tripal_bulk_loader_help.tpl.php 3.0 KB

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  1. <p>The bulk loader is a tool that Tripal provides for loading of data contained
  2. in tab
  3. delimited files. Tripal supports loading of files in standard formats (e.g.
  4. FASTA, GFF, OBO),
  5. but Chado can support a variety of different biological data types and there
  6. are often no
  7. community standard file formats for loading these data. For example, there
  8. is no file
  9. format for importing genotype and phenotype data. Those data can be stored
  10. in the feature,
  11. stock and natural diversity tables of Chado. The Bulk Loader was introduced
  12. in Tripal v1.1
  13. and provides a web interface for building custom data loader. In short, the
  14. site developer
  15. creates the bulk loader "template". This template can then be used and
  16. re-used for any tab
  17. delimited file that follows the format described by the template.
  18. Additionally, bulk loading
  19. templates can be exported allowing Tripal sites to share loaders with one
  20. another. Loading
  21. templates that have been shared are available on the Tripal website here:
  22. <?php print l('http://tripal.info/extensions/bulk-loader-templates', 'http://tripal.info/extensions/bulk-loader-templates'); ?>
  23. .</p>
  24. <br/>
  25. <h3>General Usage</h3>
  26. <ol>
  27. <li><strong>Plan how to store your data.</strong>
  28. <br/>This is the most important and often the most difficult step. This
  29. is because it requires familiarity with the Chado database schema and
  30. due to the
  31. flexibility of the schema, you may be able to store your data multiple
  32. ways. It is
  33. considered best practice to consult the GMOD website and the Chado
  34. community (via the
  35. <?php print l('gmod-schema mailing list', 'https://lists.sourceforge.net/lists/listinfo/gmod-schema'); ?>
  36. ) when deciding how to store data.
  37. </li>
  38. <li><strong>Create a new Bulk Loading Template to map the columns from your
  39. data file to chado.</strong>
  40. <br/>Creating a new template can be done by clicking on the "Templates"
  41. tab above
  42. and then the "Add Template" link. Note that the template is designed
  43. with a single line
  44. from your file in mind. Furthermore, the term "record" refers to a
  45. single entry in chado
  46. and the term "field" refers to a column in a specific chado table.
  47. </li>
  48. <li><strong>Create a Bulk Loader Job with file-specific details that uses
  49. your template to load a
  50. specific file.</strong>
  51. <br/>Create a Bulk Loading Job by clicking on the "Jobs" tab above and
  52. then "Add Bulk
  53. Loading Job". Remember to select the template you just created and to
  54. ensure that you
  55. provide the absolute path to the file. Note: The file must already be
  56. uploaded to the
  57. same server as your Drupal installation and must be readable by the
  58. command-line
  59. user who executes the tripal job.
  60. </li>
  61. </ol>
  62. <p>For the full tutorial, see
  63. the <?php print l('Tripal User Manual: The Bulk Loader', 'http://tripal.info/node/109'); ?>
  64. .</p>