Working on updating in-line documenation for Tv3 API release

legacy/tripal_analysis/includes/tripal_analysis.admin.inc

@@ -4,13 +4,13 @@
  * @file
  * Contains functions displaying administrative pages and forms.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 
 /**
  * Landing page for administration. Ensures Views are enabled & if not provides links to do so.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_admin_analysis_view() {
   $output = '';
@@ -48,7 +48,7 @@ function tripal_analysis_admin_analysis_view() {
  * @return
  *  A form API array describing an administrative form
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_admin() {
   // Create a new administrative form. We'll add main functions to the form
@@ -101,7 +101,7 @@ function tripal_analysis_admin() {
  * @form_state
  *   The user submitted values
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_admin_validate($form, &$form_state) {
 

legacy/tripal_analysis/includes/tripal_analysis.chado_node.inc

@@ -3,7 +3,7 @@
  * @file
  * Implements Drupal Node hooks to create the chado_analysis node content type.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 
 /**
@@ -12,7 +12,7 @@
  * Provide information to drupal about the node types that we're creating
  * in this module
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_node_info() {
   $nodes = array();
@@ -56,7 +56,7 @@ function chado_analysis_chado_node_sync_form($form, &$form_state) {
  * When editing or creating a new node of type 'chado_analysis' we need
  * a form.  This function creates the form that will be used for this.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function chado_analysis_form($node, &$form_state) {
   $form = array();
@@ -286,7 +286,7 @@ function chado_analysis_form($node, &$form_state) {
  * Implements hook_validate().
  * Validates the user input before creating an analysis node
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function chado_analysis_validate($node, $form, &$form_state) {
   // use the analysis parent to validate the node
@@ -299,7 +299,7 @@ function chado_analysis_validate($node, $form, &$form_state) {
  *   CASE B: Synchronizing a node from chado to drupal
  *   CASE C: Inserting a new node that exists in niether drupal nor chado
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_validate($node, $form, &$form_state) {
 
@@ -402,7 +402,7 @@ function tripal_analysis_validate($node, $form, &$form_state) {
  * to our chado_analysis table.  This function is called on insert of a new
  * node of type 'chado_analysis' and inserts the necessary information.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function chado_analysis_insert($node) {
 
@@ -482,7 +482,7 @@ function chado_analysis_insert($node) {
  * Implements hook_delete().
  * Removes analysis from the chado database.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function chado_analysis_delete($node) {
   $analysis_id = chado_get_id_from_nid('analysis', $node->nid);
@@ -509,7 +509,7 @@ function chado_analysis_delete($node) {
  * Implements hook_update().
  * Update analyses
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function chado_analysis_update($node) {
   $node->analysisname = trim($node->analysisname);
@@ -568,7 +568,7 @@ function chado_analysis_update($node) {
  * When a node is requested by the user this function is called to allow us
  * to add auxiliary data to the node object.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function chado_analysis_load($nodes) {
 
@@ -616,7 +616,7 @@ function chado_analysis_load($nodes) {
  *  access.  The only exception is when the $op == 'create'.  We will always
  *  return TRUE if the permission is set.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_node_access($node, $op, $account) {
 
@@ -655,7 +655,7 @@ function tripal_analysis_node_access($node, $op, $account) {
  * Implements hook_node_view().
  * Called for all node types.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_node_view($node, $view_mode, $langcode) {
   switch ($node->type) {
@@ -690,7 +690,7 @@ function tripal_analysis_node_view($node, $view_mode, $langcode) {
  * Implements hook_node_presave().
  * Called for all node types.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_node_presave($node) {
   $name = '';
@@ -743,7 +743,7 @@ function tripal_analysis_node_presave($node) {
  * Implements hook_node_insert().
  * Acts on all content types.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_node_insert($node) {
 
@@ -772,7 +772,7 @@ function tripal_analysis_node_insert($node) {
  * Implements hook_node_update().
  * Acts on all content types.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_node_update($node) {
 

legacy/tripal_analysis/includes/tripal_analysis.delete.inc

@@ -8,7 +8,7 @@
 /**
  * A form for indicating the analyses to delete
 *
-* @ingroup tripal_analysis
+* @ingroup tripal_legacy_analysis
 */
 function tripal_analysis_delete_form() {
   // get the list of analyses
@@ -43,7 +43,7 @@ function tripal_analysis_delete_form() {
 /**
  * Submit for the delete features form
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_delete_form_submit($form, &$form_state) {
   global $user;
@@ -77,7 +77,7 @@ function tripal_analysis_delete_form_submit($form, &$form_state) {
  * @param $job
  *   The tripal_job id
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_delete_analyses($analyses, $job = NULL) {
 

legacy/tripal_analysis/includes/tripal_analysis_privacy.inc

@@ -3,7 +3,7 @@
  * @file
  * Perform permission check (required node_privacy_byrole module).
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 
 /**
@@ -12,7 +12,7 @@
  * @param $analysis_id
  *   Which analysis to check if the user has permission to view
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_check_permission($analysis_id) {
   if (module_exists('node_privacy_byrole')) {
@@ -54,7 +54,7 @@ function tripal_analysis_check_permission($analysis_id) {
  * @param $nid
  *   The node ID of the analysis
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_set_feature_permission($analysis_id, $nid) {
 

legacy/tripal_analysis/tripal_analysis.install

@@ -3,14 +3,14 @@
  * @file
  * Implements hooks from the Schema API.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 
 /**
  * Implements hook_disable().
  * Disable default views when module is disabled
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_disable() {
 
@@ -26,7 +26,7 @@ function tripal_analysis_disable() {
 /**
  * Implementation of hook_requirements().
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_requirements($phase) {
   $requirements = array();
@@ -46,7 +46,7 @@ function tripal_analysis_requirements($phase) {
 /**
  * Implementation of hook_install().
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_install() {
 
@@ -63,7 +63,7 @@ function tripal_analysis_install() {
 /**
  * Implementation of hook_uninstall().
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_uninstall() {
 
@@ -73,7 +73,7 @@ function tripal_analysis_uninstall() {
 /**
  * Add cvs related to analyses
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_add_cvs() {
 
@@ -85,7 +85,7 @@ function tripal_analysis_add_cvs() {
 /**
  * Adds controlled vocabulary terms needed by this module.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_add_cvterms() {
 
@@ -145,7 +145,7 @@ function tripal_analysis_add_cvterms() {
  *     stores the sub-module names, such as tripal_analysis_blast, that are registered
  *     with this module.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_schema() {
 

legacy/tripal_analysis/tripal_analysis.module

@@ -4,29 +4,29 @@
  * @file
  * Contains basic functionality for the analysis module.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 
-require_once 'api/tripal_analysis.DEPRECATED.inc';
-
-require_once 'includes/tripal_analysis.delete.inc';
-require_once 'includes/tripal_analysis_privacy.inc';
-require_once 'includes/tripal_analysis.admin.inc';
-require_once 'includes/tripal_analysis.chado_node.inc';
-
 /**
- * @defgroup tripal_analysis Analysis Module
+ * @defgroup tripal_analysis Legacy Analysis Module
  * @ingroup tripal_modules
  * @{
  * Integrates the Chado Analysis module with Drupal Nodes & Views
  * @}
  */
 
+require_once 'api/tripal_analysis.DEPRECATED.inc';
+require_once 'includes/tripal_analysis.delete.inc';
+require_once 'includes/tripal_analysis_privacy.inc';
+require_once 'includes/tripal_analysis.admin.inc';
+require_once 'includes/tripal_analysis.chado_node.inc';
+
+
 /**
  * Implements hook_init().
  * Add tripal javascript to page headers
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_init() {
 
@@ -37,7 +37,7 @@ function tripal_analysis_init() {
  * Implementation of hook_menu().
  * Entry points and paths of the module
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_menu() {
   $items = array();
@@ -126,7 +126,7 @@ function tripal_analysis_search_biological_data_views() {
  * Implements hook_help().
  * Purpose: Adds a help page to the module list
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_help ($path, $arg) {
   if ($path == 'admin/help#tripal_analysis') {
@@ -141,7 +141,7 @@ function tripal_analysis_help ($path, $arg) {
  *  want permissionis that protect creation, editing and deleting of chado
  *  data objects
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_permission() {
   return array(
@@ -175,7 +175,7 @@ function tripal_analysis_permission() {
  *  We create theme functions to allow users of the module to customize the
  *  look and feel of the output generated in this module
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
@@ -225,7 +225,7 @@ function tripal_analysis_theme($existing, $type, $theme, $path) {
  *  for this module which then includes tripal_analysis.views.inc where all the
  *  views integration code is
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_views_api() {
   return array(
@@ -236,7 +236,7 @@ function tripal_analysis_views_api() {
 /**
  * Implementation of hook_form_alter().
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_form_alter(&$form, &$form_state, $form_id) {
   // turn of preview button for insert/updates
@@ -255,7 +255,7 @@ function tripal_analysis_form_alter(&$form, &$form_state, $form_id) {
  * @param $modulename
  *  The name of the module to be registered as a tripal analysis submodule
  *
- * @ingroup tripal_analysis_api
+ * @ingroup tripal_legacy_analysis_api
  */
 function tripal_register_analysis_child($modulename) {
   $sql = "SELECT * FROM {tripal_analysis} WHERE modulename = :modname";
@@ -271,7 +271,7 @@ function tripal_register_analysis_child($modulename) {
  * @param $modulename
  *  The name of the module to un-register
  *
- * @ingroup tripal_analysis_api
+ * @ingroup tripal_legacy_analysis_api
  */
 function tripal_unregister_analysis_child($modulename) {
   if (db_table_exists('tripal_analysis')) {

legacy/tripal_analysis/tripal_analysis.views_default.inc

@@ -4,13 +4,13 @@
  * @file
  * Contains the default views for the analysis module.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 
 /**
  * Implements hook_views_default_views().
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_views_default_views() {
   $views = array();
@@ -33,7 +33,7 @@ function tripal_analysis_views_default_views() {
 /**
  * Defines the analysis user search default view.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_defaultvalue_user_analysis() {
 
@@ -71,7 +71,7 @@ function tripal_analysis_defaultvalue_user_analysis() {
 /**
  * Defines the analysis admin default view.
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_legacy_analysis
  */
 function tripal_analysis_defaultvalue_admin_analysis() {
 

legacy/tripal_contact/includes/tripal_contact.admin.inc

@@ -3,14 +3,14 @@
  * @file
  * Handle administration of contacts.
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 
 /**
  * Launchpage for contact administration. Makes sure views are enabled and if not provides
  * links to enable them.
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_admin_contact_view() {
   $output = '';
@@ -45,7 +45,7 @@ function tripal_contact_admin_contact_view() {
 /**
  * Administrative settings form
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_admin() {
   $form = array();
@@ -90,7 +90,7 @@ function tripal_contact_admin() {
 /**
  * Reindex nodes for drupal search
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function get_tripal_contact_admin_form_reindex_set(&$form) {
 
@@ -100,7 +100,7 @@ function get_tripal_contact_admin_form_reindex_set(&$form) {
 /**
  * Validate the contact settings form.
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_admin_validate($form, &$form_state) {
 

legacy/tripal_contact/includes/tripal_contact.chado_node.inc

@@ -3,14 +3,14 @@
  * @file
  * Implements drupal node hooks.
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 
 /**
  * Implementation of hook_node_info().
  * This node_info, is a simple node that describes the functionallity of the module.
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_node_info() {
 
@@ -50,7 +50,7 @@ function tripal_contact_node_info() {
  *  @return $form
  *    The information that was enterd allong with
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function chado_contact_form(&$node, $form_state) {
   $form = array();
@@ -242,7 +242,7 @@ function chado_contact_form(&$node, $form_state) {
  * Implements hook_validate().
  * Validates submission of form when adding or updating a contact node.
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function chado_contact_validate($node, $form, &$form_state) {
 
@@ -315,7 +315,7 @@ function chado_contact_validate($node, $form, &$form_state) {
  *  access.  The only exception is when the $op == 'create'.  We will always
  *  return TRUE if the permission is set.
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_node_access($node, $op, $account ) {
 
@@ -362,7 +362,7 @@ function tripal_contact_node_access($node, $op, $account ) {
  *  @parm $node
  *    Then node which contains the information stored within the node-ID
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function chado_contact_insert($node) {
   $contact_id = '';
@@ -445,7 +445,7 @@ function chado_contact_insert($node) {
  * @param $node
  *   The node being updated
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function chado_contact_update($node) {
   // remove surrounding white-space on submitted values
@@ -507,7 +507,7 @@ function chado_contact_update($node) {
  * @return $node
  *   The node with the information to be loaded into the database
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function chado_contact_load($nodes) {
 
@@ -561,7 +561,7 @@ function chado_contact_load($nodes) {
  *  @parm $node
  *    Then node which contains the information stored within the node-ID
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function chado_contact_delete(&$node) {
 
@@ -591,7 +591,7 @@ function chado_contact_delete(&$node) {
 /**
  * Implements hook_node_view().
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_node_view($node, $view_mode, $langcode) {
   switch ($node->type) {
@@ -639,7 +639,7 @@ function tripal_contact_node_view($node, $view_mode, $langcode) {
 /**
  * Implements hook_node_presave().
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_node_presave($node) {
   switch ($node->type) {
@@ -661,7 +661,7 @@ function tripal_contact_node_presave($node) {
  * Implements hook_node_insert().
  * Acts on all content types.
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_node_insert($node) {
 
@@ -690,7 +690,7 @@ function tripal_contact_node_insert($node) {
  * Implements hook_node_update().
  * Acts on all content types.
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_node_update($node) {
 

legacy/tripal_contact/theme/tripal_contact.theme.inc

@@ -2,7 +2,7 @@
 /**
  *
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_preprocess_tripal_contact_relationships(&$variables) {
   $contact = $variables['node']->contact;

legacy/tripal_contact/tripal_contact.install

@@ -4,14 +4,14 @@
  * @file
  * Handles install, uninstall, disable and enable functionality including database tables.
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 
 /**
  * Implements hook_disable().
  * Disable default views when module is disabled
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_disable() {
 
@@ -27,7 +27,7 @@ function tripal_contact_disable() {
 /**
  * Implementation of hook_requirements().
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_requirements($phase) {
   $requirements = array();
@@ -47,7 +47,7 @@ function tripal_contact_requirements($phase) {
 /**
  * Implementation of hook_install().
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_install() {
 
@@ -72,7 +72,7 @@ function tripal_contact_install() {
 /**
  * Implementation of hook_uninstall().
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_uninstall() {
   /*
@@ -87,7 +87,7 @@ function tripal_contact_uninstall() {
 /**
  * Adds any cvs needed by this module.
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_add_cvs() {
 
@@ -122,7 +122,7 @@ function tripal_contact_add_cvs() {
 /**
  * Adds any cvterms needed by this module.
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_add_cvterms() {
 
@@ -131,7 +131,7 @@ function tripal_contact_add_cvterms() {
 /**
  * Implementation of hook_schema().
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_schema() {
   $schema['chado_contact'] = array(
@@ -170,7 +170,7 @@ function tripal_contact_schema() {
  * Add any custom tables needed by this module.
  * - Contactprop: keep track of properties of contact
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 // This function was moved to tripal_chado/includes/setup/tripal_chado.setup.inc
 /* function tripal_contact_add_custom_tables(){

legacy/tripal_contact/tripal_contact.module

@@ -3,7 +3,7 @@
  * @file
  * Functions related to general module functionality.
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 
 /**
@@ -27,7 +27,7 @@ require_once 'includes/tripal_contact.chado_node.inc';
  * for this module which then includes tripal_contact.views.inc where all the
  * views integration code is.
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_views_api() {
   return array(
@@ -44,7 +44,7 @@ function tripal_contact_views_api() {
  *   An array of menu items that is visible within the Drupal Menu, returned as soon
  *   as the program is ran
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_menu() {
 
@@ -134,7 +134,7 @@ function tripal_contact_search_biological_data_views() {
  * @return
  *   An array of themeing functions to register
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
@@ -182,7 +182,7 @@ function tripal_contact_theme($existing, $type, $theme, $path) {
 /**
  * Implement hook_permission().
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_permission() {
   return array(
@@ -214,7 +214,7 @@ function tripal_contact_permission() {
 /**
  * Implementation of hook_form_alter().
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_form_alter(&$form, &$form_state, $form_id) {
 

legacy/tripal_contact/tripal_contact.views_default.inc

@@ -3,13 +3,13 @@
  * @file
  * Define default views for contacts.
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 
 /**
  * Implements hook_views_default_views().
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_views_default_views() {
   $views = array();
@@ -32,7 +32,7 @@ function tripal_contact_views_default_views() {
 /**
  * Defines the contact user search default view.
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_defaultvalue_user_contacts() {
 
@@ -75,7 +75,7 @@ function tripal_contact_defaultvalue_user_contacts() {
 /**
  * Define the default view for contact administration.
  *
- * @ingroup tripal_contact
+ * @ingroup tripal_legacy_contact
  */
 function tripal_contact_defaultview_admin_contacts() {
 

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

@@ -5,8 +5,8 @@
  */
 
 /**
- * @defgroup tripal_chado_node_api Chado Node API
- * @ingroup tripal_chado_api
+ * @defgroup tripal_legacy_chado_node_api Legacy Chado Nodes
+ * @ingroup tripal_legacy_api
  * @{
  * Many Tripal modules implement Drupal node types as a means of displaying chado
  * records individually through Drupal as a single web page. In order to do this, many of
@@ -52,7 +52,7 @@
  * @return
  *   The chado id of the associated chado record
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_get_id_from_nid($table, $nid, $linking_table = NULL) {
   if (empty($linking_table)) {
@@ -82,7 +82,7 @@ function chado_get_id_from_nid($table, $nid, $linking_table = NULL) {
  * @return
  *   The nid of the associated node
  *
- *  @ingroup tripal_chado_node_api
+ *  @ingroup tripal_legacy_chado_node_api
  */
 function chado_get_nid_from_id($table, $id, $linking_table = NULL) {
   if (empty($linking_table)) {
@@ -106,7 +106,7 @@ function chado_get_nid_from_id($table, $id, $linking_table = NULL) {
  * @return
  *    The name of the chado base table for the specified content type
  *
- *  @ingroup tripal_chado_node_api
+ *  @ingroup tripal_legacy_chado_node_api
  */
 function chado_node_get_base_table($content_type, $module = FALSE) {
 
@@ -303,7 +303,7 @@ function chado_add_node_form_subtables_remove_button_submit($form, &$form_state)
  * Ajax function which returns the section of the form to be re-rendered
  * for either the properties, dbxref or relationship sub-sections.
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function chado_add_node_form_subtable_ajax_update($form, &$form_state) {
 
@@ -411,7 +411,7 @@ function chado_add_node_form_subtable_ajax_update($form, &$form_state) {
  * functions: hook_chado_node_sync_create_new_node(), hook_chado_node_sync_form(),
  * hook_chado_node_sync_select_query().
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_node_sync_form($form, &$form_state) {
   $form = array();
@@ -652,7 +652,7 @@ function chado_node_sync_form($form, &$form_state) {
 /**
  * Generic Sync Form Validate
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function chado_node_sync_form_validate($form, &$form_state) {
 
@@ -672,7 +672,7 @@ function chado_node_sync_form_validate($form, &$form_state) {
 /**
  * Generic Sync Form Submit
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function chado_node_sync_form_submit($form, $form_state) {
 
@@ -781,7 +781,7 @@ function chado_node_sync_form_submit($form, $form_state) {
  *   Optional. Used by the Trpial Jobs system when running this function
  *   as a job. It is not needed othewise.
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_node_sync_records($base_table, $max_sync = FALSE,
     $organism_id = FALSE, $types = array(), $ids = array(),
@@ -998,7 +998,7 @@ function chado_node_sync_records($base_table, $max_sync = FALSE,
  *   Optional. This should be the job id from the Tripal jobs system. Typically,
  *   only the Tripal jobs system will use the argument.
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_cleanup_orphaned_nodes($table, $nentries = 25000,
     $linking_table = NULL, $node_type = NULL, $job_id = NULL) {
@@ -1064,7 +1064,7 @@ function chado_cleanup_orphaned_nodes($table, $nentries = 25000,
  *   This should be the job id from the Tripal jobs system.  This function
  *   will update the job status using the provided job ID.
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_cleanup_orphaned_nodes_part($table, $job_id = NULL, $nentries,
     $offset, $linking_table, $node_type) {
@@ -1210,7 +1210,7 @@ function chado_cleanup_orphaned_nodes_part($table, $job_id = NULL, $nentries,
  *   A node object containing all the fields necessary to create a new node
  *   during sync
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function hook_chado_node_sync_create_new_node($new_node, $record) {
 
@@ -1233,7 +1233,7 @@ function hook_chado_node_sync_create_new_node($new_node, $record) {
  * Note: For your own module, replace hook in the function name with the
  * machine-name of your chado node type (ie: chado_feature).
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function hook_chado_node_sync_form($form, &$form_state) {
 
@@ -1255,7 +1255,7 @@ function hook_chado_node_sync_form($form, &$form_state) {
  * Note: For your own module, replace hook in the function name with the
  * machine-name of your chado node type (ie: chado_feature).
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function hook_chado_node_sync_form_submit ($form, $form_state) {
 
@@ -1311,7 +1311,7 @@ function hook_chado_node_sync_form_submit ($form, $form_state) {
  *    'where_args: An associative array of arguments to be subbed in to the
  *      where clause where the
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function hook_chado_node_sync_select_query($query) {
 

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

@@ -2,7 +2,7 @@
 
 /**
  * @file
- * API to manage the chado _dbxref table for various Tripal Node Types
+ * API to manage the Chado dbxref table for various Tripal Node Types
  *
  * How To Use:
  * @code
@@ -93,7 +93,7 @@
 
  * @endcode
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 
 /**
@@ -120,7 +120,7 @@
  *       the [value] is the human-readable name of the option. This includes all databases
  *       in the chado db table by default
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_add_node_form_dbxrefs(&$form, &$form_state, $details) {
 
@@ -437,8 +437,6 @@ function chado_add_node_form_dbxrefs(&$form, &$form_state, $details) {
 /**
  * Validate the user input for creating a new dbxref
  * Called by the add button in chado_add_node_form_dbxrefs
- *
- * @ingroup tripal_core
  */
 function chado_add_node_form_dbxrefs_add_button_validate($form, &$form_state) {
 
@@ -468,7 +466,6 @@ function chado_add_node_form_dbxrefs_add_button_validate($form, &$form_state) {
  * Create an array of additional dbxrefs in the form state. This array will then be
  * used to rebuild the form in subsequent builds
  *
- * @ingroup tripal_core
  */
 function chado_add_node_form_dbxrefs_add_button_submit($form, &$form_state) {
 
@@ -500,7 +497,6 @@ function chado_add_node_form_dbxrefs_add_button_submit($form, &$form_state) {
 /**
  * Called by the many remove buttons in chado_add_node_form_dbxrefs
  *
- * @ingroup tripal_core
  */
 function chado_add_node_form_dbxrefs_remove_button_validate($form, $form_state) {
   // No validation needed.
@@ -510,7 +506,6 @@ function chado_add_node_form_dbxrefs_remove_button_validate($form, $form_state)
  * Remove the correct dbxref from the form
  * Called by the many remove buttons in chado_add_node_form_dbxrefs
  *
- * @ingroup tripal_core
  */
 function chado_add_node_form_dbxrefs_remove_button_submit(&$form, &$form_state) {
 
@@ -545,7 +540,6 @@ function chado_add_node_form_dbxrefs_remove_button_submit(&$form, &$form_state)
  *   ),
  * );
  *
- * @ingroup tripal_core
  */
 function chado_add_node_form_dbxrefs_create_dbxref_formstate_array($form, &$form_state) {
 
@@ -572,7 +566,6 @@ function chado_add_node_form_dbxrefs_create_dbxref_formstate_array($form, &$form
 /**
  * Function to theme the add/remove dbxrefs form into a table
  *
- * @ingroup tripal_chado_node_api
  */
 function theme_chado_add_node_form_dbxrefs_table($variables) {
   $element = $variables['element'];
@@ -630,7 +623,7 @@ function theme_chado_add_node_form_dbxrefs_table($variables) {
  * @return
  *   A dbxref array
  *
- * @ingroup tripal_chado_node_api
+ *  @ingroup tripal_legacy_chado_node_api
  */
 function chado_retrieve_node_form_dbxrefs($node) {
   $dbxrefs = array();
@@ -663,7 +656,7 @@ function chado_retrieve_node_form_dbxrefs($node) {
  *   An array of databa references from chado_retrieve_node_form_dbxrefs($node).
  *   This can be used if you need special handling for some of the database references
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_update_node_form_dbxrefs($node, $details, $retrieved_dbxrefs = FALSE) {
 

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

@@ -94,7 +94,7 @@
 
  * @endcode
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 
 /**
@@ -134,7 +134,7 @@
  *       from the named vocabulary.  The array must have keys with the cvterm_id
  *       and values with the cvterm name.
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 
 function chado_add_node_form_properties(&$form, &$form_state, $details) {
@@ -646,7 +646,6 @@ function chado_add_node_form_properties(&$form, &$form_state, $details) {
  * Validate the user input for creating a new property
  * Called by the add button in chado_add_node_form_properties
  *
- * @ingroup tripal_core
  */
 function chado_add_node_form_properties_add_button_validate($form, &$form_state) {
 
@@ -676,7 +675,6 @@ function chado_add_node_form_properties_add_button_validate($form, &$form_state)
  * Create an array of properties in the form state. This array will then be
  * used to rebuild the form in subsequent builds
  *
- * @ingroup tripal_core
  */
 function chado_add_node_form_properties_add_button_submit($form, &$form_state) {
 
@@ -712,7 +710,6 @@ function chado_add_node_form_properties_add_button_submit($form, &$form_state) {
 /**
  * Called by the many remove buttons in chado_add_node_form_properties
  *
- * @ingroup tripal_core
  */
 function chado_add_node_form_properties_remove_button_validate($form, &$form_state) {
   // No validation needed.
@@ -722,7 +719,6 @@ function chado_add_node_form_properties_remove_button_validate($form, &$form_sta
  * Remove the correct property from the form
  * Called by the many remove buttons in chado_add_node_form_properties
  *
- * @ingroup tripal_core
  */
 function chado_add_node_form_properties_remove_button_submit(&$form, &$form_state) {
 
@@ -741,6 +737,12 @@ function chado_add_node_form_properties_remove_button_submit(&$form, &$form_stat
   }
 }
 
+/**
+ *
+ * @param unknown $form
+ * @param unknown $form_state
+ * @return unknown
+ */
 function chado_add_node_form_properties_ajax_desc($form, $form_state) {
   return $form['properties']['property_table']['new']['type'];
 }
@@ -761,7 +763,6 @@ function chado_add_node_form_properties_ajax_desc($form, $form_state) {
  *   ),
  * );
  *
- * @ingroup tripal_core
  */
 function chado_add_node_form_properties_create_property_formstate_array($form, &$form_state) {
 
@@ -844,7 +845,7 @@ function theme_chado_add_node_form_properties($variables) {
  * @return
  *   A property array
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_retrieve_node_form_properties($node) {
   $properties = array();
@@ -877,7 +878,7 @@ function chado_retrieve_node_form_properties($node) {
  *   An array of properties from chado_retrieve_node_form_properties($node). This can be used if you need
  *   special handling for some of the properties (See FeatureMap chado_featuremap_insert for an example)
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_update_node_form_properties($node, $details, $retrieved_properties = FALSE) {
 

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

@@ -92,7 +92,7 @@
 
  * @endcode
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 
 /**
@@ -122,7 +122,7 @@
  *     - subject_field_name: the name of the subject field in your relationship table (default: subject_id)
  *     - object_field_name: the name of the object field in your relationship table (default: object_id)
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_add_node_form_relationships(&$form, &$form_state, $details) {
 
@@ -598,7 +598,6 @@ function chado_add_node_form_relationships(&$form, &$form_state, $details) {
  * Validate the user input for creating a new relationship.
  * Called by the add button in chado_add_node_form_relationships.
  *
- * @ingroup tripal_core
  */
 function chado_add_node_form_relationships_add_button_validate($form, &$form_state) {
 
@@ -727,7 +726,6 @@ function chado_add_node_form_relationships_add_button_validate($form, &$form_sta
  * Create an array of additional relationships in the form state. This array will then be
  * used to rebuild the form in subsequent builds
  *
- * @ingroup tripal_core
  */
 function chado_add_node_form_relationships_add_button_submit($form, &$form_state) {
 
@@ -785,7 +783,6 @@ function chado_add_node_form_relationships_add_button_submit($form, &$form_state
 /**
  * Called by the many remove buttons in chado_add_node_form_relationships
  *
- * @ingroup tripal_core
  */
 function chado_add_node_form_relationships_remove_button_validate($form, &$form_state) {
   // No validation needed.
@@ -795,7 +792,6 @@ function chado_add_node_form_relationships_remove_button_validate($form, &$form_
  * Remove the correct relationship from the form
  * Called by the many remove buttons in chado_add_node_form_relationships
  *
- * @ingroup tripal_core
  */
 function chado_add_node_form_relationships_remove_button_submit(&$form, &$form_state) {
 
@@ -828,7 +824,6 @@ function chado_add_node_form_relationships_remove_button_submit(&$form, &$form_s
  *   ),
  * );
  *
- * @ingroup tripal_core
  */
 function chado_add_node_form_relationships_create_relationship_formstate_array($form, &$form_state) {
 
@@ -858,7 +853,6 @@ function chado_add_node_form_relationships_create_relationship_formstate_array($
 /**
  * Function to theme the add/remove relationships form into a table
  *
- * @ingroup tripal_chado_node_api
  */
 function theme_chado_add_node_form_relationships_table($variables) {
   $element = $variables['element'];
@@ -929,7 +923,7 @@ function theme_chado_add_node_form_relationships_table($variables) {
  * @return
  *   A relationship array
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_retrieve_node_form_relationships($node) {
   $rels = array();
@@ -961,7 +955,7 @@ function chado_retrieve_node_form_relationships($node) {
  *   An array of relationships from chado_retrieve_node_form_relationships($node). This
  *   can be used if you need special handling for some of the relationships.
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_update_node_form_relationships($node, $details, $retrieved_relationships = FALSE) {
 
@@ -1039,7 +1033,7 @@ function chado_update_node_form_relationships($node, $details, $retrieved_relati
  * @param $string
  *    The part of the string already typed in the textfield
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function chado_add_node_form_relationships_name_to_id_callback($base_table, $name_field, $string) {
   $matches = array();

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

@@ -191,7 +191,7 @@
  * @param $node
  *   The node object
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_get_node_title($node) {
   $content_type = $node->type;
@@ -240,7 +240,7 @@ function chado_get_node_title($node) {
  *     -custom_tokens: an array of custom tokens that follow the same format as those
  *      generated by chado_node_generate_tokens().
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_add_admin_form_set_title(&$form, &$form_state, $details) {
 
@@ -416,6 +416,8 @@ function chado_add_admin_form_set_title_form_submit($form, $form_state) {
  * @return
  *   A string containing tokens describing the default format for the title of nodes
  *   of the specified content type.
+ *
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_node_get_title_format($content_type, &$tokens, $base_table = NULL) {
   $format_record_format = $format = '';
@@ -474,6 +476,8 @@ function chado_node_get_title_format($content_type, &$tokens, $base_table = NULL
  * setting before this API was created. That has since been removed but
  * but to remain backwards compatible this function checks for those
  * old settings and translates them into new defaults.
+ *
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_node_get_legacy_title_default($content_type) {
   if ($content_type == 'chado_feature') {
@@ -525,7 +529,7 @@ function chado_node_get_legacy_title_default($content_type) {
  * @param $node
  *   The node object
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_get_node_url($node) {
   $content_type = $node->type;
@@ -578,6 +582,8 @@ function chado_get_node_url($node) {
  *
  * @return
  *   The URL alias that was set.
+ *
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_set_node_url($node) {
 
@@ -651,6 +657,8 @@ function chado_set_node_url($node) {
  *   The machine name of the node type to update URLs for.
  * @param $job_id
  *   The ID of the tripal job calling this function.
+ *
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_update_existing_node_urls($content_type, $job_id = 0) {
   $transaction = db_transaction();
@@ -758,7 +766,7 @@ function chado_update_existing_node_urls($content_type, $job_id = 0) {
  *     -custom_tokens: an array of custom tokens that follow the same format as those
  *      generated by chado_node_generate_tokens().
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_add_admin_form_set_url(&$form, &$form_state, $details) {
 
@@ -952,6 +960,8 @@ function chado_add_admin_form_set_url_form_submit($form, $form_state) {
  * @return
  *   A string containing tokens describing the default format for the url of nodes
  *   of the specified content type.
+ *
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_node_get_url_format($content_type, &$tokens, $base_table = NULL) {
   $format_record_format = $format = '';
@@ -1012,6 +1022,8 @@ function chado_node_get_url_format($content_type, &$tokens, $base_table = NULL)
  * setting before this API was created. That has since been removed but
  * to remain backwards compatible this function checks for those
  * old settings and translates them into new defaults.
+ *
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_node_get_legacy_url_default($content_type) {
 
@@ -1075,6 +1087,8 @@ function chado_node_get_legacy_url_default($content_type) {
  * @param $tokens
  *   An array of tokens generated by chado_node_generate_tokens(). This is saved to ensure the
  *   tokens that are available when the format is created are still available when it's used
+ *
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_node_add_token_format($application, $content_type, $format, $tokens) {
 
@@ -1114,6 +1128,8 @@ function chado_node_add_token_format($application, $content_type, $format, $toke
  *      than just the format string
  * @return
  *   A string specifying the format
+ *
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_node_get_token_format($application, $content_type, $options = array()) {
 
@@ -1149,6 +1165,8 @@ function chado_node_get_token_format($application, $content_type, $options = arr
  * @return
  *   A format string including tokens describing the unique constraint
  *   including all name fields
+ *
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_node_get_unique_constraint_format($base_table, $format_type = 'title') {
 
@@ -1230,6 +1248,8 @@ function chado_node_get_unique_constraint_format($base_table, $format_type = 'ti
  *    -location: the location of the value in a chado node variable with each level
  *     separated by an arrow (->) symbol. For example, the location for $node->feature->type_id->name
  *     is feature>type_id>name
+ *
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_node_generate_tokens($base_table, $token_prefix = FALSE, $location_prefix = FALSE) {
 
@@ -1303,6 +1323,8 @@ function chado_node_generate_tokens($base_table, $token_prefix = FALSE, $locatio
  *
  * @return
  *   The value of the token
+ *
+ * @ingroup tripal_legacy_chado_node_api
  */
 function chado_get_token_value($token_info, $node, $options = array()) {
 
@@ -1364,6 +1386,7 @@ function chado_get_token_value($token_info, $node, $options = array()) {
  *
  * @return
  *   HTML displaying the token list
+ *
  */
 function chado_node_format_tokens($tokens) {
 
@@ -1444,6 +1467,7 @@ function tripal_sort_key_length_asc($a, $b) {
  *
  * For example, given the token [feature.type_id>cvterm.cvterm_id] you don't
  * want the actual id indexed but instead would want the term name, [feature.type_id>cvterm.name]
+ *
  */
 function chado_node_get_readable_format($token) {
 

legacy/tripal_core/includes/tripal_core.form_elements.inc

@@ -7,7 +7,7 @@
 /**
  * Register form elements.
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function tripal_core_element_info() {
   $elements = array();
@@ -35,7 +35,7 @@ function tripal_core_element_info() {
 /**
  * Upload File and keep track of previously uploaded files.
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function expand_file_upload_combo($element, $form_state, $complete_form) {
 
@@ -81,7 +81,7 @@ function expand_file_upload_combo($element, $form_state, $complete_form) {
 /**
  * Theme the file upload combo form element.
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function theme_file_upload_combo($variables) {
   $element = $variables['element'];
@@ -99,7 +99,7 @@ function theme_file_upload_combo($variables) {
 /**
  * Validate all content passed into the file upload combo form element.
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function file_upload_combo_value_callback($element, $input = FALSE, &$form_state) {
   $values = array();
@@ -157,7 +157,7 @@ function file_upload_combo_value_callback($element, $input = FALSE, &$form_state
 /**
  * Retrieve Sequence bases form element.
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function expand_sequence_combo($element, $form_state, $complete_form) {
 
@@ -197,7 +197,7 @@ function expand_sequence_combo($element, $form_state, $complete_form) {
  * Validate all content passed into the sequence combo form element
  * D7 @todo: test/fix this callback.
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function sequence_combo_value_callback($element, $input = FALSE, &$form_state) {
   $upstream = $form['values'][$element['#name']]['upstream'];
@@ -222,7 +222,7 @@ function sequence_combo_value_callback($element, $input = FALSE, &$form_state) {
 /**
  * Theme the file sequence form element.
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function theme_sequence_combo($variables) {
   $element = $variables['element'];

legacy/tripal_core/tripal_core.install

@@ -7,7 +7,7 @@
 /**
  * Implementation of hook_install().
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function tripal_core_install() {
 
@@ -16,7 +16,7 @@ function tripal_core_install() {
 /**
  * Implementation of hook_schema().
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function tripal_core_schema() {
 
@@ -43,7 +43,7 @@ function tripal_core_schema() {
 /**
  * Implementation of hook_uninstall().
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function tripal_core_uninstall() {
 
@@ -61,7 +61,7 @@ function tripal_core_uninstall() {
  * can easily provide the entire list for hook_install or individual
  * tables for an update.
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function tripal_core_get_schemas() {
   $schema = array();

legacy/tripal_core/tripal_core.module

@@ -4,7 +4,23 @@
  * The Tripal Core module
  */
 
+/**
+ * @defgroup tripal_legacy_api Tripal Legacy API
+ * @{
+ * Provides an application programming interface (API) for Tripal v2
+ * backwards-compatibilty. These functions are DEPRECATED and may not
+ * be available in future version of Tripal.
+ * @}
+ */
 
+/**
+ * @defgroup tripal_legacy_core Legacy Tripal Core Module
+ * @ingroup tripal_legacy_modules
+ * @{
+ * Functionality useful for all other Tripal modules including the Tripal jobs, files,
+ * materialized views and custom table functions.
+ * @}
+ */
 require_once 'api/tripal_core.chado_nodes.api.inc';
 require_once 'api/tripal_core.chado_nodes.title_and_path.inc';
 require_once 'api/tripal_core.chado_nodes.properties.api.inc';
@@ -14,20 +30,13 @@ require_once 'api/tripal_core.tripal_variables.api.inc';
 require_once 'includes/tripal_core.form_elements.inc';
 require_once 'includes/tripal_core.search.inc';
 
-/**
- * @defgroup tripal_core Tripal Core Module
- * @ingroup tripal_modules
- * @{
- * Functionality useful for all other Tripal modules including the Tripal jobs, files,
- * materialized views and custom table functions.
- * @}
- */
+
 
 /**
  * Implements hook_init().
  * Used to set the search_path, create default content and set default variables.
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function tripal_core_init() {
 
@@ -45,7 +54,7 @@ function tripal_core_init() {
  * Implements hook_menu().
  * Defines all menu items needed by Tripal Core
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function tripal_core_menu() {
   $items = array();
@@ -108,7 +117,7 @@ function tripal_core_access_node_toc_form($node) {
  *  want permissionis that protect creation, editing and deleting of chado
  *  data objects
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function tripal_core_permission() {
   return array();
@@ -118,7 +127,7 @@ function tripal_core_permission() {
  * Implements hook_theme().
  * Registers template files/functions used by this module.
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function tripal_core_theme($existing, $type, $theme, $path) {
   return array(
@@ -199,7 +208,7 @@ function tripal_core_coder_ignore() {
  * for this module which then includes tripal_db.views.inc where all the
  * views integration code is.
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function tripal_core_views_api() {
   return array(
@@ -210,7 +219,7 @@ function tripal_core_views_api() {
 /**
  * Implements hook_node_view_alter().
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function tripal_core_node_view_alter(&$build) {
   module_load_include('inc', 'tripal_core', 'includes/tripal_core.toc');
@@ -220,7 +229,7 @@ function tripal_core_node_view_alter(&$build) {
 /**
  * Implements hook_node_view().
  *
- * @ingroup tripal_core
+ * @ingroup tripal_legacy_core
  */
 function tripal_core_node_view($node, $view_mode, $langcode) {
 

legacy/tripal_core/tripal_core.views_default.inc

@@ -7,7 +7,7 @@
 /**
  * Describes core default views
 *
-* @ingroup tripal_core
+* @ingroup tripal_legacy_core
 */
 function tripal_core_views_default_views() {
   $views = array();

legacy/tripal_cv/api/tripal_cv.api.inc

@@ -1,4 +1,20 @@
 <?php
+
+/**
+ * @file
+ * Provides legacy application programming interface (API) to manage controlled
+ * vocabularies in the Chado database.
+ */
+
+/**
+ * @defgroup tripal_legacy_chado_cv_api Legacy Chado CV
+ * @ingroup tripal_legacy_api
+ * @{
+ * Provides an application programming interface (API) to manage entities
+ * that use Chado as their base data.
+ * @}
+ */
+
 /**
  * Retreives the default vocabulary for a given table and field.
  *
@@ -23,6 +39,8 @@
  * @return
  *   The cv object of the default vocabulary or an empty array if not
  *   available.
+ *
+ * @ingroup tripal_legacy_chado_cv_api
  */
 function tripal_get_default_cv($table, $field) {
   $sql = "
@@ -55,6 +73,8 @@ function tripal_get_default_cv($table, $field) {
  * @return
  *   If an assignment is present, an object containing the 'table_name' and
  *   'field_name' is returned.
+ *
+ * @ingroup tripal_legacy_chado_cv_api
  */
 function tripal_get_default_cv_table($cv_id) {
   $default = db_select('tripal_cv_defaults', 't')
@@ -85,6 +105,8 @@ function tripal_get_default_cv_table($cv_id) {
  * @return
  *   An array(cvterm_id => name)
  *   for each cvterm in the chado cvterm table where cv_id=that supplied
+ *
+ * @ingroup tripal_legacy_chado_cv_api
  */
 function tripal_get_cvterm_default_select_options($table, $field, $field_desc) {
 

legacy/tripal_cv/tripal_cv.install

@@ -9,7 +9,7 @@
  * Implements hook_disable().
  * Disable default views when module is disabled
  *
- * @ingroup tripal_cv
+ * @ingroup tripal_legacy_cv
  */
 function tripal_cv_disable() {
 
@@ -25,7 +25,7 @@ function tripal_cv_disable() {
 /**
  * Implementation of hook_requirements().
  *
- * @ingroup tripal_cv
+ * @ingroup tripal_legacy_cv
  */
 function tripal_cv_requirements($phase) {
   $requirements = array();
@@ -45,7 +45,7 @@ function tripal_cv_requirements($phase) {
 /**
  * Implementation of hook_install().
  *
- * @ingroup tripal_cv
+ * @ingroup tripal_legacy_cv
  */
 function tripal_cv_install() {
 
@@ -54,7 +54,7 @@ function tripal_cv_install() {
 /**
  * Implementation of hook_uninstall().
  *
- * @ingroup tripal_cv
+ * @ingroup tripal_legacy_cv
  */
 function tripal_cv_uninstall() {
 

legacy/tripal_cv/tripal_cv.module

@@ -6,8 +6,8 @@
  */
 
 /**
- * @defgroup tripal_cv Controlled Vocabulary Module
- * @ingroup tripal_modules
+ * @defgroup tripal_legacy_cv Legacy Controlled Vocabulary Module
+ * @ingroup tripal_legacy_modules
  * @{
  * Provides functions for managing chado controlled vocabularies which are used ubiquitously
  * throughout chado.
@@ -25,7 +25,7 @@ require_once 'includes/tripal_cv.cvterm_form.inc';
  * Implements hook_init().
  * Adds CSS and JS needed for this modules rendered content
  *
- * @ingroup tripal_cv
+ * @ingroup tripal_legacy_cv
  */
 function tripal_cv_init() {
 
@@ -35,7 +35,7 @@ function tripal_cv_init() {
  * Implements hook_menu().
  * Registers all menu items associated with this module
  *
- * @ingroup tripal_cv
+ * @ingroup tripal_legacy_cv
  */
 function tripal_cv_menu() {
   $items = array();
@@ -205,7 +205,7 @@ function tripal_cv_help ($path, $arg) {
  *  want permissionis that protect creation, editing and deleting of chado
  *  data objects
  *
- * @ingroup tripal_cv
+ * @ingroup tripal_legacy_cv
  */
 function tripal_cv_permission() {
   return array(
@@ -219,7 +219,7 @@ function tripal_cv_permission() {
  *  for this module which then includes tripal_cv.views.inc where all the
  *  views integration code is
  *
- * @ingroup tripal_cv
+ * @ingroup tripal_legacy_cv
  */
 function tripal_cv_views_api() {
   return array('api' => 3.0);
@@ -229,7 +229,7 @@ function tripal_cv_views_api() {
  * Implements hook_coder_ignore().
  * Defines the path to the file (tripal_cv.coder_ignores.txt) where ignore rules for coder are stored
  *
- * @ingroup tripal_cv
+ * @ingroup tripal_legacy_cv
  */
 function tripal_cv_coder_ignore() {
   return array(
@@ -242,7 +242,7 @@ function tripal_cv_coder_ignore() {
  * Implements hook_form_alter().
  * Alter Forms
  *
- * @ingroup tripal_cv
+ * @ingroup tripal_legacy_cv
  */
 function tripal_cv_form_alter(&$form, &$form_state, $form_id) {
   if ($form_id == "tripal_cv_cvterm_form") {
@@ -264,7 +264,7 @@ function tripal_cv_form_alter(&$form, &$form_state, $form_id) {
  *  We create theme functions to allow users of the module to customize the
  *  look and feel of the output generated in this module
  *
- * @ingroup tripal_cv
+ * @ingroup tripal_legacy_cv
  */
 function tripal_cv_theme($existing, $type, $theme, $path) {
 

legacy/tripal_cv/tripal_cv.views_default.inc

@@ -7,7 +7,7 @@
 /**
  * Implements hook_views_default_views().
  *
- * @ingroup tripal_cv
+ * @ingroup tripal_legacy_cv
  */
 function tripal_cv_views_default_views() {
   $views = array();

legacy/tripal_db/tripal_db.install

@@ -8,7 +8,7 @@
  * Implements hook_disable().
  * Disable default views when module is disabled
  *
- * @ingroup tripal_db
+ * @ingroup tripal_legacy_db
  */
 function tripal_db_disable() {
 
@@ -24,7 +24,7 @@ function tripal_db_disable() {
 /**
  * Implementation of hook_requirements().
  *
- * @ingroup tripal_db
+ * @ingroup tripal_legacy_db
  */
 function tripal_db_requirements($phase) {
   $requirements = array();
@@ -44,7 +44,7 @@ function tripal_db_requirements($phase) {
 /**
  * Implementation of hook_install().
  *
- * @ingroup tripal_db
+ * @ingroup tripal_legacy_db
  */
 function tripal_db_install() {
 
@@ -53,7 +53,7 @@ function tripal_db_install() {
 /**
  * Implementation of hook_uninstall().
  *
- * @ingroup tripal_db
+ * @ingroup tripal_legacy_db
  */
 function tripal_db_uninstall() {
 

legacy/tripal_db/tripal_db.module

@@ -4,12 +4,9 @@
  * General functions for the db module
  */
 
-//require_once 'api/tripal_db.api.inc';
-require_once 'api/tripal_db.DEPRECATED.inc';
-
 /**
- * @defgroup tripal_db Database Reference Module
- * @ingroup tripal_modules
+ * @defgroup tripal_legacy_db Legacy Database Reference Module
+ * @ingroup tripal_legacy_modules
  * @{
  * Provides functions for managing chado database references which link chado content, such
  * as features and stocks, to records/pages in external databases/websites. For example,
@@ -19,10 +16,13 @@ require_once 'api/tripal_db.DEPRECATED.inc';
  * @}
  */
 
+require_once 'api/tripal_db.DEPRECATED.inc';
+
+
 /**
  * Implements hook_menu().
  *
- * @ingroup tripal_db
+ * @ingroup tripal_legacy_db
  */
 function tripal_db_menu() {
   $items = array();
@@ -69,7 +69,7 @@ function tripal_db_help ($path, $arg) {
  *  want permissionis that protect creation, editing and deleting of chado
  *  data objects
  *
- * @ingroup tripal_db
+ * @ingroup tripal_legacy_db
  */
 function tripal_db_permission() {
   return array(
@@ -87,7 +87,7 @@ function tripal_db_permission() {
  *  for this module which then includes tripal_db.views.inc where all the
  *  views integration code is
  *
- * @ingroup tripal_db
+ * @ingroup tripal_legacy_db
  */
 function tripal_db_views_api() {
   return array('api' => 3.0);
@@ -100,7 +100,7 @@ function tripal_db_views_api() {
  *  We create theme functions to allow users of the module to customize the
  *  look and feel of the output generated in this module
  *
- * @ingroup tripal_db
+ * @ingroup tripal_legacy_db
  */
 function tripal_db_theme($existing, $type, $theme, $path) {
 
@@ -127,7 +127,7 @@ function tripal_db_theme($existing, $type, $theme, $path) {
  * @return
  *   A json array of terms that begin with the provided string
  *
- * @ingroup tripal_db_api
+ * @ingroup tripal_legacy_db_api
  */
 function tripal_db_dbxref_accession_autocomplete($db_id, $string = '') {
   if (!$db_id) {

legacy/tripal_db/tripal_db.views_default.inc

@@ -7,7 +7,7 @@
 /**
  * Implements hook_views_default_views().
  *
- * @ingroup tripal_db
+ * @ingroup tripal_legacy_db
  */
 function tripal_db_views_default_views() {
   $views = array();

legacy/tripal_feature/includes/tripal_feature.admin.inc

@@ -7,7 +7,7 @@
 /**
  * Launchpad for feature administration.
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_admin_feature_view() {
   $output = '';
@@ -52,7 +52,7 @@ function tripal_feature_admin_feature_view() {
 /**
  * Feature Settings page
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_admin() {
 
@@ -152,7 +152,7 @@ function tripal_feature_admin() {
 /**
  * Validate the feature settings forms
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_admin_validate($form, &$form_state) {
   global $user;  // we need access to the user info

legacy/tripal_feature/includes/tripal_feature.chado_node.inc

@@ -10,7 +10,7 @@
  * Provide information to drupal about the node types that we're creating
  *  in this module
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_node_info() {
   $nodes = array();
@@ -40,7 +40,7 @@ function tripal_feature_node_info() {
 /**
  * Implementation of hook_form().
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function chado_feature_form($node, &$form_state) {
 
@@ -256,7 +256,7 @@ function chado_feature_form($node, &$form_state) {
  *   CASE B: Synchronizing a node from chado to drupal
  *   CASE C: Inserting a new node that exists in niether drupal nor chado
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function chado_feature_validate($node, $form, &$form_state) {
 
@@ -368,7 +368,7 @@ function chado_feature_validate($node, $form, &$form_state) {
  *  access.  The only exception is when the $op == 'create'.  We will always
  *  return TRUE if the permission is set.
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_node_access($node, $op, $account) {
   $node_type = $node;
@@ -410,7 +410,7 @@ function tripal_feature_node_access($node, $op, $account) {
  *  to our chado_feature table.  This function is called on insert of a new node
  *  of type 'chado_feature' and inserts the necessary information.
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function chado_feature_insert($node) {
 
@@ -507,7 +507,7 @@ function chado_feature_insert($node) {
 /**
  * Implements hook_update().
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function chado_feature_update($node) {
 
@@ -593,7 +593,7 @@ function chado_feature_update($node) {
 /**
  * Implements hook_delete().
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function chado_feature_delete($node) {
 
@@ -644,7 +644,7 @@ function chado_feature_delete($node) {
  * @param $feature_id
  *   The feature to attach the synonyms to
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function chado_feature_add_synonyms($synonyms, $feature_id) {
 
@@ -715,7 +715,7 @@ function chado_feature_add_synonyms($synonyms, $feature_id) {
  * When a node is requested by the user this function is called to allow us
  *  to add auxiliary data to the node object.
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function chado_feature_load($nodes) {
 
@@ -743,7 +743,7 @@ function chado_feature_load($nodes) {
  * Implements hook_node_presave().
  * Acts on all content types.
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_node_presave($node) {
 
@@ -787,7 +787,7 @@ function tripal_feature_node_presave($node) {
  * Implements hook_node_insert().
  * Acts on all content types.
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_node_insert($node) {
   // set the URL path after inserting.  We do it here because we do not
@@ -814,7 +814,7 @@ function tripal_feature_node_insert($node) {
  * Implements hook_node_update().
  * Acts on all content types.
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_node_update($node) {
 
@@ -836,7 +836,7 @@ function tripal_feature_node_update($node) {
  * Implements hook_node_view().
  * Acts on all content types.
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_node_view($node, $view_mode, $langcode) {
 

legacy/tripal_feature/includes/tripal_feature.delete.inc

@@ -7,7 +7,7 @@
 /**
  * A form for indicating the features to delete
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_delete_form() {
   $form['desc'] = array(
@@ -61,7 +61,7 @@ function tripal_feature_delete_form() {
 /**
  * Validation for the delete features form
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_delete_form_validate($form, &$form_state) {
   $organism_id   = $form_state['values']['organism_id'];
@@ -78,7 +78,7 @@ function tripal_feature_delete_form_validate($form, &$form_state) {
 /**
  * Submit for the delete features form
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_delete_form_submit($form, &$form_state) {
   global $user;
@@ -111,7 +111,7 @@ function tripal_feature_delete_form_submit($form, &$form_state) {
  * @param $job
  *   The tripal_job id
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_delete_features($organism_id, $analysis_id, $seq_type,
   $is_unique, $feature_names, $job = NULL) {

legacy/tripal_feature/theme/tripal_feature.theme.inc

@@ -2,7 +2,7 @@
 
 
 /**
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_preprocess_tripal_feature_sequence(&$variables) {
   // we want to provide a new variable that contains the matched features.
@@ -42,7 +42,7 @@ function tripal_feature_preprocess_tripal_feature_sequence(&$variables) {
  * @param $feature_id
  * @param $featurelocs
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_load_featureloc_sequences($feature_id, $featurelocs) {
 
@@ -178,7 +178,7 @@ function tripal_feature_load_featureloc_sequences($feature_id, $featurelocs) {
 /**
  * Used to sort the list of relationship parts by start position
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_sort_rel_parts_by_start($a, $b) {
   foreach ($a as $type_name => $details) {
@@ -201,7 +201,7 @@ function tripal_feature_sort_rel_parts_by_start($a, $b) {
  * @param $aggregate
  *   Whether or not to get the locations for related features
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_load_featurelocs($feature_id, $side = 'as_parent', $aggregate = 1) {
 
@@ -268,7 +268,7 @@ function tripal_feature_load_featurelocs($feature_id, $side = 'as_parent', $aggr
  * @return
  *   Which feature location comes first
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_sort_locations($a, $b) {
   return strnatcmp($a->fmin, $b->fmin);
@@ -281,7 +281,7 @@ function tripal_feature_sort_locations($a, $b) {
  * @param $parts
  * @param $defline
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_color_sequence($sequence, $parts, $defline) {
 
@@ -364,7 +364,7 @@ function tripal_feature_color_sequence($sequence, $parts, $defline) {
 /**
  * Used to sort the list of relationship parts by start position
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_sort_rel_parts_by_end($a, $b) {
   $val = strnatcmp($b['end'], $a['end']);
@@ -376,7 +376,7 @@ function tripal_feature_sort_rel_parts_by_end($a, $b) {
 /**
  *
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_preprocess_tripal_feature_relationships(&$variables) {
   // we want to provide a new variable that contains the matched features.
@@ -390,7 +390,7 @@ function tripal_feature_preprocess_tripal_feature_relationships(&$variables) {
 /**
  *
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_preprocess_tripal_feature_proteins(&$variables) {
   // we want to provide a new variable that contains the matched features.
@@ -403,7 +403,7 @@ function tripal_feature_preprocess_tripal_feature_proteins(&$variables) {
 /**
  *
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_preprocess_tripal_feature_alignments(&$variables) {
 
@@ -528,7 +528,7 @@ function tripal_feature_preprocess_tripal_feature_alignments(&$variables) {
    * not want to include these, so we have to filter on the SO terms:
  * match, or %_match
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_get_matched_alignments($feature) {
 
@@ -583,7 +583,7 @@ function tripal_feature_get_matched_alignments($feature) {
 /**
  *
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_preprocess_tripal_organism_feature_counts(&$variables, $hook) {
   $organism = $variables['node']->organism;
@@ -595,7 +595,7 @@ function tripal_feature_preprocess_tripal_organism_feature_counts(&$variables, $
  * @param $organism
  *  The organism of interest
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_load_organism_feature_counts($organism) {
 
@@ -692,7 +692,7 @@ function tripal_feature_load_organism_feature_counts($organism) {
  * @return
  *   An array with two objects
  *
- * @ingroup tripal_feature_api
+ * @ingroup tripal_legacy_feature_api
  */
 function tripal_feature_get_feature_relationships($feature) {
   // expand the feature object to include the feature relationships.

legacy/tripal_feature/tripal_feature.install

@@ -9,7 +9,7 @@
  *
  * Disable default views when module is disabled
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_disable() {
 
@@ -25,7 +25,7 @@ function tripal_feature_disable() {
 /**
  * Implements hook_requirements().
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_requirements($phase) {
   $requirements = array();
@@ -45,7 +45,7 @@ function tripal_feature_requirements($phase) {
 /**
  * Implements hook_install().
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_install() {
 
@@ -69,7 +69,7 @@ function tripal_feature_install() {
 /**
  * Implements hook_uninstall().
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_uninstall() {
 
@@ -77,7 +77,7 @@ function tripal_feature_uninstall() {
 /**
  * Implementation of hook_schema().
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_schema() {
 

legacy/tripal_feature/tripal_feature.module

@@ -5,8 +5,8 @@
  */
 
 /**
- * @defgroup tripal_feature Feature Module
- * @ingroup tripal_modules
+ * @defgroup tripal_legacy feature Legacy Feature Module
+ * @ingroup tripal_legacy_modules
  * @{
  * Integrates the Chado Sequence module with Drupal Nodes & Views
  * @}
@@ -27,7 +27,7 @@ require_once 'includes/tripal_feature.chado_node.inc';
  *  for this module which then includes tripal_db.views.inc where all the
  *  views integration code is
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_views_api() {
   return array(
@@ -48,7 +48,7 @@ function tripal_feature_views_api() {
  * @return
  *   help text for the path
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_help($path, $arg) {
   $output = '';
@@ -67,7 +67,7 @@ function tripal_feature_help($path, $arg) {
  *  want permissionis that protect creation, editing and deleting of chado
  *  data objects
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_permission() {
   return array(
@@ -103,7 +103,7 @@ function tripal_feature_permission() {
  *  by this module to the 'Create Content' Navigation menu item.  This function
  *  adds more menu items needed for this module.
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_menu() {
   $items = array();
@@ -199,7 +199,7 @@ function tripal_feature_search_biological_data_views() {
  *  We create theme functions to allow users of the module to customize the
  *  look and feel of the output generated in this module
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
@@ -310,7 +310,7 @@ function tripal_feature_theme($existing, $type, $theme, $path) {
  * Implements hook_job_describe_args() in order to describe the various feature jobs
  * to the tripal jobs interface.
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_job_describe_args($callback, $args) {
 
@@ -406,7 +406,7 @@ function tripal_feature_job_describe_args($callback, $args) {
  * Defines the path to the file (tripal_core.coder_ignores.txt) where ignore rules for
  * coder are stored
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_coder_ignore() {
   return array(
@@ -423,7 +423,7 @@ function tripal_feature_coder_ignore() {
  * @param $form_state
  * @param $form_id
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_form_alter(&$form, &$form_state, $form_id) {
   // turn off preview button for insert/updates
@@ -458,7 +458,7 @@ function tripal_feature_form_alter(&$form, &$form_state, $form_id) {
  * @return
  *   An array of field => criteria where the type is excluded if the criteria evaluates to TRUE
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_exclude_field_from_feature_by_default() {
   return array('residues' => 'TRUE');

legacy/tripal_feature/tripal_feature.views.inc

@@ -14,7 +14,7 @@
  *
  * @return: An array of handler definitions
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_views_handlers() {
   return array(

legacy/tripal_feature/tripal_feature.views_default.inc

@@ -7,7 +7,7 @@
 /**
  * Implements hook_views_default_views().
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_views_default_views() {
   $views = array();
@@ -30,7 +30,7 @@ function tripal_feature_views_default_views() {
 /**
  * Defines the feature user search default view.
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_defaultvalue_user_features() {
 
@@ -264,7 +264,7 @@ function tripal_feature_defaultvalue_user_features() {
 /**
  * The default feature administration view
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  */
 function tripal_feature_defaultview_admin_features() {
 

legacy/tripal_feature/views_handlers/views_handler_field_residues.inc

@@ -7,7 +7,7 @@
 /**
  * A handler to provide proper displays for sequence residues.
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_legacy_feature
  * @ingroup views_field_handlers
  */
 class views_handler_field_residues extends views_handler_field {

legacy/tripal_featuremap/includes/tripal_featuremap.admin.inc

@@ -7,7 +7,7 @@
 /**
  * Admin launchpad
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_admin_featuremaps_listing() {
   $output = '';
@@ -42,7 +42,7 @@ function tripal_featuremap_admin_featuremaps_listing() {
 /**
  * Administrative settings form
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_admin() {
   $form = array();

legacy/tripal_featuremap/includes/tripal_featuremap.chado_node.inc

@@ -10,7 +10,7 @@
  * Provide information to drupal about the node types that we're creating
  * in this module
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_node_info() {
   $nodes = array();
@@ -40,7 +40,7 @@ function tripal_featuremap_node_info() {
  *  When editing or creating a new node of type 'chado_featuremap' we need
  *  a form.  This function creates the form that will be used for this.
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function chado_featuremap_form($node, &$form_state) {
   $form = array();
@@ -151,7 +151,7 @@ function chado_featuremap_form($node, &$form_state) {
 /**
  * Validates submission of form when adding or updating a map node
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function chado_featuremap_validate($node, $form, &$form_state) {
 
@@ -219,7 +219,7 @@ function chado_featuremap_validate($node, $form, &$form_state) {
  *  access.  The only exception is when the $op == 'create'.  We will always
  *  return TRUE if the permission is set.
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_node_access($node, $op, $account) {
   $node_type = $node;
@@ -260,7 +260,7 @@ function tripal_featuremap_node_access($node, $op, $account) {
  *  to our chado_featuremap table.  This function is called on insert of a new node
  *  of type 'chado_featuremap' and inserts the necessary information.
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function chado_featuremap_insert($node) {
 
@@ -344,7 +344,7 @@ function chado_featuremap_insert($node) {
 /**
  * Implements hook_update(). Update nodes
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function chado_featuremap_update($node) {
 
@@ -413,7 +413,7 @@ function chado_featuremap_update($node) {
  *  When a node is requested by the user this function is called to allow us
  *  to add auxiliary data to the node object.
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function chado_featuremap_load($nodes) {
   foreach ($nodes as $nid => $node) {
@@ -444,7 +444,7 @@ function chado_featuremap_load($nodes) {
  * Implements hook_delete().
  *
  * Delete data from drupal and chado databases when a node is deleted
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function chado_featuremap_delete(&$node) {
 
@@ -475,7 +475,7 @@ function chado_featuremap_delete(&$node) {
 /**
  * Implements hook_node_presave(). Acts on all content types.
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_node_presave($node) {
   switch ($node->type) {
@@ -565,7 +565,7 @@ function tripal_featuremap_node_view($node, $view_mode, $langcode) {
  * Implements hook_node_insert().
  * Acts on all content types.
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_node_insert($node) {
 
@@ -592,7 +592,7 @@ function tripal_featuremap_node_insert($node) {
  * Implements hook_node_update().
  * Acts on all content types.
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_node_update($node) {
 

legacy/tripal_featuremap/tripal_featuremap.install

@@ -8,7 +8,7 @@
  * Implements hook_disable().
  * Disable default views when module is disabled
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_disable() {
 
@@ -24,7 +24,7 @@ function tripal_featuremap_disable() {
 /**
  * Implementation of hook_requirements().
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_requirements($phase) {
   $requirements = array();
@@ -44,7 +44,7 @@ function tripal_featuremap_requirements($phase) {
 /**
  * Implementation of hook_install().
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_install() {
 
@@ -64,7 +64,7 @@ function tripal_featuremap_install() {
 /**
  * Implementation of hook_uninstall().
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_uninstall() {
 
@@ -73,7 +73,7 @@ function tripal_featuremap_uninstall() {
 /**
  * Implementation of hook_schema().
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_schema() {
   $schema['chado_featuremap'] = array(
@@ -111,7 +111,7 @@ function tripal_featuremap_schema() {
 /**
  * Add cvs needed by the featuremap module
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_add_cvs() {
 
@@ -134,7 +134,7 @@ function tripal_featuremap_add_cvs() {
 /**
  * Add cv terms needed by the featuremap module
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_add_cvterms() {
 
@@ -307,7 +307,7 @@ function tripal_featuremap_add_cvterms() {
  *  - featuremap_dbxref
  *  - featureposprop
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 // This function was moved to tripal_chado/includes/setup/tripal_chado.setup.inc
 /* function tripal_featuremap_add_custom_tables(){

legacy/tripal_featuremap/tripal_featuremap.module

@@ -5,8 +5,8 @@
  */
 
 /**
- * @defgroup tripal_featuremap Feature Map Module
- * @ingroup tripal_modules
+ * @defgroup tripal_legacy_featuremap Feature Map Module
+ * @ingroup tripal_legacy_modules
  * @{
  * Integrates the Chado Map module with Drupal Nodes & Views
  * @}
@@ -30,7 +30,7 @@ require_once 'includes/tripal_featuremap.chado_node.inc';
  * @return
  *  help text for the path
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_help($path, $arg) {
   $output = '';
@@ -51,7 +51,7 @@ function tripal_featuremap_help($path, $arg) {
  * want permissionis that protect creation, editing and deleting of chado
  * data objects
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_permission() {
   return array(
@@ -87,7 +87,7 @@ function tripal_featuremap_permission() {
  * by this module to the 'Create Content' Navigation menu item.  This function
  * adds more menu items needed for this module.
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_menu() {
   $items = array();
@@ -177,7 +177,7 @@ function tripal_featuremap_search_biological_data_views() {
  *  for this module which then includes tripal_featuremap.views.inc where all the
  *  views integration code is
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_views_api() {
   return array(
@@ -192,7 +192,7 @@ function tripal_featuremap_views_api() {
  *  We create theme functions to allow users of the module to customize the
  *  look and feel of the output generated in this module
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
@@ -257,7 +257,7 @@ function tripal_featuremap_theme($existing, $type, $theme, $path) {
  * @param $form_state
  * @param $form_id
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_form_alter(&$form, &$form_state, $form_id) {
 

legacy/tripal_featuremap/tripal_featuremap.views_default.inc

@@ -7,7 +7,7 @@
 /**
  * Implements hook_views_default_views().
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_views_default_views() {
   $views = array();
@@ -30,7 +30,7 @@ function tripal_featuremap_views_default_views() {
 /**
  * Defines the featuremap user search default view.
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_defaultvalue_user_featuremaps() {
 
@@ -73,7 +73,7 @@ function tripal_featuremap_defaultvalue_user_featuremaps() {
 /**
  * Describes the default featuremap admin view
  *
- * @ingroup tripal_featuremap
+ * @ingroup tripal_legacy_featuremap
  */
 function tripal_featuremap_defaultview_admin_featuremaps() {
 

legacy/tripal_genetic/tripal_genetic.module

@@ -5,8 +5,8 @@
  */
 
 /**
- * @defgroup tripal_genetic Genetic Module
- * @ingroup tripal_modules
+ * @defgroup tripal_legacy_genetic Genetic Module
+ * @ingroup tripal_legacy_modules
  * @{
  * Provides functions for managing chado genetic data
  * @}
@@ -22,7 +22,7 @@ require_once 'includes/tripal_genetic.admin.inc';
  * Set the permission types that the chado module uses.  Essentially we
  *  want permissionis
  *
- * @ingroup tripal_genetic
+ *@ingroup tripal_legacy_genetic
  */
 function tripal_genetic_permission() {
   return array(
@@ -42,7 +42,7 @@ function tripal_genetic_permission() {
  *  by this module to the 'Create Content' Navigation menu item.  This function
  *  adds more menu items needed for this module.
  *
- * @ingroup tripal_genetic
+ *@ingroup tripal_legacy_genetic
  */
 function tripal_genetic_menu() {
   $items = array();
@@ -100,7 +100,7 @@ function tripal_genetic_search_biological_data_views() {
  *  for this module which then includes tripal_genetic.views.inc where all the
  *  views integration code is
  *
- * @ingroup tripal_genetic
+ *@ingroup tripal_legacy_genetic
  */
 function tripal_genetic_views_api() {
   return array(
@@ -111,7 +111,7 @@ function tripal_genetic_views_api() {
 /**
  * Implements hook_theme().
  *
- * @ingroup tripal_genetic
+ *@ingroup tripal_legacy_genetic
  */
 function tripal_genetic_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
@@ -139,7 +139,7 @@ function tripal_genetic_theme($existing, $type, $theme, $path) {
 /**
  * Implements hook_node_view(). Acts on all content types
  *
- * @ingroup tripal_genetic
+ *@ingroup tripal_legacy_genetic
  */
 function tripal_genetic_node_view($node, $view_mode, $langcode) {
 

legacy/tripal_library/includes/tripal_library.admin.inc

@@ -7,7 +7,7 @@
 /**
  * Admin launchpad
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_admin_libraries_listing() {
   $output = '';
@@ -42,7 +42,7 @@ function tripal_library_admin_libraries_listing() {
 /**
  * Administrative settings form
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_admin() {
   $form = array();

legacy/tripal_library/includes/tripal_library.chado_node.inc

@@ -10,7 +10,7 @@
  * Provide information to drupal about the node types that we're creating
  * in this module
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_node_info() {
   $nodes = array();
@@ -42,7 +42,7 @@ function tripal_library_node_info() {
  * When editing or creating a new node of type 'chado_library' we need
  *  a form.  This function creates the form that will be used for this.
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function chado_library_form($node, &$form_state) {
   $form = array();
@@ -224,7 +224,7 @@ function chado_library_form($node, &$form_state) {
  *
  * Validates submission of form when adding or updating a library node
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function chado_library_validate($node, $form, &$form_state) {
 
@@ -273,7 +273,7 @@ function chado_library_validate($node, $form, &$form_state) {
  *  to our chado_library table.  This function is called on insert of a new node
  *  of type 'chado_library' and inserts the necessary information.
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function chado_library_insert($node) {
 
@@ -347,7 +347,7 @@ function chado_library_insert($node) {
 /**
  * Implements hook_update().
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function chado_library_update($node) {
 
@@ -407,7 +407,7 @@ function chado_library_update($node) {
  *  When a node is requested by the user this function is called to allow us
  *  to add auxiliary data to the node object.
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function chado_library_load($nodes) {
 
@@ -439,7 +439,7 @@ function chado_library_load($nodes) {
  *
  * Delete data from drupal and chado databases when a node is deleted
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function chado_library_delete(&$node) {
 
@@ -486,7 +486,7 @@ function chado_library_delete(&$node) {
  *  access.  The only exception is when the $op == 'create'.  We will always
  *  return TRUE if the permission is set.
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_node_access($node, $op, $account) {
   $node_type = $node;
@@ -523,7 +523,7 @@ function tripal_library_node_access($node, $op, $account) {
 /**
  * Implements hook_node_view(). Acts on all content types
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_node_view($node, $view_mode, $langcode) {
 
@@ -607,7 +607,7 @@ function tripal_library_node_view($node, $view_mode, $langcode) {
 /**
  * Implements hook_node_presave(). Acts on all node content types.
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_node_presave($node) {
 
@@ -636,7 +636,7 @@ function tripal_library_node_presave($node) {
  * Implements hook_node_insert().
  * Acts on all content types.
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_node_insert($node) {
 
@@ -663,7 +663,7 @@ function tripal_library_node_insert($node) {
  * Implements hook_node_update().
  * Acts on all content types.
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_node_update($node) {
 

legacy/tripal_library/tripal_library.install

@@ -8,7 +8,7 @@
  * Implements hook_disable().
  * Disable default views when module is disabled
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_disable() {
 
@@ -24,7 +24,7 @@ function tripal_library_disable() {
 /**
  * Implementation of hook_requirements().
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_requirements($phase) {
   $requirements = array();
@@ -44,7 +44,7 @@ function tripal_library_requirements($phase) {
 /**
  * Implementation of hook_install().
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_install() {
 
@@ -60,7 +60,7 @@ function tripal_library_install() {
 /**
  * Implementation of hook_uninstall().
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_uninstall() {
 
@@ -69,7 +69,7 @@ function tripal_library_uninstall() {
 /**
  * Implementation of hook_schema().
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_schema() {
   $schema['chado_library'] = array(
@@ -107,7 +107,7 @@ function tripal_library_schema() {
 /**
  * Adds new CV's used by this module
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_add_cvs(){
   tripal_insert_cv(
@@ -123,7 +123,7 @@ function tripal_library_add_cvs(){
 /**
  * Adds cvterms needed for the library module
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_add_cvterms() {
 

legacy/tripal_library/tripal_library.module

@@ -5,8 +5,8 @@
  */
 
 /**
- * @defgroup tripal_library Library Module
- * @ingroup tripal_modules
+ * @defgroup tripal_legacy_library Library Module
+ * @ingroup tripal_legacy_modules
  * @{
  * Integrates the Chado Library module with Drupal Nodes & Views
  * @}
@@ -26,7 +26,7 @@ require_once 'includes/tripal_library.chado_node.inc';
  * want permissionis that protect creation, editing and deleting of chado
  * data objects
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_permission() {
   return array(
@@ -62,7 +62,7 @@ function tripal_library_permission() {
  * by this module to the 'Create Content' Navigation menu item.  This function
  * adds more menu items needed for this module.
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_menu() {
   $items = array();
@@ -124,7 +124,7 @@ function tripal_library_menu() {
     'access arguments' => array('administer tripal library'),
     'type' => MENU_CALLBACK,
   );
-  
+
   return $items;
 }
 
@@ -151,7 +151,7 @@ function tripal_library_search_biological_data_views() {
  *  for this module which then includes tripal_db.views.inc where all the
  *  views integration code is
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_views_api() {
   return array(
@@ -166,7 +166,7 @@ function tripal_library_views_api() {
  *  We create theme functions to allow users of the module to customize the
  *  look and feel of the output generated in this module
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
@@ -250,7 +250,7 @@ function tripal_library_theme($existing, $type, $theme, $path) {
  * Implements hook_help().
  * Adds a help page to the module list
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_help ($path, $arg) {
   if ($path == 'admin/help#tripal_library') {
@@ -265,7 +265,7 @@ function tripal_library_help ($path, $arg) {
  * @param $form_state
  * @param $form_id
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_form_alter(&$form, &$form_state, $form_id) {
 

legacy/tripal_library/tripal_library.views_default.inc

@@ -7,7 +7,7 @@
 /**
  * Implements hook_views_default_views().
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_views_default_views() {
   $views = array();
@@ -30,7 +30,7 @@ function tripal_library_views_default_views() {
 /**
  * Defines the library user search default view.
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_defaultvalue_user_library() {
 
@@ -73,7 +73,7 @@ function tripal_library_defaultvalue_user_library() {
 /**
  * Default administration library view
  *
- * @ingroup tripal_library
+ * @ingroup tripal_legacy_library
  */
 function tripal_library_admin_defaultviews_library() {
 

legacy/tripal_natural_diversity/includes/tripal_natural_diversity.admin.inc

@@ -7,7 +7,7 @@
 /**
  * Admin Launchpad
  *
- * @ingroup tripal_natural_diversity
+ * @ingroup tripal_legacy_natural_diversity
  */
 function tripal_natural_diversity_admin_natdiv_view() {
   $output = '';

legacy/tripal_natural_diversity/tripal_natural_diversity.install

@@ -8,7 +8,7 @@
  * Implements hook_disable().
  * Disable default views when module is disabled
  *
- * @ingroup tripal_natural_diversity
+ * @ingroup tripal_legacy_natural_diversity
  */
 function tripal_natural_diversity_disable() {
 
@@ -24,7 +24,7 @@ function tripal_natural_diversity_disable() {
 /**
  * Implementation of hook_requirements().
  *
- * @ingroup tripal_natural_diversity
+ * @ingroup tripal_legacy_natural_diversity
  */
 function tripal_natural_diversity_requirements($phase) {
   $requirements = array();
@@ -44,7 +44,7 @@ function tripal_natural_diversity_requirements($phase) {
 /**
  * Implementation of hook_install().
  *
- * @ingroup tripal_natural_diversity
+ * @ingroup tripal_legacy_natural_diversity
  */
 function tripal_natural_diversity_install() {
 
@@ -56,7 +56,7 @@ function tripal_natural_diversity_install() {
 /**
  * Implementation of hook_uninstall().
  *
- * @ingroup tripal_natural_diversity
+ * @ingroup tripal_legacy_natural_diversity
  */
 function tripal_natural_diversity_uninstall() {
 
@@ -65,7 +65,7 @@ function tripal_natural_diversity_uninstall() {
 /**
  * Add cvterms related to natural diversity
  *
- * @ingroup tripal_natural_diversity
+ * @ingroup tripal_legacy_natural_diversity
  */
 function tripal_natural_diversity_add_cvterms(){
 

legacy/tripal_natural_diversity/tripal_natural_diversity.module

@@ -4,25 +4,24 @@
  * Basic function for the natural diversity module
  */
 
-require_once 'theme/tripal_natural_diversity.theme.inc';
-
-require_once 'includes/tripal_natural_diversity.admin.inc';
-
 /**
- * @defgroup tripal_natural_diversity Natural Diversity Module
- * @ingroup tripal_modules
+ * @defgroup tripal_legacy_natural_diversity Legacy Natural Diversity Module
+ * @ingroup tripal_legacy_modules
  * @{
  * Provides functions for managing chado natural diversity data
  * @}
  */
 
+require_once 'theme/tripal_natural_diversity.theme.inc';
+require_once 'includes/tripal_natural_diversity.admin.inc';
+
 /**
  * Implements hook_permission().
  *
  * Set the permission types that the chado module uses.  Essentially we
  *  want permissionis
  *
- * @ingroup tripal_natural_diversity
+ * @ingroup tripal_legacy_natural_diversity
  */
 function tripal_natural_diversity_permission() {
   return array(
@@ -42,7 +41,7 @@ function tripal_natural_diversity_permission() {
  *  by this module to the 'Create Content' Navigation menu item.  This function
  *  adds more menu items needed for this module.
  *
- * @ingroup tripal_natural_diversity
+ * @ingroup tripal_legacy_natural_diversity
  */
 function tripal_natural_diversity_menu() {
   $items = array();
@@ -85,7 +84,7 @@ function tripal_natural_diversity_menu() {
  *  for this module which then includes tripal_natural_diversity.views.inc where all the
  *  views integration code is
  *
- * @ingroup tripal_natural_diversity
+ * @ingroup tripal_legacy_natural_diversity
  */
 function tripal_natural_diversity_views_api() {
   return array(
@@ -96,7 +95,7 @@ function tripal_natural_diversity_views_api() {
 /**
  * Implements hook_theme().
  *
- * @ingroup tripal_natural_diversity
+ * @ingroup tripal_legacy_natural_diversity
  */
 function tripal_natural_diversity_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
@@ -131,7 +130,7 @@ function tripal_natural_diversity_theme($existing, $type, $theme, $path) {
 /**
  * Implements hook_node_view(). Acts on all content types.
  *
- * @ingroup tripal_natural_diversity
+ * @ingroup tripal_legacy_natural_diversity
  */
 function tripal_natural_diversity_node_view($node, $view_mode, $langcode) {
   switch ($node->type) {

legacy/tripal_natural_diversity/tripal_natural_diversity.views_default.inc

@@ -7,7 +7,7 @@
 /**
  * Implements hook_views_default_views().
  *
- * @ingroup tripal_natural_diversity
+ * @ingroup tripal_legacy_natural_diversity
  */
 function tripal_natural_diversity_views_default_views() {
   $views = array();
@@ -38,7 +38,7 @@ function tripal_natural_diversity_views_default_views() {
 /**
  * Describes the default experiment administration view
  *
- * @ingroup tripal_natural_diversity
+ * @ingroup tripal_legacy_natural_diversity
  */
 function tripal_natural_diversity_defaultview_admin_natdiv_exp() {
 
@@ -159,7 +159,7 @@ function tripal_natural_diversity_defaultview_admin_natdiv_exp() {
 /**
  * Describes the default geological locations administration view
  *
- * @ingroup tripal_natural_diversity
+ * @ingroup tripal_legacy_natural_diversity
  */
 function tripal_natural_diversity_defaultview_admin_geolocations() {
 
@@ -340,7 +340,7 @@ function tripal_natural_diversity_defaultview_admin_geolocations() {
 /**
  * Describes the default reagents administration view
  *
- * @ingroup tripal_natural_diversity
+ * @ingroup tripal_legacy_natural_diversity
  */
 function tripal_natural_diversity_defaultview_admin_reagents() {
 
@@ -454,7 +454,7 @@ function tripal_natural_diversity_defaultview_admin_reagents() {
 /**
  * Describes the default protocols administration view
  *
- * @ingroup tripal_natural_diversity
+ * @ingroup tripal_legacy_natural_diversity
  */
 function tripal_natural_diversity_defaultview_admin_protocols() {
 

legacy/tripal_organism/includes/tripal_organism.admin.inc

@@ -7,7 +7,7 @@
 /**
  * Admin launchpad
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_admin_organism_view() {
   $output = '';
@@ -42,7 +42,7 @@ function tripal_organism_admin_organism_view() {
 /**
  * Administrative settings for chado_orgnism
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_admin() {
 
@@ -90,7 +90,7 @@ function tripal_organism_admin() {
 /**
  * Validate the organism settings form
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_admin_validate($form, &$form_state) {
 

legacy/tripal_organism/includes/tripal_organism.chado_node.inc

@@ -10,7 +10,7 @@
  * Provide information to drupal about the node types that we're creating
  *  in this module
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_node_info() {
   $nodes = array();
@@ -59,7 +59,7 @@ function tripal_organism_node_info() {
  *  access.  The only exception is when the $op == 'create'.  We will always
  *  return TRUE if the permission is set.
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_node_access($node, $op, $account) {
   $node_type = $node;
@@ -99,7 +99,7 @@ function tripal_organism_node_access($node, $op, $account) {
  *  When editing or creating a new node of type 'chado_organism' we need
  *  a form.  This function creates the form that will be used for this.
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function chado_organism_form($node, $form_state) {
   $form = array();
@@ -296,7 +296,7 @@ function chado_organism_form($node, $form_state) {
  * @param $form
  * @param $form_state
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function chado_organism_validate($node, $form, &$form_state) {
 
@@ -373,7 +373,7 @@ function chado_organism_validate($node, $form, &$form_state) {
  *  to our chado_organism table.  This function is called on insert of a new node
  *  of type 'chado_organism' and inserts the necessary information.
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function chado_organism_insert($node) {
 
@@ -464,7 +464,7 @@ function chado_organism_insert($node) {
 /**
  * Implements hook_update().
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function chado_organism_update($node) {
 
@@ -573,7 +573,7 @@ function chado_organism_add_image($node) {
  * Delete organism from both drupal and chado databases. Check dependency before
  * deleting from chado.
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function chado_organism_delete($node) {
   $organism_id = chado_get_id_from_nid('organism', $node->nid);
@@ -615,7 +615,7 @@ function chado_organism_delete($node) {
  *  When a node is requested by the user this function is called to allow us
  *  to add auxiliary data to the node object.
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function chado_organism_load($nodes) {
 
@@ -649,7 +649,7 @@ function chado_organism_load($nodes) {
  * @param $node
  *  The node to be saved
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_node_presave($node) {
   switch ($node->type) {
@@ -686,7 +686,7 @@ function tripal_organism_node_presave($node) {
 /**
  * Implements hook_node_view().
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_node_view($node, $view_mode, $langcode) {
 
@@ -729,7 +729,7 @@ function tripal_organism_node_view($node, $view_mode, $langcode) {
  * Implements hook_node_insert().
  * Acts on all content types.
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_node_insert($node) {
 
@@ -756,7 +756,7 @@ function tripal_organism_node_insert($node) {
  * Implements hook_node_update().
  * Acts on all content types.
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_node_update($node) {
 

legacy/tripal_organism/includes/tripal_organism.delete.inc

@@ -7,7 +7,7 @@
 /**
  * A form for indicating the organisms to delete
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_delete_form() {
   // get the list of organisms
@@ -42,7 +42,7 @@ function tripal_organism_delete_form() {
 /**
  * Submit for the delete features form
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_delete_form_submit($form, &$form_state) {
   global $user;
@@ -76,7 +76,7 @@ function tripal_organism_delete_form_submit($form, &$form_state) {
  * @param $job
  *   The tripal_job id
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_delete_organisms($organisms, $job = NULL) {
 

legacy/tripal_organism/tripal_organism.install

@@ -8,7 +8,7 @@
  * Implements hook_disable().
  * Disable default views when module is disabled
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_disable() {
 
@@ -24,7 +24,7 @@ function tripal_organism_disable() {
 /**
  * Implementation of hook_install().
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_install() {
 
@@ -36,7 +36,7 @@ function tripal_organism_install() {
 /**
  * Implementation of hook_schema().
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_schema() {
  $schema['chado_organism'] = array(
@@ -74,7 +74,7 @@ function tripal_organism_schema() {
 /**
  * Implementation of hook_uninstall().
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_uninstall() {
 
@@ -83,7 +83,7 @@ function tripal_organism_uninstall() {
 /**
  * Implementation of hook_requirements().
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_requirements($phase) {
   $requirements = array();

legacy/tripal_organism/tripal_organism.module

@@ -4,20 +4,19 @@
  * Integrates the Chado Organism module with Drupal Nodes & Views
  */
 
-require_once 'api/tripal_organism.DEPRECATED.inc';
-
-require_once 'includes/tripal_organism.admin.inc';
-require_once 'includes/tripal_organism.delete.inc';
-require_once 'includes/tripal_organism.chado_node.inc';
-
 /**
- * @defgroup tripal_organism Organism Module
- * @ingroup tripal_modules
+ * @defgroup tripal_legacy_organism Legacy Organism Module
+ * @ingroup tripal_legacy_modules
  * @{
  * Integrates the Chado Organism module with Drupal Nodes & Views
  * @}
  */
 
+require_once 'api/tripal_organism.DEPRECATED.inc';
+require_once 'includes/tripal_organism.admin.inc';
+require_once 'includes/tripal_organism.delete.inc';
+require_once 'includes/tripal_organism.chado_node.inc';
+
 /**
  *  Implements hook_menu().
  *
@@ -25,7 +24,7 @@ require_once 'includes/tripal_organism.chado_node.inc';
  *  by this module to the 'Create Content' Navigation menu item.  This function
  *  adds more menu items needed for this module.
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_menu() {
   $items = array();
@@ -124,7 +123,7 @@ function tripal_organism_search_biological_data_views() {
  * Implements hook_help().
  * Adds a help page to the module list
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_help ($path, $arg) {
   if ($path == 'admin/help#tripal_organism') {
@@ -139,7 +138,7 @@ function tripal_organism_help ($path, $arg) {
  *  We create theme functions to allow users of the module to customize the
  *  look and feel of the output generated in this module
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
@@ -187,7 +186,7 @@ function tripal_organism_theme($existing, $type, $theme, $path) {
   *  want permissionis that protect creation, editing and deleting of chado
   *  data objects
   *
-  * @ingroup tripal_organism
+  * @ingroup tripal_legacy_organism
   */
 function tripal_organism_permission() {
   return array(
@@ -223,7 +222,7 @@ function tripal_organism_permission() {
  *  for this module which then includes tripal_db.views.inc where all the
  *  views integration code is
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_views_api() {
   return array(
@@ -234,7 +233,7 @@ function tripal_organism_views_api() {
 /**
  * Implements hook_job_describe_args().
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_job_describe_args($callback, $args) {
 
@@ -254,7 +253,7 @@ function tripal_organism_job_describe_args($callback, $args) {
  * @param $form_state
  * @param $form_id
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_form_alter(&$form, &$form_state, $form_id) {
   // turn of preview button for insert/updates

legacy/tripal_organism/tripal_organism.views_default.inc

@@ -7,7 +7,7 @@
 /**
  * Implements hook_views_default_views().
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_views_default_views() {
   $views = array();
@@ -30,7 +30,7 @@ function tripal_organism_views_default_views() {
 /**
  * Defines the organism user search default view.
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_defaultvalue_user_organisms() {
 
@@ -202,7 +202,7 @@ function tripal_organism_defaultvalue_user_organisms() {
 /**
  * Describe the organism administration view.
  *
- * @ingroup tripal_organism
+ * @ingroup tripal_legacy_organism
  */
 function tripal_organism_admin_defaultview_organisms() {
 

legacy/tripal_phenotype/tripal_phenotype.install

@@ -8,7 +8,7 @@
  * Implements hook_disable().
  * Disable default views when module is disabled
  *
- * @ingroup tripal_phenotype
+ * @ingroup tripal_legacy_phenotype
  */
 function tripal_phenotype_disable() {
 

legacy/tripal_phenotype/tripal_phenotype.module

@@ -5,8 +5,8 @@
  */
 
 /**
- * @defgroup tripal_phenotype Phenotype Module
- * @ingroup tripal_modules
+ * @defgroup tripal_legacy_phenotype Legacy Phenotype Module
+ * @ingroup tripal_legacy_modules
  * @{
  * Provides functions for managing chado phenotype data
  * @}
@@ -18,7 +18,7 @@
  * Set the permission types that the chado module uses.  Essentially we
  *  want permissionis
  *
- * @ingroup tripal_phenotype
+ * @ingroup tripal_legacy_phenotype
  */
 function tripal_phenotype_permission() {
   return array(
@@ -38,7 +38,7 @@ function tripal_phenotype_permission() {
  *  by this module to the 'Create Content' Navigation menu item.  This function
  *  adds more menu items needed for this module.
  *
- * @ingroup tripal_phenotype
+ * @ingroup tripal_legacy_phenotype
  */
 function tripal_phenotype_menu() {
   $items = array();
@@ -96,7 +96,7 @@ function tripal_phenotype_search_biological_data_views() {
  *  We create theme functions to allow users of the module to customize the
  *  look and feel of the output generated in this module
  *
- * @ingroup tripal_phenotype
+ * @ingroup tripal_legacy_phenotype
  */
 function tripal_phenotype_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
@@ -123,7 +123,7 @@ function tripal_phenotype_theme($existing, $type, $theme, $path) {
  *  for this module which then includes tripal_phenotype.views.inc where all the
  *  views integration code is
  *
- * @ingroup tripal_phenotype
+ * @ingroup tripal_legacy_phenotype
  */
 function tripal_phenotype_views_api() {
   return array(
@@ -134,7 +134,7 @@ function tripal_phenotype_views_api() {
 /**
  * Admin Launchpad
  *
- * @ingroup tripal_phenotype
+ * @ingroup tripal_legacy_phenotype
  */
 function tripal_phenotype_admin_phenotypes_listing() {
   $output = '';
@@ -169,7 +169,7 @@ function tripal_phenotype_admin_phenotypes_listing() {
 /**
  * Implements hook_node_view().
  *
- * @ingroup tripal_phenotype
+ * @ingroup tripal_legacy_phenotype
  */
 function tripal_phenotype_node_view($node, $view_mode, $langcode) {
   switch ($node->type) {

legacy/tripal_phenotype/tripal_phenotype.views_default.inc

@@ -7,7 +7,7 @@
 /**
  * Implements hook_views_default_views().
  *
- * @ingroup tripal_phenotype
+ * @ingroup tripal_legacy_phenotype
  */
 function tripal_phenotype_views_default_views() {
   $views = array();
@@ -30,7 +30,7 @@ function tripal_phenotype_views_default_views() {
 /**
  * Defines the phenotype user search default view.
  *
- * @ingroup tripal_phenotype
+ * @ingroup tripal_legacy_phenotype
  */
 function tripal_phenotype_defaultvalue_user_phenotypes() {
 
@@ -70,7 +70,7 @@ function tripal_phenotype_defaultvalue_user_phenotypes() {
 /**
  * Default phenotype administration view
  *
- * @ingroup tripal_phenotype
+ * @ingroup tripal_legacy_phenotype
  */
 function tripal_phenotype_defaultview_admin_phenotypes() {
 

legacy/tripal_phylogeny/includes/tripal_phylogeny.admin.inc

@@ -3,7 +3,7 @@
 /**
  * Administrative settings form
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_admin() {
   $form = array();

legacy/tripal_phylogeny/includes/tripal_phylogeny.chado_node.inc

@@ -11,7 +11,7 @@
  * Provide information to drupal about the node types that we're creating
  * in this module.
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_node_info() {
   $nodes = array();
@@ -45,7 +45,7 @@ function tripal_phylogeny_node_info() {
 /**
  * Implements hook_node_view(). Acts on all content types
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_node_view($node, $view_mode, $langcode) {
 
@@ -107,7 +107,7 @@ function tripal_phylogeny_node_view($node, $view_mode, $langcode) {
 /**
  * Implementation of hook_form().
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function chado_phylotree_form($node, &$form_state) {
 
@@ -341,7 +341,7 @@ function chado_phylotree_validate_newick_format(stdClass $file) {
  *   CASE B: Synchronizing a node from chado to drupal
  *   CASE C: Inserting a new node that exists in niether drupal nor chado
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function chado_phylotree_validate($node, $form, &$form_state) {
 
@@ -402,7 +402,7 @@ function chado_phylotree_validate($node, $form, &$form_state) {
 /**
  * Implements hook_node_presave(). Acts on all node content types.
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_node_presave($node) {
 
@@ -431,7 +431,7 @@ function tripal_phylogeny_node_presave($node) {
  * Implements hook_node_insert().
  * Acts on all content types.
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_node_insert($node) {
 
@@ -458,7 +458,7 @@ function tripal_phylogeny_node_insert($node) {
  * Implements hook_node_update().
  * Acts on all content types.
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_node_update($node) {
 
@@ -484,7 +484,7 @@ function tripal_phylogeny_node_update($node) {
  * Defines a default title format for the Chado Node API to set the titles on
  * Chado phylotree nodes based on chado fields.
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function chado_phylotree_chado_node_default_title_format() {
   return '[phylotree.name]';
@@ -507,7 +507,7 @@ function chado_phylotree_chado_node_default_url_format() {
  *  on insert of a new node of type 'chado_phylotree' and inserts the
  *  necessary information.
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function chado_phylotree_insert($node) {
   global $user;
@@ -570,7 +570,7 @@ function chado_phylotree_insert($node) {
 /**
  * Implements hook_update().
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function chado_phylotree_update($node) {
 
@@ -620,7 +620,7 @@ function chado_phylotree_update($node) {
  *  When a node is requested by the user this function is called to allow us
  *  to add auxiliary data to the node object.
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function chado_phylotree_load($nodes) {
 
@@ -665,7 +665,7 @@ function chado_phylotree_load($nodes) {
  *
  * Delete data from drupal and chado databases when a node is deleted
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function chado_phylotree_delete(&$node) {
 
@@ -714,7 +714,7 @@ function chado_phylotree_delete(&$node) {
  *  access.  The only exception is when the $op == 'create'.  We will always
  *  return TRUE if the permission is set.
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function chado_phylotree_node_access($node, $op, $account) {
 
@@ -758,7 +758,7 @@ function chado_phylotree_node_access($node, $op, $account) {
  *
  * @param int phylotree_id
  * @return array
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function phylotree_feature_summary($phylotree_id) {
 

legacy/tripal_phylogeny/tripal_phylogeny.install

@@ -7,7 +7,7 @@
 /**
  * Implements hook_install().
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_install() {
 
@@ -51,7 +51,7 @@ function tripal_phylogeny_install() {
  *
  * Disable default views when module is disabled
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_disable() {
   // Disable all default views provided by this module
@@ -65,7 +65,7 @@ function tripal_phylogeny_disable() {
 /**
  * Implementation of hook_requirements().
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_requirements($phase) {
   $requirements = array();
@@ -85,7 +85,7 @@ function tripal_phylogeny_requirements($phase) {
 /**
  * Implementation of hook_schema().
  * Standard tripal linker table between a node and a phylotree record.
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_schema() {
   $schema['chado_phylotree'] = array(
@@ -125,7 +125,7 @@ function tripal_phylogeny_schema() {
 /**
  * Adds controlled vocabulary terms needed by this module.
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_add_cvterms() {
 
@@ -322,7 +322,7 @@ function tripal_phylogeny_integrate_view(){
  * Add any custom tables needed by this module.
  * - phylotreeprop: keep track of properties of phylotree
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_add_custom_tables() {
   $schema = array (

legacy/tripal_phylogeny/tripal_phylogeny.module

@@ -6,8 +6,8 @@
  */
 
 /**
- * @defgroup tripal_phylogeny Phylotree Module
- * @ingroup tripal_modules
+ * @defgroup tripal_legacy_phylogeny Legacy Phylotree Module
+ * @ingroup tripal_legacy_modules
  * @{
  * Integrates the Chado Phylotree module with Drupal Nodes
  * @}
@@ -26,7 +26,7 @@ require_once 'includes/tripal_phylogeny.taxonomy.inc';
  * want permissionis that protect creation, editing and deleting of chado
  * data objects
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_permission() {
   return array(
@@ -48,7 +48,7 @@ function tripal_phylogeny_permission() {
  * by this module to the 'Create Content' Navigation menu item.  This function
  * adds more menu items needed for this module.
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_menu() {
   $items = array();
@@ -148,7 +148,7 @@ function tripal_phylogeny_search_biological_data_views() {
  *  for this module which then includes tripal_db.views.inc where all the
  *  views integration code is
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_views_api() {
   return array(
@@ -163,7 +163,7 @@ function tripal_phylogeny_views_api() {
  *  We create theme functions to allow users of the module to customize the
  *  look and feel of the output generated in this module
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
@@ -231,7 +231,7 @@ function tripal_phylogeny_theme($existing, $type, $theme, $path) {
  * Implements hook_help().
  * Adds a help page to the module list
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_help ($path, $arg) {
   if ($path == 'admin/help#tripal_phylogeny') {

legacy/tripal_phylogeny/tripal_phylogeny.views.inc

@@ -14,7 +14,7 @@
  *
  * @return: An array of handler definitions
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_views_handlers() {
   return array(

legacy/tripal_phylogeny/tripal_phylogeny.views_default.inc

@@ -7,7 +7,7 @@
 /**
  * Implements hook_views_default_views().
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_views_default_views() {
   $views = array();
@@ -30,7 +30,7 @@ function tripal_phylogeny_views_default_views() {
 /**
  * The default phylotree administration view.
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_defaultview_admin_phylotree() {
   $view = new view();
@@ -157,7 +157,7 @@ function tripal_phylogeny_defaultview_admin_phylotree() {
 /**
  * Defines the phylotree user search default view.
  *
- * @ingroup tripal_phylogeny
+ * @ingroup tripal_legacy_phylogeny
  */
 function tripal_phylogeny_defaultvalue_user_phylotrees() {
 

legacy/tripal_project/includes/tripal_project.admin.inc

@@ -7,7 +7,7 @@
 /**
  * Admin launchpad
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_admin_project_view() {
   $output = '';
@@ -41,7 +41,7 @@ function tripal_project_admin_project_view() {
 /**
  * Project settings
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_admin($form, $form_state) {
   $form = array();

legacy/tripal_project/includes/tripal_project.chado_node.inc

@@ -11,7 +11,7 @@
  * that the title(Project Name) and body(Description) set to true so that they information can be
  * entered
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_node_info() {
   return array(
@@ -53,7 +53,7 @@ function tripal_project_node_info() {
  *    An array as described by the Drupal Form API
  *
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function chado_project_form(&$node, $form_state) {
   $form = array();
@@ -192,7 +192,7 @@ function chado_project_form(&$node, $form_state) {
  * Implements hook_validate().
  * Validates submission of form when adding or updating a project node
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function chado_project_validate($node, $form, &$form_state) {
 
@@ -235,7 +235,7 @@ function chado_project_validate($node, $form, &$form_state) {
  *  @parm $node
  *    Then node that has the information stored within, accessed given the nid
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function chado_project_insert($node) {
 
@@ -309,7 +309,7 @@ function chado_project_insert($node) {
  *  The node which is to be deleted, only chado project and chado_project need to be dealt with
  *  since the drupal node is deleted automagically
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function chado_project_delete($node) {
 
@@ -342,7 +342,7 @@ function chado_project_delete($node) {
  *  The node which is to have its containing information updated when the user modifies information
  *  pertaining to the specific project
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function chado_project_update($node) {
 
@@ -394,7 +394,7 @@ function chado_project_update($node) {
  * @param $node
  *   The node that is to have its containing information loaded
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function chado_project_load($nodes) {
 
@@ -443,7 +443,7 @@ function chado_project_load($nodes) {
  *  access.  The only exception is when the $op == 'create'.  We will always
  *  return TRUE if the permission is set.
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_node_access($node, $op, $account) {
 
@@ -481,7 +481,7 @@ function tripal_project_node_access($node, $op, $account) {
 /**
  * Implements hook_node_view().
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_node_view($node, $view_mode, $langcode) {
   switch ($node->type) {
@@ -534,7 +534,7 @@ function tripal_project_node_view($node, $view_mode, $langcode) {
  * Implements hook_node_insert().
  * Acts on all content types.
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_node_insert($node) {
 
@@ -563,7 +563,7 @@ function tripal_project_node_insert($node) {
  * Implements hook_node_update().
  * Acts on all content types.
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_node_update($node) {
 

legacy/tripal_project/theme/tripal_project.theme.inc

@@ -2,7 +2,7 @@
 /**
  *
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_preprocess_tripal_project_relationships(&$variables) {
   $project = $variables['node']->project;

legacy/tripal_project/tripal_project.install

@@ -8,7 +8,7 @@
  * Implements hook_disable().
  * Disable default views when module is disabled
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_disable() {
 
@@ -24,7 +24,7 @@ function tripal_project_disable() {
 /**
  * Implementation of hook_requirements().
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_requirements($phase) {
   $requirements = array();
@@ -44,7 +44,7 @@ function tripal_project_requirements($phase) {
 /**
  * Implementation of hook_install().
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_install() {
 
@@ -59,7 +59,7 @@ function tripal_project_install() {
 /**
  * Implementation of hook_uninstall().
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_uninstall() {
 
@@ -68,7 +68,7 @@ function tripal_project_uninstall() {
 /**
  * Implementation of hook_schema().
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_schema() {
   $schema['chado_project'] = array(
@@ -96,7 +96,7 @@ function tripal_project_schema() {
 /**
  * Add cvs pertaining to projects
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_add_cvs() {
   // Add the cv for project properties
@@ -115,7 +115,7 @@ function tripal_project_add_cvs() {
 /**
  * Add cvterms pertaining to projects
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_add_cvterms() {
 

legacy/tripal_project/tripal_project.module

@@ -4,21 +4,21 @@
  * Integrates the Chado Project tables with Drupal Nodes & Views
  */
 
-require_once 'api/tripal_project.DEPRECATED.inc';
-
-require_once 'theme/tripal_project.theme.inc';
-
-require_once 'includes/tripal_project.admin.inc';
-require_once 'includes/tripal_project.chado_node.inc';
-
 /**
- * @defgroup tripal_project Project Module
- * @ingroup tripal_modules
+ * @defgroup tripal_legacy_project Legacy Project Module
+ * @ingroup tripal_legacy_modules
  * @{
  * Integrates the Chado Project tables with Drupal Nodes & Views
  * @}
  */
 
+
+require_once 'api/tripal_project.DEPRECATED.inc';
+require_once 'theme/tripal_project.theme.inc';
+require_once 'includes/tripal_project.admin.inc';
+require_once 'includes/tripal_project.chado_node.inc';
+
+
 /**
  * Implements hook_views_api().
  *
@@ -26,7 +26,7 @@ require_once 'includes/tripal_project.chado_node.inc';
  *  for this module which then includes tripal_project.views.inc where all the
  *  views integration code is
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_views_api() {
   return array(
@@ -37,7 +37,7 @@ function tripal_project_views_api() {
 /**
  * Implements hook_menu().
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_menu() {
   $items = array();
@@ -121,7 +121,7 @@ function tripal_project_search_biological_data_views() {
  * Implements hook_help().
  * Adds a help page to the module list
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_help ($path, $arg) {
   if ($path == 'admin/help#tripal_project') {
@@ -135,7 +135,7 @@ function tripal_project_help ($path, $arg) {
  *  This function sets the permission for the user to access the information in the database.
  *  This includes creating, inserting, deleting and updating of information in the database
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_permission() {
   return array(
@@ -171,7 +171,7 @@ function tripal_project_permission() {
  *  We create theme functions to allow users of the module to customize the
  *  look and feel of the output generated in this module
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
@@ -229,7 +229,7 @@ function tripal_project_theme($existing, $type, $theme, $path) {
  * @param $form_state
  * @param $form_id
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_form_alter(&$form, &$form_state, $form_id) {
 

legacy/tripal_project/tripal_project.views_default.inc

@@ -7,7 +7,7 @@
 /**
  * Implements hook_views_default_views().
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_views_default_views() {
   $views = array();
@@ -30,7 +30,7 @@ function tripal_project_views_default_views() {
 /**
  * Defines the project user search default view.
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_defaultvalue_user_projects() {
 
@@ -73,7 +73,7 @@ function tripal_project_defaultvalue_user_projects() {
 /**
  * Project administration view
  *
- * @ingroup tripal_project
+ * @ingroup tripal_legacy_project
  */
 function tripal_project_defaultview_admin_projects() {
 

legacy/tripal_pub/includes/tripal_pub.admin.inc

@@ -7,7 +7,7 @@
 /**
  * Admin launchpad
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_admin_pub_view() {
   $output = '';
@@ -42,7 +42,7 @@ function tripal_pub_admin_pub_view() {
 /**
  * Administrative settings form
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_admin() {
   $form = array();
@@ -137,7 +137,7 @@ function tripal_pub_admin() {
 /**
  * Validate the admin settings form
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_admin_validate($form, &$form_state) {
   global $user;  // we need access to the user info
@@ -162,7 +162,7 @@ function tripal_pub_admin_validate($form, &$form_state) {
  * @return
  *   The url alias set
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_set_pub_url($node, $pub_id) {
 

legacy/tripal_pub/includes/tripal_pub.chado_node.inc

@@ -3,7 +3,7 @@
  * @file
  * Implements Drupal Node hooks to create the chado_analysis node content type.
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 
 /**
@@ -12,7 +12,7 @@
  * Provide information to drupal about the node types that we're creating
  * in this module
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_node_info() {
   $nodes = array();
@@ -41,7 +41,7 @@ function tripal_pub_node_info() {
 /**
  * Implements hook_form().
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function chado_pub_form($node, $form_state) {
   $form = array();
@@ -343,7 +343,7 @@ function chado_pub_form($node, $form_state) {
 /**
  * Implements hook_validate().
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function chado_pub_validate($node, $form, &$form_state) {
 
@@ -455,7 +455,7 @@ function chado_pub_validate($node, $form, &$form_state) {
  *  If an update, provide the pub_id so we don't check for a matching
  *  uniquename of the pub we are editing
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function chado_pub_validate_check_uniquename($uniquename, $pub_id = NULL) {
 
@@ -488,7 +488,7 @@ function chado_pub_validate_check_uniquename($uniquename, $pub_id = NULL) {
  *   the unique id of the publication
  *
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function chado_pub_validate_check_duplicate($title, $pyear, $series_name, $cvterm, $pub_id = NULL) {
 
@@ -549,7 +549,7 @@ function chado_pub_validate_check_duplicate($title, $pyear, $series_name, $cvter
  *  access.  The only exception is when the $op == 'create'.  We will always
  *  return TRUE if the permission is set.
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_node_access($node, $op, $account) {
   $node_type = $node;
@@ -586,7 +586,7 @@ function tripal_pub_node_access($node, $op, $account) {
 /**
  * Implements hook_insert().
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function chado_pub_insert($node) {
 
@@ -797,7 +797,7 @@ function chado_pub_insert($node) {
  * @param $node
  *   The node being updated
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function chado_pub_update($node) {
   $node->pubtitle   = trim($node->pubtitle);
@@ -987,7 +987,7 @@ function chado_pub_update($node) {
  * @return $node
  *   The node with the information to be loaded into the database
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function chado_pub_load($nodes) {
 
@@ -1030,7 +1030,7 @@ function chado_pub_load($nodes) {
  * @parm $node
  *    Then node to be deleted
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function chado_pub_delete(&$node) {
 
@@ -1059,7 +1059,7 @@ function chado_pub_delete(&$node) {
 /**
  * Implements hook_node_view(). Acts on all content types.
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_node_view($node, $view_mode, $langcode) {
   switch ($node->type) {
@@ -1148,7 +1148,7 @@ function tripal_pub_node_view($node, $view_mode, $langcode) {
  * so the nodeapi function ensures that the URL path is set after insert or update
  * of the node and when the node is loaded if it hasn't yet been set.
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_node_insert($node) {
 
@@ -1183,7 +1183,7 @@ function tripal_pub_node_insert($node) {
  * so the nodeapi function ensures that the URL path is set after insert or update
  * of the node and when the node is loaded if it hasn't yet been set.
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_node_load($nodes, $types) {
   if (count(array_intersect(array('chado_pub'), $types))) {
@@ -1206,7 +1206,7 @@ function tripal_pub_node_load($nodes, $types) {
  * so the nodeapi function ensures that the URL path is set after insert or update
  * of the node and when the node is loaded if it hasn't yet been set.
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_node_update($node) {
 
@@ -1234,7 +1234,7 @@ function tripal_pub_node_update($node) {
 /**
  * Implements hook_node_presave(). Acts on all content types.
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_node_presave($node) {
   switch ($node->type) {

legacy/tripal_pub/theme/tripal_pub.theme.inc

@@ -2,7 +2,7 @@
 /**
  *
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_preprocess_tripal_pub_relationships(&$variables) {
    $pub = $variables['node']->pub;

legacy/tripal_pub/tripal_pub.install

@@ -8,7 +8,7 @@
  * Implements hook_disable().
  * Disable default views when module is disabled
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_disable() {
 
@@ -24,7 +24,7 @@ function tripal_pub_disable() {
 /**
  * Implementation of hook_requirements().
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_requirements($phase) {
   $requirements = array();
@@ -44,7 +44,7 @@ function tripal_pub_requirements($phase) {
 /**
  * Implementation of hook_install().
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_install() {
   global $base_path;
@@ -70,7 +70,7 @@ function tripal_pub_install() {
 /**
  * Implementation of hook_uninstall().
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_uninstall() {
 
@@ -79,7 +79,7 @@ function tripal_pub_uninstall() {
 /**
  * Implements hook_enable().
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_enable() {
 
@@ -88,7 +88,7 @@ function tripal_pub_enable() {
 /**
  * Implementation of hook_schema().
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_schema() {
 
@@ -169,7 +169,7 @@ function tripal_pub_schema() {
  * Add custom table related to publications
  *  - pubauthor_contact
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 // This function was moved to tripal_chado/includes/setup/tripal_chado.setup.inc
 /* function tripal_pub_add_custom_tables() {

legacy/tripal_pub/tripal_pub.module

@@ -4,16 +4,9 @@
  * Basic functionality of the pub module
  */
 
-require_once 'api/tripal_pub.DEPRECATED.inc';
-
-require_once 'theme/tripal_pub.theme.inc';
-
-require_once 'includes/tripal_pub.admin.inc';
-require_once 'includes/tripal_pub.chado_node.inc';
-
 /**
- * @defgroup tripal_pub Publication Module
- * @ingroup tripal_modules
+ * @defgroup tripal_legacy_pub Legacy Publication Module
+ * @ingroup tripal_legacy_modules
  * @{
  * Integrates the Chado Publication module with Drupal Nodes & Views, as well as, provides
  * the ability to import publication from PubMed
@@ -25,6 +18,11 @@ require_once 'includes/tripal_pub.chado_node.inc';
  * @}
  */
 
+require_once 'api/tripal_pub.DEPRECATED.inc';
+require_once 'theme/tripal_pub.theme.inc';
+require_once 'includes/tripal_pub.admin.inc';
+require_once 'includes/tripal_pub.chado_node.inc';
+
 /**
  * Implements hook_menu().
  *
@@ -35,7 +33,7 @@ require_once 'includes/tripal_pub.chado_node.inc';
  *   An array of menu items that is visible within the Drupal Menu, returned as soon
  *   as the program is ran
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_menu() {
   $items = array();
@@ -126,7 +124,7 @@ function tripal_pub_menu() {
  * @return
  *   An array of themeing functions to register
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
@@ -214,7 +212,7 @@ function tripal_pub_theme($existing, $type, $theme, $path) {
  * Implements hook_help().
  * Adds a help page to the module list
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_help ($path, $arg) {
   if ($path == 'admin/help#tripal_pub') {
@@ -229,7 +227,7 @@ function tripal_pub_help ($path, $arg) {
  *  for this module which then includes tripal_db.views.inc where all the
  *  views integration code is
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_views_api() {
   return array(
@@ -240,7 +238,7 @@ function tripal_pub_views_api() {
 /**
  * Implement hook_permission().
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_permission() {
   return array(
@@ -270,7 +268,7 @@ function tripal_pub_permission() {
 /**
  * Implements hook_mail().
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_mail($key, &$message, $params) {
   $site_name = variable_get('site_name');
@@ -299,7 +297,7 @@ function tripal_pub_mail($key, &$message, $params) {
  * @param $form_state
  * @param $form_id
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_form_alter(&$form, &$form_state, $form_id) {
   // turn of preview button for insert/updates
@@ -335,7 +333,7 @@ function tripal_pub_form_alter(&$form, &$form_state, $form_id) {
  * @param $callback
  * @param $args
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_job_describe_args($callback, $args) {
 

legacy/tripal_pub/tripal_pub.views_default.inc

@@ -7,7 +7,7 @@
 /**
  * Implements hook_views_default_views().
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_views_default_views() {
   $views = array();
@@ -23,7 +23,7 @@ function tripal_pub_views_default_views() {
 /**
  * Default publication administration view
  *
- * @ingroup tripal_pub
+ * @ingroup tripal_legacy_pub
  */
 function tripal_pub_defaultview_admin_publications() {
 

legacy/tripal_stock/includes/tripal_stock.admin.inc

@@ -7,7 +7,7 @@
 /**
  * Admin launchpad
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_admin_stock_view() {
   $output = '';
@@ -45,7 +45,7 @@ function tripal_stock_admin_stock_view() {
  * @return
  *   Form array (as described by the drupal form api)
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_admin() {
   $form = array();
@@ -89,7 +89,7 @@ function tripal_stock_admin() {
  * @param $form_state
  *   An array describing the current state of the form including user input
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_admin_validate($form, &$form_state) {
   global $user;  // we need access to the user info

legacy/tripal_stock/includes/tripal_stock.chado_node.inc

@@ -10,7 +10,7 @@
  * @return
  *   An array describing various details of the node
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_node_info() {
   return array(
@@ -42,7 +42,7 @@ function tripal_stock_node_info() {
  * When a node is requested by the user this function is called to allow us
  *  to add auxiliary data to the node object.
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function chado_stock_load($nodes) {
 
@@ -89,7 +89,7 @@ function chado_stock_load($nodes) {
  * @return
  *   A description of the form to be rendered by drupal_get_form()
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function chado_stock_form($node, $form_state) {
 
@@ -325,7 +325,7 @@ function chado_stock_form($node, $form_state) {
  * @param $form
  *   A description of the form to be rendered by drupal_get_form()
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function chado_stock_validate(&$node, $form, &$form_state) {
 
@@ -446,7 +446,7 @@ function chado_stock_validate(&$node, $form, &$form_state) {
  * @return
  *   TRUE if the node was successfully inserted into drupal/chado; FALSE otherwise
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function chado_stock_insert($node) {
 
@@ -560,7 +560,7 @@ function chado_stock_insert($node) {
  * @return
  *   TRUE if the node was successfully updated in drupal/chado; FALSE otherwise
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function chado_stock_update($node) {
 
@@ -710,7 +710,7 @@ function chado_stock_update($node) {
  * @return
  *   TRUE if the node was successfully deleted from drupal/chado; FALSE otherwise
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function chado_stock_delete($node) {
 
@@ -724,7 +724,7 @@ function chado_stock_delete($node) {
 /**
  * Used by Tripal Chado Node API during sync'ing of nodes
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function chado_stock_chado_node_sync_create_new_node($new_node, $record) {
 
@@ -739,7 +739,7 @@ function chado_stock_chado_node_sync_create_new_node($new_node, $record) {
 /**
  * Implements hook_node_presave(). Acts on all content types.
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_node_presave($node) {
 
@@ -783,7 +783,7 @@ function tripal_stock_node_presave($node) {
 /**
  * Implements hook_node_view(). Acts on all content types.
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_node_view($node, $view_mode, $langcode) {
 
@@ -858,7 +858,7 @@ function tripal_stock_node_view($node, $view_mode, $langcode) {
  * Implements hook_node_insert().
  * Acts on all content types.
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_node_insert($node) {
 
@@ -890,7 +890,7 @@ function tripal_stock_node_insert($node) {
  * Implements hook_node_update().
  * Acts on all content types.
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_node_update($node) {
 
@@ -948,7 +948,7 @@ function chado_stock_chado_node_default_url_format() {
  *  access.  The only exception is when the $op == 'create'.  We will always
  *  return TRUE if the permission is set.
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 
 function tripal_stock_node_access($node, $op, $account) {

legacy/tripal_stock/theme/tripal_stock.theme.inc

@@ -8,7 +8,7 @@
  * Implements hook_preprocess_tripal_stock_relationships() which is the preprocess
  * hook for the tripal_stock_relationships template
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
   // we want to provide a new variable that contains the matched stocks.

legacy/tripal_stock/tripal_stock.install

@@ -8,7 +8,7 @@
  * Implements hook_disable().
  * Disable default views when module is disabled
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_disable() {
 
@@ -24,7 +24,7 @@ function tripal_stock_disable() {
 /**
  * Implementation of hook_requirements().
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_requirements($phase) {
   $requirements = array();
@@ -44,7 +44,7 @@ function tripal_stock_requirements($phase) {
 /**
  * Implementation of hook_install().
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_install() {
   // set the default vocabularies
@@ -59,7 +59,7 @@ function tripal_stock_install() {
 /**
  * Implementation of hook_uninstall().
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_uninstall() {
 
@@ -68,7 +68,7 @@ function tripal_stock_uninstall() {
 /**
  * Implementation of hook_schema().
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_schema() {
   $schema['chado_stock'] = array(

legacy/tripal_stock/tripal_stock.module

@@ -4,16 +4,9 @@
  * Basic functionality for stocks
  */
 
-require_once 'api/tripal_stock.DEPRECATED.inc';
-
-require_once 'theme/tripal_stock.theme.inc';
-
-require_once 'includes/tripal_stock.admin.inc';
-require_once 'includes/tripal_stock.chado_node.inc';
-
 /**
- * @defgroup tripal_stock Stock Module
- * @ingroup tripal_modules
+ * @defgroup tripal_legacy_stock Legacy Stock Module
+ * @ingroup tripal_legacy_modules
  * @{
  * Integrates the Chado Stock module with Drupal Nodes & Views
  *
@@ -28,6 +21,11 @@ require_once 'includes/tripal_stock.chado_node.inc';
  * @}
  */
 
+require_once 'api/tripal_stock.DEPRECATED.inc';
+require_once 'theme/tripal_stock.theme.inc';
+require_once 'includes/tripal_stock.admin.inc';
+require_once 'includes/tripal_stock.chado_node.inc';
+
 /**
  * Implements hook_menu().
  * Adds menu items for the tripal_stock
@@ -35,7 +33,7 @@ require_once 'includes/tripal_stock.chado_node.inc';
  * @return
  *   Menu definitions for the tripal_stock
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_menu() {
   $items = array();
@@ -134,7 +132,7 @@ function tripal_stock_search_biological_data_views() {
  * @return
  *   The node object with the passed in nid
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function cs_node_load($nid) {
   if (is_numeric($nid)) {
@@ -154,7 +152,7 @@ function cs_node_load($nid) {
  * @return
  *   Listing of the possible permission catagories
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_permission() {
   return array(
@@ -193,7 +191,7 @@ function tripal_stock_permission() {
  * @return
  *   An array with fields important for views integration
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_views_api() {
   return array(
@@ -208,7 +206,7 @@ function tripal_stock_views_api() {
  * @return
  *   An array of themeing functions to register
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
@@ -298,7 +296,7 @@ function tripal_stock_theme($existing, $type, $theme, $path) {
  * Implements hook_help().
  * Adds a help page to the module list
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_help ($path, $arg) {
   if ($path == 'admin/help#tripal_stock') {
@@ -311,7 +309,7 @@ function tripal_stock_help ($path, $arg) {
  * stock it will redirect to that stock page, otherwise, a list of matching
  * stocks is shown.
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_match_stocks_page($id) {
 
@@ -383,7 +381,7 @@ function tripal_stock_match_stocks_page($id) {
  * @param $form_state
  * @param $form_id
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_form_alter(&$form, &$form_state, $form_id) {
   // turn of preview button for insert/updates
@@ -401,7 +399,7 @@ function tripal_stock_form_alter(&$form, &$form_state, $form_id) {
  * @param $organism
  *  The organism of interest
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_load_organism_stock_counts($organism) {
 

legacy/tripal_stock/tripal_stock.views_default.inc

@@ -7,7 +7,7 @@
 /**
  * Implements hook_views_default_views().
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_views_default_views() {
   $views = array();
@@ -30,7 +30,7 @@ function tripal_stock_views_default_views() {
 /**
  * Defines the stock user search default view.
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_defaultvalue_user_stocks() {
 
@@ -73,7 +73,7 @@ function tripal_stock_defaultvalue_user_stocks() {
 /**
  * Default stock administration view
  *
- * @ingroup tripal_stock
+ * @ingroup tripal_legacy_stock
  */
 function tripal_stock_defaultview_admin_stocks() {
 

tripal/api/tripal.collections.api.inc

@@ -1,5 +1,27 @@
 <?php
 
+/**
+ * @file
+ *
+ * Provides the API for working with Data collections. This includes creation,
+ * experiation, and retreival.
+ */
+
+/**
+ * @defgroup tripal_data_collections_api Data Collections
+ * @ingroup tripal_api
+ * @{
+ * New with Tripal v3 are data collections. A data collection can be compared
+ * to a "shopping cart" system where site users can collect data of interest
+ * to them, and use that data later for other purposes.  By default, Tripal
+ * offers data collections with the default search interface provided by views.
+ * This interface allows end-users to create data collections after searching
+ * for items using the default search.  Once in a collection users can then
+ * generate files for downloading or use by other tools that support data
+ * collections.
+ * @}
+ */
+
 /**
  * Creates a collection of entities for a given user.
  *
@@ -12,8 +34,11 @@
  *   - ids:  An array of the entity IDs that form the collection.
  *   - fields: An array of the field IDs that the collection is limited to.
  *   - description:  A user supplied description for the collection.
+ *
  * @return TripalEntityCollection
  *   An instance of a TripalEntityCollection class or FALSE on failure.
+ *
+ * @ingroup tripal_data_collections_api
  */
 function tripal_create_collection($details) {
   global $user;
@@ -50,8 +75,11 @@ function tripal_create_collection($details) {
  *
  * @param $uid
  *   The User ID
+ *
  * @return
  *   An array of TripalEntityCollection objects.
+ *
+ * @ingroup tripal_data_collections_api
  */
 function tripal_get_user_collections($uid) {
   if (!$uid) {
@@ -77,6 +105,8 @@ function tripal_get_user_collections($uid) {
 
 /**
  * Deletes all collections that have surpassed their lifespan
+ *
+ * @ingroup tripal_data_collections_api
  */
 function tripal_expire_collections() {
   $max_hours = variable_get('tripal_data_collections_lifespan', 7);
@@ -110,6 +140,7 @@ function tripal_expire_collections() {
  * @return
  *  An instance of a TripalEntityCollection class or FALSE on failure.
  *
+ * @ingroup tripal_data_collections_api
  */
 function tripal_get_collection($values) {
   $collection_id = array_key_exists('collection_id', $values) ? $values['collection_id'] : NULL;
@@ -153,6 +184,8 @@ function tripal_get_collection($values) {
  * Generates the downloadable files for a Collection
  *
  * @param TripalEntityCollection $collection
+ *
+ * @ingroup tripal_data_collections_api
  */
 function tripal_create_collection_files($collection_id, TripalJob $job = NULL) {
    if($job) {

tripal/api/tripal.entities.api.inc

@@ -1,5 +1,143 @@
 <?php
+/**
+ * @file
+ * Provides an application programming interface (API) for working with
+ * TripalEntity content types (bundles) and their entities.
+ */
+
+/**
+ * @defgroup tripal_entities_api Tripal Entities
+ * @ingroup tripal_api
+ * @{
+ * Provides an application programming interface (API) for working with
+ * TripalEntity content types (bundles) and their entities.
+ * @}
+ *
+ */
+
+
+/**
+ * Allows a module to make changes to an entity object after creation.
+ *
+ * This function is added by Tripal to allow datastore backends to add
+ * addition properties to the entity that they themselves will use later.
+ *
+ * @param $entity
+ * @param $entity_type
+ *
+ * @ingroup tripal_entities_api
+ */
+function hook_entity_create(&$entity, $entity_type) {
+
+}
+
+/**
+ * Allows a module to perform tasks after a TripalBundle object is created.
+ *
+ * @param $bundle
+ *   The newly created TripalBundle object.
+ * @param $storage_args
+ *   Arguments passed to the storage backend for this bundle.  These arguments
+ *   typically provide details for how to associate this bundle with records
+ *   in the storage system.  Each storage system will have its own set of
+ *   arguments that it will expect.
+ *
+ * @ingroup tripal_entities_api
+ */
+function hook_bundle_create(&$bundle, $storage_args) {
+
+}
+/**
+ * Allows a module to perform tasks after fields are added to a TripalBundle.
+ *
+ * @param $bundle
+ *   The newly created TripalBundle object.
+ *
+ * @ingroup tripal_entities_api
+ */
+function hook_bundle_postcreate(&$bundle) {
+
+}
+/**
+ * Allows a module to add admin notifications to the associated tripal table
+ * during the cron run.
+ *
+ * @ingroup tripal_entities_api
+ */
+function hook_tripal_cron_notification() {
 
+}
+
+/**
+ * Allows a module to perform tasks before a TripalBundle object is deleted.
+ *
+ * @param $bundle
+ *   The newly created TripalBundle object.
+ *
+ * @ingroup tripal_entities_api
+ */
+function hook_bundle_delete($bundle) {
+
+}
+
+/**
+ * Implement this hook to define default formats for Tripal Content Types.
+ *
+ * @param TripalBundle $bundle
+ *   A tripal content type entity with information to be used for determining the default title format.
+ * @param array $available_tokens
+ *   An array of available tokens for this particular tripal content type.
+ *
+ * @return array
+ *   An array of potential formats. The lightest weighted format suggested by all modules will be chosen.
+ *   Each array item should consist of a 'weight' and 'format'. See the hook implementation below
+ *   for examples.
+ *    - weight: an integer used to determine priority of suggestions.
+ *        The smaller/lighter the number the higher the priority.
+ *        Best practice is to use a weight less than 0 for extension modules.
+ *        specifically, -2 is a good weight for calculated formats and -5 is a
+ *        good weight for hard-coded formats specific to a given type.
+ *    - format: a string including approved tokens used to determine the title
+ *        on Tripal content pages.
+ *
+ * @ingroup tripal_entities_api
+ */
+function hook_tripal_default_title_format($bundle, $available_tokens) {
+  $format = array();
+
+  // If you want to suggest a default format for a particular vocabulary term:
+  //---------------------------------------------------------------------------
+  // Load the term associated with this Tripal Content type.
+  $term = entity_load('TripalTerm', array('id' => $bundle->term_id));
+  $term = reset($term);
+
+  // If it's the term you are interested in then suggest a format.
+  if ($term->name == 'organism') {
+
+    // To suggest a format, add an element to the array with a format & weight key.
+    $format[] = array(
+      // This is the format/pattern you suggest be used to determine the title of organism pages.
+      'format' => '[organism__genus] [organism__species]',
+      // The weight/priority of your suggestion.
+      'weight' => -5
+    );
+
+  }
+
+  // Say you know that in your particular site, all 'names' are required
+  // and you want to only use the human-readable name:
+  //---------------------------------------------------------------------------
+  $name_field = preg_grep('/__name]$/', array_keys($available_tokens));
+  $name_field = reset($name_field);
+  if (is_string($name_field)) {
+    $format[] = array(
+      'format' => $name_field,
+      'weight' => -2,
+    );
+  }
+
+  return $format;
+}
 
 /**
  * A replacement for the entity_load function of Drupal.
@@ -24,6 +162,8 @@
  * @return
  *   An array of entity objects indexed by their ids. When no results are
  *   found, an empty array is returned.
+ *
+ * @ingroup tripal_entities_api
  */
 function tripal_load_entity($entity_type, $ids = FALSE, $reset = FALSE,
     $field_ids = array()) {
@@ -58,6 +198,8 @@ function tripal_load_entity($entity_type, $ids = FALSE, $reset = FALSE,
  *
  * @return
  *   A TripalTerm entity object or NULL if not found.
+ *
+ * @ingroup tripal_entities_api
  */
 function tripal_load_term_entity($values) {
   $vocabulary = array_key_exists('vocabulary', $values) ? $values['vocabulary'] : '';
@@ -98,6 +240,8 @@ function tripal_load_term_entity($values) {
  *
  * @return
  * A TripalVocab entity object or NULL if not found.
+ *
+ * @ingroup tripal_entities_api
  */
 function tripal_load_vocab_entity($values) {
   $vocabulary = array_key_exists('vocabulary', $values) ? $values['vocabulary'] : '';
@@ -134,6 +278,8 @@ function tripal_load_vocab_entity($values) {
  *
  * @return
  *   A TripalBundle entity object or NULL if not found.
+ *
+ * @ingroup tripal_entities_api
  */
 function tripal_load_bundle_entity($values) {
 
@@ -160,47 +306,6 @@ function tripal_load_bundle_entity($values) {
   return NULL;
 }
 
-
-/**
- * Allows a module to perform tasks before a TripalBundle object is deleted.
- *
- * @param $bundle
- *   The newly created TripalBundle object.
- */
-function hook_bundle_delete($bundle) {
-
-}
-/**
- * Allows a module to perform tasks after a TripalBundle object is created.
- *
- * @param $bundle
- *   The newly created TripalBundle object.
- * @param $storage_args
- *   Arguments passed to the storage backend for this bundle.  These arguments
- *   typically provide details for how to associate this bundle with records
- *   in the storage system.  Each storage system will have its own set of
- *   arguments that it will expect.
- */
-function hook_bundle_create(&$bundle, $storage_args) {
-
-}
-/**
- * Allows a module to perform tasks after fields are added to a TripalBundle.
- *
- * @param $bundle
- *   The newly created TripalBundle object.
- */
-function hook_bundle_postcreate(&$bundle) {
-
-}
-/**
- * Allows a module to add admin notifications to the associated tripal table
- * during the cron run.
- *
- */
-function hook_tripal_cron_notification() {
-
-}
 /**
  * Allows a module to write to the admin notification table
  * during the cron run.
@@ -217,6 +322,8 @@ function hook_tripal_cron_notification() {
  *   If not type is required please pass NULL.
  * @param $submitter_id
  *   A unique ID provided by the submitter for checking to make sure that the notification is not added more than once.
+ *
+ * @ingroup tripal_entities_api
  */
 function tripal_add_notification($title, $details, $type, $actions, $submitter_id) {
   $transaction = db_transaction();
@@ -259,8 +366,11 @@ function tripal_add_notification($title, $details, $type, $actions, $submitter_i
  * @param $error
  *  A string, passed by reference, that is filled with the error message
  *  if the function fails.
+ *
  * @return
  *   The bundle object or FALSE if failure.
+ *
+ * @ingroup tripal_entities_api
  */
 function tripal_create_bundle($args, &$error = '') {
   $vocabulary = $args['vocabulary'];
@@ -391,6 +501,8 @@ function tripal_entity_permissions($entity) {
  * @return
  *   An array of bundles. Each bundle is an object containing information
  *   about that bundle.
+ *
+ * @ingroup tripal_entities_api
  */
 function tripal_get_content_types() {
   return db_select('tripal_bundle', 'tb')
@@ -404,6 +516,8 @@ function tripal_get_content_types() {
  *
  * @param $bundle_name
  *   The name of the bundle to refresh (e.g. bio_data_4).
+ *
+ * @ingroup tripal_entities_api
  */
 function tripal_tripal_cron_notification() {
   $num_created = 0;
@@ -483,6 +597,8 @@ function tripal_tripal_cron_notification() {
  *
  * @return
  *   An object containing information about the bundle.
+ *
+ * @ingroup tripal_entities_api
  */
 function tripal_get_content_type($bundle_name) {
   return db_select('tripal_bundle', 'tb')
@@ -500,6 +616,8 @@ function tripal_get_content_type($bundle_name) {
  *
  * @return
  *   The array of field instance names that were added.
+ *
+ * @ingroup tripal_entities_api
  */
 function tripal_create_bundle_fields($bundle, $term) {
 
@@ -607,6 +725,7 @@ function tripal_create_bundle_fields($bundle, $term) {
  * TODO: this function really shouldn't try to create an instance and
  * attach to a bundle  at the same time.
  *
+ * @ingroup tripal_entities_api
  */
 function tripal_update_bundle_field($field_name, $field_info, $entity_type_name, $bundle_name) {
 
@@ -668,19 +787,6 @@ function tripal_update_bundle_field($field_name, $field_info, $entity_type_name,
   field_update_instance($field_instance);
 }
 
-/**
- * Allows a module to make changes to an entity object after creation.
- *
- * This function is added by Tripal to allow datastore backends to add
- * addition properties to the entity that they themselves will use later.
- *
- * @param $entity
- * @param $entity_type
- */
-function hook_entity_create(&$entity, $entity_type) {
-
-}
-
 
 /**
  * @section
@@ -696,6 +802,8 @@ function hook_entity_create(&$entity, $entity_type) {
  *   The unique identfier for the bundle you want the value for.
  * @return text
  *   The value of the specified variable for the specified bundle.
+ *
+ * @ingroup tripal_entities_api
  */
 function tripal_get_bundle_variable($variable_name, $bundle_id, $default = FALSE) {
 
@@ -731,6 +839,8 @@ function tripal_get_bundle_variable($variable_name, $bundle_id, $default = FALSE
  *   The unique identfier for the bundle you want the value for.
  * @param $text $value
  *   The value of the variable for the given bundle.
+ *
+ * @ingroup tripal_entities_api
  */
 function tripal_set_bundle_variable($variable_name, $bundle_id, $value) {
   $variable = tripal_get_variable($variable_name);
@@ -786,6 +896,8 @@ function tripal_set_bundle_variable($variable_name, $bundle_id, $value) {
  *
  * @param TripalBundle $bundle
  *   The Entity object for the Tripal Bundle the title format is for.
+ *
+ * @ingroup tripal_entities_api
  */
 function tripal_get_title_format($bundle) {
 
@@ -809,6 +921,8 @@ function tripal_get_title_format($bundle) {
  *   The Entity object for the Tripal Bundle the title format is for.
  * @param string $format
  *   The pattern to be used when generating entity titles for the above type.
+ *
+ * @ingroup tripal_entities_api
  */
 function tripal_save_title_format($entity, $format) {
 
@@ -823,6 +937,8 @@ function tripal_save_title_format($entity, $format) {
  *
  * @return string
  *   A default title format.
+ *
+ * @ingroup tripal_entities_api
  */
 function tripal_get_default_title_format($bundle) {
   $format = '';
@@ -863,62 +979,6 @@ function tripal_get_default_title_format($bundle) {
   return $format;
 }
 
-/**
- * Implement this hook to define default formats for Tripal Content Types.
- *
- * @param TripalBundle $bundle
- *   A tripal content type entity with information to be used for determining the default title format.
- * @param array $available_tokens
- *   An array of available tokens for this particular tripal content type.
- *
- * @return array
- *   An array of potential formats. The lightest weighted format suggested by all modules will be chosen.
- *   Each array item should consist of a 'weight' and 'format'. See the hook implementation below
- *   for examples.
- *    - weight: an integer used to determine priority of suggestions.
- *        The smaller/lighter the number the higher the priority.
- *        Best practice is to use a weight less than 0 for extension modules.
- *        specifically, -2 is a good weight for calculated formats and -5 is a
- *        good weight for hard-coded formats specific to a given type.
- *    - format: a string including approved tokens used to determine the title
- *        on Tripal content pages.
- */
-function hook_tripal_default_title_format($bundle, $available_tokens) {
-  $format = array();
-
-  // If you want to suggest a default format for a particular vocabulary term:
-  //---------------------------------------------------------------------------
-  // Load the term associated with this Tripal Content type.
-  $term = entity_load('TripalTerm', array('id' => $bundle->term_id));
-  $term = reset($term);
-
-  // If it's the term you are interested in then suggest a format.
-  if ($term->name == 'organism') {
-
-    // To suggest a format, add an element to the array with a format & weight key.
-    $format[] = array(
-      // This is the format/pattern you suggest be used to determine the title of organism pages.
-      'format' => '[organism__genus] [organism__species]',
-      // The weight/priority of your suggestion.
-      'weight' => -5
-    );
-
-  }
-
-  // Say you know that in your particular site, all 'names' are required
-  // and you want to only use the human-readable name:
-  //---------------------------------------------------------------------------
-  $name_field = preg_grep('/__name]$/', array_keys($available_tokens));
-  $name_field = reset($name_field);
-  if (is_string($name_field)) {
-    $format[] = array(
-      'format' => $name_field,
-      'weight' => -2,
-    );
-  }
-
-  return $format;
-}
 
 /**
  * Returns an array of tokens based on Tripal Entity Fields.
@@ -927,6 +987,8 @@ function hook_tripal_default_title_format($bundle, $available_tokens) {
  *    The bundle entity for which you want tokens.
  * @return
  *    An array of tokens where the key is the machine_name of the token.
+ *
+ * @ingroup tripal_entities_api
  */
 function tripal_get_entity_tokens($entity, $options = array()) {
   $tokens = array();
@@ -996,6 +1058,8 @@ function tripal_get_entity_tokens($entity, $options = array()) {
  *
  * @return
  *   The string will all tokens replaced with values.
+ *
+ * @ingroup tripal_entities_api
  */
 function tripal_replace_entity_tokens($string, &$entity, $bundle_entity = NULL) {
   // Determine which tokens were used in the format string
@@ -1091,6 +1155,8 @@ function tripal_replace_entity_tokens($string, &$entity, $bundle_entity = NULL)
  *   A list of tokens generated via tripal_get_entity_tokens().
  * @return
  *   Rendered output describing the available tokens.
+ *
+ * @ingroup tripal_entities_api
  */
 function theme_token_list($tokens) {
 
@@ -1113,8 +1179,9 @@ function theme_token_list($tokens) {
  * @param $entity
  *
  * @return mixed
+ *
+ * @ingroup tripal_entities_api
  */
-
 function tripal_entity_label($entity) {
   if (property_exists($entity, 'title')) {
     return $entity->title;
@@ -1122,6 +1189,12 @@ function tripal_entity_label($entity) {
   return NULL;
 }
 
+/**
+ *
+ * @param $bundle_name
+ *
+ * @ingroup tripal_entities_api
+ */
 function tripal_get_bundle_details($bundle_name) {
   global $user;
 
@@ -1203,6 +1276,8 @@ function tripal_get_bundle_details($bundle_name) {
  * A recursive helper function for the tripal_get_bundle_details.
  *
  * @param $elementInfo
+ *
+ * @ingroup tripal_entities_api
  */
 function _tripal_get_bundle_field_element_details($elements, &$field_details) {
    $field_details['elements'] = array();
@@ -1235,6 +1310,15 @@ function _tripal_get_bundle_field_element_details($elements, &$field_details) {
    }
 }
 
+/**
+ *
+ * @param unknown $bundle_name
+ * @param unknown $values
+ *
+ * @throws Exception
+ *
+ * @ingroup tripal_entities_api
+ */
 function tripal_insert_entity($bundle_name, $values){
   global $user;
 
@@ -1283,6 +1367,12 @@ function tripal_insert_entity($bundle_name, $values){
   $entity = $entity->save();
 }
 
+/**
+ * @param $bundle_name
+ * @param $values
+ *
+ * @ingroup tripal_entities_api
+ */
 function tripal_update_entity($bundle_name, $values) {
 
 

tripal/api/tripal.fields.api.inc

@@ -1,5 +1,20 @@
 <?php
 
+/**
+ * @file
+ * Provides an application programming interface (API) for working with
+ * fields attached to TripalEntity content types (bundles).
+ */
+
+/**
+ * @defgroup tripal_fields_api Tripal Fields
+ * @ingroup tripal_api
+ * @{
+ * Provides an application programming interface (API) for working with
+ * fields attached to TripalEntity content types (bundles).
+ * @}
+ *
+ */
 
 /**
  * Executes a TripalFieldQuery using the provided conditions.
@@ -26,20 +41,53 @@
  *   - orderBy: the name of the field on which the filter should be applied.
  *   - direction: either the string 'ASC' (for ascending sort) or 'DESC' (for
  *     descending).
+ *
+ * @ingroup tripal_fields_api
  */
 function hook_field_storage_tquery($conditions, $orderBy) {
   // See the tripal_chado_field_storage_tquery() function for an example.
 }
 
+/**
+ *
+ * @param unknown $entity_type
+ * @param unknown $bundle
+ *
+ * @ingroup tripal_fields_api
+ */
 function hook_bundle_fields_info($entity_type, $bundle) {
 
 }
+
+/**
+ *
+ * @param unknown $entity_type
+ * @param unknown $bundle
+ *
+ * @ingroup tripal_fields_api
+ */
 function hook_bundle_instances_info($entity_type, $bundle) {
 
 }
+/**
+ *
+ * @param unknown $info
+ * @param unknown $bundle
+ * @param unknown $term
+ *
+ * @ingroup tripal_fields_api
+ */
 function hook_bundle_fields_info_alter(&$info, $bundle, $term) {
 
 }
+/**
+ *
+ * @param unknown $info
+ * @param unknown $bundle
+ * @param unknown $term
+ *
+ * @ingroup tripal_fields_api
+ */
 function hook_bundle_instances_info_alter(&$info, $bundle, $term) {
 
 }
@@ -55,6 +103,8 @@ function hook_bundle_instances_info_alter(&$info, $bundle, $term) {
  *
  * @return
  *   A list of TripalField names.
+ *
+ * @ingroup tripal_fields_api
  */
 function tripal_get_field_types() {
   $types = array();
@@ -116,6 +166,8 @@ function tripal_get_field_types() {
  *
  * @return
  *   A list of TripalFieldWidget names.
+ *
+ * @ingroup tripal_fields_api
  */
 function tripal_get_field_widgets() {
   $widgets = array();
@@ -173,6 +225,8 @@ function tripal_get_field_widgets() {
  *
  * @return
  *   A list of TripalFieldFormatter names.
+ *
+ * @ingroup tripal_fields_api
  */
 function tripal_get_field_formatters() {
   $formatters = array();
@@ -228,6 +282,8 @@ function tripal_get_field_formatters() {
  *
  * @return
  *   TRUE if the field type class file was found, FALSE otherwise.
+ *
+ * @ingroup tripal_fields_api
  */
 function tripal_load_include_field_class($class) {
 
@@ -268,6 +324,8 @@ function tripal_load_include_field_class($class) {
  *
  * @return
  *   TRUE if the downloader class file was found, FALSE otherwise.
+ *
+ * @ingroup tripal_fields_api
  */
 function tripal_load_include_downloader_class($class) {
 
@@ -324,6 +382,8 @@ function tripal_load_include_downloader_class($class) {
  * @return
  *   The value assigned to the item's key; FALSE if the key doesn't exist or
  *   the $default argument if no value is associated with the key.
+ *
+ * @ingroup tripal_fields_api
  */
 function tripal_get_field_item_keyval($items, $delta, $key, $default='') {
   if (!array_key_exists($delta, $items)) {
@@ -354,6 +414,8 @@ function tripal_get_field_item_keyval($items, $delta, $key, $default='') {
  *   The name of the field to which the element belongs.
  * @param $term
  *   The term object as returned by tripal_get_term_details();
+ *
+ * @ingroup tripal_fields_api
  */
 function tripal_format_views_field_element($field_name, $term) {
   $element_name = $term['vocabulary']['short_name'] . '__' . $term['accession'];

tripal/api/tripal.files.api.inc

@@ -6,7 +6,7 @@
  */
 
 /**
- * @defgroup tripal_files_api Tripal Files API
+ * @defgroup tripal_files_api Files
  * @ingroup tripal_api
  * @{
  * Provides an application programming interface (API) for managing files within

tripal/api/tripal.importer.api.inc

@@ -1,4 +1,21 @@
 <?php
+
+/**
+ * @file
+ * Provides an application programming interface (API) for working with
+ * data file importers using the TripalImporter class.
+ */
+
+/**
+ * @defgroup tripal_importer_api Data Importing
+ * @ingroup tripal_api
+ * @{
+ * Provides an application programming interface (API) for working with
+ * data file importers using the TripalImporter class.
+ * @}
+ *
+ */
+
 /**
  * Implements hook_handle_uplaoded_file().
  *
@@ -14,6 +31,8 @@
  *
  * @return
  *   A Drupal managed file ID.
+ *
+ * @ingroup tripal_importer_api
  */
 function hook_handle_uploaded_file($filename, $filepath, $type) {
 
@@ -30,6 +49,8 @@ function hook_handle_uploaded_file($filename, $filepath, $type) {
  *
  * @return
  *   A list of TripalImporter names.
+ *
+ * @ingroup tripal_importer_api
  */
 function tripal_get_importers() {
   $importers = array();
@@ -59,6 +80,8 @@ function tripal_get_importers() {
  *
  * @return
  *   TRUE if the field type class file was found, FALSE otherwise.
+ *
+ * @ingroup tripal_importer_api
  */
 function tripal_load_include_importer_class($class) {
 
@@ -87,6 +110,8 @@ function tripal_load_include_importer_class($class) {
  * @param $import_id
  *   The ID of the import record.
  * @throws Exception
+ *
+ * @ingroup tripal_importer_api
  */
 function tripal_run_importer($import_id, TripalJob $job = NULL) {
 
@@ -136,6 +161,8 @@ function tripal_run_importer($import_id, TripalJob $job = NULL) {
  * @param $job
  *   The TripalJob object.$this
  * @throws Exception
+ *
+ * @ingroup tripal_importer_api
  */
 function tripal_run_importer_run($loader, $job) {
 
@@ -169,6 +196,8 @@ function tripal_run_importer_run($loader, $job) {
  * @param $job
  *   The TripalJob object.
  * @throws Exception
+ *
+ * @ingroup tripal_importer_api
  */
 function tripal_run_importer_post_run($loader, $job) {
   try {

tripal/api/tripal.jobs.api.inc

@@ -6,34 +6,27 @@
  */
 
 /**
- * @defgroup tripal_jobs_api Tripal Jobs API
+ * @defgroup tripal_jobs_api Jobs
  * @ingroup tripal_api
  * @{
  * Tripal offers a job management subsystem for managing tasks that may require
- * an extended period of time for completion.  Drupal uses a UNIX-based cron
- * job to handle tasks such as  checking  the  availability of updates,
- * indexing new nodes for searching, etc.   Drupal's cron uses the web interface
- * for launching these tasks, however, Tripal provides several administrative
- * tasks that may time out and not complete due to limitations of the web
- * server. To circumvent this, as well as provide more fine-grained control and
- * monitoring, Tripal uses a jobs management sub-system.   It is anticipated
- * that this functionality will be used for managing analysis jobs provided by
- * future tools, with eventual support for distributed computing.
+ * an extended period of time for completion. Tripal provides several
+ * administrative tasks that may time out and not complete due to limitations
+ * of the web server. To circumvent this, as well as provide more fine-grained
+ * control and monitoring, Tripal uses a jobs management system.
  *
  * The  Tripal jobs management system allows administrators to submit tasks
- * to be performed which can then  be launched through a UNIX command-line PHP
+ * to be performed which can then be launched through a UNIX command-line PHP
  * script or cron job.  This command-line script can be added to a cron
  * entry along-side the Drupal cron entry for automatic, regular launching of
  * Tripal jobs.  The order of execution of waiting jobs is determined first by
  * priority and second by the order the jobs were entered.
  *
- * The API functions described below provide a programmatic interface for
- * adding, checking and viewing jobs.
  * @}
  */
 
 /**
- * Adds a job to the Tripal Jbo queue
+ * Adds a job to the Tripal Job queue
  *
  * @param $job_name
  *    The human readable name for the job
@@ -286,8 +279,6 @@ function tripal_rerun_job($job_id, $goto_jobs_page = TRUE) {
     drupal_set_message($e->getMessage(), 'error');
     tripal_report_error('tripal', TRIPAL_ERROR, $e->getMessage());
   }
-
-
 }
 
 /**
@@ -448,7 +439,7 @@ function tripal_launch_job($do_parallel = 0, $job_id = NULL, $max_jobs = -1, $si
  * @return
  *   True on success and False otherwise
  *
- * @ingroup tripal
+ * @ingroup tripal_jobs_api
  */
 function tripal_set_job_progress($job_id, $percentage) {
 
@@ -474,6 +465,8 @@ function tripal_set_job_progress($job_id, $percentage) {
  * @return
  *   A value between 0 and 100 indicating the percentage complete of the job.
  *   FALSE on failure.
+ *
+ * @ingroup tripal_jobs_api
  */
 function tripal_get_job_progress($job_id) {
 
@@ -545,6 +538,8 @@ function tripal_get_active_jobs($modulename = NULL) {
  *   The job id to be exeuted.
  * @param bool $redirect [optional]
  *   Whether to redirect to the job page or not.
+ *
+ * @ingroup tripal_jobs_api
  */
 function tripal_execute_job($job_id, $redirect = TRUE) {
 

tripal/api/tripal.notice.api.inc

@@ -1,19 +1,19 @@
 <?php
 /**
  * @file
- * Provides an application programming interface (API) for Tripal
- *
- * The Tripal API currently provides generic functionality for all Tripal
- * extension modules.
+ * Provides an application programming interface (API) for improved user
+ * notivications.  These API functions can be used to set messages for
+ * end-users, administrators, or simple logging.
  */
 
 /**
- * @defgroup tripal_api Tripal API
+ * @defgroup tripal_notify_api Notify
+ * @ingroup tripal_api
  * @{
- * Provides an application programming interface (API) for Tripal
+ * Provides an application programming interface (API) for improved user
+ * notivications.  These API functions can be used to set messages for
+ * end-users, administrators, or simple logging.
  *
- * The Tripal API currently provides generic functionality for all Tripal
- * extension modules..
  * @}
  */
 
@@ -59,7 +59,7 @@ define('TRIPAL_DEBUG',7);
  *     - print: prints the error message to the terminal screen. Useful when
  *       display is the command-line
  *
- * @ingroup tripal_api
+ * @ingroup tripal_notify_api
  */
 function tripal_report_error($type, $severity, $message, $variables = array(), $options = array()) {
 
@@ -156,6 +156,8 @@ function tripal_report_error($type, $severity, $message, $variables = array(), $
  *     - return_html: return HTML instead of setting a drupal message. This can
  *       be used to place a tripal message in a particular place in the page.
  *       The default is FALSE.
+ *
+ * @ingroup tripal_notify_api
  */
 function tripal_set_message($message, $importance = TRIPAL_INFO, $options = array()) {
   global $user;
@@ -225,6 +227,8 @@ function tripal_set_message($message, $importance = TRIPAL_INFO, $options = arra
  *       without intervening date prefixes
  * @return
  *   The number of bytes that were written to the file, or FALSE on failure
+ *
+ * @ingroup tripal_notify_api
  */
 function tripal_log($message, $type = 'error', $options = array()) {
   global $base_url;

tripal/api/tripal.terms.api.inc

@@ -1,4 +1,27 @@
 <?php
+/**
+ * @file
+ * Provides an application programming interface (API) for working with
+ * controlled vocaublary terms.
+ */
+
+/**
+ * @defgroup tripal_terms_api CV Terms
+ * @ingroup tripal_api
+ * @{
+ * Tripal provides an application programming interface (API) for working with
+ * controlled vocaublary terms.  Tripal v3 is highly dependent on controlled
+ * vocabularies for identifying all content types and fields attached to those
+ * content types.  However, Tripal v3 is also database agnostic. Therefore, it
+ * controlled vocabularies can be stored in any database back-end.  By default
+ * the tripal_chado module is used for storing controlled vocabularies. However,
+ * if someone wanted to store controlled vocabularies in a database other than
+ * Chado they can do so. These API functions provide a convenient wrapper for
+ * accession controlled vocabularies no matter where they are stored.
+ *
+ * @}
+ */
+
 /**
  * @section
  * Vocabulary Hooks.
@@ -25,6 +48,8 @@
  *   settings: An array whose keys are the names of the settings available for
  *     the storage backend, and whose values are the default values for
  *     those settings.
+ *
+ * @ingroup tripal_terms_api
  */
 function hook_vocab_storage_info() {
   return array(
@@ -53,6 +78,8 @@ function hook_vocab_storage_info() {
  *
  * @return
  *   A form object.
+ *
+ * @ingroup tripal_terms_api
  */
 function hook_vocab_select_term_form(&$form, &$form_state) {
 
@@ -62,6 +89,8 @@ function hook_vocab_select_term_form(&$form, &$form_state) {
  * Validates the hook_vocab_select_term_form().
  *
  * @param $name
+ *
+ * @ingroup tripal_terms_api
  */
 function hook_vocab_select_term_form_validate($form, &$form_state) {
 
@@ -76,6 +105,8 @@ function hook_vocab_select_term_form_validate($form, &$form_state) {
  * @param $form
  * @param $form_state
  *
+ * @ingroup tripal_terms_api
+ *
  */
 function hook_vocab_import_form($form, &$form_state) {
   return $form;
@@ -116,6 +147,8 @@ function hook_vocab_import_form_submit($form, &$form_state) {
  *     -definition : The term's description.
  *   any other keys may be added as desired. Returns NULL if the term
  *   cannot be found.
+ *
+ * @ingroup tripal_terms_api
  */
 function hook_vocab_get_term($vocabulary, $accession) {
   // See the tripal_chado_vocab_get_term() function for an example.
@@ -142,6 +175,7 @@ function hook_vocab_get_term($vocabulary, $accession) {
  *       prefix does not support appending then the exact location for the
  *       position of the short_name and the term accession will be
  *       specified with the {db} and {accession} tags respectively.
+ * @ingroup tripal_terms_api
  */
 function hook_vocab_get_vocabulary($vocabulary) {
   // See the tripal_chado_vocab_get_vocabulary() function for an example.
@@ -167,6 +201,7 @@ function hook_vocab_get_vocabulary($vocabulary) {
  * @return
  *   TRUE if the term was added, FALSE otherwise.  If the term already exists
  *   it will be updated and the return value will be TRUE,
+ * @ingroup tripal_terms_api
  */
 function hook_vocab_add_term($details) {
   // See the tripal_chado_vocab_set_term() function for an example.
@@ -193,6 +228,7 @@ function hook_vocab_add_term($details) {
  * @return
  *   TRUE if the term was added, FALSE otherwise.  If the term already exists
  *   it will be updated and the return value will be TRUE,
+ * @ingroup tripal_terms_api
  */
 function tripal_add_term($details) {
   // TODO: we need some sort of administrative interface that lets the user
@@ -236,6 +272,8 @@ function tripal_add_term($details) {
  *     - definition : The term's description.
  *   any other keys may be added as desired. Returns NULL if the term
  *   cannot be found.
+ *
+ * @ingroup tripal_terms_api
  */
 function tripal_get_term_details($vocabulary, $accession) {
 
@@ -280,6 +318,8 @@ function tripal_get_term_details($vocabulary, $accession) {
  *       position of the short_name and the term accession will be
  *       specified with the {db} and {accession} tags respectively.
  *     - sw_url: The URL for mapping terms via the semantic web.
+ *
+ * @ingroup tripal_terms_api
  */
 function tripal_get_vocabulary_details($vocabulary) {
   // TODO: we need some sort of administrative interface that lets the user
@@ -327,6 +367,8 @@ function tripal_get_vocabulary_details($vocabulary) {
  * @param  $delta
  *   The delta value for the field if this form is being added to a field
  *   widget.
+ *
+ * @ingroup tripal_terms_api
  */
 function tripal_get_term_lookup_form(&$form, &$form_state, $default_name = '',
     $title = 'Vocabulary Term', $description = '', $is_required,
@@ -458,6 +500,8 @@ function tripal_get_term_lookup_form(&$form, &$form_state, $default_name = '',
  *
  * @return
  *   An array of term objects for each of the user selected terms.
+ *
+ * @ingroup tripal_terms_api
  */
 function tripal_get_term_lookup_form_result($form, $form_state, $field_name = '', $delta = 0) {
   $values = array();
@@ -483,6 +527,8 @@ function tripal_get_term_lookup_form_result($form, $form_state, $field_name = ''
 
 /**
  * Implements an AJAX callback for the tripal_chado_vocab_select_term_form.
+ *
+ * @ingroup tripal_terms_api
  */
 function tripal_get_term_lookup_form_ajax_callback($form, $form_state) {
   $field_name = $form_state['storage']['term_match_field'];

tripal/api/tripal.upload.api.inc

@@ -1,4 +1,105 @@
 <?php
+/**
+ * @file
+ * Provides an application programming interface (API) for working with
+ * file uploads.
+ */
+
+/**
+ * @defgroup tripal_upload_api File Upload
+ * @ingroup tripal_api
+ * @{
+ * Tripal provides a convenient HTML5 Javascript uploader. It is automatically
+ * embedded into the TripalImporter class.  This application programing
+ * interface (API) provides support for working with uploaded files.
+ *
+ * If you want to use the TripalUploader JavaScript in your own form the
+ * following must be performed:
+ *
+ * 1) Add a Drupal form to your code that contains the following:
+ *   * A Drupal-style table with 4 or 8 columns.  See the initialize
+ *     function in this class for a description of the columns.
+ *   * A button for submitting a file for upload.
+ *
+ * @code
+ * $headers = array(
+ *    array('data' => 'Sequence File'),
+ *    array('data' => 'Size', 'width' => '10%'),
+ *    array('data' => 'Upload Progress', 'width' => '20%'),
+ *    array('data' => 'Action', 'width' => '10%')
+ *  );
+ *  $rows = array();
+ *  $table_vars = array(
+ *    'header'      => $headers,
+ *    'rows'        => $rows,
+ *    'attributes'  => array('id' => 'sequence-file-upload-table'),
+ *    'sticky'      => TRUE,
+ *    'colgroups'   => array(),
+ *    'empty'       => t('There are currently no files added.'),
+ *  );
+ *  $form['upload']['sequence_file'] = array(
+ *    '#markup' => theme('table', $table_vars)
+ *  );
+ *  $form['upload']['sequence_fid'] = array(
+ *    '#type' => 'hidden',
+ *    '#value' => 0,
+ *    '#attributes' => array('id' => 'sequence-fid')
+ *  );
+ *  $form['upload']['sequence_file_submit'] = array(
+ *    '#type'     => 'submit',
+ *    '#value'    => 'Upload Sequence File',
+ *    '#name' => 'sequence_file_submit',
+ *    // We don't want this button to submit as the file upload
+ *    // is handled by the JavaScript code.
+ *    '#attributes' => array('onclick' => 'return (false);')
+ *  );
+ * @endcode
+ *
+ *
+ * 2)  Edit the theme/js/[module_name].js and in the "Drupal.behaviors.[module]"
+ * section add a JQuery show function to the form that converts the table
+ * created in the Drupal form to a TripalUploader table.  The 'table_id' must be
+ * the same as the 'id' attribute set for the table in the Drupal code above.
+ * The 'submit_id' must be the id of the upload button added in the Drupal
+ * code above.  The 'category' for the files.  This is the category that
+ * will be saved in Tripal for the file.  See the addUploadTable function
+ * for additional options.  Include a 'cardinality' setting to indicate
+ * the number of allowed files per upload, and set the 'target_id' to the
+ * name of the field that will contain the file ID (fid) after uploading.
+ *
+ * @code
+ *  // The TripalUploader object used for uploading of files using the
+ *  // HTML5 File API. Large files are uploaded as chunks and a progress
+ *  // bar is provided.
+ *  var uploader = new TripalUploader();
+ *
+ *  $('#tripal-sequences-panel-form').show(function() {
+ *    uploader.addUploadTable('sequence_file', {
+ *      'table_id' : '#sequence-file-upload-table',
+ *      'submit_id': '#edit-sequence-file-submit',
+ *      'category' : ['sequence_file'],
+ *      'cardinality' : 1,
+ *      'target_id' : 'sequence-fid',
+ *    });
+ *  });
+ * @endcode
+ *
+ *
+ * 3) Files are uploaded automatically to Tripal.  Files are saved in the
+ * Tripal user's directory.  You can retreive information about the
+ * file by querying for the file category for the current project.
+ *
+ * @code
+ *   $seq_files = TripalFeature::getFilesByTypes($user->uid, array('sequence_file'), $project_id);
+ * @endcode
+ *
+ * 4) If the 'target_id' was used in array for step #2 above, then the
+ * file ID can be retrieved in the hook_validate() and hook_submit() functions
+ * via the $form_state['input'] array (not the $form_state['values'] array.
+ *
+ * @}
+ */
+
 /**
  * Allows a module to interact with the Tripal file uploader during upload.
  *
@@ -22,6 +123,8 @@
  * @return
  *   TRUE if the upload should continue. FALSE if a problem occurs and the
  *   upload should be terminated.
+ *
+ * @ingroup tripal_upload_api
  */
 function hook_file_upload_check($action, $details, &$message){
   switch ($action) {

tripal/api/tripal.variables.api.inc

@@ -6,20 +6,19 @@
  */
 
 /**
- * @defgroup tripal_variables_api Tripal Variables API
+ * @defgroup tripal_variables_api Variables
  * @ingroup tripal_api
  * @{
  * Provides an application programming interface (API) for managing variables
  * associated with Tripal managed content. The Tripal Variables API
  * supports storing any type of variable such as a property or setting that
- * should be associated with a Tripal managed Drupal node.  Variables are
- * meant to store non-biological information only. Be aware that any data
- * stored as a Tripal Variable will not be made visible through services such
- * as Tripal Web Services and therefore can be a good place to hide application
- * specific settings.
- *
+ * should be associated with a Tripal managed content.  Variables are
+ * meant to store non-biological information only because biological data
+ * should be stored together in the primary data store (e.g. Chado). Be aware
+ * that any data stored as a Tripal Variable will not be made visible through
+ * services such as Tripal Web Services and therefore can be a good place to
+ * hide application specific settings.
  * @}
- *
  */
 
 /**
@@ -31,6 +30,8 @@
  *   The description for the variable
  * @return
  *   A record object containg the variable that was added if successful.
+ *
+ * @ingroup tripal_variables_api
  */
 function tripal_insert_variable($name, $description) {
   $name = trim($name);
@@ -69,6 +70,8 @@ function tripal_insert_variable($name, $description) {
  *   The name of the variable to retrieve
  * @return
  *   A record object containg the variable.
+ *
+ * @ingroup tripal_variables_api
  */
 function tripal_get_variable($name) {
   return db_select('tripal_variables', 'v')

tripal/includes/tripal.jobs.inc

@@ -4,18 +4,10 @@
  * Contains functions related to the display of Tripal jobs in a Tripal website.
  */
 
-/**
- * @defgroup tripal_jobs Jobs
- * @ingroup tripal
- * @{
- * Contains functions related to the display of Tripal jobs in a Tripal website.
- * @}
- */
 
 /**
  * Provides a landing page for tripal jobs admin
  *
- * @ingroup tripal_jobs
  */
 function tripal_jobs_admin_view() {
   $output = '';
@@ -47,7 +39,6 @@ function tripal_jobs_admin_view() {
 /**
  * NO LONGER USED: REPLACED BY VIEW
  *
- * @ingroup tripal_jobs
  */
 function tripal_jobs_report_form($form, &$form_state = NULL) {
   $form = array();
@@ -97,8 +88,6 @@ function tripal_jobs_report_form($form, &$form_state = NULL) {
 
 /**
  * NO LONGER USED: REPLACED BY VIEW
- *
- * @ingroup tripal_jobs
  */
 function tripal_jobs_report_form_submit($form, &$form_state = NULL) {
 
@@ -113,8 +102,6 @@ function tripal_jobs_report_form_submit($form, &$form_state = NULL) {
  *
  * @return
  *   The HTML to be rendered which describes the job report
- *
- * @ingroup tripal_jobs
  */
 function tripal_jobs_report() {
 
@@ -233,9 +220,6 @@ function tripal_jobs_report() {
  *
  * @return
  *   The HTML describing the indicated job
- * @ingroup tripal
- *
- * @ingroup tripal_jobs
  */
 function tripal_jobs_view($job_id) {
 

tripal/theme/js/TripalUploader.js

@@ -1,92 +1,7 @@
 /**
- * @file
- * TripalUploader Object
- * 
- * To use the TripalUploader Object the following must be performed:
- * 
- * 1) Add a Drupal form to your code that contains the following:
- *   * A Drupal-style table with 4 or 8 columns.  See the initialize
- *     function in this class for a description of the columns.
- *   * A button for submitting a file for upload.
- * 
- * @code
- * $headers = array(
- *    array('data' => 'Sequence File'),
- *    array('data' => 'Size', 'width' => '10%'),
- *    array('data' => 'Upload Progress', 'width' => '20%'),
- *    array('data' => 'Action', 'width' => '10%')
- *  );
- *  $rows = array();
- *  $table_vars = array(
- *    'header'      => $headers,
- *    'rows'        => $rows,
- *    'attributes'  => array('id' => 'sequence-file-upload-table'),
- *    'sticky'      => TRUE,
- *    'colgroups'   => array(),
- *    'empty'       => t('There are currently no files added.'),
- *  );
- *  $form['upload']['sequence_file'] = array(
- *    '#markup' => theme('table', $table_vars)
- *  );
- *  $form['upload']['sequence_fid'] = array(
- *    '#type' => 'hidden',
- *    '#value' => 0,
- *    '#attributes' => array('id' => 'sequence-fid')
- *  );
- *  $form['upload']['sequence_file_submit'] = array(
- *    '#type'     => 'submit',
- *    '#value'    => 'Upload Sequence File',
- *    '#name' => 'sequence_file_submit',
- *    // We don't want this button to submit as the file upload
- *    // is handled by the JavaScript code.
- *    '#attributes' => array('onclick' => 'return (false);')
- *  );
- * @endcode
- * 
- * 
- * 2)  Edit the theme/js/[module_name].js and in the "Drupal.behaviors.[module]" 
- * section add a JQuery show function to the form that converts the table 
- * created in the Drupal form to a TripalUploader table.  The 'table_id' must be
- * the same as the 'id' attribute set for the table in the Drupal code above.
- * The 'submit_id' must be the id of the upload button added in the Drupal
- * code above.  The 'category' for the files.  This is the category that
- * will be saved in Tripal for the file.  See the addUploadTable function
- * for additional options.  Include a 'cardinality' setting to indicate
- * the number of allowed files per upload, and set the 'target_id' to the
- * name of the field that will contain the file ID (fid) after uploading.
- * 
- * @code
- *  // The TripalUploader object used for uploading of files using the
- *  // HTML5 File API. Large files are uploaded as chunks and a progress
- *  // bar is provided.
- *  var uploader = new TripalUploader();
- *  
- *  $('#tripal-sequences-panel-form').show(function() {
- *    uploader.addUploadTable('sequence_file', {
- *      'table_id' : '#sequence-file-upload-table',
- *      'submit_id': '#edit-sequence-file-submit',
- *      'category' : ['sequence_file'],
- *      'cardinality' : 1,
- *      'target_id' : 'sequence-fid',
- *    });
- *  });
- * @endcode
- *
- *
- * 3) Files are uploaded automatically to Tripal.  Files are saved in the
- * Tripal user's directory.  You can retreive information about the 
- * file by querying for the file category for the current project.
- * 
- * @code
- *   $seq_files = TripalFeature::getFilesByTypes($user->uid, array('sequence_file'), $project_id);
- * @endcode
- * 
- * 4) If the 'target_id' was used in array for step #2 above, then the 
- * file ID can be retrieved in the hook_validate() and hook_submit() functions
- * via the $form_state['input'] array (not the $form_state['values'] array.
+ * See the Tripal Uploader API documenation for instructions to use this class.
  */
 
-
 (function($) {
 
   "use strict";

tripal/tripal.module

@@ -1,7 +1,25 @@
 <?php
 /**
  * @file
- * The Tripal Core module
+ * The core Tripal module
+ */
+
+ /**
+  * @defgroup tripal Tripal Module
+  * @ingroup tripal_modules
+  * @{
+  * The core Tripal module provides functionality useful for all other Tripal
+  * modules and extension modules.
+  * @}
+  */
+
+/**
+ * @defgroup tripal_api Tripal API
+ * @ingroup tripal
+ * @{
+ * Tripal provides an application programming interface (API) to support
+ * customizations and creation of new extensions.
+ * @}
  */
 
 // Import the full Tripal API into scope.
@@ -34,14 +52,6 @@ require_once "includes/TripalImporter.inc";
 require_once "includes/TripalEntityCollection.inc";
 require_once "includes/TripalFieldDownloaders/TripalFieldDownloader.inc";
 
-/**
- * @defgroup tripal Tripal Core Module
- * @ingroup tripal_modules
- * @{
- * Functionality useful for all other Tripal modules including the Tripal jobs, files,
- * materialized views and custom table functions.
- * @}
- */
 
 /**
  * Implements hook_views_api().