Error Handling

Scripts produce a numeric code on exit. By convention and by default, a successful exit has a code of 0 (zero). Within error handling, select different nonzero exit codes to indicate various error conditions.

NOTE: For Clarity LIMS v5.0, the term External Program Integration Plug-in (EPP) is deprecated and replaced with automation.

Script Error Logging and Standard Streams

Though logging information in the Clarity LIMSuser interface is useful, scripts can also write debugging/troubleshooting information into the automatedinformatics.log file using stderr (standard error). When a line is printed to stderr, a [WARN] line is written to this log, which is useful for troubleshooting interactions between the script and the automation programs. For more information on the automatedinformatics.log file, see Troubleshooting Automation. For more information on using stderr on the command line, refer to Unix and Windows documentation on standard I/O streams, especially standard error.

Error handling

In Clarity LIMS, the last line written to stdout (standard out) is automatically captured and shown in the interface.

If the exit code is zero, the message displays in green. If the exit code is nonzero, the message displays in red.

The Operations Interface Java client is deprecated in Clarity LIMS v5. All configuration and administration tasks are currently executed in the LIMS web interface.

If the script exits with a nonzero code, a sample genealogy flag is automatically added to the process outputs, with a standard error message indicating there is an External Program Error.

If the script is complex, or includes several error conditions, configure an additional result file process output (eg result.log) designed to capture status and error information. Make the external script write additional information to this file. If an error occurs, the file is still captured in the client, and is available to view for troubleshooting purposes.