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UofS-Pulse-Binfo / tripal_qtl

Provides additional fields and data import which provide support for quantitative trait loci. Additionally, it integrates with Tripal Map through shared vocabulary terms and data storage models.
GNU General Public License v2.0
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QTL Importer #3

Closed laceysanderson closed 4 years ago

laceysanderson commented 4 years ago

This importer adds QTL data to an existing map.

Testing

  1. Clone this repository, install it and Tripal Map and spin up phpunit/tripaltestsuite: composer up
  2. Load a fake map for testing purposes: ./vendor/bin/tripaltest db:seed GeneticMapSeeder
  3. Run automated testing and ensure it passes: ./vendor/bin/phpunit
  4. Create cvterms to match any traits you have in your test file. For tests/example_files/qtl.singletrait.tsv you would create a term with the name Days to Flowering. You can create cvterms through the UI at Admin > Tripal > Data Loaders > Controlled Vocabularies > Manage Chado CV Terms. Note the CV you create it in as you will have to select it in the importer.
  5. In your site, go to Admin > Tripal > Data Loaders > QTL Importer. Choose your fake map created in step 2 and the CV you noted down in step 4.
  6. Upload a test file of your choice or use tests/example_files/qtl.singletrait.tsv
  7. Choose submit and run the Tripal Job
  8. Go to Admin > Tripal > Data Storage > Chado > Materialized Views and sync both tripal_map_genetic_markers_mview and tripal_map_qtl_and_mtl_mview
  9. View your QTL using Tripal Map at localhost/MapViewer
laceysanderson commented 4 years ago

Thanks for the review. Unfortunately I cannot change the display name on Tripal Map as that is not my software. Since the loader worked perfectly for you, I'm going to merge this PR.