Assay Collection Components

Last Updated: Dec 19, 2015 10:02PM PST

Summary: This article provides a high-level overview of the components available in the Assay collection for use with ScienceCloud applications.

Covered Topics

Components Overview

The Assay collection components are installed in Components/ScienceCloud/Assay in the following top-level folders:
assay_components.png

Assay collection components

The components in these folders are used for the following tasks:

  • Connection – Configure a connection to Assay. (Note: All Assay protocols must configure one or more connections before they can use all other components described below.)
  • Administration – Access, modify or specify Assay resources based on protocols and components and defined in administration settings.
  • Automation – Create and process Runs through components following steps identical to steps followed in Assay UI.
  • Data Access and Manipulation – Get, insert or delete data related to a specific Run.

Assay Protocol Structure

A typical Assay protocol is structured as follows:

  • Always use an Assay Connection component first, to configure a connection to ScienceCloud Assay. This component makes development easier, because it encapsulates connection and authentication information that otherwise would have to be entered on every component that needs it. For specific information about how to set up this component, see Connect to ScienceCloud with Assay Components.
  • Add Assay components as necessary. Each component relates to the Assay Connection using the Connection Name present on every Assay component.

The following example illustrates how to retrieve a specific Run and get plates related to that Run.
assay_protocol_structure_run.png

Parameters to run and get plates related to that run

Connection Components

The Connection folder contains a unique component (Assay Connection) that configures a connection to the Assay, allowing to create new Runs, update a Run, or access Run data using components from other folders.
assay_connection_comp.png

Connection components

The Assay Connection component's required parameters include connection credentials and reference to the Assay data source for making a connection. For specific information about how to set up this component, see Connect to Connect to ScienceCloud with Assay Components.

Note: All Assay protocols must configure one or more connections before using any other components that need that connection information.

Administration Components

The Administration folder contains components to access or modify administration. Specifically, it provides control on resources consumed through the interface, which are based on protocols or Oracle packages, namely Readers and Visualization Templates.
assay_admin_comps.png

Administration components

For each resource, the following components are available; (in the discussion, we will abstract resource type names using the variables XXX):

  • Get XXX – Retrieves resources of a specific type as data records, with all associated metadata as data record properties.
  • Register XXX – Registers a new resource of a specific type, by providing related metadata. The component provides the same level of details than the corresponding administration screen.
  • Unregister XXX – Decommissions a resource from Assay. Some resources cannot be unregistered if existing Runs made use of them. In this case, further usage of the resource can be prevented by setting it as "hidden" through the corresponding Update component.
  • Update XXX – Modifies settings of an existing resource. This allows a seamless update of a resource of workflow without modifying. Use this component to hide resources if they cannot be unregistered once used in a Run.

Automation Components

The Automation folder contains a number of components that enable the execution of all steps that can be performed on a Run in the ScienceCloud Assay interface.
assay_automation_comps.png

Automation components

Typical actions that can be performed include:

  • Create a run
  • Upload files
  • Define Mapping
  • Perform Validation and Analysis

The results of each step are identical to the outcome of a similar action perform in the interface. The status of the Run after one of these actions is immediately modified in the Assay application, and the Run can be taken through the new available step by using the Assay application interface or other Automation components.

In a typical automation protocol, the Run ID of the run currently processed is passed from one component to the other. The progression of data records through the pipeline mirrors the progression of a Run through the different processing steps.

The following example illustrates the processing of a Run from creation to its final state.
assay_automation_protocol.png

Run from creation protocol

Data Access and Manipulation Components

The Data Access and Manipulation folder contains components that manipulate the different level of information and data that constitutes a Run.

assay_data_access_and_manipulation_comps.png

Data Access and Manipulation components

All of the components (except Assay Connection), include the Run ID parameter. It specifies the ID of the Run components for the specified action, and is usually passed from protocol parameters or obtained from upstream components, such as Get Run. The value is an integer and matches the ID displayed for each Run in the ScienceCloud Assay application.

For each level of information or data, the following components may be available; (in this discussion, we will abstract resource type names using the variables XXX):

  • Get XXX – Retrieves a specific data type as data records, with all associated metadata as data record properties. Depending on the status of a Run, some data types might not be available, in which case a single data record with no property is sent to the Fail port on the component.
  • Insert XXX – Inserts a new data type to a specific Run. These components are mainly used to design specific protocols for extending the Assay application. For automation purposes, it is better to rely on the Automation components described above. Note that the status of a Run is not modified by these components. If appropriate, this is handled using the Update Run Status component.
  • Delete XXX – Deletes a data type from a specific Run. Note that the status of a Run is not modified by these components. If appropriate, this is handled using the Update Run Status component.
  • Update XXX – Updates properties of a data type on a specific Run.
Related

Assay Collection Overview

Assay Collection Installation Instructions

Connect to ScienceCloud with Assay Components


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