Clarity LIMS Log Files
Introduction
Clarity LIMS creates various log files to help with the resolution of issues. During support request investigation, the Support team may ask for the following types of log files:
Automation Worker log file
Automation Worker creates history and log files, and stores them on laboratory computers in the logs folder of the Automation Worker installation directory.
Windows
If Automation Worker is installed on a Windows machine using the program default, find the logs folder at the following location:
Linux
If Automation Worker is installed on a Linux server, find the \logs folder at the following location:
The following log files are available:
wrapper.log - This log file outputs information on the starting, running, and stopping of the Automatic Informatics service.
automatedinformatics.log - This log file outputs messages from installed plug-ins, such as automation commands and ADC directory scans.
To monitor the automatedinformatics.log:
Log on to the server using the glsai user ID and run the following command:
If the Automation Worker is installed on a server other than the Clarity LIMS server, use the appropriate user credentials.
Browser HTML and JavaScript Logging
In the web browser, if the LIMS interface does not display items/elements correctly, provide the information and error messages to the Illumina Support team.
Instructions for finding error messages within the browser console are described in the following sections.
Google Chrome
To Start the Chrome Console:
Right-click on an element in the browser and select 'inspect element.'
A sub window opens below the main window in Chrome, showing the source HTML.
Select the Console tab, and reload the troublesome page - any JavaScript errors will be reported there. Include these errors in the Support Request ticket.
NOTE: Between stages in a protocol step you may see errors of the following type:
Such messages are expected. This is the EPP trigger checking that there is no EPP transition to fire on the page change. (This can be annoying for debug purposes, but feel free to include these in the Support Request ticket.)
To Get the JavaScript version:
Open up the Console as described in the previous section.
Go to the Network tab.
Select 'scripts' from the options listed at the bottom of the tab.
A script named isis-all.js?v=XXXXX displays.
Determine the version build number. (In the previous example, XXXXX represents the version build number).
FireFox
To Start the FireFox Console:
Right-click on an element in the browser and select 'inspect element.'
A sub window opens below the main window in Firefox, showing the source HTML
Select the Console tab, and reload the troublesome page - any JavaScript errors will be reported there. Include these errors in the Support Request ticket.
NOTE: Between stages in a protocol step you may see errors of the following type:
Such messages are expected. This is the EPP trigger checking that there is no EPP transition to fire on the page change. (This can be annoying for debug purposes, but feel free to include these in the Support Request ticket.)
To Get the JavaScript version:
Open up the Console as described in the previous section.
In the Filter options Search box and type 'isis'.
A script named isis-all.js?v=XXXXX appears.
Hover over this script with your mouse to find the V (version) build number.
Using Log Files for Troubleshooting Purposes
If you are experiencing problems and need to submit a support request, use the following guidelines to determine which log files to send to the Illumina Support team:
basespace-lims-*.log: Include if experiencing slowness in the application. (Default path: /opt/gls/clarity/tomcat/current/logs/)
automatedinformatics.log: Include if you are experiencing problems with an integration or if a process using an EPP string does not work as expected. (Default path: /opt/gls/clarity/automation_worker/)
wrapper.log: Include if the Automation Worker is unable to start (rarely needed).
search-indexer.log: Include if there is issue with search feature. (Default path: /opt/gls/clarity/search-indexer/logs/)
claritylims.log: Include if there is issue with search feature. (Default path: /var/log/elasticsearch/)
Browser Console and LIMS JavaScript version: Include for any web interface display issues. A simple refresh of the browser page may resolve the issue. However, the Support team would prefer receiving the console log and JavaScript version to investigate and make product improvements.
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