Tips and Troubleshooting

This article provides hints and tips to help you get the most out of the Cookbook recipes included in this section.

File attachments

When reading a recipe, look for file attachments. Almost all examples have an attached Groovy script to download.

Working with the attached scripts

To use the scripts with a non-production server, edit the script to include your server network address and credentials.

For illustration purposes, most scripts use populated information. You must add your own sample, process (eg, a master step in Clarity LIMS v5 and later), and other data. The non-production server has a directory set up for this purpose at

/opt/gls/clarity/customextensions/ 

Using Full Production Scripts

When using full production scripts, the following considerations must be taken:

• Cookbook scripts are written to explain concepts. They are not deeply engineered code written in a defensive programming style. Always think through the expected and unexpected input of your scripts when incorporating concepts or code from Cookbook recipe examples.

• Full production servers can require different configurations for scripting languages other than Groovy, and for the EPP/automation worker node. For example, your script directory can be accessible by the user account running the EPP/automation worker node for User Interface (UI) triggers.

Discuss the software deployment plans with your system administrator to coordinate between non-production and production servers. For more information on using production scripts, see REST General Concepts and Automation.

Version Compatibility

Each recipe was written with a specific API version. For information on how to check the version of the API on your system, see Requesting API Version Information.

Apache Groovy is required for most Cookbook examples. It is open source and is available under an Apache license from groovy-lang.org/download.html. It is installed on non-production servers, but you can also install it to your desktop. The Cookbook examples were developed with Groovy v1.7.

Python is required for some Cookbook examples. It is available from www.python.org/download. The Cookbook examples were developed with Python v2.7.

Path to Groovy

The automation worker node executing the command uses the first instance of Groovy it finds in the executable search path for the limited shell. This is the $PATH variable.

If you have multiple versions of Groovy (or multiple users using different versions) and experience problems with your command-line calls, declare the full path to Groovy/Java in your command.

To see your executable search path, and other environment variables available to you, run the following command:

bash -c "env > {outputFileLuid0}.txt"

Compare this command to the full logon shell, which is

bash -l -c "env > {outputFileLuid0}.txt"

For more information on command-line actions, see Supported Command Line Interpreters.

References

For details on the programming interface methods and data elements available, refer to the following documentation:

• https://github.com/illumina-swi/clarity-int-docs/blob/main/docs/api-docs/resources-and-references.md

• Automation Tokens

Browser Plug-Ins

Browsing for, and adjusting resources, in Firefox, Chrome, or other browsers is great for getting started or for troubleshooting.

The following plug-ins are available with Firefox:

• Text Link—Makes any URI in the XML a hyperlink.

• Linkificator—Converts text links into selectable links.

• RESTClient—Provides a simple interface to call HTTP methods on REST resources. It is useful for troubleshooting, checking error codes, and for getting comfortable with GET, PUT, and POST requests.

The following plug-ins are available with Chrome:

• Advanced REST Client—Provides similar functionality to Poster by Firefox.

• XML Tree—Displays XML data in a user-friendly way.