Moved tripal_cv_defaults to legacy... can move back if needed

legacy/tripal_analysis/includes/tripal_analysis.admin.inc

@@ -20,8 +20,8 @@ function tripal_analysis_admin_analysis_view() {
   $breadcrumb[] = l('Home', '<front>');
   $breadcrumb[] = l('Administration', 'admin');
   $breadcrumb[] = l('Tripal', 'admin/tripal');
-  $breadcrumb[] = l('Chado', 'admin/tripal/chado');
-  $breadcrumb[] = l('Analysis', 'admin/tripal/chado/tripal_analysis');
+  $breadcrumb[] = l('Chado', 'admin/tripal/legacy');
+  $breadcrumb[] = l('Analysis', 'admin/tripal/legacy/tripal_analysis');
   drupal_set_breadcrumb($breadcrumb);
 
   // Add the view
@@ -35,7 +35,7 @@ function tripal_analysis_admin_analysis_view() {
       . 'administrative interface are disabled. <strong>Click each of the following links to '
       . 'enable the pertinent views</strong>:</p>';
     $output .= '<ul>';
-      $output .= '<li>'.l('Analysis View', 'admin/tripal/chado/tripal_analysis/views/analyses/enable').'</li>';
+      $output .= '<li>'.l('Analysis View', 'admin/tripal/legacy/tripal_analysis/views/analyses/enable').'</li>';
     $output .= '</ul>';
   }
 

legacy/tripal_analysis/tripal_analysis.info

@@ -4,7 +4,7 @@ core = 7.x
 project = tripal
 package = Tripal v2 Legacy
 version = 7.x-3.0-alpha1
-configure = admin/tripal/chado/tripal_analysis/configuration
+configure = admin/tripal/legacy/tripal_analysis/configuration
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

legacy/tripal_analysis/tripal_analysis.module

@@ -42,8 +42,8 @@ function tripal_analysis_init() {
 function tripal_analysis_menu() {
   $items = array();
   // Tripal Analysis administrative settings
-  /*
-  $items['admin/tripal/chado/tripal_analysis'] = array(
+
+  $items['admin/tripal/legacy/tripal_analysis'] = array(
     'title' => 'Analyses',
     'description' => 'A bioinformatics analysis producing features.',
     'page callback' => 'tripal_analysis_admin_analysis_view',
@@ -51,7 +51,7 @@ function tripal_analysis_menu() {
     'type' => MENU_NORMAL_ITEM,
   );
 
-  $items['admin/tripal/chado/tripal_analysis/help'] = array(
+  $items['admin/tripal/legacy/tripal_analysis/help'] = array(
     'title' => 'Help',
     'description' => "A description of the Tripal Analysis module including a short description of it's usage.",
     'page callback' => 'theme',
@@ -61,7 +61,7 @@ function tripal_analysis_menu() {
     'weight' => 10,
   );
 
-  $items['admin/tripal/chado/tripal_analysis/configuration'] = array(
+  $items['admin/tripal/legacy/tripal_analysis/configuration'] = array(
     'title' => 'Settings',
     'description' => 'Settings for the displays of analysis results.',
     'page callback' => 'drupal_get_form',
@@ -71,7 +71,7 @@ function tripal_analysis_menu() {
     'weight' => 5
   );
 
-  $items['admin/tripal/chado/tripal_analysis/sync'] = array(
+  $items['admin/tripal/legacy/tripal_analysis/sync'] = array(
     'title' => ' Sync',
     'description' => 'Create pages on this site for analyses stored in Chado',
     'page callback' => 'drupal_get_form',
@@ -80,7 +80,7 @@ function tripal_analysis_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 1
   );
-  $items['admin/tripal/chado/tripal_analysis/delete'] = array(
+  $items['admin/tripal/legacy/tripal_analysis/delete'] = array(
       'title' => ' Delete',
       'description' => 'Delete multiple analyses from Chado',
       'page callback' => 'drupal_get_form',
@@ -91,7 +91,7 @@ function tripal_analysis_menu() {
       'file' =>  'includes/tripal_analysis.delete.inc',
       'weight' => 2
   );
-  $items['admin/tripal/chado/tripal_analysis/chado_analysis_toc'] = array(
+  $items['admin/tripal/legacy/tripal_analysis/chado_analysis_toc'] = array(
     'title' => ' TOC',
     'description' => 'Manage the table of contents for analysis nodes.',
     'page callback' => 'drupal_get_form',
@@ -102,7 +102,7 @@ function tripal_analysis_menu() {
     'file path' => drupal_get_path('module', 'tripal_core'),
     'weight' => 3
   );
-  */
+
   return $items;
 }
 
@@ -242,7 +242,7 @@ function tripal_analysis_form_alter(&$form, &$form_state, $form_id) {
   // turn of preview button for insert/updates
   if ($form_id == "chado_analysis_node_form") {
     $form['actions']['preview']['#access'] = FALSE;
-    
+
     //remove the body field
     unset($form['body']);
   }

legacy/tripal_analysis/tripal_analysis.views_default.inc

@@ -263,7 +263,7 @@ function tripal_analysis_defaultvalue_admin_analysis() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_analysis/analysis';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_analysis/analysis';
   $handler->display->display_options['menu']['type'] = 'default tab';
   $handler->display->display_options['menu']['title'] = 'Analyses';
   $handler->display->display_options['menu']['weight'] = '-10';

legacy/tripal_contact/includes/tripal_contact.admin.inc

@@ -20,8 +20,8 @@ function tripal_contact_admin_contact_view() {
   $breadcrumb[] = l('Home', '<front>');
   $breadcrumb[] = l('Administration', 'admin');
   $breadcrumb[] = l('Tripal', 'admin/tripal');
-  $breadcrumb[] = l('Chado', 'admin/tripal/chado');
-  $breadcrumb[] = l('Contacts', 'admin/tripal/chado/tripal_contact');
+  $breadcrumb[] = l('Chado', 'admin/tripal/legacy');
+  $breadcrumb[] = l('Contacts', 'admin/tripal/legacy/tripal_contact');
   drupal_set_breadcrumb($breadcrumb);
 
   // Add the view
@@ -35,7 +35,7 @@ function tripal_contact_admin_contact_view() {
       . 'administrative interface are disabled. <strong>Click each of the following links to '
       . 'enable the pertinent views</strong>:</p>';
     $output .= '<ul>';
-      $output .= '<li>'.l('Contacts View', 'admin/tripal/chado/tripal_contact/views/contacts/enable').'</li>';
+      $output .= '<li>'.l('Contacts View', 'admin/tripal/legacy/tripal_contact/views/contacts/enable').'</li>';
     $output .= '</ul>';
   }
 

legacy/tripal_contact/tripal_contact.module

@@ -49,8 +49,8 @@ function tripal_contact_views_api() {
 function tripal_contact_menu() {
 
   $items = array();
-  /*
-  $items['admin/tripal/chado/tripal_contact']= array(
+
+  $items['admin/tripal/legacy/tripal_contact']= array(
     'title' => 'Contacts',
     'description' => ('Model persons, institutes, groups, organizations, etc.'),
     'page callback' => 'tripal_contact_admin_contact_view',
@@ -58,7 +58,7 @@ function tripal_contact_menu() {
     'type' => MENU_NORMAL_ITEM
   );
 
-  $items['admin/tripal/chado/tripal_contact/configuration'] = array(
+  $items['admin/tripal/legacy/tripal_contact/configuration'] = array(
     'title' => 'Settings',
     'description' => 'Integration of Chado contacts.',
     'page callback' => 'drupal_get_form',
@@ -68,7 +68,7 @@ function tripal_contact_menu() {
     'weight' => 5
   );
 
-  $items['admin/tripal/chado/tripal_contact/help']= array(
+  $items['admin/tripal/legacy/tripal_contact/help']= array(
     'title' => 'Help',
     'description' => ('Help with the contact module.'),
     'page callback' => 'theme',
@@ -78,7 +78,7 @@ function tripal_contact_menu() {
     'weight' => 10
   );
 
-  $items['admin/tripal/chado/tripal_contact/sync'] = array(
+  $items['admin/tripal/legacy/tripal_contact/sync'] = array(
     'title' => ' Sync',
     'description' => 'Sync contacts in Chado with Drupal',
     'page callback' => 'drupal_get_form',
@@ -89,7 +89,7 @@ function tripal_contact_menu() {
     'weight' => 0
   );
 
-  $items['admin/tripal/chado/tripal_contact/chado_contact_toc'] = array(
+  $items['admin/tripal/legacy/tripal_contact/chado_contact_toc'] = array(
     'title' => ' TOC',
     'description' => 'Manage the table of contents for contact nodes.',
     'page callback' => 'drupal_get_form',
@@ -101,13 +101,13 @@ function tripal_contact_menu() {
     'weight' => 3
   );
 
-  $items['admin/tripal/chado/tripal_contact/contact/auto_name/%'] = array(
+  $items['admin/tripal/legacy/tripal_contact/contact/auto_name/%'] = array(
     'page callback' => 'tripal_autocomplete_contact',
     'page arguments' => array(6),
     'access arguments' => array('administer tripal contact'),
     'type' => MENU_CALLBACK,
   );
-  */
+
   return $items;
 }
 

legacy/tripal_contact/tripal_contact.views_default.inc

@@ -270,7 +270,7 @@ function tripal_contact_defaultview_admin_contacts() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_contact/contacts';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_contact/contacts';
   $handler->display->display_options['menu']['type'] = 'default tab';
   $handler->display->display_options['menu']['title'] = 'Contacts';
   $handler->display->display_options['menu']['description'] = 'Contacts can be persons, institutes, groups, or organizations.';

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

@@ -354,9 +354,9 @@ function chado_add_node_form_subtable_ajax_update($form, &$form_state) {
     // the base specified in hook_node_info
     $node_type = 'chado_example';
 
-    // This menu item will be a tab on the admin/tripal/chado/tripal_example page
+    // This menu item will be a tab on the admin/tripal/legacy/tripal_example page
     // that is not selected by default
-    $items['admin/tripal/chado/tripal_example/sync'] = array(
+    $items['admin/tripal/legacy/tripal_example/sync'] = array(
       'title' => ' Sync',
       'description' => 'Sync examples from Chado with Drupal',
       'page callback' => 'drupal_get_form',

legacy/tripal_core/api/tripal_core.chado_nodes.dbxrefs.api.inc

@@ -142,7 +142,7 @@ function chado_add_node_form_dbxrefs(&$form, &$form_state, $details) {
       $db_options[$db->db_id] = $db->name;
     }
   }
-  
+
   // Determine the node type using the name of the foreign key.
   $details['nodetype'] = str_replace('_id', '', $details['base_foreign_key']);
 
@@ -152,7 +152,7 @@ function chado_add_node_form_dbxrefs(&$form, &$form_state, $details) {
     t('To add databases to the drop down list, you need to <a href="@dblink">add
       an external database reference</a>.',
       array(
-        '@dblink' => url('admin/tripal/chado/tripal_db/add')
+        '@dblink' => url('admin/tripal/legacy/tripal_db/add')
       )
     ),
     $importance,
@@ -170,18 +170,18 @@ function chado_add_node_form_dbxrefs(&$form, &$form_state, $details) {
   );
 
   // the fieldset of the dbxref elements
-  $instructions = 'To add an external reference, select the database you want to reference from the 
-    drop-down below. Then enter the name/accession (as it is shown in the external database) of this 
-    particular %nodetype into the text box before clicking "Add". The version can be used to 
-    indicate the version of the external database or the version of the reference 
-    depending upon what is available. To remove incorrect references, click the 
-    "Remove" button. Note: you cannot edit previously added references but instead 
+  $instructions = 'To add an external reference, select the database you want to reference from the
+    drop-down below. Then enter the name/accession (as it is shown in the external database) of this
+    particular %nodetype into the text box before clicking "Add". The version can be used to
+    indicate the version of the external database or the version of the reference
+    depending upon what is available. To remove incorrect references, click the
+    "Remove" button. Note: you cannot edit previously added references but instead
     need to remove and re-add them.';
   $form['addtl_dbxrefs'] = array(
     '#type' => 'fieldset',
     '#title' => t($details['fieldset_title']),
-    '#description' => t('<p><strong>Indicate that this %nodetype either originates from 
-      or is present in another database.</strong></p><p>'. $instructions . $details['additional_instructions'] . '</p>', 
+    '#description' => t('<p><strong>Indicate that this %nodetype either originates from
+      or is present in another database.</strong></p><p>'. $instructions . $details['additional_instructions'] . '</p>',
       array('%nodetype' => $details['nodetype'])),
     '#collapsible' => TRUE,
     '#collapsed' => TRUE,
@@ -235,11 +235,11 @@ function chado_add_node_form_dbxrefs(&$form, &$form_state, $details) {
   else {
     $existing_dbxrefs = chado_query(
       "SELECT
-         db.name as db_name, 
+         db.name as db_name,
          db.db_id as db_id,
-         dbxref.dbxref_id, 
+         dbxref.dbxref_id,
          dbxref.accession as accession,
-         dbxref.description as description, 
+         dbxref.description as description,
          dbxref.version
        FROM {dbxref} dbxref
          LEFT JOIN {db} db ON db.db_id = dbxref.db_id
@@ -441,7 +441,7 @@ function chado_add_node_form_dbxrefs(&$form, &$form_state, $details) {
  * @ingroup tripal_core
  */
 function chado_add_node_form_dbxrefs_add_button_validate($form, &$form_state) {
-  
+
   // Ensure the db_id is supplied & Valid
   $db = chado_select_record(
     'db',

legacy/tripal_core/includes/tripal_core.toc.inc

@@ -19,7 +19,7 @@ function tripal_core_node_toc_form($form, &$form_state, $node) {
   );
   $admin_link = l(
     $type_info->name . " TOC administrative page",
-    "admin/tripal/chado/" . $type_info->module . "/" . $node->type . "toc",
+    "admin/tripal/legacy/" . $type_info->module . "/" . $node->type . "toc",
     array('attributes' => array('target' => '_blank'))
   );
   $form["instructions"]["main"] = array(

legacy/tripal_core/tripal_core.module

@@ -49,6 +49,17 @@ function tripal_core_init() {
 function tripal_core_menu() {
   $items = array();
 
+  // Triapl setting groups
+  $items['admin/tripal/legacy'] = array(
+    'title' => 'Tripal Legacy',
+    'description' => t("Legacy functionality from Tripal v2.0."),
+    'weight' => -8,
+    'page callback' => 'system_admin_menu_block_page',
+    'access arguments' => array('administer tripal'),
+    'file' => 'system.admin.inc',
+    'file path' => drupal_get_path('module', 'system'),
+  );
+
   // Relationshi API autocomplete callback
   $items['tripal_ajax/relationship_nodeform/%/%/name_to_id'] = array(
     'page callback' => 'chado_add_node_form_relationships_name_to_id_callback',

tripal_chado/includes/tripal_chado.cv_defaults.inc → legacy/tripal_cv/includes/tripal_cv.cv_defaults.inc

@@ -2,9 +2,9 @@
 /**
  * Provide landing page to the new admin pages
  *
- * @ingroup tripal_chado
+ * @ingroup tripal_cv
  */
-function tripal_chado_admin_cv_listing() {
+function tripal_cv_admin_cv_listing() {
   $output = '';
 
   // set the breadcrumb
@@ -12,13 +12,13 @@ function tripal_chado_admin_cv_listing() {
   $breadcrumb[] = l('Home', '<front>');
   $breadcrumb[] = l('Administration', 'admin');
   $breadcrumb[] = l('Tripal', 'admin/tripal');
-  $breadcrumb[] = l('Chado Modules', 'admin/tripal/chado');
-  $breadcrumb[] = l('Vocabularies', 'admin/tripal/vocab');
+  $breadcrumb[] = l('Chado Modules', 'admin/tripal/legacy');
+  $breadcrumb[] = l('Vocabularies', 'admin/tripal/legacy/vocab');
   drupal_set_breadcrumb($breadcrumb);
 
   // Add the view
-  $cvs_view = views_embed_view('tripal_chado_admin_cvs','default');
-  $cvterms_view = views_embed_view('tripal_chado_admin_cvterms','default');
+  $cvs_view = views_embed_view('tripal_cv_admin_cvs','default');
+  $cvterms_view = views_embed_view('tripal_cv_admin_cvterms','default');
   if (isset($cvs_view) && isset($cvterms_view)) {
     $output .= $cvs_view;
   }
@@ -43,7 +43,7 @@ function tripal_chado_admin_cv_listing() {
 /**
  *
  */
-function tripal_chado_admin_set_defaults_form($form, &$form_state) {
+function tripal_cv_admin_set_defaults_form($form, &$form_state) {
 
   $form['instructions'] = array(
     '#markup' => t('Much of the data housed in Chado is typed, meaning that a ' .
@@ -194,7 +194,7 @@ function tripal_chado_admin_set_defaults_form($form, &$form_state) {
     '#options' => $chado_tables,
     '#default_value' => 0,
     '#ajax' => array(
-      'callback' => 'tripal_chado_admin_ajax_new_default_field_callback',
+      'callback' => 'tripal_cv_admin_ajax_new_default_field_callback',
       'wrapper' => 'new-default',
     )
   );
@@ -235,7 +235,7 @@ function tripal_chado_admin_set_defaults_form($form, &$form_state) {
   return $form;
 }
 
-function tripal_chado_admin_set_defaults_form_submit($form, $form_state) {
+function tripal_cv_admin_set_defaults_form_submit($form, $form_state) {
 
   if ($form_state['triggering_element']['#value'] == 'Update Defaults') {
     foreach ($form_state['values']['settings']['existing'] as $default_cv) {
@@ -262,7 +262,7 @@ function tripal_chado_admin_set_defaults_form_submit($form, $form_state) {
   }
 }
 
-function tripal_chado_admin_ajax_new_default_field_callback($form, $form_state) {
+function tripal_cv_admin_ajax_new_default_field_callback($form, $form_state) {
   return $form['new'];
 }
 
@@ -270,7 +270,7 @@ function tripal_chado_admin_ajax_new_default_field_callback($form, $form_state)
  *
  * @param unknown $variables
  */
-function theme_tripal_chado_admin_set_defaults_form($variables) {
+function theme_tripal_cv_admin_set_defaults_form($variables) {
   $element = $variables['element'];
 
   $header = array(

legacy/tripal_cv/tripal_cv.module

@@ -15,9 +15,10 @@
  */
 
 require_once 'api/tripal_cv.DEPRECATED.inc';
-
+require_once 'api/tripal_cv.api.inc';
 require_once 'includes/tripal_cv.admin.inc';
 require_once 'includes/tripal_cv.cv_form.inc';
+require_once 'includes/tripal_cv.cv_defaults.inc';
 require_once 'includes/tripal_cv.cvterm_form.inc';
 require_once 'includes/tripal_cv.cvtermpath_form.inc';
 
@@ -40,7 +41,7 @@ function tripal_cv_init() {
 function tripal_cv_menu() {
   $items = array();
 
- /*  $items['admin/tripal/vocab'] = array(
+   $items['admin/tripal/legacy/vocab'] = array(
     'title' => 'Controlled Vocabularies',
     'description' => 'Controlled Vocabularies control the types available for entities and fields.',
     'page callback' => 'tripal_cv_admin_cv_listing',
@@ -50,7 +51,7 @@ function tripal_cv_menu() {
   );
 
 
-  $items['admin/tripal/vocab/help'] = array(
+  $items['admin/tripal/legacy/vocab/help'] = array(
     'title' => 'Help',
     'description' => "A description of the Tripal Controlled Vocabulary module including a short description of it's usage.",
     'page callback' => 'theme',
@@ -60,7 +61,7 @@ function tripal_cv_menu() {
     'weight' => 10
   );
 
-  $items['admin/tripal/vocab/cvtermpath'] = array(
+  $items['admin/tripal/legacy/vocab/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',
     'page callback' => 'drupal_get_form',
@@ -69,7 +70,7 @@ function tripal_cv_menu() {
     'type' => MENU_CALLBACK,
   );
 
-  $items['admin/tripal/vocab/cv/edit/%'] = array(
+  $items['admin/tripal/legacy/vocab/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',
@@ -79,7 +80,7 @@ function tripal_cv_menu() {
     'type' => MENU_CALLBACK,
   );
 
-  $items['admin/tripal/vocab/cv/add'] = array(
+  $items['admin/tripal/legacy/vocab/cv/add'] = array(
     'title' => 'Add a Controlled Vocabulary',
     'description' => 'Manually a new controlled vocabulary.',
     'page callback' => 'drupal_get_form',
@@ -89,7 +90,7 @@ function tripal_cv_menu() {
     'type' => MENU_CALLBACK,
   );
 
-  $items['admin/tripal/vocab/cv/%/cvterm/add'] = array(
+  $items['admin/tripal/legacy/vocab/cv/%/cvterm/add'] = array(
     'title' => 'Add a Controlled Vocabulary Term',
     'description' => 'Add a new controlled vocabulary term.',
     'page callback' => 'drupal_get_form',
@@ -97,7 +98,7 @@ function tripal_cv_menu() {
     'access arguments' => array('administer controlled vocabularies'),
     'type' => MENU_CALLBACK,
   );
-  $items['admin/tripal/vocab/cvterm/add'] = array(
+  $items['admin/tripal/legacy/vocab/cvterm/add'] = array(
     'title' => 'Add a Controlled Vocabulary Term',
     'description' => 'Add a new controlled vocabulary term.',
     'page callback' => 'drupal_get_form',
@@ -105,7 +106,7 @@ function tripal_cv_menu() {
     'access arguments' => array('administer controlled vocabularies'),
     'type' => MENU_CALLBACK,
   );
-  $items['admin/tripal/vocab/cv/%/cvterm/edit/%'] = array(
+  $items['admin/tripal/legacy/vocab/cv/%/cvterm/edit/%'] = array(
     'title' => 'Edit a Controlled Vocabulary Term',
     'description' => 'Edit an existing controlled vocabulary term.',
     'page callback' => 'drupal_get_form',
@@ -113,28 +114,37 @@ function tripal_cv_menu() {
     'access arguments' => array('administer controlled vocabularies'),
     'type' => MENU_CALLBACK,
   );
-  $items['admin/tripal/vocab/cvterm/auto_name/%/%'] = array(
+  $items['admin/tripal/legacy/vocab/cvterm/auto_name/%/%'] = array(
     'page callback' => 'tripal_cv_cvterm_name_autocomplete',
     'page arguments' => array(6, 7),
     'access arguments' => array('administer controlled vocabularies'),
     'type' => MENU_CALLBACK,
   );
 
-  $items['admin/tripal/vocab/views/cvs/enable'] = array(
+  $items['admin/tripal/legacy/vocab/views/cvs/enable'] = array(
     'title' => 'Enable Vocabulary Administrative View',
     'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_cv_admin_cvs', 'admin/tripal/vocab'),
     'access arguments' => array('administer controlled vocabularies'),
     'type' => MENU_CALLBACK,
   );
-  $items['admin/tripal/vocab/views/cvterms/enable'] = array(
+  $items['admin/tripal/legacy/vocab/views/cvterms/enable'] = array(
     'title' => 'Enable Vocabulary Terms Administrative View',
     'page callback' => 'tripal_enable_view',
     'page arguments' => array('tripal_cv_admin_cvterms', 'admin/tripal/vocab'),
     'access arguments' => array('administer controlled vocabularies'),
     'type' => MENU_CALLBACK,
   );
- */
+
+  $items['admin/tripal/legacy/chado/tripal_cv/defaults'] = array(
+    'title' => 'Defaults',
+    'description' => 'Set the default vocabularies for properties and relationships.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_cv_admin_set_defaults_form'),
+    'access arguments' => array('administer controlled vocabularies'),
+    'type' => MENU_LOCAL_TASK,
+    'weight' => 5
+  );
 
   $items['tripal_cv_chart'] = array(
     'path' => 'tripal_cv_chart',
@@ -274,6 +284,10 @@ function tripal_cv_theme($existing, $type, $theme, $path) {
       'variables' =>  array(NULL),
       'path' => "$path/theme/templates"
     ),
+   'tripal_cv_admin_set_defaults_form' => array(
+     'function' => 'theme_tripal_cv_admin_set_defaults_form',
+     'render element' => 'element',
+   ),
   );
 
   return $items;

legacy/tripal_db/tripal_db.info

@@ -4,7 +4,7 @@ core = 7.x
 project = tripal
 package = Tripal v2 Legacy
 version = 7.x-3.0-alpha1
-configure = admin/tripal/chado/tripal_db
+configure = admin/tripal/legacy/tripal_db
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

legacy/tripal_db/tripal_db.module

@@ -29,8 +29,8 @@ require_once 'includes/tripal_db.admin.inc';
 function tripal_db_menu() {
   $items = array();
 
-  /*
-  $items['admin/tripal/chado/tripal_db'] = array(
+
+  $items['admin/tripal/legacy/tripal_db'] = array(
     'title' => 'Databases',
     'description' => 'References to External Database sites such as NCBI',
     'page callback' => 'tripal_db_admin_db_listing',
@@ -38,7 +38,7 @@ function tripal_db_menu() {
     'type' => MENU_NORMAL_ITEM,
   );
 
-  $items['admin/tripal/chado/tripal_db/help'] = array(
+  $items['admin/tripal/legacy/tripal_db/help'] = array(
     'title' => 'Help',
     'description' => "A description of the Tripal Database module including a short description of it's usage.",
     'page callback' => 'theme',
@@ -48,7 +48,7 @@ function tripal_db_menu() {
     'weight' => 10
   );
 
-  $items['admin/tripal/chado/tripal_db/edit/%'] = array(
+  $items['admin/tripal/legacy/tripal_db/edit/%'] = array(
     'title' => 'Edit a Database Reference',
     'description' => 'Edit existing Database References.',
     'page callback' => 'drupal_get_form',
@@ -58,7 +58,7 @@ function tripal_db_menu() {
     'type' => MENU_CALLBACK,
   );
 
-  $items['admin/tripal/chado/tripal_db/add'] = array(
+  $items['admin/tripal/legacy/tripal_db/add'] = array(
     'title' => 'Create a Database Reference',
     'description' => 'Create a new reference to an External Database.',
     'page callback' => 'drupal_get_form',
@@ -68,27 +68,27 @@ function tripal_db_menu() {
     'type' => MENU_CALLBACK,
   );
 
-  $items['admin/tripal/chado/tripal_db/views/dbs/enable'] = array(
+  $items['admin/tripal/legacy/tripal_db/views/dbs/enable'] = array(
     'title' => 'Enable Database Administrative View',
     'page callback' => 'tripal_enable_view',
-    'page arguments' => array('tripal_db_admin_dbs', 'admin/tripal/chado/tripal_db'),
+    'page arguments' => array('tripal_db_admin_dbs', 'admin/tripal/legacy/tripal_db'),
     'access arguments' => array('administer db cross-references'),
     'type' => MENU_CALLBACK,
   );
-  $items['admin/tripal/chado/tripal_db/views/dbxrefs/enable'] = array(
+  $items['admin/tripal/legacy/tripal_db/views/dbxrefs/enable'] = array(
     'title' => 'Enable Reference Administrative View',
     'page callback' => 'tripal_enable_view',
-    'page arguments' => array('tripal_db_admin_dbxrefs', 'admin/tripal/chado/tripal_db'),
+    'page arguments' => array('tripal_db_admin_dbxrefs', 'admin/tripal/legacy/tripal_db'),
     'access arguments' => array('administer db cross-references'),
     'type' => MENU_CALLBACK,
   );
-  $items['admin/tripal/chado/tripal_db/dbxref/auto_name/%/%'] = array(
+  $items['admin/tripal/legacy/tripal_db/dbxref/auto_name/%/%'] = array(
     'page callback' => 'tripal_db_dbxref_accession_autocomplete',
     'page arguments' => array(6, 7),
     'access arguments' => array('administer db cross-references'),
     'type' => MENU_CALLBACK,
   );
- */
+
   return $items;
 }
 

legacy/tripal_db/tripal_db.views_default.inc

@@ -94,7 +94,7 @@ function tripal_db_defaultview_admin_db_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 Database',
-    'path-1' => 'admin/tripal/chado/tripal_db/add',
+    'path-1' => 'admin/tripal/legacy/tripal_db/add',
   );
   /* No results behavior: Global: Text area */
   $handler->display->display_options['empty']['text']['id'] = 'area';
@@ -139,7 +139,7 @@ function tripal_db_defaultview_admin_db_listing() {
   $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/chado/tripal_db/edit/[db_id]';
+  $handler->display->display_options['fields']['nothing']['alter']['path'] = 'admin/tripal/legacy/tripal_db/edit/[db_id]';
   /* Field: Global: Custom text */
   $handler->display->display_options['fields']['nothing_1']['id'] = 'nothing_1';
   $handler->display->display_options['fields']['nothing_1']['table'] = 'views';
@@ -148,7 +148,7 @@ function tripal_db_defaultview_admin_db_listing() {
   $handler->display->display_options['fields']['nothing_1']['exclude'] = TRUE;
   $handler->display->display_options['fields']['nothing_1']['alter']['text'] = 'References';
   $handler->display->display_options['fields']['nothing_1']['alter']['make_link'] = TRUE;
-  $handler->display->display_options['fields']['nothing_1']['alter']['path'] = 'admin/tripal/chado/tripal_db/dbxrefs?db_name=[name]';
+  $handler->display->display_options['fields']['nothing_1']['alter']['path'] = 'admin/tripal/legacy/tripal_db/dbxrefs?db_name=[name]';
   /* Field: Global: Custom text */
   $handler->display->display_options['fields']['nothing_2']['id'] = 'nothing_2';
   $handler->display->display_options['fields']['nothing_2']['table'] = 'views';
@@ -196,7 +196,7 @@ function tripal_db_defaultview_admin_db_listing() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_db/dbs';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_db/dbs';
   $handler->display->display_options['menu']['type'] = 'default tab';
   $handler->display->display_options['menu']['title'] = 'Databases';
   $handler->display->display_options['menu']['description'] = 'Lists all databases available to create database references for.';
@@ -378,7 +378,7 @@ function tripal_db_defaultview_admin_dbxref_listing() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_db/dbxrefs';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_db/dbxrefs';
   $handler->display->display_options['menu']['type'] = 'tab';
   $handler->display->display_options['menu']['title'] = 'References';
   $handler->display->display_options['menu']['weight'] = '0';

legacy/tripal_example/includes/tripal_example.admin.inc

@@ -13,8 +13,8 @@ function tripal_example_admin_examples_listing() {
   $breadcrumb[] = l('Home', '<front>');
   $breadcrumb[] = l('Administration', 'admin');
   $breadcrumb[] = l('Tripal', 'admin/tripal');
-  $breadcrumb[] = l('Chado', 'admin/tripal/chado');
-  $breadcrumb[] = l('Examples', 'admin/tripal/chado/tripal_example');
+  $breadcrumb[] = l('Chado', 'admin/tripal/legacy');
+  $breadcrumb[] = l('Examples', 'admin/tripal/legacy/tripal_example');
   drupal_set_breadcrumb($breadcrumb);
 
 
@@ -33,7 +33,7 @@ function tripal_example_admin_examples_listing() {
       . 'administrative interface are disabled. <strong>Click each of the following links to '
       . 'enable the pertinent views</strong>:</p>';
     $output .= '<ul>';
-      $output .= '<li>'.l('Example Admin', 'admin/tripal/chado/tripal_example/views/examples/enable').'</li>';
+      $output .= '<li>'.l('Example Admin', 'admin/tripal/legacy/tripal_example/views/examples/enable').'</li>';
     $output .= '</ul>';
   }
   */

legacy/tripal_example/tripal_example.module

@@ -158,11 +158,11 @@ function tripal_example_menu() {
   // This menu will provide a form similar to the one found on the node that
   // allows the user to set global TOC settings for the content type. Be sure to
   // always use a menu path of the form:
-  //   admin/tripal/chado/[module name]/[content type name]_toc
+  //   admin/tripal/legacy/[module name]/[content type name]_toc
   // this allows for a module to support TOC management when there are multiple
   // content types provided by the module, as the content type is specified
   // in the menu path.
-  $items['admin/tripal/chado/tripal_example/chado_example_toc'] = array(
+  $items['admin/tripal/legacy/tripal_example/chado_example_toc'] = array(
     'title' => ' TOC',
     'description' => 'Manage the table of contents for example nodes.',
     'page callback' => 'drupal_get_form',

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

@@ -12,15 +12,15 @@ if(property_exists($organism, 'feature_counts')) {
 
 // let admins know they can customize the terms that appear in the list
 print tripal_set_message("
-  Administrators, you can customize the types of terms that appear in this report by navigating to the " . 
-  l('Tripal feature configuration page', 'admin/tripal/chado/tripal_feature/configuration', array('attributes' => array('target' => '_blank'))) . "
+  Administrators, you can customize the types of terms that appear in this report by navigating to the " .
+  l('Tripal feature configuration page', 'admin/tripal/legacy/tripal_feature/configuration', array('attributes' => array('target' => '_blank'))) . "
   opening the section \"Feature Summary Report\" and adding the list of
   terms you want to appear in the list. You can rename terms as well. To refresh the data,re-populate the " .
-  l('organism_feature_count', 'admin/tripal/storage/chado/mviews', array('attributes' => array('target' => '_blank'))) . " 
+  l('organism_feature_count', 'admin/tripal/storage/legacy/mviews', array('attributes' => array('target' => '_blank'))) . "
   materialized view.",
   TRIPAL_INFO,
   array('return_html' => 1)
-); 
+);
 
 // the $headers array is an array of fields to use as the colum headers.
 // additional documentation can be found here
@@ -36,12 +36,12 @@ $rows = array();
 for ($j = 0; $j < count($types); $j++) {
   $type = $types[$j];
   $name = $names[$j];
-  
+
   $rows[] = array(
     "<span title=\"" . $type->definition . "\">$name</span>",
     number_format($type->num_features),
   );
-} 
+}
 // 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:

legacy/tripal_feature/tripal_feature.module

@@ -133,8 +133,7 @@ function tripal_feature_menu() {
   );
 
   // the administative settings menu
-  /*
-  $items['admin/tripal/chado/tripal_feature'] = array(
+  $items['admin/tripal/legacy/tripal_feature'] = array(
     'title' => 'Features',
     'description' => 'A biological sequence or a section of a biological sequence, or a collection of such sections.',
     'page callback' => 'tripal_feature_admin_feature_view',
@@ -142,7 +141,7 @@ function tripal_feature_menu() {
     'type' => MENU_NORMAL_ITEM,
   );
 
-  $items['admin/tripal/chado/tripal_feature/delete'] = array(
+  $items['admin/tripal/legacy/tripal_feature/delete'] = array(
     'title' => ' Delete',
     'description' => 'Delete multiple features from Chado',
     'page callback' => 'drupal_get_form',
@@ -151,7 +150,7 @@ function tripal_feature_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 2
   );
-  $items['admin/tripal/chado/tripal_feature/sync'] = array(
+  $items['admin/tripal/legacy/tripal_feature/sync'] = array(
     'title' => ' Sync',
     'description' => 'Create pages on this site for features stored in Chado',
     'page callback' => 'drupal_get_form',
@@ -160,7 +159,7 @@ function tripal_feature_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 1
   );
-  $items['admin/tripal/chado/tripal_feature/chado_feature_toc'] = array(
+  $items['admin/tripal/legacy/tripal_feature/chado_feature_toc'] = array(
     'title' => ' TOC',
     'description' => 'Manage the table of contents for feature nodes.',
     'page callback' => 'drupal_get_form',
@@ -171,7 +170,7 @@ function tripal_feature_menu() {
     'file path' => drupal_get_path('module', 'tripal_core'),
     'weight' => 3
   );
-  $items['admin/tripal/chado/tripal_feature/configuration'] = array(
+  $items['admin/tripal/legacy/tripal_feature/configuration'] = array(
     'title' => 'Settings',
     'description' => 'Configure the Tripal Feature module.',
     'page callback' => 'drupal_get_form',
@@ -180,7 +179,7 @@ function tripal_feature_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 5
   );
-  $items['admin/tripal/chado/tripal_feature/help'] = array(
+  $items['admin/tripal/legacy/tripal_feature/help'] = array(
     'title' => 'Help',
     'description' => 'Help with the Tripal Feature module.',
     'page callback' => 'theme',
@@ -198,7 +197,6 @@ function tripal_feature_menu() {
     'access arguments' => array('administer tripal feature'),
     'type' => MENU_CALLBACK,
   );
-  */
   return $items;
 }
 

legacy/tripal_featuremap/tripal_featuremap.module

@@ -93,8 +93,8 @@ function tripal_featuremap_menu() {
   $items = array();
 
   // The administative settings menu
-  /*
-  $items['admin/tripal/chado/tripal_featuremap'] = array(
+
+  $items['admin/tripal/legacy/tripal_featuremap'] = array(
     'title' => 'Feature Maps',
     'description' => 'A map of features from the chado database (e.g. genetic map)',
     'page callback' => 'tripal_featuremap_admin_featuremaps_listing',
@@ -102,7 +102,7 @@ function tripal_featuremap_menu() {
     'type' => MENU_NORMAL_ITEM,
   );
 
-  $items['admin/tripal/chado/tripal_featuremap/help'] = array(
+  $items['admin/tripal/legacy/tripal_featuremap/help'] = array(
     'title' => 'Help',
     'description' => 'Basic Description of Tripal Map Module Functionality',
     'page callback' => 'theme',
@@ -112,7 +112,7 @@ function tripal_featuremap_menu() {
     'weight' => 10
   );
 
-  $items['admin/tripal/chado/tripal_featuremap/configuration'] = array(
+  $items['admin/tripal/legacy/tripal_featuremap/configuration'] = array(
     'title' => 'Settings',
     'description' => 'Manage integration of Chado maps including associated features.',
     'page callback' => 'drupal_get_form',
@@ -122,7 +122,7 @@ function tripal_featuremap_menu() {
     'weight' => 2
   );
 
-  $items['admin/tripal/chado/tripal_featuremap/sync'] = array(
+  $items['admin/tripal/legacy/tripal_featuremap/sync'] = array(
     'title' => ' Sync',
     'description' => 'Sync featuremaps from Chado with Drupal',
     'page callback' => 'drupal_get_form',
@@ -132,7 +132,7 @@ function tripal_featuremap_menu() {
     'weight' => 0
   );
 
-  $items['admin/tripal/chado/tripal_featuremap/chado_featuremap_toc'] = array(
+  $items['admin/tripal/legacy/tripal_featuremap/chado_featuremap_toc'] = array(
     'title' => ' TOC',
     'description' => 'Manage the table of contents for feature map nodes.',
     'page callback' => 'drupal_get_form',
@@ -144,14 +144,13 @@ function tripal_featuremap_menu() {
     'weight' => 3
   );
 
-  $items['admin/tripal/chado/tripal_featuremap/views/featuremaps/enable'] = array(
+  $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'),
     'access arguments' => array('administer tripal featuremap'),
     'type' => MENU_CALLBACK,
   );
-  */
   return $items;
 }
 

legacy/tripal_genetic/includes/tripal_genetic.admin.inc

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

legacy/tripal_genetic/tripal_genetic.module

@@ -48,8 +48,8 @@ function tripal_genetic_menu() {
   $items = array();
 
     // the administative settings menu
-    /*
-  $items['admin/tripal/chado/tripal_genetic'] = array(
+
+  $items['admin/tripal/legacy/tripal_genetic'] = array(
    'title' => 'Genetics',
    'description' => 'Genetic data including Genotypes.',
    'page callback' => 'tripal_genetic_admin_genetics_listing',
@@ -57,7 +57,7 @@ function tripal_genetic_menu() {
    'type' => MENU_NORMAL_ITEM,
   );
 
-  $items['admin/tripal/chado/tripal_genetic/help'] = array(
+  $items['admin/tripal/legacy/tripal_genetic/help'] = array(
    'title' => 'Help',
    'description' => "A description of the Tripal genetic module including a short description of it's usage.",
    'page callback' => 'theme',
@@ -66,14 +66,13 @@ function tripal_genetic_menu() {
    'type' => MENU_LOCAL_TASK,
   );
 
-  $items['admin/tripal/chado/tripal_genetic/views/genetics/enable'] = array(
+  $items['admin/tripal/legacy/tripal_genetic/views/genetics/enable'] = array(
     'title' => 'Enable genetic Administrative View',
     'page callback' => 'tripal_enable_view',
-    'page arguments' => array('tripal_genetic_admin_genetics', 'admin/tripal/chado/tripal_genetic'),
+    'page arguments' => array('tripal_genetic_admin_genetics', 'admin/tripal/legacy/tripal_genetic'),
     'access arguments' => array('administer tripal genetic'),
     'type' => MENU_CALLBACK,
   );
-  */
 
   return $items;
 }

legacy/tripal_library/tripal_library.module

@@ -67,8 +67,8 @@ function tripal_library_permission() {
 function tripal_library_menu() {
   $items = array();
   // The administative settings menu
-  /*
-  $items['admin/tripal/chado/tripal_library'] = array(
+
+  $items['admin/tripal/legacy/tripal_library'] = array(
     'title' => 'Libraries',
     'description' => 'Any biological library. Examples of genomic libraries include BAC, cDNA, FOSMID, etc.',
     'page callback' => 'tripal_library_admin_libraries_listing',
@@ -76,7 +76,7 @@ function tripal_library_menu() {
     'type' => MENU_NORMAL_ITEM,
   );
 
-  $items['admin/tripal/chado/tripal_library/help'] = array(
+  $items['admin/tripal/legacy/tripal_library/help'] = array(
     'title' => 'Help',
     'description' => 'Basic Description of Tripal Library Module Functionality',
     'page callback' => 'theme',
@@ -86,7 +86,7 @@ function tripal_library_menu() {
     'weight' => 10
   );
 
-  $items['admin/tripal/chado/tripal_library/configuration'] = array(
+  $items['admin/tripal/legacy/tripal_library/configuration'] = array(
     'title' => 'Settings',
     'description' => 'Configure the Tripal Library module',
     'page callback' => 'drupal_get_form',
@@ -95,7 +95,7 @@ function tripal_library_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 5
   );
-  $items['admin/tripal/chado/tripal_library/sync'] = array(
+  $items['admin/tripal/legacy/tripal_library/sync'] = array(
     'title' => ' Sync',
     'description' => 'Create pages on this site for libraries stored in Chado',
     'page callback' => 'drupal_get_form',
@@ -104,8 +104,8 @@ function tripal_library_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 2
   );
-  
-  $items['admin/tripal/chado/tripal_library/chado_library_toc'] = array(
+
+  $items['admin/tripal/legacy/tripal_library/chado_library_toc'] = array(
     'title' => ' TOC',
     'description' => 'Manage the table of contents for library nodes.',
     'page callback' => 'drupal_get_form',
@@ -117,10 +117,10 @@ function tripal_library_menu() {
     'weight' => 3
   );
 
-  $items['admin/tripal/chado/tripal_library/views/libraries/enable'] = array(
+  $items['admin/tripal/legacy/tripal_library/views/libraries/enable'] = array(
     'title' => 'Enable Library Administrative View',
     'page callback' => 'tripal_enable_view',
-    'page arguments' => array('tripal_library_admin_libraries', 'admin/tripal/chado/tripal_library'),
+    'page arguments' => array('tripal_library_admin_libraries', 'admin/tripal/legacy/tripal_library'),
     'access arguments' => array('administer tripal library'),
     'type' => MENU_CALLBACK,
   );

legacy/tripal_natural_diversity/includes/tripal_natural_diversity.admin.inc

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

legacy/tripal_natural_diversity/tripal_natural_diversity.module

@@ -48,8 +48,8 @@ function tripal_natural_diversity_menu() {
   $items = array();
 
     // the administative settings menu
-    /*
-  $items['admin/tripal/chado/tripal_natdiv'] = array(
+
+  $items['admin/tripal/legacy/tripal_natdiv'] = array(
    'title' => 'Natural Diversity Experiments',
    'description' => 'Experiments relating to natural diversity such as genotype and phenotype experiments.',
    'page callback' => 'tripal_natural_diversity_admin_natdiv_view',
@@ -57,7 +57,7 @@ function tripal_natural_diversity_menu() {
    'type' => MENU_NORMAL_ITEM,
   );
 
-  $items['admin/tripal/chado/tripal_natdiv/help'] = array(
+  $items['admin/tripal/legacy/tripal_natdiv/help'] = array(
     'title' => 'Help',
     'description' => ('Help for the Tripal natural diversity module.'),
     'page callback' => 'theme',
@@ -67,14 +67,14 @@ function tripal_natural_diversity_menu() {
     'weight' => 10
   );
 
-  $items['admin/tripal/chado/tripal_natdiv/views/natdiv_exp/enable'] = array(
+  $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'),
     'access arguments' => array('administer tripal nd'),
     'type' => MENU_CALLBACK,
   );
-  */
+
   return $items;
 }
 

legacy/tripal_natural_diversity/tripal_natural_diversity.views_default.inc

@@ -137,7 +137,7 @@ function tripal_natural_diversity_defaultview_admin_natdiv_exp() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_natdiv/experiments';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_natdiv/experiments';
   $handler->display->display_options['menu']['type'] = 'default tab';
   $handler->display->display_options['menu']['title'] = 'Experiments';
   $handler->display->display_options['menu']['description'] = 'A single assay resulting in a single genotype or phenotype.';
@@ -325,7 +325,7 @@ function tripal_natural_diversity_defaultview_admin_geolocations() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_natdiv/locations';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_natdiv/locations';
   $handler->display->display_options['menu']['type'] = 'tab';
   $handler->display->display_options['menu']['title'] = 'Locations';
   $handler->display->display_options['menu']['description'] = 'Geographical locations in which natural diversity experiments might be performed.';
@@ -432,7 +432,7 @@ function tripal_natural_diversity_defaultview_admin_reagents() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_natdiv/reagents';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_natdiv/reagents';
   $handler->display->display_options['menu']['type'] = 'tab';
   $handler->display->display_options['menu']['title'] = 'Reagents';
   $handler->display->display_options['menu']['description'] = 'Reagents used in natural diversity experiments';
@@ -526,7 +526,7 @@ function tripal_natural_diversity_defaultview_admin_protocols() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_natdiv/protocols';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_natdiv/protocols';
   $handler->display->display_options['menu']['type'] = 'tab';
   $handler->display->display_options['menu']['title'] = 'Protocols';
   $handler->display->display_options['menu']['description'] = 'The protcols used for natural diversity experiments';

legacy/tripal_organism/includes/tripal_organism.admin.inc

@@ -17,8 +17,8 @@ function tripal_organism_admin_organism_view() {
   $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');
+  $breadcrumb[] = l('Chado', 'admin/tripal/legacy');
+  $breadcrumb[] = l('Organisms', 'admin/tripal/legacy/tripal_organism');
   drupal_set_breadcrumb($breadcrumb);
 
   // Add the view
@@ -32,7 +32,7 @@ function tripal_organism_admin_organism_view() {
       . '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 .= '<li>'.l('Organisms View', 'admin/tripal/legacy/tripal_organism/views/organisms/enable').'</li>';
     $output .= '</ul>';
   }
 

legacy/tripal_organism/tripal_organism.info

@@ -4,7 +4,7 @@ core = 7.x
 project = tripal
 package = Tripal v2 Legacy
 version = 7.x-3.0-alpha1
-configure = admin/tripal/chado/tripal_organism
+configure = admin/tripal/legacy/tripal_organism
 
 stylesheets[all][] = theme/css/tripal_organism.css
 

legacy/tripal_organism/tripal_organism.module

@@ -29,9 +29,9 @@ require_once 'includes/tripal_organism.chado_node.inc';
  */
 function tripal_organism_menu() {
   $items = array();
-/*
+
   // the administative settings menu
-  $items['admin/tripal/chado/tripal_organism'] = array(
+  $items['admin/tripal/legacy/tripal_organism'] = array(
     'title' => 'Organisms',
     'description' => 'Any living biological entity, such as an animal, plant, fungus, or bacterium.',
     'page callback' => 'tripal_organism_admin_organism_view',
@@ -39,7 +39,7 @@ function tripal_organism_menu() {
     'type' => MENU_NORMAL_ITEM,
   );
 
-  $items['admin/tripal/chado/tripal_organism/sync'] = array(
+  $items['admin/tripal/legacy/tripal_organism/sync'] = array(
     'title' => ' Sync',
     'description' => 'Create pages on this site for organisms stored in Chado',
     'page callback' => 'drupal_get_form',
@@ -48,7 +48,7 @@ function tripal_organism_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 1
   );
-  $items['admin/tripal/chado/tripal_organism/delete'] = array(
+  $items['admin/tripal/legacy/tripal_organism/delete'] = array(
     'title' => ' Delete',
     'description' => 'Delete multiple organisms from Chado',
     'page callback' => 'drupal_get_form',
@@ -59,7 +59,7 @@ function tripal_organism_menu() {
     'file' =>  'includes/tripal_organism.delete.inc',
     'weight' => 2
   );
-  $items['admin/tripal/chado/tripal_organism/chado_organism_toc'] = array(
+  $items['admin/tripal/legacy/tripal_organism/chado_organism_toc'] = array(
     'title' => ' TOC',
     'description' => 'Manage the table of contents for organism nodes.',
     'page callback' => 'drupal_get_form',
@@ -70,7 +70,7 @@ function tripal_organism_menu() {
     'file path' => drupal_get_path('module', 'tripal_core'),
     'weight' => 3
   );
-  $items['admin/tripal/chado/tripal_organism/configuration'] = array(
+  $items['admin/tripal/legacy/tripal_organism/configuration'] = array(
     'title' => 'Settings',
     'description' => 'Manage integration of Chado organisms including associated features',
     'page callback' => 'drupal_get_form',
@@ -79,7 +79,7 @@ function tripal_organism_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 5
   );
-  $items['admin/tripal/chado/tripal_organism/help'] = array(
+  $items['admin/tripal/legacy/tripal_organism/help'] = array(
     'title' => 'Help',
     'description' => "A description of the Tripal Organism module including a short description of it's usage.",
     'page callback' => 'theme',
@@ -88,20 +88,19 @@ function tripal_organism_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 10
   );
-  $items['admin/tripal/chado/tripal_organism/views/organisms/enable'] = array(
+  $items['admin/tripal/legacy/tripal_organism/views/organisms/enable'] = array(
     'title' => 'Enable Organism Administrative View',
     'page callback' => 'tripal_enable_view',
-    'page arguments' => array('tripal_organism_admin_organisms', 'admin/tripal/chado/tripal_organism'),
+    'page arguments' => array('tripal_organism_admin_organisms', 'admin/tripal/legacy/tripal_organism'),
     'access arguments' => array('administer tripal organism'),
     'type' => MENU_CALLBACK,
   );
-  $items['admin/tripal/chado/tripal_organism/organism/auto_name/%'] = array(
+  $items['admin/tripal/legacy/tripal_organism/organism/auto_name/%'] = array(
     'page callback' => 'tripal_autocomplete_organism',
     'page arguments' => array(6),
     'access arguments' => array('administer tripal organism'),
     'type' => MENU_CALLBACK,
   );
-*/
   return $items;
 }
 

legacy/tripal_organism/tripal_organism.views_default.inc

@@ -392,7 +392,7 @@ function tripal_organism_admin_defaultview_organisms() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_organism/organisms';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/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.';

legacy/tripal_phenotype/tripal_phenotype.module

@@ -44,8 +44,8 @@ function tripal_phenotype_menu() {
   $items = array();
 
     // the administative settings menu
-    /*
-  $items['admin/tripal/chado/tripal_phenotype'] = array(
+
+  $items['admin/tripal/legacy/tripal_phenotype'] = array(
    'title' => 'Phenotypes',
    'description' => 'A controlled sentence describing observable effects of non-wild type function.',
    'page callback' => 'tripal_phenotype_admin_phenotypes_listing',
@@ -53,7 +53,7 @@ function tripal_phenotype_menu() {
    'type' => MENU_NORMAL_ITEM,
   );
 
-  $items['admin/tripal/chado/tripal_phenotype/help'] = array(
+  $items['admin/tripal/legacy/tripal_phenotype/help'] = array(
    'title' => 'Help',
    'description' => "A description of the Tripal phenotype module including a short description of it's usage.",
    'page callback' => 'theme',
@@ -62,14 +62,14 @@ function tripal_phenotype_menu() {
    'type' => MENU_LOCAL_TASK,
   );
 
-  $items['admin/tripal/chado/tripal_phenotype/views/phenotypes/enable'] = array(
+  $items['admin/tripal/legacy/tripal_phenotype/views/phenotypes/enable'] = array(
     'title' => 'Enable Phenotype Administrative View',
     'page callback' => 'tripal_enable_view',
-    'page arguments' => array('tripal_phenotype_admin_phenotypes', 'admin/tripal/chado/tripal_phenotype'),
+    'page arguments' => array('tripal_phenotype_admin_phenotypes', 'admin/tripal/legacy/tripal_phenotype'),
     'access arguments' => array('administer tripal phenotype'),
     'type' => MENU_CALLBACK,
   );
-  */
+
   return $items;
 }
 
@@ -144,8 +144,8 @@ function tripal_phenotype_admin_phenotypes_listing() {
   $breadcrumb[] = l('Home', '<front>');
   $breadcrumb[] = l('Administration', 'admin');
   $breadcrumb[] = l('Tripal', 'admin/tripal');
-  $breadcrumb[] = l('Chado', 'admin/tripal/chado');
-  $breadcrumb[] = l('Phenotypes', 'admin/tripal/chado/tripal_phenotype');
+  $breadcrumb[] = l('Chado', 'admin/tripal/legacy');
+  $breadcrumb[] = l('Phenotypes', 'admin/tripal/legacy/tripal_phenotype');
   drupal_set_breadcrumb($breadcrumb);
 
   // Add the view
@@ -159,7 +159,7 @@ function tripal_phenotype_admin_phenotypes_listing() {
       . 'administrative interface are disabled. <strong>Click each of the following links to '
       . 'enable the pertinent views</strong>:</p>';
     $output .= '<ul>';
-      $output .= '<li>'.l('Phenotype Admin', 'admin/tripal/chado/tripal_phenotype/views/phenotypes/enable').'</li>';
+      $output .= '<li>'.l('Phenotype Admin', 'admin/tripal/legacy/tripal_phenotype/views/phenotypes/enable').'</li>';
     $output .= '</ul>';
   }
 

legacy/tripal_phenotype/tripal_phenotype.views_default.inc

@@ -252,7 +252,7 @@ function tripal_phenotype_defaultview_admin_phenotypes() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_phenotype/phenotypes';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_phenotype/phenotypes';
   $handler->display->display_options['menu']['type'] = 'default tab';
   $handler->display->display_options['menu']['title'] = 'Phenotypes';
   $handler->display->display_options['menu']['description'] = 'A controlled sentence describing observable effects of non-wild type function';

legacy/tripal_phylogeny/includes/tripal_phylogeny.admin.inc

@@ -13,7 +13,7 @@ function tripal_phylogeny_admin_phylotrees_listing() {
   $breadcrumb[] = l('Home', '<front>');
   $breadcrumb[] = l('Administration', 'admin');
   $breadcrumb[] = l('Tripal', 'admin/tripal');
-  $breadcrumb[] = l('Chado', 'admin/tripal/chado');
+  $breadcrumb[] = l('Chado', 'admin/tripal/legacy');
   $breadcrumb[] = l('Phylotrees', 'admin/tripal/extension/tripal_phylogeny');
   drupal_set_breadcrumb($breadcrumb);
 
@@ -183,7 +183,7 @@ function tripal_phylogeny_default_plots_form($form, &$form_state) {
     $form['node_settings']['org_table']['organism_' . $i] = array(
       '#type' => 'textfield',
       '#default_value' => array_key_exists($i, $color_defaults) ? $color_defaults[$i]['organism'] : '',
-      '#autocomplete_path' => "admin/tripal/chado/tripal_organism/organism/auto_name",
+      '#autocomplete_path' => "admin/tripal/legacy/tripal_organism/organism/auto_name",
       '#description' => t('Please enter the name of the organism.'),
       '#size' => 30,
     );

legacy/tripal_phylogeny/includes/tripal_phylogeny.chado_node.inc

@@ -222,7 +222,7 @@ function chado_phylotree_form($node, &$form_state) {
         tree. In this case, the word 'taxonomy' should be used."),
     '#required'    => TRUE,
     '#default_value' => $leaf_type,
-    '#autocomplete_path' => "admin/tripal/chado/tripal_cv/cvterm/auto_name/$cv_id",
+    '#autocomplete_path' => "admin/tripal/legacy/tripal_cv/cvterm/auto_name/$cv_id",
   );
 
   // Get the list of analyses.

legacy/tripal_phylogeny/tripal_phylogeny.module

@@ -55,7 +55,7 @@ function tripal_phylogeny_menu() {
 
   // administration landing page. currently has no content but is
   // apparently required for the Sync and Help links to work.
-  $items['admin/tripal/chado/tripal_phylogeny'] = array(
+  $items['admin/tripal/legacy/tripal_phylogeny'] = array(
     'title' => 'Phylogeny and Taxonomy',
     'description' => 'Phylogenetic and taxonomic trees.',
     'page callback' => 'tripal_phylogeny_admin_phylotrees_listing',
@@ -64,7 +64,7 @@ function tripal_phylogeny_menu() {
   );
 
   // help menu
-  $items['admin/tripal/chado/tripal_phylogeny/help'] = array(
+  $items['admin/tripal/legacy/tripal_phylogeny/help'] = array(
     'title' => 'Help',
     'description' => 'Basic Description of Tripal Phylotree Module Functionality',
     'page callback' => 'theme',
@@ -75,7 +75,7 @@ function tripal_phylogeny_menu() {
   );
 
   // configuration menu item
-  $items['admin/tripal/chado/tripal_phylogeny/configuration'] = array(
+  $items['admin/tripal/legacy/tripal_phylogeny/configuration'] = array(
     'title' => 'Settings',
     'description' => 'Configure the Tripal Phylotree module',
     'page callback' => 'drupal_get_form',
@@ -85,7 +85,7 @@ function tripal_phylogeny_menu() {
     'weight' => 1
   );
 
-  $items['admin/tripal/chado/tripal_phylogeny/plots'] = array(
+  $items['admin/tripal/legacy/tripal_phylogeny/plots'] = array(
     'title' => 'Plot Defaults',
     'description' => 'Set defaults for the trees',
     'page callback' => 'drupal_get_form',
@@ -96,7 +96,7 @@ function tripal_phylogeny_menu() {
   );
 
   // sync menu item (will be rendered as a tab by tripal)
-  $items['admin/tripal/chado/tripal_phylogeny/sync'] = array(
+  $items['admin/tripal/legacy/tripal_phylogeny/sync'] = array(
     'title' => ' Sync',
     'description' => 'Create pages on this site for phylotrees stored in Chado',
     'page callback' => 'drupal_get_form',
@@ -107,10 +107,10 @@ function tripal_phylogeny_menu() {
   );
 
   // Enable admin view
-  $items['admin/tripal/chado/tripal_phylogeny/views/phylotree/enable'] = array(
+  $items['admin/tripal/legacy/tripal_phylogeny/views/phylotree/enable'] = array(
     'title' => 'Enable Phylotree Administrative View',
     'page callback' => 'tripal_enable_view',
-    'page arguments' => array('tripal_phylogeny_admin_phylotree', 'admin/tripal/chado/tripal_phylogeny'),
+    'page arguments' => array('tripal_phylogeny_admin_phylotree', 'admin/tripal/legacy/tripal_phylogeny'),
     'access arguments' => array('administer tripal phylotree'),
     'type' => MENU_CALLBACK,
   );

legacy/tripal_phylogeny/tripal_phylogeny.views_default.inc

@@ -143,7 +143,7 @@ function tripal_phylogeny_defaultview_admin_phylotree() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_phylogeny/phylotree';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_phylogeny/phylotree';
   $handler->display->display_options['menu']['type'] = 'default tab';
   $handler->display->display_options['menu']['title'] = 'Trees';
   $handler->display->display_options['menu']['weight'] = '0';

legacy/tripal_project/includes/tripal_project.admin.inc

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

legacy/tripal_project/tripal_project.info

@@ -4,7 +4,7 @@ core = 7.x
 project = tripal
 package = Tripal v2 Legacy
 version = 7.x-3.0-alpha1
-configure = admin/tripal/chado/tripal_project
+configure = admin/tripal/legacy/tripal_project
 
 dependencies[] = tripal_core
 dependencies[] = tripal_views

legacy/tripal_project/tripal_project.module

@@ -41,8 +41,8 @@ function tripal_project_views_api() {
  */
 function tripal_project_menu() {
   $items = array();
-  /*
-  $items[ 'admin/tripal/chado/tripal_project' ]= array(
+
+  $items[ 'admin/tripal/legacy/tripal_project' ]= array(
     'title' => 'Projects',
     'description' => ('A project. Can be used for grouping data such as with the natural diversity module data.'),
     'page callback' => 'tripal_project_admin_project_view',
@@ -50,7 +50,7 @@ function tripal_project_menu() {
     'type' => MENU_NORMAL_ITEM
   );
 
-  $items['admin/tripal/chado/tripal_project/help']= array(
+  $items['admin/tripal/legacy/tripal_project/help']= array(
     'title' => 'Help',
     'description' => ("Basic Description of Tripal Project Module Functionality."),
     'page callback' => 'theme',
@@ -60,7 +60,7 @@ function tripal_project_menu() {
     'weight' => 6
   );
 
-  $items['admin/tripal/chado/tripal_project/configuration']= array(
+  $items['admin/tripal/legacy/tripal_project/configuration']= array(
     'title' => 'Settings',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_project_admin'),
@@ -69,7 +69,7 @@ function tripal_project_menu() {
     'weight' => 4
   );
 
-  $items['admin/tripal/chado/tripal_project/sync'] = array(
+  $items['admin/tripal/legacy/tripal_project/sync'] = array(
     'title' => ' Sync',
     'description' => 'Create pages on this site for projects stored in Chado',
     'page callback' => 'drupal_get_form',
@@ -78,8 +78,8 @@ function tripal_project_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 0
   );
-  
-  $items['admin/tripal/chado/tripal_project/chado_project_toc'] = array(
+
+  $items['admin/tripal/legacy/tripal_project/chado_project_toc'] = array(
     'title' => ' TOC',
     'description' => 'Manage the table of contents for project nodes.',
     'page callback' => 'drupal_get_form',
@@ -91,14 +91,13 @@ function tripal_project_menu() {
     'weight' => 3
   );
 
-  $items['admin/tripal/chado/tripal_project/views/projects/enable'] = array(
+  $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'),
     'access arguments' => array('administer tripal project'),
     'type' => MENU_CALLBACK,
   );
-  */
   return $items;
 }
 

legacy/tripal_project/tripal_project.views_default.inc

@@ -262,7 +262,7 @@ function tripal_project_defaultview_admin_projects() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_project/projects';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_project/projects';
   $handler->display->display_options['menu']['type'] = 'default tab';
   $handler->display->display_options['menu']['title'] = 'Projects';
   $handler->display->display_options['menu']['weight'] = '0';

legacy/tripal_pub/includes/tripal_pub.admin.inc

@@ -17,8 +17,8 @@ function tripal_pub_admin_pub_view() {
   $breadcrumb[] = l('Home', '<front>');
   $breadcrumb[] = l('Administration', 'admin');
   $breadcrumb[] = l('Tripal', 'admin/tripal');
-  $breadcrumb[] = l('Chado', 'admin/tripal/chado');
-  $breadcrumb[] = l('Publications', 'admin/tripal/chado/tripal_pub');
+  $breadcrumb[] = l('Chado', 'admin/tripal/legacy');
+  $breadcrumb[] = l('Publications', 'admin/tripal/legacy/tripal_pub');
   drupal_set_breadcrumb($breadcrumb);
 
   // Add the view
@@ -32,7 +32,7 @@ function tripal_pub_admin_pub_view() {
       . 'administrative interface are disabled. <strong>Click each of the following links to '
       . 'enable the pertinent views</strong>:</p>';
     $output .= '<ul>';
-      $output .= '<li>'.l('Publications View', 'admin/tripal/chado/tripal_pub/views/pubs/enable').'</li>';
+      $output .= '<li>'.l('Publications View', 'admin/tripal/legacy/tripal_pub/views/pubs/enable').'</li>';
     $output .= '</ul>';
   }
 
@@ -65,7 +65,7 @@ function tripal_pub_admin() {
   // This call adds the configuration form to your current form
   // This sub-form handles it's own validation & submit
   chado_add_admin_form_set_title($form, $form_state, $details);
-  
+
   // -----------------------------------------
   // add in the fields for selecting which fields are used when search for pubs
   $form['searching'] = array(

legacy/tripal_pub/includes/tripal_pub.pub_search.inc

@@ -178,7 +178,7 @@ function tripal_pub_search_form($form, &$form_state) {
   $form['admin-instructions'] = array(
     '#markup'  =>  tripal_set_message(
       t('Administrators, you can select the fields with which a user can use to search, by checking the desired fields on the ' .
-        l('Publication Module Settings Page', 'admin/tripal/chado/tripal_pub/configuration', array('attributes' => array('target' => '_blank'))) . '
+        l('Publication Module Settings Page', 'admin/tripal/legacy/tripal_pub/configuration', array('attributes' => array('target' => '_blank'))) . '
         in the section titled "Search Options".  The selected fields will appear in the dropdowns below.'),
       TRIPAL_INFO,
       array('return_html' => 1)),

legacy/tripal_pub/tripal_pub.module

@@ -68,7 +68,7 @@ function tripal_pub_menu() {
     'type ' => MENU_CALLBACK,
   );
 
-  $items['admin/tripal/chado/tripal_pub']= array(
+  $items['admin/tripal/legacy/tripal_pub']= array(
     'title' => 'Publications',
     'description' => ('A documented provenance artefact - publications, documents, personal communication.'),
     'page callback' => 'tripal_pub_admin_pub_view',
@@ -76,7 +76,7 @@ function tripal_pub_menu() {
     'type' => MENU_NORMAL_ITEM
   );
 
-  $items['admin/tripal/chado/tripal_pub/help']= array(
+  $items['admin/tripal/legacy/tripal_pub/help']= array(
     'title' => 'Help',
     'description' => ('A module for interfacing the GMOD chado database with Drupal, providing viewing of publications'),
     'page callback' => 'theme',
@@ -86,7 +86,7 @@ function tripal_pub_menu() {
     'weight' => 10
   );
 
-  $items['admin/tripal/chado/tripal_pub/configuration'] = array(
+  $items['admin/tripal/legacy/tripal_pub/configuration'] = array(
     'title' => 'Settings',
     'description' => 'Configure the Tripal publication module.',
     'page callback' => 'drupal_get_form',
@@ -96,7 +96,7 @@ function tripal_pub_menu() {
     'weight' => 5
   );
 
-  $items['admin/tripal/chado/tripal_pub/sync'] = array(
+  $items['admin/tripal/legacy/tripal_pub/sync'] = array(
     'title' => ' Sync',
     'description' => 'Create pages on this site for libraries stored in Chado',
     'page callback' => 'drupal_get_form',
@@ -106,7 +106,7 @@ function tripal_pub_menu() {
     'weight' => 2
   );
 
-  $items['admin/tripal/chado/tripal_pub/chado_pub_toc'] = array(
+  $items['admin/tripal/legacy/tripal_pub/chado_pub_toc'] = array(
     'title' => ' TOC',
     'description' => 'Manage the table of contents for pub nodes.',
     'page callback' => 'drupal_get_form',
@@ -118,7 +118,7 @@ function tripal_pub_menu() {
     'weight' => 3
   );
 
-  $items['admin/tripal/chado/tripal_pub/citation'] = array(
+  $items['admin/tripal/legacy/tripal_pub/citation'] = array(
     'title' => 'Citations',
     'description' => 'Update publication citations',
     'page callback' => 'drupal_get_form',

legacy/tripal_pub/tripal_pub.views_default.inc

@@ -198,7 +198,7 @@ function tripal_pub_defaultview_admin_publications() {
 
   /* Display: Page */
   $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->display->display_options['path'] = 'admin/tripal/chado/tripal_pub/publications';
+  $handler->display->display_options['path'] = 'admin/tripal/legacy/tripal_pub/publications';
   $handler->display->display_options['menu']['type'] = 'default tab';
   $handler->display->display_options['menu']['title'] = 'Publications';
   $handler->display->display_options['menu']['description'] = 'A published article, book, conference proceeding, etc.';

legacy/tripal_stock/includes/tripal_stock.admin.inc

@@ -17,8 +17,8 @@ function tripal_stock_admin_stock_view() {
   $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');
+  $breadcrumb[] = l('Chado', 'admin/tripal/legacy');
+  $breadcrumb[] = l('Stocks', 'admin/tripal/legacy/tripal_stock');
   drupal_set_breadcrumb($breadcrumb);
 
   // Add the view
@@ -32,7 +32,7 @@ function tripal_stock_admin_stock_view() {
       . '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 .= '<li>'.l('Stocks View', 'admin/tripal/legacy/tripal_stock/views/stocks/enable').'</li>';
     $output .= '</ul>';
   }
 

legacy/tripal_stock/includes/tripal_stock.chado_node.inc

@@ -249,7 +249,7 @@ function chado_stock_form($node, $form_state) {
         about this stock, please provide the name of the database, the accession
         and an optional description using the fields below. If the database
         is not present in the list, then please ') .
-        l(t('add the database '), 'admin/tripal/chado/tripal_db/add', array('attributes' => array('target' => '_blank'))) .
+        l(t('add the database '), 'admin/tripal/legacy/tripal_db/add', array('attributes' => array('target' => '_blank'))) .
         t('then refresh this page.'),
   );
 

legacy/tripal_stock/tripal_stock.module

@@ -49,8 +49,8 @@ function tripal_stock_menu() {
   );
 
   //Administrative settings menu-----------------
-  /*
-  $items['admin/tripal/chado/tripal_stock'] = array(
+
+  $items['admin/tripal/legacy/tripal_stock'] = array(
     'title' => 'Stocks',
     'description' => 'A stock is the physical entities of an organism, either living or preserved.',
     'page callback' => 'tripal_stock_admin_stock_view',
@@ -58,7 +58,7 @@ function tripal_stock_menu() {
     'type' => MENU_NORMAL_ITEM
   );
 
-  $items['admin/tripal/chado/tripal_stock/configuration'] = array(
+  $items['admin/tripal/legacy/tripal_stock/configuration'] = array(
     'title' => 'Settings',
     'description' => 'Settings for Chado Stocks',
     'page callback' => 'drupal_get_form',
@@ -68,7 +68,7 @@ function tripal_stock_menu() {
     'weight' => 5
   );
 
-  $items['admin/tripal/chado/tripal_stock/sync'] = array(
+  $items['admin/tripal/legacy/tripal_stock/sync'] = array(
     'title' => ' Sync',
     'description' => 'Sync stocks from Chado with Drupal',
     'page callback' => 'drupal_get_form',
@@ -79,7 +79,7 @@ function tripal_stock_menu() {
     'weight' => 0
   );
 
-  $items['admin/tripal/chado/tripal_stock/chado_stock_toc'] = array(
+  $items['admin/tripal/legacy/tripal_stock/chado_stock_toc'] = array(
     'title' => ' TOC',
     'description' => 'Manage the table of contents for stock nodes.',
     'page callback' => 'drupal_get_form',
@@ -91,7 +91,7 @@ function tripal_stock_menu() {
     'weight' => 3
   );
 
-  $items['admin/tripal/chado/tripal_stock/help'] = array(
+  $items['admin/tripal/legacy/tripal_stock/help'] = array(
     'title' => 'Help',
     'description' => 'Basic Description of Tripal Stock Module Functionality',
     'page callback' => 'theme',
@@ -100,7 +100,6 @@ function tripal_stock_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 10
   );
-  */
 
   return $items;
 }

tripal_chado/api/modules/tripal_chado.cv.api.inc

@@ -1154,71 +1154,6 @@ function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE) {
   }
 }
 
-/**
- * Retreives the default vocabulary for a given table and field.
- *
- * Each table in Chado that has a 'type_id' (or foreign key constraint to
- * the cvterm table) will have a default vocabulary assigned. This indicates to
- * Tripal that terms in that vocabulary are used to set the type_id for that
- * table. An example where this is used is the
- * tripal_get_cvterm_select_options() function which generates a list of options
- * for a select box used in a Drupal form.  The select box will list the terms
- * from the default vocabulary in the drop down.
- *
- * This function uses the Chado table and field name (e.g. 'type_id') to
- * retreive the vocabulary assgined.
- *
- * @param $table
- *   The name of the table that contains a field with a foreign key
- *   relationship to the cvterm table
- * @param $field
- *   The table field name that has the foreign key relationship to the
- *   cvterm table for which the default vocabulary will be set
- *
- * @return
- *   The cv object of the default vocabulary or an empty array if not
- *   available.
- */
-function tripal_get_default_cv($table, $field) {
-  $sql = "
-    SELECT cv_id
-    FROM {tripal_cv_defaults}
-    WHERE table_name = :table and field_name = :field
-  ";
-  $cv_id = db_query($sql, array(':table' => $table, ':field' => $field))->fetchField();
-
-  return tripal_get_cv(array('cv_id' => $cv_id));
-}
-
-/**
- * Retrieves the Chado table to which a vocbulary is set as default.
- *
- * Each table in Chado that has a 'type_id' (or foreign key constraint to
- * the cvterm table) will have a default vocabulary assigned. This indicates to
- * Tripal that terms in that vocabulary are used to set the type_id for that
- * table. An example where this is used is the
- * tripal_get_cvterm_select_options() function which generates a list of options
- * for a select box used in a Drupal form.  The select box will list the terms
- * from the default vocabulary in the drop down.
- *
- * This function uses the vocabulary ID to get the Chado table to which it
- * is assigned.
- *
- * @param $cv_id
- *  The ID of the vocabulary.
- *
- * @return
- *   If an assignment is present, an object containing the 'table_name' and
- *   'field_name' is returned.
- */
-function tripal_get_default_cv_table($cv_id) {
-  $default = db_select('tripal_cv_defaults', 't')
-    ->fields('t', array('table_name', 'field_name'))
-    ->condition('cv_id', $cv_id)
-    ->execute()
-    ->fetchObject();
-  return $default;
-}
 
 /**
  * Create an options array to be used in a form element

tripal_chado/includes/loaders/tripal_chado.pub_importers.inc

@@ -64,7 +64,7 @@ function tripal_pub_importers_list() {
           link labeled 'Import Pubs' to schedule a job to import the publications</li>
       <li>The first method only performs the import once.  However, you can schedule the
           importer to run peridically by adding a cron job. See the " .
-     l("Pub Module help instructions", "admin/tripal/chado/tripal_pub/help") . " to learn how to
+     l("Pub Module help instructions", "admin/tripal/legacy/tripal_pub/help") . " to learn how to
      set the importers to run automatically.") . '</li>
      </ol><br>';
 

tripal_chado/tripal_chado.module

@@ -169,17 +169,6 @@ function tripal_chado_menu() {
     'weight' => 2
   );
 
-  $items['admin/tripal/storage/chado/vocab'] = array(
-    'title' => 'Vocabulary Defaults',
-    'description' => 'Set the default vocabularies for properties and relationships.',
-    'page callback' => 'drupal_get_form',
-    'page arguments' => array('tripal_chado_admin_set_defaults_form'),
-    'file' => 'includes/tripal_chado.cv_defaults.inc',
-    'file path' => drupal_get_path('module', 'tripal_chado'),
-    'access arguments' => array('administer controlled vocabularies'),
-    'type' => MENU_NORMAL_ITEM,
-  );
-
 
   //////////////////////////////////////////////////////////////////////////////
   //                       Materialized Views
@@ -631,10 +620,6 @@ function tripal_chado_theme($existing, $type, $theme, $path) {
       'render element' => 'form',
       'file' => 'includes/loaders/tripal_chado.pub_importers.inc',
     ),
-    'tripal_chado_admin_set_defaults_form' => array(
-      'function' => 'theme_tripal_chado_admin_set_defaults_form',
-      'render element' => 'element',
-    ),
   );
 
   // Override the theme for each entity to use the legacy modules

tripal_ws/tripal_ws.info

@@ -4,6 +4,5 @@ core = 7.x
 project = tripal
 package = Tripal
 version = 7.x-3.0-alpha1
-configure = admin/tripal/chado/tripal_ws
 
 dependencies[] = tripal