Supported Command Line Interpreters
LIMS automations typically call scripts or third-party programs written for a shell or command-line interpreter, of either a Linux or Windows operating system (OS). Although the use of any system shell if acceptable, Bash is recommended.
Depending on the systems that integrate with the given automations, various restrictions apply to the string parameters/tokens and formatting used in the automation command line.
For BaseSpace Clarity LIMS v5, several terms are deprecated:
| • | Automation replaced External Program Integration Plug-in (EPP). |
| • | Automation worker / AW node replaced EPP/AI node. |
| • | Token replaced Parameter. |
Environment Variables
Environment variables can be used to aid in configuration. However, automation commands are generated with a limited shell. For full access to environment variables, the recommended practice is to start the command to instantiate a 'full' user shell. For example, for Bash use the following command:
bash -l -c
This procedure provides the following advantages:
| • | Ensures updates of the environment variables, removing the need for repeated AI node/automation worker restarts. |
| • | Ensures access to all environment variables, including the full path to Groovy. |
| • | Allows certainty of the shell being used. |
Operating system shell formatting, spaces, and special characters
The various operating system (OS) shells each have their own rules and regulations. When creating command-line strings, be aware of the considerations described in the following sections.
Operating System Shell Formatting Differences
Windows shell command-line interpreters require different syntax and formatting than Linux shell variants. For example, the following scripts are identical, but are formatted for different AI nodes/automation workers running on different operating systems.
On Linux
groovy -cp ../../scripts ../../scripts/flexcontrol_drivergen.groovy -l {processU:v1:http} -a {artifactsU:v1:http} -u {username} -p {password} -f {compoundOutputFile0}.txt
On Windows
C:\Windows\System32\cmd /c "groovy -cp ..\..\scripts ..\..\scripts\flexcontrol_drivergen.groovy -l {processU:v1:http} -a {artifactsU:v1:http} -u {username} -p {password} -f {compoundOutputFile0}.txt"
Most of the examples in this specification use Windows formatting, because Windows is the most common platform found in the lab.
Spaces
Spaces in paths, file names, or parameter/token data can cause commands to be misinterpreted as information passes between systems.
Many OS shells automatically parse command-line contents by space, which cannot be what is intended. Enclose commands in double quotes " " to avoid misinterpretation of spaces by the OS shell command-line interpreter.
Special Characters
OS shell command-line interpreters can attempt to interpret and act upon certain special characters, rather than passing them along as textual information. A character can have a rule applied to it within one OS shell environment, and a different rule under another environment. To use a character in its literal form, escape the characters. The escape character used varies depending on your OS shell. The most common escape character is the backslash character.
The most common OS shell characters that require escaping are:
% ( ) / \ * & |
To make sure that a configured command in the client is properly interpreted, test it on the AI node/automation worker machine command line.
