Validate Complete Plate

Clarity LIMS NGS Extensions Package v5.17 and later includes the validateCompletePlateStarted script. This script checks that all samples in a container were started together on the current step. This section provides details on the script and its parameters, and LIMS configuration requirements.

Script Overview

The purpose of the validateCompletePlateStarted script is to make sure that all of the samples in the input plate were started together. The validation supports partially-filled plates and multiple plates.

You can supply additional parameters to the script, to optionally enforce:

• 'Cannot proceed with partial plate' logic for only for the samples that are queued to the current step, instead of the entire plate contents. Default is false—the entire plate contents are verified.

• Contiguous row-major or column-major layout. This makes sure that the input plate(s) are in the expected layout and contain no gaps between the first and last sample. By default, this is not enforced.

Script Parameters

Parameter	Description
-u {username} -username {username}	(Required) LIMS login username
-p {password} -password {password}	(Required) LIMS login password
-i {stepURI:v2} -stepURI {stepURI:v2}	(Required) LIMS step URI
-log {logFileLIMSID} -logFileName {logFileLIMSID}	(Required) LIMS ID of the log file placeholder
-layout <'ROW'/'COLUMN'>	(Optional) One of 'ROW' or 'COLUMN', if provided. When present, script enforces that the samples are laid out in gap-free, row-major or column-major order.
-queuedOnly <true/false>	(Optional) When provided and set to true, the script ensures that samples queued to the started step were started together. Samples dropped earlier in the workflow will are ignored. Default is false.
-t <true/false> -testMode <true/false>	(Optional) When provided and set to true the script reports errors in accordance with 'Record Details button' mode, instead of the default 'screen transition' mode. Default is false.

Command Line Examples

Example 1

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-log {compoundOutputFileLuid0} \
script:validateCompletePlateStarted"

Example 2

bash -l -c "/opt/gls/clarity/bin/java -jar/opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar \
-i {stepURI:v2} \
-u {username} \
-p {password} \
-log {compoundOutputFileLuid0} \
script:validateCompletePlateStarted" \
-layout 'ROW' \
-queuedOnly true -t true

Configuration

The validateCompletePlateStarted script is intended to run when the user selects the Begin Work button on the Ice Bucket screen and starts the step.

To achieve this, configure the automation trigger as follows:

• Trigger Location: Step

• Trigger Style: Automatic upon entry