Organism: Added default admin view and switched to new UI

tripal_organism/includes/tripal_organism.admin.inc

@@ -1,5 +1,38 @@
 <?php
 
+/**
+ *
+ */
+function tripal_organism_admin_organism_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');
+  $breadcrumb[] = l('Organisms', 'admin/tripal/chado/tripal_organism');
+  drupal_set_breadcrumb($breadcrumb);
+
+  // Add the view
+  $view = views_embed_view('tripal_organism_admin_organisms','default');
+  if (isset($view)) {
+    $output .= $view;
+  }
+  else {
+    $output .= '<p>The Organism 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('Organisms View', 'admin/tripal/chado/tripal_organism/views/organisms/enable').'</li>';
+    $output .= '</ul>';
+  }
+
+  return $output;
+}
+
 /**
  * Administrative settings for chado_orgnism
  *
@@ -10,7 +43,7 @@ function tripal_organism_admin() {
   $form = array();
 
   get_tripal_organism_admin_form_reindex_set($form);
-  get_tripal_organism_admin_form_taxonomy_set($form);  
+  get_tripal_organism_admin_form_taxonomy_set($form);
 
   return system_settings_form($form);
 }
@@ -41,7 +74,7 @@ function get_tripal_organism_admin_form_taxonomy_set(&$form) {
     '#value' => t(
       "Drupal allows for assignment of \"taxonomy\" or catagorical terms to " .
       "nodes. These terms allow for advanced filtering during searching. This option allows " .
-      "for setting taxonomy only for features that belong to the selected organisms below.  All " . 
+      "for setting taxonomy only for features that belong to the selected organisms below.  All " .
       "other features will be unaffected.  To set taxonomy for all features in the site see the Feature Administration page."),
     '#weight' => 1,
   );
@@ -161,9 +194,9 @@ function tripal_organism_reindex_features($organism_id = NULL, $job_id = NULL) {
   }
 
   $sql = "
-    SELECT * 
-    FROM {feature} 
-    WHERE organism_id = :organism_id 
+    SELECT *
+    FROM {feature}
+    WHERE organism_id = :organism_id
     ORDER BY feature_id";
   $results = chado_query($sql, array(':organism_id' => $organism_id));
 
@@ -196,9 +229,9 @@ function tripal_organism_taxonify_features($organism_id = NULL, $job_id = NULL)
   }
 
   $sql = "
-    SELECT * 
-    FROM {feature} 
-    WHERE organism_id = :organism_id 
+    SELECT *
+    FROM {feature}
+    WHERE organism_id = :organism_id
     ORDER BY feature_id
   ";
   $results = chado_query($sql, array(':organism_id' => $organism_id));

tripal_organism/tripal_organism.module

@@ -101,6 +101,7 @@ function tripal_organism_menu() {
   $items['admin/tripal/chado/tripal_organism'] = array(
    'title' => 'Organisms',
    'description' => 'Basic Description of Tripal Organism Module Functionality',
+   'page callback' => 'tripal_organism_admin_organism_view',
    'access arguments' => array('adminster tripal organism'),
    'type' => MENU_NORMAL_ITEM,
   );
@@ -111,25 +112,33 @@ function tripal_organism_menu() {
    'page callback' => 'theme',
    'page arguments' => array('tripal_organism_help'),
    'access arguments' => array('adminster tripal organism'),
-   'type' => MENU_NORMAL_ITEM,
+   'type' => MENU_LOCAL_TASK,
   );
 
   $items['admin/tripal/chado/tripal_organism/configuration'] = array(
-   'title' => 'Configuration',
+   'title' => 'Settings',
    'description' => 'Manage integration of Chado organisms including associated features',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_organism_admin'),
    'access arguments' => array('adminster tripal organism'),
-   'type' => MENU_NORMAL_ITEM,
+   'type' => MENU_LOCAL_TASK,
   );
 
   $items['admin/tripal/chado/tripal_organism/sync'] = array(
-    'title' => 'Sync Organisms',
+    'title' => 'Sync',
     'description' => 'Sync Chado organisms with Drupal',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_organism_sync'),
     'access arguments' => array('adminster tripal organism'),
-    'type' => MENU_NORMAL_ITEM,
+    'type' => MENU_LOCAL_TASK,
+  );
+
+  $items['admin/tripal/chado/tripal_organism/views/organisms/enable'] = array(
+    'title' => 'Enable Organism Administrative View',
+    'page callback' => 'tripal_views_admin_enable_view',
+    'page arguments' => array('tripal_organism_admin_organisms', 'admin/tripal/chado/tripal_organism'),
+    'access arguments' => array('administer tripal_bulk_loader'),
+    'type' => MENU_CALLBACK,
   );
 
   return $items;
@@ -154,7 +163,7 @@ function tripal_organism_help ($path, $arg) {
  */
 function tripal_organism_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
-  
+
   $items = array(
     'node__chado_organism' => array(
       'template' => 'node--chado-generic',
@@ -329,7 +338,7 @@ function chado_organism_validate($node, $form, &$form_state) {
   $node->abbreviation = trim($node->abbreviation);
   $node->common_name  = trim($node->common_name);
   $node->description  = trim($node->description);
-  
+
   // if this is an update, we want to make sure that a different organism doesn't
   // already have this genus and speces
   if (property_exists($node, 'organism_id')) {
@@ -383,7 +392,7 @@ function chado_organism_insert($node) {
   $node->abbreviation = trim($node->abbreviation);
   $node->common_name  = trim($node->common_name);
   $node->description  = trim($node->description);
-  
+
   // if there is an organism_id in the $node object then this must be a sync so
   // we can skip adding the organism as it is already there, although
   // we do need to proceed with the rest of the insert
@@ -410,7 +419,7 @@ function chado_organism_insert($node) {
 
   // Make sure the entry for this organism doesn't already exist in the
   // chado_organism table if it doesn't exist then we want to add it.
-  $check_org_id = chado_get_id_for_node('organism', $node->nid);  
+  $check_org_id = chado_get_id_for_node('organism', $node->nid);
   if (!$check_org_id) {
     $record = new stdClass();
     $record->nid = $node->nid;
@@ -441,7 +450,7 @@ function chado_organism_update($node) {
   $node->abbreviation = trim($node->abbreviation);
   $node->common_name  = trim($node->common_name);
   $node->description  = trim($node->description);
-  
+
   if ($node->revision) {
     // there is no way to handle revisions in Chado but leave
     // this here just to make not we've addressed it.
@@ -546,17 +555,17 @@ function chado_organism_add_image($node) {
  */
 function chado_organism_form($node, $form_state) {
   $form = array();
-  
+
   // we have a file upload element on the form soe we need the multipart encoding type
   $form['#attributes']['enctype'] = 'multipart/form-data';
-  
+
   // if the organism is part of the node object then we are editing. If not we are inserting
   if (property_exists($node, 'organism')) {
     $organism = $node->organism;
 
     // add in the comment since it is a text field and may not be included if too big
     $organism = tripal_core_expand_chado_vars($organism, 'field', 'organism.comment');
-    
+
     // get form defaults
     $abbreviation   = property_exists($node, 'abbreviation')   ? property_exists($node, 'abbreviation')   : $organism->abbreviation;
     $genus          = property_exists($node, 'genus')          ? property_exists($node, 'genus')          : $organism->genus;
@@ -564,7 +573,7 @@ function chado_organism_form($node, $form_state) {
     $common_name    = property_exists($node, 'common_name')    ? property_exists($node, 'common_name')    : $organism->common_name;
     $description    = property_exists($node, 'description')    ? property_exists($node, 'description')    : $organism->comment;
     $organism_image = property_exists($node, 'organism_image') ? property_exists($node, 'organism_image') : '';
-    
+
     // set the organism_id in the form
     $form['organism_id'] = array(
       '#type' => 'value',
@@ -635,7 +644,7 @@ function chado_organism_load($nodes) {
     // build the organism variable
     $values = array('organism_id' => $organism_id);
     $organism = tripal_core_generate_chado_var('organism', $values);
-    
+
 
     // add in the description field
     $organism = tripal_core_expand_chado_vars($organism, 'field', 'organism.comment');

tripal_organism/tripal_organism.views_default.inc

@@ -7,293 +7,190 @@
 function tripal_organism_views_default_views() {
   $views = array();
 
-  if (!module_exists('tripal_views')) {
-    return $views;
-  }
+  $view = tripal_organism_admin_defaultview_organisms();
+  $views[$view->name] = $view;
+
+  return $views;
+}
+
+function tripal_organism_admin_defaultview_organisms() {
 
-  // Main default view
-  $view = new view;
-  $view->name = 'organism_listing';
+  $view = new view();
+  $view->name = 'tripal_organism_admin_organisms';
   $view->description = 'A listing of all organism in chado';
-  $view->tag = 'chado default';
+  $view->tag = 'tripal admin';
   $view->base_table = 'organism';
+  $view->human_name = 'Organism 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'] = 'Organisms';
+  $handler->display->display_options['use_more_always'] = FALSE;
+  $handler->display->display_options['access']['type'] = 'perm';
+  $handler->display->display_options['access']['perm'] = 'adminster tripal organism';
+  $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['exposed_form']['options']['submit_button'] = 'Filter';
+  $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(
+    'common_name' => 'common_name',
+    'genus' => 'genus',
+    'species' => 'species',
+    'abbreviation' => 'abbreviation',
+  );
+  $handler->display->display_options['style_options']['default'] = '-1';
+  $handler->display->display_options['style_options']['info'] = array(
     'common_name' => array(
-      'label' => 'Common 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' => 'common_name',
-      'table' => 'organism',
-      'field' => 'common_name',
-      'relationship' => 'none',
+      'sortable' => 1,
+      'separator' => '',
     ),
     'genus' => array(
-      'label' => 'Genus',
-      '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' => 'genus',
-      'table' => 'organism',
-      'field' => 'genus',
-      'relationship' => 'none',
+      'sortable' => 1,
+      'separator' => '',
     ),
     'species' => array(
-      'label' => 'Species',
-      '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' => 'species',
-      'table' => 'organism',
-      'field' => 'species',
-      'relationship' => 'none',
+      'sortable' => 1,
+      'separator' => '',
     ),
     'abbreviation' => array(
-      'label' => 'Abbreviation',
-      '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' => 0,
-      'exclude' => 0,
-      'id' => 'abbreviation',
-      'table' => 'organism',
-      'field' => 'abbreviation',
-      'relationship' => 'none',
-    ),
-  ));
-  $handler->override_option('sorts', array(
-    'genus' => array(
-      'order' => 'ASC',
-      'id' => 'genus',
-      'table' => 'organism',
-      'field' => 'genus',
-      'relationship' => 'none',
+      'sortable' => 1,
+      'separator' => '',
     ),
-    'species' => array(
-      'order' => 'ASC',
-      'id' => 'species',
-      'table' => 'organism',
-      'field' => 'species',
-      'relationship' => 'none',
-    ),
-  ));
-  $handler->override_option('access', array(
-    'type' => 'perm',
-    'perm' => 'access chado_organism content',
-  ));
-  $handler->override_option('cache', array(
-    'type' => 'none',
-  ));
-  $handler->override_option('title', 'Organisms');
-  $handler->override_option('empty', 'No organisms matched the supplied criteria.');
-  $handler->override_option('empty_format', '1');
-  $handler->override_option('items_per_page', 0);
-  $handler->override_option('style_plugin', 'table');
-  $handler->override_option('style_options', array(
-    'grouping' => '',
-    'override' => 1,
-    'sticky' => 0,
-    'order' => 'asc',
-    'summary' => '',
-    'columns' => array(
-      'common_name' => 'common_name',
-      'genus' => 'genus',
-      'species' => 'species',
-      'abbreviation' => 'abbreviation',
-    ),
-    'info' => array(
-      'common_name' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'genus' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'species' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-      'abbreviation' => array(
-        'sortable' => 1,
-        'separator' => '',
-      ),
-    ),
-    'default' => '-1',
-  ));
-  $default_handler = $handler;
+  );
+  /* Header: Global: Text area */
+  $handler->display->display_options['header']['area']['id'] = 'area';
+  $handler->display->display_options['header']['area']['table'] = 'views';
+  $handler->display->display_options['header']['area']['field'] = 'area';
+  $handler->display->display_options['header']['area']['label'] = 'Add Organism';
+  $handler->display->display_options['header']['area']['empty'] = TRUE;
+  $handler->display->display_options['header']['area']['content'] = '<ul class="action-links">
+          <li><a href="node/add/tripal_cv">Add Organism</a></li>
+     </ul>';
+  $handler->display->display_options['header']['area']['format'] = 'full_html';
+  /* 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 organisms matched the supplied criteria.';
+  $handler->display->display_options['empty']['text']['format'] = '1';
+  /* Relationship: Organism: Organism => Node */
+  $handler->display->display_options['relationships']['organism_id']['id'] = 'organism_id';
+  $handler->display->display_options['relationships']['organism_id']['table'] = 'chado_organism';
+  $handler->display->display_options['relationships']['organism_id']['field'] = 'organism_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 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']['alter']['make_link'] = TRUE;
+  $handler->display->display_options['fields']['common_name']['alter']['path'] = 'node/[nid]';
+  /* Field: Chado Organism: Genus */
+  $handler->display->display_options['fields']['genus']['id'] = 'genus';
+  $handler->display->display_options['fields']['genus']['table'] = 'organism';
+  $handler->display->display_options['fields']['genus']['field'] = 'genus';
+  /* Field: Chado Organism: Species */
+  $handler->display->display_options['fields']['species']['id'] = 'species';
+  $handler->display->display_options['fields']['species']['table'] = 'organism';
+  $handler->display->display_options['fields']['species']['field'] = 'species';
+  /* Field: Chado Organism: Abbreviation */
+  $handler->display->display_options['fields']['abbreviation']['id'] = 'abbreviation';
+  $handler->display->display_options['fields']['abbreviation']['table'] = 'organism';
+  $handler->display->display_options['fields']['abbreviation']['field'] = 'abbreviation';
+  /* 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'] = 'organism_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'] = 'organism_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: Genus */
+  $handler->display->display_options['sorts']['genus']['id'] = 'genus';
+  $handler->display->display_options['sorts']['genus']['table'] = 'organism';
+  $handler->display->display_options['sorts']['genus']['field'] = 'genus';
+  /* Sort criterion: Chado Organism: Species */
+  $handler->display->display_options['sorts']['species']['id'] = 'species';
+  $handler->display->display_options['sorts']['species']['table'] = 'organism';
+  $handler->display->display_options['sorts']['species']['field'] = 'species';
+  /* 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']['operator'] = 'contains';
+  $handler->display->display_options['filters']['common_name']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['common_name']['expose']['operator_id'] = '';
+  $handler->display->display_options['filters']['common_name']['expose']['label'] = 'Common Name Contains';
+  $handler->display->display_options['filters']['common_name']['expose']['identifier'] = 'common_name';
+  $handler->display->display_options['filters']['common_name']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+  /* Filter criterion: Chado Organism: Genus */
+  $handler->display->display_options['filters']['genus']['id'] = 'genus';
+  $handler->display->display_options['filters']['genus']['table'] = 'organism';
+  $handler->display->display_options['filters']['genus']['field'] = 'genus';
+  $handler->display->display_options['filters']['genus']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['genus']['expose']['operator_id'] = 'genus_op';
+  $handler->display->display_options['filters']['genus']['expose']['label'] = 'Genus';
+  $handler->display->display_options['filters']['genus']['expose']['operator'] = 'genus_op';
+  $handler->display->display_options['filters']['genus']['expose']['identifier'] = 'genus';
+  $handler->display->display_options['filters']['genus']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+  /* Filter criterion: Chado Organism: Species */
+  $handler->display->display_options['filters']['species']['id'] = 'species';
+  $handler->display->display_options['filters']['species']['table'] = 'organism';
+  $handler->display->display_options['filters']['species']['field'] = 'species';
+  $handler->display->display_options['filters']['species']['exposed'] = TRUE;
+  $handler->display->display_options['filters']['species']['expose']['operator_id'] = 'species_op';
+  $handler->display->display_options['filters']['species']['expose']['label'] = 'Species';
+  $handler->display->display_options['filters']['species']['expose']['operator'] = 'species_op';
+  $handler->display->display_options['filters']['species']['expose']['identifier'] = 'species';
+  $handler->display->display_options['filters']['species']['expose']['remember_roles'] = array(
+    2 => '2',
+    1 => 0,
+    3 => 0,
+  );
+
+  /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->override_option('path', 'chado/organisms');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Organisms',
-    'description' => 'A biological organism.',
-    '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;
-    // Adds organism => Node relationship
-    $default_handler->override_option('relationships', array(
-      'nid' => array(
-        'label' => 'Organism to Node',
-        'required' => 0,
-        'id' => 'nid',
-        'table' => 'chado_organism',
-        'field' => 'nid',
-        'relationship' => 'none',
-      ),
-    ));
-    // Change analysis.name to have a link to the node
-    $fields['common_name']['alter']['link_to_node'] = 1;
-    $default_handler->override_option('fields', $fields);
-    // 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_organism/organisms';
+  $handler->display->display_options['menu']['type'] = 'default tab';
+  $handler->display->display_options['menu']['title'] = 'Organisms';
+  $handler->display->display_options['menu']['description'] = 'A biological organism.';
+  $handler->display->display_options['menu']['weight'] = '-10';
+  $handler->display->display_options['menu']['name'] = 'management';
+  $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;
+  return $view;
 }