fixing the formatting on the files to meet drupal requirements

tripal_chado/api/tripal_chado.api.inc

@@ -164,7 +164,7 @@ function tripal_chado_publish_records($values, $job_id = NULL) {
   // Perform the query.
   $sql = $select . $from . $where;
   $records = chado_query($sql, $args);
-  $transaction = db_transaction();
+  //$transaction = db_transaction();
 
   print "\nNOTE: publishing records is performed using a database transaction. \n" .
       "If the load fails or is terminated prematurely then the entire set of \n" .

tripal_ds/includes/tripal_ds.field_formatter.inc

@@ -96,7 +96,7 @@ function tripal_ds_field_group_delete_field_group($group) {
  * checks for changes from tripalpane to another type
  */
 function tripal_ds_field_group_update_field_group($group) {
-  //change from tripal pane to another type
+  //Change from tripal pane to another type.
   if(!empty($group->bundle)){
     $result = db_select('tripal_ds', 't')
       ->fields('t')
@@ -105,7 +105,7 @@ function tripal_ds_field_group_update_field_group($group) {
       ->execute()
       ->fetchAssoc();
 
-    //change from tripal pane to another type
+    //Change from tripal pane to another type.
     if($group->format_type !== 'tripalpane' && !empty($result)){
        db_delete('tripal_ds')
       ->condition('bundle', $result['bundle'], '=')
@@ -113,7 +113,7 @@ function tripal_ds_field_group_update_field_group($group) {
       ->execute();
     }
 
-    //change from other type to tripalpane
+    //Change from other type to tripalpane.
     if($group->format_type == 'tripalpane' && empty($result)){
 
       if(strpos($group->group_name, 'Tripal Pane')){

tripal_ds/includes/tripal_ds.field_group.inc

@@ -1,397 +1,396 @@
 <?php
 /**
- * Implements hook_field_group_info().
- */
+* Implements hook_field_group_info().
+*/
 
 function _summary_field_group_info($bundle_name, $fields){
-    
-    //tripalpane  to nest the fieldset within
-    $field_group_tripalpane = new stdClass();
-    $field_group_tripalpane->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
-    $field_group_tripalpane->api_version = 1;
-    $field_group_tripalpane->identifier = 'group_summary_tripalpane|TripalEntity|'.$bundle_name.'|default';
-    $field_group_tripalpane->group_name = 'group_summary_tripalpane';
-    $field_group_tripalpane->entity_type = 'TripalEntity';
-    $field_group_tripalpane->bundle = $bundle_name;
-    $field_group_tripalpane->mode = 'default';
-    $field_group_tripalpane->parent_name = '';
-    $field_group_tripalpane->data = array(
-        'label' => 'Tripal Pane Summary',
-        'weight' => '1',
-        'children' => array(
-            0 => 'group_summary',
-        ),
-        'format_type' => 'tripalpane',
-        'format_settings' => array(
-            'label' => 'Tripal Pane Summary',
-            'instance_settings' => array(
-                'id' => 'tripal_ds-fieldset-group_summary_tripalpane',
-                'classes' => 'group-summary-tripalpane field-group-tripalpane',
-                'description' => '',
-            ),
-        ),
-    );
-    drupal_write_record('field_group', $field_group_tripalpane);
-
-    //write to the tripal_ds table to record the new tripal pane
-    $field_for_table = new stdClass();
-    $field_for_table->tripal_ds_field_name = 'group_summary_tripalpane';
-    $field_for_table->tripal_ds_field_label = 'Summary';
-    $field_for_table->entity_type = 'TripalEntity';
-    $field_for_table->bundle = $bundle_name;
-
-    drupal_write_record('tripal_ds', $field_for_table);
-
-    //fieldset field to nest the table within
-    $field_group_fieldset = new stdClass();
-    $field_group_fieldset->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
-    $field_group_fieldset->api_version = 1;
-    $field_group_fieldset->identifier = 'group_summary|TripalEntity|'.$bundle_name.'|default';
-    $field_group_fieldset->group_name = 'group_summary';
-    $field_group_fieldset->entity_type = 'TripalEntity';
-    $field_group_fieldset->bundle = $bundle_name;
-    $field_group_fieldset->mode = 'default';
-    $field_group_fieldset->parent_name = 'group_summary_tripalpane';
-    $field_group_fieldset->data = array(
-        'label' => 'Summary',
-        'weight' => '5',
-        'children' => array(
-            0 => 'group_summary_table',
-        ),
-        'format_type' => 'fieldset',
-        'format_settings' => array(
-            'label' => 'Summary',
-            'instance_settings' => array(
-                'id' => '',
-                'classes' => 'group-summary field-group-fieldset',
-                'description' => '',
-            ),
-            'formatter' => 'collapsible',
-        ),
-    );
-
-    drupal_write_record('field_group', $field_group_fieldset);
-
-    //table of fields
-    $field_group = new stdClass();
-    $field_group->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
-    $field_group->api_version = 1;
-    $field_group->identifier = 'group_summary_table|TripalEntity|'.$bundle_name.'|default';
-    $field_group->group_name = 'group_summary_table';
-    $field_group->entity_type = 'TripalEntity';
-    $field_group->bundle = $bundle_name;
-    $field_group->mode = 'default';
-    $field_group->parent_name = 'group_summary';
-    $field_group->data = array(
-        'label' => 'Summary Table',
-        'weight' => '30',
-        'children' => $fields,
-        'format_type' => 'table',
-        'format_settings' => array(
-            'label' => 'Summary Table',
-            'instance_settings' => array(
-                'label_visibility' => '1',
-                'desc' => '',
-                'first_column' => '',
-                'second_column' => '',
-                'empty_label_behavior' => '1',
-                'table_row_striping' => 0,
-                'always_show_field_label' => 0,
-                'classes' => 'group-summary-table field-group-table',
-            ),
-        ),
-    );
 
-    drupal_write_record('field_group', $field_group);
+  //Tripal pane to nest the summary fieldset within.
+  $field_group_tripalpane = new stdClass();
+  $field_group_tripalpane->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
+  $field_group_tripalpane->api_version = 1;
+  $field_group_tripalpane->identifier = 'group_summary_tripalpane|TripalEntity|'.$bundle_name.'|default';
+  $field_group_tripalpane->group_name = 'group_summary_tripalpane';
+  $field_group_tripalpane->entity_type = 'TripalEntity';
+  $field_group_tripalpane->bundle = $bundle_name;
+  $field_group_tripalpane->mode = 'default';
+  $field_group_tripalpane->parent_name = '';
+  $field_group_tripalpane->data = array(
+    'label' => 'Tripal Pane Summary',
+    'weight' => '1',
+    'children' => array(
+      0 => 'group_summary',
+    ),
+    'format_type' => 'tripalpane',
+    'format_settings' => array(
+      'label' => 'Tripal Pane Summary',
+      'instance_settings' => array(
+        'id' => 'tripal_ds-fieldset-group_summary_tripalpane',
+        'classes' => 'group-summary-tripalpane field-group-tripalpane',
+        'description' => '',
+      ),
+    ),
+  );
+  drupal_write_record('field_group', $field_group_tripalpane);
+
+  //Write to the tripal_ds table to record the new tripal pane.
+  $field_for_table = new stdClass();
+  $field_for_table->tripal_ds_field_name = 'group_summary_tripalpane';
+  $field_for_table->tripal_ds_field_label = 'Summary';
+  $field_for_table->entity_type = 'TripalEntity';
+  $field_for_table->bundle = $bundle_name;
+
+  drupal_write_record('tripal_ds', $field_for_table);
+
+  //Fieldset field to nest the table within.
+  $field_group_fieldset = new stdClass();
+  $field_group_fieldset->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
+  $field_group_fieldset->api_version = 1;
+  $field_group_fieldset->identifier = 'group_summary|TripalEntity|'.$bundle_name.'|default';
+  $field_group_fieldset->group_name = 'group_summary';
+  $field_group_fieldset->entity_type = 'TripalEntity';
+  $field_group_fieldset->bundle = $bundle_name;
+  $field_group_fieldset->mode = 'default';
+  $field_group_fieldset->parent_name = 'group_summary_tripalpane';
+  $field_group_fieldset->data = array(
+    'label' => 'Summary',
+    'weight' => '5',
+    'children' => array(
+      0 => 'group_summary_table',
+    ),
+    'format_type' => 'fieldset',
+    'format_settings' => array(
+      'label' => 'Summary',
+      'instance_settings' => array(
+        'id' => '',
+        'classes' => 'group-summary field-group-fieldset',
+        'description' => '',
+      ),
+      'formatter' => 'collapsible',
+    ),
+  );
+
+  drupal_write_record('field_group', $field_group_fieldset);
+
+  //Table of fields.
+  $field_group = new stdClass();
+  $field_group->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
+  $field_group->api_version = 1;
+  $field_group->identifier = 'group_summary_table|TripalEntity|'.$bundle_name.'|default';
+  $field_group->group_name = 'group_summary_table';
+  $field_group->entity_type = 'TripalEntity';
+  $field_group->bundle = $bundle_name;
+  $field_group->mode = 'default';
+  $field_group->parent_name = 'group_summary';
+  $field_group->data = array(
+    'label' => 'Summary Table',
+    'weight' => '30',
+    'children' => $fields,
+    'format_type' => 'table',
+    'format_settings' => array(
+      'label' => 'Summary Table',
+      'instance_settings' => array(
+        'label_visibility' => '1',
+        'desc' => '',
+        'first_column' => '',
+        'second_column' => '',
+        'empty_label_behavior' => '1',
+        'table_row_striping' => 0,
+        'always_show_field_label' => 0,
+        'classes' => 'group-summary-table field-group-table',
+      ),
+    ),
+  );
+
+  drupal_write_record('field_group', $field_group);
 
 
 }
 /**
- * Implements hook_field_group_info().
- */
+* Implements hook_field_group_info().
+*/
 
 function _prop_field_group_info($bundle_name, $fields){
-    //tripalpane  to nest the fieldset within
-    $field_group_tripalpane = new stdClass();
-    $field_group_tripalpane->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
-    $field_group_tripalpane->api_version = 1;
-    $field_group_tripalpane->identifier = 'group_prop_tripalpane|TripalEntity|'.$bundle_name.'|default';
-    $field_group_tripalpane->group_name = 'group_prop_tripalpane';
-    $field_group_tripalpane->entity_type = 'TripalEntity';
-    $field_group_tripalpane->bundle = $bundle_name;
-    $field_group_tripalpane->mode = 'default';
-    $field_group_tripalpane->parent_name = '';
-    $field_group_tripalpane->data = array(
-        'label' => 'Tripal Pane Properties',
-        'weight' => '2',
-        'children' => array(
-            0 => 'group_prop',
-        ),
-        'format_type' => 'tripalpane',
-        'format_settings' => array(
-            'label' => 'Tripal Pane Properties',
-            'instance_settings' => array(
-                'id' => 'tripal_ds-fieldset-group_prop_tripalpane',
-                'classes' => 'group-prop-tripalpane field-group-tripalpane',
-                'description' => '',
-            ),
+  //Tripal pane  to nest the fieldset within.
+  $field_group_tripalpane = new stdClass();
+  $field_group_tripalpane->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
+  $field_group_tripalpane->api_version = 1;
+  $field_group_tripalpane->identifier = 'group_prop_tripalpane|TripalEntity|'.$bundle_name.'|default';
+  $field_group_tripalpane->group_name = 'group_prop_tripalpane';
+  $field_group_tripalpane->entity_type = 'TripalEntity';
+  $field_group_tripalpane->bundle = $bundle_name;
+  $field_group_tripalpane->mode = 'default';
+  $field_group_tripalpane->parent_name = '';
+  $field_group_tripalpane->data = array(
+    'label' => 'Tripal Pane Properties',
+    'weight' => '2',
+    'children' => array(
+        0 => 'group_prop',
+    ),
+    'format_type' => 'tripalpane',
+    'format_settings' => array(
+      'label' => 'Tripal Pane Properties',
+      'instance_settings' => array(
+        'id' => 'tripal_ds-fieldset-group_prop_tripalpane',
+        'classes' => 'group-prop-tripalpane field-group-tripalpane',
+        'description' => '',
+      ),
+    ),
+  );
+  drupal_write_record('field_group', $field_group_tripalpane);
+
+  //write to the tripal_ds table to record the new tripal pane.
+  $field_for_table = new stdClass();
+  $field_for_table->tripal_ds_field_name = 'group_prop_tripalpane';
+  $field_for_table->tripal_ds_field_label = 'Properties';
+  $field_for_table->entity_type = 'TripalEntity';
+  $field_for_table->bundle = $bundle_name;
+
+  drupal_write_record('tripal_ds', $field_for_table);
+
+
+  //Fieldset field to nest the table within.
+  $field_group_fieldset = new stdClass();
+  $field_group_fieldset->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
+  $field_group_fieldset->api_version = 1;
+  $field_group_fieldset->identifier = 'group_prop|TripalEntity|'.$bundle_name.'|default';
+  $field_group_fieldset->group_name = 'group_prop';
+  $field_group_fieldset->entity_type = 'TripalEntity';
+  $field_group_fieldset->bundle = $bundle_name;
+  $field_group_fieldset->mode = 'default';
+  $field_group_fieldset->parent_name = 'group_prop_tripalpane';
+  $field_group_fieldset->data = array(
+    'label' => 'Properties',
+    'weight' => '3',
+    'children' => array(
+      0 => 'group_prop_table',
+    ),
+    'format_type' => 'fieldset',
+    'format_settings' => array(
+      'label' => 'Properties',
+      'instance_settings' => array(
+        'id' => '',
+        'classes' => 'group-prop field-group-fieldset',
+        'description' => '',
         ),
-    );
-    drupal_write_record('field_group', $field_group_tripalpane);
-    
-    //write to the tripal_ds table to record the new tripal pane
-    $field_for_table = new stdClass();
-    $field_for_table->tripal_ds_field_name = 'group_prop_tripalpane';
-    $field_for_table->tripal_ds_field_label = 'Properties';
-    $field_for_table->entity_type = 'TripalEntity';
-    $field_for_table->bundle = $bundle_name;
-
-    drupal_write_record('tripal_ds', $field_for_table);
-
-
-    //fieldset field to nest the table within
-    $field_group_fieldset = new stdClass();
-    $field_group_fieldset->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
-    $field_group_fieldset->api_version = 1;
-    $field_group_fieldset->identifier = 'group_prop|TripalEntity|'.$bundle_name.'|default';
-    $field_group_fieldset->group_name = 'group_prop';
-    $field_group_fieldset->entity_type = 'TripalEntity';
-    $field_group_fieldset->bundle = $bundle_name;
-    $field_group_fieldset->mode = 'default';
-    $field_group_fieldset->parent_name = 'group_prop_tripalpane';
-    $field_group_fieldset->data = array(
-        'label' => 'Properties',
-        'weight' => '3',
-        'children' => array(
-            0 => 'group_prop_table',
-        ),
-        'format_type' => 'fieldset',
-        'format_settings' => array(
-            'label' => 'Properties',
-            'instance_settings' => array(
-                'id' => '',
-                'classes' => 'group-prop field-group-fieldset',
-                'description' => '',
-                ),
-            'formatter' => 'collapsible',
-        ),
-    );
-
-    drupal_write_record('field_group', $field_group_fieldset);
-
-    //table of fields
-    $field_group = new stdClass();
-    $field_group->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
-    $field_group->api_version = 1;
-    $field_group->identifier = 'group_prop_table|TripalEntity|'.$bundle_name.'|default';
-    $field_group->group_name = 'group_prop_table';
-    $field_group->entity_type = 'TripalEntity';
-    $field_group->bundle = $bundle_name;
-    $field_group->mode = 'default';
-    $field_group->parent_name = 'group_prop';
-    $field_group->data = array(
-        'label' => 'Properties Table',
-        'weight' => '30',
-        'children' => $fields,
-        'format_type' => 'table',
-        'format_settings' => array(
-            'label' => 'Properties Table',
-            'instance_settings' => array(
-                'label_visibility' => '1',
-                'desc' => '',
-                'first_column' => '',
-                'second_column' => '',
-                'empty_label_behavior' => '1',
-                'table_row_striping' => 0,
-                'always_show_field_label' => 0,
-                'classes' => 'group-prop-table field-group-table',
-            ),
-        ),
-    );
-
-    drupal_write_record('field_group', $field_group);
+      'formatter' => 'collapsible',
+    ),
+  );
+
+  drupal_write_record('field_group', $field_group_fieldset);
+
+  //Table of fields.
+  $field_group = new stdClass();
+  $field_group->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
+  $field_group->api_version = 1;
+  $field_group->identifier = 'group_prop_table|TripalEntity|'.$bundle_name.'|default';
+  $field_group->group_name = 'group_prop_table';
+  $field_group->entity_type = 'TripalEntity';
+  $field_group->bundle = $bundle_name;
+  $field_group->mode = 'default';
+  $field_group->parent_name = 'group_prop';
+  $field_group->data = array(
+    'label' => 'Properties Table',
+    'weight' => '30',
+    'children' => $fields,
+    'format_type' => 'table',
+    'format_settings' => array(
+      'label' => 'Properties Table',
+      'instance_settings' => array(
+        'label_visibility' => '1',
+        'desc' => '',
+        'first_column' => '',
+        'second_column' => '',
+        'empty_label_behavior' => '1',
+        'table_row_striping' => 0,
+        'always_show_field_label' => 0,
+        'classes' => 'group-prop-table field-group-table',
+      ),
+    ),
+  );
+
+  drupal_write_record('field_group', $field_group);
 }
 /**
- * Implements hook_field_group_info().
- */
+* Implements hook_field_group_info().
+*/
 
 function _data_sequence_field_group_info($bundle_name, $fields){
-    //tripalpane  to nest the fieldset within
-    $field_group_tripalpane = new stdClass();
-    $field_group_tripalpane->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
-    $field_group_tripalpane->api_version = 1;
-    $field_group_tripalpane->identifier = 'group_sequence_tripalpane|TripalEntity|'.$bundle_name.'|default';
-    $field_group_tripalpane->group_name = 'group_sequence_tripalpane';
-    $field_group_tripalpane->entity_type = 'TripalEntity';
-    $field_group_tripalpane->bundle = $bundle_name;
-    $field_group_tripalpane->mode = 'default';
-    $field_group_tripalpane->parent_name = '';
-    $field_group_tripalpane->data = array(
-        'label' => 'Tripal Pane Data Sequences',
-        'weight' => '2',
-        'children' => array(
-            0 => 'group_sequence',
-        ),
-        'format_type' => 'tripalpane',
-        'format_settings' => array(
-            'label' => 'Tripal Pane Data Sequences',
-            'instance_settings' => array(
-                'id' => 'tripal_ds-fieldset-group_sequence_tripalpane',
-                'classes' => 'group-sequence-tripalpane field-group-tripalpane',
-                'description' => '',
-            ),
-        ),
-    );
-    drupal_write_record('field_group', $field_group_tripalpane);
-
-    //write to the tripal_ds table to record the new tripal pane
-    $field_for_table = new stdClass();
-    $field_for_table->tripal_ds_field_name = 'group_sequence_tripalpane';
-    $field_for_table->tripal_ds_field_label = 'Data Sequences';
-    $field_for_table->entity_type = 'TripalEntity';
-    $field_for_table->bundle = $bundle_name;
-
-    drupal_write_record('tripal_ds', $field_for_table);
-
-    //fieldset field to nest the table within
-    $field_group_fieldset = new stdClass();
-    $field_group_fieldset->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
-    $field_group_fieldset->api_version = 1;
-    $field_group_fieldset->identifier = 'group_sequence|TripalEntity|'.$bundle_name.'|default';
-    $field_group_fieldset->group_name = 'group_sequence';
-    $field_group_fieldset->entity_type = 'TripalEntity';
-    $field_group_fieldset->bundle = $bundle_name;
-    $field_group_fieldset->mode = 'default';
-    $field_group_fieldset->parent_name = 'group_sequence_tripalpane';
-    $field_group_fieldset->data = array(
-        'label' => 'Data Sequences',
-        'weight' => '3',
-        'children' => array(
-            0 => 'group_sequence_table',
-        ),
-        'format_type' => 'fieldset',
-        'format_settings' => array(
-            'label' => 'Data Sequences',
-            'instance_settings' => array(
-                'id' => '',
-                'classes' => 'group-sequence field-group-fieldset',
-                'description' => '',
-            ),
-            'formatter' => 'collapsible',
-        ),
-    );
-
-    drupal_write_record('field_group', $field_group_fieldset);
-
-    //table of fields
-    $field_group = new stdClass();
-    $field_group->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
-    $field_group->api_version = 1;
-    $field_group->identifier = 'group_sequence_table|TripalEntity|'.$bundle_name.'|default';
-    $field_group->group_name = 'group_sequence_table';
-    $field_group->entity_type = 'TripalEntity';
-    $field_group->bundle = $bundle_name;
-    $field_group->mode = 'default';
-    $field_group->parent_name = 'group_sequence';
-    $field_group->data = array(
-        'label' => 'Data Sequences Table',
-        'weight' => '30',
-        'children' => $fields,
-        'format_type' => 'table',
-        'format_settings' => array(
-            'label' => 'Data Sequences Table',
-            'instance_settings' => array(
-                'label_visibility' => '1',
-                'desc' => '',
-                'first_column' => '',
-                'second_column' => '',
-                'empty_label_behavior' => '1',
-                'table_row_striping' => 0,
-                'always_show_field_label' => 0,
-                'classes' => 'group-sequence-table field-group-table',
-            ),
-        ),
-    );
-
-    drupal_write_record('field_group', $field_group);
+  //Tripal pane  to nest the fieldset within.
+  $field_group_tripalpane = new stdClass();
+  $field_group_tripalpane->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
+  $field_group_tripalpane->api_version = 1;
+  $field_group_tripalpane->identifier = 'group_sequence_tripalpane|TripalEntity|'.$bundle_name.'|default';
+  $field_group_tripalpane->group_name = 'group_sequence_tripalpane';
+  $field_group_tripalpane->entity_type = 'TripalEntity';
+  $field_group_tripalpane->bundle = $bundle_name;
+  $field_group_tripalpane->mode = 'default';
+  $field_group_tripalpane->parent_name = '';
+  $field_group_tripalpane->data = array(
+    'label' => 'Tripal Pane Data Sequences',
+    'weight' => '2',
+    'children' => array(
+        0 => 'group_sequence',
+    ),
+    'format_type' => 'tripalpane',
+    'format_settings' => array(
+      'label' => 'Tripal Pane Data Sequences',
+      'instance_settings' => array(
+        'id' => 'tripal_ds-fieldset-group_sequence_tripalpane',
+        'classes' => 'group-sequence-tripalpane field-group-tripalpane',
+        'description' => '',
+      ),
+    ),
+  );
+  drupal_write_record('field_group', $field_group_tripalpane);
+
+  //Write to the tripal_ds table to record the new tripal pane.
+  $field_for_table = new stdClass();
+  $field_for_table->tripal_ds_field_name = 'group_sequence_tripalpane';
+  $field_for_table->tripal_ds_field_label = 'Data Sequences';
+  $field_for_table->entity_type = 'TripalEntity';
+  $field_for_table->bundle = $bundle_name;
+
+  drupal_write_record('tripal_ds', $field_for_table);
+
+  //Fieldset field to nest the table within.
+  $field_group_fieldset = new stdClass();
+  $field_group_fieldset->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
+  $field_group_fieldset->api_version = 1;
+  $field_group_fieldset->identifier = 'group_sequence|TripalEntity|'.$bundle_name.'|default';
+  $field_group_fieldset->group_name = 'group_sequence';
+  $field_group_fieldset->entity_type = 'TripalEntity';
+  $field_group_fieldset->bundle = $bundle_name;
+  $field_group_fieldset->mode = 'default';
+  $field_group_fieldset->parent_name = 'group_sequence_tripalpane';
+  $field_group_fieldset->data = array(
+    'label' => 'Data Sequences',
+    'weight' => '3',
+    'children' => array(
+      0 => 'group_sequence_table',
+    ),
+    'format_type' => 'fieldset',
+    'format_settings' => array(
+      'label' => 'Data Sequences',
+      'instance_settings' => array(
+        'id' => '',
+        'classes' => 'group-sequence field-group-fieldset',
+        'description' => '',
+      ),
+      'formatter' => 'collapsible',
+    ),
+  );
+
+  drupal_write_record('field_group', $field_group_fieldset);
+
+  //Table of fields.
+  $field_group = new stdClass();
+  $field_group->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
+  $field_group->api_version = 1;
+  $field_group->identifier = 'group_sequence_table|TripalEntity|'.$bundle_name.'|default';
+  $field_group->group_name = 'group_sequence_table';
+  $field_group->entity_type = 'TripalEntity';
+  $field_group->bundle = $bundle_name;
+  $field_group->mode = 'default';
+  $field_group->parent_name = 'group_sequence';
+  $field_group->data = array(
+    'label' => 'Data Sequences Table',
+    'weight' => '30',
+    'children' => $fields,
+    'format_type' => 'table',
+    'format_settings' => array(
+      'label' => 'Data Sequences Table',
+      'instance_settings' => array(
+        'label_visibility' => '1',
+        'desc' => '',
+        'first_column' => '',
+        'second_column' => '',
+        'empty_label_behavior' => '1',
+        'table_row_striping' => 0,
+        'always_show_field_label' => 0,
+        'classes' => 'group-sequence-table field-group-table',
+      ),
+    ),
+  );
+
+  drupal_write_record('field_group', $field_group);
 }
 
 /**
- * Implements hook_field_group_info().
- * Processes all additional fields into Tripal Panes
- */
+* Implements hook_field_group_info().
+* Processes all additional fields into Tripal Panes
+*/
 
 function _additional_fields_field_group_info($bundle_name, $field_label, $group_field_name, $fieldset_field_name, $field_name){
-    //write to the tripal_ds table to record the new tripal pane
-    $field_for_table = new stdClass();
-    $field_for_table->tripal_ds_field_name = $group_field_name;
-    $field_for_table->tripal_ds_field_label = $field_label;
-    $field_for_table->entity_type = 'TripalEntity';
-    $field_for_table->bundle = $bundle_name;
-
-    drupal_write_record('tripal_ds', $field_for_table);
-
-    //fieldset field to nest the table within
-    $field_group_fieldset = new stdClass();
-    $field_group_fieldset->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
-    $field_group_fieldset->api_version = 1;
-    $field_group_fieldset->identifier = $group_field_name.'|TripalEntity|'.$bundle_name.'|default';
-    $field_group_fieldset->group_name = $group_field_name;
-    $field_group_fieldset->entity_type = 'TripalEntity';
-    $field_group_fieldset->bundle = $bundle_name;
-    $field_group_fieldset->mode = 'default';
-    $field_group_fieldset->parent_name = '';
-    $field_group_fieldset->data = array(
-        'label' => $field_label.' TripalPane',
-        'weight' => '5',
-        'children' => array(
-            0 => $fieldset_field_name,
-        ),
-        'format_type' => 'tripalpane',
-        'format_settings' => array(
-            'label' => $field_label.' TripalPane',
-            'instance_settings' => array(
-                'id' => 'tripal_ds-fieldset-'.$group_field_name,
-                'classes' => $group_field_name.' field-group-tripalpane',
-                'description' => '',
-            ),
-            'formatter' => 'collapsible',
-        ),
-    );
-
-    drupal_write_record('field_group', $field_group_fieldset);
-
-    //table of fields
-    $field_group = new stdClass();
-    $field_group->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
-    $field_group->api_version = 1;
-    $field_group->identifier =  $fieldset_field_name.'|TripalEntity|'.$bundle_name.'|default';
-    $field_group->group_name =  $fieldset_field_name;
-    $field_group->entity_type = 'TripalEntity';
-    $field_group->bundle = $bundle_name;
-    $field_group->mode = 'default';
-    $field_group->parent_name =  $group_field_name;
-    $field_group->data = array(
-        'label' => $field_label,
-        'weight' => '30',
-        'children' => array(
-            0 =>$field_name,
-        ),
-        'format_type' => 'table',
-        'format_type' => 'fieldset',
-        'format_settings' => array(
-            'label' => $field_label,
-            'instance_settings' => array(
-                'label_visibility' => '1',
-                'id' => '',
-                'classes' => $fieldset_field_name.' field-group-fieldset',
-                'description' => '',
-            ),
-            'formatter' => 'collapsible',
-        ),
-    );
-
-    drupal_write_record('field_group', $field_group);
+  //Write to the tripal_ds table to record the new tripal pane.
+  $field_for_table = new stdClass();
+  $field_for_table->tripal_ds_field_name = $group_field_name;
+  $field_for_table->tripal_ds_field_label = $field_label;
+  $field_for_table->entity_type = 'TripalEntity';
+  $field_for_table->bundle = $bundle_name;
+
+  drupal_write_record('tripal_ds', $field_for_table);
+
+  //Tripal pane to nest the fieldset within.
+  $field_group_fieldset = new stdClass();
+  $field_group_fieldset->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
+  $field_group_fieldset->api_version = 1;
+  $field_group_fieldset->identifier = $group_field_name.'|TripalEntity|'.$bundle_name.'|default';
+  $field_group_fieldset->group_name = $group_field_name;
+  $field_group_fieldset->entity_type = 'TripalEntity';
+  $field_group_fieldset->bundle = $bundle_name;
+  $field_group_fieldset->mode = 'default';
+  $field_group_fieldset->parent_name = '';
+  $field_group_fieldset->data = array(
+    'label' => $field_label.' TripalPane',
+    'weight' => '5',
+    'children' => array(
+      0 => $fieldset_field_name,
+    ),
+    'format_type' => 'tripalpane',
+    'format_settings' => array(
+      'label' => $field_label.' TripalPane',
+      'instance_settings' => array(
+        'id' => 'tripal_ds-fieldset-'.$group_field_name,
+        'classes' => $group_field_name.' field-group-tripalpane',
+        'description' => '',
+      ),
+      'formatter' => 'collapsible',
+    ),
+  );
+
+  drupal_write_record('field_group', $field_group_fieldset);
+
+  //Fieldset to nest the field within the tripal pane.
+  $field_group = new stdClass();
+  $field_group->disabled = FALSE; /* Edit this to true to make a default field_group disabled initially*/
+  $field_group->api_version = 1;
+  $field_group->identifier =  $fieldset_field_name.'|TripalEntity|'.$bundle_name.'|default';
+  $field_group->group_name =  $fieldset_field_name;
+  $field_group->entity_type = 'TripalEntity';
+  $field_group->bundle = $bundle_name;
+  $field_group->mode = 'default';
+  $field_group->parent_name =  $group_field_name;
+  $field_group->data = array(
+    'label' => $field_label,
+    'weight' => '30',
+    'children' => array(
+      0 =>$field_name,
+    ),
+    'format_type' => 'fieldset',
+    'format_settings' => array(
+      'label' => $field_label,
+      'instance_settings' => array(
+        'label_visibility' => '1',
+        'id' => '',
+        'classes' => $fieldset_field_name.' field-group-fieldset',
+        'description' => '',
+      ),
+      'formatter' => 'collapsible',
+    ),
+  );
+
+  drupal_write_record('field_group', $field_group);
 
 }
 

tripal_ds/includes/views/tripal_ds.views.inc

@@ -3,78 +3,77 @@
 
 
 /**
- * Implements hook_views_data().
- */
+* Implements hook_views_data().
+*/
 function tripal_ds_views_data() {
 
-    $data = array();
+  $data = array();
 
-    $data['tripal_ds']['table']['group'] = t('Tripal Panes');
+  $data['tripal_ds']['table']['group'] = t('Tripal Panes');
 
-    $data['tripal_ds']['table']['base'] = array(
-        'title' => t('Tripal Panes'),
-        'help' => t('Contains Tripal Pane records we want exposed to Views.'),
-    );
+  $data['tripal_ds']['table']['base'] = array(
+      'title' => t('Tripal Panes'),
+      'help' => t('Contains Tripal Pane records we want exposed to Views.'),
+  );
 
-    $data['tripal_ds']['bundle'] = array(
-	   'title' => t('Bundle ID'),
-	   'help' => t('This the unque bundle name, eg bio_data_1.'),
-		'relationship' => array(
-		      'base' => 'tripal_entity', // The name of the table to join with.
-		      'base field' => 'bundle', // The name of the field on the joined table.
-		      // 'field' => 'nid' -- see hook_views_data_alter(); not needed here.
-		      'handler' => 'views_handler_relationship',
-		      'label' => t('Default label for the relationship'),
-		      'title' => t('Title shown when adding the relationship'),
-		      'help' => t('More information on this relationship'),
-		    ),    	
-		'filter' => array(
-      		'handler' => 'views_handler_filter_bundle',
-     	),
-    	'argument' => array(
-      		'handler' => 'views_handler_argument_string',
-    	),
-    	'field' => array(
-      		'handler' => 'views_handler_field',
-    	),
-  	);
+  $data['tripal_ds']['bundle'] = array(
+   'title' => t('Bundle ID'),
+   'help' => t('This the unque bundle name, eg bio_data_1.'),
+  'relationship' => array(
+        'base' => 'tripal_entity', // The name of the table to join with.
+        'base field' => 'bundle', // The name of the field on the joined table.
+        'handler' => 'views_handler_relationship',
+        'label' => t('Bundle relationship with tripal_entity table'),
+        'title' => t('Bundle and tripal_entity relationship'),
+        'help' => t('This relationship links the tripal_ds table with the tripal_entity table via the bundle.'),
+      ),
+  'filter' => array(
+        'handler' => 'views_handler_filter_bundle',
+    ),
+    'argument' => array(
+        'handler' => 'views_handler_argument_string',
+    ),
+    'field' => array(
+        'handler' => 'views_handler_field',
+    ),
+  );
 
-    $data['tripal_ds']['tripal_ds_field_name'] = array(
-	   'title' => t('Field Name'),
-	   'help' => t('This the field name, it is not necessarily unique, like "summary" which might feature across several bundles.'),
-	   'field' => array(
-      		'handler' => 'views_handler_field',
-      		'click sortable' => TRUE, // This is use by the table display plugin.
-    	),
-	    'sort' => array(
-	      'handler' => 'views_handler_sort',
-	    ),
-	    'filter' => array(
-	      'handler' => 'views_handler_filter_string',
-	    ),
-	    'argument' => array(
-	      'handler' => 'views_handler_argument_string',
-	    ),
-    );
+  $data['tripal_ds']['tripal_ds_field_name'] = array(
+   'title' => t('Field Name'),
+   'help' => t('This the field name, it is not necessarily unique, like "summary" which might feature across several bundles.'),
+   'field' => array(
+        'handler' => 'views_handler_field',
+        'click sortable' => TRUE, // This is use by the table display plugin.
+    ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
 
-    $data['tripal_ds']['tripal_ds_field_label'] = array(
-	   'title' => t('Field Label'),
-	   'help' => t('The human readable name of the field, like "Data Sequences".'),
-	   'field' => array(
-      		'handler' => 'views_handler_field',
-      		'click sortable' => TRUE, // This is use by the table display plugin.
-    	),
-	    'sort' => array(
-	      'handler' => 'views_handler_sort',
-	    ),
-	    'filter' => array(
-	      'handler' => 'views_handler_filter_string',
-	    ),
-	    'argument' => array(
-	      'handler' => 'views_handler_argument_string',
-	    ),
-    );
+  $data['tripal_ds']['tripal_ds_field_label'] = array(
+   'title' => t('Field Label'),
+   'help' => t('The human readable name of the field, like "Data Sequences".'),
+   'field' => array(
+        'handler' => 'views_handler_field',
+        'click sortable' => TRUE, // This is use by the table display plugin.
+    ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
 
-    return $data;
+  return $data;
 }
 

tripal_ds/includes/views/tripal_ds.views_default.inc

@@ -1,88 +1,88 @@
 <?php
 
 /**
- * Implements hook_views_default_views().
- */
+* Implements hook_views_default_views().
+*/
 function tripal_ds_views_default_views() {
- 
-	$view = new view();
-	$view->name = 'tripal_content_type_toc';
-	$view->description = '';
-	$view->tag = 'default';
-	$view->base_table = 'tripal_ds';
-	$view->human_name = 'Tripal Content Type Table of Contents';
-	$view->core = 7;
-	$view->api_version = '3.0';
-	$view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
 
-	/* Display: Master */
-	$handler = $view->new_display('default', 'Master', 'default');
-	$handler->display->display_options['title'] = 'Table of Contents';
-	$handler->display->display_options['use_more_always'] = FALSE;
-	$handler->display->display_options['access']['type'] = 'none';
-	$handler->display->display_options['cache']['type'] = 'none';
-	$handler->display->display_options['query']['type'] = 'views_query';
-	$handler->display->display_options['exposed_form']['type'] = 'basic';
-	$handler->display->display_options['pager']['type'] = 'full';
-	$handler->display->display_options['pager']['options']['items_per_page'] = '10';
-	$handler->display->display_options['style_plugin'] = 'default';
-	$handler->display->display_options['row_plugin'] = 'fields';
-	/* Field: Tripal Panes: Field Name */
-	$handler->display->display_options['fields']['tripal_ds_field_name']['id'] = 'tripal_ds_field_name';
-	$handler->display->display_options['fields']['tripal_ds_field_name']['table'] = 'tripal_ds';
-	$handler->display->display_options['fields']['tripal_ds_field_name']['field'] = 'tripal_ds_field_name';
-	$handler->display->display_options['fields']['tripal_ds_field_name']['label'] = '';
-	$handler->display->display_options['fields']['tripal_ds_field_name']['exclude'] = TRUE;
-	$handler->display->display_options['fields']['tripal_ds_field_name']['element_label_colon'] = FALSE;
-	/* Field: Tripal Panes: Bundle ID */
-	$handler->display->display_options['fields']['bundle']['id'] = 'bundle';
-	$handler->display->display_options['fields']['bundle']['table'] = 'tripal_ds';
-	$handler->display->display_options['fields']['bundle']['field'] = 'bundle';
-	$handler->display->display_options['fields']['bundle']['label'] = '';
-	$handler->display->display_options['fields']['bundle']['exclude'] = TRUE;
-	$handler->display->display_options['fields']['bundle']['element_label_colon'] = FALSE;
-	/* Field: Tripal Panes: Field Label */
-	$handler->display->display_options['fields']['tripal_ds_field_label']['id'] = 'tripal_ds_field_label';
-	$handler->display->display_options['fields']['tripal_ds_field_label']['table'] = 'tripal_ds';
-	$handler->display->display_options['fields']['tripal_ds_field_label']['field'] = 'tripal_ds_field_label';
-	$handler->display->display_options['fields']['tripal_ds_field_label']['label'] = '';
-	$handler->display->display_options['fields']['tripal_ds_field_label']['alter']['alter_text'] = TRUE;
-	$handler->display->display_options['fields']['tripal_ds_field_label']['alter']['text'] = '<a href="#" class="tripal_pane-toc-list-item-link" id ="[tripal_ds_field_name]">[tripal_ds_field_label] </a>';
-	$handler->display->display_options['fields']['tripal_ds_field_label']['element_label_colon'] = FALSE;
-	/* Contextual filter: Tripal Panes: Bundle ID */
-	$handler->display->display_options['arguments']['bundle']['id'] = 'bundle';
-	$handler->display->display_options['arguments']['bundle']['table'] = 'tripal_ds';
-	$handler->display->display_options['arguments']['bundle']['field'] = 'bundle';
-	$handler->display->display_options['arguments']['bundle']['default_action'] = 'default';
-	$handler->display->display_options['arguments']['bundle']['default_argument_type'] = 'php';
-	$handler->display->display_options['arguments']['bundle']['default_argument_options']['code'] = '$url = current_path();
-	$url_exploded = explode("/", $url);
-	$tripal_entity_id = (int)$url_exploded[1];
+$view = new view();
+$view->name = 'tripal_content_type_toc';
+$view->description = '';
+$view->tag = 'default';
+$view->base_table = 'tripal_ds';
+$view->human_name = 'Tripal Content Type Table of Contents';
+$view->core = 7;
+$view->api_version = '3.0';
+$view->disabled = FALSE; /* Edit this to true to make a default view disabled initially. */
 
-	    $result = db_select(\'tripal_entity\', \'te\')
-	      ->fields(\'te\', array(\'bundle\'))
-	      ->condition(\'id\', $tripal_entity_id, \'=\')
-	      ->execute()
-	      ->fetchField();
+/* Display: Master */
+$handler = $view->new_display('default', 'Master', 'default');
+$handler->display->display_options['title'] = 'Table of Contents';
+$handler->display->display_options['use_more_always'] = FALSE;
+$handler->display->display_options['access']['type'] = 'none';
+$handler->display->display_options['cache']['type'] = 'none';
+$handler->display->display_options['query']['type'] = 'views_query';
+$handler->display->display_options['exposed_form']['type'] = 'basic';
+$handler->display->display_options['pager']['type'] = 'full';
+$handler->display->display_options['pager']['options']['items_per_page'] = '10';
+$handler->display->display_options['style_plugin'] = 'default';
+$handler->display->display_options['row_plugin'] = 'fields';
+/* Field: Tripal Panes: Field Name */
+$handler->display->display_options['fields']['tripal_ds_field_name']['id'] = 'tripal_ds_field_name';
+$handler->display->display_options['fields']['tripal_ds_field_name']['table'] = 'tripal_ds';
+$handler->display->display_options['fields']['tripal_ds_field_name']['field'] = 'tripal_ds_field_name';
+$handler->display->display_options['fields']['tripal_ds_field_name']['label'] = '';
+$handler->display->display_options['fields']['tripal_ds_field_name']['exclude'] = TRUE;
+$handler->display->display_options['fields']['tripal_ds_field_name']['element_label_colon'] = FALSE;
+/* Field: Tripal Panes: Bundle ID */
+$handler->display->display_options['fields']['bundle']['id'] = 'bundle';
+$handler->display->display_options['fields']['bundle']['table'] = 'tripal_ds';
+$handler->display->display_options['fields']['bundle']['field'] = 'bundle';
+$handler->display->display_options['fields']['bundle']['label'] = '';
+$handler->display->display_options['fields']['bundle']['exclude'] = TRUE;
+$handler->display->display_options['fields']['bundle']['element_label_colon'] = FALSE;
+/* Field: Tripal Panes: Field Label */
+$handler->display->display_options['fields']['tripal_ds_field_label']['id'] = 'tripal_ds_field_label';
+$handler->display->display_options['fields']['tripal_ds_field_label']['table'] = 'tripal_ds';
+$handler->display->display_options['fields']['tripal_ds_field_label']['field'] = 'tripal_ds_field_label';
+$handler->display->display_options['fields']['tripal_ds_field_label']['label'] = '';
+$handler->display->display_options['fields']['tripal_ds_field_label']['alter']['alter_text'] = TRUE;
+$handler->display->display_options['fields']['tripal_ds_field_label']['alter']['text'] = '<a href="#" class="tripal_pane-toc-list-item-link" id ="[tripal_ds_field_name]">[tripal_ds_field_label] </a>';
+$handler->display->display_options['fields']['tripal_ds_field_label']['element_label_colon'] = FALSE;
+/* Contextual filter: Tripal Panes: Bundle ID */
+$handler->display->display_options['arguments']['bundle']['id'] = 'bundle';
+$handler->display->display_options['arguments']['bundle']['table'] = 'tripal_ds';
+$handler->display->display_options['arguments']['bundle']['field'] = 'bundle';
+$handler->display->display_options['arguments']['bundle']['default_action'] = 'default';
+$handler->display->display_options['arguments']['bundle']['default_argument_type'] = 'php';
+$handler->display->display_options['arguments']['bundle']['default_argument_options']['code'] = '$url = current_path();
+$url_exploded = explode("/", $url);
+$tripal_entity_id = (int)$url_exploded[1];
 
-	return $result;';
-	$handler->display->display_options['arguments']['bundle']['summary']['number_of_records'] = '0';
-	$handler->display->display_options['arguments']['bundle']['summary']['format'] = 'default_summary';
-	$handler->display->display_options['arguments']['bundle']['summary_options']['items_per_page'] = '25';
-	$handler->display->display_options['arguments']['bundle']['limit'] = '0';
+    $result = db_select(\'tripal_entity\', \'te\')
+      ->fields(\'te\', array(\'bundle\'))
+      ->condition(\'id\', $tripal_entity_id, \'=\')
+      ->execute()
+      ->fetchField();
 
-	/* Display: Page */
-	$handler = $view->new_display('page', 'Page', 'page');
-	$handler->display->display_options['path'] = 'tripal_ct_toc';
+return $result;';
+$handler->display->display_options['arguments']['bundle']['summary']['number_of_records'] = '0';
+$handler->display->display_options['arguments']['bundle']['summary']['format'] = 'default_summary';
+$handler->display->display_options['arguments']['bundle']['summary_options']['items_per_page'] = '25';
+$handler->display->display_options['arguments']['bundle']['limit'] = '0';
 
-	/* Display: Block */
-	$handler = $view->new_display('block', 'Block', 'block');
-	$handler->display->display_options['defaults']['pager'] = FALSE;
-	$handler->display->display_options['pager']['type'] = 'none';
-	$handler->display->display_options['pager']['options']['offset'] = '0';
-	 
-	$views[$view->name] = $view;
-	 
-	// return views
-	return $views;
+/* Display: Page */
+$handler = $view->new_display('page', 'Page', 'page');
+$handler->display->display_options['path'] = 'tripal_ct_toc';
+
+/* Display: Block */
+$handler = $view->new_display('block', 'Block', 'block');
+$handler->display->display_options['defaults']['pager'] = FALSE;
+$handler->display->display_options['pager']['type'] = 'none';
+$handler->display->display_options['pager']['options']['offset'] = '0';
+
+$views[$view->name] = $view;
+
+// Return views.
+return $views;
 }