Template File Generator

Available from: BaseSpace Clarity LIMS v4.2.x

The Template File Generator is a file-generation solution that allows Clarity LIMS admins, such as lab managers, to produce custom template files without requiring scripting or development knowledge or resources.

At run time, the Template File Generator uses a script (driver_file_generator) and the supplied template file to generate a file. This may be a simple file that includes a subset of LIMS data, or a more complex sample sheet file for upload to the sequencing instrument to start a run.

The format of a template file is typically a comma-delimited CSV file. However, the following file formats are also supported: .bak, .groovy, .md5, .tsv, .txt, .xml.

How the Template File Generator Works

1. In Clarity LIMS:

   • An automation is configured and enabled on a step.

   • The driver_file_generator script is triggered from the automation command line.

2. The script uses the template file to generate a file, the contents of which are based on the specifications provided in the template.

3. The script extracts data from the LIMS via the API, based on tokens defined within the template file.

4. The script parses the template file and processes the sections, metadata, and tokens it contains. Sections may include header block, header, data, and footer, each of which is enclosed inside tags.

For example:

<HEADER_BLOCK> 
    Header block entry one, two, three 
    More information
</HEADER_BLOCK>
<DATA>
    Data row entry
    Data row entry
</DATA>

For details on template sections and the tokens you can use in your template files, see Creating Template Files article.

• Several special options are available for inclusion in the template. These options do not directly pull data from the LIMS API. Instead, they modify what has been gathered in the template file.

• For details, refer to TOKEN FORMAT section of the Creating Template Files article.