Fixed bug in FASTA downloaders. Removed hidden fields from inclusion in collections

tripal/includes/TripalFieldDownloaders/TripalNucFASTADownloader.inc

@@ -73,7 +73,10 @@ class TripalNucFASTADownloader extends TripalFieldDownloader {
                 // Skip the identifier fields and the residues fields.
                 if (!in_array($fname, array('data__identifier',
                     'schema__name', 'data__protein_sequence', $field_name))) {
-                  $defline .= $instance['label'] . ': ' . $entity->{$fname}['und'][0]['value'] . '; ';
+                  $fvalue = $entity->{$fname}['und'][0]['value'];
+                  if ($fvalue) {
+                    $defline .= $instance['label'] . ': ' . $fvalue . '; ';
+                  }
                 }
               }
               else {

tripal/includes/TripalFieldDownloaders/TripalProteinFASTADownloader.inc

@@ -72,7 +72,10 @@ class TripalProteinFASTADownloader extends TripalFieldDownloader {
                 // Skip the identifier fields and the residues fields.
                 if (!in_array($fname, array('data__identifier',
                   'schema__name', 'data__sequence', $field_name))) {
-                  $defline .= $instance['label'] . ': ' . $entity->{$fname}['und'][0]['value'] . '; ';
+                  $fvalue = $entity->{$fname}['und'][0]['value'];
+                  if ($fvalue) {
+                    $defline .= $instance['label'] . ': ' . $fvalue . '; ';
+                  }
                 }
               }
               else {

tripal/views_handlers/tripal_views_handler_area_collections.inc

@@ -91,6 +91,10 @@ function tripal_views_handler_area_collections_form($form, $form_state, $view, $
     if ($instance['field_name'] == 'entity_id') {
       continue;
     }
+    // Skip hidden fields.
+    if ($instance['display']['default']['type'] == 'hidden') {
+      continue;
+    }
     $field_ids[$instance['field_id']] = $instance['label'];
   }
   $form['save_collection']['field_ids'] = array(
@@ -136,7 +140,7 @@ function tripal_views_handler_area_collections_form_submit($form, $form_state) {
   $bundle = $form_state['values']['bundle'];
   $view = $form_state['values']['view'];
   $query = $form_state['values']['query'];
-  $collection_name = $form_state['values']['collection_name'];
+  $collection_name = trim($form_state['values']['collection_name']);
   $description = $form_state['values']['collection_desc'];
   $field_ids = array_key_exists('field_ids', $form_state['values']) ? $form_state['values']['field_ids'] : array();
   $uid = $user->uid;
@@ -155,6 +159,10 @@ function tripal_views_handler_area_collections_form_submit($form, $form_state) {
       if ($instance['field_name'] == 'entity_id') {
         continue;
       }
+      // Skip hidden fields.
+      if ($instance['display']['default']['type'] == 'hidden') {
+        continue;
+      }
       $selected_fids[] = $instance['field_id'];
     }
   }