Merge pull request #52 from UofS-Pulse-Binfo/issue51

Issue #51: Improve Documentation
UofS-Pulse-Binfo · Dec 5, 2020 · afd1c99 · afd1c99
2 parents 148940e + f01edcc
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diff --git a/docs/contribute.rst b/docs/contribute.rst
@@ -25,7 +25,7 @@ This will run all tests associated with the ND Genotypes extension module. If yo
 Manual Testing (Demonstration)
 --------------------------------
 
-We have provided a `Tripal Test Suite Database Seeder <https://tripaltestsuite.readthedocs.io/en/latest/db-seeders.html>` to make development and demonstration of functionality easier. To populate your development database with fake phenotypic data:
+We have provided a `Tripal Test Suite Database Seeder <https://tripaltestsuite.readthedocs.io/en/latest/db-seeders.html>`_ to make development and demonstration of functionality easier. To populate your development database with fake phenotypic data:
 
 1. Install this module according to the instructions in the administration guide.
 2. Create an organism (genus: Tripalus; species: databasica)
@@ -39,7 +39,7 @@ We have provided a `Tripal Test Suite Database Seeder <https://tripaltestsuite.r
 
 4. Populate the materialized views by going to Administration » Tripal » Extensions » Natural Diversity Genotypes » Sync and Choose "Tripalus" then click the "Sync" button. Finally run the Tripal jobs submitted.
 5. To play with the genotype matrix go to ``[your drupal site]/chado/genotype/[genus]``. You can see what germplasm are available by typing a single random letter in the autocomplete box.
-6. To play with marker/variant pages, go to Administration » Content » Tripal Content » Publish Tripal Content and then select "Genetic Marker"/"Sequence Variant" and publish to create pages. Remember to run the tripal jobs submitted.
+6. To play with marker/variant pages, go to Administration » Content » Tripal Content » Publish Tripal Content and then select "Genetic Marker"/"Sequence Variant" and publish to create pages. Remember to run the tripal jobs submitted on the command-line using Drush ``trp-job-run``.
 
 .. warning::
 

diff --git a/includes/nd_genotypes.admin.inc b/includes/nd_genotypes.admin.inc
@@ -440,7 +440,8 @@ function nd_genotypes_admin_sync_mviews($form, $form_state) {
     '#title' => 'Materialized Views',
     '#description' => 'Materialized views are used extensively by this module to
       speed up quering and provide flexibility on how you choose to store your data. <strong>It is important to update these
-      materialized views whenever you load in new genotype data.</strong>',
+      materialized views whenever you load in new genotype data.</strong>
+      <div class="messages notice">It is important the sync Tripal job be run on the command-line through Drush using the command displayed when you submit this form.</div>',
     '#collapsible' => TRUE,
     '#collapsed' => FALSE
   );