In General Purpose Assay (GPAT) designs, you can enable reporting of warnings in a transformation script. Ordinarily, errors will stop the execution of a script and the assay import, but if warnings are configured, you can have the import pause on warnings and allow an operator to examine transformed results and elect to proceed or cancel the upload. Note that this feature applies only to the General Purpose Assay Type (GPAT) and is not a generic assay feature. Warning reporting is optional, and invisible unless you explicitly enable it. If your script does not update maximumSeverity, then no warnings will be triggered and no user interaction will be required. Warnings are not supported for assays set to Import in Background.

Enable Support for Warnings in a Transformation Script

To raise a warning from within your transformation script, set maximumSeverity to WARN within the transformedRunProperties file. To report an error, set maximumSeverity to ERROR. To display a specific message with either a warning or error, write the message to errors.html in the current directory. For example, this snippet from an R transformation script defines a warning and error handler:

# writes the maximumSeverity level to the transformRunProperties file and the error/warning message to the error.html file.
# LK server will read these files after execution to determine if an error or warning occurred and handle it appropriately
handleErrorsAndWarnings <- function()
if(run.error.level > 0)
if(run.error.level == 1)
writeLines(c(paste("maximumSeverity","WARN",sep="t")), fileConn);
writeLines(c(paste("maximumSeverity","ERROR",sep="t")), fileConn);

# This file gets read and displayed directly as warnings or errors, depending on maximumSeverity level.
writeLines(run.error.msg, fileConn);


Click here to download a sample transformation script including this handler and other configuration required for warning reporting.

Workflow for Warnings from Transformation Scripts

When a warning is triggered during assay import, the user will see a screen similar to this with the option to Proceed or Cancel the import after examining the output files:

After examining the output and transformed data files, if the user clicks Proceed the transform script will be rerun and no warnings will be raised the on second pass. Quieting warnings on the approved import is handled using the value of an internal property called severityLevel in the run properties file. Errors will still be raised if necessary.

Priority of Errors and Warnings:

  • 1. Script error (syntax, runtime, etc...) <- Error
  • 2. Script returns a non-zero value <- Error
  • 3. Script writes ERROR to maximumSeverity in the transformedRunProperties file <- Error
    • If the script also writes a message to errors.html, it will be displayed, otherwise a server generated message will be shown.
  • 4. Script writes WARN to maximumSeverity in the transformedRunProperties file <- Warning
    • If the script also writes a message to errors.html, it will be displayed, otherwise a server generated message will be shown.
    • The Proceed and Cancel buttons are shown, requiring a user selection to continue.
  • 5. Script does not write a value to maximumSeverity in transformedRunProperties but does write a message to errors.html. This will be interpreted as an error.

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