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- <p>The bulk loader is a tool that Tripal provides for loading of data contained
- in tab
- delimited files. Tripal supports loading of files in standard formats (e.g.
- FASTA, GFF, OBO),
- but Chado can support a variety of different biological data types and there
- are often no
- community standard file formats for loading these data. For example, there
- is no file
- format for importing genotype and phenotype data. Those data can be stored
- in the feature,
- stock and natural diversity tables of Chado. The Bulk Loader was introduced
- in Tripal v1.1
- and provides a web interface for building custom data loader. In short, the
- site developer
- creates the bulk loader "template". This template can then be used and
- re-used for any tab
- delimited file that follows the format described by the template.
- Additionally, bulk loading
- templates can be exported allowing Tripal sites to share loaders with one
- another. Loading
- templates that have been shared are available on the Tripal website here:
- <?php print l('http://tripal.info/extensions/bulk-loader-templates', 'http://tripal.info/extensions/bulk-loader-templates'); ?>
- .</p>
- <br/>
- <h3>General Usage</h3>
- <ol>
- <li><strong>Plan how to store your data.</strong>
- <br/>This is the most important and often the most difficult step. This
- is because it requires familiarity with the Chado database schema and
- due to the
- flexibility of the schema, you may be able to store your data multiple
- ways. It is
- considered best practice to consult the GMOD website and the Chado
- community (via the
- <?php print l('gmod-schema mailing list', 'https://lists.sourceforge.net/lists/listinfo/gmod-schema'); ?>
- ) when deciding how to store data.
- </li>
- <li><strong>Create a new Bulk Loading Template to map the columns from your
- data file to chado.</strong>
- <br/>Creating a new template can be done by clicking on the "Templates"
- tab above
- and then the "Add Template" link. Note that the template is designed
- with a single line
- from your file in mind. Furthermore, the term "record" refers to a
- single entry in chado
- and the term "field" refers to a column in a specific chado table.
- </li>
- <li><strong>Create a Bulk Loader Job with file-specific details that uses
- your template to load a
- specific file.</strong>
- <br/>Create a Bulk Loading Job by clicking on the "Jobs" tab above and
- then "Add Bulk
- Loading Job". Remember to select the template you just created and to
- ensure that you
- provide the absolute path to the file. Note: The file must already be
- uploaded to the
- same server as your Drupal installation and must be readable by the
- command-line
- user who executes the tripal job.
- </li>
- </ol>
- <p>For the full tutorial, see
- the <?php print l('Tripal User Manual: The Bulk Loader', 'http://tripal.info/node/109'); ?>
- .</p>
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