All Classes and Interfaces
Class
Description
Base for date adapters.
Identifies the resource that represents the actions applied or to be applied by the step.
Address contains the related fields of a mailing address.
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.
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 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).
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.
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.
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.
Exception thrown when an attempt is made to change an object that
cannot be altered in such a manner through the Clarity API.
The representation of a list of resource details.
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.
The representation for a list of container type links.
The available options for the automation context.
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.
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 ControlTypes
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.
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.
Factory for creating a singleton EhCache 3
CacheManager
from
XML configuration.EPP trigger configuration for the Master Step.
EPP trigger configuration for the Protocol Step.
Sample next action or step.
Escalation details.
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.
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.
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.
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.
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).
Interface for classes that are links to real LIMS objects.
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.
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
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.artifact package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.artifactgroup package.
This object contains factory methods for each Java content interface and Java
element interface generated in the com.genologics.ri.automation package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.configuration package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.container package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.containertype package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.controltype package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.exception package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.file package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.instrument package.
This object contains factory methods for each Java content interface and Java
element interface generated in the com.genologics.ri.instrumenttype package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.lab package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.permission package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.process package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.processexecution package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.processtemplate package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.processtype package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.project package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.property package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.protocolconfiguration package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.queue package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.reagentkit package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.reagentlot package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.reagenttype package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.researcher package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.role package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.routing package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.sample package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.stage package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.step package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.stepconfiguration package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.userdefined package.
This object contains factory methods for each
Java content interface and Java element interface
generated in the com.genologics.ri.version package.
This object contains factory methods for each
Java content interface and Java element interface
generated 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 artifact and container placement.
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.
Permission-link is a child element type of permissions and provides a URI
linking to the detailed representation of a Permission.
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.
Protocol link for the stage.
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 the stage.
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
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.
The detailed representation of a Reagent Lot
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.
The representation of a list of Reagent Lots
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 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.
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 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.
Identifies the configuration information for the step run.
A request to create a step.
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.
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.
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.
The trigger-point enumeration lists the possible values of the EPP Trigger point attribute.
The trigger-status enumeration lists the possible values of the EPP Trigger status attribute.
The trigger-type enumeration lists the possible values of the EPP Trigger type attribute.
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.
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 the 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.