkable<?>) - Method in class com.genologics.ri.Links
ADD_REAGENT - Enum constant in enum com.genologics.ri.processtype.TriggerStatus
ADD_REAGENT - Enum constant in enum 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 com.genologics.ri.stepconfiguration.TriggerStatus
addAll(Links) - Method in class com.genologics.ri.Links
addAll(Collection<? extends Linkable<Artifact>>) - Method in class com.genologics.ri.routing.ExtArtifactAssignments
addAll(Collection<Link>) - Method in class com.genologics.ri.Links
addArtifact(Linkable<Artifact>) - Method in class com.genologics.ri.routing.ExtArtifactAssignments
addArtifactGroup(Linkable<ArtifactGroup>) - Method in class com.genologics.ri.artifact.Artifact
addAttribute(Attribute) - Method in class com.genologics.ri.reagenttype.SpecialType
addAttribute(String, String) - Method in class com.genologics.ri.reagenttype.SpecialType
addAvailableInput(Linkable<Artifact>) - Method in class com.genologics.ri.step.Pools
addAvailableInput(Input) - Method in class com.genologics.ri.step.Pools
addAvailableProgram(AvailableProgram) - Method in class com.genologics.ri.step.ProcessStep
addEppTriggers(EppTrigger) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
addEscalatedArtifact(Linkable<Artifact>) - Method in class com.genologics.ri.step.Escalation
addEscalatedArtifact(EscalatedArtifact) - Method in class com.genologics.ri.step.Escalation
addField(UDF) - Method in class com.genologics.ri.userdefined.UDT
addField(String, FieldType, String) - Method in class com.genologics.ri.userdefined.UDT
addFile(ClarityFile) - Method in class com.genologics.ri.process.ClarityProcess
addFile(ClarityFile) - Method in class com.genologics.ri.project.Project
addFile(ClarityFile) - Method in class com.genologics.ri.sample.SampleBase
addFile(SharedResultFile) - Method in class com.genologics.ri.step.StepSetup
addFile(SharedResultFile) - Method in class com.genologics.ri.stepconfiguration.StepSetup
addForCreate(Collection<Artifact>) - Method in class com.genologics.ri.artifact.ArtifactBatchFetchResult
addForCreate(Collection<Container>) - Method in class com.genologics.ri.container.ContainerBatchFetchResult
addForCreate(Collection<ClarityFile>) - Method in class com.genologics.ri.file.ClarityFileBatchFetchResult
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
addForUpdate(Collection<Container>) - Method in class com.genologics.ri.container.ContainerBatchFetchResult
addForUpdate(Collection<ClarityFile>) - Method in class com.genologics.ri.file.ClarityFileBatchFetchResult
addForUpdate(Collection<Sample>) - Method in class com.genologics.ri.sample.SampleBatchFetchResult
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
addInput(Linkable<Artifact>) - Method in class com.genologics.ri.step.PooledInputs
addInput(Linkable<Artifact>, Linkable<ControlType>, Long) - Method in class com.genologics.ri.step.StepCreation
addInput(Linkable<Artifact>, QCFlag) - Method in class com.genologics.ri.processexecution.ExecutableInputOutputMap
addInput(Input) - Method in class com.genologics.ri.processexecution.ExecutableInputOutputMap
addInput(CreationInput) - Method in class com.genologics.ri.step.StepCreation
addInput(Input) - Method in class com.genologics.ri.step.PooledInputs
addInputOutputMap(LimsEntityLinkable<Artifact>, LimsEntityLinkable<Artifact>) - Method in class com.genologics.ri.step.StepDetails
addInputOutputMap(InputOutputMap) - Method in class com.genologics.ri.process.ClarityProcess
addInputOutputMap(ExecutableInputOutputMap) - Method in class com.genologics.ri.processexecution.ExecutableProcess
addInputOutputMap(InputOutputMap) - Method in class com.genologics.ri.step.StepDetails
addOutputPlacement(Linkable<Artifact>, Linkable<Container>, String) - Method in class com.genologics.ri.step.Placements
addOutputPlacement(OutputPlacement) - Method in class com.genologics.ri.step.Placements
addOutputReagent(Output) - Method in class com.genologics.ri.step.Reagents
addPermittedContainer(ContainerType) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
addPermittedContainer(String) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
addPermittedControlType(Linkable<ControlType>) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
addPermittedReagentCategory(ReagentType) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
addPermittedReagentCategory(String) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
addPlacement(Placement) - Method in class com.genologics.ri.container.Container
addPlacement(LimsEntityLinkable<Artifact>, String) - Method in class com.genologics.ri.container.Container
addPooledInputs(PooledInputs) - Method in class com.genologics.ri.step.Pools
addPooledInputs(Collection<? extends Linkable<Artifact>>, String, Linkable<Artifact>) - Method in class com.genologics.ri.step.Pools
addProtocol(Linkable<Protocol>) - Method in class com.genologics.ri.workflowconfiguration.Workflow
addQueueField(QueueField) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
addReagentLabel(ReagentLabel) - Method in class com.genologics.ri.artifact.Artifact
addReagentLabel(String) - Method in class com.genologics.ri.artifact.Artifact
addReagentLot(LimsEntityLinkable<ReagentLot>) - Method in class com.genologics.ri.step.ReagentLots
addReagentLot(ReagentLotLink) - Method in class com.genologics.ri.step.ReagentLots
addRequiredReagentKit(Linkable<ReagentKit>) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
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
addRole(String) - Method in class com.genologics.ri.researcher.Credentials
addSelectedContainer(Linkable<Container>) - Method in class com.genologics.ri.step.Placements
addStage(Linkable<Stage>) - Method in class com.genologics.ri.workflowconfiguration.Workflow
addStepField(Field) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
addStepProperty(StepProperty) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
addStepProperty(String, String) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
addTransition(NextStep) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
addTypeDefinition(Linkable<Field>) - Method in class com.genologics.ri.processtype.ProcessType
addUserDefinedField(UDF) - Method in class com.genologics.ri.artifact.Artifact: Deprecated.
addUserDefinedField(UDF) - Method in class com.genologics.ri.container.Container: Deprecated.
addUserDefinedField(UDF) - Method in class com.genologics.ri.lab.Lab: Deprecated.
addUserDefinedField(UDF) - Method in class com.genologics.ri.process.ClarityProcess: Deprecated.
addUserDefinedField(UDF) - Method in class com.genologics.ri.processexecution.ExecutableProcess: Deprecated.
addUserDefinedField(UDF) - Method in class com.genologics.ri.processtemplate.ProcessTemplate: Deprecated.
addUserDefinedField(UDF) - Method in class com.genologics.ri.project.Project: Deprecated.
addUserDefinedField(UDF) - Method in class com.genologics.ri.researcher.Researcher: Deprecated.
addUserDefinedField(UDF) - Method in class com.genologics.ri.sample.SampleBase: Deprecated.
addUserDefinedField(UDF) - Method in class com.genologics.ri.step.StepDetails: Deprecated.
addUserDefinedField(String, FieldType, String) - Method in class com.genologics.ri.artifact.Artifact: Deprecated.
addUserDefinedField(String, FieldType, String) - Method in class com.genologics.ri.container.Container: Deprecated.
addUserDefinedField(String, FieldType, String) - Method in class com.genologics.ri.lab.Lab: Deprecated.
addUserDefinedField(String, FieldType, String) - Method in class com.genologics.ri.process.ClarityProcess: Deprecated.
addUserDefinedField(String, FieldType, String) - Method in class com.genologics.ri.processexecution.ExecutableProcess: Deprecated.
addUserDefinedField(String, FieldType, String) - Method in class com.genologics.ri.processtemplate.ProcessTemplate: Deprecated.
addUserDefinedField(String, FieldType, String) - Method in class com.genologics.ri.project.Project: Deprecated.
addUserDefinedField(String, FieldType, String) - Method in class com.genologics.ri.researcher.Researcher: Deprecated.
addUserDefinedField(String, FieldType, String) - Method in class com.genologics.ri.sample.SampleBase: Deprecated.
addUserDefinedField(String, FieldType, String) - Method in class com.genologics.ri.step.StepDetails: Deprecated.
addWorkflowStage(WorkflowStage) - Method in class com.genologics.ri.artifact.Artifact
ADMIN_ROLE - Static variable in class com.genologics.ri.researcher.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 com.genologics.ri.processtype.TriggerPoint
AFTER - Enum constant in enum com.genologics.ri.stepconfiguration.TriggerPoint
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
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 com.genologics.ri.artifact.OutputType
ANY - Enum constant in enum 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.
apiCacheControl - Variable in class org.cruk.clarity.api.cache.ClarityAPICache: The API again, but via its internal interface.
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
archived - Variable in class com.genologics.ri.instrument.Instrument
archived - Variable in class com.genologics.ri.reagentkit.ReagentKit
ARCHIVED - Enum constant in enum com.genologics.ri.reagentlot.Status
ARCHIVED - Enum constant in enum com.genologics.ri.workflowconfiguration.Status
artifact - Variable in class com.genologics.ri.artifact.Demux
artifact - Variable in class com.genologics.ri.sample.SampleBase
Artifact - Class in com.genologics.ri.artifact: The detailed representation of an Artifact.
Artifact() - Constructor for class com.genologics.ri.artifact.Artifact
ARTIFACT_GROUP_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
ARTIFACT_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
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
ArtifactBatchFetchResult() - Constructor for class com.genologics.ri.artifact.ArtifactBatchFetchResult
ArtifactBatchFetchResult(Collection<Artifact>) - Constructor for class com.genologics.ri.artifact.ArtifactBatchFetchResult
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
ArtifactGroupLink() - Constructor for class com.genologics.ri.artifactgroup.ArtifactGroupLink
ArtifactGroupLink(Linkable<ArtifactGroup>) - Constructor for class com.genologics.ri.artifact.ArtifactGroupLink
ArtifactGroupLink(Linkable<ArtifactGroup>) - Constructor for class com.genologics.ri.artifactgroup.ArtifactGroupLink
ArtifactGroupLink(URI) - Constructor for class com.genologics.ri.artifact.ArtifactGroupLink
ArtifactGroupLink(URI) - Constructor for class com.genologics.ri.artifactgroup.ArtifactGroupLink
ArtifactGroupLink(URI, String) - Constructor for class com.genologics.ri.artifact.ArtifactGroupLink
ArtifactGroupLink(URI, String) - Constructor for class com.genologics.ri.artifactgroup.ArtifactGroupLink
artifactGroups - Variable in class com.genologics.ri.artifact.Artifact
artifactGroups - Variable in class com.genologics.ri.artifactgroup.ArtifactGroups
ArtifactGroups - Class in com.genologics.ri.artifactgroup: The representation of a list of artifactGroup links.
ArtifactGroups() - Constructor for class com.genologics.ri.artifactgroup.ArtifactGroups
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
ArtifactLink - Class in com.genologics.ri.routing
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
ArtifactLink() - Constructor for class com.genologics.ri.process.ArtifactLink
ArtifactLink() - Constructor for class com.genologics.ri.queue.ArtifactLink
ArtifactLink() - Constructor for class com.genologics.ri.routing.ArtifactLink
ArtifactLink() - Constructor for class com.genologics.ri.sample.ArtifactLink
ArtifactLink() - Constructor for class com.genologics.ri.step.ArtifactLink
ArtifactLink(LimsEntityLinkable<Artifact>) - Constructor for class com.genologics.ri.artifact.ArtifactLink
ArtifactLink(LimsEntityLinkable<Artifact>) - Constructor for class com.genologics.ri.process.ArtifactLink
ArtifactLink(LimsEntityLinkable<Artifact>) - Constructor for class com.genologics.ri.sample.ArtifactLink
ArtifactLink(LimsEntityLinkable<Artifact>) - Constructor for class com.genologics.ri.step.ArtifactLink
ArtifactLink(Linkable<Artifact>) - Constructor for class com.genologics.ri.process.ArtifactLink
ArtifactLink(Linkable<Artifact>) - Constructor for class com.genologics.ri.routing.ArtifactLink
ArtifactLink(Linkable<Artifact>) - Constructor for class com.genologics.ri.step.ArtifactLink
ArtifactLink(URI) - Constructor for class com.genologics.ri.artifact.ArtifactLink
ArtifactLink(URI) - Constructor for class com.genologics.ri.process.ArtifactLink
ArtifactLink(URI) - Constructor for class com.genologics.ri.queue.ArtifactLink
ArtifactLink(URI) - Constructor for class com.genologics.ri.routing.ArtifactLink
ArtifactLink(URI) - Constructor for class com.genologics.ri.sample.ArtifactLink
ArtifactLink(URI) - Constructor for class com.genologics.ri.step.ArtifactLink
ArtifactLink(URI, String) - Constructor for class com.genologics.ri.artifact.ArtifactLink
ArtifactLink(URI, String) - Constructor for class com.genologics.ri.process.ArtifactLink
ArtifactLink(URI, String) - Constructor for class com.genologics.ri.queue.ArtifactLink
ArtifactLink(URI, String) - Constructor for class com.genologics.ri.sample.ArtifactLink
ArtifactLink(URI, String) - Constructor for class com.genologics.ri.step.ArtifactLink
artifacts - Variable in class com.genologics.ri.artifact.ArtifactBatchFetchResult
artifacts - Variable in class com.genologics.ri.artifact.Artifacts
artifacts - Variable in class com.genologics.ri.artifact.DemuxDetails
artifacts - Variable in class com.genologics.ri.artifactgroup.ArtifactGroup
artifacts - Variable in class com.genologics.ri.queue.Queue
artifacts - Variable in class com.genologics.ri.routing.ExtArtifactAssignments
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
Artifacts() - Constructor for class com.genologics.ri.artifactgroup.Artifacts
artifactType - Variable in class com.genologics.ri.processtype.ProcessInput
artifactType - Variable in class com.genologics.ri.processtype.ProcessOutput
artifactUri - Variable in class com.genologics.ri.step.NextAction
artifactUri - Variable in class com.genologics.ri.step.Output
artifactUri - Variable in class com.genologics.ri.step.SharedResultFile
assignedRoutes - Variable in class com.genologics.ri.routing.Routing
assignWorkingFlag - Variable in class com.genologics.ri.processtype.ProcessOutput: Deprecated.
attachedTo - Variable in class com.genologics.ri.file.ClarityFile
attachTo - Variable in class com.genologics.ri.processtype.Field
attachTo - Variable in class com.genologics.ri.stepconfiguration.Field
attachToCategory - Variable in class com.genologics.ri.configuration.Field
attachToCategory - Variable in class com.genologics.ri.configuration.Type
attachToCategory - Variable in class com.genologics.ri.configuration.UdfConfigLink
attachToCategory - Variable in class com.genologics.ri.configuration.UdtConfigLink
attachToName - Variable in class com.genologics.ri.configuration.Field
attachToName - Variable in class com.genologics.ri.configuration.Type
attachToName - Variable in class com.genologics.ri.configuration.UdfConfigLink
attachToName - Variable in class com.genologics.ri.configuration.UdtConfigLink
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
Attribute(String) - Constructor for class com.genologics.ri.reagenttype.Attribute
Attribute(String, String) - Constructor for class com.genologics.ri.reagenttype.Attribute
attributes - Variable in class com.genologics.ri.reagenttype.SpecialType
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
author - Variable in class com.genologics.ri.step.EscalationReview
AUTOMATIC - Enum constant in enum com.genologics.ri.processtype.TriggerType
AUTOMATIC - Enum constant in enum com.genologics.ri.stepconfiguration.TriggerType
automaticNextStep - Variable in class com.genologics.ri.step.ProcessStep
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
AutomaticNextStepLink(Linkable<ProcessStep>) - Constructor for class com.genologics.ri.step.AutomaticNextStepLink
AutomaticNextStepLink(URI) - Constructor for class com.genologics.ri.step.AutomaticNextStepLink
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
AUTOMATION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
AutomationLink - Class in com.genologics.ri.automation
AutomationLink() - Constructor for class com.genologics.ri.automation.AutomationLink
AutomationLink(URI) - Constructor for class com.genologics.ri.automation.AutomationLink
AutomationLink(URI, String) - Constructor for class com.genologics.ri.automation.AutomationLink
automations - Variable in class com.genologics.ri.automation.Automations
Automations - Class in com.genologics.ri.automation
Automations() - Constructor for class com.genologics.ri.automation.Automations
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
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
AvailableProgram(URI) - Constructor for class com.genologics.ri.step.AvailableProgram
AvailableProgram(URI, String) - Constructor for class com.genologics.ri.step.AvailableProgram
availablePrograms - Variable in class com.genologics.ri.step.ProcessStep

B

Batch<L> - Interface in com.genologics.ri: Interface for objects that hold batches of linkable items (links or entities).
batchCreate() - Element in annotation type com.genologics.ri.ClarityBatchRetrieveResult: Flag indicating that the annotated entity can be created using a batch creation call.
batchUpdate() - Element in annotation type 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 com.genologics.ri.processtype.TriggerPoint
BEFORE - Enum constant in enum com.genologics.ri.stepconfiguration.TriggerPoint
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
bioSource - Variable in class com.genologics.ri.sample.SampleBase: Deprecated.
BioSource - Class in com.genologics.ri.sample: Deprecated.
Biosource is not supported in Clarity.
BioSource() - Constructor for class com.genologics.ri.sample.BioSource: Deprecated.
BioSource(String) - Constructor for class com.genologics.ri.sample.BioSource: Deprecated.
BOOLEAN - Enum constant in enum com.genologics.ri.configuration.FieldType
BUILT_IN - Enum constant in enum com.genologics.ri.processtype.Style
BUILT_IN - Enum constant in enum com.genologics.ri.stepconfiguration.Style
builtIn - Variable in class com.genologics.ri.role.Role

C

cacheable() - Element in annotation type com.genologics.ri.ClarityEntity: Whether entities of the class can be cached.
cacheManager - Variable in class org.cruk.clarity.api.cache.ClarityAPICache: The cache manager.
CacheStatefulBehaviour - Enum 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.
CalibrantWell(String) - Constructor for class com.genologics.ri.containertype.CalibrantWell: Deprecated.
CalibrantWell(String, String) - Constructor for class com.genologics.ri.containertype.CalibrantWell: Deprecated.
calibrantWells - Variable in class com.genologics.ri.containertype.ContainerType: Deprecated.
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
catalogueNumber - Variable in class com.genologics.ri.reagentkit.ReagentKit
category - Variable in class com.genologics.ri.exception.Exception
category - Variable in exception org.cruk.clarity.api.ClarityException
channel - Variable in class com.genologics.ri.automation.Automation
channel - Variable in class com.genologics.ri.processtype.Parameter
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
city - Variable in class com.genologics.ri.Address
CLARITY_ROLE - Static variable in class com.genologics.ri.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.
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
ClarityAutomationException(String) - Constructor for exception org.cruk.clarity.api.automation.ClarityAutomationException
ClarityAutomationException(String, Throwable) - Constructor for exception org.cruk.clarity.api.automation.ClarityAutomationException
ClarityAutomationException(Throwable) - Constructor for exception org.cruk.clarity.api.automation.ClarityAutomationException
ClarityBatchRetrieveResult - Annotation Type in com.genologics.ri: Annotation for classes that contain lists of entities fetched from the API's batch retrieve mechanism.
ClarityEntity - Annotation Type 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, HttpStatus) - Constructor for exception org.cruk.clarity.api.ClarityException: Initialise from the given API exception with an HTTP status code.
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.
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
ClarityFile(ClarityFile) - Constructor for class com.genologics.ri.file.ClarityFile
ClarityFile(URI) - Constructor for class com.genologics.ri.file.ClarityFile
ClarityFile(URI, String) - Constructor for class com.genologics.ri.file.ClarityFile
ClarityFileBatchFetchResult - Class in com.genologics.ri.file: The representation of a batch of file resources.
ClarityFileBatchFetchResult() - Constructor for class com.genologics.ri.file.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
ClarityProcess - Class in com.genologics.ri.process: The detailed representation of a process.
ClarityProcess() - Constructor for class com.genologics.ri.process.ClarityProcess
ClarityProcess(URI) - Constructor for class com.genologics.ri.process.ClarityProcess
ClarityProcess(URI, String) - Constructor for class com.genologics.ri.process.ClarityProcess
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
ClarityQueryResult - Annotation Type in com.genologics.ri: Annotation to put on classes that are the results of querying the API for entities.
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.
closeCacheManager() - Method in class org.cruk.clarity.api.cache.EhCacheManagerFactory: Close the cache manager.
closeDate - Variable in class com.genologics.ri.project.Project
code - Variable in class com.genologics.ri.exception.Exception
code - Variable in exception org.cruk.clarity.api.ClarityException
columns - Variable in class com.genologics.ri.containertype.ContainerType
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
com.genologics.ri.artifactgroup - package com.genologics.ri.artifactgroup
com.genologics.ri.automation - package com.genologics.ri.automation
com.genologics.ri.configuration - package com.genologics.ri.configuration
com.genologics.ri.container - package com.genologics.ri.container
com.genologics.ri.containertype - package com.genologics.ri.containertype
com.genologics.ri.controltype - package com.genologics.ri.controltype
com.genologics.ri.exception - package com.genologics.ri.exception
com.genologics.ri.file - package com.genologics.ri.file
com.genologics.ri.instrument - package com.genologics.ri.instrument
com.genologics.ri.instrumenttype - package com.genologics.ri.instrumenttype
com.genologics.ri.lab - package com.genologics.ri.lab
com.genologics.ri.permission - package com.genologics.ri.permission
com.genologics.ri.process - package com.genologics.ri.process
com.genologics.ri.processexecution - package com.genologics.ri.processexecution
com.genologics.ri.processtemplate - package com.genologics.ri.processtemplate
com.genologics.ri.processtype - package com.genologics.ri.processtype
com.genologics.ri.project - package com.genologics.ri.project
com.genologics.ri.property - package com.genologics.ri.property
com.genologics.ri.protocolconfiguration - package com.genologics.ri.protocolconfiguration
com.genologics.ri.queue - package com.genologics.ri.queue
com.genologics.ri.reagentkit - package com.genologics.ri.reagentkit
com.genologics.ri.reagentlot - package com.genologics.ri.reagentlot
com.genologics.ri.reagenttype - package com.genologics.ri.reagenttype
com.genologics.ri.researcher - package com.genologics.ri.researcher
com.genologics.ri.role - package com.genologics.ri.role
com.genologics.ri.routing - package com.genologics.ri.routing
com.genologics.ri.sample - package com.genologics.ri.sample
com.genologics.ri.stage - package com.genologics.ri.stage
com.genologics.ri.step - package com.genologics.ri.step
com.genologics.ri.stepconfiguration - package com.genologics.ri.stepconfiguration
com.genologics.ri.userdefined - package com.genologics.ri.userdefined
com.genologics.ri.version - package com.genologics.ri.version
com.genologics.ri.workflowconfiguration - package com.genologics.ri.workflowconfiguration
comment - Variable in class com.genologics.ri.step.EscalationRequest
comment - Variable in class com.genologics.ri.step.EscalationReview
compareTo(Placement) - Method in class com.genologics.ri.container.Placement
compareTo(Location) - Method in class com.genologics.ri.Location
COMPLETE - Enum constant in enum com.genologics.ri.artifact.Status
COMPLETE - Enum constant in enum com.genologics.ri.processtype.TriggerStatus
COMPLETE - Enum constant in enum com.genologics.ri.step.ActionType
COMPLETE - Enum constant in enum com.genologics.ri.stepconfiguration.TriggerStatus
COMPLETE_REPEAT - Enum constant in enum com.genologics.ri.step.ActionType
COMPLETED - Enum constant in enum com.genologics.ri.step.ProcessState: The step state when the step is complete.
concentration - Variable in class com.genologics.ri.controltype.ControlType
configuration - Variable in class com.genologics.ri.step.Actions
configuration - Variable in class com.genologics.ri.step.Placements
configuration - Variable in class com.genologics.ri.step.Pools
configuration - Variable in class com.genologics.ri.step.ProcessStep
configuration - Variable in class com.genologics.ri.step.ProgramStatus
configuration - Variable in class com.genologics.ri.step.ReagentLots
configuration - Variable in class com.genologics.ri.step.Reagents
configuration - Variable in class com.genologics.ri.step.StepCreation
configuration - Variable in class com.genologics.ri.step.StepDetails
configuration - Variable in class com.genologics.ri.step.StepSetup
CONFIGURATION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
Container - Class in com.genologics.ri.container
Container() - Constructor for class com.genologics.ri.container.Container
Container(ContainerType) - Constructor for class com.genologics.ri.container.Container
Container(Linkable<ContainerType>) - Constructor for class com.genologics.ri.container.Container
Container(Linkable<ContainerType>, String) - Constructor for class com.genologics.ri.container.Container
CONTAINER_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
CONTAINER_TYPE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
ContainerBatchFetchResult - Class in com.genologics.ri.container: The representation of a list of resource details.
ContainerBatchFetchResult() - Constructor for class com.genologics.ri.container.ContainerBatchFetchResult
ContainerBatchFetchResult(Collection<Container>) - Constructor for class com.genologics.ri.container.ContainerBatchFetchResult
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
ContainerLink() - Constructor for class com.genologics.ri.ContainerLink
ContainerLink() - Constructor for class com.genologics.ri.step.ContainerLink
ContainerLink(LimsEntityLinkable<Container>) - Constructor for class com.genologics.ri.container.ContainerLink
ContainerLink(LimsEntityLinkable<Container>) - Constructor for class com.genologics.ri.ContainerLink
ContainerLink(Linkable<Container>) - Constructor for class com.genologics.ri.ContainerLink
ContainerLink(Linkable<Container>) - Constructor for class com.genologics.ri.step.ContainerLink
ContainerLink(URI) - Constructor for class com.genologics.ri.container.ContainerLink
ContainerLink(URI) - Constructor for class com.genologics.ri.ContainerLink
ContainerLink(URI) - Constructor for class com.genologics.ri.step.ContainerLink
ContainerLink(URI, String) - Constructor for class com.genologics.ri.container.ContainerLink
ContainerLink(URI, String) - Constructor for class com.genologics.ri.ContainerLink
ContainerLink(URI, String, String) - Constructor for class com.genologics.ri.container.ContainerLink
containers - Variable in class com.genologics.ri.container.ContainerBatchFetchResult
containers - Variable in class com.genologics.ri.container.Containers
Containers - Class in com.genologics.ri.container: The representation for a list of container links.
Containers() - Constructor for class com.genologics.ri.container.Containers
ContainerState - Enum 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
containerType - Variable in class com.genologics.ri.step.StepCreation
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
ContainerTypeLink() - Constructor for class com.genologics.ri.container.ContainerTypeLink
ContainerTypeLink() - Constructor for class com.genologics.ri.containertype.ContainerTypeLink
ContainerTypeLink() - Constructor for class com.genologics.ri.processtype.ContainerTypeLink
ContainerTypeLink(Linkable<ContainerType>) - Constructor for class com.genologics.ri.container.ContainerTypeLink
ContainerTypeLink(Linkable<ContainerType>) - Constructor for class com.genologics.ri.containertype.ContainerTypeLink
ContainerTypeLink(URI) - Constructor for class com.genologics.ri.container.ContainerTypeLink
ContainerTypeLink(URI) - Constructor for class com.genologics.ri.containertype.ContainerTypeLink
ContainerTypeLink(URI, String) - Constructor for class com.genologics.ri.container.ContainerTypeLink
ContainerTypeLink(URI, String) - Constructor for class com.genologics.ri.containertype.ContainerTypeLink
containerTypes - Variable in class com.genologics.ri.containertype.ContainerTypes
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
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
context - Variable in class com.genologics.ri.automation.Automation
Context - Enum in com.genologics.ri.automation: The available options for the automation context.
CONTINUE - Enum constant in enum com.genologics.ri.artifact.QCFlag
CONTINUE - Enum constant in enum com.genologics.ri.processexecution.QCFlag
CONTROL_TYPE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
controlledVocabulary - Variable in class com.genologics.ri.configuration.Field
controlType - Variable in class com.genologics.ri.artifact.Artifact
controlType - Variable in class com.genologics.ri.sample.SampleBase
ControlType - Class in com.genologics.ri.controltype
ControlType() - Constructor for class com.genologics.ri.controltype.ControlType
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
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
ControlTypeLink() - Constructor for class com.genologics.ri.controltype.ControlTypeLink
ControlTypeLink() - Constructor for class com.genologics.ri.processtype.ControlTypeLink
ControlTypeLink() - Constructor for class com.genologics.ri.sample.ControlTypeLink
ControlTypeLink() - Constructor for class com.genologics.ri.stepconfiguration.ControlTypeLink
ControlTypeLink(Linkable<ControlType>) - Constructor for class com.genologics.ri.artifact.ControlTypeLink
ControlTypeLink(Linkable<ControlType>) - Constructor for class com.genologics.ri.sample.ControlTypeLink
ControlTypeLink(Linkable<ControlType>) - Constructor for class com.genologics.ri.stepconfiguration.ControlTypeLink
ControlTypeLink(URI) - Constructor for class com.genologics.ri.artifact.ControlTypeLink
ControlTypeLink(URI) - Constructor for class com.genologics.ri.controltype.ControlTypeLink
ControlTypeLink(URI) - Constructor for class com.genologics.ri.sample.ControlTypeLink
ControlTypeLink(URI) - Constructor for class com.genologics.ri.stepconfiguration.ControlTypeLink
ControlTypeLink(URI, String) - Constructor for class com.genologics.ri.controltype.ControlTypeLink
ControlTypeLink(URI, String) - Constructor for class com.genologics.ri.sample.ControlTypeLink
ControlTypeLink(URI, String) - Constructor for class com.genologics.ri.stepconfiguration.ControlTypeLink
controlTypes - Variable in class com.genologics.ri.controltype.ControlTypes
ControlTypes - Class in com.genologics.ri.controltype: The representation of a list of ControlTypes
ControlTypes() - Constructor for class com.genologics.ri.controltype.ControlTypes
controlTypeUri - Variable in class com.genologics.ri.step.CreationInput
country - Variable in class com.genologics.ri.Address
creatable() - Element in annotation type 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
createActions(Actions) - Method in class com.genologics.ri.step.ObjectFactory
createActionsLink() - Method in class com.genologics.ri.step.ObjectFactory
createAddress() - Method in class com.genologics.ri.ObjectFactory
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
createArtifact() - Method in class com.genologics.ri.process.ObjectFactory
createArtifact() - Method in class com.genologics.ri.routing.ObjectFactory
createArtifact() - Method in class com.genologics.ri.sample.ObjectFactory
createArtifact() - Method in class com.genologics.ri.step.ObjectFactory
createArtifact(Artifact) - Method in class com.genologics.ri.artifact.ObjectFactory
createArtifactgroup() - Method in class com.genologics.ri.artifact.ObjectFactory
createArtifactgroup() - Method in class com.genologics.ri.artifactgroup.ObjectFactory
createArtifactgroup(ArtifactGroup) - Method in class com.genologics.ri.artifactgroup.ObjectFactory
createArtifactgroupLink() - Method in class com.genologics.ri.artifactgroup.ObjectFactory
createArtifactgroups() - Method in class com.genologics.ri.artifactgroup.ObjectFactory
createArtifactgroups(ArtifactGroups) - Method in class com.genologics.ri.artifactgroup.ObjectFactory
createArtifactLink() - Method in class com.genologics.ri.artifact.ObjectFactory
createArtifactLink() - Method in class com.genologics.ri.queue.ObjectFactory
createArtifacts() - Method in class com.genologics.ri.artifact.ObjectFactory
createArtifacts() - Method in class com.genologics.ri.artifactgroup.ObjectFactory
createArtifacts(Artifacts) - Method in class com.genologics.ri.artifact.ObjectFactory
createAttribute() - Method in class com.genologics.ri.reagenttype.ObjectFactory
createAutomaticNextStepLink() - Method in class com.genologics.ri.step.ObjectFactory
createAutomation() - Method in class com.genologics.ri.automation.ObjectFactory
createAutomation(Automation) - Method in class com.genologics.ri.automation.ObjectFactory
createAutomationLink() - Method in class com.genologics.ri.automation.ObjectFactory
createAutomations() - Method in class com.genologics.ri.automation.ObjectFactory
createAutomations(Automations) - Method in class com.genologics.ri.automation.ObjectFactory
createAvailableProgram() - Method in class com.genologics.ri.step.ObjectFactory
createBiosource() - Method in class com.genologics.ri.sample.ObjectFactory: Deprecated.
createCacheManager() - Method in class org.cruk.clarity.api.cache.EhCacheManagerFactory: Create and initialise the cache manager by reading the configuration XML file.
createCalibrantWell() - Method in class com.genologics.ri.containertype.ObjectFactory: Deprecated.
createContainer() - Method in class com.genologics.ri.container.ObjectFactory
createContainer() - Method in class com.genologics.ri.ObjectFactory
createContainer() - Method in class com.genologics.ri.step.ObjectFactory
createContainer(Container) - Method in class com.genologics.ri.container.ObjectFactory
createContainerLink() - Method in class com.genologics.ri.container.ObjectFactory
createContainerName(String) - Method in class com.genologics.ri.container.ObjectFactory
createContainerOccupiedWells(Long) - Method in class com.genologics.ri.container.ObjectFactory
createContainerPlacement(Placement) - Method in class com.genologics.ri.container.ObjectFactory
createContainers() - Method in class com.genologics.ri.container.ObjectFactory
createContainers(Containers) - Method in class com.genologics.ri.container.ObjectFactory
createContainerState(String) - Method in class com.genologics.ri.container.ObjectFactory
createContainerType() - Method in class com.genologics.ri.container.ObjectFactory
createContainerType() - Method in class com.genologics.ri.containertype.ObjectFactory
createContainerType(ContainerTypeLink) - Method in class com.genologics.ri.container.ObjectFactory
createContainerType(ContainerType) - Method in class com.genologics.ri.containertype.ObjectFactory
createContainerTypeLink() - Method in class com.genologics.ri.containertype.ObjectFactory
createContainerTypeLink() - Method in class com.genologics.ri.processtype.ObjectFactory
createContainerTypes() - Method in class com.genologics.ri.containertype.ObjectFactory
createContainerTypes(ContainerTypes) - Method in class com.genologics.ri.containertype.ObjectFactory
createControlType() - Method in class com.genologics.ri.controltype.ObjectFactory
createControlType(ControlType) - Method in class com.genologics.ri.controltype.ObjectFactory
createControlTypeLink() - Method in class com.genologics.ri.artifact.ObjectFactory
createControlTypeLink() - Method in class com.genologics.ri.controltype.ObjectFactory
createControlTypeLink() - Method in class com.genologics.ri.processtype.ObjectFactory
createControlTypeLink() - Method in class com.genologics.ri.sample.ObjectFactory
createControlTypeLink() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory
createControlTypes() - Method in class com.genologics.ri.controltype.ObjectFactory
createControlTypes(ControlTypes) - Method in class com.genologics.ri.controltype.ObjectFactory
createCreationInput() - Method in class com.genologics.ri.step.ObjectFactory
createCredentials() - Method in class com.genologics.ri.researcher.ObjectFactory
createdBy - Variable in class com.genologics.ri.reagentlot.ReagentLot
createdDate - Variable in class com.genologics.ri.reagentlot.ReagentLot
createDemux() - Method in class com.genologics.ri.artifact.ObjectFactory
createDemux(Demux) - Method in class com.genologics.ri.artifact.ObjectFactory
createDemuxArtifact() - Method in class com.genologics.ri.artifact.ObjectFactory
createDemuxArtifactSample() - Method in class com.genologics.ri.artifact.ObjectFactory
createDemuxDetails() - Method in class com.genologics.ri.artifact.ObjectFactory
createDemuxDetails(DemuxDetails) - Method in class com.genologics.ri.artifact.ObjectFactory
createDemuxLink() - Method in class com.genologics.ri.artifact.ObjectFactory
createDemuxSourceArtifact() - Method in class com.genologics.ri.artifact.ObjectFactory
createDetails() - Method in class com.genologics.ri.artifact.ObjectFactory
createDetails() - Method in class com.genologics.ri.container.ObjectFactory
createDetails() - Method in class com.genologics.ri.file.ObjectFactory
createDetails() - Method in class com.genologics.ri.sample.ObjectFactory
createDetails() - Method in class com.genologics.ri.step.ObjectFactory
createDetails(ArtifactBatchFetchResult) - Method in class com.genologics.ri.artifact.ObjectFactory
createDetails(ContainerBatchFetchResult) - Method in class com.genologics.ri.container.ObjectFactory
createDetails(ClarityFileBatchFetchResult) - Method in class com.genologics.ri.file.ObjectFactory
createDetails(SampleBatchFetchResult) - Method in class com.genologics.ri.sample.ObjectFactory
createDetails(StepDetails) - Method in class com.genologics.ri.step.ObjectFactory
createDetailsLink() - Method in class com.genologics.ri.step.ObjectFactory
createDimension() - Method in class com.genologics.ri.containertype.ObjectFactory
createEppTrigger() - Method in class com.genologics.ri.processtype.ObjectFactory
createEppTrigger() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory
createEscalatedArtifact() - Method in class com.genologics.ri.step.ObjectFactory
createEscalation() - Method in class com.genologics.ri.step.ObjectFactory
createEscalationRequest() - Method in class com.genologics.ri.step.ObjectFactory
createEscalationReview() - Method in class com.genologics.ri.step.ObjectFactory
createException() - Method in class com.genologics.ri.exception.ObjectFactory
createException(Exception) - Method in class com.genologics.ri.exception.ObjectFactory
createExternalArtifactAssignments() - Method in class com.genologics.ri.routing.ObjectFactory
createExternalid() - Method in class com.genologics.ri.ObjectFactory
createExternalid(ExternalId) - Method in class com.genologics.ri.ObjectFactory
createField() - Method in class com.genologics.ri.configuration.ObjectFactory
createField() - Method in class com.genologics.ri.processtype.ObjectFactory
createField() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory
createField() - Method in class com.genologics.ri.userdefined.ObjectFactory
createField(Field) - Method in class com.genologics.ri.configuration.ObjectFactory
createField(UDF) - Method in class com.genologics.ri.userdefined.ObjectFactory
createFieldLink() - Method in class com.genologics.ri.configuration.ObjectFactory
createFile() - Method in class com.genologics.ri.file.ObjectFactory
createFile() - Method in class com.genologics.ri.step.ObjectFactory
createFile(ClarityFile) - Method in class com.genologics.ri.file.ObjectFactory
createFileLink() - Method in class com.genologics.ri.file.ObjectFactory
createFiles() - Method in class com.genologics.ri.file.ObjectFactory
createFiles(ClarityFiles) - Method in class com.genologics.ri.file.ObjectFactory
createFormatter() - Method in class org.cruk.clarity.api.jaxb.AbstractDateAdapter: Create the correct date format object for the type of dates expected.
createFormatter() - Method in class org.cruk.clarity.api.jaxb.LongTimestampAdapter: Create a date formatter for the long timestamp format.
createFormatter() - Method in class org.cruk.clarity.api.jaxb.ShortDateAdapter: Create a date formatter for the short date format.
createGenericTypeLink() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory
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
createIceBucketField() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory
createIndex() - Method in class com.genologics.ri.ObjectFactory
createIndex(Index) - Method in class com.genologics.ri.ObjectFactory
createInput() - Method in class com.genologics.ri.processexecution.ObjectFactory
createInput() - Method in class com.genologics.ri.step.ObjectFactory
createInputOutputMap() - Method in class com.genologics.ri.process.ObjectFactory
createInputOutputMap() - Method in class com.genologics.ri.processexecution.ObjectFactory
createInputOutputMap() - Method in class com.genologics.ri.step.ObjectFactory
createInstrument() - Method in class com.genologics.ri.instrument.ObjectFactory
createInstrument() - Method in class com.genologics.ri.process.ObjectFactory
createInstrument() - Method in class com.genologics.ri.processexecution.ObjectFactory
createInstrument() - Method in class com.genologics.ri.processtemplate.ObjectFactory
createInstrument() - Method in class com.genologics.ri.step.ObjectFactory
createInstrument(Instrument) - Method in class com.genologics.ri.instrument.ObjectFactory
createInstrumentLink() - Method in class com.genologics.ri.instrument.ObjectFactory
createInstruments() - Method in class com.genologics.ri.instrument.ObjectFactory
createInstruments(Instruments) - Method in class com.genologics.ri.instrument.ObjectFactory
createInstrumentType() - Method in class com.genologics.ri.instrumenttype.ObjectFactory
createInstrumentType(InstrumentType) - Method in class com.genologics.ri.instrumenttype.ObjectFactory
createInstrumentTypeLink() - Method in class com.genologics.ri.instrumenttype.ObjectFactory
createInstrumentTypeProcessType() - Method in class com.genologics.ri.instrumenttype.ObjectFactory
createInstrumentTypes() - Method in class com.genologics.ri.instrumenttype.ObjectFactory
createInstrumentTypes(InstrumentTypes) - Method in class com.genologics.ri.instrumenttype.ObjectFactory
createLab() - Method in class com.genologics.ri.lab.ObjectFactory
createLab() - Method in class com.genologics.ri.researcher.ObjectFactory
createLab(Lab) - Method in class com.genologics.ri.lab.ObjectFactory
createLabLink() - Method in class com.genologics.ri.lab.ObjectFactory
createLabs() - Method in class com.genologics.ri.lab.ObjectFactory
createLabs(Labs) - Method in class com.genologics.ri.lab.ObjectFactory
createLink() - Method in class com.genologics.ri.ObjectFactory
createLinks() - Method in class com.genologics.ri.ObjectFactory
createLinks(Links) - Method in class com.genologics.ri.ObjectFactory
createLocation() - Method in class com.genologics.ri.ObjectFactory
createLockableSetting() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory
createLots(ReagentLots) - Method in class com.genologics.ri.step.ObjectFactory
createNextAction() - Method in class com.genologics.ri.step.ObjectFactory
createNextStep() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory
createOutput() - Method in class com.genologics.ri.processexecution.ObjectFactory
createOutput() - Method in class com.genologics.ri.step.ObjectFactory
createOutputPlacement() - Method in class com.genologics.ri.step.ObjectFactory
createPage() - Method in class com.genologics.ri.ObjectFactory
createParameter() - Method in class com.genologics.ri.process.ObjectFactory
createParameter() - Method in class com.genologics.ri.processexecution.ObjectFactory
createParameter() - Method in class com.genologics.ri.processtemplate.ObjectFactory
createParameter() - Method in class com.genologics.ri.processtype.ObjectFactory
createParentProcess() - Method in class com.genologics.ri.artifact.ObjectFactory
createParentProcess() - Method in class com.genologics.ri.process.ObjectFactory
createPermission() - Method in class com.genologics.ri.permission.ObjectFactory
createPermission(Permission) - Method in class com.genologics.ri.permission.ObjectFactory
createPermissionLink() - Method in class com.genologics.ri.permission.ObjectFactory
createPermissionLink() - Method in class com.genologics.ri.role.ObjectFactory
createPermissions() - Method in class com.genologics.ri.permission.ObjectFactory
createPermissions(Permissions) - Method in class com.genologics.ri.permission.ObjectFactory
createPlacement() - Method in class com.genologics.ri.container.ObjectFactory
createPlacements() - Method in class com.genologics.ri.step.ObjectFactory
createPlacements(Placements) - Method in class com.genologics.ri.step.ObjectFactory
createPlacementsLink() - Method in class com.genologics.ri.step.ObjectFactory
createPooledInputs() - Method in class com.genologics.ri.step.ObjectFactory
createPools() - Method in class com.genologics.ri.step.ObjectFactory
createPools(Pools) - Method in class com.genologics.ri.step.ObjectFactory
createPoolsLink() - Method in class com.genologics.ri.step.ObjectFactory
createPoolStep() - Method in class com.genologics.ri.artifact.ObjectFactory
createProcess() - Method in class com.genologics.ri.process.ObjectFactory
createProcess() - Method in class com.genologics.ri.processexecution.ObjectFactory
createProcess(ClarityProcess) - Method in class com.genologics.ri.process.ObjectFactory
createProcess(ExecutableProcess) - Method in class com.genologics.ri.processexecution.ObjectFactory
createProcessDateRun(String) - Method in class com.genologics.ri.process.ObjectFactory
createProcessDateRun(String) - Method in class com.genologics.ri.processexecution.ObjectFactory
createProcesses() - Method in class com.genologics.ri.process.ObjectFactory
createProcesses(ClarityProcesses) - Method in class com.genologics.ri.process.ObjectFactory
createProcessInput() - Method in class com.genologics.ri.processtype.ObjectFactory
createProcessInputOutputMap(InputOutputMap) - Method in class com.genologics.ri.process.ObjectFactory
createProcessInputOutputMap(ExecutableInputOutputMap) - Method in class com.genologics.ri.processexecution.ObjectFactory
createProcessInstrument(InstrumentLink) - Method in class com.genologics.ri.process.ObjectFactory
createProcessInstrument(InstrumentLink) - Method in class com.genologics.ri.processexecution.ObjectFactory
createProcessLink() - Method in class com.genologics.ri.process.ObjectFactory
createProcessOutput() - Method in class com.genologics.ri.processtype.ObjectFactory
createProcessProcessParameter(Parameter) - Method in class com.genologics.ri.process.ObjectFactory
createProcessProcessParameter(Parameter) - Method in class com.genologics.ri.processexecution.ObjectFactory
createProcessProtocolName(String) - Method in class com.genologics.ri.process.ObjectFactory
createProcessTechnician(Technician) - Method in class com.genologics.ri.process.ObjectFactory
createProcessTechnician(Technician) - Method in class com.genologics.ri.processexecution.ObjectFactory
createProcessTemplate() - Method in class com.genologics.ri.processtemplate.ObjectFactory
createProcessTemplate(ProcessTemplate) - Method in class com.genologics.ri.processtemplate.ObjectFactory
createProcessTemplateInstrument(InstrumentLink) - Method in class com.genologics.ri.processtemplate.ObjectFactory
createProcessTemplateIsDefault(Boolean) - Method in class com.genologics.ri.processtemplate.ObjectFactory
createProcessTemplateLink() - Method in class com.genologics.ri.processtemplate.ObjectFactory
createProcessTemplateName(String) - Method in class com.genologics.ri.processtemplate.ObjectFactory
createProcessTemplateProcessParameter(Parameter) - Method in class com.genologics.ri.processtemplate.ObjectFactory
createProcessTemplates() - Method in class com.genologics.ri.processtemplate.ObjectFactory
createProcessTemplates(ProcessTemplates) - Method in class com.genologics.ri.processtemplate.ObjectFactory
createProcessTemplateTechnician(Technician) - Method in class com.genologics.ri.processtemplate.ObjectFactory
createProcessTemplateType(ProcessTypeLink) - Method in class com.genologics.ri.processtemplate.ObjectFactory
createProcessType() - Method in class com.genologics.ri.process.ObjectFactory
createProcessType() - Method in class com.genologics.ri.processtemplate.ObjectFactory
createProcessType() - Method in class com.genologics.ri.processtype.ObjectFactory
createProcessType(ProcessTypeLink) - Method in class com.genologics.ri.process.ObjectFactory
createProcessType(ProcessType) - Method in class com.genologics.ri.processtype.ObjectFactory
createProcessType(String) - Method in class com.genologics.ri.processexecution.ObjectFactory
createProcessTypeAttribute() - Method in class com.genologics.ri.processtype.ObjectFactory
createProcessTypeLink() - Method in class com.genologics.ri.automation.ObjectFactory
createProcessTypeLink() - Method in class com.genologics.ri.processtype.ObjectFactory
createProcessTypeLink() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory
createProcessTypes() - Method in class com.genologics.ri.processtype.ObjectFactory
createProcessTypes(ProcessTypes) - Method in class com.genologics.ri.processtype.ObjectFactory
createProgramStatus() - Method in class com.genologics.ri.step.ObjectFactory
createProgramStatus(ProgramStatus) - Method in class com.genologics.ri.step.ObjectFactory
createProgramStatusLink() - Method in class com.genologics.ri.step.ObjectFactory
createProject() - Method in class com.genologics.ri.project.ObjectFactory
createProject() - Method in class com.genologics.ri.sample.ObjectFactory
createProject(Project) - Method in class com.genologics.ri.project.ObjectFactory
createProjectLink() - Method in class com.genologics.ri.project.ObjectFactory
createProjects() - Method in class com.genologics.ri.project.ObjectFactory
createProjects(Projects) - Method in class com.genologics.ri.project.ObjectFactory
createProperties() - Method in class com.genologics.ri.property.ObjectFactory
createProperties(Properties) - Method in class com.genologics.ri.property.ObjectFactory
createPropertyLink() - Method in class com.genologics.ri.property.ObjectFactory
createProtocol() - Method in class com.genologics.ri.protocolconfiguration.ObjectFactory
createProtocol(Protocol) - Method in class com.genologics.ri.protocolconfiguration.ObjectFactory
createProtocolLink() - Method in class com.genologics.ri.protocolconfiguration.ObjectFactory
createProtocolLink() - Method in class com.genologics.ri.stage.ObjectFactory
createProtocolLink() - Method in class com.genologics.ri.workflowconfiguration.ObjectFactory
createProtocolProperty() - Method in class com.genologics.ri.protocolconfiguration.ObjectFactory
createProtocols() - Method in class com.genologics.ri.protocolconfiguration.ObjectFactory
createProtocols(Protocols) - Method in class com.genologics.ri.protocolconfiguration.ObjectFactory
createProtocolStep() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory
createProtocolStepLink() - Method in class com.genologics.ri.stage.ObjectFactory
createQueue() - Method in class com.genologics.ri.queue.ObjectFactory
createQueue(Queue) - Method in class com.genologics.ri.queue.ObjectFactory
createQueueField() - Method in class com.genologics.ri.processtype.ObjectFactory
createQueueField() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory
createReagentKit() - Method in class com.genologics.ri.reagentkit.ObjectFactory
createReagentKit(ReagentKit) - Method in class com.genologics.ri.reagentkit.ObjectFactory
createReagentKitLink() - Method in class com.genologics.ri.processtype.ObjectFactory
createReagentKitLink() - Method in class com.genologics.ri.reagentkit.ObjectFactory
createReagentKitLink() - Method in class com.genologics.ri.reagentlot.ObjectFactory
createReagentKitLink() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory
createReagentKits() - Method in class com.genologics.ri.reagentkit.ObjectFactory
createReagentKits(ReagentKits) - Method in class com.genologics.ri.reagentkit.ObjectFactory
createReagentLabel() - Method in class com.genologics.ri.artifact.ObjectFactory
createReagentLabel() - Method in class com.genologics.ri.step.ObjectFactory
createReagentLot() - Method in class com.genologics.ri.reagentlot.ObjectFactory
createReagentLot(ReagentLot) - Method in class com.genologics.ri.reagentlot.ObjectFactory
createReagentLotLink() - Method in class com.genologics.ri.reagentlot.ObjectFactory
createReagentLotLink() - Method in class com.genologics.ri.step.ObjectFactory
createReagentLots() - Method in class com.genologics.ri.reagentlot.ObjectFactory
createReagentLots(ReagentLots) - Method in class com.genologics.ri.reagentlot.ObjectFactory
createReagentLotsLink() - Method in class com.genologics.ri.step.ObjectFactory
createReagents() - Method in class com.genologics.ri.step.ObjectFactory
createReagents(Reagents) - Method in class com.genologics.ri.step.ObjectFactory
createReagentsLink() - Method in class com.genologics.ri.step.ObjectFactory
createReagentsLots() - Method in class com.genologics.ri.step.ObjectFactory
createReagentType() - Method in class com.genologics.ri.reagenttype.ObjectFactory
createReagentType(ReagentType) - Method in class com.genologics.ri.reagenttype.ObjectFactory
createReagentTypeLink() - Method in class com.genologics.ri.reagenttype.ObjectFactory
createReagentTypes() - Method in class com.genologics.ri.reagenttype.ObjectFactory
createReagentTypes(ReagentTypes) - Method in class com.genologics.ri.reagenttype.ObjectFactory
createResearcher() - Method in class com.genologics.ri.project.ObjectFactory
createResearcher() - Method in class com.genologics.ri.reagentlot.ObjectFactory
createResearcher() - Method in class com.genologics.ri.researcher.ObjectFactory
createResearcher(Researcher) - Method in class com.genologics.ri.researcher.ObjectFactory
createResearcherLink() - Method in class com.genologics.ri.researcher.ObjectFactory
createResearcherLink() - Method in class com.genologics.ri.role.ObjectFactory
createResearchers() - Method in class com.genologics.ri.researcher.ObjectFactory
createResearchers(Researchers) - Method in class com.genologics.ri.researcher.ObjectFactory
createRole() - Method in class com.genologics.ri.researcher.ObjectFactory
createRole() - Method in class com.genologics.ri.role.ObjectFactory
createRole(Role) - Method in class com.genologics.ri.role.ObjectFactory
createRoleLink() - Method in class com.genologics.ri.role.ObjectFactory
createRoles() - Method in class com.genologics.ri.role.ObjectFactory
createRoles(Roles) - Method in class com.genologics.ri.role.ObjectFactory
createRouting() - Method in class com.genologics.ri.routing.ObjectFactory
createRouting(Routing) - Method in class com.genologics.ri.routing.ObjectFactory
createSample() - Method in class com.genologics.ri.artifact.ObjectFactory
createSample() - Method in class com.genologics.ri.sample.ObjectFactory
createSample(Sample) - Method in class com.genologics.ri.sample.ObjectFactory
createSamplebase() - Method in class com.genologics.ri.sample.ObjectFactory
createSamplecreation() - Method in class com.genologics.ri.sample.ObjectFactory
createSamplecreation(SampleCreation) - Method in class com.genologics.ri.sample.ObjectFactory
createSampleLink() - Method in class com.genologics.ri.sample.ObjectFactory
createSamples() - Method in class com.genologics.ri.sample.ObjectFactory
createSamples(Samples) - Method in class com.genologics.ri.sample.ObjectFactory
createSetup() - Method in class com.genologics.ri.step.ObjectFactory
createSetup(StepSetup) - Method in class com.genologics.ri.step.ObjectFactory
createSetupLink() - Method in class com.genologics.ri.step.ObjectFactory
createSharedResultFile() - Method in class com.genologics.ri.processtype.ObjectFactory
createSharedResultFile() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory
createSpecialType() - Method in class com.genologics.ri.reagenttype.ObjectFactory
createStage() - Method in class com.genologics.ri.stage.ObjectFactory
createStage(Stage) - Method in class com.genologics.ri.stage.ObjectFactory
createStageLink() - Method in class com.genologics.ri.workflowconfiguration.ObjectFactory
createStep() - Method in class com.genologics.ri.step.ObjectFactory
createStep(ProcessStep) - Method in class com.genologics.ri.step.ObjectFactory
createStep(ProtocolStep) - Method in class com.genologics.ri.stepconfiguration.ObjectFactory
createStepConfiguration() - Method in class com.genologics.ri.step.ObjectFactory
createStepCreation() - Method in class com.genologics.ri.step.ObjectFactory
createStepCreation(StepCreation) - Method in class com.genologics.ri.step.ObjectFactory
createStepProperty() - Method in class com.genologics.ri.processtype.ObjectFactory
createStepProperty() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory
createStepSetup() - Method in class com.genologics.ri.processtype.ObjectFactory
createStepSetup() - Method in class com.genologics.ri.stepconfiguration.ObjectFactory
createSubmitter() - Method in class com.genologics.ri.sample.ObjectFactory
createTechnician() - Method in class com.genologics.ri.process.ObjectFactory
createTechnician() - Method in class com.genologics.ri.processexecution.ObjectFactory
createTechnician() - Method in class com.genologics.ri.processtemplate.ObjectFactory
createType() - Method in class com.genologics.ri.configuration.ObjectFactory
createType() - Method in class com.genologics.ri.userdefined.ObjectFactory
createType(Type) - Method in class com.genologics.ri.configuration.ObjectFactory
createType(UDT) - Method in class com.genologics.ri.userdefined.ObjectFactory
createTypeDefinition() - Method in class com.genologics.ri.configuration.ObjectFactory
createTypeDefinition() - Method in class com.genologics.ri.processtype.ObjectFactory
createUdfconfigLink() - Method in class com.genologics.ri.configuration.ObjectFactory
createUdfconfigLink(UdfConfigLink) - Method in class com.genologics.ri.configuration.ObjectFactory
createUdfs() - Method in class com.genologics.ri.configuration.ObjectFactory
createUdfs(Udfs) - Method in class com.genologics.ri.configuration.ObjectFactory
createUdtconfigLink() - Method in class com.genologics.ri.configuration.ObjectFactory
createUdtconfigLink(UdtConfigLink) - Method in class com.genologics.ri.configuration.ObjectFactory
createUdts() - Method in class com.genologics.ri.configuration.ObjectFactory
createUdts(Udts) - Method in class com.genologics.ri.configuration.ObjectFactory
createUser() - Method in class com.genologics.ri.step.ObjectFactory
createVersion() - Method in class com.genologics.ri.version.ObjectFactory
createVersion(Version) - Method in class com.genologics.ri.version.ObjectFactory
createVersions() - Method in class com.genologics.ri.version.ObjectFactory
createVersions(Versions) - Method in class com.genologics.ri.version.ObjectFactory
createWorkflow() - Method in class com.genologics.ri.workflowconfiguration.ObjectFactory
createWorkflow(Workflow) - Method in class com.genologics.ri.workflowconfiguration.ObjectFactory
createWorkflowLink() - Method in class com.genologics.ri.stage.ObjectFactory
createWorkflowLink() - Method in class com.genologics.ri.workflowconfiguration.ObjectFactory
createWorkflows() - Method in class com.genologics.ri.workflowconfiguration.ObjectFactory
createWorkflows(Workflows) - Method in class com.genologics.ri.workflowconfiguration.ObjectFactory
creationClass() - Element in annotation type 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
CreationInput(Linkable<Artifact>) - Constructor for class com.genologics.ri.step.CreationInput
CreationInput(Linkable<Artifact>, Linkable<ControlType>) - Constructor for class com.genologics.ri.step.CreationInput
CreationInput(Linkable<Artifact>, Linkable<ControlType>, Long) - Constructor for class com.genologics.ri.step.CreationInput
CreationInput(URI) - Constructor for class com.genologics.ri.step.CreationInput
CreationInput(URI, URI) - Constructor for class com.genologics.ri.step.CreationInput
CreationInput(URI, URI, Long) - Constructor for class com.genologics.ri.step.CreationInput
credentials - Variable in class com.genologics.ri.researcher.Researcher
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: Now an enumeration since release 2.31.3 of the client.
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
date - Variable in class com.genologics.ri.step.EscalationReview
DATE - Enum constant in enum com.genologics.ri.configuration.FieldType
dateCompleted - Variable in class com.genologics.ri.sample.SampleBase
dateCompleted - Variable in class com.genologics.ri.step.ProcessStep
dateReceived - Variable in class com.genologics.ri.sample.SampleBase
dateRun - Variable in class com.genologics.ri.process.ClarityProcess
dateRun - Variable in class com.genologics.ri.processexecution.ExecutableProcess
dateStarted - Variable in class com.genologics.ri.step.ProcessStep
defaultGrouping - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep: Deprecated.
defaultTemplate - Variable in class com.genologics.ri.processtemplate.ProcessTemplate
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
demux - Variable in class com.genologics.ri.artifact.DemuxArtifact
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
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
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
DemuxArtifactSample(URI) - Constructor for class com.genologics.ri.artifact.DemuxArtifactSample
demuxDetails - Variable in class com.genologics.ri.artifact.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
DemuxLink - Class in com.genologics.ri.artifact: Identifies the resource that will demultiplex this artifact.
DemuxLink() - Constructor for class com.genologics.ri.artifact.DemuxLink
DemuxLink(URI) - Constructor for class com.genologics.ri.artifact.DemuxLink
DemuxSourceArtifact - Class in com.genologics.ri.artifact
DemuxSourceArtifact() - Constructor for class com.genologics.ri.artifact.DemuxSourceArtifact
DemuxSourceArtifact(URI) - Constructor for class com.genologics.ri.artifact.DemuxSourceArtifact
DemuxSourceArtifact(URI, String) - Constructor for class com.genologics.ri.artifact.DemuxSourceArtifact
department - Variable in class com.genologics.ri.Address
DEPLETED - Enum constant in enum com.genologics.ri.container.ContainerState: The container state when the container is depleted.
DERIVED_SAMPLE - Enum constant in enum com.genologics.ri.automation.Context
description - Variable in class com.genologics.ri.permission.Permission
description - Variable in class com.genologics.ri.sample.BioSource: Deprecated.
detail - Variable in class com.genologics.ri.processtype.IceBucketField
detail - Variable in class com.genologics.ri.processtype.QueueField
detail - Variable in class com.genologics.ri.stepconfiguration.IceBucketField
detail - Variable in class com.genologics.ri.stepconfiguration.QueueField
details - Variable in class com.genologics.ri.step.ProcessStep
deviation - Variable in class com.genologics.ri.configuration.Field
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
Dimension(Integer) - Constructor for class com.genologics.ri.containertype.Dimension
DISCARDED - Enum constant in enum com.genologics.ri.container.ContainerState: The container state when the container has been discarded.
displayName - Variable in enum com.genologics.ri.container.ContainerState: The display name of the state.
displayName - Variable in class com.genologics.ri.processtype.ProcessInput
displayName - Variable in class com.genologics.ri.processtype.ProcessOutput
displayName - Variable in enum com.genologics.ri.step.ProcessState: The display name of the state.
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.

E

editable - Variable in class com.genologics.ri.configuration.Field
EhCacheManagerFactory - Class in org.cruk.clarity.api.cache: Factory for creating a singleton EhCache 3 CacheManager from XML configuration.
EhCacheManagerFactory() - Constructor for class org.cruk.clarity.api.cache.EhCacheManagerFactory: Constructor.
email - Variable in class com.genologics.ri.researcher.Researcher
EMPTY - Enum constant in enum 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
enabled - Variable in class com.genologics.ri.stepconfiguration.StepSetup
entityClass() - Element in annotation type com.genologics.ri.ClarityBatchRetrieveResult: The class of entity indicated by the links returned in the annotated object.
entityClass() - Element in annotation type 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
EppTrigger() - Constructor for class com.genologics.ri.stepconfiguration.EppTrigger
EppTrigger(String) - Constructor for class com.genologics.ri.processtype.EppTrigger
eppTriggers - Variable in class com.genologics.ri.processtype.ProcessType
eppTriggers - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep
equals(Object) - Method in class com.genologics.ri.ContainerLink
equals(Object) - Method in class com.genologics.ri.Location
equals(Object) - Method in class org.cruk.clarity.api.impl.URLInputStreamResource: Test for equality.
ERROR - Enum constant in enum com.genologics.ri.step.Status
EscalatedArtifact - Class in com.genologics.ri.step: Sample next action or step.
EscalatedArtifact() - Constructor for class com.genologics.ri.step.EscalatedArtifact
EscalatedArtifact(Linkable<Artifact>) - Constructor for class com.genologics.ri.step.EscalatedArtifact
EscalatedArtifact(URI) - Constructor for class com.genologics.ri.step.EscalatedArtifact
escalatedArtifacts - Variable in class com.genologics.ri.step.Escalation
escalation - Variable in class com.genologics.ri.step.Actions
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
EscalationRequest() - Constructor for class com.genologics.ri.step.EscalationRequest
EscalationReview - Class in com.genologics.ri.step
EscalationReview() - Constructor for class com.genologics.ri.step.EscalationReview
EXACT - Enum constant in enum 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 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
EXCEPTION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
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
ExecutableInputOutputMap(Boolean) - Constructor for class com.genologics.ri.processexecution.ExecutableInputOutputMap
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
ExecutableProcess(String) - Constructor for class com.genologics.ri.processexecution.ExecutableProcess
ExecutableProcess(String, Linkable<Researcher>) - Constructor for class com.genologics.ri.processexecution.ExecutableProcess
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
expiryDate - Variable in class com.genologics.ri.reagentlot.ReagentLot
ExtArtifactAssignments - Class in com.genologics.ri.routing
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
ExternalId(URI) - Constructor for class com.genologics.ri.ExternalId
ExternalId(URI, URI) - Constructor for class com.genologics.ri.ExternalId
externalIds - Variable in class com.genologics.ri.lab.Lab
externalIds - Variable in class com.genologics.ri.project.Project
externalIds - Variable in class com.genologics.ri.researcher.Researcher
externalIds - Variable in class com.genologics.ri.sample.SampleBase

F

FAILED - Enum constant in enum com.genologics.ri.artifact.QCFlag
FAILED - Enum constant in enum com.genologics.ri.processexecution.QCFlag
fax - Variable in class com.genologics.ri.researcher.Researcher
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
Field() - Constructor for class com.genologics.ri.processtype.Field
Field() - Constructor for class com.genologics.ri.stepconfiguration.Field
Field(String) - Constructor for class com.genologics.ri.processtype.Field
Field(String) - Constructor for class com.genologics.ri.stepconfiguration.Field
Field(String, String) - Constructor for class com.genologics.ri.stepconfiguration.Field
fieldDefinitions - Variable in class com.genologics.ri.configuration.Type
fieldDefinitions - Variable in class com.genologics.ri.processtype.ProcessOutput: Deprecated.
fieldDefinitions - Variable in class com.genologics.ri.processtype.ProcessType: Deprecated.
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
FieldLink(Linkable<Field>) - Constructor for class com.genologics.ri.configuration.FieldLink
FieldLink(URI) - Constructor for class com.genologics.ri.configuration.FieldLink
FieldLink(URI, String) - Constructor for class com.genologics.ri.configuration.FieldLink
fields - Variable in class com.genologics.ri.artifact.Artifact
fields - Variable in class com.genologics.ri.container.Container
fields - Variable in class com.genologics.ri.lab.Lab
fields - Variable in class com.genologics.ri.process.ClarityProcess
fields - Variable in class com.genologics.ri.processexecution.ExecutableProcess
fields - Variable in class com.genologics.ri.processtemplate.ProcessTemplate
fields - Variable in class com.genologics.ri.project.Project
fields - Variable in class com.genologics.ri.researcher.Researcher
fields - Variable in class com.genologics.ri.sample.BioSource: Deprecated.
fields - Variable in class com.genologics.ri.sample.SampleBase
fields - Variable in class com.genologics.ri.step.StepDetails
fields - Variable in class com.genologics.ri.userdefined.UDT
FieldType - Enum in com.genologics.ri.configuration: UDF field types.
file - Variable in class com.genologics.ri.artifact.Artifact
file - Variable in class com.genologics.ri.processtype.Parameter: Deprecated.
FILE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
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
FileLink(LimsEntityLinkable<ClarityFile>) - Constructor for class com.genologics.ri.file.FileLink
FileLink(URI) - Constructor for class com.genologics.ri.file.FileLink
FileLink(URI, String) - Constructor for class com.genologics.ri.file.FileLink
files - Variable in class com.genologics.ri.automation.Automation
files - Variable in class com.genologics.ri.file.ClarityFileBatchFetchResult
files - Variable in class com.genologics.ri.file.ClarityFiles
files - Variable in class com.genologics.ri.process.ClarityProcess
files - Variable in class com.genologics.ri.processtype.Parameter
files - Variable in class com.genologics.ri.processtype.StepSetup
files - Variable in class com.genologics.ri.project.Project
files - Variable in class com.genologics.ri.sample.SampleBase
files - Variable in class com.genologics.ri.step.StepSetup
files - Variable in class com.genologics.ri.stepconfiguration.StepSetup
filestoreCredentials - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl: User name and password credentials for accessing the file store.
filestoreSessionFactory - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl: Session factory for JSch connections to the file store over SFTP.
fileUploadClient - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl: Adapted REST client for uploading files through the HTTP mechanism.
finalize() - Method in class org.cruk.clarity.api.impl.URLInputStreamResource: Make sure things are closed.
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
firstName - Variable in class com.genologics.ri.processtemplate.Technician
firstName - Variable in class com.genologics.ri.researcher.Researcher
firstName - Variable in class com.genologics.ri.researcher.ResearcherLink
firstName - Variable in class com.genologics.ri.role.ResearcherLink
firstName - Variable in class com.genologics.ri.sample.Submitter
firstName - Variable in class com.genologics.ri.step.UserLink
firstPresetIsDefaultValue - Variable in class com.genologics.ri.configuration.Field
FIXED - Enum constant in enum com.genologics.ri.processtype.VariabilityType
fromValue(String) - Static method in enum com.genologics.ri.artifact.OutputType
fromValue(String) - Static method in enum com.genologics.ri.artifact.QCFlag
fromValue(String) - Static method in enum com.genologics.ri.artifact.Status
fromValue(String) - Static method in enum com.genologics.ri.automation.Context
fromValue(String) - Static method in enum com.genologics.ri.configuration.FieldType
fromValue(String) - Static method in enum com.genologics.ri.container.ContainerState: Get the container state that has the given display name.
fromValue(String) - Static method in enum com.genologics.ri.process.OutputGenerationType
fromValue(String) - Static method in enum com.genologics.ri.processexecution.QCFlag
fromValue(String) - Static method in enum com.genologics.ri.processtype.InvocationType
fromValue(String) - Static method in enum com.genologics.ri.processtype.OutputGenerationType
fromValue(String) - Static method in enum com.genologics.ri.processtype.Style
fromValue(String) - Static method in enum com.genologics.ri.processtype.TriggerPoint
fromValue(String) - Static method in enum com.genologics.ri.processtype.TriggerStatus
fromValue(String) - Static method in enum com.genologics.ri.processtype.TriggerType
fromValue(String) - Static method in enum com.genologics.ri.processtype.VariabilityType
fromValue(String) - Static method in enum com.genologics.ri.reagentlot.Status
fromValue(String) - Static method in enum com.genologics.ri.step.ActionType
fromValue(String) - Static method in enum com.genologics.ri.step.OutputGenerationType
fromValue(String) - Static method in enum com.genologics.ri.step.ProcessState: Get the process state that has the given display name.
fromValue(String) - Static method in enum com.genologics.ri.step.Status
fromValue(String) - Static method in enum com.genologics.ri.stepconfiguration.Style
fromValue(String) - Static method in enum com.genologics.ri.stepconfiguration.TriggerPoint
fromValue(String) - Static method in enum com.genologics.ri.stepconfiguration.TriggerStatus
fromValue(String) - Static method in enum com.genologics.ri.stepconfiguration.TriggerType
fromValue(String) - Static method in enum com.genologics.ri.workflowconfiguration.Status

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
GenericTypeLink(String) - Constructor for class com.genologics.ri.stepconfiguration.GenericTypeLink
getAction() - Method in class com.genologics.ri.permission.Permission
getAction() - Method in class com.genologics.ri.permission.PermissionLink
getAction() - Method in class com.genologics.ri.role.PermissionLink
getAction() - Method in class com.genologics.ri.step.NextAction
getActions() - Method in class com.genologics.ri.step.ProcessStep
getArchived() - Method in class com.genologics.ri.controltype.ControlType
getArchived() - Method in class com.genologics.ri.instrument.Instrument
getArchived() - Method in class com.genologics.ri.reagentkit.ReagentKit
getArtifact() - Method in class com.genologics.ri.artifact.Demux
getArtifact() - Method in class com.genologics.ri.sample.SampleBase
getArtifactGroups() - Method in class com.genologics.ri.artifact.Artifact
getArtifactGroups() - Method in class com.genologics.ri.artifactgroup.ArtifactGroups
getArtifacts() - Method in class com.genologics.ri.artifact.ArtifactBatchFetchResult
getArtifacts() - Method in class com.genologics.ri.artifact.Artifacts
getArtifacts() - Method in class com.genologics.ri.artifact.DemuxDetails
getArtifacts() - Method in class com.genologics.ri.artifactgroup.ArtifactGroup
getArtifacts() - Method in class com.genologics.ri.queue.Queue
getArtifacts() - Method in class com.genologics.ri.routing.ExtArtifactAssignments
getArtifactType() - Method in class com.genologics.ri.processtype.ProcessInput
getArtifactType() - Method in class com.genologics.ri.processtype.ProcessOutput: Artifact type for this output.
getArtifactUri() - Method in class com.genologics.ri.step.NextAction
getAssign() - Method in class com.genologics.ri.routing.Routing
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
getAttachTo() - Method in class com.genologics.ri.stepconfiguration.Field
getAttachToCategory() - Method in class com.genologics.ri.configuration.Field
getAttachToCategory() - Method in class com.genologics.ri.configuration.Type
getAttachToCategory() - Method in class com.genologics.ri.configuration.UdfConfigLink
getAttachToCategory() - Method in class com.genologics.ri.configuration.UdtConfigLink
getAttachToName() - Method in class com.genologics.ri.configuration.Field
getAttachToName() - Method in class com.genologics.ri.configuration.Type
getAttachToName() - Method in class com.genologics.ri.configuration.UdfConfigLink
getAttachToName() - Method in class com.genologics.ri.configuration.UdtConfigLink
getAttributes() - Method in class com.genologics.ri.reagenttype.SpecialType
getAuthor() - Method in class com.genologics.ri.step.EscalationRequest
getAuthor() - Method in class com.genologics.ri.step.EscalationReview
getAutomaticNextStep() - Method in class com.genologics.ri.step.ProcessStep
getAutomations() - Method in class com.genologics.ri.automation.Automations
getAvailableInputs() - Method in class com.genologics.ri.step.Pools
getAvailablePrograms() - Method in class com.genologics.ri.step.ProcessStep
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
getBioSource() - Method in class com.genologics.ri.sample.SampleBase: Deprecated.
getBuiltIn() - Method in class com.genologics.ri.role.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
getCatalogueNumber() - Method in class com.genologics.ri.reagentkit.ReagentKit
getCategory() - Method in class com.genologics.ri.exception.Exception
getCategory() - Method in exception org.cruk.clarity.api.ClarityException: Get the error category.
getChannel() - Method in class com.genologics.ri.automation.Automation
getChannel() - Method in class com.genologics.ri.processtype.Parameter
getChildUris() - Method in class com.genologics.ri.configuration.Field
getCity() - Method in class com.genologics.ri.Address
getCloseDate() - Method in class com.genologics.ri.project.Project
getCode() - Method in class com.genologics.ri.exception.Exception
getCode() - Method in exception org.cruk.clarity.api.ClarityException: Get the error code.
getColumns() - Method in class com.genologics.ri.containertype.ContainerType
getComment() - Method in class com.genologics.ri.step.EscalationRequest
getComment() - Method in class com.genologics.ri.step.EscalationReview
getConcentration() - Method in class com.genologics.ri.controltype.ControlType
getConfiguration() - Method in class com.genologics.ri.step.Actions
getConfiguration() - Method in class com.genologics.ri.step.Placements
getConfiguration() - Method in class com.genologics.ri.step.Pools
getConfiguration() - Method in class com.genologics.ri.step.ProcessStep
getConfiguration() - Method in class com.genologics.ri.step.ProgramStatus
getConfiguration() - Method in class com.genologics.ri.step.ReagentLots
getConfiguration() - Method in class com.genologics.ri.step.Reagents
getConfiguration() - Method in class com.genologics.ri.step.StepCreation
getConfiguration() - Method in class com.genologics.ri.step.StepDetails
getConfiguration() - Method in class com.genologics.ri.step.StepSetup
getContainer() - Method in class com.genologics.ri.Location
getContainers() - Method in class com.genologics.ri.container.ContainerBatchFetchResult
getContainers() - Method in class com.genologics.ri.container.Containers
getContainerType() - Method in class com.genologics.ri.container.Container
getContainerType() - Method in class com.genologics.ri.step.StepCreation
getContainerTypes() - Method in class com.genologics.ri.containertype.ContainerTypes
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
getControlType() - Method in class com.genologics.ri.artifact.Artifact
getControlType() - Method in class com.genologics.ri.sample.SampleBase
getControlTypes() - Method in class com.genologics.ri.controltype.ControlTypes
getControlTypeUri() - Method in class com.genologics.ri.step.CreationInput
getCountry() - Method in class com.genologics.ri.Address
getCreatedBy() - Method in class com.genologics.ri.reagentlot.ReagentLot
getCreatedDate() - Method in class com.genologics.ri.reagentlot.ReagentLot
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
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
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
getDate() - Method in class com.genologics.ri.step.EscalationRequest
getDate() - Method in class com.genologics.ri.step.EscalationReview
getDateCompleted() - Method in class com.genologics.ri.sample.SampleBase
getDateCompleted() - Method in class com.genologics.ri.step.ProcessStep
getDateReceived() - Method in class com.genologics.ri.sample.SampleBase
getDateRun() - Method in class com.genologics.ri.process.ClarityProcess
getDateRun() - Method in class com.genologics.ri.processexecution.ExecutableProcess
getDateStarted() - Method in class com.genologics.ri.step.ProcessStep
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
getDemux() - Method in class com.genologics.ri.artifact.DemuxArtifact
getDemuxDetails() - Method in class com.genologics.ri.artifact.Demux
getDepartment() - Method in class com.genologics.ri.Address
getDescription() - Method in class com.genologics.ri.permission.Permission
getDescription() - Method in class com.genologics.ri.sample.BioSource: Deprecated.
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
getDetail() - Method in class com.genologics.ri.processtype.QueueField
getDetail() - Method in class com.genologics.ri.stepconfiguration.IceBucketField
getDetail() - Method in class com.genologics.ri.stepconfiguration.QueueField
getDisplayName() - Method in class com.genologics.ri.processtype.ProcessInput
getDisplayName() - Method in class com.genologics.ri.processtype.ProcessOutput: The display name for the output.
getDisplayPrecision() - Method in class com.genologics.ri.configuration.Field
getEmail() - Method in class com.genologics.ri.researcher.Researcher: The researcher's e-mail address.
getEnabled() - Method in class com.genologics.ri.processtype.StepSetup
getEntityClass() - Method in class com.genologics.ri.artifact.ArtifactGroupLink
getEntityClass() - Method in class com.genologics.ri.artifact.ArtifactLink
getEntityClass() - Method in class com.genologics.ri.artifact.ControlTypeLink
getEntityClass() - Method in class com.genologics.ri.artifact.DemuxArtifactSample
getEntityClass() - Method in class com.genologics.ri.artifact.DemuxLink
getEntityClass() - Method in class com.genologics.ri.artifact.DemuxSourceArtifact
getEntityClass() - Method in class com.genologics.ri.artifact.ParentProcessLink
getEntityClass() - Method in class com.genologics.ri.artifact.PoolStep
getEntityClass() - Method in class com.genologics.ri.artifact.SampleLink
getEntityClass() - Method in class com.genologics.ri.artifact.WorkflowStage
getEntityClass() - Method in class com.genologics.ri.artifactgroup.ArtifactGroupLink
getEntityClass() - Method in class com.genologics.ri.automation.AutomationLink
getEntityClass() - Method in class com.genologics.ri.automation.ProcessTypeLink
getEntityClass() - Method in class com.genologics.ri.configuration.FieldLink
getEntityClass() - Method in class com.genologics.ri.configuration.TypeDefinition
getEntityClass() - Method in class com.genologics.ri.configuration.UdfConfigLink
getEntityClass() - Method in class com.genologics.ri.configuration.UdtConfigLink
getEntityClass() - Method in class com.genologics.ri.container.ContainerLink
getEntityClass() - Method in class com.genologics.ri.container.ContainerTypeLink
getEntityClass() - Method in class com.genologics.ri.container.Placement
getEntityClass() - Method in class com.genologics.ri.ContainerLink
getEntityClass() - Method in class com.genologics.ri.containertype.ContainerTypeLink
getEntityClass() - Method in class com.genologics.ri.controltype.ControlTypeLink
getEntityClass() - Method in class com.genologics.ri.file.ClarityFile
getEntityClass() - Method in class com.genologics.ri.file.FileLink
getEntityClass() - Method in class com.genologics.ri.instrument.InstrumentLink
getEntityClass() - Method in class com.genologics.ri.instrumenttype.InstrumentTypeLink
getEntityClass() - Method in class com.genologics.ri.instrumenttype.InstrumentTypeProcessType
getEntityClass() - Method in class com.genologics.ri.lab.LabLink
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
getEntityClass() - Method in class com.genologics.ri.permission.PermissionLink
getEntityClass() - Method in class com.genologics.ri.process.ArtifactLink
getEntityClass() - Method in class com.genologics.ri.process.InstrumentLink
getEntityClass() - Method in class com.genologics.ri.process.ParentProcessLink
getEntityClass() - Method in class com.genologics.ri.process.ProcessLink
getEntityClass() - Method in class com.genologics.ri.process.ProcessTypeLink
getEntityClass() - Method in class com.genologics.ri.process.Technician
getEntityClass() - Method in class com.genologics.ri.processexecution.Input
getEntityClass() - Method in class com.genologics.ri.processexecution.InstrumentLink
getEntityClass() - Method in class com.genologics.ri.processexecution.Technician
getEntityClass() - Method in class com.genologics.ri.processtemplate.InstrumentLink
getEntityClass() - Method in class com.genologics.ri.processtemplate.ProcessTemplateLink
getEntityClass() - Method in class com.genologics.ri.processtemplate.ProcessTypeLink
getEntityClass() - Method in class com.genologics.ri.processtemplate.Technician
getEntityClass() - Method in class com.genologics.ri.processtype.ContainerTypeLink
getEntityClass() - Method in class com.genologics.ri.processtype.ControlTypeLink
getEntityClass() - Method in class com.genologics.ri.processtype.ProcessTypeLink
getEntityClass() - Method in class com.genologics.ri.processtype.ReagentKitLink
getEntityClass() - Method in class com.genologics.ri.processtype.TypeDefinition
getEntityClass() - Method in class com.genologics.ri.project.ProjectLink
getEntityClass() - Method in class com.genologics.ri.project.ResearcherLink
getEntityClass() - Method in class com.genologics.ri.protocolconfiguration.ProtocolLink
getEntityClass() - Method in class com.genologics.ri.queue.ArtifactLink
getEntityClass() - Method in class com.genologics.ri.reagentkit.ReagentKitLink
getEntityClass() - Method in class com.genologics.ri.reagentlot.ReagentKitLink
getEntityClass() - Method in class com.genologics.ri.reagentlot.ReagentLotLink
getEntityClass() - Method in class com.genologics.ri.reagentlot.ResearcherLink
getEntityClass() - Method in class com.genologics.ri.reagenttype.ReagentTypeLink
getEntityClass() - Method in class com.genologics.ri.researcher.LabLink
getEntityClass() - Method in class com.genologics.ri.researcher.ResearcherLink
getEntityClass() - Method in class com.genologics.ri.researcher.Role
getEntityClass() - Method in class com.genologics.ri.role.PermissionLink
getEntityClass() - Method in class com.genologics.ri.role.ResearcherLink
getEntityClass() - Method in class com.genologics.ri.role.RoleLink
getEntityClass() - Method in class com.genologics.ri.routing.ArtifactLink
getEntityClass() - Method in class com.genologics.ri.sample.ArtifactLink
getEntityClass() - Method in class com.genologics.ri.sample.ControlTypeLink
getEntityClass() - Method in class com.genologics.ri.sample.ProjectLink
getEntityClass() - Method in class com.genologics.ri.sample.SampleLink
getEntityClass() - Method in class com.genologics.ri.sample.Submitter
getEntityClass() - Method in class com.genologics.ri.stage.ProtocolLink
getEntityClass() - Method in class com.genologics.ri.stage.ProtocolStepLink
getEntityClass() - Method in class com.genologics.ri.stage.WorkflowLink
getEntityClass() - Method in class com.genologics.ri.step.ActionsLink
getEntityClass() - Method in class com.genologics.ri.step.ArtifactLink
getEntityClass() - Method in class com.genologics.ri.step.AutomaticNextStepLink
getEntityClass() - Method in class com.genologics.ri.step.ContainerLink
getEntityClass() - Method in class com.genologics.ri.step.CreationInput
getEntityClass() - Method in class com.genologics.ri.step.EscalatedArtifact
getEntityClass() - Method in class com.genologics.ri.step.Input
getEntityClass() - Method in class com.genologics.ri.step.InstrumentLink
getEntityClass() - Method in class com.genologics.ri.step.NextAction
getEntityClass() - Method in class com.genologics.ri.step.Output
getEntityClass() - Method in class com.genologics.ri.step.OutputPlacement
getEntityClass() - Method in class com.genologics.ri.step.PlacementsLink
getEntityClass() - Method in class com.genologics.ri.step.PoolsLink
getEntityClass() - Method in class com.genologics.ri.step.ProgramStatusLink
getEntityClass() - Method in class com.genologics.ri.step.ReagentLotLink
getEntityClass() - Method in class com.genologics.ri.step.ReagentLotsLink
getEntityClass() - Method in class com.genologics.ri.step.ReagentsLink
getEntityClass() - Method in class com.genologics.ri.step.SharedResultFile
getEntityClass() - Method in class com.genologics.ri.step.StepConfiguration
getEntityClass() - Method in class com.genologics.ri.step.StepDetailsLink
getEntityClass() - Method in class com.genologics.ri.step.StepSetupLink
getEntityClass() - Method in class com.genologics.ri.step.UserLink
getEntityClass() - Method in class com.genologics.ri.stepconfiguration.ControlTypeLink
getEntityClass() - Method in class com.genologics.ri.stepconfiguration.NextStep
getEntityClass() - Method in class com.genologics.ri.stepconfiguration.ProcessTypeLink
getEntityClass() - Method in class com.genologics.ri.stepconfiguration.ReagentKitLink
getEntityClass() - Method in class com.genologics.ri.workflowconfiguration.ProtocolLink
getEntityClass() - Method in class com.genologics.ri.workflowconfiguration.StageLink
getEntityClass() - Method in class com.genologics.ri.workflowconfiguration.WorkflowLink
getEppTriggers() - Method in class com.genologics.ri.processtype.ProcessType
getEppTriggers() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
getEscalatedArtifacts() - Method in class com.genologics.ri.step.Escalation
getEscalation() - Method in class com.genologics.ri.step.Actions
getExpiryDate() - Method in class com.genologics.ri.instrument.Instrument
getExpiryDate() - Method in class com.genologics.ri.reagentlot.ReagentLot
getExternalid() - Method in class com.genologics.ri.lab.Lab
getExternalIds() - Method in class com.genologics.ri.project.Project
getExternalIds() - Method in class com.genologics.ri.researcher.Researcher
getExternalIds() - Method in class com.genologics.ri.sample.SampleBase
getFax() - Method in class com.genologics.ri.researcher.Researcher
getFieldDefinitions() - Method in class com.genologics.ri.configuration.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: Deprecated.
These field definitions are ignored as of Clarity LIMS 5.0.
getFieldName() - Method in exception com.genologics.ri.userdefined.MissingUDFException
getFields() - Method in class com.genologics.ri.sample.BioSource: Deprecated.
getFields() - Method in class com.genologics.ri.userdefined.UDT
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
getFiles() - Method in class com.genologics.ri.file.ClarityFileBatchFetchResult
getFiles() - Method in class com.genologics.ri.file.ClarityFiles
getFiles() - Method in class com.genologics.ri.process.ClarityProcess
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
getFiles() - Method in class com.genologics.ri.project.Project
getFiles() - Method in class com.genologics.ri.sample.SampleBase
getFiles() - Method in class com.genologics.ri.step.StepSetup
getFiles() - Method in class com.genologics.ri.stepconfiguration.StepSetup
getFilestoreServer() - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl: Get the host currently set on the file store.
getFirstName() - Method in class com.genologics.ri.process.Technician
getFirstName() - Method in class com.genologics.ri.processtemplate.Technician
getFirstName() - Method in class com.genologics.ri.researcher.Researcher
getFirstName() - Method in class com.genologics.ri.researcher.ResearcherLink
getFirstName() - Method in class com.genologics.ri.role.ResearcherLink
getFirstName() - Method in class com.genologics.ri.sample.Submitter
getFirstName() - Method in class com.genologics.ri.step.UserLink
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.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.
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
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
getIceBucketFields() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
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.ExternalId
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.stage.Stage: Get 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
getIndex() - Method in class com.genologics.ri.stage.Stage
getInitials() - Method in class com.genologics.ri.researcher.Researcher
getInput() - Method in class com.genologics.ri.process.InputOutputMap
getInput() - Method in class com.genologics.ri.step.InputOutputMap
getInputOutputMaps() - Method in class com.genologics.ri.process.ClarityProcess
getInputOutputMaps() - Method in class com.genologics.ri.processexecution.ExecutableProcess
getInputOutputMaps() - Method in class com.genologics.ri.step.StepDetails
getInputs() - Method in class com.genologics.ri.processexecution.ExecutableInputOutputMap
getInputs() - Method in class com.genologics.ri.step.PooledInputs
getInputs() - Method in class com.genologics.ri.step.StepCreation
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
getInstrument() - Method in class com.genologics.ri.process.ClarityProcess
getInstrument() - Method in class com.genologics.ri.processexecution.ExecutableProcess
getInstrument() - Method in class com.genologics.ri.processtemplate.ProcessTemplate
getInstrument() - Method in class com.genologics.ri.step.StepDetails
getInstruments() - Method in class com.genologics.ri.instrument.Instruments
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
getLab() - Method in class com.genologics.ri.researcher.Researcher
getLabs() - Method in class com.genologics.ri.lab.Labs
getLastModifiedBy() - Method in class com.genologics.ri.reagentlot.ReagentLot
getLastModifiedDate() - Method in class com.genologics.ri.reagentlot.ReagentLot
getLastName() - Method in class com.genologics.ri.process.Technician
getLastName() - Method in class com.genologics.ri.processtemplate.Technician
getLastName() - Method in class com.genologics.ri.researcher.Researcher
getLastName() - Method in class com.genologics.ri.researcher.ResearcherLink
getLastName() - Method in class com.genologics.ri.role.ResearcherLink
getLastName() - Method in class com.genologics.ri.sample.Submitter
getLastName() - Method in class com.genologics.ri.step.UserLink
getLimsid() - Method in class com.genologics.ri.artifact.Artifact
getLimsid() - Method in class com.genologics.ri.artifact.ArtifactLink
getLimsid() - Method in class com.genologics.ri.artifact.DemuxArtifactSample
getLimsid() - Method in class com.genologics.ri.artifact.ParentProcessLink
getLimsid() - Method in class com.genologics.ri.artifact.SampleLink
getLimsid() - Method in class com.genologics.ri.container.Container
getLimsid() - Method in class com.genologics.ri.container.ContainerLink
getLimsid() - Method in class com.genologics.ri.container.Placement
getLimsid() - Method in class com.genologics.ri.ContainerLink
getLimsid() - Method in class com.genologics.ri.file.ClarityFile
getLimsid() - Method in class com.genologics.ri.file.FileLink
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
getLimsid() - Method in class com.genologics.ri.lab.Lab
getLimsid() - Method in class com.genologics.ri.lab.LabLink
getLimsid() - Method in interface com.genologics.ri.LimsEntityLinkable: Get the LIMS id for this object.
getLimsid() - Method in class com.genologics.ri.Location
getLimsid() - Method in class com.genologics.ri.process.ArtifactLink
getLimsid() - Method in class com.genologics.ri.process.ClarityProcess
getLimsid() - Method in class com.genologics.ri.process.InstrumentLink
getLimsid() - Method in class com.genologics.ri.process.ParentProcessLink
getLimsid() - Method in class com.genologics.ri.process.ProcessLink
getLimsid() - Method in class com.genologics.ri.processexecution.InstrumentLink
getLimsid() - Method in class com.genologics.ri.processtemplate.InstrumentLink
getLimsid() - Method in class com.genologics.ri.project.Project
getLimsid() - Method in class com.genologics.ri.project.ProjectLink
getLimsid() - Method in class com.genologics.ri.project.ResearcherLink
getLimsid() - Method in class com.genologics.ri.queue.ArtifactLink
getLimsid() - Method in class com.genologics.ri.reagentlot.ReagentLot
getLimsid() - Method in class com.genologics.ri.reagentlot.ReagentLotLink
getLimsid() - Method in class com.genologics.ri.reagentlot.ResearcherLink
getLimsid() - Method in class com.genologics.ri.reagenttype.ReagentType
getLimsid() - Method in class com.genologics.ri.reagenttype.ReagentTypeLink
getLimsid() - Method in class com.genologics.ri.researcher.LabLink
getLimsid() - Method in class com.genologics.ri.researcher.Researcher
getLimsid() - Method in class com.genologics.ri.researcher.ResearcherLink
getLimsid() - Method in class com.genologics.ri.role.ResearcherLink
getLimsid() - Method in class com.genologics.ri.sample.ArtifactLink
getLimsid() - Method in class com.genologics.ri.sample.ProjectLink
getLimsid() - Method in class com.genologics.ri.sample.SampleBase
getLimsid() - Method in class com.genologics.ri.sample.SampleLink
getLimsid() - Method in class com.genologics.ri.step.ArtifactLink
getLimsid() - Method in class com.genologics.ri.step.InstrumentLink
getLimsid() - Method in class com.genologics.ri.step.ProcessStep
getLimsid() - Method in class com.genologics.ri.step.ReagentLotLink
getLimsid() - Method in class com.genologics.ri.step.SharedResultFile
getLimsId() - Method in interface com.genologics.ri.LimsEntityLinkable: Same as getLimsid() but written in a more pleasing form for camel case.
getLinks() - Method in class com.genologics.ri.configuration.Udfs
getLinks() - Method in class com.genologics.ri.configuration.Udts
getLinks() - Method in class com.genologics.ri.Index
getLinks() - Method in class com.genologics.ri.Links
getList() - Method in class com.genologics.ri.artifact.ArtifactBatchFetchResult
getList() - Method in class com.genologics.ri.artifact.Artifacts
getList() - Method in class com.genologics.ri.artifactgroup.ArtifactGroups
getList() - Method in class com.genologics.ri.automation.Automations
getList() - Method in interface com.genologics.ri.Batch
getList() - Method in class com.genologics.ri.configuration.Type
getList() - Method in class com.genologics.ri.configuration.Udfs
getList() - Method in class com.genologics.ri.configuration.Udts
getList() - Method in class com.genologics.ri.container.ContainerBatchFetchResult
getList() - Method in class com.genologics.ri.container.Containers
getList() - Method in class com.genologics.ri.containertype.ContainerTypes
getList() - Method in class com.genologics.ri.controltype.ControlTypes
getList() - Method in class com.genologics.ri.file.ClarityFileBatchFetchResult
getList() - Method in class com.genologics.ri.file.ClarityFiles
getList() - Method in class com.genologics.ri.Index
getList() - Method in class com.genologics.ri.instrument.Instruments
getList() - Method in class com.genologics.ri.instrumenttype.InstrumentTypes
getList() - Method in class com.genologics.ri.lab.Labs
getList() - Method in class com.genologics.ri.Links
getList() - Method in class com.genologics.ri.permission.Permissions
getList() - Method in class com.genologics.ri.process.ClarityProcesses
getList() - Method in class com.genologics.ri.processtemplate.ProcessTemplates
getList() - Method in class com.genologics.ri.processtype.ProcessTypes
getList() - Method in class com.genologics.ri.project.Projects
getList() - Method in class com.genologics.ri.property.Properties
getList() - Method in class com.genologics.ri.protocolconfiguration.Protocols
getList() - Method in class com.genologics.ri.queue.Queue
getList() - Method in class com.genologics.ri.reagentkit.ReagentKits
getList() - Method in class com.genologics.ri.reagentlot.ReagentLots
getList() - Method in class com.genologics.ri.reagenttype.ReagentTypes
getList() - Method in class com.genologics.ri.researcher.Researchers
getList() - Method in class com.genologics.ri.role.Roles
getList() - Method in class com.genologics.ri.sample.SampleBatchFetchResult
getList() - Method in class com.genologics.ri.sample.Samples
getList() - Method in class com.genologics.ri.version.Versions
getList() - Method in class com.genologics.ri.workflowconfiguration.Workflows
getLocation() - Method in class com.genologics.ri.artifact.Artifact
getLocation() - Method in class com.genologics.ri.processexecution.Output
getLocation() - Method in class com.genologics.ri.queue.ArtifactLink
getLocation() - Method in class com.genologics.ri.sample.SampleCreation
getLocation() - Method in class com.genologics.ri.step.OutputPlacement
getLocked() - Method in class com.genologics.ri.stepconfiguration.GenericTypeLink
getLotNumber() - Method in class com.genologics.ri.reagentlot.ReagentLot
getMajor() - Method in class com.genologics.ri.version.Version
getMaxValue() - Method in class com.genologics.ri.configuration.Field
getMessage() - Method in class com.genologics.ri.exception.Exception
getMessage() - Method in class com.genologics.ri.processtype.SharedResultFile
getMessage() - Method in class com.genologics.ri.step.ProgramStatus
getMessage() - Method in class com.genologics.ri.step.SharedResultFile
getMessage() - Method in class com.genologics.ri.stepconfiguration.SharedResultFile
getMinor() - Method in class com.genologics.ri.version.Version
getMinValue() - Method in class com.genologics.ri.configuration.Field
getName() - Method in class com.genologics.ri.artifact.Artifact
getName() - Method in class com.genologics.ri.artifact.ArtifactGroupLink
getName() - Method in class com.genologics.ri.artifact.DemuxArtifact
getName() - Method in class com.genologics.ri.artifact.DemuxSourceArtifact
getName() - Method in class com.genologics.ri.artifact.PoolStep
getName() - Method in class com.genologics.ri.artifact.ReagentLabel
getName() - Method in class com.genologics.ri.artifact.WorkflowStage
getName() - Method in class com.genologics.ri.artifactgroup.ArtifactGroup
getName() - Method in class com.genologics.ri.artifactgroup.ArtifactGroupLink
getName() - Method in class com.genologics.ri.automation.Automation
getName() - Method in class com.genologics.ri.automation.AutomationLink
getName() - Method in class com.genologics.ri.automation.ProcessTypeLink
getName() - Method in class com.genologics.ri.configuration.Field
getName() - Method in class com.genologics.ri.configuration.FieldLink
getName() - Method in class com.genologics.ri.configuration.Type
getName() - Method in class com.genologics.ri.configuration.TypeDefinition
getName() - Method in class com.genologics.ri.configuration.UdfConfigLink
getName() - Method in class com.genologics.ri.configuration.UdtConfigLink
getName() - Method in class com.genologics.ri.container.Container
getName() - Method in class com.genologics.ri.container.ContainerLink
getName() - Method in class com.genologics.ri.container.ContainerTypeLink
getName() - Method in class com.genologics.ri.containertype.CalibrantWell: Deprecated.
getName() - Method in class com.genologics.ri.containertype.ContainerType
getName() - Method in class com.genologics.ri.containertype.ContainerTypeLink
getName() - Method in class com.genologics.ri.controltype.ControlType
getName() - Method in class com.genologics.ri.controltype.ControlTypeLink
getName() - Method in class com.genologics.ri.instrument.Instrument
getName() - Method in class com.genologics.ri.instrument.InstrumentLink
getName() - Method in class com.genologics.ri.instrumenttype.InstrumentType
getName() - Method in class com.genologics.ri.instrumenttype.InstrumentTypeLink
getName() - Method in class com.genologics.ri.instrumenttype.InstrumentTypeProcessType
getName() - Method in class com.genologics.ri.lab.Lab
getName() - Method in class com.genologics.ri.lab.LabLink
getName() - Method in class com.genologics.ri.permission.Permission
getName() - Method in class com.genologics.ri.permission.PermissionLink
getName() - Method in class com.genologics.ri.process.Parameter
getName() - Method in class com.genologics.ri.process.ProcessTypeLink
getName() - Method in class com.genologics.ri.processexecution.Parameter
getName() - Method in class com.genologics.ri.processtemplate.Parameter
getName() - Method in class com.genologics.ri.processtemplate.ProcessTemplate
getName() - Method in class com.genologics.ri.processtemplate.ProcessTemplateLink
getName() - Method in class com.genologics.ri.processtemplate.ProcessTypeLink
getName() - Method in class com.genologics.ri.processtype.ContainerTypeLink
getName() - Method in class com.genologics.ri.processtype.ControlTypeLink
getName() - Method in class com.genologics.ri.processtype.EppTrigger
getName() - Method in class com.genologics.ri.processtype.Field
getName() - Method in class com.genologics.ri.processtype.Parameter
getName() - Method in class com.genologics.ri.processtype.ProcessType
getName() - Method in class com.genologics.ri.processtype.ProcessTypeAttribute
getName() - Method in class com.genologics.ri.processtype.ProcessTypeLink
getName() - Method in class com.genologics.ri.processtype.ReagentKitLink
getName() - Method in class com.genologics.ri.processtype.StepProperty
getName() - Method in class com.genologics.ri.processtype.TypeDefinition
getName() - Method in class com.genologics.ri.project.Project
getName() - Method in class com.genologics.ri.project.ProjectLink
getName() - Method in class com.genologics.ri.property.PropertyLink
getName() - Method in class com.genologics.ri.protocolconfiguration.Protocol
getName() - Method in class com.genologics.ri.protocolconfiguration.ProtocolLink
getName() - Method in class com.genologics.ri.protocolconfiguration.ProtocolProperty
getName() - Method in class com.genologics.ri.queue.Queue
getName() - Method in class com.genologics.ri.reagentkit.ReagentKit
getName() - Method in class com.genologics.ri.reagentkit.ReagentKitLink
getName() - Method in class com.genologics.ri.reagentlot.ReagentKitLink
getName() - Method in class com.genologics.ri.reagentlot.ReagentLot
getName() - Method in class com.genologics.ri.reagentlot.ReagentLotLink
getName() - Method in class com.genologics.ri.reagenttype.Attribute
getName() - Method in class com.genologics.ri.reagenttype.ReagentType
getName() - Method in class com.genologics.ri.reagenttype.ReagentTypeLink
getName() - Method in class com.genologics.ri.reagenttype.SpecialType
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
getName() - Method in class com.genologics.ri.role.Role
getName() - Method in class com.genologics.ri.role.RoleLink
getName() - Method in class com.genologics.ri.sample.BioSource: Deprecated.
getName() - Method in class com.genologics.ri.sample.ControlTypeLink
getName() - Method in class com.genologics.ri.sample.SampleBase
getName() - Method in class com.genologics.ri.stage.Stage
getName() - Method in class com.genologics.ri.step.AvailableProgram
getName() - Method in class com.genologics.ri.step.InstrumentLink
getName() - Method in class com.genologics.ri.step.PooledInputs
getName() - Method in class com.genologics.ri.step.ReagentLabel
getName() - Method in class com.genologics.ri.step.SharedResultFile
getName() - Method in class com.genologics.ri.stepconfiguration.ControlTypeLink
getName() - Method in class com.genologics.ri.stepconfiguration.EppTrigger
getName() - Method in class com.genologics.ri.stepconfiguration.Field
getName() - Method in class com.genologics.ri.stepconfiguration.NextStep
getName() - Method in class com.genologics.ri.stepconfiguration.ProcessTypeLink
getName() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
getName() - Method in class com.genologics.ri.stepconfiguration.ReagentKitLink
getName() - Method in class com.genologics.ri.stepconfiguration.StepProperty
getName() - Method in class com.genologics.ri.userdefined.UDF
getName() - Method in class com.genologics.ri.userdefined.UDT
getName() - Method in class com.genologics.ri.workflowconfiguration.ProtocolLink
getName() - Method in class com.genologics.ri.workflowconfiguration.StageLink
getName() - Method in class com.genologics.ri.workflowconfiguration.Workflow
getName() - Method in class com.genologics.ri.workflowconfiguration.WorkflowLink
getNextActions() - Method in class com.genologics.ri.step.Actions
getNextPage() - Method in class com.genologics.ri.artifact.Artifacts
getNextPage() - Method in class com.genologics.ri.artifactgroup.ArtifactGroups
getNextPage() - Method in class com.genologics.ri.automation.Automations
getNextPage() - Method in class com.genologics.ri.configuration.Udfs
getNextPage() - Method in class com.genologics.ri.configuration.Udts
getNextPage() - Method in class com.genologics.ri.container.Containers
getNextPage() - Method in class com.genologics.ri.containertype.ContainerTypes
getNextPage() - Method in class com.genologics.ri.file.ClarityFiles
getNextPage() - Method in class com.genologics.ri.instrument.Instruments
getNextPage() - Method in class com.genologics.ri.instrumenttype.InstrumentTypes
getNextPage() - Method in class com.genologics.ri.lab.Labs
getNextPage() - Method in interface com.genologics.ri.PaginatedBatch
getNextPage() - Method in class com.genologics.ri.process.ClarityProcesses
getNextPage() - Method in class com.genologics.ri.processtemplate.ProcessTemplates
getNextPage() - Method in class com.genologics.ri.processtype.ProcessTypes
getNextPage() - Method in class com.genologics.ri.project.Projects
getNextPage() - Method in class com.genologics.ri.property.Properties
getNextPage() - Method in class com.genologics.ri.queue.Queue
getNextPage() - Method in class com.genologics.ri.reagentkit.ReagentKits
getNextPage() - Method in class com.genologics.ri.reagentlot.ReagentLots
getNextPage() - Method in class com.genologics.ri.reagenttype.ReagentTypes
getNextPage() - Method in class com.genologics.ri.researcher.Researchers
getNextPage() - Method in class com.genologics.ri.sample.Samples
getNextStepUri() - Method in class com.genologics.ri.stepconfiguration.NextStep
getNotes() - Method in class com.genologics.ri.reagentlot.ReagentLot
getNumberOfOutputs() - Method in class com.genologics.ri.processtype.ProcessOutput: Number of outputs to generate (only applies if variabilityType is FIXED).
getObject() - Method in class org.cruk.clarity.api.cache.EhCacheManagerFactory
getObjectType() - Method in class org.cruk.clarity.api.cache.EhCacheManagerFactory
getOccupiedWells() - Method in class com.genologics.ri.container.Container
getOffset() - Method in class com.genologics.ri.containertype.Dimension
getOpenDate() - Method in class com.genologics.ri.project.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
getOutput() - Method in class com.genologics.ri.processexecution.ExecutableInputOutputMap
getOutput() - Method in class com.genologics.ri.step.InputOutputMap
getOutputGenerationType() - Method in class com.genologics.ri.process.ArtifactLink
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
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
getOutputReagents() - Method in class com.genologics.ri.step.Reagents
getOutputType() - Method in class com.genologics.ri.artifact.Artifact
getOutputType() - Method in class com.genologics.ri.process.ArtifactLink
getOutputUri() - Method in class com.genologics.ri.step.PooledInputs
getParameter() - Method in class com.genologics.ri.process.ClarityProcess
getParameter() - Method in class com.genologics.ri.processexecution.ExecutableProcess
getParameter() - Method in class com.genologics.ri.processtemplate.ProcessTemplate
getParameters() - Method in class com.genologics.ri.processtype.ProcessType
getParentProcess() - Method in class com.genologics.ri.artifact.Artifact
getParentProcess() - Method in class com.genologics.ri.process.ArtifactLink
getParentUri() - Method in class com.genologics.ri.configuration.Field
getPassword() - Method in class com.genologics.ri.researcher.Credentials
getPermissions() - Method in class com.genologics.ri.permission.Permissions
getPermissions() - Method in class com.genologics.ri.role.Role
getPermittedContainers() - Method in class com.genologics.ri.processtype.ProcessType
getPermittedContainerTypes() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
getPermittedControlTypes() - Method in class com.genologics.ri.processtype.ProcessType
getPermittedControlTypes() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
getPermittedInstrumentTypes() - Method in class com.genologics.ri.processtype.ProcessType
getPermittedInstrumentTypes() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
getPermittedReagentCategories() - Method in class com.genologics.ri.processtype.ProcessType
getPermittedReagentCategories() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
getPhone() - Method in class com.genologics.ri.researcher.Researcher
getPlacements() - Method in class com.genologics.ri.container.Container
getPlacements() - Method in class com.genologics.ri.step.ProcessStep
getPoint() - Method in class com.genologics.ri.processtype.EppTrigger
getPoint() - Method in class com.genologics.ri.stepconfiguration.EppTrigger
getPooledInputs() - Method in class com.genologics.ri.step.Pools
getPools() - Method in class com.genologics.ri.step.ProcessStep
getPoolStep() - Method in class com.genologics.ri.artifact.DemuxDetails
getPostalCode() - Method in class com.genologics.ri.Address
getPostProcessUri() - Method in class com.genologics.ri.process.ArtifactLink
getPreset() - Method in class com.genologics.ri.step.StepDetails
getPresets() - Method in class com.genologics.ri.configuration.Field
getPreviousPage() - Method in class com.genologics.ri.artifact.Artifacts
getPreviousPage() - Method in class com.genologics.ri.artifactgroup.ArtifactGroups
getPreviousPage() - Method in class com.genologics.ri.automation.Automations
getPreviousPage() - Method in class com.genologics.ri.configuration.Udfs
getPreviousPage() - Method in class com.genologics.ri.configuration.Udts
getPreviousPage() - Method in class com.genologics.ri.container.Containers
getPreviousPage() - Method in class com.genologics.ri.containertype.ContainerTypes
getPreviousPage() - Method in class com.genologics.ri.file.ClarityFiles
getPreviousPage() - Method in class com.genologics.ri.instrument.Instruments
getPreviousPage() - Method in class com.genologics.ri.instrumenttype.InstrumentTypes
getPreviousPage() - Method in class com.genologics.ri.lab.Labs
getPreviousPage() - Method in interface com.genologics.ri.PaginatedBatch
getPreviousPage() - Method in class com.genologics.ri.process.ClarityProcesses
getPreviousPage() - Method in class com.genologics.ri.processtemplate.ProcessTemplates
getPreviousPage() - Method in class com.genologics.ri.processtype.ProcessTypes
getPreviousPage() - Method in class com.genologics.ri.project.Projects
getPreviousPage() - Method in class com.genologics.ri.property.Properties
getPreviousPage() - Method in class com.genologics.ri.queue.Queue
getPreviousPage() - Method in class com.genologics.ri.reagentkit.ReagentKits
getPreviousPage() - Method in class com.genologics.ri.reagentlot.ReagentLots
getPreviousPage() - Method in class com.genologics.ri.reagenttype.ReagentTypes
getPreviousPage() - Method in class com.genologics.ri.researcher.Researchers
getPreviousPage() - Method in class com.genologics.ri.sample.Samples
getProcesses() - Method in class com.genologics.ri.process.ClarityProcesses
getProcessInputs() - Method in class com.genologics.ri.processtype.ProcessType
getProcessOutputs() - Method in class com.genologics.ri.processtype.ProcessType
getProcessTemplates() - Method in class com.genologics.ri.processtemplate.ProcessTemplates
getProcessType() - Method in class com.genologics.ri.process.ClarityProcess
getProcessType() - Method in class com.genologics.ri.processexecution.ExecutableProcess
getProcessType() - Method in class com.genologics.ri.processtemplate.ProcessTemplate
getProcessType() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
getProcessTypeAttributes() - Method in class com.genologics.ri.processtype.ProcessType
getProcessTypes() - Method in class com.genologics.ri.automation.Automation
getProcessTypes() - Method in class com.genologics.ri.instrumenttype.InstrumentType
getProcessTypes() - Method in class com.genologics.ri.processtype.ProcessTypes
getProgramStatus() - Method in class com.genologics.ri.step.ProcessStep
getProject() - Method in class com.genologics.ri.sample.SampleBase
getProjects() - Method in class com.genologics.ri.project.Projects
getProperties() - Method in class com.genologics.ri.property.Properties
getProtocol() - Method in class com.genologics.ri.stage.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
getProtocolProperties() - Method in class com.genologics.ri.protocolconfiguration.Protocol
getProtocols() - Method in class com.genologics.ri.protocolconfiguration.Protocols
getProtocols() - Method in class com.genologics.ri.workflowconfiguration.Workflow
getProtocolStepIndex() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
getProtocolStepUri() - Method in class com.genologics.ri.queue.Queue
getProtocolStepUri() - Method in class com.genologics.ri.step.StepConfiguration
getProtocolUri() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
getQCFlag() - Method in class com.genologics.ri.artifact.Artifact
getQCFlag() - Method in class com.genologics.ri.processexecution.ArtifactBase
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
getQueueFields() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
getQueueTime() - Method in class com.genologics.ri.queue.ArtifactLink
getReagentCategory() - Method in class com.genologics.ri.reagenttype.ReagentType
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
getReagentKit() - Method in class com.genologics.ri.reagentlot.ReagentLot
getReagentKits() - Method in class com.genologics.ri.reagentkit.ReagentKits
getReagentLabels() - Method in class com.genologics.ri.artifact.Artifact
getReagentLabels() - Method in class com.genologics.ri.artifact.DemuxArtifact
getReagentLabels() - Method in class com.genologics.ri.step.Output
getReagentLots() - Method in class com.genologics.ri.reagentlot.ReagentLots
getReagentLots() - Method in class com.genologics.ri.step.ProcessStep
getReagentLots() - Method in class com.genologics.ri.step.ReagentLots
getReagents() - Method in class com.genologics.ri.step.ProcessStep
getReagentTypes() - Method in class com.genologics.ri.reagenttype.ReagentTypes
getRelative() - Method in class com.genologics.ri.Link
getReplicates() - Method in class com.genologics.ri.step.CreationInput
getReplicates() - Method in class com.genologics.ri.step.Input
getRequest() - Method in class com.genologics.ri.step.Escalation
getRequiredReagentKits() - Method in class com.genologics.ri.processtype.ProcessType
getRequiredReagentKits() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
getResearcher() - Method in class com.genologics.ri.project.Project
getResearchers() - Method in class com.genologics.ri.researcher.Researchers
getResearchers() - Method in class com.genologics.ri.role.Role
getReview() - Method in class com.genologics.ri.step.Escalation
getReviewer() - Method in class com.genologics.ri.step.EscalationRequest
getReworkStepUri() - Method in class com.genologics.ri.step.NextAction
getRoleName() - Method in class com.genologics.ri.researcher.Role: Deprecated.
Deprecated from version 2.19.
getRoles() - Method in class com.genologics.ri.researcher.Credentials
getRoles() - Method in class com.genologics.ri.role.Roles
getRows() - Method in class com.genologics.ri.containertype.ContainerType
getSampleCreations() - Method in class com.genologics.ri.sample.SampleBatchFetchResult
getSampleFields() - Method in class com.genologics.ri.processtype.ProcessType
getSampleFields() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
getSamples() - Method in class com.genologics.ri.artifact.Artifact
getSamples() - Method in class com.genologics.ri.artifact.DemuxArtifact
getSamples() - Method in class com.genologics.ri.sample.SampleBatchFetchResult
getSamples() - Method in class com.genologics.ri.sample.Samples
getScript() - Method in class com.genologics.ri.automation.Automation
getScript() - Method in class com.genologics.ri.processtype.Parameter
getSearchTerm() - Method in exception org.cruk.clarity.api.IllegalSearchTermException: Get the search term that caused the error.
getSelectedContainers() - Method in class com.genologics.ri.step.Placements
getSequence() - Method in class com.genologics.ri.stepconfiguration.NextStep
getSerialNumber() - Method in class com.genologics.ri.instrument.Instrument
getServer() - Method in interface org.cruk.clarity.api.ClarityAPI: Get the base URL of the Clarity server.
getServer() - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl: Get the base URL of the Clarity server.
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.
getSetup() - Method in class com.genologics.ri.step.ProcessStep
getSharedResultFileIndex() - Method in class com.genologics.ri.processtype.SharedResultFile
getSharedResultFileIndex() - Method in class com.genologics.ri.step.SharedResultFile
getSharedResultFileIndex() - Method in class com.genologics.ri.stepconfiguration.SharedResultFile
getShippingAddress() - Method in class com.genologics.ri.lab.Lab
getSingleStep() - Method in class com.genologics.ri.controltype.ControlType
getSize() - Method in class com.genologics.ri.artifact.ArtifactBatchFetchResult
getSize() - Method in class com.genologics.ri.artifact.Artifacts
getSize() - Method in class com.genologics.ri.artifactgroup.ArtifactGroups
getSize() - Method in class com.genologics.ri.automation.Automations
getSize() - Method in interface com.genologics.ri.Batch
getSize() - Method in class com.genologics.ri.configuration.Type
getSize() - Method in class com.genologics.ri.configuration.Udfs
getSize() - Method in class com.genologics.ri.configuration.Udts
getSize() - Method in class com.genologics.ri.container.ContainerBatchFetchResult
getSize() - Method in class com.genologics.ri.container.Containers
getSize() - Method in class com.genologics.ri.containertype.ContainerTypes
getSize() - Method in class com.genologics.ri.containertype.Dimension
getSize() - Method in class com.genologics.ri.controltype.ControlTypes
getSize() - Method in class com.genologics.ri.file.ClarityFileBatchFetchResult
getSize() - Method in class com.genologics.ri.file.ClarityFiles
getSize() - Method in class com.genologics.ri.Index
getSize() - Method in class com.genologics.ri.instrument.Instruments
getSize() - Method in class com.genologics.ri.instrumenttype.InstrumentTypes
getSize() - Method in class com.genologics.ri.lab.Labs
getSize() - Method in class com.genologics.ri.Links
getSize() - Method in class com.genologics.ri.permission.Permissions
getSize() - Method in class com.genologics.ri.process.ClarityProcesses
getSize() - Method in class com.genologics.ri.processtemplate.ProcessTemplates
getSize() - Method in class com.genologics.ri.processtype.ProcessTypes
getSize() - Method in class com.genologics.ri.project.Projects
getSize() - Method in class com.genologics.ri.property.Properties
getSize() - Method in class com.genologics.ri.protocolconfiguration.Protocols
getSize() - Method in class com.genologics.ri.queue.Queue
getSize() - Method in class com.genologics.ri.reagentkit.ReagentKits
getSize() - Method in class com.genologics.ri.reagentlot.ReagentLots
getSize() - Method in class com.genologics.ri.reagenttype.ReagentTypes
getSize() - Method in class com.genologics.ri.researcher.Researchers
getSize() - Method in class com.genologics.ri.role.Roles
getSize() - Method in class com.genologics.ri.sample.SampleBatchFetchResult
getSize() - Method in class com.genologics.ri.sample.Samples
getSize() - Method in class com.genologics.ri.version.Versions
getSize() - Method in class com.genologics.ri.workflowconfiguration.Workflows
getSpecialType() - Method in class com.genologics.ri.reagenttype.ReagentType
getStages() - Method in class com.genologics.ri.workflowconfiguration.Workflow
getStageUri() - Method in class com.genologics.ri.routing.ExtArtifactAssignments
getState() - Method in class com.genologics.ri.Address
getState() - Method in class com.genologics.ri.container.Container
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
getStatus() - Method in class com.genologics.ri.processtype.EppTrigger
getStatus() - Method in class com.genologics.ri.reagentlot.ReagentLot
getStatus() - Method in class com.genologics.ri.step.ProgramStatus
getStatus() - Method in class com.genologics.ri.stepconfiguration.EppTrigger
getStatus() - Method in class com.genologics.ri.workflowconfiguration.Workflow
getStatus() - Method in class com.genologics.ri.workflowconfiguration.WorkflowLink
getStep() - Method in class com.genologics.ri.stage.Stage
getStep() - Method in class com.genologics.ri.step.Actions
getStep() - Method in class com.genologics.ri.step.Placements
getStep() - Method in class com.genologics.ri.step.Pools
getStep() - Method in class com.genologics.ri.step.ProgramStatus
getStep() - Method in class com.genologics.ri.step.ReagentLots
getStep() - Method in class com.genologics.ri.step.Reagents
getStep() - Method in class com.genologics.ri.step.StepDetails
getStep() - Method in class com.genologics.ri.step.StepSetup
getStepDetails() - Method in class com.genologics.ri.step.ProcessStep
getStepFields() - Method in class com.genologics.ri.processtype.ProcessType
getStepFields() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
getStepName() - Method in class com.genologics.ri.step.StepConfiguration
getStepProperties() - Method in class com.genologics.ri.processtype.ProcessType
getStepProperties() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
getSteps() - Method in class com.genologics.ri.protocolconfiguration.Protocol
getStepSetup() - Method in class com.genologics.ri.processtype.ProcessType
getStepSetup() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
getStepUri() - Method in class com.genologics.ri.step.NextAction
getStorageLocation() - Method in class com.genologics.ri.reagentlot.ReagentLot
getStreet() - Method in class com.genologics.ri.Address
getStyle() - Method in class com.genologics.ri.processtype.Field
getStyle() - Method in class com.genologics.ri.stepconfiguration.Field
getSubmitter() - Method in class com.genologics.ri.sample.SampleBase
getSuggestedActions() - Method in class com.genologics.ri.exception.Exception
getSuggestedActions() - Method in exception org.cruk.clarity.api.ClarityException: Get the "suggested actions" text.
getSupplier() - Method in class com.genologics.ri.controltype.ControlType
getSupplier() - Method in class com.genologics.ri.reagentkit.ReagentKit
getTechnician() - Method in class com.genologics.ri.process.ClarityProcess
getTechnician() - Method in class com.genologics.ri.processexecution.ExecutableProcess
getTechnician() - Method in class com.genologics.ri.processtemplate.ProcessTemplate
getTransitions() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
getType() - Method in class com.genologics.ri.artifact.Artifact
getType() - Method in class com.genologics.ri.configuration.Field
getType() - Method in class com.genologics.ri.instrument.Instrument
getType() - Method in class com.genologics.ri.processexecution.Output
getType() - Method in class com.genologics.ri.processtype.EppTrigger
getType() - Method in class com.genologics.ri.step.ArtifactLink
getType() - Method in class com.genologics.ri.stepconfiguration.EppTrigger
getType() - Method in class com.genologics.ri.userdefined.UDF
getTypeDefinition() - Method in class com.genologics.ri.configuration.Field
getTypeDefinitions() - Method in class com.genologics.ri.processtype.ProcessType
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
getUnavailableWells() - Method in class com.genologics.ri.containertype.ContainerType
getUnit() - Method in class com.genologics.ri.userdefined.UDF
getUnitLabel() - Method in class com.genologics.ri.configuration.Field
getUri() - Method in class com.genologics.ri.artifact.Artifact
getUri() - Method in class com.genologics.ri.artifact.ArtifactGroupLink
getUri() - Method in class com.genologics.ri.artifact.ArtifactLink
getUri() - Method in class com.genologics.ri.artifact.ControlTypeLink
getUri() - Method in class com.genologics.ri.artifact.Demux
getUri() - Method in class com.genologics.ri.artifact.DemuxArtifact
getUri() - Method in class com.genologics.ri.artifact.DemuxArtifactSample
getUri() - Method in class com.genologics.ri.artifact.DemuxLink
getUri() - Method in class com.genologics.ri.artifact.DemuxSourceArtifact
getUri() - Method in class com.genologics.ri.artifact.ParentProcessLink
getUri() - Method in class com.genologics.ri.artifact.PoolStep
getUri() - Method in class com.genologics.ri.artifact.SampleLink
getUri() - Method in class com.genologics.ri.artifact.WorkflowStage
getUri() - Method in class com.genologics.ri.artifactgroup.ArtifactGroup
getUri() - Method in class com.genologics.ri.artifactgroup.ArtifactGroupLink
getUri() - Method in class com.genologics.ri.artifactgroup.Artifacts
getUri() - Method in class com.genologics.ri.automation.Automation
getUri() - Method in class com.genologics.ri.automation.AutomationLink
getUri() - Method in class com.genologics.ri.automation.Automations
getUri() - Method in class com.genologics.ri.automation.ProcessTypeLink
getUri() - Method in class com.genologics.ri.configuration.Field
getUri() - Method in class com.genologics.ri.configuration.FieldLink
getUri() - Method in class com.genologics.ri.configuration.Type
getUri() - Method in class com.genologics.ri.configuration.TypeDefinition
getUri() - Method in class com.genologics.ri.configuration.UdfConfigLink
getUri() - Method in class com.genologics.ri.configuration.UdtConfigLink
getUri() - Method in class com.genologics.ri.container.Container
getUri() - Method in class com.genologics.ri.container.ContainerLink
getUri() - Method in class com.genologics.ri.container.ContainerTypeLink
getUri() - Method in class com.genologics.ri.container.Placement
getUri() - Method in class com.genologics.ri.ContainerLink
getUri() - Method in class com.genologics.ri.containertype.ContainerType
getUri() - Method in class com.genologics.ri.containertype.ContainerTypeLink
getUri() - Method in class com.genologics.ri.controltype.ControlType
getUri() - Method in class com.genologics.ri.controltype.ControlTypeLink
getUri() - Method in class com.genologics.ri.controltype.ControlTypes
getUri() - Method in class com.genologics.ri.ExternalId
getUri() - Method in class com.genologics.ri.file.ClarityFile
getUri() - Method in class com.genologics.ri.file.FileLink
getUri() - Method in class com.genologics.ri.instrument.Instrument
getUri() - Method in class com.genologics.ri.instrument.InstrumentLink
getUri() - Method in class com.genologics.ri.instrumenttype.InstrumentType
getUri() - Method in class com.genologics.ri.instrumenttype.InstrumentTypeLink
getUri() - Method in class com.genologics.ri.instrumenttype.InstrumentTypeProcessType
getUri() - Method in class com.genologics.ri.lab.Lab
getUri() - Method in class com.genologics.ri.lab.LabLink
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
getUri() - Method in interface com.genologics.ri.Locatable: Get the URI of this object.
getUri() - Method in class com.genologics.ri.Location
getUri() - Method in class com.genologics.ri.Page
getUri() - Method in class com.genologics.ri.permission.Permission
getUri() - Method in class com.genologics.ri.permission.PermissionLink
getUri() - Method in class com.genologics.ri.permission.Permissions
getUri() - Method in class com.genologics.ri.process.ArtifactLink
getUri() - Method in class com.genologics.ri.process.ClarityProcess
getUri() - Method in class com.genologics.ri.process.InstrumentLink
getUri() - Method in class com.genologics.ri.process.ParentProcessLink
getUri() - Method in class com.genologics.ri.process.ProcessLink
getUri() - Method in class com.genologics.ri.process.ProcessTypeLink
getUri() - Method in class com.genologics.ri.process.Technician
getUri() - Method in class com.genologics.ri.processexecution.Input
getUri() - Method in class com.genologics.ri.processexecution.InstrumentLink
getUri() - Method in class com.genologics.ri.processexecution.Technician
getUri() - Method in class com.genologics.ri.processtemplate.InstrumentLink
getUri() - Method in class com.genologics.ri.processtemplate.ProcessTemplate
getUri() - Method in class com.genologics.ri.processtemplate.ProcessTemplateLink
getUri() - Method in class com.genologics.ri.processtemplate.ProcessTypeLink
getUri() - Method in class com.genologics.ri.processtemplate.Technician
getUri() - Method in class com.genologics.ri.processtype.ContainerTypeLink
getUri() - Method in class com.genologics.ri.processtype.ControlTypeLink
getUri() - Method in class com.genologics.ri.processtype.ProcessType
getUri() - Method in class com.genologics.ri.processtype.ProcessTypeLink
getUri() - Method in class com.genologics.ri.processtype.ReagentKitLink
getUri() - Method in class com.genologics.ri.processtype.TypeDefinition
getUri() - Method in class com.genologics.ri.project.Project
getUri() - Method in class com.genologics.ri.project.ProjectLink
getUri() - Method in class com.genologics.ri.project.ResearcherLink
getUri() - Method in class com.genologics.ri.property.PropertyLink
getUri() - Method in class com.genologics.ri.protocolconfiguration.Protocol
getUri() - Method in class com.genologics.ri.protocolconfiguration.ProtocolLink
getUri() - Method in class com.genologics.ri.queue.ArtifactLink
getUri() - Method in class com.genologics.ri.queue.Queue
getUri() - Method in class com.genologics.ri.reagentkit.ReagentKit
getUri() - Method in class com.genologics.ri.reagentkit.ReagentKitLink
getUri() - Method in class com.genologics.ri.reagentkit.ReagentKits
getUri() - Method in class com.genologics.ri.reagentlot.ReagentKitLink
getUri() - Method in class com.genologics.ri.reagentlot.ReagentLot
getUri() - Method in class com.genologics.ri.reagentlot.ReagentLotLink
getUri() - Method in class com.genologics.ri.reagentlot.ReagentLots
getUri() - Method in class com.genologics.ri.reagentlot.ResearcherLink
getUri() - Method in class com.genologics.ri.reagenttype.ReagentType
getUri() - Method in class com.genologics.ri.reagenttype.ReagentTypeLink
getUri() - Method in class com.genologics.ri.researcher.LabLink
getUri() - Method in class com.genologics.ri.researcher.Researcher
getUri() - Method in class com.genologics.ri.researcher.ResearcherLink
getUri() - Method in class com.genologics.ri.researcher.Role: Get the URI to the researcher.
getUri() - Method in class com.genologics.ri.role.PermissionLink
getUri() - Method in class com.genologics.ri.role.ResearcherLink
getUri() - Method in class com.genologics.ri.role.Role
getUri() - Method in class com.genologics.ri.role.RoleLink
getUri() - Method in class com.genologics.ri.role.Roles
getUri() - Method in class com.genologics.ri.routing.ArtifactLink
getUri() - Method in class com.genologics.ri.sample.ArtifactLink
getUri() - Method in class com.genologics.ri.sample.ControlTypeLink
getUri() - Method in class com.genologics.ri.sample.ProjectLink
getUri() - Method in class com.genologics.ri.sample.SampleBase
getUri() - Method in class com.genologics.ri.sample.SampleLink
getUri() - Method in class com.genologics.ri.sample.Submitter
getUri() - Method in class com.genologics.ri.stage.ProtocolLink
getUri() - Method in class com.genologics.ri.stage.ProtocolStepLink
getUri() - Method in class com.genologics.ri.stage.Stage
getUri() - Method in class com.genologics.ri.stage.WorkflowLink
getUri() - Method in class com.genologics.ri.step.Actions
getUri() - Method in class com.genologics.ri.step.ActionsLink
getUri() - Method in class com.genologics.ri.step.ArtifactLink
getUri() - Method in class com.genologics.ri.step.AutomaticNextStepLink
getUri() - Method in class com.genologics.ri.step.AvailableProgram
getUri() - Method in class com.genologics.ri.step.ContainerLink
getUri() - Method in class com.genologics.ri.step.CreationInput
getUri() - Method in class com.genologics.ri.step.EscalatedArtifact
getUri() - Method in class com.genologics.ri.step.Input
getUri() - Method in class com.genologics.ri.step.InstrumentLink
getUri() - Method in class com.genologics.ri.step.NextAction
getUri() - Method in class com.genologics.ri.step.Output
getUri() - Method in class com.genologics.ri.step.OutputPlacement
getUri() - Method in class com.genologics.ri.step.Placements
getUri() - Method in class com.genologics.ri.step.PlacementsLink
getUri() - Method in class com.genologics.ri.step.Pools
getUri() - Method in class com.genologics.ri.step.PoolsLink
getUri() - Method in class com.genologics.ri.step.ProcessStep
getUri() - Method in class com.genologics.ri.step.ProgramStatus
getUri() - Method in class com.genologics.ri.step.ProgramStatusLink
getUri() - Method in class com.genologics.ri.step.ReagentLotLink
getUri() - Method in class com.genologics.ri.step.ReagentLots
getUri() - Method in class com.genologics.ri.step.ReagentLotsLink
getUri() - Method in class com.genologics.ri.step.Reagents
getUri() - Method in class com.genologics.ri.step.ReagentsLink
getUri() - Method in class com.genologics.ri.step.SharedResultFile
getUri() - Method in class com.genologics.ri.step.StepConfiguration
getUri() - Method in class com.genologics.ri.step.StepDetails
getUri() - Method in class com.genologics.ri.step.StepDetailsLink
getUri() - Method in class com.genologics.ri.step.StepSetup
getUri() - Method in class com.genologics.ri.step.StepSetupLink
getUri() - Method in class com.genologics.ri.step.UserLink
getUri() - Method in class com.genologics.ri.stepconfiguration.ControlTypeLink
getUri() - Method in class com.genologics.ri.stepconfiguration.NextStep
getUri() - Method in class com.genologics.ri.stepconfiguration.ProcessTypeLink
getUri() - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
getUri() - Method in class com.genologics.ri.stepconfiguration.ReagentKitLink
getUri() - Method in class com.genologics.ri.version.Version
getUri() - Method in class com.genologics.ri.workflowconfiguration.ProtocolLink
getUri() - Method in class com.genologics.ri.workflowconfiguration.StageLink
getUri() - Method in class com.genologics.ri.workflowconfiguration.Workflow
getUri() - Method in class com.genologics.ri.workflowconfiguration.WorkflowLink
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
getUserDefinedField(String) - Method in class com.genologics.ri.artifact.Artifact: Deprecated.
getUserDefinedField(String) - Method in class com.genologics.ri.container.Container: Deprecated.
getUserDefinedField(String) - Method in class com.genologics.ri.lab.Lab: Deprecated.
getUserDefinedField(String) - Method in class com.genologics.ri.process.ClarityProcess: Deprecated.
getUserDefinedField(String) - Method in class com.genologics.ri.project.Project: Deprecated.
getUserDefinedField(String) - Method in class com.genologics.ri.researcher.Researcher: Deprecated.
getUserDefinedField(String) - Method in class com.genologics.ri.sample.SampleBase: Deprecated.
getUserDefinedField(String) - Method in class com.genologics.ri.step.StepDetails: Deprecated.
getUserDefinedFields() - Method in class com.genologics.ri.artifact.Artifact
getUserDefinedFields() - Method in class com.genologics.ri.container.Container
getUserDefinedFields() - Method in class com.genologics.ri.lab.Lab
getUserDefinedFields() - Method in class com.genologics.ri.process.ClarityProcess
getUserDefinedFields() - Method in class com.genologics.ri.processexecution.ExecutableProcess
getUserDefinedFields() - Method in class com.genologics.ri.processtemplate.ProcessTemplate
getUserDefinedFields() - Method in class com.genologics.ri.project.Project
getUserDefinedFields() - Method in class com.genologics.ri.researcher.Researcher
getUserDefinedFields() - Method in class com.genologics.ri.sample.SampleBase
getUserDefinedFields() - Method in class com.genologics.ri.step.StepDetails
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
getUserDefinedType() - Method in class com.genologics.ri.lab.Lab
getUserDefinedType() - Method in class com.genologics.ri.process.ClarityProcess
getUserDefinedType() - Method in class com.genologics.ri.processexecution.ExecutableProcess
getUserDefinedType() - Method in class com.genologics.ri.processtemplate.ProcessTemplate
getUserDefinedType() - Method in class com.genologics.ri.project.Project
getUserDefinedType() - Method in class com.genologics.ri.researcher.Researcher
getUserDefinedType() - Method in class com.genologics.ri.sample.SampleBase
getUsername() - Method in class com.genologics.ri.researcher.Credentials
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.containertype.CalibrantWell: Deprecated.
getValue() - Method in class com.genologics.ri.processtype.ProcessTypeAttribute
getValue() - Method in class com.genologics.ri.processtype.StepProperty
getValue() - Method in class com.genologics.ri.property.PropertyLink
getValue() - Method in class com.genologics.ri.protocolconfiguration.ProtocolProperty
getValue() - Method in class com.genologics.ri.reagenttype.Attribute
getValue() - Method in class com.genologics.ri.stepconfiguration.GenericTypeLink
getValue() - Method in class com.genologics.ri.stepconfiguration.StepProperty
getValue() - Method in class com.genologics.ri.userdefined.UDF
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
getVendor() - Method in class com.genologics.ri.instrumenttype.InstrumentTypeLink
getVersions() - Method in class com.genologics.ri.version.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
getWebsite() - Method in class com.genologics.ri.lab.Lab
getWebsite() - Method in class com.genologics.ri.reagentkit.ReagentKit
getWellPosition() - Method in class com.genologics.ri.container.Placement
getWellPosition() - Method in class com.genologics.ri.Location
getWorkflow() - Method in class com.genologics.ri.stage.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: Get the numeric identifier for this stage's workflow from its URI.
getWorkflows() - Method in class com.genologics.ri.workflowconfiguration.Workflows
getWorkflowStages() - Method in class com.genologics.ri.artifact.Artifact
getWorkflowUri() - Method in class com.genologics.ri.routing.ExtArtifactAssignments

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(HttpStatus) - 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.ContainerLink
hashCode() - Method in class com.genologics.ri.Location
hashCode() - Method in class org.cruk.clarity.api.impl.URLInputStreamResource: Get a hash code for this URLInputStreamResource.
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.
httpStatus - Variable in exception org.cruk.clarity.api.ClarityException
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 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
IceBucketField() - Constructor for class com.genologics.ri.stepconfiguration.IceBucketField
IceBucketField(String) - Constructor for class com.genologics.ri.stepconfiguration.IceBucketField
IceBucketField(String, String) - Constructor for class com.genologics.ri.stepconfiguration.IceBucketField
iceBucketFields - Variable in class com.genologics.ri.processtype.ProcessType
iceBucketFields - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep
id - Variable in class com.genologics.ri.ExternalId
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 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 com.genologics.ri.artifact.Status
index - Variable in class com.genologics.ri.protocolconfiguration.Protocol
index - Variable in class com.genologics.ri.stage.Stage
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
initials - Variable in class com.genologics.ri.researcher.Researcher
input - Variable in class com.genologics.ri.process.InputOutputMap
input - Variable in class com.genologics.ri.step.InputOutputMap
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
Input() - Constructor for class com.genologics.ri.step.Input
Input(Linkable<Artifact>) - Constructor for class com.genologics.ri.processexecution.Input
Input(Linkable<Artifact>) - Constructor for class com.genologics.ri.step.Input
Input(URI) - Constructor for class com.genologics.ri.processexecution.Input
Input(URI) - Constructor for class com.genologics.ri.step.Input
Input(URI, QCFlag) - Constructor for class com.genologics.ri.processexecution.Input
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
InputOutputMap() - Constructor for class com.genologics.ri.step.InputOutputMap
InputOutputMap(LimsEntityLinkable<Artifact>, LimsEntityLinkable<Artifact>) - Constructor for class com.genologics.ri.process.InputOutputMap
InputOutputMap(LimsEntityLinkable<Artifact>, LimsEntityLinkable<Artifact>) - Constructor for class com.genologics.ri.step.InputOutputMap
InputOutputMap(Linkable<Artifact>, Linkable<Artifact>) - Constructor for class com.genologics.ri.process.InputOutputMap
InputOutputMap(Linkable<Artifact>, Linkable<Artifact>) - Constructor for class com.genologics.ri.step.InputOutputMap
InputOutputMap(ArtifactLink, ArtifactLink) - Constructor for class com.genologics.ri.process.InputOutputMap
InputOutputMap(ArtifactLink, ArtifactLink) - Constructor for class com.genologics.ri.step.InputOutputMap
inputOutputMaps - Variable in class com.genologics.ri.process.ClarityProcess
inputOutputMaps - Variable in class com.genologics.ri.processexecution.ExecutableProcess
inputOutputMaps - Variable in class com.genologics.ri.step.StepDetails
inputs - Variable in class com.genologics.ri.processexecution.ExecutableInputOutputMap
inputs - Variable in class com.genologics.ri.step.PooledInputs
inputs - Variable in class com.genologics.ri.step.StepCreation
institution - Variable in class com.genologics.ri.Address
instrument - Variable in class com.genologics.ri.process.ClarityProcess
instrument - Variable in class com.genologics.ri.processexecution.ExecutableProcess
instrument - Variable in class com.genologics.ri.processtemplate.ProcessTemplate
instrument - Variable in class com.genologics.ri.step.StepDetails
Instrument - Class in com.genologics.ri.instrument: The detailed representation of an instrument.
Instrument() - Constructor for class com.genologics.ri.instrument.Instrument
Instrument(String) - Constructor for class com.genologics.ri.instrument.Instrument
Instrument(String, String) - Constructor for class com.genologics.ri.instrument.Instrument
INSTRUMENT_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
INSTRUMENT_TYPE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
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
InstrumentLink() - Constructor for class com.genologics.ri.process.InstrumentLink
InstrumentLink() - Constructor for class com.genologics.ri.processexecution.InstrumentLink
InstrumentLink() - Constructor for class com.genologics.ri.processtemplate.InstrumentLink
InstrumentLink() - Constructor for class com.genologics.ri.step.InstrumentLink
InstrumentLink(Linkable<Instrument>) - Constructor for class com.genologics.ri.instrument.InstrumentLink
InstrumentLink(Linkable<Instrument>) - Constructor for class com.genologics.ri.process.InstrumentLink
InstrumentLink(Linkable<Instrument>) - Constructor for class com.genologics.ri.processexecution.InstrumentLink
InstrumentLink(Linkable<Instrument>) - Constructor for class com.genologics.ri.processtemplate.InstrumentLink
InstrumentLink(Linkable<Instrument>) - Constructor for class com.genologics.ri.step.InstrumentLink
InstrumentLink(URI) - Constructor for class com.genologics.ri.instrument.InstrumentLink
InstrumentLink(URI) - Constructor for class com.genologics.ri.process.InstrumentLink
InstrumentLink(URI) - Constructor for class com.genologics.ri.processexecution.InstrumentLink
InstrumentLink(URI) - Constructor for class com.genologics.ri.processtemplate.InstrumentLink
InstrumentLink(URI) - Constructor for class com.genologics.ri.step.InstrumentLink
InstrumentLink(URI, String) - Constructor for class com.genologics.ri.instrument.InstrumentLink
InstrumentLink(URI, String) - Constructor for class com.genologics.ri.step.InstrumentLink
instruments - Variable in class com.genologics.ri.instrument.Instruments
Instruments - Class in com.genologics.ri.instrument: The representation of a list of instrument links.
Instruments() - Constructor for class com.genologics.ri.instrument.Instruments
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
InstrumentType(URI) - Constructor for class com.genologics.ri.instrumenttype.InstrumentType
InstrumentType(URI, String) - Constructor for class com.genologics.ri.instrumenttype.InstrumentType
InstrumentTypeLink - Class in com.genologics.ri.instrumenttype
InstrumentTypeLink() - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypeLink
InstrumentTypeLink(URI) - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypeLink
InstrumentTypeLink(URI, String) - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypeLink
InstrumentTypeProcessType - Class in com.genologics.ri.instrumenttype
InstrumentTypeProcessType() - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypeProcessType
InstrumentTypeProcessType(URI) - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypeProcessType
InstrumentTypeProcessType(URI, String) - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypeProcessType
instrumentTypes - Variable in class com.genologics.ri.instrumenttype.InstrumentTypes
InstrumentTypes - Class in com.genologics.ri.instrumenttype
InstrumentTypes() - Constructor for class com.genologics.ri.instrumenttype.InstrumentTypes
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.
InvocationType - Enum in com.genologics.ri.processtype
invoiceDate - Variable in class com.genologics.ri.project.Project
isAccountLocked() - Method in class com.genologics.ri.researcher.Credentials
isAllowNonPresetValues() - Method in class com.genologics.ri.configuration.Field
isAlpha() - Method in class com.genologics.ri.containertype.Dimension
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
isControlSample() - Method in class com.genologics.ri.sample.SampleBase
isDefault() - Method in class com.genologics.ri.processtemplate.ProcessTemplate
isDeviation() - Method in class com.genologics.ri.configuration.Field
isEditable() - Method in class com.genologics.ri.configuration.Field
isEnabled() - Method in class com.genologics.ri.stepconfiguration.StepSetup
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
isLocked() - Method in class com.genologics.ri.stepconfiguration.LockableSetting
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.
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
isRunProgramPerEvent() - Method in class com.genologics.ri.automation.Automation
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
isShowInLablink() - Method in class com.genologics.ri.configuration.Field
isShowInTables() - Method in class com.genologics.ri.configuration.Field
isSingleton() - Method in class org.cruk.clarity.api.cache.EhCacheManagerFactory
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
isWorkingFlag() - Method in class com.genologics.ri.artifact.Artifact
iterator() - Method in class com.genologics.ri.artifact.ArtifactBatchFetchResult
iterator() - Method in class com.genologics.ri.artifact.Artifacts
iterator() - Method in class com.genologics.ri.artifactgroup.ArtifactGroups
iterator() - Method in class com.genologics.ri.automation.Automations
iterator() - Method in class com.genologics.ri.configuration.Type
iterator() - Method in class com.genologics.ri.configuration.Udfs
iterator() - Method in class com.genologics.ri.configuration.Udts
iterator() - Method in class com.genologics.ri.container.ContainerBatchFetchResult
iterator() - Method in class com.genologics.ri.container.Containers
iterator() - Method in class com.genologics.ri.containertype.ContainerTypes
iterator() - Method in class com.genologics.ri.controltype.ControlTypes
iterator() - Method in class com.genologics.ri.file.ClarityFileBatchFetchResult
iterator() - Method in class com.genologics.ri.file.ClarityFiles
iterator() - Method in class com.genologics.ri.Index
iterator() - Method in class com.genologics.ri.instrument.Instruments
iterator() - Method in class com.genologics.ri.instrumenttype.InstrumentTypes
iterator() - Method in class com.genologics.ri.lab.Labs
iterator() - Method in class com.genologics.ri.Links
iterator() - Method in class com.genologics.ri.permission.Permissions
iterator() - Method in class com.genologics.ri.process.ClarityProcesses
iterator() - Method in class com.genologics.ri.processtemplate.ProcessTemplates
iterator() - Method in class com.genologics.ri.processtype.ProcessTypes
iterator() - Method in class com.genologics.ri.project.Projects
iterator() - Method in class com.genologics.ri.property.Properties
iterator() - Method in class com.genologics.ri.protocolconfiguration.Protocols
iterator() - Method in class com.genologics.ri.queue.Queue
iterator() - Method in class com.genologics.ri.reagentkit.ReagentKits
iterator() - Method in class com.genologics.ri.reagentlot.ReagentLots
iterator() - Method in class com.genologics.ri.reagenttype.ReagentTypes
iterator() - Method in class com.genologics.ri.researcher.Researchers
iterator() - Method in class com.genologics.ri.role.Roles
iterator() - Method in class com.genologics.ri.sample.SampleBatchFetchResult
iterator() - Method in class com.genologics.ri.sample.Samples
iterator() - Method in class com.genologics.ri.version.Versions
iterator() - Method in class com.genologics.ri.workflowconfiguration.Workflows

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
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
Lab - Class in com.genologics.ri.lab: The detailed representation of a lab.
Lab() - Constructor for class com.genologics.ri.lab.Lab
Lab(URI) - Constructor for class com.genologics.ri.lab.Lab
Lab(URI, String) - Constructor for class com.genologics.ri.lab.Lab
LAB_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
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
LabLink() - Constructor for class com.genologics.ri.researcher.LabLink
LabLink(Linkable<Lab>) - Constructor for class com.genologics.ri.lab.LabLink
LabLink(Linkable<Lab>) - Constructor for class com.genologics.ri.researcher.LabLink
LabLink(URI) - Constructor for class com.genologics.ri.lab.LabLink
LabLink(URI) - Constructor for class com.genologics.ri.researcher.LabLink
LabLink(URI, String) - Constructor for class com.genologics.ri.lab.LabLink
LABLINK_ROLE - Static variable in class com.genologics.ri.researcher.Role
labs - Variable in class com.genologics.ri.lab.Labs
Labs - Class in com.genologics.ri.lab: The representation of a list of lab links.
Labs() - Constructor for class com.genologics.ri.lab.Labs
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
lastModifiedDate - Variable in class com.genologics.ri.reagentlot.ReagentLot
lastName - Variable in class com.genologics.ri.process.Technician
lastName - Variable in class com.genologics.ri.processtemplate.Technician
lastName - Variable in class com.genologics.ri.researcher.Researcher
lastName - Variable in class com.genologics.ri.researcher.ResearcherLink
lastName - Variable in class com.genologics.ri.role.ResearcherLink
lastName - Variable in class com.genologics.ri.sample.Submitter
lastName - Variable in class com.genologics.ri.step.UserLink
LATEST - Enum constant in enum 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 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.
LEAVE - Enum constant in enum com.genologics.ri.step.ActionType
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).
limsid - Variable in class com.genologics.ri.artifact.Artifact
limsid - Variable in class com.genologics.ri.artifact.ArtifactLink
limsid - Variable in class com.genologics.ri.artifact.DemuxArtifactSample
limsid - Variable in class com.genologics.ri.artifact.ParentProcessLink
limsid - Variable in class com.genologics.ri.artifact.SampleLink
limsid - Variable in class com.genologics.ri.container.Container
limsid - Variable in class com.genologics.ri.container.ContainerLink
limsid - Variable in class com.genologics.ri.container.Placement
limsid - Variable in class com.genologics.ri.ContainerLink
limsid - Variable in class com.genologics.ri.file.ClarityFile
limsid - Variable in class com.genologics.ri.file.FileLink
limsid - Variable in class com.genologics.ri.instrument.Instrument
limsid - Variable in class com.genologics.ri.process.ArtifactLink
limsid - Variable in class com.genologics.ri.process.ClarityProcess
limsid - Variable in class com.genologics.ri.process.ParentProcessLink
limsid - Variable in class com.genologics.ri.process.ProcessLink
limsid - Variable in class com.genologics.ri.project.Project
limsid - Variable in class com.genologics.ri.project.ProjectLink
limsid - Variable in class com.genologics.ri.queue.ArtifactLink
limsid - Variable in class com.genologics.ri.reagentlot.ReagentLot
limsid - Variable in class com.genologics.ri.reagentlot.ReagentLotLink
limsid - Variable in class com.genologics.ri.sample.ArtifactLink
limsid - Variable in class com.genologics.ri.sample.ProjectLink
limsid - Variable in class com.genologics.ri.sample.SampleBase
limsid - Variable in class com.genologics.ri.sample.SampleLink
limsid - Variable in class com.genologics.ri.step.ArtifactLink
limsid - Variable in class com.genologics.ri.step.ProcessStep
limsid - Variable in class com.genologics.ri.step.ReagentLotLink
limsid - Variable in class com.genologics.ri.step.SharedResultFile
limsIdFromUri(Locatable) - Static method in class com.genologics.ri.Link: Extract the LIMS identifier from the URI of a Locatable object.
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.
Link - Class in com.genologics.ri: A link provides a URI linking to an additional resource.
Link() - Constructor for class com.genologics.ri.Link
Link(Linkable<?>) - Constructor for class com.genologics.ri.Link
Link(String) - Constructor for class com.genologics.ri.Link
Link(String, URI) - Constructor for class com.genologics.ri.Link
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
links - Variable in class com.genologics.ri.Index
Links - Class in com.genologics.ri: The representation of a list of resource links.
Links() - Constructor for class com.genologics.ri.Links
Links(int) - Constructor for class com.genologics.ri.Links
Links(Links) - Constructor for class com.genologics.ri.Links
Links(Collection<Link>) - Constructor for class com.genologics.ri.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
location - Variable in class com.genologics.ri.processexecution.Output
location - Variable in class com.genologics.ri.queue.ArtifactLink
location - Variable in class com.genologics.ri.sample.SampleCreation
location - Variable in class com.genologics.ri.step.OutputPlacement
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
Location(LimsEntityLinkable<Container>, String) - Constructor for class com.genologics.ri.Location
Location(Linkable<Container>, String) - Constructor for class com.genologics.ri.Location
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
locked - Variable in class com.genologics.ri.stepconfiguration.GenericTypeLink
locked - Variable in class com.genologics.ri.stepconfiguration.LockableSetting
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.cache.EhCacheManagerFactory
logger - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl: Logger.
LongTimestampAdapter - Class in org.cruk.clarity.api.jaxb: Adapter for those dates that are exchanged with the API in the long timestamp format.
LongTimestampAdapter() - Constructor for class org.cruk.clarity.api.jaxb.LongTimestampAdapter: Empty constructor.
lotNumber - Variable in class com.genologics.ri.reagentlot.ReagentLot

M

major - Variable in class com.genologics.ri.version.Version
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 com.genologics.ri.processtype.TriggerType
MANUAL - Enum constant in enum com.genologics.ri.stepconfiguration.TriggerType
marshal(Object) - Method in class org.cruk.clarity.api.jaxb.JaxbMarshallingTool: Marshals the object into a string of XML.
marshal(URI) - Method in class org.cruk.clarity.api.jaxb.URIAdapter: Convert the given URI into its string format.
marshal(Date) - Method in class org.cruk.clarity.api.jaxb.AbstractDateAdapter: Convert the given date into the expected date format.
maxValue - Variable in class com.genologics.ri.configuration.Field
message - Variable in class com.genologics.ri.exception.Exception
message - Variable in class com.genologics.ri.processtype.SharedResultFile
message - Variable in class com.genologics.ri.step.ProgramStatus
message - Variable in class com.genologics.ri.step.SharedResultFile
message - Variable in class com.genologics.ri.stepconfiguration.SharedResultFile
minor - Variable in class com.genologics.ri.version.Version
minValue - Variable in class com.genologics.ri.configuration.Field
MissingUDFException - Exception in com.genologics.ri.userdefined
MissingUDFException(String) - Constructor for exception com.genologics.ri.userdefined.MissingUDFException
MissingUDFException(String, String) - Constructor for exception com.genologics.ri.userdefined.MissingUDFException

N

name - Variable in class com.genologics.ri.artifact.Artifact
name - Variable in class com.genologics.ri.artifact.ArtifactGroupLink
name - Variable in class com.genologics.ri.artifact.DemuxArtifact
name - Variable in class com.genologics.ri.artifact.DemuxSourceArtifact
name - Variable in class com.genologics.ri.artifact.PoolStep
name - Variable in class com.genologics.ri.artifact.ReagentLabel
name - Variable in class com.genologics.ri.artifact.WorkflowStage
name - Variable in class com.genologics.ri.artifactgroup.ArtifactGroup
name - Variable in class com.genologics.ri.artifactgroup.ArtifactGroupLink
name - Variable in class com.genologics.ri.automation.Automation
name - Variable in class com.genologics.ri.automation.AutomationLink
name - Variable in class com.genologics.ri.automation.ProcessTypeLink
name - Variable in class com.genologics.ri.configuration.Field
name - Variable in class com.genologics.ri.configuration.FieldLink
name - Variable in class com.genologics.ri.configuration.Type
name - Variable in class com.genologics.ri.configuration.TypeDefinition
name - Variable in class com.genologics.ri.configuration.UdfConfigLink
name - Variable in class com.genologics.ri.configuration.UdtConfigLink
name - Variable in class com.genologics.ri.container.Container
name - Variable in class com.genologics.ri.container.ContainerLink
name - Variable in class com.genologics.ri.container.ContainerTypeLink
name - Variable in class com.genologics.ri.containertype.CalibrantWell: Deprecated.
name - Variable in class com.genologics.ri.containertype.ContainerType
name - Variable in class com.genologics.ri.containertype.ContainerTypeLink
name - Variable in class com.genologics.ri.controltype.ControlType
name - Variable in class com.genologics.ri.controltype.ControlTypeLink
name - Variable in class com.genologics.ri.instrument.Instrument
name - Variable in class com.genologics.ri.instrument.InstrumentLink
name - Variable in class com.genologics.ri.instrumenttype.InstrumentType
name - Variable in class com.genologics.ri.instrumenttype.InstrumentTypeLink
name - Variable in class com.genologics.ri.instrumenttype.InstrumentTypeProcessType
name - Variable in class com.genologics.ri.lab.Lab
name - Variable in class com.genologics.ri.lab.LabLink
name - Variable in class com.genologics.ri.permission.Permission
name - Variable in class com.genologics.ri.permission.PermissionLink
name - Variable in class com.genologics.ri.process.Parameter
name - Variable in class com.genologics.ri.process.ProcessTypeLink
name - Variable in class com.genologics.ri.processexecution.Parameter
name - Variable in class com.genologics.ri.processtemplate.Parameter
name - Variable in class com.genologics.ri.processtemplate.ProcessTemplate
name - Variable in class com.genologics.ri.processtemplate.ProcessTemplateLink
name - Variable in class com.genologics.ri.processtemplate.ProcessTypeLink
name - Variable in class com.genologics.ri.processtype.ContainerTypeLink
name - Variable in class com.genologics.ri.processtype.ControlTypeLink
name - Variable in class com.genologics.ri.processtype.EppTrigger
name - Variable in class com.genologics.ri.processtype.Field
name - Variable in class com.genologics.ri.processtype.Parameter
name - Variable in class com.genologics.ri.processtype.ProcessType
name - Variable in class com.genologics.ri.processtype.ProcessTypeAttribute
name - Variable in class com.genologics.ri.processtype.ProcessTypeLink
name - Variable in class com.genologics.ri.processtype.ReagentKitLink
name - Variable in class com.genologics.ri.processtype.StepProperty
name - Variable in class com.genologics.ri.processtype.TypeDefinition
name - Variable in class com.genologics.ri.project.Project
name - Variable in class com.genologics.ri.project.ProjectLink
name - Variable in class com.genologics.ri.property.PropertyLink
name - Variable in class com.genologics.ri.protocolconfiguration.Protocol
name - Variable in class com.genologics.ri.protocolconfiguration.ProtocolLink
name - Variable in class com.genologics.ri.protocolconfiguration.ProtocolProperty
name - Variable in class com.genologics.ri.queue.Queue
name - Variable in class com.genologics.ri.reagentkit.ReagentKit
name - Variable in class com.genologics.ri.reagentkit.ReagentKitLink
name - Variable in class com.genologics.ri.reagentlot.ReagentKitLink
name - Variable in class com.genologics.ri.reagentlot.ReagentLot
name - Variable in class com.genologics.ri.reagentlot.ReagentLotLink: The name of the Reagent Lot.
name - Variable in class com.genologics.ri.reagenttype.Attribute
name - Variable in class com.genologics.ri.reagenttype.ReagentType
name - Variable in class com.genologics.ri.reagenttype.ReagentTypeLink
name - Variable in class com.genologics.ri.reagenttype.SpecialType
name - Variable in class com.genologics.ri.researcher.Role
name - Variable in class com.genologics.ri.role.PermissionLink
name - Variable in class com.genologics.ri.role.Role
name - Variable in class com.genologics.ri.role.RoleLink
name - Variable in class com.genologics.ri.sample.BioSource: Deprecated.
name - Variable in class com.genologics.ri.sample.ControlTypeLink
name - Variable in class com.genologics.ri.sample.SampleBase
name - Variable in class com.genologics.ri.stage.Stage
name - Variable in class com.genologics.ri.step.AvailableProgram
name - Variable in class com.genologics.ri.step.InstrumentLink
name - Variable in class com.genologics.ri.step.PooledInputs
name - Variable in class com.genologics.ri.step.ReagentLabel
name - Variable in class com.genologics.ri.step.SharedResultFile
name - Variable in class com.genologics.ri.stepconfiguration.ControlTypeLink
name - Variable in class com.genologics.ri.stepconfiguration.EppTrigger
name - Variable in class com.genologics.ri.stepconfiguration.Field
name - Variable in class com.genologics.ri.stepconfiguration.NextStep
name - Variable in class com.genologics.ri.stepconfiguration.ProcessTypeLink
name - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep
name - Variable in class com.genologics.ri.stepconfiguration.ReagentKitLink
name - Variable in class com.genologics.ri.stepconfiguration.StepProperty
name - Variable in class com.genologics.ri.userdefined.UDF
name - Variable in class com.genologics.ri.userdefined.UDT
name - Variable in class com.genologics.ri.workflowconfiguration.ProtocolLink
name - Variable in class com.genologics.ri.workflowconfiguration.StageLink
name - Variable in class com.genologics.ri.workflowconfiguration.Workflow
name - Variable in class com.genologics.ri.workflowconfiguration.WorkflowLink
Namespaces - Class in com.genologics.ri: Static list of all the namespaces in the Genologics API.
Namespaces() - Constructor for class com.genologics.ri.Namespaces
NEW - Enum constant in enum com.genologics.ri.container.ContainerState: The container state when the container is newly created.
newInputOutputMap() - Method in class com.genologics.ri.processexecution.ExecutableProcess
NEXT_STEPS - Enum constant in enum 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
NextAction(Linkable<Artifact>) - Constructor for class com.genologics.ri.step.NextAction
NextAction(Linkable<Artifact>, ActionType) - Constructor for class com.genologics.ri.step.NextAction
NextAction(Linkable<Artifact>, ActionType, Linkable<ProtocolStep>) - Constructor for class com.genologics.ri.step.NextAction
NextAction(URI) - Constructor for class com.genologics.ri.step.NextAction
NextAction(URI, ActionType) - Constructor for class com.genologics.ri.step.NextAction
NextAction(URI, ActionType, Linkable<ProtocolStep>) - Constructor for class com.genologics.ri.step.NextAction
nextActions - Variable in class com.genologics.ri.step.Actions
nextCallCacheOverride(CacheStatefulBehaviour) - Method in interface org.cruk.clarity.api.ClarityAPI: Deprecated.
Calls through to ClarityAPI.overrideStateful(StatefulOverride) with a conversion of the behaviour value to StatefulOverride, so behaviour is maintained but one should update code to use overrideStateful.
nextCallCacheOverride(CacheStatefulBehaviour) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl: Deprecated.
nextPage - Variable in class com.genologics.ri.artifact.Artifacts
nextPage - Variable in class com.genologics.ri.artifactgroup.ArtifactGroups
nextPage - Variable in class com.genologics.ri.automation.Automations
nextPage - Variable in class com.genologics.ri.configuration.Udfs
nextPage - Variable in class com.genologics.ri.configuration.Udts
nextPage - Variable in class com.genologics.ri.container.Containers
nextPage - Variable in class com.genologics.ri.containertype.ContainerTypes
nextPage - Variable in class com.genologics.ri.file.ClarityFiles
nextPage - Variable in class com.genologics.ri.instrument.Instruments
nextPage - Variable in class com.genologics.ri.instrumenttype.InstrumentTypes
nextPage - Variable in class com.genologics.ri.lab.Labs
nextPage - Variable in class com.genologics.ri.process.ClarityProcesses
nextPage - Variable in class com.genologics.ri.processtemplate.ProcessTemplates
nextPage - Variable in class com.genologics.ri.processtype.ProcessTypes
nextPage - Variable in class com.genologics.ri.project.Projects
nextPage - Variable in class com.genologics.ri.property.Properties
nextPage - Variable in class com.genologics.ri.queue.Queue
nextPage - Variable in class com.genologics.ri.reagentkit.ReagentKits
nextPage - Variable in class com.genologics.ri.reagentlot.ReagentLots
nextPage - Variable in class com.genologics.ri.reagenttype.ReagentTypes
nextPage - Variable in class com.genologics.ri.researcher.Researchers
nextPage - Variable in class com.genologics.ri.sample.Samples
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
NEXTSTEP - Enum constant in enum com.genologics.ri.step.ActionType
nextStepUri - Variable in class com.genologics.ri.stepconfiguration.NextStep
notes - Variable in class com.genologics.ri.reagentlot.ReagentLot
numberOfOutputs - Variable in class com.genologics.ri.processtype.ProcessOutput
NUMERIC - Enum constant in enum com.genologics.ri.configuration.FieldType

O

ObjectFactory - Class in com.genologics.ri.artifact: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.artifact package.
ObjectFactory - Class in com.genologics.ri.artifactgroup: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.artifactgroup package.
ObjectFactory - Class in com.genologics.ri.automation: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.automation package.
ObjectFactory - Class in com.genologics.ri.configuration: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.configuration package.
ObjectFactory - Class in com.genologics.ri.container: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.container package.
ObjectFactory - Class in com.genologics.ri.containertype: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.containertype package.
ObjectFactory - Class in com.genologics.ri.controltype: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.controltype package.
ObjectFactory - Class in com.genologics.ri.exception: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.exception package.
ObjectFactory - Class in com.genologics.ri.file: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.file package.
ObjectFactory - Class in com.genologics.ri.instrument: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.instrument package.
ObjectFactory - Class in com.genologics.ri.instrumenttype: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.instrumenttype package.
ObjectFactory - Class in com.genologics.ri.lab: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.lab package.
ObjectFactory - Class in com.genologics.ri: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri package.
ObjectFactory - Class in com.genologics.ri.permission: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.permission package.
ObjectFactory - Class in com.genologics.ri.process: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.process package.
ObjectFactory - Class in com.genologics.ri.processexecution: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.processexecution package.
ObjectFactory - Class in com.genologics.ri.processtemplate: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.processtemplate package.
ObjectFactory - Class in com.genologics.ri.processtype: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.processtype package.
ObjectFactory - Class in com.genologics.ri.project: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.project package.
ObjectFactory - Class in com.genologics.ri.property: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.property package.
ObjectFactory - Class in com.genologics.ri.protocolconfiguration: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.protocolconfiguration package.
ObjectFactory - Class in com.genologics.ri.queue: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.queue package.
ObjectFactory - Class in com.genologics.ri.reagentkit: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.reagentkit package.
ObjectFactory - Class in com.genologics.ri.reagentlot: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.reagentlot package.
ObjectFactory - Class in com.genologics.ri.reagenttype: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.reagenttype package.
ObjectFactory - Class in com.genologics.ri.researcher: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.researcher package.
ObjectFactory - Class in com.genologics.ri.role: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.role package.
ObjectFactory - Class in com.genologics.ri.routing: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.routing package.
ObjectFactory - Class in com.genologics.ri.sample: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.sample package.
ObjectFactory - Class in com.genologics.ri.stage: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.stage package.
ObjectFactory - Class in com.genologics.ri.step: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.step package.
ObjectFactory - Class in com.genologics.ri.stepconfiguration: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.stepconfiguration package.
ObjectFactory - Class in com.genologics.ri.userdefined: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.userdefined package.
ObjectFactory - Class in com.genologics.ri.version: This object contains factory methods for each Java content interface and Java element interface generated in the com.genologics.ri.version package.
ObjectFactory - Class in com.genologics.ri.workflowconfiguration: This object contains factory methods for each Java content interface and Java element interface generated 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
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: Create 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: Create 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: Create 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.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: Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: com.genologics.ri
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: Create 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.stage.ObjectFactory: Create 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: Create 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
offset - Variable in class com.genologics.ri.containertype.Dimension
OK - Enum constant in enum com.genologics.ri.step.Status
openDate - Variable in class com.genologics.ri.project.Project
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 - 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.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.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.
originalLocation - Variable in class com.genologics.ri.file.ClarityFile
originalName - Variable in class com.genologics.ri.file.ClarityFile
output - Variable in class com.genologics.ri.process.InputOutputMap
output - Variable in class com.genologics.ri.processexecution.ExecutableInputOutputMap
output - Variable in class com.genologics.ri.step.InputOutputMap
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
Output() - Constructor for class com.genologics.ri.step.Output
Output(OutputType) - Constructor for class com.genologics.ri.processexecution.Output
Output(OutputType, LimsEntityLinkable<Container>, String) - Constructor for class com.genologics.ri.processexecution.Output
outputGenerationType - Variable in class com.genologics.ri.process.ArtifactLink
outputGenerationType - Variable in class com.genologics.ri.processtype.ProcessOutput
outputGenerationType - Variable in class com.genologics.ri.step.ArtifactLink
OutputGenerationType - Enum in com.genologics.ri.process
OutputGenerationType - Enum in com.genologics.ri.processtype
OutputGenerationType - Enum in com.genologics.ri.step
outputName - Variable in class com.genologics.ri.processtype.ProcessOutput
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
OutputPlacement(Linkable<Artifact>) - Constructor for class com.genologics.ri.step.OutputPlacement
OutputPlacement(Linkable<Artifact>, LimsEntityLinkable<Container>, String) - Constructor for class com.genologics.ri.step.OutputPlacement
OutputPlacement(Linkable<Artifact>, Linkable<Container>, String) - Constructor for class com.genologics.ri.step.OutputPlacement
outputPlacements - Variable in class com.genologics.ri.step.Placements
outputReagents - Variable in class com.genologics.ri.step.Reagents
outputType - Variable in class com.genologics.ri.artifact.Artifact
outputType - Variable in class com.genologics.ri.process.ArtifactLink
OutputType - Enum in com.genologics.ri.artifact
outputUri - Variable in class com.genologics.ri.step.PooledInputs
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
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
parameter - Variable in class com.genologics.ri.processexecution.ExecutableProcess
parameter - Variable in class com.genologics.ri.processtemplate.ProcessTemplate
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
Parameter() - Constructor for class com.genologics.ri.processexecution.Parameter
Parameter() - Constructor for class com.genologics.ri.processtemplate.Parameter
Parameter() - Constructor for class com.genologics.ri.processtype.Parameter
Parameter(String) - Constructor for class com.genologics.ri.process.Parameter
Parameter(String) - Constructor for class com.genologics.ri.processexecution.Parameter
Parameter(String) - Constructor for class com.genologics.ri.processtemplate.Parameter
parameters - Variable in class com.genologics.ri.processtype.ProcessType
parentProcess - Variable in class com.genologics.ri.artifact.Artifact
parentProcess - Variable in class com.genologics.ri.process.ArtifactLink
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
ParentProcessLink() - Constructor for class com.genologics.ri.process.ParentProcessLink
ParentProcessLink(LimsEntityLinkable<ClarityProcess>) - Constructor for class com.genologics.ri.artifact.ParentProcessLink
ParentProcessLink(LimsEntityLinkable<ClarityProcess>) - Constructor for class com.genologics.ri.process.ParentProcessLink
ParentProcessLink(URI) - Constructor for class com.genologics.ri.artifact.ParentProcessLink
ParentProcessLink(URI) - Constructor for class com.genologics.ri.process.ParentProcessLink
ParentProcessLink(URI, String) - Constructor for class com.genologics.ri.artifact.ParentProcessLink
ParentProcessLink(URI, String) - Constructor for class com.genologics.ri.process.ParentProcessLink
parentUri - Variable in class com.genologics.ri.configuration.Field
PASSED - Enum constant in enum com.genologics.ri.artifact.QCFlag
PASSED - Enum constant in enum com.genologics.ri.processexecution.QCFlag
password - Variable in class com.genologics.ri.researcher.Credentials
PENDING - Enum constant in enum com.genologics.ri.reagentlot.Status
PENDING - Enum constant in enum com.genologics.ri.workflowconfiguration.Status
PER_ALL_INPUTS - Enum constant in enum com.genologics.ri.process.OutputGenerationType
PER_ALL_INPUTS - Enum constant in enum com.genologics.ri.processtype.OutputGenerationType
PER_ALL_INPUTS - Enum constant in enum com.genologics.ri.step.OutputGenerationType
PER_INPUT - Enum constant in enum com.genologics.ri.process.OutputGenerationType
PER_INPUT - Enum constant in enum com.genologics.ri.processtype.OutputGenerationType
PER_INPUT - Enum constant in enum com.genologics.ri.step.OutputGenerationType
PER_REAGENT_LABEL - Enum constant in enum com.genologics.ri.process.OutputGenerationType
PER_REAGENT_LABEL - Enum constant in enum com.genologics.ri.processtype.OutputGenerationType
PER_REAGENT_LABEL - Enum constant in enum com.genologics.ri.step.OutputGenerationType
Permission - Class in com.genologics.ri.permission
Permission() - Constructor for class com.genologics.ri.permission.Permission
Permission(URI) - Constructor for class com.genologics.ri.permission.Permission
Permission(URI, String) - Constructor for class com.genologics.ri.permission.Permission
PERMISSION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
PermissionLink - Class in com.genologics.ri.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
PermissionLink() - Constructor for class com.genologics.ri.role.PermissionLink
PermissionLink(URI) - Constructor for class com.genologics.ri.permission.PermissionLink
PermissionLink(URI) - Constructor for class com.genologics.ri.role.PermissionLink
PermissionLink(URI, String) - Constructor for class com.genologics.ri.role.PermissionLink
permissions - Variable in class com.genologics.ri.permission.Permissions
permissions - Variable in class com.genologics.ri.role.Role
Permissions - Class in com.genologics.ri.permission
Permissions() - Constructor for class com.genologics.ri.permission.Permissions
Permissions(String) - Constructor for class com.genologics.ri.permission.Permissions
permittedContainers - Variable in class com.genologics.ri.processtype.ProcessType
permittedContainerTypes - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep
permittedControlTypes - Variable in class com.genologics.ri.processtype.ProcessType
permittedControlTypes - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep
permittedInstrumentTypes - Variable in class com.genologics.ri.processtype.ProcessType
permittedInstrumentTypes - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep
permittedReagentCategories - Variable in class com.genologics.ri.processtype.ProcessType
permittedReagentCategories - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep
phone - Variable in class com.genologics.ri.researcher.Researcher
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
Placement(LimsEntityLinkable<Artifact>) - Constructor for class com.genologics.ri.container.Placement
Placement(LimsEntityLinkable<Artifact>, String) - Constructor for class com.genologics.ri.container.Placement
Placement(URI) - Constructor for class com.genologics.ri.container.Placement
Placement(URI, String) - Constructor for class com.genologics.ri.container.Placement
Placement(URI, String, String) - Constructor for class com.genologics.ri.container.Placement
PLACEMENT - Enum constant in enum com.genologics.ri.processtype.TriggerStatus
PLACEMENT - Enum constant in enum com.genologics.ri.step.ProcessState: The step state when the step is in the sample placement stage.
PLACEMENT - Enum constant in enum com.genologics.ri.stepconfiguration.TriggerStatus
placements - Variable in class com.genologics.ri.container.Container
placements - Variable in class com.genologics.ri.step.ProcessStep
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
Placements(URI) - Constructor for class com.genologics.ri.step.Placements
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
PlacementsLink(Linkable<Placements>) - Constructor for class com.genologics.ri.step.PlacementsLink
PlacementsLink(URI) - Constructor for class com.genologics.ri.step.PlacementsLink
point - Variable in class com.genologics.ri.processtype.EppTrigger
point - Variable in class com.genologics.ri.stepconfiguration.EppTrigger
pooledInputs - Variable in class com.genologics.ri.step.Pools
PooledInputs - Class in com.genologics.ri.step: Provides pooled input groups.
PooledInputs() - Constructor for class com.genologics.ri.step.PooledInputs
PooledInputs(Collection<? extends Linkable<Artifact>>, String) - Constructor for class com.genologics.ri.step.PooledInputs
PooledInputs(Collection<? extends Linkable<Artifact>>, String, Linkable<Artifact>) - Constructor for class com.genologics.ri.step.PooledInputs
POOLING - Enum constant in enum com.genologics.ri.processtype.TriggerStatus
POOLING - Enum constant in enum com.genologics.ri.step.ProcessState: The step state when the step is in the pooling stage.
POOLING - Enum constant in enum com.genologics.ri.stepconfiguration.TriggerStatus
pools - Variable in class com.genologics.ri.step.ProcessStep
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
Pools(URI) - Constructor for class com.genologics.ri.step.Pools
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
PoolsLink(Linkable<Pools>) - Constructor for class com.genologics.ri.step.PoolsLink
PoolsLink(URI) - Constructor for class com.genologics.ri.step.PoolsLink
poolStep - Variable in class com.genologics.ri.artifact.DemuxDetails
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
PoolStep(URI) - Constructor for class com.genologics.ri.artifact.PoolStep
PoolStep(URI, String) - Constructor for class com.genologics.ri.artifact.PoolStep
POPULATED - Enum constant in enum com.genologics.ri.container.ContainerState: The container state when the container has something in it.
POST_PROCESS - Enum constant in enum com.genologics.ri.processtype.InvocationType
postalCode - Variable in class com.genologics.ri.Address
postProcessUri - Variable in class com.genologics.ri.process.ArtifactLink
PRE_PROCESS - Enum constant in enum com.genologics.ri.processtype.InvocationType
precision - Variable in class com.genologics.ri.configuration.Field
preset - Variable in class com.genologics.ri.step.StepDetails
presets - Variable in class com.genologics.ri.configuration.Field
previousPage - Variable in class com.genologics.ri.artifact.Artifacts
previousPage - Variable in class com.genologics.ri.artifactgroup.ArtifactGroups
previousPage - Variable in class com.genologics.ri.automation.Automations
previousPage - Variable in class com.genologics.ri.configuration.Udfs
previousPage - Variable in class com.genologics.ri.configuration.Udts
previousPage - Variable in class com.genologics.ri.container.Containers
previousPage - Variable in class com.genologics.ri.containertype.ContainerTypes
previousPage - Variable in class com.genologics.ri.file.ClarityFiles
previousPage - Variable in class com.genologics.ri.instrument.Instruments
previousPage - Variable in class com.genologics.ri.instrumenttype.InstrumentTypes
previousPage - Variable in class com.genologics.ri.lab.Labs
previousPage - Variable in class com.genologics.ri.process.ClarityProcesses
previousPage - Variable in class com.genologics.ri.processtemplate.ProcessTemplates
previousPage - Variable in class com.genologics.ri.processtype.ProcessTypes
previousPage - Variable in class com.genologics.ri.project.Projects
previousPage - Variable in class com.genologics.ri.property.Properties
previousPage - Variable in class com.genologics.ri.queue.Queue
previousPage - Variable in class com.genologics.ri.reagentkit.ReagentKits
previousPage - Variable in class com.genologics.ri.reagentlot.ReagentLots
previousPage - Variable in class com.genologics.ri.reagenttype.ReagentTypes
previousPage - Variable in class com.genologics.ri.researcher.Researchers
previousPage - Variable in class com.genologics.ri.sample.Samples
primaryEntity() - Element in annotation type com.genologics.ri.ClarityEntity: Specifies the outer entity of the API for which the annotated class is the inner entity.
PROCESS_EXECUTION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
PROCESS_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
PROCESS_TEMPLATE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
PROCESS_TYPE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
processes - Variable in class com.genologics.ri.process.ClarityProcesses
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
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
ProcessLink(LimsEntityLinkable<ClarityProcess>) - Constructor for class com.genologics.ri.process.ProcessLink
ProcessLink(URI) - Constructor for class com.genologics.ri.process.ProcessLink
ProcessLink(URI, String) - Constructor for class com.genologics.ri.process.ProcessLink
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
ProcessState - Enum 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
ProcessStep(URI) - Constructor for class com.genologics.ri.step.ProcessStep
ProcessStep(URI, String) - Constructor for class com.genologics.ri.step.ProcessStep
ProcessTemplate - Class in com.genologics.ri.processtemplate: The detailed representation of a Process Template.
ProcessTemplate() - Constructor for class com.genologics.ri.processtemplate.ProcessTemplate
ProcessTemplate(URI) - Constructor for class com.genologics.ri.processtemplate.ProcessTemplate
ProcessTemplate(URI, String) - Constructor for class com.genologics.ri.processtemplate.ProcessTemplate
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
ProcessTemplateLink(Linkable<ProcessTemplate>) - Constructor for class com.genologics.ri.processtemplate.ProcessTemplateLink
ProcessTemplateLink(URI) - Constructor for class com.genologics.ri.processtemplate.ProcessTemplateLink
ProcessTemplateLink(URI, String) - Constructor for class com.genologics.ri.processtemplate.ProcessTemplateLink
processTemplates - Variable in class com.genologics.ri.processtemplate.ProcessTemplates
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
processType - Variable in class com.genologics.ri.process.ClarityProcess
processType - Variable in class com.genologics.ri.processexecution.ExecutableProcess
processType - Variable in class com.genologics.ri.processtemplate.ProcessTemplate
processType - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep
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
ProcessType(URI) - Constructor for class com.genologics.ri.processtype.ProcessType
ProcessType(URI, String) - Constructor for class com.genologics.ri.processtype.ProcessType
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
ProcessTypeAttribute(String) - Constructor for class com.genologics.ri.processtype.ProcessTypeAttribute
ProcessTypeAttribute(String, String) - Constructor for class com.genologics.ri.processtype.ProcessTypeAttribute
processTypeAttributes - Variable in class com.genologics.ri.processtype.ProcessType
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
ProcessTypeLink() - Constructor for class com.genologics.ri.process.ProcessTypeLink
ProcessTypeLink() - Constructor for class com.genologics.ri.processtemplate.ProcessTypeLink
ProcessTypeLink() - Constructor for class com.genologics.ri.processtype.ProcessTypeLink
ProcessTypeLink() - Constructor for class com.genologics.ri.stepconfiguration.ProcessTypeLink
ProcessTypeLink(Linkable<ProcessType>) - Constructor for class com.genologics.ri.process.ProcessTypeLink
ProcessTypeLink(Linkable<ProcessType>) - Constructor for class com.genologics.ri.processtemplate.ProcessTypeLink
ProcessTypeLink(Linkable<ProcessType>) - Constructor for class com.genologics.ri.processtype.ProcessTypeLink
ProcessTypeLink(Linkable<ProcessType>) - Constructor for class com.genologics.ri.stepconfiguration.ProcessTypeLink
ProcessTypeLink(ProcessType) - Constructor for class com.genologics.ri.process.ProcessTypeLink
ProcessTypeLink(URI) - Constructor for class com.genologics.ri.automation.ProcessTypeLink
ProcessTypeLink(URI) - Constructor for class com.genologics.ri.process.ProcessTypeLink
ProcessTypeLink(URI) - Constructor for class com.genologics.ri.processtemplate.ProcessTypeLink
ProcessTypeLink(URI) - Constructor for class com.genologics.ri.processtype.ProcessTypeLink
ProcessTypeLink(URI) - Constructor for class com.genologics.ri.stepconfiguration.ProcessTypeLink
ProcessTypeLink(URI, String) - Constructor for class com.genologics.ri.automation.ProcessTypeLink
ProcessTypeLink(URI, String) - Constructor for class com.genologics.ri.process.ProcessTypeLink
ProcessTypeLink(URI, String) - Constructor for class com.genologics.ri.processtemplate.ProcessTypeLink
ProcessTypeLink(URI, String) - Constructor for class com.genologics.ri.processtype.ProcessTypeLink
ProcessTypeLink(URI, String) - Constructor for class com.genologics.ri.stepconfiguration.ProcessTypeLink
processTypes - Variable in class com.genologics.ri.automation.Automation
processTypes - Variable in class com.genologics.ri.instrumenttype.InstrumentType
processTypes - Variable in class com.genologics.ri.processtype.ProcessTypes
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
programStatus - Variable in class com.genologics.ri.step.ProcessStep
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
ProgramStatus(URI) - Constructor for class com.genologics.ri.step.ProgramStatus
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
ProgramStatusLink(Linkable<ProgramStatus>) - Constructor for class com.genologics.ri.step.ProgramStatusLink
ProgramStatusLink(URI) - Constructor for class com.genologics.ri.step.ProgramStatusLink
project - Variable in class com.genologics.ri.sample.SampleBase
Project - Class in com.genologics.ri.project: The detailed representation of a Project.
Project() - Constructor for class com.genologics.ri.project.Project
Project(URI) - Constructor for class com.genologics.ri.project.Project
Project(URI, String) - Constructor for class com.genologics.ri.project.Project
PROJECT - Enum constant in enum com.genologics.ri.automation.Context
PROJECT_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
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
ProjectLink() - Constructor for class com.genologics.ri.sample.ProjectLink
ProjectLink(LimsEntityLinkable<Project>) - Constructor for class com.genologics.ri.project.ProjectLink
ProjectLink(LimsEntityLinkable<Project>) - Constructor for class com.genologics.ri.sample.ProjectLink
ProjectLink(URI) - Constructor for class com.genologics.ri.project.ProjectLink
ProjectLink(URI) - Constructor for class com.genologics.ri.sample.ProjectLink
ProjectLink(URI, String) - Constructor for class com.genologics.ri.project.ProjectLink
ProjectLink(URI, String) - Constructor for class com.genologics.ri.sample.ProjectLink
ProjectLink(URI, String, String) - Constructor for class com.genologics.ri.project.ProjectLink
projects - Variable in class com.genologics.ri.project.Projects
Projects - Class in com.genologics.ri.project: The representation of a list of project links.
Projects() - Constructor for class com.genologics.ri.project.Projects
properties - Variable in class com.genologics.ri.property.Properties
Properties - Class in com.genologics.ri.property: The representation for a list of property links.
Properties() - Constructor for class com.genologics.ri.property.Properties
PROPERTY_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
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
PropertyLink(URI) - Constructor for class com.genologics.ri.property.PropertyLink
PropertyLink(URI, String, String) - Constructor for class com.genologics.ri.property.PropertyLink
protocol - Variable in class com.genologics.ri.stage.Stage
Protocol - Class in com.genologics.ri.protocolconfiguration: Detailed representation of a protocol.
Protocol() - Constructor for class com.genologics.ri.protocolconfiguration.Protocol
Protocol(URI) - Constructor for class com.genologics.ri.protocolconfiguration.Protocol
Protocol(URI, String) - Constructor for class com.genologics.ri.protocolconfiguration.Protocol
Protocol(URI, String, Integer) - Constructor for class com.genologics.ri.protocolconfiguration.Protocol
PROTOCOL_CONFIGURATION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
ProtocolLink - Class in com.genologics.ri.protocolconfiguration
ProtocolLink - Class in com.genologics.ri.stage: Protocol link for the stage.
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
ProtocolLink() - Constructor for class com.genologics.ri.stage.ProtocolLink
ProtocolLink() - Constructor for class com.genologics.ri.workflowconfiguration.ProtocolLink
ProtocolLink(Linkable<Protocol>) - Constructor for class com.genologics.ri.protocolconfiguration.ProtocolLink
ProtocolLink(Linkable<Protocol>) - Constructor for class com.genologics.ri.stage.ProtocolLink
ProtocolLink(Linkable<Protocol>) - Constructor for class com.genologics.ri.workflowconfiguration.ProtocolLink
ProtocolLink(URI) - Constructor for class com.genologics.ri.protocolconfiguration.ProtocolLink
ProtocolLink(URI) - Constructor for class com.genologics.ri.stage.ProtocolLink
ProtocolLink(URI) - Constructor for class com.genologics.ri.workflowconfiguration.ProtocolLink
ProtocolLink(URI, String) - Constructor for class com.genologics.ri.protocolconfiguration.ProtocolLink
ProtocolLink(URI, String) - Constructor for class com.genologics.ri.workflowconfiguration.ProtocolLink
protocolName - Variable in class com.genologics.ri.process.ClarityProcess
protocolProperties - Variable in class com.genologics.ri.protocolconfiguration.Protocol
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
ProtocolProperty(String, String) - Constructor for class com.genologics.ri.protocolconfiguration.ProtocolProperty
protocols - Variable in class com.genologics.ri.protocolconfiguration.Protocols
protocols - Variable in class com.genologics.ri.workflowconfiguration.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
ProtocolStep - Class in com.genologics.ri.stepconfiguration: Detailed representation of a Step
ProtocolStep() - Constructor for class com.genologics.ri.stepconfiguration.ProtocolStep
ProtocolStep(URI) - Constructor for class com.genologics.ri.stepconfiguration.ProtocolStep
ProtocolStep(URI, String) - Constructor for class com.genologics.ri.stepconfiguration.ProtocolStep
protocolStepIndex - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep
ProtocolStepLink - Class in com.genologics.ri.stage: Protocol Step link for the stage.
ProtocolStepLink() - Constructor for class com.genologics.ri.stage.ProtocolStepLink
ProtocolStepLink(Linkable<ProtocolStep>) - Constructor for class com.genologics.ri.stage.ProtocolStepLink
ProtocolStepLink(URI) - Constructor for class com.genologics.ri.stage.ProtocolStepLink
protocolStepUri - Variable in class com.genologics.ri.queue.Queue
protocolStepUri - Variable in class com.genologics.ri.step.StepConfiguration
protocolUri - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep
published - Variable in class com.genologics.ri.file.ClarityFile

Q

qcFlag - Variable in class com.genologics.ri.artifact.Artifact
qcFlag - Variable in class com.genologics.ri.processexecution.ArtifactBase
QCFlag - Enum in com.genologics.ri.artifact
QCFlag - Enum in com.genologics.ri.processexecution
Queue - Class in com.genologics.ri.queue: The representation of a queue.
Queue() - Constructor for class com.genologics.ri.queue.Queue
Queue(URI) - Constructor for class com.genologics.ri.queue.Queue
Queue(URI, String) - Constructor for class com.genologics.ri.queue.Queue
QUEUE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
QUEUED - Enum constant in enum com.genologics.ri.artifact.Status
QUEUED - Enum constant in enum com.genologics.ri.step.Status
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
QueueField() - Constructor for class com.genologics.ri.stepconfiguration.QueueField
QueueField(String) - Constructor for class com.genologics.ri.stepconfiguration.QueueField
QueueField(String, String) - Constructor for class com.genologics.ri.stepconfiguration.QueueField
QueueField(String, String, Boolean) - Constructor for class com.genologics.ri.stepconfiguration.QueueField
queueFields - Variable in class com.genologics.ri.processtype.ProcessType: queueFields
queueFields - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep
queueTime - Variable in class com.genologics.ri.queue.ArtifactLink

R

REAGENT_KIT_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
REAGENT_LOT_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
REAGENT_ONLY - Enum constant in enum 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
reagentCategory - Variable in class com.genologics.ri.reagenttype.ReagentType
reagentCategory - Variable in class com.genologics.ri.step.Reagents
reagentCategory - Variable in class com.genologics.ri.step.StepCreation
reagentKit - Variable in class com.genologics.ri.reagentlot.ReagentLot
ReagentKit - Class in com.genologics.ri.reagentkit: The detailed representation of a reagent kit.
ReagentKit() - Constructor for class com.genologics.ri.reagentkit.ReagentKit
ReagentKit(URI) - Constructor for class com.genologics.ri.reagentkit.ReagentKit
ReagentKit(URI, String) - Constructor for class com.genologics.ri.reagentkit.ReagentKit
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
ReagentKitLink() - Constructor for class com.genologics.ri.reagentkit.ReagentKitLink
ReagentKitLink() - Constructor for class com.genologics.ri.reagentlot.ReagentKitLink
ReagentKitLink() - Constructor for class com.genologics.ri.stepconfiguration.ReagentKitLink
ReagentKitLink(Linkable<ReagentKit>) - Constructor for class com.genologics.ri.reagentkit.ReagentKitLink
ReagentKitLink(Linkable<ReagentKit>) - Constructor for class com.genologics.ri.reagentlot.ReagentKitLink
ReagentKitLink(Linkable<ReagentKit>) - Constructor for class com.genologics.ri.stepconfiguration.ReagentKitLink
ReagentKitLink(String) - Constructor for class com.genologics.ri.processtype.ReagentKitLink
ReagentKitLink(URI) - Constructor for class com.genologics.ri.reagentkit.ReagentKitLink
ReagentKitLink(URI) - Constructor for class com.genologics.ri.reagentlot.ReagentKitLink
ReagentKitLink(URI) - Constructor for class com.genologics.ri.stepconfiguration.ReagentKitLink
ReagentKitLink(URI, String) - Constructor for class com.genologics.ri.reagentkit.ReagentKitLink
ReagentKitLink(URI, String) - Constructor for class com.genologics.ri.reagentlot.ReagentKitLink
ReagentKitLink(URI, String) - Constructor for class com.genologics.ri.stepconfiguration.ReagentKitLink
reagentKits - Variable in class com.genologics.ri.reagentkit.ReagentKits
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
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
ReagentLabel() - Constructor for class com.genologics.ri.step.ReagentLabel
ReagentLabel(String) - Constructor for class com.genologics.ri.artifact.ReagentLabel
ReagentLabel(String) - Constructor for class com.genologics.ri.step.ReagentLabel
reagentLabels - Variable in class com.genologics.ri.artifact.Artifact
reagentLabels - Variable in class com.genologics.ri.artifact.DemuxArtifact
reagentLabels - Variable in class com.genologics.ri.step.Output
ReagentLot - Class in com.genologics.ri.reagentlot: The detailed representation of a Reagent Lot
ReagentLot() - Constructor for class com.genologics.ri.reagentlot.ReagentLot
ReagentLot(LimsEntityLinkable<ReagentLot>) - Constructor for class com.genologics.ri.reagentlot.ReagentLot
ReagentLot(URI) - Constructor for class com.genologics.ri.reagentlot.ReagentLot
ReagentLot(URI, String) - Constructor for class com.genologics.ri.reagentlot.ReagentLot
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
ReagentLotLink() - Constructor for class com.genologics.ri.step.ReagentLotLink
ReagentLotLink(LimsEntityLinkable<ReagentLot>) - Constructor for class com.genologics.ri.reagentlot.ReagentLotLink
ReagentLotLink(LimsEntityLinkable<ReagentLot>) - Constructor for class com.genologics.ri.step.ReagentLotLink
ReagentLotLink(URI) - Constructor for class com.genologics.ri.reagentlot.ReagentLotLink
ReagentLotLink(URI) - Constructor for class com.genologics.ri.step.ReagentLotLink
ReagentLotLink(URI, String) - Constructor for class com.genologics.ri.reagentlot.ReagentLotLink
ReagentLotLink(URI, String) - Constructor for class com.genologics.ri.step.ReagentLotLink
reagentLots - Variable in class com.genologics.ri.reagentlot.ReagentLots
reagentLots - Variable in class com.genologics.ri.step.ProcessStep
reagentLots - Variable in class com.genologics.ri.step.ReagentLots
ReagentLots - Class in com.genologics.ri.reagentlot: The representation of a list of Reagent Lots
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
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
ReagentLotsLink(Linkable<ReagentLots>) - Constructor for class com.genologics.ri.step.ReagentLotsLink
ReagentLotsLink(URI) - Constructor for class com.genologics.ri.step.ReagentLotsLink
reagents - Variable in class com.genologics.ri.step.ProcessStep
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
Reagents(URI) - Constructor for class com.genologics.ri.step.Reagents
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
ReagentsLink(Linkable<Reagents>) - Constructor for class com.genologics.ri.step.ReagentsLink
ReagentsLink(URI) - Constructor for class com.genologics.ri.step.ReagentsLink
ReagentType - Class in com.genologics.ri.reagenttype: The detailed representation of a reagent type.
ReagentType() - Constructor for class com.genologics.ri.reagenttype.ReagentType
ReagentType(URI) - Constructor for class com.genologics.ri.reagenttype.ReagentType
ReagentType(URI, String) - Constructor for class com.genologics.ri.reagenttype.ReagentType
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
ReagentTypeLink(Linkable<ReagentType>) - Constructor for class com.genologics.ri.reagenttype.ReagentTypeLink
ReagentTypeLink(URI) - Constructor for class com.genologics.ri.reagenttype.ReagentTypeLink
ReagentTypeLink(URI, String) - Constructor for class com.genologics.ri.reagenttype.ReagentTypeLink
reagentTypes - Variable in class com.genologics.ri.reagenttype.ReagentTypes
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
RECORD_DETAILS - Enum constant in enum com.genologics.ri.processtype.TriggerStatus
RECORD_DETAILS - Enum constant in enum com.genologics.ri.step.ProcessState: The step state when the step is in the record details stage.
RECORD_DETAILS - Enum constant in enum com.genologics.ri.stepconfiguration.TriggerStatus
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
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 type 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 com.genologics.ri.step.ActionType
REMOVED - Enum constant in enum com.genologics.ri.artifact.Status
removeStateParameter(String) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl: Strip the state parameter from a URI in string form.
removeStateParameter(String) - Static method in class org.cruk.clarity.api.jaxb.URIAdapter: Remove any "state=" parameter from the given URI.
removeStateParameter(URI) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl: Strip the state parameter from a URI.
removeStateParameter(URI) - Static method in class org.cruk.clarity.api.jaxb.URIAdapter: Remove any "state=" parameter from the given URI.
removeWorkingFlag - Variable in class com.genologics.ri.processtype.ProcessInput: Deprecated.
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 com.genologics.ri.step.ActionType
replicates - Variable in class com.genologics.ri.step.CreationInput
replicates - Variable in class com.genologics.ri.step.Input
request - Variable in class com.genologics.ri.step.Escalation
required - Variable in class com.genologics.ri.configuration.Field
requiredReagentKits - Variable in class com.genologics.ri.processtype.ProcessType
requiredReagentKits - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep
researcher - Variable in class com.genologics.ri.project.Project
Researcher - Class in com.genologics.ri.researcher: The detailed representation of a researcher.
Researcher() - Constructor for class com.genologics.ri.researcher.Researcher
Researcher(URI) - Constructor for class com.genologics.ri.researcher.Researcher
RESEARCHER_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
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
ResearcherLink() - Constructor for class com.genologics.ri.reagentlot.ResearcherLink
ResearcherLink() - Constructor for class com.genologics.ri.researcher.ResearcherLink
ResearcherLink() - Constructor for class com.genologics.ri.role.ResearcherLink
ResearcherLink(Linkable<Researcher>) - Constructor for class com.genologics.ri.project.ResearcherLink
ResearcherLink(Linkable<Researcher>) - Constructor for class com.genologics.ri.reagentlot.ResearcherLink
ResearcherLink(Linkable<Researcher>) - Constructor for class com.genologics.ri.researcher.ResearcherLink
ResearcherLink(URI) - Constructor for class com.genologics.ri.project.ResearcherLink
ResearcherLink(URI) - Constructor for class com.genologics.ri.reagentlot.ResearcherLink
ResearcherLink(URI) - Constructor for class com.genologics.ri.researcher.ResearcherLink
ResearcherLink(URI) - Constructor for class com.genologics.ri.role.ResearcherLink
researchers - Variable in class com.genologics.ri.researcher.Researchers
researchers - Variable in class com.genologics.ri.role.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
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
RESULT_FILE - Enum constant in enum com.genologics.ri.artifact.OutputType
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
REVIEW - Enum constant in enum com.genologics.ri.step.ActionType
reviewer - Variable in class com.genologics.ri.step.EscalationRequest
REWORK - Enum constant in enum com.genologics.ri.step.ActionType
REWORKED - Enum constant in enum com.genologics.ri.artifact.Status
reworkStepUri - Variable in class com.genologics.ri.step.NextAction
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
Role() - Constructor for class com.genologics.ri.role.Role
Role(Linkable<Role>) - Constructor for class com.genologics.ri.researcher.Role
Role(Role) - Constructor for class com.genologics.ri.researcher.Role
Role(URI) - Constructor for class com.genologics.ri.researcher.Role
Role(URI) - Constructor for class com.genologics.ri.role.Role
Role(URI, String) - Constructor for class com.genologics.ri.researcher.Role
Role(URI, String) - Constructor for class com.genologics.ri.role.Role
ROLE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
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
RoleLink(URI) - Constructor for class com.genologics.ri.role.RoleLink
RoleLink(URI, String) - Constructor for class com.genologics.ri.role.RoleLink
roleName - Variable in class com.genologics.ri.researcher.Role: Deprecated.
Deprecated from version 2.19.
roles - Variable in class com.genologics.ri.researcher.Credentials
roles - Variable in class com.genologics.ri.role.Roles
Roles - Class in com.genologics.ri.role
Roles() - Constructor for class com.genologics.ri.role.Roles
Roles(URI) - Constructor for class com.genologics.ri.role.Roles
ROOT_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
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
rows - Variable in class com.genologics.ri.containertype.ContainerType
RUNNING - Enum constant in enum com.genologics.ri.step.Status
runProgramPerEvent - Variable in class com.genologics.ri.automation.Automation
runProgramPerEvent - Variable in class com.genologics.ri.processtype.Parameter: Deprecated.
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
SAMPLE - Enum constant in enum com.genologics.ri.artifact.OutputType
SAMPLE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
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
SampleBase(SampleBase) - Constructor for class com.genologics.ri.sample.SampleBase
SampleBatchFetchResult - Class in com.genologics.ri.sample: Batch fetch and update holder for samples.
SampleBatchFetchResult() - Constructor for class com.genologics.ri.sample.SampleBatchFetchResult
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
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
sampleFields - Variable in class com.genologics.ri.processtype.ProcessType
sampleFields - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep
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
SampleLink() - Constructor for class com.genologics.ri.sample.SampleLink
SampleLink(LimsEntityLinkable<Sample>) - Constructor for class com.genologics.ri.artifact.SampleLink
SampleLink(LimsEntityLinkable<Sample>) - Constructor for class com.genologics.ri.sample.SampleLink
SampleLink(URI) - Constructor for class com.genologics.ri.artifact.SampleLink
SampleLink(URI) - Constructor for class com.genologics.ri.sample.SampleLink
SampleLink(URI, String) - Constructor for class com.genologics.ri.artifact.SampleLink
SampleLink(URI, String) - Constructor for class com.genologics.ri.sample.SampleLink
samples - Variable in class com.genologics.ri.artifact.Artifact
samples - Variable in class com.genologics.ri.artifact.DemuxArtifact
samples - Variable in class com.genologics.ri.sample.SampleBatchFetchResult
samples - Variable in class com.genologics.ri.sample.Samples
Samples - Class in com.genologics.ri.sample: The representation for a list of sample links.
Samples() - Constructor for class com.genologics.ri.sample.Samples
SCANNED - Enum constant in enum 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
script - Variable in class com.genologics.ri.processtype.Parameter: The EPP script text that will actually run.
SEARCH_RESULT_FILE - Enum constant in enum com.genologics.ri.artifact.OutputType
selectedContainers - Variable in class com.genologics.ri.step.Placements
sequence - Variable in class com.genologics.ri.stepconfiguration.NextStep
serialNumber - Variable in class com.genologics.ri.instrument.Instrument
serverAddress - Variable in class org.cruk.clarity.api.impl.ClarityAPIImpl: The root URL to the Clarity server.
setAccountLocked(Boolean) - Method in class com.genologics.ri.researcher.Credentials
setAction(ActionType) - Method in class com.genologics.ri.step.NextAction
setAction(String) - Method in class com.genologics.ri.permission.Permission
setAction(String) - Method in class com.genologics.ri.permission.PermissionLink
setAction(String) - Method in class com.genologics.ri.role.PermissionLink
setActions(ActionsLink) - Method in class com.genologics.ri.step.ProcessStep
setAllowNonPresetValues(Boolean) - Method in class com.genologics.ri.configuration.Field
setAlpha(Boolean) - Method in class com.genologics.ri.containertype.Dimension
setArchived(Boolean) - Method in class com.genologics.ri.controltype.ControlType
setArchived(Boolean) - Method in class com.genologics.ri.instrument.Instrument
setArchived(Boolean) - Method in class com.genologics.ri.reagentkit.ReagentKit
setArtifact(DemuxSourceArtifact) - Method in class com.genologics.ri.artifact.Demux
setArtifact(LimsEntityLinkable<Artifact>) - Method in class com.genologics.ri.sample.SampleBase
setArtifact(Linkable<Artifact>) - Method in class com.genologics.ri.artifact.DemuxSourceArtifact
setArtifact(Linkable<Artifact>) - Method in class com.genologics.ri.step.CreationInput
setArtifact(Linkable<Artifact>) - Method in class com.genologics.ri.step.NextAction
setArtifact(Linkable<Artifact>) - Method in class com.genologics.ri.step.Output
setArtifact(Linkable<Artifact>) - Method in class com.genologics.ri.step.OutputPlacement
setArtifact(Linkable<DemuxArtifact>) - Method in class com.genologics.ri.artifact.DemuxLink
setArtifactGroups(Collection<? extends Linkable<ArtifactGroup>>) - Method in class com.genologics.ri.artifact.Artifact
setArtifacts(Artifacts) - Method in class com.genologics.ri.artifactgroup.ArtifactGroup
setArtifactType(String) - Method in class com.genologics.ri.processtype.ProcessInput
setArtifactType(String) - Method in class com.genologics.ri.processtype.ProcessOutput
setArtifactUri(URI) - Method in class com.genologics.ri.step.NextAction
setAssignWorkingFlag(Boolean) - Method in class com.genologics.ri.processtype.ProcessOutput: Deprecated.
setAttachedTo(Linkable<?>) - Method in class com.genologics.ri.file.ClarityFile
setAttachTo(String) - Method in class com.genologics.ri.processtype.Field
setAttachTo(String) - Method in class com.genologics.ri.stepconfiguration.Field
setAttachToCategory(String) - Method in class com.genologics.ri.configuration.Field
setAttachToCategory(String) - Method in class com.genologics.ri.configuration.Type
setAttachToCategory(String) - Method in class com.genologics.ri.configuration.UdfConfigLink
setAttachToCategory(String) - Method in class com.genologics.ri.configuration.UdtConfigLink
setAttachToName(String) - Method in class com.genologics.ri.configuration.Field
setAttachToName(String) - Method in class com.genologics.ri.configuration.Type
setAttachToName(String) - Method in class com.genologics.ri.configuration.UdfConfigLink
setAttachToName(String) - Method in class com.genologics.ri.configuration.UdtConfigLink
setAuthor(Linkable<Researcher>) - Method in class com.genologics.ri.step.EscalationRequest
setAuthor(Linkable<Researcher>) - Method in class com.genologics.ri.step.EscalationReview
setAutomaticNextStep(Linkable<ProcessStep>) - Method in class com.genologics.ri.step.ProcessStep
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
setBioSource(BioSource) - Method in class com.genologics.ri.sample.SampleBase: Deprecated.
setBuiltIn(Boolean) - Method in class com.genologics.ri.role.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
setCatalogueNumber(String) - Method in class com.genologics.ri.reagentkit.ReagentKit
setCategory(String) - Method in class com.genologics.ri.exception.Exception
setChannel(String) - Method in class com.genologics.ri.automation.Automation
setChannel(String) - Method in class com.genologics.ri.processtype.Parameter
setCity(String) - Method in class com.genologics.ri.Address
setClarityAPI(ClarityAPI) - Method in class org.cruk.clarity.api.automation.impl.ClarityProcessAutomationImpl: Set the API.
setClarityAPI(ClarityAPI) - 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.
setCloseDate(Date) - Method in class com.genologics.ri.project.Project
setCode(String) - Method in class com.genologics.ri.exception.Exception
setColumns(Dimension) - Method in class com.genologics.ri.containertype.ContainerType
setComment(String) - Method in class com.genologics.ri.step.EscalationRequest
setComment(String) - Method in class com.genologics.ri.step.EscalationReview
setConcentration(String) - Method in class com.genologics.ri.controltype.ControlType
setConfigLocation(Resource) - Method in class org.cruk.clarity.api.cache.EhCacheManagerFactory: Set the location of the EhCache config file.
setConfiguration(Linkable<ProtocolStep>) - Method in class com.genologics.ri.step.StepCreation
setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.Actions
setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.Placements
setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.Pools
setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.ProcessStep
setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.ProgramStatus
setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.ReagentLots
setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.Reagents
setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.StepCreation
setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.StepDetails
setConfiguration(StepConfiguration) - Method in class com.genologics.ri.step.StepSetup
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
setContainerType(ContainerType) - Method in class com.genologics.ri.step.StepCreation
setContainerType(Linkable<ContainerType>) - Method in class com.genologics.ri.container.Container
setContainerType(String) - Method in class com.genologics.ri.step.StepCreation
setContentLocation(URI) - Method in class com.genologics.ri.file.ClarityFile
setContext(Context) - Method in class com.genologics.ri.automation.Automation
setControlledVocabulary(Boolean) - Method in class com.genologics.ri.configuration.Field
setControlType(Linkable<ControlType>) - Method in class com.genologics.ri.artifact.Artifact
setControlType(Linkable<ControlType>) - Method in class com.genologics.ri.sample.SampleBase
setControlType(Linkable<ControlType>) - Method in class com.genologics.ri.step.CreationInput
setControlTypeUri(URI) - Method in class com.genologics.ri.step.CreationInput
setCountry(String) - Method in class com.genologics.ri.Address
setCreatedBy(Linkable<Researcher>) - Method in class com.genologics.ri.reagentlot.ReagentLot
setCreatedDate(Date) - Method in class com.genologics.ri.reagentlot.ReagentLot
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
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(URL, Credentials) - Method in interface org.cruk.clarity.api.http.AuthenticatingClientHttpRequestFactory: Set the credentials based on the protocol, host and port in the URL.
setCredentials(URL, Credentials) - Method in class org.cruk.clarity.api.http.HttpComponentsClientHttpRequestFactoryBasicAuth
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
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
setDate(Date) - Method in class com.genologics.ri.step.EscalationRequest
setDate(Date) - Method in class com.genologics.ri.step.EscalationReview
setDateCompleted(Date) - Method in class com.genologics.ri.sample.SampleBase
setDateCompleted(Date) - Method in class com.genologics.ri.step.ProcessStep
setDateReceived(Date) - Method in class com.genologics.ri.sample.SampleBase
setDateRun(Date) - Method in class com.genologics.ri.process.ClarityProcess
setDateRun(Date) - Method in class com.genologics.ri.processexecution.ExecutableProcess
setDateStarted(Date) - Method in class com.genologics.ri.step.ProcessStep
setDefault(Boolean) - Method in class com.genologics.ri.processtemplate.ProcessTemplate
setDefaultGrouping(GenericTypeLink) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep: Deprecated.
setDemux(DemuxDetails) - Method in class com.genologics.ri.artifact.DemuxArtifact
setDemux(Linkable<Demux>) - Method in class com.genologics.ri.artifact.Artifact
setDemuxDetails(DemuxDetails) - Method in class com.genologics.ri.artifact.Demux
setDepartment(String) - Method in class com.genologics.ri.Address
setDescription(String) - Method in class com.genologics.ri.permission.Permission
setDescription(String) - Method in class com.genologics.ri.sample.BioSource: Deprecated.
setDetail(Boolean) - Method in class com.genologics.ri.processtype.IceBucketField
setDetail(Boolean) - Method in class com.genologics.ri.processtype.QueueField
setDetail(Boolean) - Method in class com.genologics.ri.stepconfiguration.IceBucketField
setDetail(Boolean) - Method in class com.genologics.ri.stepconfiguration.QueueField
setDetails(Linkable<StepDetails>) - Method in class com.genologics.ri.step.ProcessStep
setDeviation(Boolean) - Method in class com.genologics.ri.configuration.Field
setDisplayName(String) - Method in class com.genologics.ri.processtype.ProcessInput
setDisplayName(String) - Method in class com.genologics.ri.processtype.ProcessOutput
setDisplayPrecision(Integer) - Method in class com.genologics.ri.configuration.Field
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).
setEditable(Boolean) - Method in class com.genologics.ri.configuration.Field
setEmail(String) - Method in class com.genologics.ri.researcher.Researcher
setEnabled(boolean) - Method in class com.genologics.ri.stepconfiguration.StepSetup
setEnabled(Boolean) - Method in class com.genologics.ri.processtype.StepSetup
setEscalation(Escalation) - Method in class com.genologics.ri.step.Actions
setExpiryDate(String) - Method in class com.genologics.ri.instrument.Instrument
setExpiryDate(Date) - Method in class com.genologics.ri.reagentlot.ReagentLot
setFax(String) - Method in class com.genologics.ri.researcher.Researcher
setFile(ClarityFile) - Method in class com.genologics.ri.artifact.Artifact
setFile(String) - Method in class com.genologics.ri.processtype.Parameter: Deprecated.
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 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.
setFilestoreSessionFactory(DefaultSftpSessionFactory) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl: Set the file store session factory for SFTP connections.
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
setFirstName(String) - Method in class com.genologics.ri.processtemplate.Technician
setFirstName(String) - Method in class com.genologics.ri.researcher.Researcher
setFirstName(String) - Method in class com.genologics.ri.researcher.ResearcherLink
setFirstName(String) - Method in class com.genologics.ri.role.ResearcherLink
setFirstName(String) - Method in class com.genologics.ri.sample.Submitter
setFirstName(String) - Method in class com.genologics.ri.step.UserLink
setFirstPresetDefaultValue(Boolean) - Method in class com.genologics.ri.configuration.Field
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.
setHttpStatus(HttpStatus) - 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(URI) - Method in class com.genologics.ri.ExternalId
setIndex(Integer) - Method in class com.genologics.ri.protocolconfiguration.Protocol
setIndex(Integer) - Method in class com.genologics.ri.stage.Stage
setInitials(String) - Method in class com.genologics.ri.researcher.Researcher
setInput(LimsEntityLinkable<Artifact>) - Method in class com.genologics.ri.process.InputOutputMap
setInput(LimsEntityLinkable<Artifact>) - Method in class com.genologics.ri.step.InputOutputMap
setInput(Linkable<Artifact>) - Method in class com.genologics.ri.process.InputOutputMap
setInput(Linkable<Artifact>) - Method in class com.genologics.ri.step.InputOutputMap
setInput(ArtifactLink) - Method in class com.genologics.ri.process.InputOutputMap
setInput(ArtifactLink) - Method in class com.genologics.ri.step.InputOutputMap
setInputArtifacts(Collection<? extends Linkable<Artifact>>) - Method in class com.genologics.ri.step.PooledInputs
setInputs(Collection<? extends Linkable<Artifact>>) - Method in class com.genologics.ri.processexecution.ExecutableInputOutputMap
setInstitution(String) - Method in class com.genologics.ri.Address
setInstrument(Instrument) - Method in class com.genologics.ri.processtemplate.ProcessTemplate
setInstrument(Linkable<Instrument>) - Method in class com.genologics.ri.process.ClarityProcess
setInstrument(Linkable<Instrument>) - Method in class com.genologics.ri.processexecution.ExecutableProcess
setInstrument(Linkable<Instrument>) - Method in class com.genologics.ri.step.StepDetails
setInstrument(InstrumentLink) - Method in class com.genologics.ri.processtemplate.ProcessTemplate
setInternalClarityAPI(ClarityAPIInternal) - Method in class org.cruk.clarity.api.cache.ClarityAPICache: Set the internal interface access to the API.
setInvocationType(InvocationType) - Method in class com.genologics.ri.processtype.Parameter: Deprecated.
setInvoiceDate(Date) - Method in class com.genologics.ri.project.Project
setJaxbMarshaller(Jaxb2Marshaller) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl: Set the Jaxb marshaller.
setLab(Linkable<Lab>) - Method in class com.genologics.ri.researcher.Researcher
setLastModifiedBy(Linkable<Researcher>) - Method in class com.genologics.ri.reagentlot.ReagentLot
setLastModifiedDate(Date) - Method in class com.genologics.ri.reagentlot.ReagentLot
setLastName(String) - Method in class com.genologics.ri.process.Technician
setLastName(String) - Method in class com.genologics.ri.processtemplate.Technician
setLastName(String) - Method in class com.genologics.ri.researcher.Researcher
setLastName(String) - Method in class com.genologics.ri.researcher.ResearcherLink
setLastName(String) - Method in class com.genologics.ri.role.ResearcherLink
setLastName(String) - Method in class com.genologics.ri.sample.Submitter
setLastName(String) - Method in class com.genologics.ri.step.UserLink
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
setLimsid(String) - Method in class com.genologics.ri.artifact.ArtifactLink
setLimsid(String) - Method in class com.genologics.ri.artifact.DemuxArtifactSample
setLimsid(String) - Method in class com.genologics.ri.artifact.ParentProcessLink
setLimsid(String) - Method in class com.genologics.ri.artifact.SampleLink
setLimsid(String) - Method in class com.genologics.ri.container.Container
setLimsid(String) - Method in class com.genologics.ri.container.ContainerLink
setLimsid(String) - Method in class com.genologics.ri.container.Placement
setLimsid(String) - Method in class com.genologics.ri.ContainerLink
setLimsid(String) - Method in class com.genologics.ri.file.ClarityFile
setLimsid(String) - Method in class com.genologics.ri.file.FileLink
setLimsid(String) - Method in class com.genologics.ri.instrument.Instrument
setLimsid(String) - Method in class com.genologics.ri.instrument.InstrumentLink
setLimsid(String) - Method in class com.genologics.ri.lab.Lab
setLimsid(String) - Method in class com.genologics.ri.lab.LabLink
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
setLimsid(String) - Method in class com.genologics.ri.process.ArtifactLink
setLimsid(String) - Method in class com.genologics.ri.process.ClarityProcess
setLimsid(String) - Method in class com.genologics.ri.process.InstrumentLink
setLimsid(String) - Method in class com.genologics.ri.process.ParentProcessLink
setLimsid(String) - Method in class com.genologics.ri.process.ProcessLink
setLimsid(String) - Method in class com.genologics.ri.processexecution.InstrumentLink
setLimsid(String) - Method in class com.genologics.ri.processtemplate.InstrumentLink
setLimsid(String) - Method in class com.genologics.ri.project.Project
setLimsid(String) - Method in class com.genologics.ri.project.ProjectLink
setLimsid(String) - Method in class com.genologics.ri.project.ResearcherLink
setLimsid(String) - Method in class com.genologics.ri.queue.ArtifactLink
setLimsid(String) - Method in class com.genologics.ri.reagentlot.ReagentLot
setLimsid(String) - Method in class com.genologics.ri.reagentlot.ReagentLotLink
setLimsid(String) - Method in class com.genologics.ri.reagentlot.ResearcherLink
setLimsid(String) - Method in class com.genologics.ri.reagenttype.ReagentType
setLimsid(String) - Method in class com.genologics.ri.reagenttype.ReagentTypeLink
setLimsid(String) - Method in class com.genologics.ri.researcher.LabLink
setLimsid(String) - Method in class com.genologics.ri.researcher.Researcher
setLimsid(String) - Method in class com.genologics.ri.researcher.ResearcherLink
setLimsid(String) - Method in class com.genologics.ri.role.ResearcherLink
setLimsid(String) - Method in class com.genologics.ri.sample.ArtifactLink
setLimsid(String) - Method in class com.genologics.ri.sample.ProjectLink
setLimsid(String) - Method in class com.genologics.ri.sample.SampleBase
setLimsid(String) - Method in class com.genologics.ri.sample.SampleLink
setLimsid(String) - Method in class com.genologics.ri.step.ArtifactLink
setLimsid(String) - Method in class com.genologics.ri.step.InstrumentLink
setLimsid(String) - Method in class com.genologics.ri.step.ProcessStep
setLimsid(String) - Method in class com.genologics.ri.step.ReagentLotLink
setLimsid(String) - Method in class com.genologics.ri.step.SharedResultFile
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
setLocation(LimsEntityLinkable<Container>, String) - Method in class com.genologics.ri.step.OutputPlacement
setLocation(Linkable<Container>, String) - Method in class com.genologics.ri.step.OutputPlacement
setLocation(Location) - Method in class com.genologics.ri.artifact.Artifact
setLocation(Location) - Method in class com.genologics.ri.processexecution.Output
setLocation(Location) - Method in class com.genologics.ri.queue.ArtifactLink
setLocation(Location) - Method in class com.genologics.ri.sample.SampleCreation
setLocation(Location) - Method in class com.genologics.ri.step.OutputPlacement
setLocked(Boolean) - Method in class com.genologics.ri.stepconfiguration.GenericTypeLink
setLocked(Boolean) - Method in class com.genologics.ri.stepconfiguration.LockableSetting
setLotNumber(String) - Method in class com.genologics.ri.reagentlot.ReagentLot
setMajor(String) - Method in class com.genologics.ri.version.Version
setMarshaller(JaxbMarshallingTool) - Method in class org.cruk.clarity.api.debugging.RestClientSnoopingAspect: Set the tool to convert an object back into XML for printing.
setMarshaller(Jaxb2Marshaller) - Method in class org.cruk.clarity.api.http.ClarityFailureResponseErrorHandler: Set the marshaller used to create the XML.
setMarshaller(Jaxb2Marshaller) - 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
setMessage(String) - Method in class com.genologics.ri.exception.Exception
setMessage(String) - Method in class com.genologics.ri.processtype.SharedResultFile
setMessage(String) - Method in class com.genologics.ri.step.ProgramStatus
setMessage(String) - Method in class com.genologics.ri.step.SharedResultFile
setMessage(String) - Method in class com.genologics.ri.stepconfiguration.SharedResultFile
setMinor(String) - Method in class com.genologics.ri.version.Version
setMinValue(Double) - Method in class com.genologics.ri.configuration.Field
setName(String) - Method in class com.genologics.ri.artifact.Artifact
setName(String) - Method in class com.genologics.ri.artifact.ArtifactGroupLink
setName(String) - Method in class com.genologics.ri.artifact.DemuxArtifact
setName(String) - Method in class com.genologics.ri.artifact.DemuxSourceArtifact
setName(String) - Method in class com.genologics.ri.artifact.PoolStep
setName(String) - Method in class com.genologics.ri.artifact.ReagentLabel
setName(String) - Method in class com.genologics.ri.artifact.WorkflowStage
setName(String) - Method in class com.genologics.ri.artifactgroup.ArtifactGroup
setName(String) - Method in class com.genologics.ri.artifactgroup.ArtifactGroupLink
setName(String) - Method in class com.genologics.ri.automation.Automation
setName(String) - Method in class com.genologics.ri.automation.AutomationLink
setName(String) - Method in class com.genologics.ri.automation.ProcessTypeLink
setName(String) - Method in class com.genologics.ri.configuration.Field
setName(String) - Method in class com.genologics.ri.configuration.FieldLink
setName(String) - Method in class com.genologics.ri.configuration.Type
setName(String) - Method in class com.genologics.ri.configuration.TypeDefinition
setName(String) - Method in class com.genologics.ri.configuration.UdfConfigLink
setName(String) - Method in class com.genologics.ri.configuration.UdtConfigLink
setName(String) - Method in class com.genologics.ri.container.Container
setName(String) - Method in class com.genologics.ri.container.ContainerLink
setName(String) - Method in class com.genologics.ri.container.ContainerTypeLink
setName(String) - Method in class com.genologics.ri.containertype.CalibrantWell: Deprecated.
setName(String) - Method in class com.genologics.ri.containertype.ContainerType
setName(String) - Method in class com.genologics.ri.containertype.ContainerTypeLink
setName(String) - Method in class com.genologics.ri.controltype.ControlType
setName(String) - Method in class com.genologics.ri.controltype.ControlTypeLink
setName(String) - Method in class com.genologics.ri.instrument.Instrument
setName(String) - Method in class com.genologics.ri.instrument.InstrumentLink
setName(String) - Method in class com.genologics.ri.instrumenttype.InstrumentType
setName(String) - Method in class com.genologics.ri.instrumenttype.InstrumentTypeLink
setName(String) - Method in class com.genologics.ri.instrumenttype.InstrumentTypeProcessType
setName(String) - Method in class com.genologics.ri.lab.Lab
setName(String) - Method in class com.genologics.ri.lab.LabLink
setName(String) - Method in class com.genologics.ri.permission.Permission
setName(String) - Method in class com.genologics.ri.permission.PermissionLink
setName(String) - Method in class com.genologics.ri.process.Parameter
setName(String) - Method in class com.genologics.ri.process.ProcessTypeLink
setName(String) - Method in class com.genologics.ri.processexecution.Parameter
setName(String) - Method in class com.genologics.ri.processtemplate.Parameter
setName(String) - Method in class com.genologics.ri.processtemplate.ProcessTemplate
setName(String) - Method in class com.genologics.ri.processtemplate.ProcessTemplateLink
setName(String) - Method in class com.genologics.ri.processtemplate.ProcessTypeLink
setName(String) - Method in class com.genologics.ri.processtype.ContainerTypeLink
setName(String) - Method in class com.genologics.ri.processtype.ControlTypeLink
setName(String) - Method in class com.genologics.ri.processtype.EppTrigger
setName(String) - Method in class com.genologics.ri.processtype.Field
setName(String) - Method in class com.genologics.ri.processtype.Parameter
setName(String) - Method in class com.genologics.ri.processtype.ProcessType
setName(String) - Method in class com.genologics.ri.processtype.ProcessTypeAttribute
setName(String) - Method in class com.genologics.ri.processtype.ProcessTypeLink
setName(String) - Method in class com.genologics.ri.processtype.ReagentKitLink
setName(String) - Method in class com.genologics.ri.processtype.StepProperty
setName(String) - Method in class com.genologics.ri.processtype.TypeDefinition
setName(String) - Method in class com.genologics.ri.project.Project
setName(String) - Method in class com.genologics.ri.project.ProjectLink
setName(String) - Method in class com.genologics.ri.property.PropertyLink
setName(String) - Method in class com.genologics.ri.protocolconfiguration.Protocol
setName(String) - Method in class com.genologics.ri.protocolconfiguration.ProtocolLink
setName(String) - Method in class com.genologics.ri.protocolconfiguration.ProtocolProperty
setName(String) - Method in class com.genologics.ri.queue.Queue
setName(String) - Method in class com.genologics.ri.reagentkit.ReagentKit
setName(String) - Method in class com.genologics.ri.reagentkit.ReagentKitLink
setName(String) - Method in class com.genologics.ri.reagentlot.ReagentKitLink
setName(String) - Method in class com.genologics.ri.reagentlot.ReagentLot
setName(String) - Method in class com.genologics.ri.reagentlot.ReagentLotLink
setName(String) - Method in class com.genologics.ri.reagenttype.Attribute
setName(String) - Method in class com.genologics.ri.reagenttype.ReagentType
setName(String) - Method in class com.genologics.ri.reagenttype.ReagentTypeLink
setName(String) - Method in class com.genologics.ri.reagenttype.SpecialType
setName(String) - Method in class com.genologics.ri.researcher.Role: Set the role name.
setName(String) - Method in class com.genologics.ri.role.PermissionLink
setName(String) - Method in class com.genologics.ri.role.Role
setName(String) - Method in class com.genologics.ri.role.RoleLink
setName(String) - Method in class com.genologics.ri.sample.BioSource: Deprecated.
setName(String) - Method in class com.genologics.ri.sample.ControlTypeLink
setName(String) - Method in class com.genologics.ri.sample.SampleBase
setName(String) - Method in class com.genologics.ri.stage.Stage
setName(String) - Method in class com.genologics.ri.step.AvailableProgram
setName(String) - Method in class com.genologics.ri.step.InstrumentLink
setName(String) - Method in class com.genologics.ri.step.PooledInputs
setName(String) - Method in class com.genologics.ri.step.ReagentLabel
setName(String) - Method in class com.genologics.ri.step.SharedResultFile
setName(String) - Method in class com.genologics.ri.stepconfiguration.ControlTypeLink
setName(String) - Method in class com.genologics.ri.stepconfiguration.EppTrigger
setName(String) - Method in class com.genologics.ri.stepconfiguration.Field
setName(String) - Method in class com.genologics.ri.stepconfiguration.NextStep
setName(String) - Method in class com.genologics.ri.stepconfiguration.ProcessTypeLink
setName(String) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
setName(String) - Method in class com.genologics.ri.stepconfiguration.ReagentKitLink
setName(String) - Method in class com.genologics.ri.stepconfiguration.StepProperty
setName(String) - Method in class com.genologics.ri.userdefined.UDF
setName(String) - Method in class com.genologics.ri.userdefined.UDT
setName(String) - Method in class com.genologics.ri.workflowconfiguration.ProtocolLink
setName(String) - Method in class com.genologics.ri.workflowconfiguration.StageLink
setName(String) - Method in class com.genologics.ri.workflowconfiguration.Workflow
setName(String) - Method in class com.genologics.ri.workflowconfiguration.WorkflowLink
setNextPage(Page) - Method in class com.genologics.ri.artifact.Artifacts
setNextPage(Page) - Method in class com.genologics.ri.artifactgroup.ArtifactGroups
setNextPage(Page) - Method in class com.genologics.ri.automation.Automations
setNextPage(Page) - Method in class com.genologics.ri.configuration.Udfs
setNextPage(Page) - Method in class com.genologics.ri.configuration.Udts
setNextPage(Page) - Method in class com.genologics.ri.container.Containers
setNextPage(Page) - Method in class com.genologics.ri.containertype.ContainerTypes
setNextPage(Page) - Method in class com.genologics.ri.file.ClarityFiles
setNextPage(Page) - Method in class com.genologics.ri.instrument.Instruments
setNextPage(Page) - Method in class com.genologics.ri.instrumenttype.InstrumentTypes
setNextPage(Page) - Method in class com.genologics.ri.lab.Labs
setNextPage(Page) - Method in interface com.genologics.ri.PaginatedBatch
setNextPage(Page) - Method in class com.genologics.ri.process.ClarityProcesses
setNextPage(Page) - Method in class com.genologics.ri.processtemplate.ProcessTemplates
setNextPage(Page) - Method in class com.genologics.ri.processtype.ProcessTypes
setNextPage(Page) - Method in class com.genologics.ri.project.Projects
setNextPage(Page) - Method in class com.genologics.ri.property.Properties
setNextPage(Page) - Method in class com.genologics.ri.queue.Queue
setNextPage(Page) - Method in class com.genologics.ri.reagentkit.ReagentKits
setNextPage(Page) - Method in class com.genologics.ri.reagentlot.ReagentLots
setNextPage(Page) - Method in class com.genologics.ri.reagenttype.ReagentTypes
setNextPage(Page) - Method in class com.genologics.ri.researcher.Researchers
setNextPage(Page) - Method in class com.genologics.ri.sample.Samples
setNextStep(Linkable<ProtocolStep>) - Method in class com.genologics.ri.stepconfiguration.NextStep
setNextStepUri(URI) - Method in class com.genologics.ri.stepconfiguration.NextStep
setNotes(String) - Method in class com.genologics.ri.reagentlot.ReagentLot
setNumberOfOutputs(Integer) - Method in class com.genologics.ri.processtype.ProcessOutput
setOccupiedWells(Long) - Method in class com.genologics.ri.container.Container
setOffset(Integer) - Method in class com.genologics.ri.containertype.Dimension
setOpenDate(Date) - Method in class com.genologics.ri.project.Project
setOriginalLocation(String) - Method in class com.genologics.ri.file.ClarityFile
setOriginalName(String) - Method in class com.genologics.ri.file.ClarityFile
setOutput(OutputType, LimsEntityLinkable<Container>, String) - Method in class com.genologics.ri.processexecution.ExecutableInputOutputMap
setOutput(LimsEntityLinkable<Artifact>) - Method in class com.genologics.ri.process.InputOutputMap
setOutput(LimsEntityLinkable<Artifact>) - Method in class com.genologics.ri.step.InputOutputMap
setOutput(Linkable<Artifact>) - Method in class com.genologics.ri.process.InputOutputMap
setOutput(Linkable<Artifact>) - Method in class com.genologics.ri.step.InputOutputMap
setOutput(ArtifactLink) - Method in class com.genologics.ri.process.InputOutputMap
setOutput(Output) - Method in class com.genologics.ri.processexecution.ExecutableInputOutputMap
setOutput(ArtifactLink) - Method in class com.genologics.ri.step.InputOutputMap
setOutput(Output) - Method in class com.genologics.ri.step.PooledInputs
setOutputArtifact(Linkable<Artifact>) - Method in class com.genologics.ri.step.PooledInputs
setOutputGenerationType(OutputGenerationType) - Method in class com.genologics.ri.process.ArtifactLink
setOutputGenerationType(OutputGenerationType) - Method in class com.genologics.ri.processtype.ProcessOutput
setOutputGenerationType(OutputGenerationType) - Method in class com.genologics.ri.step.ArtifactLink
setOutputName(String) - Method in class com.genologics.ri.processtype.ProcessOutput
setOutputType(OutputType) - Method in class com.genologics.ri.artifact.Artifact
setOutputType(OutputType) - Method in class com.genologics.ri.process.ArtifactLink
setOutputUri(URI) - Method in class com.genologics.ri.step.PooledInputs
setParameter(Parameter) - Method in class com.genologics.ri.process.ClarityProcess
setParameter(Parameter) - Method in class com.genologics.ri.processexecution.ExecutableProcess
setParameter(Parameter) - Method in class com.genologics.ri.processtemplate.ProcessTemplate
setParentProcess(LimsEntityLinkable<ClarityProcess>) - Method in class com.genologics.ri.artifact.Artifact
setParentProcess(LimsEntityLinkable<ClarityProcess>) - Method in class com.genologics.ri.process.ArtifactLink
setParentUri(URI) - Method in class com.genologics.ri.configuration.Field
setPassword(String) - Method in class com.genologics.ri.researcher.Credentials
setPhone(String) - Method in class com.genologics.ri.researcher.Researcher
setPlacements(Linkable<Placements>) - Method in class com.genologics.ri.step.ProcessStep
setPlacements(Collection<? extends LimsEntityLinkable<Artifact>>) - Method in class com.genologics.ri.container.Container
setPoint(TriggerPoint) - Method in class com.genologics.ri.processtype.EppTrigger
setPoint(TriggerPoint) - Method in class com.genologics.ri.stepconfiguration.EppTrigger
setPools(Linkable<Pools>) - Method in class com.genologics.ri.step.ProcessStep
setPoolStep(PoolStep) - Method in class com.genologics.ri.artifact.DemuxDetails
setPoolStep(Linkable<ProcessStep>) - Method in class com.genologics.ri.artifact.DemuxDetails
setPostalCode(String) - Method in class com.genologics.ri.Address
setPostProcessUri(URI) - Method in class com.genologics.ri.process.ArtifactLink
setPreset(String) - Method in class com.genologics.ri.step.StepDetails
setPreviousPage(Page) - Method in class com.genologics.ri.artifact.Artifacts
setPreviousPage(Page) - Method in class com.genologics.ri.artifactgroup.ArtifactGroups
setPreviousPage(Page) - Method in class com.genologics.ri.automation.Automations
setPreviousPage(Page) - Method in class com.genologics.ri.configuration.Udfs
setPreviousPage(Page) - Method in class com.genologics.ri.configuration.Udts
setPreviousPage(Page) - Method in class com.genologics.ri.container.Containers
setPreviousPage(Page) - Method in class com.genologics.ri.containertype.ContainerTypes
setPreviousPage(Page) - Method in class com.genologics.ri.file.ClarityFiles
setPreviousPage(Page) - Method in class com.genologics.ri.instrument.Instruments
setPreviousPage(Page) - Method in class com.genologics.ri.instrumenttype.InstrumentTypes
setPreviousPage(Page) - Method in class com.genologics.ri.lab.Labs
setPreviousPage(Page) - Method in interface com.genologics.ri.PaginatedBatch
setPreviousPage(Page) - Method in class com.genologics.ri.process.ClarityProcesses
setPreviousPage(Page) - Method in class com.genologics.ri.processtemplate.ProcessTemplates
setPreviousPage(Page) - Method in class com.genologics.ri.processtype.ProcessTypes
setPreviousPage(Page) - Method in class com.genologics.ri.project.Projects
setPreviousPage(Page) - Method in class com.genologics.ri.property.Properties
setPreviousPage(Page) - Method in class com.genologics.ri.queue.Queue
setPreviousPage(Page) - Method in class com.genologics.ri.reagentkit.ReagentKits
setPreviousPage(Page) - Method in class com.genologics.ri.reagentlot.ReagentLots
setPreviousPage(Page) - Method in class com.genologics.ri.reagenttype.ReagentTypes
setPreviousPage(Page) - Method in class com.genologics.ri.researcher.Researchers
setPreviousPage(Page) - Method in class com.genologics.ri.sample.Samples
setProcessType(Linkable<ProcessType>) - Method in class com.genologics.ri.automation.ProcessTypeLink
setProcessType(Linkable<ProcessType>) - Method in class com.genologics.ri.process.ClarityProcess
setProcessType(Linkable<ProcessType>) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
setProcessType(ProcessTypeLink) - Method in class com.genologics.ri.processtemplate.ProcessTemplate
setProcessType(ProcessType) - Method in class com.genologics.ri.process.ClarityProcess
setProcessType(ProcessType) - Method in class com.genologics.ri.processexecution.ExecutableProcess
setProcessType(ProcessType) - Method in class com.genologics.ri.processtemplate.ProcessTemplate
setProcessType(String) - Method in class com.genologics.ri.processexecution.ExecutableProcess
setProgramStatus(Linkable<ProgramStatus>) - Method in class com.genologics.ri.step.ProcessStep
setProject(LimsEntityLinkable<Project>) - Method in class com.genologics.ri.sample.SampleBase
setProtocol(Linkable<Protocol>) - Method in class com.genologics.ri.stage.Stage
setProtocolName(String) - Method in class com.genologics.ri.process.ClarityProcess
setProtocolStep(Linkable<ProtocolStep>) - Method in class com.genologics.ri.step.StepConfiguration
setProtocolStepIndex(Integer) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
setProtocolStepUri(URI) - Method in class com.genologics.ri.queue.Queue
setProtocolStepUri(URI) - Method in class com.genologics.ri.step.StepConfiguration
setProtocolUri(URI) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
setPublished(Boolean) - Method in class com.genologics.ri.file.ClarityFile
setQCFlag(QCFlag) - Method in class com.genologics.ri.artifact.Artifact
setQCFlag(QCFlag) - Method in class com.genologics.ri.processexecution.ArtifactBase
setQueueTime(Date) - Method in class com.genologics.ri.queue.ArtifactLink
setReagentCategory(String) - Method in class com.genologics.ri.reagenttype.ReagentType
setReagentCategory(String) - Method in class com.genologics.ri.step.Reagents
setReagentCategory(String) - Method in class com.genologics.ri.step.StepCreation
setReagentKit(Linkable<ReagentKit>) - Method in class com.genologics.ri.reagentlot.ReagentLot
setReagentLots(Linkable<ReagentLots>) - Method in class com.genologics.ri.step.ProcessStep
setReagents(Linkable<Reagents>) - Method in class com.genologics.ri.step.ProcessStep
setRelative(String) - Method in class com.genologics.ri.Link
setRemoveWorkingFlag(Boolean) - Method in class com.genologics.ri.processtype.ProcessInput: Deprecated.
setReplicates(Long) - Method in class com.genologics.ri.step.CreationInput
setReplicates(Long) - Method in class com.genologics.ri.step.Input
setRequest(EscalationRequest) - Method in class com.genologics.ri.step.Escalation
setRequired(Boolean) - Method in class com.genologics.ri.configuration.Field
setResearcher(Linkable<Researcher>) - Method in class com.genologics.ri.project.Project
setRestClient(RestOperations) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl: Set the REST client.
setReview(EscalationReview) - Method in class com.genologics.ri.step.Escalation
setReviewer(Linkable<Researcher>) - Method in class com.genologics.ri.step.EscalationRequest
setReworkStep(Linkable<ProtocolStep>) - Method in class com.genologics.ri.step.NextAction
setReworkStepUri(URI) - Method in class com.genologics.ri.step.NextAction
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
setRunProgramPerEvent(Boolean) - Method in class com.genologics.ri.automation.Automation
setRunProgramPerEvent(Boolean) - Method in class com.genologics.ri.processtype.Parameter: Deprecated.
setSampleFields(Field) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
setSamples(Collection<? extends LimsEntityLinkable<Sample>>) - Method in class com.genologics.ri.artifact.Artifact
setScript(String) - Method in class com.genologics.ri.automation.Automation
setScript(String) - Method in class com.genologics.ri.processtype.Parameter
setSequence(Integer) - Method in class com.genologics.ri.stepconfiguration.NextStep
setSerialNumber(String) - Method in class com.genologics.ri.instrument.Instrument
setServer(URL) - Method in interface org.cruk.clarity.api.ClarityAPI: Set the base URL to the Clarity server.
setServer(URL) - Method in class org.cruk.clarity.api.impl.ClarityAPIImpl: Set the base URL to the Clarity server.
setSetup(Linkable<StepSetup>) - Method in class com.genologics.ri.step.ProcessStep
setShared(Boolean) - Method in class com.genologics.ri.processexecution.ExecutableInputOutputMap
setSharedResultFileIndex(String) - Method in class com.genologics.ri.processtype.SharedResultFile
setSharedResultFileIndex(String) - Method in class com.genologics.ri.step.SharedResultFile
setSharedResultFileIndex(String) - Method in class com.genologics.ri.stepconfiguration.SharedResultFile
setShippingAddress(Address) - Method in class com.genologics.ri.lab.Lab
setShowInLablink(Boolean) - Method in class com.genologics.ri.configuration.Field
setShowInTables(Boolean) - Method in class com.genologics.ri.configuration.Field
setSingleStep(Boolean) - Method in class com.genologics.ri.controltype.ControlType
setSize(Integer) - Method in class com.genologics.ri.containertype.Dimension
setSpecialType(SpecialType) - Method in class com.genologics.ri.reagenttype.ReagentType
setStage(Linkable<Stage>) - Method in class com.genologics.ri.routing.ExtArtifactAssignments
setStageUri(URI) - Method in class com.genologics.ri.routing.ExtArtifactAssignments
setState(ContainerState) - Method in class com.genologics.ri.container.Container
setState(String) - Method in class com.genologics.ri.Address
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
setStatus(TriggerStatus) - Method in class com.genologics.ri.processtype.EppTrigger
setStatus(Status) - Method in class com.genologics.ri.reagentlot.ReagentLot
setStatus(Status) - Method in class com.genologics.ri.step.ProgramStatus
setStatus(TriggerStatus) - Method in class com.genologics.ri.stepconfiguration.EppTrigger
setStatus(Status) - Method in class com.genologics.ri.workflowconfiguration.Workflow
setStatus(Status) - Method in class com.genologics.ri.workflowconfiguration.WorkflowLink
setStep(Link) - Method in class com.genologics.ri.step.Actions
setStep(Link) - Method in class com.genologics.ri.step.Placements
setStep(Link) - Method in class com.genologics.ri.step.Pools
setStep(Link) - Method in class com.genologics.ri.step.ProgramStatus
setStep(Link) - Method in class com.genologics.ri.step.ReagentLots
setStep(Link) - Method in class com.genologics.ri.step.Reagents
setStep(Link) - Method in class com.genologics.ri.step.StepDetails
setStep(Link) - Method in class com.genologics.ri.step.StepSetup
setStep(Linkable<ProcessStep>) - Method in class com.genologics.ri.step.Placements
setStep(Linkable<ProtocolStep>) - Method in class com.genologics.ri.stage.Stage
setStep(Linkable<ProtocolStep>) - Method in class com.genologics.ri.step.NextAction
setStepName(String) - Method in class com.genologics.ri.step.StepConfiguration
setStepSetup(StepSetup) - Method in class com.genologics.ri.processtype.ProcessType
setStepSetup(StepSetup) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
setStepUri(URI) - Method in class com.genologics.ri.step.NextAction
setStorageLocation(String) - Method in class com.genologics.ri.reagentlot.ReagentLot
setStreet(String) - Method in class com.genologics.ri.Address
setStyle(Style) - Method in class com.genologics.ri.processtype.Field
setStyle(Style) - Method in class com.genologics.ri.stepconfiguration.Field
setSubmitter(Linkable<Researcher>) - Method in class com.genologics.ri.sample.SampleBase
setSuggestedActions(String) - Method in class com.genologics.ri.exception.Exception
setSupplier(String) - Method in class com.genologics.ri.controltype.ControlType
setSupplier(String) - Method in class com.genologics.ri.reagentkit.ReagentKit
setTechnician(Linkable<Researcher>) - Method in class com.genologics.ri.process.ClarityProcess
setTechnician(Linkable<Researcher>) - Method in class com.genologics.ri.processexecution.ExecutableProcess
setTechnician(Technician) - Method in class com.genologics.ri.processtemplate.ProcessTemplate
setTechnician(Researcher) - Method in class com.genologics.ri.processtemplate.ProcessTemplate
setTube(Boolean) - Method in class com.genologics.ri.containertype.ContainerType
setType(OutputType) - Method in class com.genologics.ri.processexecution.Output
setType(OutputType) - Method in class com.genologics.ri.step.ArtifactLink
setType(FieldType) - Method in class com.genologics.ri.configuration.Field
setType(FieldType) - Method in class com.genologics.ri.userdefined.UDF
setType(TriggerType) - Method in class com.genologics.ri.processtype.EppTrigger
setType(TriggerType) - Method in class com.genologics.ri.stepconfiguration.EppTrigger
setType(String) - Method in class com.genologics.ri.artifact.Artifact
setType(String) - Method in class com.genologics.ri.instrument.Instrument
setTypeDefinition(TypeDefinition) - Method in class com.genologics.ri.configuration.Field
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
setup - Variable in class com.genologics.ri.step.ProcessStep
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
setUri(String) - Method in class com.genologics.ri.reagentlot.ReagentLots
setUri(URI) - Method in class com.genologics.ri.artifact.Artifact
setUri(URI) - Method in class com.genologics.ri.artifact.ArtifactGroupLink
setUri(URI) - Method in class com.genologics.ri.artifact.ArtifactLink
setUri(URI) - Method in class com.genologics.ri.artifact.ControlTypeLink
setUri(URI) - Method in class com.genologics.ri.artifact.Demux
setUri(URI) - Method in class com.genologics.ri.artifact.DemuxArtifact
setUri(URI) - Method in class com.genologics.ri.artifact.DemuxArtifactSample
setUri(URI) - Method in class com.genologics.ri.artifact.DemuxLink
setUri(URI) - Method in class com.genologics.ri.artifact.DemuxSourceArtifact
setUri(URI) - Method in class com.genologics.ri.artifact.ParentProcessLink
setUri(URI) - Method in class com.genologics.ri.artifact.PoolStep
setUri(URI) - Method in class com.genologics.ri.artifact.SampleLink
setUri(URI) - Method in class com.genologics.ri.artifact.WorkflowStage
setUri(URI) - Method in class com.genologics.ri.artifactgroup.ArtifactGroup
setUri(URI) - Method in class com.genologics.ri.artifactgroup.ArtifactGroupLink
setUri(URI) - Method in class com.genologics.ri.artifactgroup.Artifacts
setUri(URI) - Method in class com.genologics.ri.automation.Automation
setUri(URI) - Method in class com.genologics.ri.automation.AutomationLink
setUri(URI) - Method in class com.genologics.ri.automation.Automations
setUri(URI) - Method in class com.genologics.ri.automation.ProcessTypeLink
setUri(URI) - Method in class com.genologics.ri.configuration.Field
setUri(URI) - Method in class com.genologics.ri.configuration.FieldLink
setUri(URI) - Method in class com.genologics.ri.configuration.Type
setUri(URI) - Method in class com.genologics.ri.configuration.TypeDefinition
setUri(URI) - Method in class com.genologics.ri.configuration.UdfConfigLink
setUri(URI) - Method in class com.genologics.ri.configuration.UdtConfigLink
setUri(URI) - Method in class com.genologics.ri.container.Container
setUri(URI) - Method in class com.genologics.ri.container.ContainerLink
setUri(URI) - Method in class com.genologics.ri.container.ContainerTypeLink
setUri(URI) - Method in class com.genologics.ri.container.Placement
setUri(URI) - Method in class com.genologics.ri.ContainerLink
setUri(URI) - Method in class com.genologics.ri.containertype.ContainerType
setUri(URI) - Method in class com.genologics.ri.containertype.ContainerTypeLink
setUri(URI) - Method in class com.genologics.ri.controltype.ControlType
setUri(URI) - Method in class com.genologics.ri.controltype.ControlTypeLink
setUri(URI) - Method in class com.genologics.ri.controltype.ControlTypes
setUri(URI) - Method in class com.genologics.ri.ExternalId
setUri(URI) - Method in class com.genologics.ri.file.ClarityFile
setUri(URI) - Method in class com.genologics.ri.file.FileLink
setUri(URI) - Method in class com.genologics.ri.instrument.Instrument
setUri(URI) - Method in class com.genologics.ri.instrument.InstrumentLink
setUri(URI) - Method in class com.genologics.ri.instrumenttype.InstrumentType
setUri(URI) - Method in class com.genologics.ri.instrumenttype.InstrumentTypeLink
setUri(URI) - Method in class com.genologics.ri.instrumenttype.InstrumentTypeProcessType
setUri(URI) - Method in class com.genologics.ri.lab.Lab
setUri(URI) - Method in class com.genologics.ri.lab.LabLink
setUri(URI) - Method in class com.genologics.ri.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
setUri(URI) - Method in class com.genologics.ri.Page
setUri(URI) - Method in class com.genologics.ri.permission.Permission
setUri(URI) - Method in class com.genologics.ri.permission.PermissionLink
setUri(URI) - Method in class com.genologics.ri.process.ArtifactLink
setUri(URI) - Method in class com.genologics.ri.process.ClarityProcess
setUri(URI) - Method in class com.genologics.ri.process.InstrumentLink
setUri(URI) - Method in class com.genologics.ri.process.ParentProcessLink
setUri(URI) - Method in class com.genologics.ri.process.ProcessLink
setUri(URI) - Method in class com.genologics.ri.process.ProcessTypeLink
setUri(URI) - Method in class com.genologics.ri.process.Technician
setUri(URI) - Method in class com.genologics.ri.processexecution.Input
setUri(URI) - Method in class com.genologics.ri.processexecution.InstrumentLink
setUri(URI) - Method in class com.genologics.ri.processexecution.Technician
setUri(URI) - Method in class com.genologics.ri.processtemplate.InstrumentLink
setUri(URI) - Method in class com.genologics.ri.processtemplate.ProcessTemplate
setUri(URI) - Method in class com.genologics.ri.processtemplate.ProcessTemplateLink
setUri(URI) - Method in class com.genologics.ri.processtemplate.ProcessTypeLink
setUri(URI) - Method in class com.genologics.ri.processtemplate.Technician
setUri(URI) - Method in class com.genologics.ri.processtype.ContainerTypeLink
setUri(URI) - Method in class com.genologics.ri.processtype.ControlTypeLink
setUri(URI) - Method in class com.genologics.ri.processtype.ProcessType
setUri(URI) - Method in class com.genologics.ri.processtype.ProcessTypeLink
setUri(URI) - Method in class com.genologics.ri.processtype.ReagentKitLink
setUri(URI) - Method in class com.genologics.ri.processtype.TypeDefinition
setUri(URI) - Method in class com.genologics.ri.project.Project
setUri(URI) - Method in class com.genologics.ri.project.ProjectLink
setUri(URI) - Method in class com.genologics.ri.project.ResearcherLink
setUri(URI) - Method in class com.genologics.ri.property.PropertyLink
setUri(URI) - Method in class com.genologics.ri.protocolconfiguration.Protocol
setUri(URI) - Method in class com.genologics.ri.protocolconfiguration.ProtocolLink
setUri(URI) - Method in class com.genologics.ri.queue.ArtifactLink
setUri(URI) - Method in class com.genologics.ri.queue.Queue
setUri(URI) - Method in class com.genologics.ri.reagentkit.ReagentKit
setUri(URI) - Method in class com.genologics.ri.reagentkit.ReagentKitLink
setUri(URI) - Method in class com.genologics.ri.reagentkit.ReagentKits
setUri(URI) - Method in class com.genologics.ri.reagentlot.ReagentKitLink
setUri(URI) - Method in class com.genologics.ri.reagentlot.ReagentLot
setUri(URI) - Method in class com.genologics.ri.reagentlot.ReagentLotLink
setUri(URI) - Method in class com.genologics.ri.reagentlot.ResearcherLink
setUri(URI) - Method in class com.genologics.ri.reagenttype.ReagentType
setUri(URI) - Method in class com.genologics.ri.reagenttype.ReagentTypeLink
setUri(URI) - Method in class com.genologics.ri.researcher.LabLink
setUri(URI) - Method in class com.genologics.ri.researcher.Researcher
setUri(URI) - Method in class com.genologics.ri.researcher.ResearcherLink
setUri(URI) - Method in class com.genologics.ri.researcher.Role: Set the URI to the researcher.
setUri(URI) - Method in class com.genologics.ri.role.PermissionLink
setUri(URI) - Method in class com.genologics.ri.role.ResearcherLink
setUri(URI) - Method in class com.genologics.ri.role.Role
setUri(URI) - Method in class com.genologics.ri.role.RoleLink
setUri(URI) - Method in class com.genologics.ri.role.Roles
setUri(URI) - Method in class com.genologics.ri.routing.ArtifactLink
setUri(URI) - Method in class com.genologics.ri.sample.ArtifactLink
setUri(URI) - Method in class com.genologics.ri.sample.ControlTypeLink
setUri(URI) - Method in class com.genologics.ri.sample.ProjectLink
setUri(URI) - Method in class com.genologics.ri.sample.SampleBase
setUri(URI) - Method in class com.genologics.ri.sample.SampleLink
setUri(URI) - Method in class com.genologics.ri.sample.Submitter
setUri(URI) - Method in class com.genologics.ri.stage.ProtocolLink
setUri(URI) - Method in class com.genologics.ri.stage.ProtocolStepLink
setUri(URI) - Method in class com.genologics.ri.stage.Stage
setUri(URI) - Method in class com.genologics.ri.stage.WorkflowLink
setUri(URI) - Method in class com.genologics.ri.step.Actions
setUri(URI) - Method in class com.genologics.ri.step.ActionsLink
setUri(URI) - Method in class com.genologics.ri.step.ArtifactLink
setUri(URI) - Method in class com.genologics.ri.step.AutomaticNextStepLink
setUri(URI) - Method in class com.genologics.ri.step.AvailableProgram
setUri(URI) - Method in class com.genologics.ri.step.ContainerLink
setUri(URI) - Method in class com.genologics.ri.step.CreationInput
setUri(URI) - Method in class com.genologics.ri.step.EscalatedArtifact
setUri(URI) - Method in class com.genologics.ri.step.Input
setUri(URI) - Method in class com.genologics.ri.step.InstrumentLink
setUri(URI) - Method in class com.genologics.ri.step.NextAction
setUri(URI) - Method in class com.genologics.ri.step.Output
setUri(URI) - Method in class com.genologics.ri.step.OutputPlacement
setUri(URI) - Method in class com.genologics.ri.step.Placements
setUri(URI) - Method in class com.genologics.ri.step.PlacementsLink
setUri(URI) - Method in class com.genologics.ri.step.Pools
setUri(URI) - Method in class com.genologics.ri.step.PoolsLink
setUri(URI) - Method in class com.genologics.ri.step.ProcessStep
setUri(URI) - Method in class com.genologics.ri.step.ProgramStatus
setUri(URI) - Method in class com.genologics.ri.step.ProgramStatusLink
setUri(URI) - Method in class com.genologics.ri.step.ReagentLotLink
setUri(URI) - Method in class com.genologics.ri.step.ReagentLots
setUri(URI) - Method in class com.genologics.ri.step.ReagentLotsLink
setUri(URI) - Method in class com.genologics.ri.step.Reagents
setUri(URI) - Method in class com.genologics.ri.step.ReagentsLink
setUri(URI) - Method in class com.genologics.ri.step.SharedResultFile
setUri(URI) - Method in class com.genologics.ri.step.StepConfiguration
setUri(URI) - Method in class com.genologics.ri.step.StepDetails
setUri(URI) - Method in class com.genologics.ri.step.StepDetailsLink
setUri(URI) - Method in class com.genologics.ri.step.StepSetup
setUri(URI) - Method in class com.genologics.ri.step.StepSetupLink
setUri(URI) - Method in class com.genologics.ri.step.UserLink
setUri(URI) - Method in class com.genologics.ri.stepconfiguration.ControlTypeLink
setUri(URI) - Method in class com.genologics.ri.stepconfiguration.NextStep
setUri(URI) - Method in class com.genologics.ri.stepconfiguration.ProcessTypeLink
setUri(URI) - Method in class com.genologics.ri.stepconfiguration.ProtocolStep
setUri(URI) - Method in class com.genologics.ri.stepconfiguration.ReagentKitLink
setUri(URI) - Method in class com.genologics.ri.version.Version
setUri(URI) - Method in class com.genologics.ri.workflowconfiguration.ProtocolLink
setUri(URI) - Method in class com.genologics.ri.workflowconfiguration.StageLink
setUri(URI) - Method in class com.genologics.ri.workflowconfiguration.Workflow
setUri(URI) - Method in class com.genologics.ri.workflowconfiguration.WorkflowLink
setUsageCount(Long) - Method in class com.genologics.ri.reagentlot.ReagentLot
setUserDefinedType(UDT) - Method in class com.genologics.ri.container.Container
setUserDefinedType(UDT) - Method in class com.genologics.ri.lab.Lab
setUserDefinedType(UDT) - Method in class com.genologics.ri.process.ClarityProcess
setUserDefinedType(UDT) - Method in class com.genologics.ri.processexecution.ExecutableProcess
setUserDefinedType(UDT) - Method in class com.genologics.ri.processtemplate.ProcessTemplate
setUserDefinedType(UDT) - Method in class com.genologics.ri.project.Project
setUserDefinedType(UDT) - Method in class com.genologics.ri.researcher.Researcher
setUserDefinedType(UDT) - Method in class com.genologics.ri.sample.SampleBase
setUserDefinedType(String) - Method in class com.genologics.ri.container.Container
setUserDefinedType(String) - Method in class com.genologics.ri.lab.Lab
setUserDefinedType(String) - Method in class com.genologics.ri.process.ClarityProcess
setUserDefinedType(String) - Method in class com.genologics.ri.processexecution.ExecutableProcess
setUserDefinedType(String) - Method in class com.genologics.ri.processtemplate.ProcessTemplate
setUserDefinedType(String) - Method in class com.genologics.ri.project.Project
setUserDefinedType(String) - Method in class com.genologics.ri.researcher.Researcher
setUserDefinedType(String) - Method in class com.genologics.ri.sample.SampleBase
setUsername(String) - Method in class com.genologics.ri.researcher.Credentials
setValue(Object) - Method in class com.genologics.ri.userdefined.UDF
setValue(String) - Method in class com.genologics.ri.containertype.CalibrantWell: Deprecated.
setValue(String) - Method in class com.genologics.ri.processtype.ProcessTypeAttribute
setValue(String) - Method in class com.genologics.ri.processtype.StepProperty
setValue(String) - Method in class com.genologics.ri.property.PropertyLink
setValue(String) - Method in class com.genologics.ri.protocolconfiguration.ProtocolProperty
setValue(String) - Method in class com.genologics.ri.reagenttype.Attribute
setValue(String) - Method in class com.genologics.ri.stepconfiguration.GenericTypeLink
setValue(String) - Method in class com.genologics.ri.stepconfiguration.StepProperty
setVariabilityType(VariabilityType) - Method in class com.genologics.ri.processtype.ProcessOutput
setVendor(String) - Method in class com.genologics.ri.instrumenttype.InstrumentType
setVendor(String) - Method in class com.genologics.ri.instrumenttype.InstrumentTypeLink
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
setWebsite(String) - Method in class com.genologics.ri.lab.Lab
setWebsite(String) - Method in class com.genologics.ri.reagentkit.ReagentKit
setWellPosition(String) - Method in class com.genologics.ri.container.Placement
setWellPosition(String) - Method in class com.genologics.ri.Location
setWorkflow(Linkable<Workflow>) - Method in class com.genologics.ri.routing.ExtArtifactAssignments
setWorkflow(Linkable<Workflow>) - Method in class com.genologics.ri.stage.Stage
setWorkflowStages(Collection<WorkflowStage>) - Method in class com.genologics.ri.artifact.Artifact
setWorkflowUri(URI) - Method in class com.genologics.ri.routing.ExtArtifactAssignments
setWorkingFlag(Boolean) - Method in class com.genologics.ri.artifact.Artifact
shared - Variable in class com.genologics.ri.processexecution.ExecutableInputOutputMap
SHARED_RESULT_FILE - Enum constant in enum com.genologics.ri.artifact.OutputType
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
SharedResultFile() - Constructor for class com.genologics.ri.step.SharedResultFile
SharedResultFile() - Constructor for class com.genologics.ri.stepconfiguration.SharedResultFile
SharedResultFile(LimsEntityLinkable<Artifact>) - Constructor for class com.genologics.ri.step.SharedResultFile
SharedResultFile(URI) - Constructor for class com.genologics.ri.step.SharedResultFile
SharedResultFile(URI, String) - Constructor for class com.genologics.ri.step.SharedResultFile
sharedResultFileIndex - Variable in class com.genologics.ri.processtype.SharedResultFile
sharedResultFileIndex - Variable in class com.genologics.ri.step.SharedResultFile
sharedResultFileIndex - Variable in class com.genologics.ri.stepconfiguration.SharedResultFile
shippingAddress - Variable in class com.genologics.ri.lab.Lab
ShortDateAdapter - Class in org.cruk.clarity.api.jaxb: Adapter for those dates that are exchanged with the API in the short date only format.
ShortDateAdapter() - Constructor for class org.cruk.clarity.api.jaxb.ShortDateAdapter: Empty constructor.
showInLablink - Variable in class com.genologics.ri.configuration.Field
showInTables - Variable in class com.genologics.ri.configuration.Field
singleStep - Variable in class com.genologics.ri.controltype.ControlType
size - Variable in class com.genologics.ri.containertype.Dimension
SKIPPED - Enum constant in enum com.genologics.ri.artifact.Status
specialType - Variable in class com.genologics.ri.reagenttype.ReagentType
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
SpecialType(String) - Constructor for class com.genologics.ri.reagenttype.SpecialType
SPOT_LIST - Enum constant in enum com.genologics.ri.artifact.OutputType
Stage - Class in com.genologics.ri.stage: The detailed representation of a stage.
Stage() - Constructor for class com.genologics.ri.stage.Stage
Stage(URI) - Constructor for class com.genologics.ri.stage.Stage
Stage(URI, String) - Constructor for class com.genologics.ri.stage.Stage
STAGE_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
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
StageLink(Linkable<Stage>) - Constructor for class com.genologics.ri.workflowconfiguration.StageLink
StageLink(URI) - Constructor for class com.genologics.ri.workflowconfiguration.StageLink
StageLink(URI, String) - Constructor for class com.genologics.ri.workflowconfiguration.StageLink
stages - Variable in class com.genologics.ri.workflowconfiguration.Workflow
stageUri - Variable in class com.genologics.ri.routing.ExtArtifactAssignments
STARTED - Enum constant in enum com.genologics.ri.processtype.TriggerStatus
STARTED - Enum constant in enum com.genologics.ri.step.ProcessState: The step state when the step is in the sample placement stage.
STARTED - Enum constant in enum com.genologics.ri.stepconfiguration.TriggerStatus
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
state - Variable in class com.genologics.ri.container.Container: Container state.
stateful() - Element in annotation type 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 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 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
status - Variable in class com.genologics.ri.processtype.EppTrigger
status - Variable in class com.genologics.ri.reagentlot.ReagentLot
status - Variable in class com.genologics.ri.step.ProgramStatus
status - Variable in class com.genologics.ri.stepconfiguration.EppTrigger
status - Variable in class com.genologics.ri.workflowconfiguration.Workflow
status - Variable in class com.genologics.ri.workflowconfiguration.WorkflowLink
Status - Enum in com.genologics.ri.artifact: The workflow stage status for the artifact.
Status - Enum in com.genologics.ri.reagentlot
Status - Enum in com.genologics.ri.step
Status - Enum in com.genologics.ri.workflowconfiguration
step - Variable in class com.genologics.ri.stage.Stage
step - Variable in class com.genologics.ri.step.Actions
step - Variable in class com.genologics.ri.step.Placements
step - Variable in class com.genologics.ri.step.Pools
step - Variable in class com.genologics.ri.step.ProgramStatus
step - Variable in class com.genologics.ri.step.ReagentLots
step - Variable in class com.genologics.ri.step.Reagents
step - Variable in class com.genologics.ri.step.StepDetails
step - Variable in class com.genologics.ri.step.StepSetup
STEP - Enum constant in enum com.genologics.ri.automation.Context
STEP_CONFIGURATION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
STEP_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
STEP_SETUP - Enum constant in enum com.genologics.ri.processtype.TriggerStatus
STEP_SETUP - Enum constant in enum com.genologics.ri.stepconfiguration.TriggerStatus
StepConfiguration - Class in com.genologics.ri.step: Identifies the configuration information for the step run.
StepConfiguration() - Constructor for class com.genologics.ri.step.StepConfiguration
StepConfiguration(Linkable<ProtocolStep>) - Constructor for class com.genologics.ri.step.StepConfiguration
StepConfiguration(URI) - Constructor for class com.genologics.ri.step.StepConfiguration
StepConfiguration(URI, String) - Constructor for class com.genologics.ri.step.StepConfiguration
StepCreation - Class in com.genologics.ri.step: A request to create a step.
StepCreation() - Constructor for class com.genologics.ri.step.StepCreation
StepCreation(Linkable<ProtocolStep>) - Constructor for class com.genologics.ri.step.StepCreation
StepCreation(StepConfiguration) - Constructor for class com.genologics.ri.step.StepCreation
StepDetails - Class in com.genologics.ri.step
StepDetails() - Constructor for class com.genologics.ri.step.StepDetails
StepDetails(URI) - Constructor for class com.genologics.ri.step.StepDetails
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
StepDetailsLink(Linkable<StepDetails>) - Constructor for class com.genologics.ri.step.StepDetailsLink
StepDetailsLink(URI) - Constructor for class com.genologics.ri.step.StepDetailsLink
stepFields - Variable in class com.genologics.ri.processtype.ProcessType
stepFields - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep
stepName - Variable in class com.genologics.ri.step.StepConfiguration
stepProperties - Variable in class com.genologics.ri.processtype.ProcessType
stepProperties - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep
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
StepProperty() - Constructor for class com.genologics.ri.stepconfiguration.StepProperty
StepProperty(String) - Constructor for class com.genologics.ri.stepconfiguration.StepProperty
StepProperty(String, String) - Constructor for class com.genologics.ri.stepconfiguration.StepProperty
steps - Variable in class com.genologics.ri.protocolconfiguration.Protocol
stepSetup - Variable in class com.genologics.ri.processtype.ProcessType
stepSetup - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep
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
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
StepSetup() - Constructor for class com.genologics.ri.step.StepSetup
StepSetup() - Constructor for class com.genologics.ri.stepconfiguration.StepSetup
StepSetup(URI) - Constructor for class com.genologics.ri.step.StepSetup
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
StepSetupLink(Linkable<StepSetup>) - Constructor for class com.genologics.ri.step.StepSetupLink
StepSetupLink(URI) - Constructor for class com.genologics.ri.step.StepSetupLink
stepUri - Variable in class com.genologics.ri.step.NextAction
storageLocation - Variable in class com.genologics.ri.reagentlot.ReagentLot
STORE - Enum constant in enum com.genologics.ri.step.ActionType
street - Variable in class com.genologics.ri.Address
STRING - Enum constant in enum com.genologics.ri.configuration.FieldType
style - Variable in class com.genologics.ri.processtype.Field
style - Variable in class com.genologics.ri.stepconfiguration.Field
Style - Enum in com.genologics.ri.processtype: The different styles of Fields.
Style - Enum in com.genologics.ri.stepconfiguration
submitter - Variable in class com.genologics.ri.sample.SampleBase
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
Submitter(Linkable<Researcher>) - Constructor for class com.genologics.ri.sample.Submitter
Submitter(URI) - Constructor for class com.genologics.ri.sample.Submitter
suggestedActions - Variable in class com.genologics.ri.exception.Exception
suggestedActions - Variable in exception org.cruk.clarity.api.ClarityException
supplier - Variable in class com.genologics.ri.controltype.ControlType
supplier - Variable in class com.genologics.ri.reagentkit.ReagentKit
SYSTEM_ADMIN_ROLE - Static variable in class com.genologics.ri.researcher.Role

T

technician - Variable in class com.genologics.ri.process.ClarityProcess
technician - Variable in class com.genologics.ri.processexecution.ExecutableProcess
technician - Variable in class com.genologics.ri.processtemplate.ProcessTemplate
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() - Constructor for class com.genologics.ri.process.Technician
Technician() - Constructor for class com.genologics.ri.processexecution.Technician
Technician() - Constructor for class com.genologics.ri.processtemplate.Technician
Technician(Linkable<Researcher>) - Constructor for class com.genologics.ri.process.Technician
Technician(Linkable<Researcher>) - Constructor for class com.genologics.ri.processexecution.Technician
Technician(Linkable<Researcher>) - Constructor for class com.genologics.ri.processtemplate.Technician
Technician(URI) - Constructor for class com.genologics.ri.process.Technician
Technician(URI) - Constructor for class com.genologics.ri.processexecution.Technician
Technician(URI) - Constructor for class com.genologics.ri.processtemplate.Technician
TEXT - Enum constant in enum com.genologics.ri.configuration.FieldType
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
toString() - Method in class com.genologics.ri.artifact.ArtifactGroupLink
toString() - Method in class com.genologics.ri.artifact.ArtifactLink
toString() - Method in class com.genologics.ri.artifact.DemuxArtifactSample
toString() - Method in class com.genologics.ri.artifact.DemuxSourceArtifact
toString() - Method in class com.genologics.ri.artifact.ParentProcessLink
toString() - Method in class com.genologics.ri.artifact.PoolStep
toString() - Method in class com.genologics.ri.artifact.ReagentLabel
toString() - Method in class com.genologics.ri.artifact.SampleLink
toString() - Method in class com.genologics.ri.artifact.WorkflowStage
toString() - Method in class com.genologics.ri.artifactgroup.ArtifactGroupLink
toString() - Method in class com.genologics.ri.automation.AutomationLink
toString() - Method in class com.genologics.ri.automation.ProcessTypeLink
toString() - Method in class com.genologics.ri.configuration.FieldLink
toString() - Method in class com.genologics.ri.configuration.TypeDefinition
toString() - Method in class com.genologics.ri.configuration.UdfConfigLink
toString() - Method in class com.genologics.ri.configuration.UdtConfigLink
toString() - Method in class com.genologics.ri.container.Container
toString() - Method in class com.genologics.ri.container.ContainerLink
toString() - Method in enum com.genologics.ri.container.ContainerState
toString() - Method in class com.genologics.ri.container.ContainerTypeLink
toString() - Method in class com.genologics.ri.container.Placement
toString() - Method in class com.genologics.ri.ContainerLink
toString() - Method in class com.genologics.ri.containertype.ContainerType
toString() - Method in class com.genologics.ri.containertype.ContainerTypeLink
toString() - Method in class com.genologics.ri.controltype.ControlTypeLink
toString() - Method in class com.genologics.ri.file.ClarityFile
toString() - Method in class com.genologics.ri.file.FileLink
toString() - Method in class com.genologics.ri.instrument.InstrumentLink
toString() - Method in class com.genologics.ri.lab.Lab
toString() - Method in class com.genologics.ri.lab.LabLink
toString() - Method in class com.genologics.ri.Link
toString() - Method in class com.genologics.ri.Location
toString() - Method in class com.genologics.ri.Page
toString() - Method in class com.genologics.ri.process.ArtifactLink
toString() - Method in class com.genologics.ri.process.ClarityProcess
toString() - Method in class com.genologics.ri.process.ParentProcessLink
toString() - Method in class com.genologics.ri.process.ProcessLink
toString() - Method in class com.genologics.ri.process.ProcessTypeLink
toString() - Method in class com.genologics.ri.process.Technician
toString() - Method in class com.genologics.ri.processtemplate.ProcessTemplateLink
toString() - Method in class com.genologics.ri.processtemplate.ProcessTypeLink
toString() - Method in class com.genologics.ri.processtemplate.Technician
toString() - Method in class com.genologics.ri.processtype.Field
toString() - Method in class com.genologics.ri.processtype.ProcessTypeLink
toString() - Method in class com.genologics.ri.processtype.TypeDefinition
toString() - Method in class com.genologics.ri.project.Project
toString() - Method in class com.genologics.ri.project.ProjectLink
toString() - Method in class com.genologics.ri.project.ResearcherLink
toString() - Method in class com.genologics.ri.protocolconfiguration.ProtocolLink
toString() - Method in class com.genologics.ri.queue.ArtifactLink
toString() - Method in class com.genologics.ri.reagentkit.ReagentKitLink
toString() - Method in class com.genologics.ri.reagentlot.ReagentKitLink
toString() - Method in class com.genologics.ri.reagentlot.ReagentLot
toString() - Method in class com.genologics.ri.reagentlot.ReagentLotLink
toString() - Method in class com.genologics.ri.reagenttype.ReagentType
toString() - Method in class com.genologics.ri.reagenttype.ReagentTypeLink
toString() - Method in class com.genologics.ri.researcher.Researcher
toString() - Method in class com.genologics.ri.researcher.ResearcherLink
toString() - Method in class com.genologics.ri.researcher.Role
toString() - Method in class com.genologics.ri.role.ResearcherLink
toString() - Method in class com.genologics.ri.role.RoleLink
toString() - Method in class com.genologics.ri.sample.ArtifactLink
toString() - Method in class com.genologics.ri.sample.ControlTypeLink
toString() - Method in class com.genologics.ri.sample.ProjectLink
toString() - Method in class com.genologics.ri.sample.SampleBase
toString() - Method in class com.genologics.ri.sample.SampleLink
toString() - Method in class com.genologics.ri.sample.Submitter
toString() - Method in class com.genologics.ri.step.Actions
toString() - Method in class com.genologics.ri.step.ArtifactLink
toString() - Method in class com.genologics.ri.step.InstrumentLink
toString() - Method in class com.genologics.ri.step.NextAction
toString() - Method in class com.genologics.ri.step.OutputPlacement
toString() - Method in enum com.genologics.ri.step.ProcessState
toString() - Method in class com.genologics.ri.step.ReagentLabel
toString() - Method in class com.genologics.ri.step.ReagentLotLink
toString() - Method in class com.genologics.ri.step.SharedResultFile
toString() - Method in class com.genologics.ri.step.UserLink
toString() - Method in class com.genologics.ri.stepconfiguration.ControlTypeLink
toString() - Method in class com.genologics.ri.stepconfiguration.GenericTypeLink
toString() - Method in class com.genologics.ri.stepconfiguration.ProcessTypeLink
toString() - Method in class com.genologics.ri.stepconfiguration.ReagentKitLink
toString() - Method in class com.genologics.ri.userdefined.UDF
toString() - Method in class com.genologics.ri.workflowconfiguration.ProtocolLink
toString() - Method in class com.genologics.ri.workflowconfiguration.StageLink
toString() - Method in class com.genologics.ri.workflowconfiguration.WorkflowLink
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.
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
TriggerPoint - Enum in com.genologics.ri.processtype: The trigger-point enumeration lists the possible values of the EPP Trigger point attribute.
TriggerPoint - Enum in com.genologics.ri.stepconfiguration
TriggerStatus - Enum in com.genologics.ri.processtype: The trigger-status enumeration lists the possible values of the EPP Trigger status attribute.
TriggerStatus - Enum in com.genologics.ri.stepconfiguration
TriggerType - Enum in com.genologics.ri.processtype: The trigger-type enumeration lists the possible values of the EPP Trigger type attribute.
TriggerType - Enum in com.genologics.ri.stepconfiguration
tube - Variable in class com.genologics.ri.containertype.ContainerType
type - Variable in class com.genologics.ri.artifact.Artifact
type - Variable in class com.genologics.ri.configuration.Field
type - Variable in class com.genologics.ri.container.Container
type - Variable in class com.genologics.ri.instrument.Instrument
type - Variable in class com.genologics.ri.lab.Lab
type - Variable in class com.genologics.ri.process.ClarityProcess
type - Variable in class com.genologics.ri.processexecution.ExecutableProcess
type - Variable in class com.genologics.ri.processexecution.Output
type - Variable in class com.genologics.ri.processtemplate.ProcessTemplate
type - Variable in class com.genologics.ri.processtype.EppTrigger
type - Variable in class com.genologics.ri.project.Project
type - Variable in class com.genologics.ri.researcher.Researcher
type - Variable in class com.genologics.ri.sample.SampleBase
type - Variable in class com.genologics.ri.step.ArtifactLink
type - Variable in class com.genologics.ri.stepconfiguration.EppTrigger
type - Variable in class com.genologics.ri.userdefined.UDF
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
typeDefinition - Variable in class com.genologics.ri.configuration.Field
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
TypeDefinition() - Constructor for class com.genologics.ri.processtype.TypeDefinition
TypeDefinition(Linkable<Field>) - Constructor for class com.genologics.ri.processtype.TypeDefinition
TypeDefinition(Linkable<Type>) - Constructor for class com.genologics.ri.configuration.TypeDefinition
TypeDefinition(URI) - Constructor for class com.genologics.ri.configuration.TypeDefinition
TypeDefinition(URI) - Constructor for class com.genologics.ri.processtype.TypeDefinition
TypeDefinition(URI, String) - Constructor for class com.genologics.ri.configuration.TypeDefinition
TypeDefinition(URI, String) - Constructor for class com.genologics.ri.processtype.TypeDefinition
typeDefinitions - Variable in class com.genologics.ri.processtype.ProcessType

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
UDF(String, FieldType) - Constructor for class com.genologics.ri.userdefined.UDF
UDF(String, FieldType, Object) - Constructor for class com.genologics.ri.userdefined.UDF
UDF(String, Object) - Constructor for class com.genologics.ri.userdefined.UDF
UDF_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
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
UdfConfigLink(Field) - Constructor for class com.genologics.ri.configuration.UdfConfigLink
UdfConfigLink(URI) - Constructor for class com.genologics.ri.configuration.UdfConfigLink
udfConfigLinks - Variable in class com.genologics.ri.configuration.Udfs
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
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
UDT(String) - Constructor for class com.genologics.ri.userdefined.UDT
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
UdtConfigLink(Type) - Constructor for class com.genologics.ri.configuration.UdtConfigLink
UdtConfigLink(URI) - Constructor for class com.genologics.ri.configuration.UdtConfigLink
udtConfigLinks - Variable in class com.genologics.ri.configuration.Udts
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
unassignedRoutes - Variable in class com.genologics.ri.routing.Routing
unavailableWells - Variable in class com.genologics.ri.containertype.ContainerType
unit - Variable in class com.genologics.ri.userdefined.UDF
unitLabel - Variable in class com.genologics.ri.configuration.Field
UNKNOWN - Enum constant in enum com.genologics.ri.artifact.QCFlag
UNKNOWN - Enum constant in enum com.genologics.ri.processexecution.QCFlag
UNKNOWN - Enum constant in enum com.genologics.ri.step.ActionType
unmarshal(String) - Method in class org.cruk.clarity.api.jaxb.AbstractDateAdapter: Parse the string into a Date object.
unmarshal(String) - Method in class org.cruk.clarity.api.jaxb.URIAdapter: Convert a string into a URI.
UNUSED - Enum constant in enum com.genologics.ri.processtype.TriggerType
UNUSED - Enum constant in enum com.genologics.ri.stepconfiguration.TriggerType
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 type 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
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.
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
uri - Variable in class com.genologics.ri.artifact.ArtifactGroupLink
uri - Variable in class com.genologics.ri.artifact.ArtifactLink
uri - Variable in class com.genologics.ri.artifact.ControlTypeLink
uri - Variable in class com.genologics.ri.artifact.Demux
uri - Variable in class com.genologics.ri.artifact.DemuxArtifact
uri - Variable in class com.genologics.ri.artifact.DemuxArtifactSample
uri - Variable in class com.genologics.ri.artifact.DemuxLink
uri - Variable in class com.genologics.ri.artifact.DemuxSourceArtifact
uri - Variable in class com.genologics.ri.artifact.ParentProcessLink
uri - Variable in class com.genologics.ri.artifact.PoolStep
uri - Variable in class com.genologics.ri.artifact.SampleLink
uri - Variable in class com.genologics.ri.artifact.WorkflowStage
uri - Variable in class com.genologics.ri.artifactgroup.ArtifactGroup
uri - Variable in class com.genologics.ri.artifactgroup.ArtifactGroupLink
uri - Variable in class com.genologics.ri.artifactgroup.Artifacts
uri - Variable in class com.genologics.ri.automation.Automation
uri - Variable in class com.genologics.ri.automation.AutomationLink
uri - Variable in class com.genologics.ri.automation.Automations
uri - Variable in class com.genologics.ri.automation.ProcessTypeLink
uri - Variable in class com.genologics.ri.configuration.Field
uri - Variable in class com.genologics.ri.configuration.FieldLink
uri - Variable in class com.genologics.ri.configuration.Type
uri - Variable in class com.genologics.ri.configuration.TypeDefinition
uri - Variable in class com.genologics.ri.configuration.UdfConfigLink
uri - Variable in class com.genologics.ri.configuration.UdtConfigLink
uri - Variable in class com.genologics.ri.container.Container
uri - Variable in class com.genologics.ri.container.ContainerLink
uri - Variable in class com.genologics.ri.container.ContainerTypeLink
uri - Variable in class com.genologics.ri.container.Placement
uri - Variable in class com.genologics.ri.ContainerLink
uri - Variable in class com.genologics.ri.containertype.ContainerType
uri - Variable in class com.genologics.ri.containertype.ContainerTypeLink
uri - Variable in class com.genologics.ri.controltype.ControlType
uri - Variable in class com.genologics.ri.controltype.ControlTypeLink
uri - Variable in class com.genologics.ri.controltype.ControlTypes
uri - Variable in class com.genologics.ri.ExternalId
uri - Variable in class com.genologics.ri.file.ClarityFile
uri - Variable in class com.genologics.ri.file.FileLink
uri - Variable in class com.genologics.ri.instrument.Instrument
uri - Variable in class com.genologics.ri.instrument.InstrumentLink
uri - Variable in class com.genologics.ri.instrumenttype.InstrumentType
uri - Variable in class com.genologics.ri.instrumenttype.InstrumentTypeLink
uri - Variable in class com.genologics.ri.instrumenttype.InstrumentTypeProcessType
uri - Variable in class com.genologics.ri.lab.Lab
uri - Variable in class com.genologics.ri.lab.LabLink
uri - Variable in class com.genologics.ri.Link
uri - Variable in class com.genologics.ri.Page
uri - Variable in class com.genologics.ri.permission.Permission
uri - Variable in class com.genologics.ri.permission.PermissionLink
uri - Variable in class com.genologics.ri.permission.Permissions
uri - Variable in class com.genologics.ri.process.ArtifactLink
uri - Variable in class com.genologics.ri.process.ClarityProcess
uri - Variable in class com.genologics.ri.process.InstrumentLink
uri - Variable in class com.genologics.ri.process.ParentProcessLink
uri - Variable in class com.genologics.ri.process.ProcessLink
uri - Variable in class com.genologics.ri.process.ProcessTypeLink
uri - Variable in class com.genologics.ri.process.Technician
uri - Variable in class com.genologics.ri.processexecution.Input
uri - Variable in class com.genologics.ri.processexecution.InstrumentLink
uri - Variable in class com.genologics.ri.processexecution.Technician
uri - Variable in class com.genologics.ri.processtemplate.InstrumentLink
uri - Variable in class com.genologics.ri.processtemplate.ProcessTemplate
uri - Variable in class com.genologics.ri.processtemplate.ProcessTemplateLink
uri - Variable in class com.genologics.ri.processtemplate.ProcessTypeLink
uri - Variable in class com.genologics.ri.processtemplate.Technician
uri - Variable in class com.genologics.ri.processtype.ContainerTypeLink
uri - Variable in class com.genologics.ri.processtype.ControlTypeLink
uri - Variable in class com.genologics.ri.processtype.ProcessType
uri - Variable in class com.genologics.ri.processtype.ProcessTypeLink
uri - Variable in class com.genologics.ri.processtype.ReagentKitLink
uri - Variable in class com.genologics.ri.processtype.TypeDefinition
uri - Variable in class com.genologics.ri.project.Project
uri - Variable in class com.genologics.ri.project.ProjectLink
uri - Variable in class com.genologics.ri.project.ResearcherLink
uri - Variable in class com.genologics.ri.property.PropertyLink
uri - Variable in class com.genologics.ri.protocolconfiguration.Protocol
uri - Variable in class com.genologics.ri.protocolconfiguration.ProtocolLink
uri - Variable in class com.genologics.ri.queue.ArtifactLink
uri - Variable in class com.genologics.ri.queue.Queue
uri - Variable in class com.genologics.ri.reagentkit.ReagentKit
uri - Variable in class com.genologics.ri.reagentkit.ReagentKitLink
uri - Variable in class com.genologics.ri.reagentkit.ReagentKits
uri - Variable in class com.genologics.ri.reagentlot.ReagentKitLink
uri - Variable in class com.genologics.ri.reagentlot.ReagentLot
uri - Variable in class com.genologics.ri.reagentlot.ReagentLotLink
uri - Variable in class com.genologics.ri.reagentlot.ReagentLots
uri - Variable in class com.genologics.ri.reagentlot.ResearcherLink
uri - Variable in class com.genologics.ri.reagenttype.ReagentType
uri - Variable in class com.genologics.ri.reagenttype.ReagentTypeLink
uri - Variable in class com.genologics.ri.researcher.LabLink
uri - Variable in class com.genologics.ri.researcher.Researcher
uri - Variable in class com.genologics.ri.researcher.ResearcherLink
uri - Variable in class com.genologics.ri.researcher.Role
uri - Variable in class com.genologics.ri.role.PermissionLink
uri - Variable in class com.genologics.ri.role.ResearcherLink
uri - Variable in class com.genologics.ri.role.Role
uri - Variable in class com.genologics.ri.role.RoleLink
uri - Variable in class com.genologics.ri.role.Roles
uri - Variable in class com.genologics.ri.routing.ArtifactLink
uri - Variable in class com.genologics.ri.sample.ArtifactLink
uri - Variable in class com.genologics.ri.sample.ControlTypeLink
uri - Variable in class com.genologics.ri.sample.ProjectLink
uri - Variable in class com.genologics.ri.sample.SampleBase
uri - Variable in class com.genologics.ri.sample.SampleLink
uri - Variable in class com.genologics.ri.sample.Submitter
uri - Variable in class com.genologics.ri.stage.ProtocolLink
uri - Variable in class com.genologics.ri.stage.ProtocolStepLink
uri - Variable in class com.genologics.ri.stage.Stage
uri - Variable in class com.genologics.ri.stage.WorkflowLink
uri - Variable in class com.genologics.ri.step.Actions
uri - Variable in class com.genologics.ri.step.ActionsLink
uri - Variable in class com.genologics.ri.step.ArtifactLink
uri - Variable in class com.genologics.ri.step.AutomaticNextStepLink
uri - Variable in class com.genologics.ri.step.AvailableProgram
uri - Variable in class com.genologics.ri.step.ContainerLink
uri - Variable in class com.genologics.ri.step.CreationInput
uri - Variable in class com.genologics.ri.step.EscalatedArtifact
uri - Variable in class com.genologics.ri.step.Input
uri - Variable in class com.genologics.ri.step.InstrumentLink
uri - Variable in class com.genologics.ri.step.OutputPlacement
uri - Variable in class com.genologics.ri.step.Placements
uri - Variable in class com.genologics.ri.step.PlacementsLink
uri - Variable in class com.genologics.ri.step.Pools
uri - Variable in class com.genologics.ri.step.PoolsLink
uri - Variable in class com.genologics.ri.step.ProcessStep
uri - Variable in class com.genologics.ri.step.ProgramStatus
uri - Variable in class com.genologics.ri.step.ProgramStatusLink
uri - Variable in class com.genologics.ri.step.ReagentLotLink
uri - Variable in class com.genologics.ri.step.ReagentLots
uri - Variable in class com.genologics.ri.step.ReagentLotsLink
uri - Variable in class com.genologics.ri.step.Reagents
uri - Variable in class com.genologics.ri.step.ReagentsLink
uri - Variable in class com.genologics.ri.step.StepDetails
uri - Variable in class com.genologics.ri.step.StepDetailsLink
uri - Variable in class com.genologics.ri.step.StepSetup
uri - Variable in class com.genologics.ri.step.StepSetupLink
uri - Variable in class com.genologics.ri.step.UserLink
uri - Variable in class com.genologics.ri.stepconfiguration.ControlTypeLink
uri - Variable in class com.genologics.ri.stepconfiguration.ProcessTypeLink
uri - Variable in class com.genologics.ri.stepconfiguration.ProtocolStep
uri - Variable in class com.genologics.ri.stepconfiguration.ReagentKitLink
uri - Variable in class com.genologics.ri.version.Version
uri - Variable in class com.genologics.ri.workflowconfiguration.ProtocolLink
uri - Variable in class com.genologics.ri.workflowconfiguration.StageLink
uri - Variable in class com.genologics.ri.workflowconfiguration.Workflow
uri - Variable in class com.genologics.ri.workflowconfiguration.WorkflowLink
URI - Enum constant in enum com.genologics.ri.configuration.FieldType
URIAdapter - Class in org.cruk.clarity.api.jaxb: Convert to and from URI objects, correctly encoding the query string.
URIAdapter() - Constructor for class org.cruk.clarity.api.jaxb.URIAdapter
uriSection() - Element in annotation type 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 type 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
USER_DEFINED - Enum constant in enum com.genologics.ri.processtype.Style
USER_DEFINED - Enum constant in enum com.genologics.ri.stepconfiguration.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
UserLink(Linkable<Researcher>) - Constructor for class com.genologics.ri.step.UserLink
UserLink(URI) - Constructor for class com.genologics.ri.step.UserLink
username - Variable in class com.genologics.ri.researcher.Credentials

V

value - Variable in class com.genologics.ri.containertype.CalibrantWell: Deprecated.
value - Variable in class com.genologics.ri.processtype.ProcessTypeAttribute
value - Variable in class com.genologics.ri.processtype.StepProperty
value - Variable in class com.genologics.ri.property.PropertyLink
value - Variable in class com.genologics.ri.protocolconfiguration.ProtocolProperty
value - Variable in class com.genologics.ri.reagenttype.Attribute
value - Variable in class com.genologics.ri.stepconfiguration.GenericTypeLink
value - Variable in class com.genologics.ri.stepconfiguration.StepProperty
value - Variable in class com.genologics.ri.userdefined.UDF
value() - Method in enum com.genologics.ri.artifact.OutputType
value() - Method in enum com.genologics.ri.artifact.QCFlag
value() - Method in enum com.genologics.ri.artifact.Status
value() - Method in enum com.genologics.ri.automation.Context
value() - Method in enum com.genologics.ri.configuration.FieldType
value() - Method in enum com.genologics.ri.container.ContainerState
value() - Method in enum com.genologics.ri.process.OutputGenerationType
value() - Method in enum com.genologics.ri.processexecution.QCFlag
value() - Method in enum com.genologics.ri.processtype.InvocationType
value() - Method in enum com.genologics.ri.processtype.OutputGenerationType
value() - Method in enum com.genologics.ri.processtype.Style
value() - Method in enum com.genologics.ri.processtype.TriggerPoint
value() - Method in enum com.genologics.ri.processtype.TriggerStatus
value() - Method in enum com.genologics.ri.processtype.TriggerType
value() - Method in enum com.genologics.ri.processtype.VariabilityType
value() - Method in enum com.genologics.ri.step.ActionType
value() - Method in enum com.genologics.ri.step.OutputGenerationType
value() - Method in enum com.genologics.ri.step.ProcessState
value() - Method in enum com.genologics.ri.step.Status
value() - Method in enum com.genologics.ri.stepconfiguration.Style
value() - Method in enum com.genologics.ri.stepconfiguration.TriggerPoint
value() - Method in enum com.genologics.ri.stepconfiguration.TriggerStatus
value() - Method in enum com.genologics.ri.stepconfiguration.TriggerType
value() - Method in enum com.genologics.ri.workflowconfiguration.Status
valueOf(String) - Static method in enum com.genologics.ri.artifact.OutputType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.artifact.QCFlag: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.artifact.Status: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.automation.Context: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.configuration.FieldType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.container.ContainerState: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.process.OutputGenerationType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.processexecution.QCFlag: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.processtype.InvocationType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.processtype.OutputGenerationType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.processtype.Style: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.processtype.TriggerPoint: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.processtype.TriggerStatus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.processtype.TriggerType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.processtype.VariabilityType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.reagentlot.Status: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.step.ActionType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.step.OutputGenerationType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.step.ProcessState: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.step.Status: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.stepconfiguration.Style: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.stepconfiguration.TriggerPoint: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.stepconfiguration.TriggerStatus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.stepconfiguration.TriggerType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.genologics.ri.workflowconfiguration.Status: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.cruk.clarity.api.cache.CacheStatefulBehaviour: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.cruk.clarity.api.StatefulOverride: Returns the enum constant of this type with the specified name.
values() - Static method in enum com.genologics.ri.artifact.OutputType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.artifact.QCFlag: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.artifact.Status: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.automation.Context: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.configuration.FieldType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.container.ContainerState: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.process.OutputGenerationType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.processexecution.QCFlag: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.processtype.InvocationType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.processtype.OutputGenerationType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.processtype.Style: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.processtype.TriggerPoint: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.processtype.TriggerStatus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.processtype.TriggerType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.processtype.VariabilityType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.reagentlot.Status: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.step.ActionType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.step.OutputGenerationType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.step.ProcessState: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.step.Status: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.stepconfiguration.Style: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.stepconfiguration.TriggerPoint: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.stepconfiguration.TriggerStatus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.stepconfiguration.TriggerType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.genologics.ri.workflowconfiguration.Status: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.cruk.clarity.api.cache.CacheStatefulBehaviour: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.cruk.clarity.api.StatefulOverride: Returns an array containing the constants of this enum type, in the order they are declared.
variabilityType - Variable in class com.genologics.ri.processtype.ProcessOutput
VariabilityType - Enum in com.genologics.ri.processtype
VARIABLE - Enum constant in enum com.genologics.ri.processtype.VariabilityType
VARIABLE_BY_INPUT - Enum constant in enum com.genologics.ri.processtype.VariabilityType
vendor - Variable in class com.genologics.ri.instrumenttype.InstrumentType
vendor - Variable in class com.genologics.ri.instrumenttype.InstrumentTypeLink
Version - Class in com.genologics.ri.version
Version() - Constructor for class com.genologics.ri.version.Version
VERSION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
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
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

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 com.genologics.ri.step.Status
website - Variable in class com.genologics.ri.controltype.ControlType
website - Variable in class com.genologics.ri.lab.Lab
website - Variable in class com.genologics.ri.reagentkit.ReagentKit
WELL_POSITION_SPLITTER - Static variable in class com.genologics.ri.Location
wellPosition - Variable in class com.genologics.ri.container.Placement
workflow - Variable in class com.genologics.ri.stage.Stage
Workflow - Class in com.genologics.ri.workflowconfiguration: The detailed representation of a Workflow.
Workflow() - Constructor for class com.genologics.ri.workflowconfiguration.Workflow
Workflow(URI) - Constructor for class com.genologics.ri.workflowconfiguration.Workflow
Workflow(URI, String) - Constructor for class com.genologics.ri.workflowconfiguration.Workflow
WORKFLOW_CONFIGURATION_NAMESPACE - Static variable in class com.genologics.ri.Namespaces
WorkflowLink - Class in com.genologics.ri.stage: Workflow link for the 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
WorkflowLink() - Constructor for class com.genologics.ri.workflowconfiguration.WorkflowLink
WorkflowLink(Linkable<Workflow>) - Constructor for class com.genologics.ri.stage.WorkflowLink
WorkflowLink(Linkable<Workflow>) - Constructor for class com.genologics.ri.workflowconfiguration.WorkflowLink
WorkflowLink(URI) - Constructor for class com.genologics.ri.stage.WorkflowLink
WorkflowLink(URI) - Constructor for class com.genologics.ri.workflowconfiguration.WorkflowLink
WorkflowLink(URI, String) - Constructor for class com.genologics.ri.workflowconfiguration.WorkflowLink
workflows - Variable in class com.genologics.ri.workflowconfiguration.Workflows
Workflows - Class in com.genologics.ri.workflowconfiguration: The representation of a list of Workflow links.
Workflows() - Constructor for class com.genologics.ri.workflowconfiguration.Workflows
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
WorkflowStage(URI) - Constructor for class com.genologics.ri.artifact.WorkflowStage
WorkflowStage(URI, String) - Constructor for class com.genologics.ri.artifact.WorkflowStage
WorkflowStage(URI, String, Status) - Constructor for class com.genologics.ri.artifact.WorkflowStage
workflowStages - Variable in class com.genologics.ri.artifact.Artifact
workflowUri - Variable in class com.genologics.ri.routing.ExtArtifactAssignments
workingFlag - Variable in class com.genologics.ri.artifact.Artifact

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