Useful Tools
To help with learning, BaseSpace Clarity LIMS documentation includes:
| • | An introduction to the API architecture (see REST General Concepts). |
| • | Details of the methods and interfaces (see REST API documentation and Automation Overview). |
| • | Example code (see About the Cookbook). |
However, there is more to the Clarity LIMS Rapid Scripting™ API package than these resources.
Details on tools, training, and best practices are covered in the following sections and in Development Prerequisites.
Nonproduction Scripting Sandbox Server
Nonproduction server licenses and training are essential. A nonproduction scripting sandbox server is set up with Groovy, BaseSpace Clarity LIMS, and automation ready to be used with the scripts provided in the About the Cookbook and with the Clarity LIMS API Application Examples.
| • | Have the nonproduction servers set up before learning to script (see Development Prerequisites). |
| • | All the examples in the Cookbook are intended to be used with the nonproduction scripting sandbox server. This server has all the software packaged up to start scripting with the API. |
| • | The Cookbook examples do not explain how to configure the servers for process configuration. Server installation and server-side configuration instructions are covered during implementation, as part of the installation and training services. |
| • | For more information and to understand the importance of a dedicated scripting server, see Development Prerequisites. |
Cookbook Examples for Learning the API on Nonproduction Servers
The nonproduction server license and the Cookbook examples are not for production use. It is not practical to integrate actual instruments to this server permanently, but it does provide a great way to learn to script.
The nonproduction scripting sandbox server provides a safe place to learn the API, using the Cookbook example scripts as a guide. The typical installation includes the Clarity LIMS software, the Automation Informatics node (referred to as the automation worker in Clarity LIMS v5), and Groovy.
Installation and Administration Training
Installation and administration training enables IT administrators to support multiple script writers with multiple nonproduction servers for development and testing. Administrators learn about server-side tools and procedures, such as the backup and restore procedure. This procedure moves scripts between systems.
| • | The production and nonproduction server installation training is provided to IT administrators at the start of each implementation or when the Rapid Scripting API package is purchased. |
| • | Automation Worker (AW) node training is also included. This component can be installed on multiple computers using the Automation Worker software package. |
| • | Explore other training, consulting, and issue management services available from Illumina in case the packaged services are exceeded. |
Contact Illumina for additional training or support installing and maintaining servers and AW nodes.
API Training and Consulting
The script training includes instructor-led, hands-on sessions and the training included on this site.
Instructors start from a basic Hello World script kicked off from within Clarity LIMS using automation, then progress to more in-depth concepts.
Also provided in the package is on-demand consulting. For quality service, all requests are handled via the Support team. However, expert script writers are available in technical services to consult by email, phone, or web-based sessions.
Script Deployment
Illumina recommends placing scripts in subdirectories starting from a common root, namely /opt/gls/clarity/customextensions/.
This makes moving scripts between development, test, and production systems much easier and less error-prone. This directory is assumed by the backup and restore process.
Use a directory structure beneath this root to expand the deployed scripts over time. This customextensions folder is reserved exclusively for your custom scripts.
At Illumina, this practice is called deploying on the rails. The following directories illustrate how this method is used to deploy multiple instrument integrations.
/opt/gls/clarity/extensions/
/opt/gls/clarity/extensions/Illumina/HiSeq/v1.1
/opt/gls/clarity/extensions/ABI/SOLiD/v1.0
/opt/gls/clarity/customextensions/'YourRootDirectory'
- root dir for all automation scripts
- Integration from Illumina, do not modify
- Another integration for Illumina
- Scripts created by you
Putting all the scripts into a common root directory also allows multiple teams to work on the implementation independently. For example, when Illumina provides custom integrations and you are scripting at the same time. The backup and restore process allows you to transfer all files in the root directory between systems. It is important to not place server-specific settings, such as IP addresses or login details, in these directories.
To learn more about the backup and restore process, talk to the IT Administrator (who attended the installation and administration training) and refer to the Clarity LIMS Installation Procedure documentation (accessible from the Installation section of the Clarity LIMS documentation).
Groovy
The Cookbook how-to examples and the nonproduction server use scripts written in Groovy, a Java-based scripting language.
You can use other languages with the API. However, Groovy is easy to understand. Groovy scripts look similar to pseudocode.
In addition, Groovy is particularly suited to real scripting because it handles and manipulates the major inputs, outputs, and interfaces within Clarity LIMS well.
