Fixed defline to wrap better, and bug with non-initalized items

tripal_chado/api/modules/tripal_chado.feature.api.inc

@@ -785,21 +785,21 @@ function chado_get_fasta_defline($feature, $notes = '', $featureloc = NULL, $typ
 
   // Construct the definition line.
   $defline = $feature->uniquename . " " .
-    'ID=' . $feature->uniquename . "|" .
-    'Name=' . $feature->name . "|" .
-    'organism=' . $feature->organism_id->genus . " " . $feature->organism_id->species . "|" .
-    'type=' . $type . '|';
+    'ID=' . $feature->uniquename . "; " .
+    'Name=' . $feature->name . "; " .
+    'organism=' . $feature->organism_id->genus . " " . $feature->organism_id->species . "; " .
+    'type=' . $type . '; ';
   if ($length > 0) {
-    $defline .= "length=" . $length . "bp|";
+    $defline .= "length=" . $length . "bp; ";
   }
   if ($featureloc) {
     $defline .= "location=Sequence derived from: " . chado_get_location_string($featureloc);
     $defline .= " (" . $featureloc->srcfeature_id->organism_id->genus . " " . $featureloc->srcfeature_id->organism_id->species . ")|";
   }
   if ($notes) {
-    $defline .= "Notes=$notes|";
+    $defline .= "Notes=$notes; ";
   }
-  $defline = substr($defline, 0, -1); // remove the trailing |
+  $defline = substr($defline, 0, -2); // remove the trailing "; "
   return $defline;
 }
 

tripal_chado/includes/TripalFields/data__sequence_record/data__sequence_record.inc

@@ -75,6 +75,9 @@ class data__sequence_record extends ChadoField {
     $field_name = $this->field['field_name'];
     $feature = $entity->chado_record;
 
+    // Intialize the field items array
+    $entity->{$field_name}['und'] = [];
+
     // Add the primary sequence from the Chada feature table, residues column.
     $feature = chado_expand_var($feature, 'field', 'feature.residues');
 

tripal_chado/includes/TripalFields/data__sequence_record/data__sequence_record_formatter.inc

@@ -51,7 +51,6 @@ class data__sequence_record_formatter extends ChadoFieldFormatter {
 
     }
 
-
     if (empty($content)) {
       $element[0] = [
         '#type' => 'markup',