Stock: Added default admin view for new UI

tripal_stock/includes/tripal_stock.admin.inc

@@ -4,6 +4,40 @@
  * @todo Add file header description
  */
 
+/**
+ *
+ */
+function tripal_stock_admin_stock_view() {
+  $output = '';
+
+  // set the breadcrumb
+  $breadcrumb = array();
+  $breadcrumb[] = l('Home', '<front>');
+  $breadcrumb[] = l('Administration', 'admin');
+  $breadcrumb[] = l('Tripal', 'admin/tripal');
+  $breadcrumb[] = l('Chado', 'admin/tripal/chado');
+  $breadcrumb[] = l('Stocks', 'admin/tripal/chado/tripal_stock');
+  drupal_set_breadcrumb($breadcrumb);
+
+  // Add the view
+  $view = views_embed_view('tripal_stock_admin_stocks','default');
+  if (isset($view)) {
+    $output .= $view;
+  }
+  else {
+    $output .= '<p>The Stock module uses primarily views to provide an '
+      . 'administrative interface. Currently one or more views needed for this '
+      . 'administrative interface are disabled. <strong>Click each of the following links to '
+      . 'enable the pertinent views</strong>:</p>';
+    $output .= '<ul>';
+      $output .= '<li>'.l('Stocks View', 'admin/tripal/chado/tripal_stock/views/stocks/enable').'</li>';
+    $output .= '</ul>';
+  }
+
+  return $output;
+}
+
+
 /**
  * Purpose: Provide administration options for chado_stocks
  *
@@ -17,9 +51,9 @@ function tripal_stock_admin() {
 
   get_tripal_stock_admin_form_title_set($form);
   get_tripal_stock_admin_form_url_set($form);
-  get_tripal_stock_admin_form_vocabulary_set($form);       
+  get_tripal_stock_admin_form_vocabulary_set($form);
   get_tripal_stock_admin_form_cleanup_set($form);
-  
+
 
   return system_settings_form($form);
 
@@ -41,18 +75,18 @@ function tripal_stock_admin_validate($form, &$form_state) {
 
   variable_set('chado_stock_types_cv', $form_state['values']['stock_types_cv']);
   variable_set('chado_stock_prop_types_cv', $form_state['values']['stock_prop_types_cv']);
-  variable_set('chado_stock_relationship_cv', $form_state['values']['stock_relationship_cv']);  
+  variable_set('chado_stock_relationship_cv', $form_state['values']['stock_relationship_cv']);
   variable_set('chado_stock_url_string', $form_state['values']['chado_stock_url_string']);
-  
+
   switch ($form_state['values']['op']) {
-    case  t('Set Controlled Vacabularies') :      
+    case  t('Set Controlled Vacabularies') :
       break;
-      
+
     case t('Clean up orphaned stocks') :
       tripal_add_job('Cleanup orphaned stocks', 'tripal_stock',
          'tripal_stock_cleanup', $job_args, $user->uid);
       break;
-    
+
     case t('Set Stock URLs') :
       tripal_add_job('Set Stock URLs', 'tripal_stock',
         'tripal_stock_set_urls', $job_args, $user->uid);
@@ -62,7 +96,7 @@ function tripal_stock_admin_validate($form, &$form_state) {
 }
 
 /**
- * 
+ *
  * @param $form
  */
 function get_tripal_stock_admin_form_title_set(&$form) {
@@ -76,9 +110,9 @@ function get_tripal_stock_admin_form_title_set(&$form) {
   $form['title']['desc'] = array(
     '#type'  => 'markup',
     '#value' => t('Each synced stock must have a unique page title, however, stocks
-      may have the same name if they are of different types or from different 
-      organisms.  Therefore, we must be sure that the page titles can uniquely 
-      identify the stock being viewed.  Select an option below that will 
+      may have the same name if they are of different types or from different
+      organisms.  Therefore, we must be sure that the page titles can uniquely
+      identify the stock being viewed.  Select an option below that will
       uniquely identify all stocks on your site.'),
   );
   $options = array(
@@ -89,9 +123,9 @@ function get_tripal_stock_admin_form_title_set(&$form) {
   $form['title']['chado_stock_title'] = array(
     '#title'         => t('Stock Page Titles'),
     '#type'          => 'radios',
-    '#description'   => t('Choose a title type  from the list above that is 
-      guaranteed to be unique for all stocks If in doubt it is safest to choose 
-      the last option as that guarantees uniqueness. Click the 
+    '#description'   => t('Choose a title type  from the list above that is
+      guaranteed to be unique for all stocks If in doubt it is safest to choose
+      the last option as that guarantees uniqueness. Click the
       \'Save Configuration\' button at the bottom to save your selection.'),
     '#required'      => FALSE,
     '#options'       => $options,
@@ -99,7 +133,7 @@ function get_tripal_stock_admin_form_title_set(&$form) {
   );
 }
 /**
- * 
+ *
  * @param  $form
  */
 function get_tripal_stock_admin_form_url_set(&$form) {
@@ -121,7 +155,7 @@ function get_tripal_stock_admin_form_url_set(&$form) {
     '[name]'       => '[name]:' . t('The stock name'),
     'reset'        => t('Reset'),
   );
-  
+
 
   $form['url']['chado_stock_url_string'] = array(
     '#title' => 'URL Syntax',
@@ -129,15 +163,15 @@ function get_tripal_stock_admin_form_url_set(&$form) {
     '#description' => t('You may rearrange elements in this text box to
       customize the URLs.  The available tags include: [id],
       [uniquename]. [name], [species], [genus], [type]. You can separate or
-      include any text between the tags. Click the "Set Stock URLs" button to 
+      include any text between the tags. Click the "Set Stock URLs" button to
       reset the URLs for all stock pages.  Click the "Save Configuration" button to
       simply save this setup. <b>Important</b>: be sure that whatever you choose will always be unique even considering
-      future data that may be added.  If you include the Chado table name, genus, species, type 
+      future data that may be added.  If you include the Chado table name, genus, species, type
       and uniquename you are guaranteed to have a unique URL. For example stock/[genus]/[species]/[type]/[uniquename]'),
     '#size' => 150,
-    '#default_value' => variable_get('chado_stock_url_string', '/stock/[genus]/[species]/[type]/[uniquename]'), 
+    '#default_value' => variable_get('chado_stock_url_string', '/stock/[genus]/[species]/[type]/[uniquename]'),
   );
-  
+
   $form['url']['chado_stock_url'] = array(
     '#title'         => t('URL components'),
     '#type'          => 'checkboxes',
@@ -150,21 +184,21 @@ function get_tripal_stock_admin_form_url_set(&$form) {
         if (this.value == \'reset\') {
           box.val(\'\');
         }
-        else {        
-          box.val(box.val() + "/" + this.value);          
+        else {
+          box.val(box.val() + "/" + this.value);
         }
         this.checked = false;
       ',
     ),
-  );  
-  
+  );
+
   $form['url']['button'] = array(
     '#type' => 'submit',
     '#value' => t('Set Stock URLs'),
   );
 }
 /**
- * 
+ *
  * @param $form
  */
 function get_tripal_stock_admin_form_vocabulary_set(&$form) {

tripal_stock/tripal_stock.module

@@ -41,31 +41,42 @@ function tripal_stock_menu() {
   $items = array();
 
   //Administrative settings menu-----------------
-  $items['admin/tripal/tripal_stock'] = array(
+  $items['admin/tripal/chado/tripal_stock'] = array(
     'title' => 'Stocks',
-    'description' => 'Basic Description of Tripal Stock Module Functionality',
-    'page callback' => 'theme',
-    'page arguments' => array('tripal_stock_help'),
+    'description' => 'A stock is the physical entities of an organism, either living or preserved.',
+    'page callback' => 'tripal_stock_admin_stock_view',
     'access arguments' => array('administer tripal stocks'),
     'type' => MENU_NORMAL_ITEM
   );
 
-  $items['admin/tripal/tripal_stock/configuration'] = array(
-    'title' => 'Configuration',
+  $items['admin/tripal/chado/tripal_stock/configuration'] = array(
+    'title' => 'Settings',
     'description' => 'Settings for Chado Stocks',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_stock_help'),
     'access arguments' => array('administer tripal stocks'),
-    'type' => MENU_NORMAL_ITEM
+    'type' => MENU_LOCAL_TASK,
+    'weight' => 5
   );
-  
-  $items['admin/tripal/tripal_stock/sync'] = array(
-    'title' => ' Sync Stocks',
+
+  $items['admin/tripal/chado/tripal_stock/sync'] = array(
+    'title' => ' Sync',
     'description' => 'Sync stocks from Chado with Drupal',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_stock_sync_form'),
     'access arguments' => array('administer tripal stocks'),
-    'type' => MENU_NORMAL_ITEM,
+    'type' => MENU_LOCAL_TASK,
+    'weight' => 0
+  );
+
+  $items['admin/tripal/chado/tripal_stock/help'] = array(
+    'title' => 'Help',
+    'description' => 'Basic Description of Tripal Stock Module Functionality',
+    'page callback' => 'theme',
+    'page arguments' => array('tripal_stock_help'),
+    'access arguments' => array('administer tripal stocks'),
+    'type' => MENU_LOCAL_TASK,
+    'weight' => 10
   );
 
   // Adding Secondary Properties-----------------
@@ -126,7 +137,7 @@ function tripal_stock_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 10,
   );
-  
+
   // the menu link for addressing any stock (by name, uniquename, synonym)
   $items['stock/%'] = array(
     'page callback' => 'tripal_stock_match_stocks_page',
@@ -203,7 +214,7 @@ function tripal_stock_permissions() {
  * Implement hook_access().
  *
  * This hook allows node modules to limit access to the node types they define.
- * 
+ *
  *  @param $node
  *  The node on which the operation is to be performed, or, if it does not yet exist, the
  *  type of node to be created
@@ -217,7 +228,7 @@ function tripal_stock_permissions() {
  *  @return
  *  If the permission for the specified operation is not set then return FALSE. If the
  *  permission is set then return NULL as this allows other modules to disable
- *  access.  The only exception is when the $op == 'create'.  We will always 
+ *  access.  The only exception is when the $op == 'create'.  We will always
  *  return TRUE if the permission is set.
  *
  * @ingroup tripal_stock
@@ -335,18 +346,18 @@ function tripal_stock_theme() {
       'arguments' => array('node' => NULL),
       'template' => 'tripal_stock_locations',
       'path' => "$theme_path/tripal_stock",
-    ),    
+    ),
     // tripal_organism templates
     'tripal_organism_stocks' => array(
       'arguments' => array('node' => NULL),
       'template' => 'tripal_organism_stocks',
       'path' => "$theme_path/tripal_organism",
-    ),    
+    ),
     // help template
     'tripal_stock_help' => array(
-      'template' => 'tripal_stock_help',  
-      'arguments' =>  array(NULL),  
-      'path' => $theme_path, 
+      'template' => 'tripal_stock_help',
+      'arguments' =>  array(NULL),
+      'path' => $theme_path,
     ),
   );
   return $items;
@@ -395,12 +406,12 @@ function chado_stock_load($node) {
 
   // get the stock details from chado
   $stock_id = chado_get_id_for_node('stock', $node->nid);
-  
+
   // build the variable with all the stock details
   $values = array('stock_id' => $stock_id);
   $stock = tripal_core_generate_chado_var('stock', $values);
-  
-  
+
+
   // by default, the titles are saved using the unique constraint.  We will
   // keep it the same, but remove the duplicate name if the unique name and name
   // are identical
@@ -409,10 +420,10 @@ function chado_stock_load($node) {
     if (strcmp($stock->name, $stock->uniquename)==0) {
       $node->title = $stock->name . " (" . $stock->type_id->name . ") " . $stock->organism_id->genus . " " . $stock->organism_id->species ;
     }
-    // in previous version of Tripal, the stock title was simply the unique name. 
+    // in previous version of Tripal, the stock title was simply the unique name.
     // so, we recreate the title just to be sure all of our stock pages are consistent
     else {
-      $node->title = $stock->name . ", " . $stock->uniquename . " (" . $stock->type_id->name . ") " . $stock->organism_id->genus . " " . $stock->organism_id->species ;  
+      $node->title = $stock->name . ", " . $stock->uniquename . " (" . $stock->type_id->name . ") " . $stock->organism_id->genus . " " . $stock->organism_id->species ;
     }
   }
   // set the title to be the stock name or uniquename as configured
@@ -420,9 +431,9 @@ function chado_stock_load($node) {
     $node->title = $stock->name;
   }
   if($title_type == 'stock_unique_name') {
-    $node->title = $stock->uniquename;  
+    $node->title = $stock->uniquename;
   }
-  
+
   // add this to the node
   $additions = new stdClass();
   $additions->stock = $stock;
@@ -518,10 +529,10 @@ function chado_stock_form($node, $form_state) {
   $type_options = tripal_cv_get_cvterm_options( variable_get('chado_stock_types_cv', 'NULL') );
   $type_options[0] = 'Select a Type';
   if ($node->nid == '') {
-    $type_default = 0; 
+    $type_default = 0;
   }
-  else { 
-    $type_default = $node->stock->type_id->cvterm_id; 
+  else {
+    $type_default = $node->stock->type_id->cvterm_id;
   }
   $form['details']['type_id'] = array(
     '#type' => 'select',
@@ -531,7 +542,7 @@ function chado_stock_form($node, $form_state) {
     '#required'    => TRUE,
   );
 
- 
+
   // get the list of organisms
   $sql = "SELECT * FROM {Organism} ORDER BY genus, species";
   $org_rset = chado_query($sql);
@@ -612,12 +623,12 @@ function chado_stock_validate($node, &$form) {
       SELECT *
       FROM {stock} S
         INNER JOIN {cvterm} CVT ON S.type_id = CVT.cvterm_id
-      WHERE 
-        uniquename = :uname AND organism_id = :organism_id AND 
+      WHERE
+        uniquename = :uname AND organism_id = :organism_id AND
         CVT.name = :cvtname AND NOT stock_id = :stock_id
     ";
-    $result = chado_query($sql, array(':uname' => $node->uniquename, 
-      ':organism_id' => $node->organism_id, ':cvtname' => $node->stock_type, 
+    $result = chado_query($sql, array(':uname' => $node->uniquename,
+      ':organism_id' => $node->organism_id, ':cvtname' => $node->stock_type,
       ':stock_id' => $node->stock_id))->fetchObject();
     if ($result) {
       form_set_error('uniquename', t("Stock update cannot proceed. The stock name '$node->uniquename' is not unique for this organism. Please provide a unique name for this stock."));
@@ -632,13 +643,13 @@ function chado_stock_validate($node, &$form) {
       FROM {Stock} S
         INNER JOIN {cvterm} CVT ON S.type_id = CVT.cvterm_id
       WHERE uniquename = :uname'AND organism_id = :organism_id AND CVT.name = :cvtname";
-    $result = chado_query($sql, array(':uname' => $node->uniquename, 
+    $result = chado_query($sql, array(':uname' => $node->uniquename,
       ':organism_id' => $node->organism_id, ':cvtname' => $node->stock_type))->fetchObject();
     if ($result) {
       form_set_error('uniquename', t("Stock insert cannot proceed. The stock name '$node->uniquename' already exists for this organism. Please provide a unique name for this stock."));
     }
   }
-  
+
 
   // Check Type of Stock is valid cvterm_id in chado ( $form['values']['details']['type_id'] )
   if ( $node->type_id == 0) {
@@ -695,7 +706,7 @@ function chado_stock_validate($node, &$form) {
  * @ingroup tripal_stock
  */
 function chado_stock_insert($node) {
-  
+
   // If the chado stock exists (e.g. this is only a syncing operation)
   // then don't create but simply link to node
   if ($node->chado_stock_exists) {
@@ -703,7 +714,7 @@ function chado_stock_insert($node) {
       $sql = "INSERT INTO {chado_stock} (nid, vid, stock_id) VALUES (:nid, :vid, :stock_id)";
       db_query($sql, array(':nid' => $node->nid, ':vid' => $node->vid, ':stock_id' => $node->stock_id));
     }
-    
+
     return $node;
   }
 
@@ -729,7 +740,7 @@ function chado_stock_insert($node) {
           );
         }
       }
-      else { 
+      else {
         $dbxref_status = 1;
       }
     }
@@ -762,11 +773,11 @@ function chado_stock_insert($node) {
     );
     $stock = tripal_core_chado_insert('stock', $values);
   }
-  
+
   // if the stock creation was succesful then add the URL and the entry in the
   // chado_stock table
   if (is_array($stock)) {
-    
+
     // convert the stock into an object
     $stock = (object) $stock;
 
@@ -778,7 +789,7 @@ function chado_stock_insert($node) {
     if ($node->simulate_multipart) {
       $next_stage_path = preg_replace('/%node/', $node->nid, $node->next_step_path);
       $_REQUEST['destination'] = $next_stage_path;
-    }    
+    }
   }
   else {
     drupal_set_message(t('Error during stock creation.'), 'error');
@@ -888,7 +899,7 @@ function chado_stock_update($node) {
     );
   }
   $status = tripal_core_chado_update('stock', array('stock_id' => $node->stock_id), $update_values);
-    
+
 
   if (!$status) {
     drupal_set_message(t('Unable to update stock'), 'error');
@@ -902,7 +913,7 @@ function chado_stock_update($node) {
   else {
     // set the URL for this stock page
     $values = array('stock_id' => $node->stock_id);
-    $stock = tripal_core_chado_select('stock', array('*'), $values);    
+    $stock = tripal_core_chado_select('stock', array('*'), $values);
   }
 }
 
@@ -946,26 +957,26 @@ function tripal_stock_block_info() {
 
   $blocks['synonyms']['info'] = t('Tripal Stock Synonyms');
   $blocks['synonyms']['cache'] = BLOCK_NO_CACHE;
-  
+
   $blocks['collections']['info'] = t('Tripal Stock Collections');
   $blocks['collections']['cache'] = BLOCK_NO_CACHE;
-  
+
   $blocks['phenotypes']['info'] = t('Tripal Stock Phenotypes');
   $blocks['phenotypes']['cache'] = BLOCK_NO_CACHE;
-  
+
   $blocks['genotypes']['info'] = t('Tripal Stock Genotypes');
   $blocks['genotypes']['cache'] = BLOCK_NO_CACHE;
-  
+
   $blocks['locations']['info'] = t('Tripal Stock Locations');
   $blocks['locations']['cache'] = BLOCK_NO_CACHE;
-  
+
   $blocks['orgstocks']['info'] = t('Tripal Organism Stocks');
   $blocks['orgstocks']['cache'] = BLOCK_NO_CACHE;
 
   return $blocks;
 }
 /**
- * 
+ *
  * @ingroup tripal_stock
  */
 function tripal_stock_block_view($delta = '') {
@@ -973,59 +984,59 @@ function tripal_stock_block_view($delta = '') {
   if (user_access('access chado_stock content') and arg(0) == 'node' and is_numeric(arg(1))) {
     $nid = arg(1);
     $node = node_load($nid);
-  
+
     $block = array();
     switch ($delta) {
       case 'base':
         $block['subject'] = t('Stock Details');
         $block['content'] = theme('tripal_stock_base', $node);
         break;
-  
+
       case 'properties':
         $block['subject'] = t('Properties');
         $block['content'] = theme('tripal_stock_properties', $node);
         break;
-  
+
       case 'references':
         $block['subject'] = t('References');
         $block['content'] = theme('tripal_stock_references', $node);
         break;
-  
+
       case 'relationships':
         $block['subject'] = t('Relationships');
         $block['content'] = theme('tripal_stock_relationships', $node);
         break;
-  
+
       case 'synonyms':
         $block['subject'] = t('Synonyms');
         $block['content'] = theme('tripal_stock_synonyms', $node);
         break;
-        
+
       case 'collections':
         $block['subject'] = t('Stock Collections');
         $block['content'] = theme('tripal_stock_collections', $node);
         break;
-        
+
       case 'phenotypes':
         $block['subject'] = t('Stock Phenotypes');
         $block['content'] = theme('tripal_stock_phenotypes', $node);
         break;
-        
+
       case 'genotypes':
         $block['subject'] = t('Stock Genotypes');
         $block['content'] = theme('tripal_stock_genotypes', $node);
         break;
-        
+
       case 'locations':
         $block['subject'] = t('Stock Locations');
         $block['content'] = theme('tripal_stock_locations', $node);
         break;
-        
+
       case 'orgstocks':
         $block['subject'] = t('Organism Stocks');
         $block['content'] = theme('tripal_organism_stocks', $node);
         break;
-  
+
     }
     return $block;
   }
@@ -1039,14 +1050,14 @@ function tripal_stock_block_view($delta = '') {
 function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
   // we want to provide a new variable that contains the matched stocks.
   $stock = $variables['node']->stock;
-   
+
   // normally we would use tripal_core_expand_chado_vars to expand our
   // organism object and add in the relationships, however whan a large
   // number of relationships are present this significantly slows the
   // query, therefore we will manually perform the query
   $sql = "
-    SELECT 
-      S.name, S.uniquename, S.stock_id, CS.nid, 
+    SELECT
+      S.name, S.uniquename, S.stock_id, CS.nid,
       CVT.name as rel_type, CVTs.name as obj_type,
       SR.value
     FROM {stock_relationship} SR
@@ -1058,8 +1069,8 @@ function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
   ";
   $as_subject = chado_query($sql, array(':stock_id' => $stock->stock_id));
   $sql = "
-    SELECT 
-      S.name, S.uniquename,  S.stock_id, CS.nid, 
+    SELECT
+      S.name, S.uniquename,  S.stock_id, CS.nid,
       CVT.name as rel_type, CVTs.name as sub_type,
       SR.value
     FROM {stock_relationship} SR
@@ -1070,45 +1081,45 @@ function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
     WHERE SR.object_id = :stock_id
   ";
   $as_object = chado_query($sql, array(':stock_id' => $stock->stock_id));
-  
+
   // combine both object and subject relationshisp into a single array
   $relationships = array();
   $relationships['object'] = array();
   $relationships['subject'] = array();
-  
+
   // iterate through the object relationships
   while ($relationship = $as_object->fetchObject()) {
-     
+
      // get the relationship and child types
      $rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));
      $sub_type = t(preg_replace('/_/', " ", $relationship->sub_type));
-     
+
      if (!array_key_exists($rel_type, $relationships['object'])) {
-       $relationships['object'][$rel_type] = array();   
+       $relationships['object'][$rel_type] = array();
      }
      if (!array_key_exists($sub_type, $relationships['object'][$rel_type])) {
-       $relationships['object'][$rel_type][$sub_type] = array();   
+       $relationships['object'][$rel_type][$sub_type] = array();
      }
-     $relationships['object'][$rel_type][$sub_type][] = $relationship;     
+     $relationships['object'][$rel_type][$sub_type][] = $relationship;
   }
-  
+
   // now add in the subject relationships
   while ($relationship = $as_subject->fetchObject()) {
-     
+
      // get the relationship and child types
      $rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));
      $obj_type = t(preg_replace('/_/', " ", $relationship->obj_type));
-     
+
      if (!array_key_exists($rel_type, $relationships['subject'])) {
-       $relationships['subject'][$rel_type] = array();   
+       $relationships['subject'][$rel_type] = array();
      }
      if (!array_key_exists($obj_type, $relationships['subject'][$rel_type])) {
-       $relationships['subject'][$rel_type][$obj_type] = array();   
+       $relationships['subject'][$rel_type][$obj_type] = array();
      }
-     $relationships['subject'][$rel_type][$obj_type][] = $relationship;     
+     $relationships['subject'][$rel_type][$obj_type][] = $relationship;
   }
-  
-  
+
+
   $stock->all_relationships = $relationships;
 
 }
@@ -1138,10 +1149,10 @@ function tripal_stock_node_insert($node) {
         $chado_stock = db_query($sql, array(':nid' => $node->nid))->fetchObject();
         $node->stock_id = $chado_stock->stock_id;
       }
-      
+
       // remove any previous alias
       db_query("DELETE FROM {url_alias} WHERE src = :src", array(':src' => "node/$node->nid"));
-      
+
       // set the URL for this stock page
       $url_alias = tripal_stock_get_stock_url($node);
       path_set_alias("node/$node->nid", $url_alias);
@@ -1155,10 +1166,10 @@ function tripal_stock_node_update($node) {
 
   switch ($node->type) {
     case 'chado_stock':
-      
+
       // remove any previous alias
       db_query("DELETE FROM {url_alias} WHERE src = :src", array(':src' => "node/$node->nid"));
-      
+
       // set the URL for this stock page
       $url_alias = tripal_stock_get_stock_url($node);
       path_set_alias("node/$node->nid", $url_alias);
@@ -1190,19 +1201,19 @@ function tripal_stock_node_view($node, $view_mode, $langcode) {
  * stocks is shown.
  */
 function tripal_stock_match_stocks_page($id) {
-  
+
   // if the URL alias configuration is set such that the URL
   // always begins with 'stock' then we want to use the ID as it is and
   // forward it on. Otherwise, try to find the matching stock.
-  $url_alias = variable_get('chado_stock_url_string', '/stock/[genus]/[species]/[type]/[uniquename]'); 
+  $url_alias = variable_get('chado_stock_url_string', '/stock/[genus]/[species]/[type]/[uniquename]');
   if (!$url_alias) {
     $url_alias = '/stock/[genus]/[species]/[type]/[uniquename]';
-  } 
-  $url_alias = preg_replace('/^\//', '', $url_alias); // remove any preceeding forward slash  
+  }
+  $url_alias = preg_replace('/^\//', '', $url_alias); // remove any preceeding forward slash
   if (preg_match('/^stock\//', $url_alias)) {
     drupal_goto($id);
   }
-  
+
 
   $sql = "
     SELECT

tripal_stock/tripal_stock.views_default.inc

@@ -7,400 +7,239 @@
 function tripal_stock_views_default_views() {
   $views = array();
 
-  if (!module_exists('tripal_views')) {
-    return $views;
-  }
+  $view = tripal_stock_defaultview_admin_stocks();
+  $views[$view->name] = $view;
+
+  return $views;
+}
 
-  // Main default view
-  $view = new view;
-  $view->name = 'stock_listing';
-  $view->description = 'This view lists all stocks by default.';
-  $view->tag = 'chado default';
+function tripal_stock_defaultview_admin_stocks() {
+
+  $view = new view();
+  $view->name = 'tripal_stock_admin_stocks';
+  $view->description = 'DO NOT DISABLE';
+  $view->tag = 'tripal admin';
   $view->base_table = 'stock';
+  $view->human_name = 'Stock Admin';
   $view->core = 0;
-  $view->api_version = '2';
+  $view->api_version = '3.0';
   $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
+
+  /* Display: Defaults */
   $handler = $view->new_display('default', 'Defaults', 'default');
-  $handler->override_option('fields', array(
+  $handler->display->display_options['title'] = 'Stocks';
+  $handler->display->display_options['use_more_always'] = FALSE;
+  $handler->display->display_options['access']['type'] = 'perm';
+  $handler->display->display_options['access']['perm'] = 'access chado_stock content';
+  $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'] = '25';
+  $handler->display->display_options['pager']['options']['offset'] = '0';
+  $handler->display->display_options['pager']['options']['id'] = '0';
+  $handler->display->display_options['pager']['options']['quantity'] = '9';
+  $handler->display->display_options['style_plugin'] = 'table';
+  $handler->display->display_options['style_options']['grouping'] = '';
+  $handler->display->display_options['style_options']['columns'] = array(
+    'uniquename' => 'uniquename',
+    'name_2' => 'name_2',
+    'name' => 'name',
+    'common_name' => 'common_name',
+    'all_dbxref' => 'all_dbxref',
+    'all_properties' => 'all_properties',
+    'all_relationships' => 'all_relationships',
+  );
+  $handler->display->display_options['style_options']['default'] = '-1';
+  $handler->display->display_options['style_options']['info'] = array(
     'uniquename' => array(
-      'label' => 'Unique Name',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'link_to_node' => 1,
-      'exclude' => 0,
-      'id' => 'uniquename',
-      'table' => 'stock',
-      'field' => 'uniquename',
-      'relationship' => 'none',
+      'sortable' => 1,
+      'separator' => '',
     ),
     'name_2' => array(
-      'label' => 'Name',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'link_to_node' => 1,
-      'exclude' => 0,
-      'id' => 'name_2',
-      'table' => 'stock',
-      'field' => 'name',
-      'relationship' => 'none',
+      'sortable' => 1,
+      'separator' => '',
     ),
     'name' => array(
-      'label' => 'Type',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'exclude' => 0,
-      'id' => 'name',
-      'table' => 'cvterm',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-    'common_name' => array(
-      'label' => 'Organism',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'link_to_node' => 1,
-      'exclude' => 0,
-      'id' => 'common_name',
-      'table' => 'organism',
-      'field' => 'common_name',
-      'relationship' => 'none',
-    ),
-  ));
-  $handler->override_option('sorts', array(
-    'common_name' => array(
-      'order' => 'ASC',
-      'id' => 'common_name',
-      'table' => 'organism',
-      'field' => 'common_name',
-      'relationship' => 'none',
+      'sortable' => 1,
+      'separator' => '',
     ),
-    'uniquename' => array(
-      'order' => 'ASC',
-      'id' => 'uniquename',
-      'table' => 'stock',
-      'field' => 'uniquename',
-      'relationship' => 'none',
-    ),
-  ));
-  $handler->override_option('filters', array(
     'common_name' => array(
-      'operator' => '=',
-      'value' => array(),
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'common_name_op',
-        'identifier' => 'organism_common_name',
-        'label' => 'Organism',
-        'remember' => 0,
-      ),
-      'case' => 1,
-      'id' => 'common_name',
-      'table' => 'organism',
-      'field' => 'common_name',
-      'relationship' => 'none',
-      'values_form_type' => 'select',
-      'multiple' => 1,
-      'optional' => 0,
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 1,
-      ),
-    ),
-    'search_results' => array(
-      'operator' => '=',
-      'value' => '',
-      'group' => '0',
-      'exposed' => FALSE,
-      'expose' => array(
-        'operator' => FALSE,
-        'label' => '',
-      ),
-      'id' => 'search_results',
-      'table' => 'views',
-      'field' => 'search_results',
-      'relationship' => 'none',
-      'apply_button' => 'Show',
-      'no_results_text' => 'Click "Show" to see a list of all stocks matching the entered criteria. If you leave a any of the criteria blank then the stocks will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all stocks will be listed.',
+      'sortable' => 1,
+      'separator' => '',
     ),
-    'type_id' => array(
-      'operator' => '=',
-      'value' => '',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'type_id_op',
-        'identifier' => 'type_id',
-        'label' => 'Type',
-        'remember' => 0,
-      ),
-      'case' => 1,
-      'id' => 'type_id',
-      'table' => 'stock',
-      'field' => 'type_id',
-      'relationship' => 'none',
-      'values_form_type' => 'select',
-      'multiple' => 1,
-      'optional' => 0,
-      'show_all' => 0,
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 1,
-      ),
-    ),
-    'name' => array(
-      'operator' => '~',
-      'value' => '',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'name_op',
-        'identifier' => 'name',
-        'label' => 'Name Contains',
-        'remember' => 0,
-      ),
-      'case' => 0,
-      'id' => 'name',
-      'table' => 'stock',
-      'field' => 'name',
-      'relationship' => 'none',
-      'agg' => array(
-        'records_with' => 1,
-        'aggregates_with' => 1,
-      ),
+    'all_dbxref' => array(
+      'separator' => '',
     ),
-  ));
-  $handler->override_option('access', array(
-    'type' => 'perm',
-    'perm' => 'access chado_stock content',
-  ));
-  $handler->override_option('cache', array(
-    'type' => 'none',
-  ));
-  $handler->override_option('title', 'Stocks');
-  $handler->override_option('header', 'Click "Show" to see a list of all stocks matching the entered criteria. If you leave a any of the criteria blank then the stocks will be not be filtered based on that field. Furthermore, if you leave all criteria blank then all stocks will be listed.');
-  $handler->override_option('header_format', '2');
-  $handler->override_option('header_empty', 0);
-  $handler->override_option('empty', 'No stocks match the supplied criteria.');
-  $handler->override_option('empty_format', '1');
-  $handler->override_option('items_per_page', 50);
-  $handler->override_option('use_pager', '1');
-  $handler->override_option('style_plugin', 'table');
-  $handler->override_option('style_options', array(
-    'grouping' => '',
-    'override' => 1,
-    'sticky' => 0,
-    'order' => 'asc',
-    'columns' => array(
-      'uniquename' => 'uniquename',
-      'name_2' => 'name_2',
-      'name' => 'name',
-      'common_name' => 'common_name',
-      'all_dbxref' => 'all_dbxref',
-      'all_properties' => 'all_properties',
-      'all_relationships' => 'all_relationships',
+    'all_properties' => array(
+      'separator' => '',
     ),
-    'info' => array(
-      'uniquename' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'name_2' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'name' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'common_name' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'all_dbxref' => array(
-        'separator' => '',
-      ),
-      'all_properties' => array(
-        'separator' => '',
-      ),
-      'all_relationships' => array(
-        'separator' => '',
-      ),
+    'all_relationships' => array(
+      'separator' => '',
     ),
-    'default' => '-1',
-  ));
-  $default_handler = $handler;
+  );
+  /* Header: Global: Action Links */
+  $handler->display->display_options['header']['action_links_area']['id'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['table'] = 'views';
+  $handler->display->display_options['header']['action_links_area']['field'] = 'action_links_area';
+  $handler->display->display_options['header']['action_links_area']['label'] = 'Action Links';
+  $handler->display->display_options['header']['action_links_area']['empty'] = TRUE;
+  $handler->display->display_options['header']['action_links_area']['link-1'] = array(
+    'label-1' => 'Add Stock',
+    'path-1' => 'node/add/tripal-stock',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-2'] = array(
+    'label-2' => '',
+    'path-2' => '',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-3'] = array(
+    'label-3' => '',
+    'path-3' => '',
+  );
+  $handler->display->display_options['header']['action_links_area']['link-4'] = array(
+    'label-4' => '',
+    'path-4' => '',
+  );
+  /* No results behavior: Global: Text area */
+  $handler->display->display_options['empty']['text']['id'] = 'area';
+  $handler->display->display_options['empty']['text']['table'] = 'views';
+  $handler->display->display_options['empty']['text']['field'] = 'area';
+  $handler->display->display_options['empty']['text']['content'] = 'No stocks match the supplied criteria.';
+  $handler->display->display_options['empty']['text']['format'] = '1';
+  /* Relationship: Stock: Stock => Node */
+  $handler->display->display_options['relationships']['stock_id']['id'] = 'stock_id';
+  $handler->display->display_options['relationships']['stock_id']['table'] = 'chado_stock';
+  $handler->display->display_options['relationships']['stock_id']['field'] = 'stock_id';
+  /* Field: Content: Nid */
+  $handler->display->display_options['fields']['nid']['id'] = 'nid';
+  $handler->display->display_options['fields']['nid']['table'] = 'node';
+  $handler->display->display_options['fields']['nid']['field'] = 'nid';
+  $handler->display->display_options['fields']['nid']['exclude'] = TRUE;
+  /* Field: Chado Stock: Uniquename */
+  $handler->display->display_options['fields']['uniquename']['id'] = 'uniquename';
+  $handler->display->display_options['fields']['uniquename']['table'] = 'stock';
+  $handler->display->display_options['fields']['uniquename']['field'] = 'uniquename';
+  $handler->display->display_options['fields']['uniquename']['label'] = 'Unique Name';
+  /* Field: Chado Stock: Name */
+  $handler->display->display_options['fields']['name_2']['id'] = 'name_2';
+  $handler->display->display_options['fields']['name_2']['table'] = 'stock';
+  $handler->display->display_options['fields']['name_2']['field'] = 'name';
+  /* Field: Chado Cvterm: Name */
+  $handler->display->display_options['fields']['name']['id'] = 'name';
+  $handler->display->display_options['fields']['name']['table'] = 'cvterm';
+  $handler->display->display_options['fields']['name']['field'] = 'name';
+  $handler->display->display_options['fields']['name']['label'] = 'Type';
+  /* Field: Chado Organism: Common Name */
+  $handler->display->display_options['fields']['common_name']['id'] = 'common_name';
+  $handler->display->display_options['fields']['common_name']['table'] = 'organism';
+  $handler->display->display_options['fields']['common_name']['field'] = 'common_name';
+  $handler->display->display_options['fields']['common_name']['label'] = 'Organism';
+  /* Field: Content: Delete link */
+  $handler->display->display_options['fields']['delete_node']['id'] = 'delete_node';
+  $handler->display->display_options['fields']['delete_node']['table'] = 'views_entity_node';
+  $handler->display->display_options['fields']['delete_node']['field'] = 'delete_node';
+  $handler->display->display_options['fields']['delete_node']['relationship'] = 'stock_id';
+  $handler->display->display_options['fields']['delete_node']['exclude'] = TRUE;
+  /* Field: Content: Edit link */
+  $handler->display->display_options['fields']['edit_node']['id'] = 'edit_node';
+  $handler->display->display_options['fields']['edit_node']['table'] = 'views_entity_node';
+  $handler->display->display_options['fields']['edit_node']['field'] = 'edit_node';
+  $handler->display->display_options['fields']['edit_node']['relationship'] = 'stock_id';
+  $handler->display->display_options['fields']['edit_node']['exclude'] = TRUE;
+  /* Field: Global: Custom text */
+  $handler->display->display_options['fields']['nothing']['id'] = 'nothing';
+  $handler->display->display_options['fields']['nothing']['table'] = 'views';
+  $handler->display->display_options['fields']['nothing']['field'] = 'nothing';
+  $handler->display->display_options['fields']['nothing']['label'] = '';
+  $handler->display->display_options['fields']['nothing']['alter']['text'] = '[edit_node]   [delete_node]';
+  $handler->display->display_options['fields']['nothing']['element_label_colon'] = FALSE;
+  /* Sort criterion: Chado Organism: Common Name */
+  $handler->display->display_options['sorts']['common_name']['id'] = 'common_name';
+  $handler->display->display_options['sorts']['common_name']['table'] = 'organism';
+  $handler->display->display_options['sorts']['common_name']['field'] = 'common_name';
+  /* Sort criterion: Chado Stock: Uniquename */
+  $handler->display->display_options['sorts']['uniquename']['id'] = 'uniquename';
+  $handler->display->display_options['sorts']['uniquename']['table'] = 'stock';
+  $handler->display->display_options['sorts']['uniquename']['field'] = 'uniquename';
+  /* Filter criterion: Chado Organism: Common Name */
+  $handler->display->display_options['filters']['common_name']['id'] = 'common_name';
+  $handler->display->display_options['filters']['common_name']['table'] = 'organism';
+  $handler->display->display_options['filters']['common_name']['field'] = 'common_name';
+  $handler->display->display_options['filters']['common_name']['value'] = 'All';
+  $handler->display->display_options['filters']['common_name']['group'] = '0';
+  $handler->display->display_options['filters']['common_name']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['common_name']['expose']['operator_id'] = 'common_name_op';
+  $handler->display->display_options['filters']['common_name']['expose']['label'] = 'Organism';
+  $handler->display->display_options['filters']['common_name']['expose']['operator'] = 'common_name_op';
+  $handler->display->display_options['filters']['common_name']['expose']['identifier'] = 'organism_common_name';
+  $handler->display->display_options['filters']['common_name']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+  /* Filter criterion: Chado Stock: Type Id */
+  $handler->display->display_options['filters']['type_id']['id'] = 'type_id';
+  $handler->display->display_options['filters']['type_id']['table'] = 'stock';
+  $handler->display->display_options['filters']['type_id']['field'] = 'type_id';
+  $handler->display->display_options['filters']['type_id']['value'] = 'All';
+  $handler->display->display_options['filters']['type_id']['group'] = '0';
+  $handler->display->display_options['filters']['type_id']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['type_id']['expose']['operator_id'] = 'type_id_op';
+  $handler->display->display_options['filters']['type_id']['expose']['label'] = 'Type';
+  $handler->display->display_options['filters']['type_id']['expose']['operator'] = 'type_id_op';
+  $handler->display->display_options['filters']['type_id']['expose']['identifier'] = 'type_id';
+  $handler->display->display_options['filters']['type_id']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+  /* Filter criterion: Chado Stock: Name */
+  $handler->display->display_options['filters']['name']['id'] = 'name';
+  $handler->display->display_options['filters']['name']['table'] = 'stock';
+  $handler->display->display_options['filters']['name']['field'] = 'name';
+  $handler->display->display_options['filters']['name']['operator'] = 'contains';
+  $handler->display->display_options['filters']['name']['group'] = '0';
+  $handler->display->display_options['filters']['name']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['name']['expose']['operator_id'] = 'name_op';
+  $handler->display->display_options['filters']['name']['expose']['label'] = 'Name Contains';
+  $handler->display->display_options['filters']['name']['expose']['operator'] = 'name_op';
+  $handler->display->display_options['filters']['name']['expose']['identifier'] = 'name';
+  $handler->display->display_options['filters']['name']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+
+  /** MANUALLY ADD since filter handler no exporting correctly */
+  $handler->display->display_options['filters']['common_name']['expose']['values_form_type'] = 'select';
+  $handler->display->display_options['filters']['common_name']['expose']['select_multiple'] = FALSE;
+  $handler->display->display_options['filters']['common_name']['expose']['select_optional'] = TRUE;
+  $handler->display->display_options['filters']['common_name']['expose']['max_length'] = 40;
+  $handler->display->display_options['filters']['type_id']['expose']['values_form_type'] = 'select';
+  $handler->display->display_options['filters']['type_id']['expose']['select_multiple'] = FALSE;
+  $handler->display->display_options['filters']['type_id']['expose']['select_optional'] = TRUE;
+  $handler->display->display_options['filters']['type_id']['expose']['max_length'] = 40;
+
+  /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->override_option('path', 'chado/stocks');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Stocks',
-    'description' => 'A stock is the physical entities, either living or preserved, held by collections and can be globally identified by the combination of organism, uniquename and stock type.',
-    'weight' => '10',
-    'name' => 'navigation',
-  ));
-  $handler->override_option('tab_options', array(
-    'type' => 'none',
-    'title' => '',
-    'description' => '',
-    'weight' => 0,
-    'name' => 'navigation',
-  ));
-  // Add code specific to a local chado installation
-  // NOTE: Edit $handler above to $default_handler for the default display
-  if (tripal_core_chado_schema_exists()) {
-    // Add nid field
-    $fields = $view->get_items('field', 'default');
-    $new_fields = array(
-      'nid' => array(
-        'label' => 'Nid',
-        'alter' => array(
-          'alter_text' => 0,
-          'text' => '',
-          'make_link' => 0,
-          'path' => '',
-          'absolute' => 0,
-          'link_class' => '',
-          'alt' => '',
-          'rel' => '',
-          'prefix' => '',
-          'suffix' => '',
-          'target' => '',
-          'help' => '',
-          'trim' => 0,
-          'max_length' => '',
-          'word_boundary' => 1,
-          'ellipsis' => 1,
-          'html' => 0,
-          'strip_tags' => 0,
-        ),
-        'empty' => '',
-        'hide_empty' => 0,
-        'empty_zero' => 0,
-        'hide_alter_empty' => 1,
-        'link_to_node' => 0,
-        'exclude' => 1,
-        'id' => 'nid',
-        'table' => 'node',
-        'field' => 'nid',
-        'relationship' => 'none',
-      )
-    );
-    $fields = $new_fields + $fields;
-    // Change analysis.name to have a link to the node
-    $fields['name_2']['alter']['link_to_node'] = 1;
-    $default_handler->override_option('fields', $fields);
-    // Adds stock => Node relationship
-    $default_handler->override_option('relationships', array(
-      'nid' => array(
-        'label' => 'Stock to Node',
-        'required' => 0,
-        'id' => 'nid',
-        'table' => 'chado_stock',
-        'field' => 'nid',
-        'relationship' => 'none',
-      ),
-    ));
-    // Only show records with published nodes
-    /**
-    $filters = $view->get_items('filter', 'default');
-    $filters['status'] = array(
-      'operator' => '=',
-      'value' => '1',
-      'group' => '0',
-      'exposed' => FALSE,
-      'expose' => array(
-        'operator' => FALSE,
-        'label' => '',
-      ),
-      'id' => 'status',
-      'table' => 'node',
-      'field' => 'status',
-      'relationship' => 'none',
-    );
-    $default_handler->override_option('filters', $filters);
-    */
-  }
-  $views[$view->name] = $view;
+  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_stock/stocks';
+  $handler->display->display_options['menu']['type'] = 'default tab';
+  $handler->display->display_options['menu']['title'] = 'Stocks';
+  $handler->display->display_options['menu']['description'] = 'A stock is the physical entities, either living or preserved';
+  $handler->display->display_options['menu']['weight'] = '-10';
+  $handler->display->display_options['menu']['context'] = 0;
+  $handler->display->display_options['menu']['context_only_inline'] = 0;
+  $handler->display->display_options['tab_options']['weight'] = '0';
 
-  return $views;
+  /** MANUALLY ADD since filter handler no exporting correctly
+  $handler->display->display_options['filters']['common_name']['expose']['values_form_type'] = 'select';
+  $handler->display->display_options['filters']['common_name']['expose']['select_multiple'] = FALSE;
+  $handler->display->display_options['filters']['common_name']['expose']['select_optional'] = TRUE;
+  $handler->display->display_options['filters']['common_name']['expose']['max_length'] = 40;
+  $handler->display->display_options['filters']['type_id']['expose']['values_form_type'] = 'select';
+  $handler->display->display_options['filters']['type_id']['expose']['select_multiple'] = FALSE;
+  $handler->display->display_options['filters']['type_id']['expose']['select_optional'] = TRUE;
+  $handler->display->display_options['filters']['type_id']['expose']['max_length'] = 40;
+  */
+  return $view;
 }