When configuring automations in BaseSpace Clarity LIMS, copy tokens from the Tokens list and paste them into the Command Line field.
These tokens are available for use in project automations. If using multiple variables, add a space between each entry. All tokens and parameters are case-sensitive.
| Token | Purpose | Example |
|---|---|---|
{username}
Supplies the username of the current user running the step to the triggered automation script
cmd /c "C:\ai\ai.bat {username}"
resolves to:
cmd /c C:\ai\ai.bat adminuser
{password}
Supplies the password of the current user running the step to the triggered automation script.
cmd /c "C:\ai\ai.bat {password}"
resolves to:
cmd /c C:\ai\ai.bat 3BlindMice
In log files, the password supplied on the command line is replaced with a series of *** characters
{baseURI}
Supplies the base API URI to the triggered automation script.
cmd /c "C:\ai\ai.bat {baseURI}"
resolves to:
cmd /c C:\ai\ai.bat https://lims.lan.29/api/
cmd /c "C:\ai\ai.bat {baseURI}v2"
resolves to:
cmd /c C:\ai\ai.bat https://lims.lan.29/api/v2
NOTE: To access the endpoints, make sure that the {baseURI} is appended with v2. You can include this in the token in the command line, as shown above, or in the script itself.
{projectLuid}
Supplies the URI of the step to the triggered automation script. Include the version parameter (ie, {stepURI:version}) to specify the version of the REST API to be accessed.
cmd /c "C:\ai\ai.bat {C:\ai\ai.bat {projectLuid}"
resolves to:
cmd /c C:\ai\ai.bat ADM123
This section provides information to help you work with Clarity LIMS automation tokens in Clarity LIMS v5 and later.
When configuring automations in the BaseSpace Clarity LIMS, copy tokens from the Tokens list and paste them into the Command-Line field.
These tokens are available for use in derived sample automations. If using multiple variables, add a space between each entry. All tokens and parameters are case-sensitive.
| Token | Purpose | Example |
|---|---|---|
{username}
Supplies the username of the current user running the step to the triggered automation script.
cmd /c "C:\ai\ai.bat {username}"
resolves to:
cmd /c C:\ai\ai.bat adminuser
{password}
Supplies the password of the current user running the step to the triggered automation script.
cmd /c "C:\ai\ai.bat {password}"
resolves to:
cmd /c C:\ai\ai.bat 3BlindMice
In log files, the password supplied on the command line is replaced with a series of *** characters.
{baseURI}
Supplies the base API URI to the triggered automation script.
cmd /c "C:\ai\ai.bat {baseURI}"
resolves to:
cmd /c C:\ai\ai.bat https://lims.lan.29/api
{derivedSampleLuids}
Supplies the derived sample LIMS IDs to the triggered automation script.
cmd /c "C:\ai\ai.bat {derivedSampleLuids}"
resolves to:
cmd /c C:\ai\ai.bat 2-1641 2-1642 2-1643
{userinput:customParameterName}
Allows for data input to supply the triggered automation script. Custom parameters are identified with the prefix 'userinput:'
The following command line requires the user to input a value for 'more_yield':
yieldscript.sh -y {userinput:more_yield} -u {username}
When configuring automations in BaseSpace Clarity LIMS, copy tokens from the Tokens list and paste them into the Command Line field. These tokens are available for use in step automations. If using multiple variables, add a space between each entry. All tokens and parameters are case-sensitive.
| Token | Purpose | Example |
|---|---|---|
{username}
Supplies the username of the current user running the step to the triggered automation script
cmd /c "C:\ai\ai.bat {username}"
resolves to:
cmd /c C:\ai\ai.bat adminuser
{password}
Supplies the password of the current user running the step to the triggered automation script.
cmd /c "C:\ai\ai.bat {password}"
resolves to:
cmd /c C:\ai\ai.bat 3BlindMice
In log files, the password supplied on the command line is replaced with a series of *** characters.
{baseURI}
Supplies the base API URI to the triggered automation script.
cmd /c "C:\ai\ai.bat {baseURI}"
resolves to:
cmd /c C:\ai\ai.bat https://lims.lan.29/api
{stepURI}
Supplies the URI of the step to the triggered automation script. Include the version parameter (ie, {stepURI:version}) to specify the version of the REST API to be accessed.
cmd /c "C:\ai\ai.bat {stepURI:v2}"
resolves to:
cmd /c C:\ai\ai.bat https://yourServerNameOrIP/api/v2/steps/CAM-CSB-100212-24-197
{artifactsURI}
Supplies the URI of the artifacts root to the triggered automation script.
Include the version parameter (ie, {artifactsURI:version}) to specify the version of the REST API to be accessed.
cmd /c "C:\ai\ai.bat {artifactsURI:v2}"
resolves to:
cmd /c C:\ai\ai.bat https://yourServerNameOrIP/api/v2/artifacts
{processURI}
{stepURI} token is preferred.
{processURI} is deprecated and less accurate. May be removed in future versions.
Supplies the URI of the step to the triggered automation script.
If using the deprecated {processURI} token, the addition of the version and scheme parameters is recommended ({processURI:version:scheme}).
Adding the version and scheme reduces the chance of a server and REST version upgrade unknowingly affecting your scripts.
cmd /c "C:\ai\ai.bat {processURI:v2:http}"
resolves to:
cmd /c C:\ai\ai.bat https://yourServerNameOrIP/api/v2/processes/CAM-CSB-100212-24-197
{processLuid}
Supplies the LIMS ID of the step that triggered the automation script.
cmd /c "C:\ai\ai.bat {processLuid}"
resolves to:
cmd /c C:\ai\ai.bat CAM-CSB-100212-24-169
{udf:nameOfUDF}
Supplies the current value stored within a UDF configured as nameofUDF.
cmd /c "C:\ai\ai.bat {udf:injection_volume}"
resolves to:
cmd /c C:\ai\ai.bat 12.4
{parentProcessUdf:nameOfUDF}
Supplies the current value stored within a UDF configured as nameofUDF of the immediate parent step to the step that triggered the automation script.
The parent step must provide the inputs (derived samples) to the step.
In cases where there are multiple parents (ie, the inputs are derived from various steps) only the first of these parents is returned.
cmd /c "C:\ai\ai.bat {parentProcessUdf:RunID}"
resolves to:
cmd /c C:\ai\ai.bat RUN_BW1765
{parentProcessUdfN:nameOfUDF}
Supplies the current value stored within a UDF configured as nameofUDF of the immediate parent step to the step that triggered the automation script. The parent step must provide the inputs (derived samples) to the step.
In cases where there are multiple parents (ie, the inputs are derived from various steps) all parent step IDs are treated as an array-based list.
N specifies the array list index position 0..n of the desired step.
{parentProcessUdf0:nameofUDF} is equivalent to {parentProcessUdf:nameofUDF}.
cmd /c "C:\ai\ai.bat {parentProcessUdf1:RunID}"
resolves to:
cmd /c C:\ai\ai.bat RUN_HJ1865
{outputFileLuids}
Supplies the LIMS IDs of all step output file placeholders.
cmd /c "C:\ai\ai.bat {outputFileLuids}"
resolves to:
cmd /c C:\ai\ai.bat "BAR103A1CO248" "BAR103A1CO249" "BAR103A1CO250" "BAR103A1CO251" "BAR103A3CO158" "BAR103A3CO159" "BAR103A3CO160" "BAR103A3CO161"
{outputFileLuidN}
Supplies the LIMS ID for the specified step output file placeholder. All output file placeholders applying to inputs of the step are treated as an array-based list, where N specifies the array list index position [0..n] of the desired file.
Assuming the same eight output files as in the previous example:
cmd /c "C:\ai\ai.bat {outputFileLuid0}"
resolves to:
cmd /c C:\ai\ai.bat BAR103A1CO248
cmd /c "C:\ai\ai.bat {outputFileLuid1}"
resolves to:
cmd /c C:\ai\ai.bat BAR103A1CO249
cmd /c "C:\ai\ai.bat {outputFileLuid7}"
resolves to:
cmd /c C:\ai\ai.bat BAR103A3CO161
{compoundOutputFileLuids}
Supplies the LIMS IDs for all shared step output file placeholders.
cmd /c "C:\ai\ai.bat {compoundOutputFileLuids}"
resolves to:
cmd /c C:\ai\ai.bat "92-527" "92-528" "100-541" "100-544"
{compoundOutputFileLuidN}
Supplies the LIMS ID for the specified step output file placeholder that applies to an individual input. All output file placeholders applying to individual inputs for the step are treated as an array-based list, where *N specifies the array list index position [0..n] of the desired file.
Assuming the same four output files as in the previous example:
cmd /c "C:\ai\ai.bat {compoundOutputFileLuid0}"
resolves to:
cmd /c C:\ai\ai.bat 92-527
cmd /c "C:\ai\ai.bat {compoundOutputFileLuid1}"
resolves to:
cmd /c C:\ai\ai.bat 92-528
cmd /c "C:\ai\ai.bat {compoundOutputFileLuid2}"
resolves to:
cmd /c C:\ai\ai.bat 100-541
cmd /c "C:\ai\ai.bat {compoundOutputFileLuid3}"
resolves to:
cmd /c C:\ai\ai.bat 100-544
Deprecated {parentProcessLuid*} tokens
The following tokens have been deprecated:
• {parentProcessLuid}
• {parentProcessLuids}
• {parentProcessLuidN}
These tokens were only applicable to steps that take file inputs. File inputs are no longer supported in the Clarity LIMS.