Tweaks to menus and text

legacy/tripal_db/includes/tripal_db.admin.inc

@@ -17,8 +17,8 @@ function tripal_db_admin_db_listing() {
   $breadcrumb[] = l('Home', '<front>');
   $breadcrumb[] = l('Administration', 'admin');
   $breadcrumb[] = l('Tripal', 'admin/tripal');
-  $breadcrumb[] = l('Chado Modules', 'admin/tripal/chado');
-  $breadcrumb[] = l('Databases', 'admin/tripal/chado/tripal_db');
+  $breadcrumb[] = l('Chado Modules', 'admin/tripal/legacy');
+  $breadcrumb[] = l('Databases', 'admin/tripal/legacy/tripal_db');
   drupal_set_breadcrumb($breadcrumb);
 
   // Add the view
@@ -34,10 +34,10 @@ function tripal_db_admin_db_listing() {
       . 'enable the pertinent views</strong>:</p>';
     $output .= '<ul>';
     if (!isset($dbs_view)) {
-      $output .= '<li>'.l('DB Admin', 'admin/tripal/chado/tripal_db/views/dbs/enable').'</li>';
+      $output .= '<li>'.l('DB Admin', 'admin/tripal/legacy/tripal_db/views/dbs/enable').'</li>';
     }
     if (!isset($dbxrefs_view)) {
-      $output .= '<li>'.l('DB Reference Admin', 'admin/tripal/chado/tripal_db/views/dbxrefs/enable').'</li>';
+      $output .= '<li>'.l('DB Reference Admin', 'admin/tripal/legacy/tripal_db/views/dbxrefs/enable').'</li>';
     }
     $output .= '</ul>';
   }

legacy/tripal_feature/includes/tripal_feature.admin.inc

@@ -17,8 +17,8 @@ function tripal_feature_admin_feature_view() {
   $breadcrumb[] = l('Home', '<front>');
   $breadcrumb[] = l('Administration', 'admin');
   $breadcrumb[] = l('Tripal', 'admin/tripal');
-  $breadcrumb[] = l('Chado', 'admin/tripal/chado');
-  $breadcrumb[] = l('Features', 'admin/tripal/chado/tripal_feature');
+  $breadcrumb[] = l('Chado', 'admin/tripal/legacy');
+  $breadcrumb[] = l('Features', 'admin/tripal/legacy/tripal_feature');
   drupal_set_breadcrumb($breadcrumb);
 
   // Add the view
@@ -32,7 +32,7 @@ function tripal_feature_admin_feature_view() {
       . 'administrative interface are disabled. <strong>Click each of the following links to '
       . 'enable the pertinent views</strong>:</p>';
     $output .= '<ul>';
-      $output .= '<li>'.l('Features View', 'admin/tripal/chado/tripal_feature/views/features/enable').'</li>';
+      $output .= '<li>'.l('Features View', 'admin/tripal/legacy/tripal_feature/views/features/enable').'</li>';
     $output .= '</ul>';
   }
 

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

@@ -10,50 +10,50 @@ $terms = $feature->feature_cvterm;
 $s_terms = array();
 if ($terms) {
   foreach ($terms as $term) {
-    $s_terms[$term->cvterm_id->cv_id->name][] = $term;  
+    $s_terms[$term->cvterm_id->cv_id->name][] = $term;
   }
 }
 
 if (count($s_terms) > 0) { ?>
   <div class="tripal_feature-data-block-desc tripal-data-block-desc">The following terms have been associated with this <?php print $node->feature->type_id->name ?>:</div>  <?php
-  
+
   // iterate through each term
   $i = 0;
-  foreach ($s_terms as $cv => $terms) {  
+  foreach ($s_terms as $cv => $terms) {
     // the $headers array is an array of fields to use as the colum headers.
     // additional documentation can be found here
     // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
     $headers = array('Term', 'Definition');
-    
+
     // the $rows array contains an array of rows where each row is an array
     // of values for each column of the table in that row.  Additional documentation
     // can be found here:
     // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
     $rows = array();
 
-    foreach ($terms as $term) { 
+    foreach ($terms as $term) {
       $accession = $term->cvterm_id->dbxref_id->accession;
       if (is_numeric($term->cvterm_id->dbxref_id->accession)) {
         $accession = $term->cvterm_id->dbxref_id->db_id->name . ":" . $term->cvterm_id->dbxref_id->accession;
       }
       if ($term->cvterm_id->dbxref_id->db_id->urlprefix) {
         $accession = l($accession, $term->cvterm_id->dbxref_id->db_id->urlprefix . $accession, array('attributes' => array("target" => '_blank')));
-      } 
-      
+      }
+
       $rows[] = array(
         array('data' => $accession, 'width' => '15%'),
         $term->cvterm_id->name
       );
-    } 
-    
+    }
+
     // generate the link to configure a database, b ut only if the user is
     // a tripal administrator
     $configure_link = '';
     if (user_access('view ids')) {
       $db_id = $term->cvterm_id->dbxref_id->db_id->db_id;
-      $configure_link = l('[configure term links]', "admin/tripal/chado/tripal_db/edit/$db_id", array('attributes' => array("target" => '_blank')));
+      $configure_link = l('[configure term links]', "admin/tripal/legacy/tripal_db/edit/$db_id", array('attributes' => array("target" => '_blank')));
     }
-    
+
     // the $table array contains the headers and rows array as well as other
     // options for controlling the display of the table.  Additional
     // documentation can be found here:
@@ -70,7 +70,7 @@ if (count($s_terms) > 0) { ?>
       'colgroups' => array(),
       'empty' => '',
     );
-    
+
     // once we have our table array structure defined, we call Drupal's theme_table()
     // function to generate the table.
     print theme_table($table);

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

@@ -67,7 +67,7 @@ if (count($so_terms) > 0) {
     print tripal_set_message("Administrators, you can specify the feature types ".
       "that should appear in this browser or remove it from the list of resources ".
       "by navigating to the ".
-      l("Tripal feature settings page", "admin/tripal/chado/tripal_feature/configuration", array('attributes' => array('target' => '_blank'))),
+      l("Tripal feature settings page", "admin/tripal/legacy/tripal_feature/configuration", array('attributes' => array('target' => '_blank'))),
       TRIPAL_INFO,
       array('return_html' => 1)
     );

legacy/tripal_feature/tripal_feature.module

@@ -190,10 +190,10 @@ function tripal_feature_menu() {
   );
 
   // Enable admin view
-  $items['admin/tripal/chado/tripal_feature/views/features/enable'] = array(
+  $items['admin/tripal/legacy/tripal_feature/views/features/enable'] = array(
     'title' => 'Enable feature Administrative View',
     'page callback' => 'tripal_enable_view',
-    'page arguments' => array('tripal_feature_admin_features', 'admin/tripal/chado/tripal_feature'),
+    'page arguments' => array('tripal_feature_admin_features', 'admin/tripal/legacy/tripal_feature'),
     'access arguments' => array('administer tripal feature'),
     'type' => MENU_CALLBACK,
   );

legacy/tripal_feature/tripal_feature.views_default.inc

@@ -526,7 +526,7 @@ function tripal_feature_defaultview_admin_features() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_feature/features';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_feature/features';
   $handler->display->display_options['menu']['type'] = 'default tab';
   $handler->display->display_options['menu']['title'] = 'Features';
   $handler->display->display_options['menu']['description'] = 'A feature is a biological sequence or a section of a biological sequence, or a collection of such sections.';

legacy/tripal_featuremap/includes/tripal_featuremap.admin.inc

@@ -17,8 +17,8 @@ function tripal_featuremap_admin_featuremaps_listing() {
   $breadcrumb[] = l('Home', '<front>');
   $breadcrumb[] = l('Administration', 'admin');
   $breadcrumb[] = l('Tripal', 'admin/tripal');
-  $breadcrumb[] = l('Chado', 'admin/tripal/chado');
-  $breadcrumb[] = l('Maps', 'admin/tripal/chado/tripal_featuremap');
+  $breadcrumb[] = l('Chado', 'admin/tripal/legacy');
+  $breadcrumb[] = l('Maps', 'admin/tripal/legacy/tripal_featuremap');
   drupal_set_breadcrumb($breadcrumb);
 
   // Add the view
@@ -32,7 +32,7 @@ function tripal_featuremap_admin_featuremaps_listing() {
       . 'administrative interface are disabled. <strong>Click each of the following links to '
       . 'enable the pertinent views</strong>:</p>';
     $output .= '<ul>';
-      $output .= '<li>'.l('Feature Map Admin', 'admin/tripal/chado/tripal_featuremap/views/featuremaps/enable').'</li>';
+      $output .= '<li>'.l('Feature Map Admin', 'admin/tripal/legacy/tripal_featuremap/views/featuremaps/enable').'</li>';
     $output .= '</ul>';
   }
 

legacy/tripal_featuremap/tripal_featuremap.module

@@ -147,7 +147,7 @@ function tripal_featuremap_menu() {
   $items['admin/tripal/legacy/tripal_featuremap/views/featuremaps/enable'] = array(
     'title' => 'Enable featuremap Administrative View',
     'page callback' => 'tripal_enable_view',
-    'page arguments' => array('tripal_featuremap_admin_featuremaps', 'admin/tripal/chado/tripal_featuremap'),
+    'page arguments' => array('tripal_featuremap_admin_featuremaps', 'admin/tripal/legacy/tripal_featuremap'),
     'access arguments' => array('administer tripal featuremap'),
     'type' => MENU_CALLBACK,
   );

legacy/tripal_featuremap/tripal_featuremap.views_default.inc

@@ -253,7 +253,7 @@ function tripal_featuremap_defaultview_admin_featuremaps() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_featuremap/featuremaps';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_featuremap/featuremaps';
   $handler->display->display_options['menu']['type'] = 'default tab';
   $handler->display->display_options['menu']['title'] = 'Maps';
   $handler->display->display_options['menu']['description'] = 'A listing of chado feature maps.';

legacy/tripal_genetic/tripal_genetic.views_default.inc

@@ -180,7 +180,7 @@ function tripal_genetic_defaultviews_admin_genotypes() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_genetic/genotypes';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_genetic/genotypes';
   $handler->display->display_options['menu']['type'] = 'default tab';
   $handler->display->display_options['menu']['title'] = 'Genotypes';
   $handler->display->display_options['menu']['description'] = 'A genotype is defined by a collection of features, mutations, etc.';

legacy/tripal_library/includes/tripal_library.admin.inc

@@ -17,8 +17,8 @@ function tripal_library_admin_libraries_listing() {
   $breadcrumb[] = l('Home', '<front>');
   $breadcrumb[] = l('Administration', 'admin');
   $breadcrumb[] = l('Tripal', 'admin/tripal');
-  $breadcrumb[] = l('Chado', 'admin/tripal/chado');
-  $breadcrumb[] = l('Libraries', 'admin/tripal/chado/tripal_library');
+  $breadcrumb[] = l('Chado', 'admin/tripal/legacy');
+  $breadcrumb[] = l('Libraries', 'admin/tripal/legacy/tripal_library');
   drupal_set_breadcrumb($breadcrumb);
 
   // Add the view
@@ -32,7 +32,7 @@ function tripal_library_admin_libraries_listing() {
       . 'administrative interface are disabled. <strong>Click each of the following links to '
       . 'enable the pertinent views</strong>:</p>';
     $output .= '<ul>';
-      $output .= '<li>'.l('Library Admin', 'admin/tripal/chado/tripal_library/views/libraries/enable').'</li>';
+      $output .= '<li>'.l('Library Admin', 'admin/tripal/legacy/tripal_library/views/libraries/enable').'</li>';
     $output .= '</ul>';
   }
 

legacy/tripal_library/tripal_library.views_default.inc

@@ -282,7 +282,7 @@ function tripal_library_admin_defaultviews_library() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_library/libraries';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_library/libraries';
   $handler->display->display_options['menu']['type'] = 'default tab';
   $handler->display->display_options['menu']['title'] = 'Libraries';
   $handler->display->display_options['menu']['description'] = 'A library is a collection of features of a given type. For example, a cDNA or BAC clone library.';

legacy/tripal_natural_diversity/tripal_natural_diversity.module

@@ -70,7 +70,7 @@ function tripal_natural_diversity_menu() {
   $items['admin/tripal/legacy/tripal_natdiv/views/natdiv_exp/enable'] = array(
     'title' => 'Enable Natural Diversity Administrative View',
     'page callback' => 'tripal_enable_view',
-    'page arguments' => array('tripal_natural_diversity_admin_natdiv_exp', 'admin/tripal/chado/tripal_natdiv'),
+    'page arguments' => array('tripal_natural_diversity_admin_natdiv_exp', 'admin/tripal/legacy/tripal_natdiv'),
     'access arguments' => array('administer tripal nd'),
     'type' => MENU_CALLBACK,
   );

legacy/tripal_project/tripal_project.module

@@ -94,7 +94,7 @@ function tripal_project_menu() {
   $items['admin/tripal/legacy/tripal_project/views/projects/enable'] = array(
     'title' => 'Enable Project Administrative View',
     'page callback' => 'tripal_enable_view',
-    'page arguments' => array('tripal_project_admin_projects', 'admin/tripal/chado/tripal_project'),
+    'page arguments' => array('tripal_project_admin_projects', 'admin/tripal/legacy/tripal_project'),
     'access arguments' => array('administer tripal project'),
     'type' => MENU_CALLBACK,
   );

legacy/tripal_pub/tripal_pub.module

@@ -329,10 +329,10 @@ function tripal_pub_form_alter(&$form, &$form_state, $form_id) {
     // the form to the ahah callback URL. We need to set it back
     // to the normal form URL
     if (array_key_exists('values', $form_state) and $form_state['values']['action'] == 'edit') {
-      $form['#action'] = url("admin/tripal/chado/tripal_pub/import/edit/" . $form_state['values']['pub_import_id']);
+      $form['#action'] = url("admin/tripal/legacy/tripal_pub/import/edit/" . $form_state['values']['pub_import_id']);
     }
     if (array_key_exists('values', $form_state) and $form_state['values']['action'] == 'new') {
-      $form['#action'] = url("admin/tripal/chado/tripal_pub/import/new");
+      $form['#action'] = url("admin/tripal/legacy/tripal_pub/import/new");
     }
     */
   }

legacy/tripal_stock/tripal_stock.views_default.inc

@@ -299,7 +299,7 @@ function tripal_stock_defaultview_admin_stocks() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_stock/stocks';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/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';

tripal_chado/includes/fields/chado_base__dbxref_id.inc

@@ -299,7 +299,7 @@ class chado_base__dbxref_id extends TripalField {
     );
     $widget['links'] = array(
       '#type' => 'item',
-      '#markup' => l('Add a new database', 'admin/tripal/chado/tripal_db/add', array('attributes' => array('target' => '_blank')))
+      '#markup' => l('Add a new database', 'admin/tripal/legacy/tripal_db/add', array('attributes' => array('target' => '_blank')))
     );
   }
 

tripal_chado/includes/fields/chado_linker__dbxref.inc

@@ -322,7 +322,7 @@ class chado_linker__dbxref extends TripalField {
     if (!$db_id) {
       $widget['links'] = array(
         '#type' => 'item',
-        '#markup' => l('Add a database', 'admin/tripal/chado/tripal_db/add', array('attributes' => array('target' => '_blank')))
+        '#markup' => l('Add a database', 'admin/tripal/legacy/tripal_db/add', array('attributes' => array('target' => '_blank')))
       );
     }
   }

tripal_chado/includes/loaders/tripal_chado.pub_importers.inc

@@ -115,7 +115,7 @@ function tripal_pub_importer_setup_page($action = 'new', $pub_import_id = NULL)
   }
 
   if(!extension_loaded ('yaz')){
-    drupal_set_message(t('<b>Note:</b> In order to create an importer using the USDA National Agricultural Library (AGL) you must install the yaz libraries. See the ') . l(t('Pub Module help page'), 'admin/tripal/chado/tripal_pub/help') . ' for assistance.  If you do not want to use AGL you can ignore this warning.', 'warning');
+    drupal_set_message(t('<b>Note:</b> In order to create an importer using the USDA National Agricultural Library (AGL) you must install the yaz libraries. See the ') . l(t('Pub Module help page'), 'admin/tripal/legacy/tripal_pub/help') . ' for assistance.  If you do not want to use AGL you can ignore this warning.', 'warning');
   }
 
   // generate the search form