All Classes and Interfaces

Class
Description
Base for date adapters.
Represents actions applied or to be applied by a step in the workflow.
Identifies the resource that represents the actions applied or to be applied by the step.
Enumeration of action types that can be performed on artifacts in a step.
Address contains the related fields of a mailing address.
The detailed representation of a step's output container Tube Rack arrangements only for an Add Label Step.
Identifies the resource that represents the arrangements (if any) for the step.
The detailed representation of an Artifact.
The base representation of an Artifact in the context of Process execution, defining common elements for both input and output Artifacts.
The representation of a batch fetch result for artifacts.
ArtifactGroups are created by the Lab Scientist interface for each workflow.
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.
artifactGroup-link is a child element type of artifactGroup and provides a URI linking to the detailed representation of a artifactGroup.
The representation of a list of artifactGroup links.
Artifact-link is a child element type of artifacts and provides a URI linking to the detailed representation of an artifact.
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.
Artifact-Link provides a URI linking to the detailed representation of an artifact in a queue.
Link to an artifact for routing purposes.
Artifact is a child element of Sample and provides a URI linking to the detailed representation of the artifact for the Sample.
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.
The representation of a list of artifact links.
Artifacts is a link to 1...n child artifacts, that belong to the artifactGroup The link to an artifactList, filtered on artifactgroupID
Attribute is a child element of special type and provides a name-value pair of the special type.
Extension of the ClientHttpRequestFactory interface to allow authentication to be used with the REST client.
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.
The automation element integrates the process with the Automation Worker (previously called External Program Plugin or EPP).
A link to an Automation entity.
A list of automation links returned from a query.
Identifies a program that is available for a step.
Interface for objects that hold batches of linkable items (links or entities).
Extension of the Batch interface for classes that support bulk create or update operations for entities.
Deprecated.
Biosource is not supported in Clarity.
Options for how the API cache handles entities that are stateful.
Deprecated.
This type is no longer supported.
Interface to the Clarity API version 2 via REST.
A cache optionally deployed around a ClarityAPI bean as an aspect.
Implementation of ClarityAPI using the Clarity REST operations.
Interface to the Clarity API for internal use, mostly by the cache.
Aspect for replaying server exchanges from a directory containing XML representations of entities as would be returned from a real Clarity server.
Aspect for recording server exchanges with a real Clarity server as XML files to a directory on disk.
Runtime exception when there is a failure in automating a Clarity process.
Annotation for classes that contain lists of entities fetched from the API's batch retrieve mechanism.
Spring configuration class for the Clarity API cache.
Main Spring configuration for the Clarity Client.
Spring configuration for playback.
Spring configuration for recording.
Spring configuration for the Clarity Client with searches.
Annotation to put on classes that are entities in the Clarity LIMS.
Exception decoded when a response from an API call gives an exception object.
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.
The file element contains information about a file in the system.
The representation of a batch of file resources.
The representation for a list of file links.
The detailed representation of a process.
Helper for moving Clarity processes through their stages using the "click through" newer methods rather than the API's ExecutableProcess end point.
Helper for moving Clarity processes through their stages using the "click through" newer methods rather than the API's ExecutableProcess end point.
The representation of a list of process links.
Annotation to put on classes that are the results of querying the API for entities.
Interface for SFTP file store upload and delete implementations to adhere to.
Exception thrown when an attempt is made to change an object that cannot be altered in such a manner through the Clarity API.
Container entity representing a physical container in the Clarity LIMS.
The representation of a list of resource details for batch operations on containers.
Container-link is a child element type of containers and provides a URI linking to the detailed representation of a container.
Container is a child element of location and provides a URI linking to the detailed representation of the Container for the location.
Provides a URI linking to a selected container to be used for placement.
The representation for a list of container links.
An enumeration of the values possible in the Container.state attribute.
The detailed representation of a container type.
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.
Container-type-link is a child element type of containers and provides a URI linking to the detailed representation of a container type.
Link to a container type within a process type configuration.
The representation for a list of container type links.
The available options for the automation context.
Represents a control type in the Clarity LIMS system.
Provide a URI linking to the control type if this artifact is a control sample.
Control-type-link is a child element type of controlTypes and provides a URI linking to the detailed representation of a ControlType.
Link to a control type within a process type configuration.
Control Type provides a name and a URI linking to the detailed representation of the Control Type associated with the Sample.
Control-type-link is a child element type of controlTypes and provides a URI linking to the detailed representation of a ControlType.
The representation of a list of control types in the Clarity LIMS system.
Typically, provides a URI linking to the input artifact.
The credentials element contains information about a researcher's access to the client software interface.
The detailed representation of the demultiplexing of a pooled artifact.
Details of an individual artifact that is part of a pooled artifact.
The details of a sample that is part of a pooled artifact.
Demultiplexing of the Artifact showing all pooling steps that this artifact has been part of.
Identifies the resource that will demultiplex this artifact.
Link to a source artifact for demultiplexing.
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.
EPP trigger configuration for the Master Step.
EPP trigger configuration for the Protocol Step.
Sample next action or step.
Escalation details.
Represents an escalation request in a step.
Represents an escalation review in a step.
Exception is a descriptive error message that is returned instead of the standard response for any request that the system was unable to process.
Processes link inputs to outputs and this relationship is called an input-output map.
The process element defines the XML needed to run a process.
External artifact assignments for routing to workflows and stages.
An external id is a reference to an identifier in an external system that contains additional information about a representation within the API.
The detailed representation of the configuration of a user-defined field.
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
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.
The detailed representation of a field dynamic UDF preset.
The representation of a list of field dynamic UDF preset.
Field definition represents a user-defined field configured in the parent entity.
UDF field types.
The file-link type provides a URI that links to information about a file in the system.
Generic-type is a lockable child element that provides a name linking an entity to the step.
Clarity global token.
global-token-link is a child element type of global tokens and provides a URI linking to the detailed representation of a global token.
List of global token links.
Testing aspect that reports on the calls being made by the HTTP client talking to the Clarity API.
Client HTTP request factory adding basic authentication to the request.
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.
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
Exception raised when a search for entities is provided with search terms that are illegal.
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.
The input element provides URIs to one or more Artifacts that will be used by the Process.
Provides input URI links.
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.
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.
The detailed representation of an instrument.
Instrument-link is a child element type of instruments and provides a URI linking to the detailed representation of an instrument.
The instrument element provides a URI to the instrument that is responsible for running the process.
The instrument element provides a URI to the instrument that is responsible for running the process.
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.
The instrument element provides a URI to the selected instrument for the step.
The representation of a list of instrument links.
An instrument describes properties common to all instruments of that type.
Instrument-type-link provides a URI linking to the detailed representation of an instrument type.
Process type link for instrument types.
The representation of a list of instrument type links.
Exception raised when a URI or URL object is created from a string but the string isn't a valid URI or URL.
Enumeration of EPP invocation types.
Tool to help debugging: a short cut for marshalling an object to a string.
Aspect that wraps the unmarshalling of responses from the Clarity API.
The detailed representation of a lab.
Lab-link is a child element type of labs and provides a URI linking to the detailed representation of a lab.
Lab is a child element of researcher and provides a URI linking to the detailed representation of the lab for the researcher.
The representation of a list of lab links.
Aspect to ensure that the API will not fetch the latest versions of stateful entities on the next call.
Interface for all objects that are real LIMS entities (i.e. not links or other references).
Interface for links to LimsEntity objects.
Interface for entities and links to entities that are identifiable in the system (i.e. have a LIMS id).
Helper base class for LimsEntityLink implementations extending from LimsLinkBase.
Interface for classes that are links to real LIMS objects.
JAXB adapter for dealing with LimsLink objects.
Helper base class for LimsLink implementations that implements LimsLinkBase.hashCode() and LimsLinkBase.equals(Object) to consider links that point to the same entities as equivalent.
A link provides a URI linking to an additional resource.
Marker interface that indicates a locatable object can be linked to.
The representation of a list of resource links.
Interface for LIMS objects that can be located via a URI.
Location provides a URI linking to the detailed representation of a Container along with the well location within that Container.
A protocol step setting is considered locked if the Master Step has defined that setting.
Adapter for those dates that are exchanged with the API in the long timestamp format.
Exception thrown when a required user-defined field is not found.
Static list of all the namespaces in the Genologics API.
Sample next action or step.
List of step transitions including the URI allowing access to the specific next step
Exception thrown when an entity or search is requested that has no recording in the playback message directory.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.artifact package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.artifactgroup package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.automation package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.configuration package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.container package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.containertype package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.controltype package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.exception package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.file package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.globaltoken package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.instrument package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.instrumenttype package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.lab package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.permission package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.process package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.processexecution package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.processtemplate package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.processtype package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.project package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.property package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.protocolconfiguration package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.queue package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.reagentkit package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.reagentlot package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.reagenttype package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.researcher package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.role package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.routing package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.sample package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.savedquery package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.stage package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.step package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.stepconfiguration package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.userdefined package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.version package.
Factory class for creating instances of JAXB content classes defined in the com.genologics.ri.workflowconfiguration package.
The output element provides information about the Artifacts that will be created by the Process.
Provides a URI linking to the output artifact and reagent label.
Provides a URI linking to the output container and Tube Rack arrangement.
The output generation type enumeration.
Enumeration of output generation types for process outputs.
Enumeration of output generation types for step artifacts.
Provides a URI linking to the output artifact and container placement.
Enumeration of artifact output types.
The link to a page of additional content.
Interface for objects that hold paginated batches of links to entities.
The parameter is a child element of process that integrates the Process with the External Program Integration plug-in (EPP).
The parameter is a child element of process execution that integrates the Process with the External Program Integration plug-in (EPP).
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).
The parameter element integrates the process with the External Program Integration plug-in (EPP).
Parent-process is a child element of Artifact and provides a URI linking to the detailed representation of the process that produced the Artifact.
Parent-process is a child element of Artifact and provides a URI linking to the Process that created the Artifact.
The detailed representation of a permission.
Permission-link provides a URI linking to the detailed representation of a permission.
Permission-link is a child element type of permissions and provides a URI linking to the detailed representation of a Permission.
The representation of a list of permission links.
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.
The detailed representation of a step's output artifact container placements
Identifies the resource that represents the output placements for the step.
Provides pooled input groups.
The detailed representation of a step's pooled inputs.
Identifies the resource that represents the pools added by the step.
The details of the pooling step that created the pooled sample(s).
Process-input is a child element of process type specifying the available input types for the process
Process-link is a child element type of process and provides a URI linking to the detailed representation of a process.
Process-output is a child element of process type specifying the configured output generation types for the process
An enumeration of the values possible in the ProcessStep.currentState attribute.
The detailed representation of a step.
The detailed representation of a Process Template.
process-template-link is a child element type of Process Templates and provides a URI linking to the detailed representation of a Process Template.
The representation of a list of Process Template links.
The process-type element contains the XML representation of a type of process configured in the system.
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.
Provides links to process types the automation is enabled on.
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.
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.
Process-type-link is a child element type of process types and provides a URI linking to the detailed representation of a process type.
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.
The representation for a list of process type links.
The current EPP status for a step (supports automatically triggered programs only).
Identifies the resource that represents the program status for the step.
The detailed representation of a Project.
Project-link is a child element type of projects and provides a URI linking to the detailed representation of a project.
Project is a child element of Sample and provides a URI linking to the detailed representation of the Project for the Sample.
The representation of a list of project links.
The representation for a list of property links.
property-link is a child element type of property and provides a URI linking to the detailed representation of a property.
Detailed representation of a protocol.
Link to a protocol configuration.
Protocol link for a stage in a workflow.
Protocol-link is a child element type of workflow and provides a URI linking to the detailed representation of a protocol.
Protocol-property is a child element of protocol containing key/value pairs for setting specific attributes of protocols.
Returns the representation of a list of protocols
Detailed representation of a Step
Protocol step link for a stage in a workflow.
Enumeration of quality control flag values.
Quality control flag enumeration for artifacts in process execution.
The representation of a queue.
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
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
Provides the row and column location within a Tube Rack.
The detailed representation of a reagent kit.
Reagent-kit-link is a child element type of reagentKits and provides a URI linking to the detailed representation of a 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.
Reagent-Kit-Link is an element providing a URI linking to the detailed representation of a reagent kit.
Reagent-Kit-Link is an element providing a URI linking to the detailed representation of a reagent kit.
The representation for a list of reagent type links.
Reagent-label is a child element of Artifact and provides the name of a label or reagent that has been added to the Artifact.
Reagent-label is a child element of ExtStepReagentListElement and provides the name of a label or reagent that has been added to the Artifact.
Represents a reagent lot in the Clarity LIMS system.
Reagent-lot-link is a child element type of Reagent Lots and provides a URI linking to the detailed representation of a Reagent Lot.
Provides a URI linking to the reagent lot details.
Represents a paginated collection of reagent lot links returned by the API.
The list representation of a step's reagent lots.
Identifies the resource that represents the reagent lots for the step.
The detailed representation of a step's output artifact reagents.
Identifies the resource that represents the reagents added by the step.
The detailed representation of a reagent type.
Reagent-type-link is a child element type of reagent types and provides a URI linking to the detailed representation of a reagent type.
The representation for a list of reagent type links.
The detailed representation of a researcher.
Researcher is a child element of Project and provides a URI linking to the detailed representation of the Researcher for the Project.
Researcher is a child element of the reagent lot.
Researcher-link is a child element type of researchers and provides a URI linking to the detailed representation of a researcher.
Researcher-link is a child element type of researchers and provides a URI linking to the detailed representation of a researcher.
The representation of a list of researcher links.
Aspect used to examine calls from the REST template to the Clarity API.
The role element defines a researcher's level of access in the system.
The detailed representation of a Role
Role-link is a child element type of roles and provides a URI linking to the detailed representation of a Role.
The representation for a list of role links.
The root element for a routing API call.
The detailed representation of a sample.
The base representation of a Sample, defining common elements for both Sample and Sample creation.
Batch fetch and update holder for samples.
Sample creation is the detailed representation required when creating a new Sample in the system.
Sample is a child element of Artifact and provides a URI linking to the detailed representation of a submitted Sample for the Artifact.
Sample-link is a child element type of samples and provides a URI linking to the detailed representation of a sample.
The representation for a list of sample links.
Represents a paginated list of saved queries.
Represents a saved query in the Clarity LIMS system.
Link to a saved query entity.
Extraction of code to run a saved query to simplify ClarityAPIImpl.
The summary of a result of running a saved query.
Search<E extends Locatable>
A class holding both the parameters of a search and the links returned from that search.
Class recording an individual parameter and its value or values of a call to the API's find method.
Class recording the parameters and entity class of a call to the API's find method.
The file element describes a shared result file output that will be displayed in the step-setup view.
The file element describes a shared result file output that will be displayed in the step-setup view.
The file element describes a shared result file output that will be displayed in the step-setup view.
Adapter for those dates that are exchanged with the API in the short date only format.
Special-type is a child element of reagent type and provides a name and attributes describing a special type of reagent type.
The detailed representation of a workflow stage.
The detailed representation of a Stage (the portion of a workflow to which samples can be associated in order to be queued)
Enumeration of the ways to override the normal behaviour of the API and the cache to get specific versions of stateful entities.
The workflow stage status for the artifact.
The status of a reagent lot.
Enumeration of status values for a step.
Enumeration representing the status of a workflow.
Identifies the configuration information for the step run.
A request to create a step.
Represents the detailed view of a step, including configuration, input/output mappings, user-defined fields, and associated resources.
Identifies the resource that represents the details for the step.
Step-property is a child element of master step containing key/value pairs for setting specific attributes of master steps.
Step-property is a child element of protocol step containing key/value pairs for setting specific attributes of protocol steps.
Step-setup is a child element that describes the shared result file placeholder information for the step-setup view.
Represents the setup configuration for a step, including files and configuration settings.
Step-setup is a child element that describes the shared result file placeholder information for the step-setup view.
Identifies the resource that represents the setup for the step.
The different styles of Fields.
Enumeration of field styles.
Submitter is a child element of Sample and provides a URI linking to the detailed representation of the submitter for the Sample.
Technician is a child element of Process and provides a URI linking to the detailed representation of the technician that ran the Process.
The technician element provides a URI to the user that is responsible for the Process.
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 is a child element of Step and provides a URI linking to the detailed representation of the technician that ran the Step.
The trigger-point enumeration lists the possible values of the EPP Trigger point attribute.
Enumeration of EPP trigger execution points.
The trigger-status enumeration lists the possible values of the EPP Trigger status attribute.
Enumeration of step statuses at which EPP triggers can execute.
The trigger-type enumeration lists the possible values of the EPP Trigger type attribute.
Enumeration of EPP trigger types.
The detailed representation of the configuration of a user defined type.
Type-definition provides a URI linking to the user defined type associated with the user-defined field, if applicable.
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.
Field is the value and data type of a user-defined field.
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.
Interface for any entity or other object that holds user defined fields (UDFs).
The representation of a list of user defined field configuration links.
Type is the name and user-defined fields of a user-defined type.
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.
The representation of a list of user defined type configuration links.
Convert to and from URI objects, correctly encoding the query string.
Resource implementation based around a URL.
Describes a user as required in the context of step escalations.
Enumeration of variability types for process outputs.
Represents a Clarity LIMS API version.
Index is the base entry point to the API, providing a list of supported versions in the system.
The detailed representation of a Workflow.
Workflow link for a stage.
Workflow-link is a child element type of workflows and provides a URI linking to the detailed representation of a workflow.
The representation of a list of Workflow links.
Provides links to workflow stages, stage names and their respective statuses.