Merge pull request #23 from UofS-Pulse-Binfo/22-infraspecific_bug

infraspecific name bug

Author: laceysanderson

includes/TripalImporter/GermplasmAccessionImporter.inc

@@ -347,20 +347,23 @@
         'genus' => $genus,
         'species' => $one_accession['germplasm_species']
       );
-      if ($one_accession['subtaxa']){
+      if (!empty($one_accession['subtaxa'])){
         $match['infraspecific_name'] = $one_accession['subtaxa'];
       }
+      else {
+        $match['infraspecific_name'] = NULL;
+      }
       $results = chado_select_record('organism', ['organism_id'], $match);
       if (count($results) > 1){
-          $this->logMessage('ERROR: The genus, !genus, species, !species, has more than one matched organism in chado.organism.',['!genus' => $genus, '!species' => $one_accession['germplasm_species']], TRIPAL_WARNING);
+          $this->logMessage('ERROR: The genus, !genus, species, !species, infraspecific, !infraspecific, has more than one matched organism in chado.organism.',['!genus' => $genus, '!species' => $one_accession['germplasm_species'], '!infraspecific' => $one_accession['subtaxa']], TRIPAL_WARNING);
           break;
       }
       elseif (count($results) == 1){
         //@log $this->logMessage('The stock, !stock, has one matched name in chado.stock.',['!stock' =>  $one_accession['name']], TRIPAL_WARNING);
         $organism_id = $results[0]->organism_id;
       }
       else{
-        $this->logMessage('ERROR: The genus, !genus, species, !species, has no matched organism in chado.organism.',['!genus' => $genus, '!species' => $one_accession['germplasm_species']], TRIPAL_WARNING);
+        $this->logMessage('ERROR: The genus, !genus, species, !species, infraspecific, !infraspecific, has no matched organism in chado.organism.',['!genus' => $genus, '!species' => $one_accession['germplasm_species'], '!infraspecific' => $one_accession['subtaxa']], TRIPAL_WARNING);
         break;
       }
 

includes/TripalImporter/GermplasmCrossImporter.inc

@@ -74,7 +74,12 @@
     $organisms = array();
     $organisms[''] = '';
     while ($organism = $org_rset->fetchObject()) {
-      $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
+      if ($organism->infraspecific_name){
+        $organisms[$organism->organism_id] = "$organism->genus $organism->species $organism->infraspecific_name  ($organism->common_name)";
+      }
+      else{
+        $organisms[$organism->organism_id] = "$organism->genus $organism->species  ($organism->common_name)";
+      }
     }
 
     $form['instructions'] = [