Fixes to GFF uploader class

tripal/api/tripal.importer.api.inc

@@ -113,6 +113,9 @@ function tripal_run_importer($import_id, $job_id = NULL) {
         $loader->preRun($details);
         $loader->run($details, $job_id);
         $loader->postRun($details);
+
+        // Check for new fields and notify the user.
+        tripal_tripal_cron_notification();
       }
       catch (Exception $e) {
         throw new Exception('Cannot run loader, ' . $loader_name . ': ' .  $e->getMessage());

tripal_chado/includes/TripalImporter/GFF3Importer.inc

@@ -77,7 +77,18 @@ class GFF3Importer extends TripalImporter {
       '#options'     => $analyses,
     );
 
-    $form['line_number']= array(
+
+
+    // Advanced Options
+    $form['advanced'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Additional Options'),
+      '#collapsible' => TRUE,
+      '#collapsed' => TRUE,
+    );
+
+
+    $form['advanced']['line_number']= array(
       '#type'          => 'textfield',
       '#title'         => t('Start Line Number'),
       '#description'   => t('Enter the line number in the GFF file where you would like to begin processing.  The
@@ -85,7 +96,7 @@ class GFF3Importer extends TripalImporter {
       '#size' => 10,
     );
 
-    $form['landmark_type'] = array(
+    $form['advanced']['landmark_type'] = array(
       '#title'       => t('Landmark Type'),
       '#type'        => t('textfield'),
       '#description' => t("Optional. Use this field to specify a Sequence Ontology type
@@ -96,7 +107,7 @@ class GFF3Importer extends TripalImporter {
        field is not used."),
     );
 
-    $form['alt_id_attr'] = array(
+    $form['advanced']['alt_id_attr'] = array(
       '#title'       => t('ID Attribute'),
       '#type'        => t('textfield'),
       '#description' => t("Optional. Sometimes lines in the GFF file are missing the
@@ -105,14 +116,6 @@ class GFF3Importer extends TripalImporter {
       you may specify the name of the attribute to use for the name."),
     );
 
-    // Advanced Options
-    $form['advanced'] = array(
-      '#type' => 'fieldset',
-      '#title' => t('Advanced Options'),
-      '#collapsible' => TRUE,
-      '#collapsed' => TRUE,
-    );
-
     $form['advanced']['protein_names'] = array(
       '#type' => 'fieldset',
       '#title' => t('Protein Names'),
@@ -147,15 +150,8 @@ class GFF3Importer extends TripalImporter {
        expression would be "$1-P$2".')
     );
 
-    $form['advanced']['import_options'] = array(
-      '#type' => 'fieldset',
-      '#title' => t('Import Options'),
-      '#collapsible' => TRUE,
-      '#collapsed' => FALSE,
-      '#weight' => 0,
-    );
 
-    $form['advanced']['import_options']['use_transaction']= array(
+    $form['advanced']['use_transaction']= array(
       '#type' => 'checkbox',
       '#title' => t('Use a transaction'),
       '#required' => FALSE,
@@ -165,14 +161,14 @@ class GFF3Importer extends TripalImporter {
       of failure will be present in the database.'),
       '#default_value' => 1,
     );
-    $form['advanced']['import_options']['add_only']= array(
+    $form['advanced']['add_only']= array(
       '#type' => 'checkbox',
       '#title' => t('Import only new features'),
       '#required' => FALSE,
       '#description' => t('The job will skip features in the GFF file that already
                          exist in the database and import only new features.'),
     );
-    $form['advanced']['import_options']['update']= array(
+    $form['advanced']['update']= array(
       '#type' => 'checkbox',
       '#title' => t('Import all and update'),
       '#required' => FALSE,
@@ -202,7 +198,7 @@ class GFF3Importer extends TripalImporter {
     //     '#description' => t('Features present in the GFF file that exist in the database
     //                          will be removed rather than imported'),
     //   );
-    $form['advanced']['import_options']['create_organism']= array(
+    $form['advanced']['create_organism']= array(
       '#type' => 'checkbox',
       '#title' => t('Create organism'),
       '#required' => FALSE,