Derived Sample Naming Convention Tokens
Last updated
Last updated
By default, the name of the outputs generated by a step in the LIMS follows the naming convention of the inputs to the step.
When configuring a master step, you can use tokens to configure the naming convention so that it resolves to other unique attributes of the output. These tokens function as placeholders that are replaced with actual values at runtime. For example, for the Standard step type, the default naming convention resolves to the value of the {InputItemName} token (shown below).
The Tokens list provides a list of tokens you can use. You can copy and paste these directly into the Naming Convention text box.
If using multiple tokens, add a space between each entry.
Below the Naming Convention field, you will see a preview of how the token(s) will resolve.
Note that some runtime-specific items, such as dates and times, will not preview exactly as they will resolve at runtime.
NOTE:
Output names are limited to 100 characters. If a name exceeds this limit, the LIMS automatically removes characters from the middle of the name.
To pad a resolved value, add a colon (:) and a whole number to indicate the desired number of digits. For example, if {OutputItemNumber} resolves to 23, {OutputItemNumber:4} will resolve to 0023.
You can use simple tokens that will resolve to system-specified results, such as container location and LIMS ID of an output. These tokens are replaced with the appropriate value of the specified item at runtime. Tokens are case sensitive.
{InputItemName}
The name of the input used to generate the output.
{InputItemNameNoSpaces}
The name of the input used to generate the output, but with spaces removed.
{InputWellLocation}
The location or name of the well where the input resides.
To get a sub-string of the location or name of the well, add a colon (:), and one or two whole numbers to indicate the start index (zero-based, i.e. starts with 0. Inclusive) and end index (Exclusive). {InputWellLocation:<startIndex>,<endIndex>}
Example
If {InputWellLocation} has the value of A:3, the following examples show the derived values with the new format:
Lane {InputWellLocation} -> Lane A:3
Lane {InputWellLocation:0,1} -> Lane A
Lane {InputWellLocation:1,3} -> Lane :3
Lane {InputWellLocation:1} -> Lane :3
{InputContainerIdentifier}
The container identifier in which the input resides.
{InputItemNumber}
The number of the input used to generate the output, such as 7 of 20. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.
{InputItemTotal}
The total number of inputs used to generate the outputs. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.
{OutputItemLIMSID}
The LIMS ID of the output.
{OutputItemNumber}
The current output's absolute position within the order of all outputs, such as 9 of 40. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.
{OutputItemTotal}
The total number of outputs generated. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.
{OutputItemSubsetNumber}
The current output's relative position within its relative set, such as 1 of 2. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.
{OutputItemSubsetTotal}
The fixed count of relative outputs per input. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.
{AppliedReagentLabels}
The type of reagent label applied to the input.
{SubmittedSampleName}
The name of the sample’s related submitted sample - the original parent sample that was submitted to the LIMS.
{ProjectName}
The name of the project that contains the inputs to the step.
{ProcessLIMSID}
The LIMS ID of the step that created the outputs.
{ProcessTechnicianFullName}
The name of the lab scientist who runs the step.
{ProcessTechnicianFirstName}
The first name of the lab scientist who runs the step.
{ProcessTechnicianLastName}
The last name of the lab scientist who runs the step.
{ProcessTechnicianInitials}
The initials of the lab scientist who runs the step.
{DATE:MMM d, yyyy}
The date the step was run, according to the computer's clock.
{LIST:a,b,c}
With this variable, you can specify a comma-delimited list of words that will be used when generating output names. Clarity LIMS will cycle through the words from left to right, applying one word to each output name. When the last word has been used and there are further outputs that require names, Clarity LIMS will restart at the beginning of the list.
Complex tokens provide further flexibility with the use of parameters.
You can combine any alpha-numeric text with simple and complex tokens for highly specialized and unique output names.
When using complex tokens, you must specify parameters that will be used when the token is resolved.
You can only use one LIST and one DATE token per output string, but you can use any combination of parameters within those tokens.
With the DATE token, if you would like to include a word between parameters, enclose the word in single quotes (‘x‘).
Times and dates resolve to the time and date the process was run, according to the computer's clock.
Tokens and parameters are case sensitive.
| Token | Resolves to | Usage | Example |
|---|---|---|---|
a | AM/PM marker | The system returns the marker in the same format, regardless of how many times the token is repeated. | If runtime is in the afternoon: a resolves to PM |
H | Hour in day (24-hour clock) | The number of times you repeat the token determines the minimum number of digits returned, with the system padding the value with zeros if necessary. | If runtime is 11 PM: H resolves to 23 HHH resolves to 023 |
h | Hour in AM/PM (12-hour clock) | The number of times you repeat the token determines the minimum number of digits returned, with the system padding the value with zeros if necessary. | If runtime is 11 PM: h resolves to 11 hhh resolves to 011 |
m | Minute in hour | The number of times you repeat the token determines the minimum number of digits returned, with the system padding the value with zeros if necessary. | If runtime is 11:10: m resolves to 10 mmm resolves to 010 |
s | Second in minute | The number of times you repeat the token determines the minimum number of digits returned, with the system padding the value with zeros if necessary. | If runtime is 11:10:23: s resolves to 23 sss resolves to 023 |
S | Millisecond | The number of times you repeat the token determines the minimum number of digits returned, with the system padding the value with zeros if necessary. | If runtime is 1:10:23:01: S resolves to 1 SS resolves to 01 |
z | Time zone - general | One token results in the abbreviated time zone. Four tokens results in the entire name. | If runtime is in the Pacific time zone, during daylight savings: z resolves to PDT zzzz resolves to Pacific Daylight Time |
Z | Time zone - RFC 822 | The system returns the time zone in the same format, regardless of how many times the token is repeated. | If runtime is in the Pacific time zone, during daylight savings: Z resolves to -0800 |
