Reorganized the vocabulary loader links and consolidated them into a single location

legacy/tripal_core/api/tripal_core.chado_nodes.properties.api.inc

@@ -293,7 +293,7 @@ function chado_add_node_form_properties(&$form, &$form_state, $details) {
         to the %cv_name controlled vocabulary.',
         array(
           '%cv_name' => $details['cv_name'],
-          '@cvtermlink' => url('admin/tripal/loaders/chado_cv/' . $details['cv_id'] . '/cvterm/add')
+          '@cvtermlink' => url('admin/tripal/loaders/chado_vocabs/chado_cv/' . $details['cv_id'] . '/cvterm/add')
         )
       ),
       TRIPAL_NOTICE,
@@ -306,7 +306,7 @@ function chado_add_node_form_properties(&$form, &$form_state, $details) {
         a controlled vocabulary term</a> to the %cv_name controlled vocabulary.',
         array(
           '%cv_name' => $details['cv_name'],
-          '@cvtermlink' => url('admin/tripal/loaders/chado_cv/' . $details['cv_id'] . '/cvterm/add')
+          '@cvtermlink' => url('admin/tripal/loaders/chado_vocabs/chado_cv/' . $details['cv_id'] . '/cvterm/add')
         )
       ),
       TRIPAL_INFO,

legacy/tripal_core/api/tripal_core.chado_nodes.relationships.api.inc

@@ -254,7 +254,7 @@ function chado_add_node_form_relationships(&$form, &$form_state, $details) {
         to the %cv_name controlled vocabulary.',
         array(
           '%cv_name' => $details['cv_name'],
-          '@cvtermlink' => url('admin/tripal/loaders/chado_cv/'.$details['cv_id'].'/cvterm/add')
+          '@cvtermlink' => url('admin/tripal/loaders/chado_vocabs/chado_cv/'.$details['cv_id'].'/cvterm/add')
         )
       ),
       TRIPAL_WARNING,
@@ -267,7 +267,7 @@ function chado_add_node_form_relationships(&$form, &$form_state, $details) {
         a controlled vocabulary term</a> to the %cv_name controlled vocabulary.',
         array(
           '%cv_name' => $details['cv_name'],
-          '@cvtermlink' => url('admin/tripal/loaders/chado_cv/' . $details['cv_id'] . '/cvterm/add')
+          '@cvtermlink' => url('admin/tripal/loaders/chado_vocabs/chado_cv/' . $details['cv_id'] . '/cvterm/add')
         )
       ),
       TRIPAL_INFO,

legacy/tripal_cv/api/tripal_cv.api.inc

@@ -97,7 +97,7 @@ function tripal_get_cvterm_default_select_options($table, $field, $field_desc) {
     if (count($options) == 0) {
       tripal_set_message('There are no ' . $field_desc . '. Please ' .
           l('add terms',
-              'admin/tripal/loaders/chado_cv/' .$default_cv->cv_id. '/cvterm/add',
+              'admin/tripal/loaders/chado_vocabs/chado_cv/' .$default_cv->cv_id. '/cvterm/add',
               array('attributes' => array('target' => '_blank'))) . ' to the ' .
           $default_cv->name .' vocabulary.',
           TRIPAL_WARNING);

legacy/tripal_cv/includes/tripal_cv.cv_defaults.inc

@@ -79,18 +79,18 @@ function tripal_cv_admin_set_defaults_form($form, &$form_state) {
     );
 
     // Actions
-    $view_terms = l('New Vocabulary', 'admin/tripal/loaders/chado_cv/add');
+    $view_terms = l('New Vocabulary', 'admin/tripal/loaders/chado_vocabs/chado_cv/add');
     $add_term = '';
     if (!empty($cv)) {
       $view_terms = l(
           'View Terms',
-          'admin/tripal/loaders/chado_cvterms',
+          'admin/tripal/loaders/chado_vocabs/chado_cvterms',
           array('query' => array('cv' => $cv->name))
       );
 
       $add_term = l(
           'Add Term',
-          'admin/tripal/loaders/chado_cv/' . $cv->cv_id . '/cvterm/add'
+          'admin/tripal/loaders/chado_vocabs/chado_cv/' . $cv->cv_id . '/cvterm/add'
       );
     }
     $form['settings']['existing'][$cv_default_id]["view-terms"] = array(

legacy/tripal_cv/theme/templates/tripal_cv_help.tpl.php

@@ -15,7 +15,7 @@
    users access to view content and create a special role for creating, editing and other administrative tasks.</p></li>
 
       <li><p><b>Loading of Ontologies/Controlled Vocabularies</b>: You can access this loader at <?php
-        print l('Admin->Tripal Management->Tripal CV->Load Ontology With OBO File', 'admin/tripal/loaders/chado_obo_loader')
+        print l('Admin->Tripal Management->Tripal CV->Load Ontology With OBO File', 'admin/tripal/loaders/chado_vocabs/obo_loader')
         ?>. This loader allows you to choose from a list of common ontologies or
         enter the URL or location to an OBO file. Even the list of common
         ontologies is using a URL ensuring you get the most up to date ontology.</p>

legacy/tripal_feature/theme/templates/tripal_feature_help.tpl.php

@@ -11,7 +11,7 @@
 
    <li><p><b>Loading of Ontologies</b>:
      Before loading genomic features you must also have several vocabularies loaded as well. Using the
-     <?php print l('OGO loader','admin/tripal/tripal_cv/obo_loader')?> you should load the following
+     <?php print l('OGO loader','admin/tripal/loaders/chado_vocabs/obo_loader')?> you should load the following
      ontologies:</p>
      <ul>
         <li>Sequence Ontology</li>

legacy/tripal_library/includes/tripal_library.chado_node.inc

@@ -128,7 +128,7 @@ function chado_library_form($node, &$form_state) {
   $lt_message = tripal_set_message("To add additional items to the library type drop down list,
      add a term to the " .
      l($lt_cv->name . " controlled vocabulary",
-       "admin/tripal/loaders/chado_cv/" . $lt_cv->cv_id . "/cvterm/add",
+       "admin/tripal/loaders/chado_vocabs/chado_cv/" . $lt_cv->cv_id . "/cvterm/add",
        array('attributes' => array('target' => '_blank'))
       ),
      TRIPAL_INFO, array('return_html' => TRUE)

legacy/tripal_pub/includes/tripal_pub.chado_node.inc

@@ -53,7 +53,7 @@ function chado_pub_form($node, $form_state) {
     drupal_set_message(t('The Tripal Pub vocabulary is currently not loaded. ' .
         'This vocabulary is required to be loaded before adding ' .
         'publications.  <br>Please !import',
-        array('!import' => l('load the Tripal Publication vocabulary', 'admin/tripal/loaders/obo_loader'))), 'warning');
+        array('!import' => l('load the Tripal Publication vocabulary', 'admin/tripal/loaders/chado_vocabs/obo_loader'))), 'warning');
   }
 
   // Default values can come in the following ways:

legacy/tripal_stock/includes/tripal_stock.chado_node.inc

@@ -202,7 +202,7 @@ function chado_stock_form($node, $form_state) {
   $st_message = tripal_set_message("To add additional items to the stock type drop down list,
      add a term to the " .
     l($st_cv->name . " controlled vocabulary",
-      "admin/tripal/loaders/chado_cv/" . $st_cv->cv_id . "/cvterm/add",
+      "admin/tripal/loaders/chado_vocabs/chado_cv/" . $st_cv->cv_id . "/cvterm/add",
       array('attributes' => array('target' => '_blank'))
     ),
     TRIPAL_INFO, array('return_html' => TRUE)

tripal/includes/TripalImporter.inc

@@ -105,6 +105,15 @@ class TripalImporter {
    */
   public static $cardinality = 1;
 
+
+  /**
+   * Be default, all loaders are automaticlly added to the Admin >
+   * Tripal > Data Laders menu.  However, if this loader should be
+   * made available via a different menu path, then set it here.  If the
+   * value is empty then the path will be the default.
+   */
+  public static $menu_path = '';
+
   // --------------------------------------------------------------------------
   //                  PRIVATE MEMBERS -- DO NOT EDIT or OVERRIDE
   // --------------------------------------------------------------------------

tripal/tripal.module

@@ -323,7 +323,11 @@ function tripal_menu() {
   foreach ($importers as $class_name) {
     tripal_load_include_importer_class($class_name);
     if (class_exists($class_name)) {
-      $items['admin/tripal/loaders/' . $class_name::$machine_name] = array(
+      $menu_path = 'admin/tripal/loaders/' . $class_name::$machine_name;
+      if ($class_name::$menu_path) {
+        $menu_path = $class_name::$menu_path;
+      }
+      $items[$menu_path] = array(
         'title' => $class_name::$name,
         'description' =>  $class_name::$description,
         'page callback' => 'drupal_get_form',

tripal_chado/includes/TripalImporter/OBOImporter.inc

@@ -14,7 +14,7 @@ class OBOImporter extends TripalImporter {
    * The name of this loader.  This name will be presented to the site
    * user.
    */
-  public static $name = 'Chado OBO Loader';
+  public static $name = 'OBO Vocabulary Loader';
 
   /**
    * The machine name for this loader. This name will be used to construct
@@ -81,8 +81,17 @@ class OBOImporter extends TripalImporter {
     'file_remote' => FALSE,
   );
 
+  /**
+   * Be default, all loaders are automaticlly added to the Admin >
+   * Tripal > Data Laders menu.  However, if this loader should be
+   * made available via a different menu path, then set it here.  If the
+   * value is empty then the path will be the default.
+   */
+  public static $menu_path = 'admin/tripal/loaders/chado_vocabs/obo_loader';
+
   public static $file_required = FALSE;
 
+
   /**
    * Keep track of vocabularies that have been added.
    *

tripal_chado/includes/loaders/tripal_chado.pub_importers.inc

@@ -22,7 +22,7 @@ function tripal_pub_importers_list() {
     drupal_set_message(t('The Tripal Pub vocabulary is currently not loaded. ' .
         'This vocabulary is required to be loaded before importing of ' .
         'publications.  <br>Please !import',
-        array('!import' => l('load the Tripal Publication vocabulary', 'admin/tripal/loaders/obo_loader'))), 'warning');
+        array('!import' => l('load the Tripal Publication vocabulary', 'aadmin/tripal/loaders/chado_vocabs/obo_loader'))), 'warning');
   }
 
   // clear out the session variable when we view the list.
@@ -117,12 +117,12 @@ function tripal_pub_importer_setup_page($action = 'new', $pub_import_id = NULL)
   $values = array('name' => 'tripal_pub');
   $tpub_cv = chado_select_record('cv', array('cv_id'), $values);
   if (count($tpub_cv) == 0) {
-    drupal_set_message(t('Before importing publications you must first ') . l(t('load the Tripal Pub Ontology'), 'admin/tripal/tripal_cv/obo_loader'), 'error');
+    drupal_set_message(t('Before importing publications you must first ') . l(t('load the Tripal Pub Ontology'), 'admin/tripal/loaders/chado_vocabs/obo_loader'), 'error');
   }
   $values = array('name' => 'tripal_contact');
   $tpub_cv = chado_select_record('cv', array('cv_id'), $values);
   if (count($tpub_cv) == 0) {
-    drupal_set_message(t('If you want to create contact pages for authors, you must first ') . l(t('load the Tripal Contact Ontology'), 'admin/tripal/tripal_cv/obo_loader'), 'error');
+    drupal_set_message(t('If you want to create contact pages for authors, you must first ') . l(t('load the Tripal Contact Ontology'), 'admin/tripal/loaders/chado_vocabs/obo_loader'), 'error');
   }
 
   if(!extension_loaded ('yaz')){

tripal_chado/tripal_chado.module

@@ -569,8 +569,15 @@ function tripal_chado_menu() {
   //////////////////////////////////////////////////////////////////////////////
   //                          Controlled Vocabularies
   //////////////////////////////////////////////////////////////////////////////
-  $items['admin/tripal/loaders/chado_cv'] = array(
-    'title' => 'Chado Controlled Vocabularies',
+  $items['admin/tripal/loaders/chado_vocabs'] = array(
+    'title' => 'Chado Vocabularies',
+    'description' => t('Tools facilitating import of controlled vocabularies and terms.'),
+    'access arguments' => array('administer tripal'),
+    'type' => MENU_NORMAL_ITEM,
+    'weight' => 6
+  );
+  $items['admin/tripal/loaders/chado_vocabs/chado_cv'] = array(
+    'title' => 'Manage Controlled Vocabularies',
     'description' => 'Controlled Vocabularies control the terms available for various chado fields.',
     'page callback' => 'tripal_cv_admin_cv_listing',
     'access arguments' => array('administer controlled vocabularies'),
@@ -578,7 +585,7 @@ function tripal_chado_menu() {
     'file path' => drupal_get_path('module', 'tripal_chado'),
     'type' => MENU_NORMAL_ITEM,
   );
-  $items['admin/tripal/loaders/chado_cv/edit/%'] = array(
+  $items['admin/tripal/loaders/chado_vocabs/chado_cv/edit/%'] = array(
     'title' => 'Edit a Controlled Vocabulary',
     'description' => 'Edit the details such as name and description for an existing controlled vocabulary.',
     'page callback' => 'drupal_get_form',
@@ -589,7 +596,7 @@ function tripal_chado_menu() {
     'file path' => drupal_get_path('module', 'tripal_chado'),
     'type' => MENU_CALLBACK,
   );
-  $items['admin/tripal/loaders/chado_cv/add'] = array(
+  $items['admin/tripal/loaders/chado_vocabs/chado_cv/add'] = array(
     'title' => 'Add a Controlled Vocabulary',
     'description' => 'Manually a new controlled vocabulary.',
     'page callback' => 'drupal_get_form',
@@ -600,7 +607,7 @@ function tripal_chado_menu() {
     'file path' => drupal_get_path('module', 'tripal_chado'),
     'type' => MENU_CALLBACK,
   );
-  $items['admin/tripal/loaders/chado_cv/%/cvterm/add'] = array(
+  $items['admin/tripal/loaders/chado_vocabs/chado_cv/%/cvterm/add'] = array(
     'title' => 'Add a Controlled Vocabulary Term',
     'description' => 'Add a new controlled vocabulary term.',
     'page callback' => 'drupal_get_form',
@@ -610,7 +617,7 @@ function tripal_chado_menu() {
     'file path' => drupal_get_path('module', 'tripal_chado'),
     'type' => MENU_CALLBACK,
   );
-  $items['admin/tripal/loaders/chado_cv/cvterm/add'] = array(
+  $items['admin/tripal/loaders/chado_vocabs/chado_cv/cvterm/add'] = array(
     'title' => 'Add a Controlled Vocabulary Term',
     'description' => 'Add a new controlled vocabulary term.',
     'page callback' => 'drupal_get_form',
@@ -620,7 +627,7 @@ function tripal_chado_menu() {
     'file path' => drupal_get_path('module', 'tripal_chado'),
     'type' => MENU_CALLBACK,
   );
-  $items['admin/tripal/loaders/chado_cv/%/cvterm/edit/%'] = array(
+  $items['admin/tripal/loaders/chado_vocabs/chado_cv/%/cvterm/edit/%'] = array(
     'title' => 'Edit a Controlled Vocabulary Term',
     'description' => 'Edit an existing controlled vocabulary term.',
     'page callback' => 'drupal_get_form',
@@ -631,9 +638,14 @@ function tripal_chado_menu() {
     'type' => MENU_CALLBACK,
   );
 
-  $items['admin/tripal/storage/chado/cvtermpath'] = array(
-    'title' => 'Update Chado cvtermpath table',
-    'description' => 'The Chado cvtermpath table provides lineage for terms and is useful for quickly finding any ancestor parent of a term.  However, this table must be populated.  This page allows for populating of this table one vocabulary at a time',
+  $items['admin/tripal/loaders/chado_vocabs/cvtermpath'] = array(
+    'title' => 'Update CV Term Paths',
+    'description' => 'The Chado cvtermpath table provides lineage for
+      controlled vocabulary terms and is useful for quickly finding any
+      ancestor parent of a term.  If controlled vocabularies are loaded
+      using the OBO Importer then the vocabulary is automatically added to
+      the cvtermpath table.  However, if it is needed, the addition of terms
+      to the cvtermpath table can be manually executed here.',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_cv_cvtermpath_form'),
     'access arguments' => array('administer controlled vocabularies'),

tripal_chado/tripal_chado.views_default.inc

@@ -504,7 +504,7 @@ function tripal_chado_defaultview_admin_cvs_listing() {
   $handler->display->display_options['header']['action_links_area']['empty'] = TRUE;
   $handler->display->display_options['header']['action_links_area']['link-1'] = array(
     'label-1' => 'Add Vocabulary',
-    'path-1' => 'admin/tripal/loaders/chado_cv/add',
+    'path-1' => 'admin/tripal/loaders/chado_vocabs/chado_cv/add',
   );
   /* No results behavior: Global: Text area */
   $handler->display->display_options['empty']['text']['id'] = 'area';
@@ -534,7 +534,7 @@ function tripal_chado_defaultview_admin_cvs_listing() {
   $handler->display->display_options['fields']['nothing_1']['exclude'] = TRUE;
   $handler->display->display_options['fields']['nothing_1']['alter']['text'] = 'edit';
   $handler->display->display_options['fields']['nothing_1']['alter']['make_link'] = TRUE;
-  $handler->display->display_options['fields']['nothing_1']['alter']['path'] = 'admin/tripal/loaders/chado_cv/edit/[cv_id]';
+  $handler->display->display_options['fields']['nothing_1']['alter']['path'] = 'admin/tripal/loaders/chado_vocabs/chado_cv/edit/[cv_id]';
   /* Field: Global: Custom text */
   $handler->display->display_options['fields']['nothing']['id'] = 'nothing';
   $handler->display->display_options['fields']['nothing']['table'] = 'views';
@@ -543,7 +543,7 @@ function tripal_chado_defaultview_admin_cvs_listing() {
   $handler->display->display_options['fields']['nothing']['exclude'] = TRUE;
   $handler->display->display_options['fields']['nothing']['alter']['text'] = 'View Terms';
   $handler->display->display_options['fields']['nothing']['alter']['make_link'] = TRUE;
-  $handler->display->display_options['fields']['nothing']['alter']['path'] = 'admin/tripal/loaders/chado_cvterms?cv=[name]';
+  $handler->display->display_options['fields']['nothing']['alter']['path'] = 'admin/tripal/loaders/chado_vocabs/chado_cvterms?cv=[name]';
   $handler->display->display_options['fields']['nothing']['hide_alter_empty'] = TRUE;
   /* Field: Global: Custom text */
   $handler->display->display_options['fields']['nothing_3']['id'] = 'nothing_3';
@@ -553,7 +553,7 @@ function tripal_chado_defaultview_admin_cvs_listing() {
   $handler->display->display_options['fields']['nothing_3']['exclude'] = TRUE;
   $handler->display->display_options['fields']['nothing_3']['alter']['text'] = 'Add Term';
   $handler->display->display_options['fields']['nothing_3']['alter']['make_link'] = TRUE;
-  $handler->display->display_options['fields']['nothing_3']['alter']['path'] = 'admin/tripal/loaders/chado_cv/[cv_id]/cvterm/add';
+  $handler->display->display_options['fields']['nothing_3']['alter']['path'] = 'aadmin/tripal/loaders/chado_vocabs/chado_cv/[cv_id]/cvterm/add';
   /* Field: Global: Custom text */
   $handler->display->display_options['fields']['nothing_2']['id'] = 'nothing_2';
   $handler->display->display_options['fields']['nothing_2']['table'] = 'views';
@@ -609,7 +609,7 @@ function tripal_chado_defaultview_admin_cvs_listing() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/loaders/chado_cvs';
+  $handler->display->display_options['path'] = 'admin/tripal/loaders/chado_vocabs/chado_cvs';
   $handler->display->display_options['menu']['type'] = 'default tab';
   $handler->display->display_options['menu']['title'] = 'Chado Controlled Vocabularies';
   $handler->display->display_options['menu']['description'] = 'A listing of all controlled vocabularies';
@@ -704,7 +704,7 @@ $handler->display->display_options['header']['action_links_area']['label'] = 'Ac
 $handler->display->display_options['header']['action_links_area']['empty'] = TRUE;
 $handler->display->display_options['header']['action_links_area']['link-1'] = array(
   'label-1' => 'Add Term',
-  'path-1' => 'admin/tripal/loaders/chado_cv/cvterm/add',
+  'path-1' => 'admin/tripal/loaders/chado_vocabs/chado_cv/cvterm/add',
 );
 /* No results behavior: Global: Text area */
 $handler->display->display_options['empty']['text']['id'] = 'area';
@@ -724,7 +724,7 @@ $handler->display->display_options['fields']['name_1']['table'] = 'cv';
 $handler->display->display_options['fields']['name_1']['field'] = 'name';
 $handler->display->display_options['fields']['name_1']['label'] = 'Vocabulary';
 $handler->display->display_options['fields']['name_1']['alter']['make_link'] = TRUE;
-$handler->display->display_options['fields']['name_1']['alter']['path'] = 'admin/tripal/loaders/chado_cvs?name=[name_1]';
+$handler->display->display_options['fields']['name_1']['alter']['path'] = 'admin/tripal/loaders/chado_vocabs/chado_cvs?name=[name_1]';
 /* Field: Chado Cvterm: Cvterm Id */
 $handler->display->display_options['fields']['cvterm_id']['id'] = 'cvterm_id';
 $handler->display->display_options['fields']['cvterm_id']['table'] = 'cvterm';
@@ -773,7 +773,7 @@ $handler->display->display_options['fields']['nothing']['label'] = 'Edit Link';
 $handler->display->display_options['fields']['nothing']['exclude'] = TRUE;
 $handler->display->display_options['fields']['nothing']['alter']['text'] = 'edit';
 $handler->display->display_options['fields']['nothing']['alter']['make_link'] = TRUE;
-$handler->display->display_options['fields']['nothing']['alter']['path'] = 'admin/tripal/loaders/chado_cv/[cv_id]/cvterm/edit/[cvterm_id]';
+$handler->display->display_options['fields']['nothing']['alter']['path'] = 'admin/tripal/loaders/chado_vocabs/chado_cv/[cv_id]/cvterm/edit/[cvterm_id]';
 /* Field: Global: Custom text */
 $handler->display->display_options['fields']['nothing_1']['id'] = 'nothing_1';
 $handler->display->display_options['fields']['nothing_1']['table'] = 'views';
@@ -843,10 +843,10 @@ $handler->display->display_options['filters']['definition']['expose']['remember_
 
 /* Display: Page */
 $handler = $view->new_display('page', 'Page', 'page_1');
-$handler->display->display_options['path'] = 'admin/tripal/loaders/chado_cvterms';
+$handler->display->display_options['path'] = 'admin/tripal/loaders/chado_vocabs/chado_cvterms';
 $handler->display->display_options['menu']['type'] = 'normal';
-$handler->display->display_options['menu']['title'] = 'Chado CV Terms';
-$handler->display->display_options['menu']['description'] = 'A listing of a controlled vocabulary terms for a given vocabulary';
+$handler->display->display_options['menu']['title'] = 'Manage Chado CV Terms';
+$handler->display->display_options['menu']['description'] = 'View and edit controlled vocabulary terms.';
 $handler->display->display_options['menu']['weight'] = '-8';
 $handler->display->display_options['menu']['name'] = 'management';
 $handler->display->display_options['menu']['context'] = 0;