Run properties are defined as part of assay design and values are specified at run upload. The server creates a runProperties.tsv file and rewrites the uploaded data in TSV format. Assay-specific properties from both the run and batch levels are included.

There are standard default assay properties which apply to most assay types, as well as additional properties specific to the assay type. For example, NAb, Luminex, and ELISpot assays can include specimen, analyte, and antigen properties which correspond to locations on a plate associated with the assay instance.

The runProperties.tsv file also contains additional context information that the validation script might need, such as username, container path, assay instance name, assay id. Since the uploaded assay data will be written out to a file in TSV format, the runProperties.tsv also specifies the destination file's location.

Run Properties Format

The runProperties file has three (or four) tab-delimited columns in the following order:

  1. property name
  2. property value
  3. data type – The java class name of the property value (java.lang.String). This column may have a different meaning for properties like the run data, transformed data, or errors file. More information can be found in the property description below.
  4. transformed data location – The full path to the location where the transformed data are rewritten in order for the server to load them into the database.
The file does not contain a column header row because the column order is fixed.

Generic Assay Run Properties

Property NameData TypeProperty Description
assayIdStringThe value entered in the Assay Id field of the run properties section.
assayNameStringThe name of the assay design given when the new assay design was created.
assayTypeStringThe type of this assay design. (GenericAssay, Luminex, Microarray, etc.)
baseUrlURL StringFor example, http://localhost:8080/labkey
containerPathStringThe container location of the assay. (for example, /home/AssayTutorial)
errorsFileFull PathThe full path to a .tsv file where any validation errors are written. See details below.
originalFileLocationFull PathThe full path to the original location of the file being imported as an assay.
protocolDescriptionStringThe description of the assay definition when the new assay design was created.
protocolIdStringThe ID of this assay definition.
protocolLsidStringThe assay definition LSID.
runCommentsStringThe value entered into the Comments field of the run properties section.
runDataUploadedFileFull PathThe original data file that was selected by the user and uploaded to the server as part of an import process. This can be an Excel file, a tab-separated text file, or a comma-separated text file.
runDataFileFull PathThe imported data file after the assay framework has attempted to convert the file to .tsv format and match its columns to the assay data result set definition.
transformedRunPropertiesFileFull PathFile where the script writes out the updated values of batch- and run-level properties that are listed in the runProperties file.
userNameStringThe user who created the assay design.
workingDirStringThe temp location that this script is executed in. (e.g. C:\AssayId_209\39\)

errorsFile

Validation errors can be written to a TSV file as specified by full path with the errorsFile property. This output file is formatted with three columns:

  • Type - "error" or "warn"
  • Property - the name of the property raising the validation error
  • Message - the actual error message
For additional information about handling errors and warnings in transformation scripts, see: Warnings in Tranformation Scripts.

Additional Assay Specific Run Properties

ELISpot

Property NameData TypeProperty Description
sampleDataStringThe path to a file that contains sample data written in a tab-delimited format. The file will contain all of the columns from the sample group section of the assay design. A wellgroup column will be written that corresponds to the well group name in the plate template associated with this assay instance. A row of data will be written for each well position in the plate template.
antigenDataStringThe path to a file that contains antigen data written in a tab-delimited format. The file contains all of the columns from the antigen group section of the assay design. A wellgroup column corresponds to the well group name in the plate template associated with this assay instance. A row of data is written for each well position in the plate template.

Luminex

Property NameData TypeProperty Description
DerivativeString 
AdditiveString 
SpecimenTypeString 
DateModifiedDate 
ReplacesPreviousFileBoolean 
TestDateDate 
ConjugateString 
IsotypeString 

NAb (TZM-bl Neutralizing Antibody) Assay

Property NameData TypeProperty Description
sampleDataStringThe path to a file that contains sample data written in a tab-delimited format. The file contains all of the columns from the sample group section of the assay design. A wellgroup column corresponds to the well group name in the plate template associated with this assay instance. A row of data is written for each well position in the plate template.

General Purpose Assay Type (GPAT)

Property NameData TypeProperty Description
severityLevel (reserved)StringThis is a property name used internally for error and warning handling. Do not define your own property with the same name in a GPAT assay.
maximumSeverity (reserved)StringThis is a property name reserved for use in error and warning handling. Do not define your own property with the same name in a GPAT assay. See Warnings in Tranformation Scripts for details.

Discussion

previousnext
 
expand all collapse all