Fixed merge conflict

.github/ISSUE-TEMPLATE.md

@@ -0,0 +1,18 @@
+INSTRUCTIONS: The following template is meant to provide the information that will help other Tripal developers diagnose and reproduce your issue. Follow the directions below to complete the template. If the template is not appropriate for your issue you may remove it and describe your issue.
+
+### System information
+<!--Please enter the following information (if able). All information is available in your site's administrator report area (Administration Toolbar > Reports > Status Report) -->
+
+* Tripal Version:
+* Drupal Version:
+* PostgreSQL Version:
+* PHP Version:
+
+
+### Issue description
+<!-- Please describe your issue here 
+Some information you might want to include: the page you're seeing the issue on,  what behaviour you're experiencing versus what you expect, steps to reproduce...  really anything you think might best help us help you! -->
+
+
+
+<-- PS. Also feel free to ask questions, start discussions, suggest improvements We welcome any and all feedback! -->

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') {
 
@@ -1199,7 +1217,7 @@ function chado_node_get_unique_constraint_format($base_table, $format_type = 'ti
     tripal_report_error(
       'tripal_node_api',
       TRIPAL_ERROR,
-      'Unable to determine the format for the unique contraint since the format type (%format-type) is not supported (only "title" and "url" are at this time).',
+      'Unable to determine the format for the unique constraint since the format type (%format-type) is not supported (only "title" and "url" are at this time).',
       array('%format-type' => $format_type)
     );
   }
@@ -1230,6 +1248,8 @@ function chado_node_get_unique_constraint_format($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

@@ -1,6 +1,22 @@
 <?php
+
 /**
- * Retreives the default vocabulary for a given table and field.
+ * @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.
+ * @}
+ */
+
+/**
+ * Retrieves the default vocabulary for a given table and field.
  *
  * Each table in Chado that has a 'type_id' (or foreign key constraint to
  * the cvterm table) will have a default vocabulary assigned. This indicates to
@@ -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) {
 
@@ -114,4 +136,63 @@ function tripal_get_cvterm_default_select_options($table, $field, $field_desc) {
   }
 
   return $options;
+}
+
+
+/**
+ * This function sets the default vocabulary for a given table and field.
+ *
+ * @param $table
+ *   The name of the table that contains a field with a foreign key
+ *   relationship to the cvterm table
+ * @param $field
+ *   The table field name that has the foreign key relationship to the
+ *   cvterm table for which the default vocabulary will be set
+ * @param $cv_name
+ *   The name of the vocabulary
+ *
+ * @return
+ *   TRUE if set, FALSE if an error occured
+ *
+ * @ingroup tripal_legacy_chado_cv_api
+ */
+function tripal_set_default_cv($table, $field, $cv_name, $cv_id = FALSE) {
+
+  // Get the CV object
+  if ($cv_id) {
+    $cv = tripal_get_cv(array('cv_id' => $cv_id));
+  }
+  else {
+    $cv = tripal_get_cv(array('name' => $cv_name));
+  }
+
+  if ($cv) {
+    // first delete any entries for this table and field
+    $num_deleted = db_delete('tripal_cv_defaults')
+      ->condition('table_name', $table)
+      ->condition('field_name', $field)
+      ->execute();
+
+    // now add the default value
+    $cv_default_id = db_insert('tripal_cv_defaults')
+      ->fields(array(
+        'table_name' => $table,
+        'field_name' => $field,
+        'cv_id'      => $cv->cv_id,
+      ))
+      ->execute();
+
+    if (!$cv_default_id) {
+      tripal_report_error('tripal_chado', TRIPAL_WARNING,
+        "Cannot set default vocabulary for %table.%field. Check the error logs.",
+        array('%table' => $table, '%field' => $field));
+      return FALSE;
+    }
+  }
+  else {
+    tripal_report_error('tripal_chado', TRIPAL_WARNING,
+      "Cannot set default vocabulary for %table.%field. The vocabulary name, '%cvname', doesn't exist.",
+      array('%table' => $table, '%field' => $field, '%cvname' => $cv_name));
+    return FALSE;
+  }
 }

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.drush.inc

@@ -43,7 +43,7 @@ function tripal_feature_drush_command() {
       'parent'   => dt('Set this argument to 1 to retrieve the sequence from the parent in an alignment rather than the residues column of the feature itself.'),
       'agg'      => dt('Set this argument to 1 to aggregate sub features into a single sequence.  This is useful, for example, for obtaining CDS sequence from an mRNA'),
       'child'    => dt('Set this argument to the exact sequence ontology term for the children to aggregate.  This is useful in the case where a gene has exons as well as CDSs and UTRs.  You may sepcify as many feature types as desired by separating each with a single comma (no spaces). Term matching is case-sensitive.'),
-      'relationship'  => dt('Retreives the sequence of any feature in the specified relationship with the matched features.'),
+      'relationship'  => dt('Retrieves the sequence of any feature in the specified relationship with the matched features.'),
       'rel_part' => dt('If a relationship is provided, then this will be "subject" or "object" indicating the side of the relationship for the matched features. If the matched features are the "object" then the "subject" features will have their sequences included in the output (and vice versa).'),
       'width'    => dt('The number of nucleotides per row (defaults to 50).')
     ),

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) {
   $form = array();
@@ -209,7 +209,7 @@ function chado_organism_form($node, $form_state) {
       $terms = tripal_get_cvterm_select_options($cv->cv_id);
 
       // Unfortunately the taxonomic_rank vocabulary is not properly organized
-      // such that we an only include terms below 'species'. Therefore we will
+      // such that we only include terms below 'species'. Therefore we will
       // just list them here and hope we haven't missed one.
       $valid_terms = array('subspecies', 'varietas', 'subvariety', 'forma', 'subforma');
       foreach  ($terms as $cvterm_id => $name) {
@@ -296,7 +296,7 @@ function chado_organism_form($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 $user;
@@ -44,8 +69,11 @@ function tripal_create_collection($details) {
  *
  * @param $uid
  *   The User ID
+ *
  * @return
  *   An array of TripalEntityCollection objects.
+ *
+ * @ingroup tripal_data_collections_api
  */
 function tripal_get_user_collections($uid) {
   if (!$uid) {
@@ -71,6 +99,8 @@ function tripal_get_user_collections($uid) {
 
 /**
  * Deletes all collections that have surpassed their lifespan
+ *
+ * @ingroup tripal_data_collections_api
  */
 function tripal_expire_collections() {
   $max_days = variable_get('tripal_data_collections_lifespan', 30);
@@ -104,6 +134,7 @@ function tripal_expire_collections() {
  * @return
  *  An instance of a TripalEntityCollection class or FALSE on failure.
  *
+ * @ingroup tripal_data_collections_api
  */
 function tripal_get_collection($values) {
   $collection_id = array_key_exists('collection_id', $values) ? $values['collection_id'] : NULL;
@@ -147,6 +178,8 @@ function tripal_get_collection($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() {
   $widgets = array();
@@ -202,6 +254,8 @@ function tripal_get_field_field_formatters($field) {
  *
  * @return
  *   A list of TripalFieldFormatter names.
+ *
+ * @ingroup tripal_fields_api
  */
 function tripal_get_field_formatters() {
   $formatters = array();
@@ -257,6 +311,8 @@ function tripal_get_field_formatters() {
  *
  * @return
  *   TRUE if the field type class file was found, FALSE otherwise.
+ *
+ * @ingroup tripal_fields_api
  */
 function tripal_load_include_field_class($class) {
 
@@ -297,6 +353,8 @@ 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) {
 
@@ -353,6 +411,8 @@ 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, $items)) {
@@ -383,6 +443,8 @@ function tripal_get_field_item_keyval($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
@@ -65,7 +65,7 @@ function tripal_create_files_dir($module_name, $path = FALSE) {
 }
 
 /**
- * Retreives the Drupal relative directory for a Tripal module.
+ * Retrieves the Drupal relative directory for a Tripal module.
  *
  * Each Tripal module has a unique data directory which was created using the
  * tripal_create_files_dir function during installation.  This function
@@ -97,7 +97,7 @@ function tripal_get_files_dir($module_name = FALSE) {
 }
 
 /**
- * Retreives the Drupal stream (e.g. public://...) for a Tripal module.
+ * Retrieves the Drupal stream (e.g. public://...) for a Tripal module.
  *
  * Each Tripal module has a unique data directory which was created using the
  * tripal_create_files_dir function during installation.  This function

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
@@ -52,6 +45,10 @@
  *    An array of paths to files that should be included in order to execute
  *    the job. Use the module_load_include function to get a path for a given
  *    file.
+ * @param $ignore_duplicate.
+ *   Set to TRUE to not add the job if it has
+ *   the same name as another job which has not yet run. The default is TRUE.
+ *
  * @return
  *    The job_id of the registered job, or FALSE on failure.
  *
@@ -78,13 +75,13 @@
  * @ingroup tripal_jobs_api
  */
 function tripal_add_job($job_name, $modulename, $callback, $arguments, $uid,
-    $priority = 10, $includes = array()) {
+    $priority = 10, $includes = array(), $ignore_duplicate = FALSE) {
 
   $user = user_load($uid);
 
   try {
     $job = new TripalJob();
-    $job->create(array(
+    $is_created = $job->create(array(
       'job_name' => $job_name,
       'modulename' => $modulename,
       'callback' => $callback,
@@ -92,21 +89,27 @@ function tripal_add_job($job_name, $modulename, $callback, $arguments, $uid,
       'uid' => $uid,
       'priority' => $priority,
       'includes' => $includes,
+      'ignore_duplicate' => $ignore_duplicate,
     ));
 
-    // If no exceptions were thrown then we know the creation worked.  So
-    // let the user know!
-    drupal_set_message(t("Job '%job_name' submitted.", array('%job_name' => $job_name)));
-
-    // If this is the Tripal admin user then give a bit more information
-    // about how to run the job.
-    if (user_access('administer tripal')) {
-      $jobs_url = url("admin/tripal/tripal_jobs");
-      drupal_set_message(t("Check the <a href='!jobs_url'>jobs page</a> for status.",
-          array('!jobs_url' => $jobs_url)));
-      drupal_set_message(t("You can execute the job queue manually on the command line " .
-          "using the following Drush command: <br>drush trp-run-jobs --username=%uname --root=%base_path",
-          array('%base_path' => DRUPAL_ROOT, '%uname' => $user->name)));
+    if ($is_created) {
+      // If no exceptions were thrown then we know the creation worked.  So
+      // let the user know!
+      drupal_set_message(t("Job '%job_name' submitted.", array('%job_name' => $job_name)));
+
+      // If this is the Tripal admin user then give a bit more information
+      // about how to run the job.
+      if (user_access('administer tripal')) {
+        $jobs_url = url("admin/tripal/tripal_jobs");
+        drupal_set_message(t("Check the <a href='!jobs_url'>jobs page</a> for status.",
+            array('!jobs_url' => $jobs_url)));
+        drupal_set_message(t("You can execute the job queue manually on the command line " .
+            "using the following Drush command: <br>drush trp-run-jobs --username=%uname --root=%base_path",
+            array('%base_path' => DRUPAL_ROOT, '%uname' => $user->name)));
+      }
+    }
+    else {
+      drupal_set_message(t("Job '%job_name' already exists in the queue and was not re-submitted.", array('%job_name' => $job_name)), 'warning');
     }
     return $job->getJobID();
   }
@@ -281,8 +284,6 @@ function tripal_rerun_job($job_id, $goto_jobs_page = TRUE) {
     drupal_set_message($e->getMessage(), 'error');
     tripal_report_error('tripal', TRIPAL_ERROR, $e->getMessage());
   }
-
-
 }
 
 /**
@@ -443,7 +444,7 @@ 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) {
 
@@ -469,6 +470,8 @@ 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) {
 
@@ -540,6 +543,8 @@ 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 $form;
@@ -116,10 +147,68 @@ function hook_vocab_import_form_submit($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.
 
+}
+/**
+ * Retrieves a paged list of terms from a vocabulary.
+ *
+ * @param $vocabulary
+ *   The short name of the vocabulary.
+ * @param $limit
+ *   The number of results to return.
+ * @param $element
+ *   The pager element. This is equivalent to the element from the
+ *   pager_default_initialize() function of Drupal.
+ */
+function hook_vocab_get_terms($vocabulary, $limit = 25, $element = 0) {
+
+}
+/**
+ * Hook used by the default term storage backend to provide children for a term.
+ *
+ * This hook is called by the tripal_entity module to retrieve a list of
+ * children for a term from the storage backend.  It must return an array
+ * of terms where each term contains the same structure as that of the
+ * hook_vocab_get_term().
+ *
+ * @param $vocabulary
+ *   The vocabulary of the vocabulary in which the term is found.
+ * @param $accession
+ *   The unique identifier (accession) for this term.
+ *
+ * @return
+ *   An array of terms where each term contains the same structure as that of
+ *   the hook_vocab_get_term(), or an empty array if no children are present.
+ *
+ * @ingroup tripal_terms_api
+ */
+function hook_vocab_get_term_children($vocabulary, $accession) {
+
+}
+/**
+ * Hook used by the default term storage backend to provide root terms.
+ *
+ * This hook is called by the tripal_entity module to retrieve a list of
+ * root terms for a given vocabulary from the storage backend.  It must return
+ * an array of terms where each term contains the same structure as that of the
+ * hook_vocab_get_term().
+ *
+ * @param $vocabulary
+ *   The vocabulary of the vocabulary in which the term is found.
+ *
+ * @return
+ *   An array of root terms where each term contains the same structure as that
+ *   of the hook_vocab_get_term(), or an empty array if no children are present.
+ *
+ * @ingroup tripal_terms_api
+ */
+function hook_vocab_get_root_terms($vocabulary) {
+
 }
 /**
  * Hook used by the default term storage backend to provide details for a vocab.
@@ -142,10 +231,23 @@ 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.
 }
+
+/**
+ * Retrieves the list of vocabularies that are available on the site.
+ *
+ * @return
+ *   An array of vocabularies where each entry in the array is compatible
+ *   with the array returned by the tripal_get_vocabulary_details()
+ *   function.
+ */
+function hook_vocab_get_vocabularies() {
+  // See the tripal_chado_vocab_get_vocabularies() function for an example.
+}
 /**
  * Hook used by the default term storage backend to add new terms.
  *
@@ -167,6 +269,7 @@ 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 +296,7 @@ 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 +340,8 @@ 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) {
 
@@ -256,6 +362,67 @@ function tripal_get_term_details($vocabulary, $accession) {
     }
   }
 }
+/**
+ * Retrieves the immediate children of the given term.
+ *
+ * @param $vocabulary
+ *   The vocabulary of the vocabulary in which the term is found.
+ * @param $accession
+ *   The unique identifier (accession) for this term.
+ *
+ * @return
+ *   Returns an array of terms where each term is compatible with the
+ *   array returned by the tripal_get_term_details() function.
+ *
+ * @ingroup tripal_terms_api
+ */
+function tripal_get_vocabulary_root_terms($vocabulary) {
+  if (empty($vocabulary)) {
+    tripal_report_error('tripal_term', TRIPAL_ERROR, 'Unable to retrieve details for term due to missing vocabulary.');
+  }
+
+  // TODO: we need some sort of administrative interface that lets the user
+  // switch to the desired vocabulary type. For now, we'll just use the
+  // first one in the list.
+  $stores = module_invoke_all('vocab_storage_info');
+  if (is_array($stores) and count($stores) > 0) {
+    $keys = array_keys($stores);
+    $module = $stores[$keys[0]]['module'];
+    $function = $module . '_vocab_get_root_terms';
+    if (function_exists($function)) {
+      return $function($vocabulary);
+    }
+  }
+}
+/**
+ * Retrieves the immediate children of the given term.
+ *
+ * @param $vocabulary
+ *   The vocabulary of the vocabulary in which the term is found.
+ * @param $accession
+ *   The unique identifier (accession) for this term.
+ *
+ * @return
+ *   Returns an array of terms where each term is compatible with the
+ *   array returned by the tripal_get_term_details() function.
+ *
+ * @ingroup tripal_terms_api
+ */
+function tripal_get_term_children($vocabulary, $accession) {
+  if (empty($vocabulary) OR empty($accession)) {
+    tripal_report_error('tripal_term', TRIPAL_ERROR, 'Unable to retrieve details for term due to missing vocabulary and/or accession.');
+  }
+
+  $stores = module_invoke_all('vocab_storage_info');
+  if (is_array($stores) and count($stores) > 0) {
+    $keys = array_keys($stores);
+    $module = $stores[$keys[0]]['module'];
+    $function = $module . '_vocab_get_term_children';
+    if (function_exists($function)) {
+      return $function($vocabulary, $accession);
+    }
+  }
+}
 /**
  * Retrieves full information about a vocabulary.
  *
@@ -280,6 +447,9 @@ function tripal_get_term_details($vocabulary, $accession) {
  *       position of the short_name and the term accession will be
  *       specified with the {db} and {accession} tags respectively.
  *     - sw_url: The URL for mapping terms via the semantic web.
+ *     - num_terms: The number of terms loaded in the vocabulary.
+ *
+ * @ingroup tripal_terms_api
  */
 function tripal_get_vocabulary_details($vocabulary) {
   // TODO: we need some sort of administrative interface that lets the user
@@ -297,6 +467,50 @@ function tripal_get_vocabulary_details($vocabulary) {
 }
 
 
+/**
+ * Retrieves a paged list of terms from a vocabulary.
+ *
+ * @param $vocabulary
+ *   The short name of the vocabulary.
+ * @param $limit
+ *   The number of results to return.
+ * @param $element
+ *   The pager element. This is equivalent to the element from the
+ *   pager_default_initialize() function of Drupal.
+ */
+function tripal_get_vocabulary_terms($vocabulary, $limit = 25, $element = 0) {
+  $stores = module_invoke_all('vocab_storage_info');
+  if (is_array($stores) and count($stores) > 0) {
+    $keys = array_keys($stores);
+    $module = $stores[$keys[0]]['module'];
+    $function = $module . '_vocab_get_terms';
+    if (function_exists($function)) {
+      return $function($vocabulary, $limit, $element);
+    }
+  }
+}
+
+/**
+ * Retrieves the list of vocabularies that are available on the site.
+ *
+ * @return
+ *   An array of vocabularies where each entry in the array is compatible
+ *   with the array returned by the tripal_get_vocabulary_details()
+ *   function.
+ */
+function tripal_get_vocabularies() {
+  $stores = module_invoke_all('vocab_storage_info');
+  if (is_array($stores) and count($stores) > 0) {
+    $keys = array_keys($stores);
+    $module = $stores[$keys[0]]['module'];
+    $function = $module . '_vocab_get_vocabularies';
+    if (function_exists($function)) {
+      return $function();
+    }
+  }
+}
+
+
 /**
  * Provides a term lookup form.
  *
@@ -327,6 +541,8 @@ function tripal_get_vocabulary_details($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 = '', $is_required,
@@ -458,6 +674,8 @@ function tripal_get_term_lookup_form(&$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) {
   $values = array();
@@ -483,6 +701,8 @@ function tripal_get_term_lookup_form_result($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/TripalBundleUIController.inc

@@ -661,7 +661,7 @@ function tripal_admin_add_type_form_ajax_callback($form, $form_state) {
  */
 function tripal_admin_add_type_form_validate($form, &$form_state) {
   $stores = module_invoke_all('vocab_storage_info');
-  $store_select = $form_state['values']['store_select'];
+  $store_select = (isset($form_state['values']['store_select'])) ? $form_state['values']['store_select'] : NULL;
 
   if (array_key_exists('clicked_button', $form_state) and
       $form_state['clicked_button']['#name'] =='use_cvterm') {
@@ -768,6 +768,7 @@ function tripal_admin_add_type_form_submit($form, &$form_state) {
  * Checks access permissions for a given entity.
  */
 function tripal_admin_access($entity) {
+
   if ($entity) {
     $bundle_name = $entity->name;
   }
@@ -793,5 +794,6 @@ function tripal_admin_access($entity) {
   foreach($roles as $role => $value){
     user_role_change_permissions($role, $permission_for_role);
   }
+
   return TRUE;
 }