Process Input File Parameters

• This section relates to processes run from the LIMS Operations Interface.
• Steps run from the LIMS web interface only support analyte (derived sample) inputs.

The inputs to a process may sometimes be files that were created from a previous process. For the EPP/automation script, such process input files supply additional information, or raw data, for processing. Input files display in the process summary tab in the Operations Interface:

This section describes parameters for input files. In the following list, parameters are categorized according to their purpose in the EPP/automation script.

• Parameters That Copy Files
– inputFiles
– inputFileN
• Parameters That Identify Files
– inputFileLuids
– inputFileLuidN
• Parameters That Print Path and File Names
– originalInputFileNames
– originalInputFileNameN

Copy File parameters are only available for use when both of the following conditions exist:

• The Run each time a file attachment event occurs option is deselected (Operations Interface, in the Add/Modify Process Parameter dialog).
• The EPP/automation is triggered by a process completion event.

The following parameters are used to automatically transfer input files from Clarity LIMS to the processing EPP/AI node. Note the following:

• Input files are named with their unique LIMS ID and the original file extension.
• Input files can be accessed directly by your script.
• Any file-related commands used by your script can assume these files are located in its current working directory.

{inputFiles}

Purpose—Transfers all of the input files to the temporary working directory.

Example: In the configured parameter string:

cmd /c "C:\ai\ai.bat {inputFiles}"

The parameter is replaced with:

cmd /c C:\ai\ai.bat "BAR103A1MA9.txt" "BAR103A3MA9.txt"

{inputFileN}

Purpose—Transfers the specified input file to the temporary working directory.

• All input files for this process are treated as an array based list.
• N specifies the array list index position [0..n] of the file desired.

Example:

In the configured parameter string:

cmd /c "C:\ai\ai.bat {inputFile0}"

The parameter is replaced with:

cmd /c C:\ai\ai.bat BAR103A1MA9.txt

Similarly, in the configured parameter string:

cmd /c "C:\ai\ai.bat {inputFile1}"

The parameter is replaced with:

cmd /c C:\ai\ai.bat BAR103A3MA9.txt

The following parameters are used to supply the external script with the unique LIMS IDs of the input files, without transferring the input files to the temporary working directory.

This mechanism allows the input files to be identified by the external script without actually transferring those files over the network.

This is particularly useful when the files are very large and stored in a location already known and accessible by the external script.

{inputFileLuids}

Purpose—Supplies the LIMS IDs for all input files.

Example:

In the configured parameter string:

cmd /c "C:\ai\ai.bat {inputFileLuids}"

The parameter is replaced with:

cmd /c C:\ai\ai.bat "BAR103A1MA9" "BAR103A3MA9"

{inputFileLuidN}

Purpose—Supplies the LIMS ID for the specified input file.

• All input files for this process are treated as an array based list.
• N specifies the array list index position [0..n] of the file desired.

Example:

In the configured parameter string:

cmd /c "C:\ai\ai.bat {inputFileLuid0}"

The parameter is replaced with:

cmd /c C:\ai\ai.bat BAR103A1MA9

Similarly, in the configured parameter string:

cmd /c "C:\ai\ai.bat {inputFileLuid1}"

The parameter is replaced with:

cmd /c C:\ai\ai.bat BAR103A3MA9

Within the LIMS, generated IDs are most often referred to as 'LIMS IDs', but may occasionally be referred to as LUIDs (Lims Unique IDs).

The following parameters are used to supply the external script with the original path and file name of the input files, without transferring the input files to the temporary working directory.

This mechanism allows the input files to be identified by the external script without actually transferring those files over the network. This is particularly useful when the files are very large and stored in a location already known and accessible by the external script.

If you would like external scripts to access files directly using the supplied path and name:

• Be sure that your standard operating procedures for attaching files through the Operations Interface require attaching the files from universal network paths – rather than from a locally referenced directory (i.e., a network path that any machine on your network could access to locate the file).

{originalInputFileNames}

Purpose—Supplies the original path and file names for all input files.

Example:

In the configured parameter string:

cmd /c "C:\ai\ai.bat {originalInputFileNames}"

The parameter is replaced with:

cmd /c C:\ai\ai.bat "\\nas\testdata\if-1.txt" "\\nas\testdata\if-3.txt"

{originalInputFileNameN}

Purpose—Supplies the original path and file name for the specified input file.

• All input files for this process are treated as an array based list.
• N specifies the array list index position [0..n] of the file desired.

Example:

In the configured parameter string:

cmd /c "C:\ai\ai.bat {originalInputFileName0}"

The parameter is replaced with:

cmd /c C:\ai\ai.bat \\nas\testdata\if-1.txt

Similarly, in the configured parameter string:

cmd /c "C:\ai\ai.bat {originalInputFileName1}"

The parameter is replaced with:

cmd /c C:\ai\ai.bat \\nas\testdata\if-3.txt

Check that the EPP/AI node machine can resolve the base network path as it is returned from the API.