In QC steps, some items have a QC flag associated with them. This flag can be read and set from script expressions. The value may be set to true or false.

Example expressions:

-exp 'input.QC = input.::Concentration:: >= step.::minConcentration:: && input.::Concentration:: <= step.::maxConcentration::' -exp 'output.QC = input.QC'-exp 'if(Step.::Concentration:: >= 1) { input.QC = true } else { input.QC = false }'

The following tables summarize the mapping of UDF/custom field types.

Working with Toggle Switches

The LIMS and API treat the toggle switch field type as boolean when its value is set to true or false. However, it is possible to configure a toggle switch to not have to set a boolean true / false value. In this case, the value of the field is None Set and the field is treated as a 'nonexistent' field. To make sure that a toggle switch value has been set, you can use the hasValue function. For details, see Handling Non-Existent UDFs/Custom Fields.

Script Parameters and Usage

The following table defines the parameters used by the evaluateDynamicExpression script.

Automation Command Line

Using Special Characters—Rules and Constraints

Joining Multiple Evaluations

Use the following special syntax to join multiple evaluations within an expression:

• AND = &&

• OR = ||

• NOT = !

Boolean expressions should evaluate to true or false.

Troubleshooting

For debugging errors, run through the following steps to determine the cause.

1. Check custom field format (eg, step.::UDF Name::).

2. Make sure that the custom fields have been created for the correct entity type.

3. Check the mapping of the field type (see section) — if doing Math they need to be numeric.

4. Check that the step has a log file placeholder configured.

   • The 'unexpanded placeholders in string' error often refers to the last -log parameter — where the step has not been configured to produce one.

   • If no log file is created, find additional error logging from the command line of the instance. This often shows the location of a syntax error. Find the log file at /opt/gls/clarity/automation_worker/node/logs/automatedinformatics.log.

5. Set -t parameter to false if an automatic trigger is used.

Use the fail() method to halt the script and display an error message. If the script is used on a step transition, this method also prevents the step from proceeding to the next screen.

Example expression:

-exp 'if (!step.hasValue( ::Batch ID:: )) { fail(::Batch ID step UDF is required::) }'

Note that this example also uses the hasValue function (see Handling Non-Existent UDFs/Custom Fields).

The following table summarizes the non-UDF/custom field properties available for each entity type. Column headers are the types available. The bold row entries are the properties available.

LIMSID is supported via Groovy node access. See section.

name

The name read-only property makes the name of the entity available to the scripting engine.

Example basic expression:

workflowName

The workflowName read-only property makes the workflow name of input samples available to the scripting engine.

This property contains a string representing the current IN_PROGRESS workflow names. The string is formatted as a comma-delimited list, with a space inserted before each new item.

Example basic expressions:

replicateCount

The replicateCount read-only property is available for input samples.

This property contains an integer value representing the number of output replicates (samples or result files / measurements or files / file placeholders) generated from the input sample in the current step.

Example basic expressions:

pooledInputsCount

The number of input analytes/derived samples that contributed to this analyte / derived sample.

• For pooled analytes / derived samples, this is > 1.

• For non-pooled analytes this is 1.

• Replicated samples that are then pooled are still counted separately in pooledInputsCount.

Example basic expression:

When working with the pooledInputsCount property, the script looks at the step that created the derived sample or result file / measurement, and doesnot look upstream for a pooling step.

Example scenario:

Step 1: Pooling step that creates pooled samples.

Step 2: Nonpooling step that takes in the pooled samples and creates new derived samples (that are themselves still pools).

Step 3: Nonpooling step with expression that calls input.pooledInputsCount.

The expression in step 3 returns '1' because it onlys look at the previous step (step 2)—the step that created the current derived samples.

limsid

You can access the limsid field with some knowledge of Groovy and the LLTK. Use the following examples with any supported entity:

Example basic expressions:

well

The well read-only property makes the well location of input, output, or submittedSample available to dynamic expressions. Result file / measurement outputs are supported if they have placement information (eg, on QC steps).

Example basic expression:

When working with the Lab Logic Toolkit evaluateDynamicExpression script, custom field values can originate from the following data collection entities (these will differ, depending on the step from which the script is being run):

• input (analyte/derived sample)

• output (analyte/derived sample or per-input result file, measurement, or file placeholder)¹

• step

• container

• submittedSample / submittedSamples²

¹ Shared and per-reagent-label result files / measurements (e.g., those produced by a demultiplexing step) are not supported.

² Use 'submittedSamples' with pooled derived samples, and 'submittedSample' for single-source derived samples.

The nextStep property is similar to the input, output, submittedSample, container, and step entities. However, nextStep can only be used on the left side of a dynamic expression; it cannot be used in the calculation on the right side of the expression.

The basic syntax is as follows:

nextStep = <next step value>

Depending on how the step is configured, a nextStep expression may set the next action for the step inputs or the step outputs. For example, in steps that do not produce output samples — such as QC steps, it is the step inputs that proceed (provided they pass QC) to the next step in the workflow.

When creating an expression that calls the nextStep property, there is no need to differentiate between step inputs and step outputs. The LIMS is able to determine this from how the API represents the entities that are available to set next actions on.

Note also that this property is evaluated for each input/output, and can set a different nextStep value for each.

Supported Values for nextStep

For samples to advance to the next step via an LLTK expression, the next step must be specified in the Configuration area of the LIMS.

Configure next steps on the protocol configuration form, in the Next Steps table.

The possible next step values listed in the following table are intended for non-QC protocols. There is no nextStep entity for a QC protocol. However, samples in a QC step in a QC protocol can move to REMOVE or ESCALATE via LLTK.

<next step value> can be one of the following:

• Any Groovy expression that includes the top-level entity UDFs/custom fields on input, output, submittedSample, and evaluates to one of the options described.

• A valid next step name, for example, ::Sample Pooling:: (remember that text / string values must be inside double colon delimiters).

• One of the following 'special values' described in the following table.

The following conditions must be met:

• If <next step value> is not a valid next step, or is not one of the special values described in the table above, an error is raised and the script will fail by returning a nonzero value.

• The <next step value> must be in 'choose next steps' or 'record details' transition when the script is executed. If not, the script will fail and will return an error message.

Example expressions:

-exp 'nextStep = ::ADVANCE::'

-exp 'if (input.QC == true) { nextStep = ::ADVANCE:: } else { nextStep = ::ESCALATE:: }'

-exp 'if (output.QC == true) { nextStep = ::ADVANCE:: } else { nextStep = ::ESCALATE:: }'

-exp 'if (input.::QC:: == true) { nextStep = ::TP53 Make Master Mix Deep Well Plate:: } else { nextStep = ::Dilute/Concentrate:: }'

-exp ‘if (step.::Concentration:: >= 25) { input.QC = true } else {input.QC = false }'

-exp 'if ( step.::Visual QC Result:: == ::Passed Visual QC:: ) { nextStep = ::SEMI-AUTOMATED - Make DNA Quant and Eval Standard Quant:: } else { nextStep = ::REMOVE:: }'

-exp 'if (input.::Avg Concentration:: > 25) { nextStep = ::Cluster Generation (LLT):: } else { nextStep = ::ESCALATE:: }'

Handling Control Samples

When working with control samples, single-use control samples cannot have their next steps set to anything other than REMOVE.

Supplying the optional -excludeControls parameter with a value of true ensures the following:

• The script calculation is only evaluated for noncontrol samples.

• If next steps are set, the value is set to REMOVE for control samples.

Note also that the Java contains() method provides a simple way of identifying controls to be removed:

-exp 'if (input.name.contains( ::No Template Control::)) { nextStep = ::REMOVE:: }' 
-exp 'if (input.name.contains( ::CTLl::)) { nextStep = ::REMOVE:: }’

For a pooled derived sample consisting of several submitted samples, Lab Logic Toolkit exposes a submittedSamples property that is a collection of the submitted samples represented in the well.

• submittedSamples returns a list of submitted samples.

• If it is not a pooled sample, it will return a list of 1.

• submittedSample returns an error if sample is pooled.

Use this collection to read and/or update all related submitted samples.

For example:

• To set the sample level UDF/custom field for each of the related submitted samples:

  Copy

  -exp 'submittedSamples.each { sample -> sample.::My Sample-Level UDF:: = 123 }'

• To sum the Volume UDF/custom field on all the related submitted samples into a single value written to the input analyte / derived sample:

  Copy

  -exp 'input.::Total Origin Sample Volume:: = submittedSamples.sum { sample -> sample.::Volume:: }'

For information on Groovy syntax and closures, see Groovy Closures.

The container entity makes the input, output, or submittedSample container available to the scripting engine.

• The container can be queried for its name, for example:

  Copy

  input.::container::.::name::

• Container name, UDFs / fields, and entity information can be read or written, for example:

  Copy

  output.::container::.::example udf1:: = input.::container::.::example udf1::

Example basic expressions:

-exp 'output.container.::containerUDF:: = ::This is a string::'
-exp 'input.::container::.::containerUDF:: = ::This is a string::'
-exp 'submittedSample.container.::containerUDF:: = ::This is a string::'

The word 'container' may be optionally surrounded by "::"

Each custom field is specified by using one of the data collection entity names (see ), followed by a dot separator, followed by the field name enclosed in :: characters.

For example:

Rules and Constraints

• The expression is evaluated and the target field value set for each input/output pair in the step.

• Where there are replicates or pooling this may mean that a particular input or output item is evaluated multiple times.

• Lab Logic Toolkit can write to read-only fields.

• Lab Logic Toolkit can write to all hidden fields.

The evaluateDynamicExpression script evaluates the expression and sets the target field value for each input/output pair in the step.

• Where there are replicates or pooling this may mean that a particular input or output item will be evaluated multiple times.

• The output data collection is treated specially. The script performs the following actions:

  • Searches the per-input output sample and the per-input output result file/measurement (if they exist) for any output field names found in the expression.

  • Returns any values found.

• In the event of a name collision (ie, the same field name exists on both sample output and result file / measurement output) the sample value is used.

Example Expressions

Example 1

In this example expression, the sample output DNA Concentration field is assigned the value resulting from the following calculation:

1. Multiplying the value of the step Ideal Volume by the value of its Ideal Concentration.

2. Dividing that result by the Volume defined on the sample input.

Note the following:

• step.::Ideal Volume:: is the value of a UDF/custom field. The period between step and Ideal Volume signifies that Ideal Volume is associated with the step.

• The part of the expression to the left of the = sign is always the destination or result of the expression, that is:
• The part of the expression to the right of the = sign is always the source of the value to be stored in the destination, that is:
• In this case, multiplying the value of the protocol step Ideal Volume by the value of its Ideal Concentration, and then dividing the result by the Volume defined on the sample input.

Example 2

Copy a step or analyte / derived sample field value to a field configured on the step output - for use in downstream steps:

This expression will be evaluated one time for each output.

Example 3

Copy a result file or measurement field value to the output analyte / derived field for use in downstream step:

Example 4

Automatically set a text-string field value:

Handling Non-Existent UDFs/Custom Fields

In the API, fields that do not exist and fields that do not have a value set are considered the same and are handled in the same way.

Attempting to access a nonexistent UDF / custom field will usually result in an error. Sometimes this may not be the desired behavior.

Before attempting to access a field, you can use the hasValue function to check if it exists.

The hasValue function:

• May be used on any item.

• Takes one parameter - the name of the field.

• Returns true if the field exists and has a non-null value.

Example Expressions:

The following expression checks that the Concentration field has a non-null value, and then checks that this value is greater than 1:

The following expression checks that a toggle switch field has a non-null value - ie, that it is set to true or false, and then checks that the value is set to true: