Merge pull request #1301 from tripal/1300-tv3-fasta-loader-infraspecific

Issue 1300 FASTA importer organism selector infraspecific nomenclature
tripal · Sep 26, 2022 · 48e2aff · 48e2aff
2 parents 2de02c0 + 8a90e37
commit 48e2aff
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Showing 2 changed files with 2 additions and 15 deletions.
diff --git a/tripal_chado/includes/TripalImporter/FASTAImporter.inc b/tripal_chado/includes/TripalImporter/FASTAImporter.inc
@@ -71,13 +71,7 @@ class FASTAImporter extends TripalImporter {
   public function form($form, &$form_state) {
 
     // get the list of organisms
-    $sql = "SELECT * FROM {organism} ORDER BY genus, species";
-    $org_rset = chado_query($sql);
-    $organisms = [];
-    $organisms[''] = '';
-    while ($organism = $org_rset->fetchObject()) {
-      $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
-    }
+    $organisms = chado_get_organism_select_options(FALSE);
     $form['organism_id'] = [
       '#title' => t('Organism'),
       '#type' => t('select'),

diff --git a/tripal_chado/includes/TripalImporter/GFF3Importer.inc b/tripal_chado/includes/TripalImporter/GFF3Importer.inc
@@ -298,14 +298,7 @@ class GFF3Importer extends TripalImporter {
   public function form($form, &$form_state) {
 
     // get the list of organisms
-    $sql = "SELECT * FROM {organism} ORDER BY genus, species";
-    $org_rset = chado_query($sql);
-    $organisms = [];
-    $organisms[''] = '';
-    while ($organism = $org_rset->fetchObject()) {
-      $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
-    }
-
+    $organisms = chado_get_organism_select_options(FALSE);
     $form['organism_id'] = [
       '#title' => t('Existing Organism'),
       '#type' => 'select',