Merged api_changes branch and fixed merged conflict with contact module

tripal_contact/api/tripal_contact.api.inc

@@ -1,4 +1,11 @@
 <?php
+/**
+ * @file
+ * Functions to interact with contacts.
+ *
+ * @ingroup tripal_contact
+ */
+
 /**
  * @defgroup tripal_contact_api Contact Module API
  * @ingroup tripal_api
@@ -68,6 +75,7 @@ function tripal_contact_insert_property($contact_id, $property, $value, $update_
 function tripal_contact_update_property($contact_id, $property, $value, $insert_if_missing = 0) {
   return chado_update_property('contact', $contact_id, $property, 'tripal_contact', $value, $insert_if_missing);
 }
+
 /**
  * Delete a given property
  *
@@ -108,7 +116,6 @@ function tripal_contact_delete_property($contact_id, $property) {
  *   returned
  *
  * @ingroup tripal_contact_api
- *
  */
 function tripal_contact_add_contact($name, $description, $type, $properties) {
 
@@ -156,4 +163,4 @@ function tripal_contact_add_contact($name, $description, $type, $properties) {
     }
   }
   return $contact;
-}
+}

tripal_contact/includes/tripal_contact.admin.inc

@@ -1,7 +1,16 @@
 <?php
+/**
+ * @file
+ * Handle administration of contacts.
+ *
+ * @ingroup tripal_contact
+ */
 
 /**
+ * Launchpage for contact administration. Makes sure views are enabled and if not provides
+ * links to enable them.
  *
+ * @ingroup tripal_contact
  */
 function tripal_contact_admin_contact_view() {
   $output = '';
@@ -33,7 +42,6 @@ function tripal_contact_admin_contact_view() {
   return $output;
 }
 
-
 /**
  * Administrative settings form
  *
@@ -51,19 +59,20 @@ function tripal_contact_admin() {
 
 
 /**
+ * Reindex nodes for drupal search
  *
  * @ingroup tripal_contact
  */
 function get_tripal_contact_admin_form_reindex_set(&$form) {
 
- 
+
 }
+
 /**
+ * Validate the contact settings form.
  *
  * @ingroup tripal_contact
  */
 function tripal_contact_admin_validate($form, &$form_state) {
-  global $user;  // we need access to the user info
-  $job_args = array();
-}
 
+}

tripal_contact/includes/tripal_contact.chado_node.inc

@@ -1,9 +1,16 @@
 <?php
 /**
- * Implementation of hook_tripal_contact_node_info().
+ * @file
+ * Implements drupal node hooks.
  *
+ * @ingroup tripal_contact
+ */
+
+/**
+ * Implementation of hook_node_info().
  * This node_info, is a simple node that describes the functionallity of the module.
  *
+ * @ingroup tripal_contact
  */
 function tripal_contact_node_info() {
 
@@ -31,10 +38,9 @@ function tripal_contact_node_info() {
     ),
   );
 }
+
 /**
- * Implementation of tripal_contact_form().
- *
- *
+ * Implementation of hook_form().
  *
  *  @parm $node
  *    The node that is created when the database is initialized
@@ -46,6 +52,7 @@ function tripal_contact_node_info() {
  *  @return $form
  *    The information that was enterd allong with
  *
+ * @ingroup tripal_contact
  */
 function chado_contact_form(&$node, $form_state) {
   $form = array();
@@ -228,7 +235,8 @@ function chado_contact_form(&$node, $form_state) {
 }
 
 /**
- *  validates submission of form when adding or updating a contact node
+ * Implements hook_validate().
+ * Validates submission of form when adding or updating a contact node.
  *
  * @ingroup tripal_contact
  */
@@ -280,7 +288,7 @@ function chado_contact_validate($node, $form, &$form_state) {
 }
 
 /**
- * Implement hook_access().
+ * Implements hook_access().
  *
  * This hook allows node modules to limit access to the node types they define.
  *
@@ -300,6 +308,7 @@ function chado_contact_validate($node, $form, &$form_state) {
  *  access.  The only exception is when the $op == 'create'.  We will always
  *  return TRUE if the permission is set.
  *
+ * @ingroup tripal_contact
  */
 function chado_contact_node_access($node, $op, $account ) {
   if ($op == 'create') {
@@ -330,7 +339,7 @@ function chado_contact_node_access($node, $op, $account ) {
 
 
 /**
- * Implementation of tripal_contact_insert().
+ * Implements of hook_insert().
  *
  * This function inserts user entered information pertaining to the contact instance into the
  * 'contactauthor', 'contactprop', 'chado_contact', 'contact' talble of the database.
@@ -338,7 +347,7 @@ function chado_contact_node_access($node, $op, $account ) {
  *  @parm $node
  *    Then node which contains the information stored within the node-ID
  *
- *
+ * @ingroup tripal_contact
  */
 function chado_contact_insert($node) {
 
@@ -404,19 +413,18 @@ function chado_contact_insert($node) {
   return TRUE;
 }
 
-/*
+/**
+ * Implements hook_update
+ *
+ * The purpose of the function is to allow the module to take action when an edited node is being
+ * updated. It updates any name changes to the database tables that werec reated upon registering a contact.
+ * As well, the database will be changed, so the user changed information will be saved to the database.
+ *
+ * @param $node
+ *   The node being updated
  *
-* Implements hook_update
-*
-* The purpose of the function is to allow the module to take action when an edited node is being
-* updated. It updates any name changes to the database tables that werec reated upon registering a contact.
-* As well, the database will be changed, so the user changed information will be saved to the database.
-*
-* @param $node
-*   The node being updated
-*
-* @ingroup tripal_contact
-*/
+ * @ingroup tripal_contact
+ */
 function chado_contact_update($node) {
   // remove surrounding white-space on submitted values
   $node->contactname          = trim($node->contactname);
@@ -466,8 +474,7 @@ function chado_contact_update($node) {
 
 
 /**
- * Implementation of tripal_contact_load().
- *
+ * Implements hook_load().
  *
  * @param $node
  *   The node that is to be accessed from the database
@@ -475,6 +482,7 @@ function chado_contact_update($node) {
  * @return $node
  *   The node with the information to be loaded into the database
  *
+ * @ingroup tripal_contact
  */
 function chado_contact_load($nodes) {
 
@@ -510,7 +518,7 @@ function chado_contact_load($nodes) {
 }
 
 /**
- * Implementation of tripal_contact_delete().
+ * Implements hook_delete().
  *
  * This function takes a node and if the delete button has been chosen by the user, the contact
  * and it's details will be removed.Following,given the node-ID, the instance will be deleted from
@@ -519,6 +527,7 @@ function chado_contact_load($nodes) {
  *  @parm $node
  *    Then node which contains the information stored within the node-ID
  *
+ * @ingroup tripal_contact
  */
 function chado_contact_delete(&$node) {
 
@@ -546,8 +555,9 @@ function chado_contact_delete(&$node) {
 
 
 /**
+ * Implements hook_node_view().
  *
- * @ingroup tripal_feature
+ * @ingroup tripal_contact
  */
 function tripal_contact_node_view($node, $view_mode, $langcode) {
   switch ($node->type) {
@@ -586,8 +596,9 @@ function tripal_contact_node_view($node, $view_mode, $langcode) {
 }
 
 /**
+ * Implements hook_node_presave().
  *
- * @param $node
+ * @ingroup tripal_contact
  */
 function tripal_contact_node_presave($node) {
   switch ($node->type) {

tripal_contact/tripal_contact.install

@@ -2,16 +2,16 @@
 
 /**
  * @file
- * This file contains all the functions which describe and implement drupal database tables
- * needed by this module. This module was developed by Chad N.A. Krilow and Lacey-Anne Sanderson,
- * University of Saskatchewan.
+ * Handles install, uninstall, disable and enable functionality including database tables.
  *
- * The contact manamgenet module allows you to sync data in a chado/Tripal instance with
- * multiple contact/mysql instances as well as manage and create such contact instances
+ * @ingroup tripal_contact
  */
 
 /**
+ * Implements hook_disable().
  * Disable default views when module is disabled
+ *
+ * @ingroup tripal_contact
  */
 function tripal_contact_disable() {
 
@@ -27,6 +27,7 @@ function tripal_contact_disable() {
 /**
  * Implementation of hook_requirements().
  *
+ * @ingroup tripal_contact
  */
 function tripal_contact_requirements($phase) {
   $requirements = array();
@@ -45,6 +46,8 @@ function tripal_contact_requirements($phase) {
 
 /**
  * Implementation of hook_install().
+ *
+ * @ingroup tripal_contact
  */
 function tripal_contact_install() {
 
@@ -78,6 +81,8 @@ function tripal_contact_install() {
 
 /**
  * Implementation of hook_uninstall().
+ *
+ * @ingroup tripal_contact
  */
 function tripal_contact_uninstall() {
   /*
@@ -89,6 +94,11 @@ function tripal_contact_uninstall() {
     */
 }
 
+/**
+ * Adds any cvs needed by this module.
+ *
+ * @ingroup tripal_contact
+ */
 function tripal_contact_add_cvs() {
 
   tripal_cv_add_cv(
@@ -98,12 +108,19 @@ function tripal_contact_add_cvs() {
 
 }
 
+/**
+ * Adds any cvterms needed by this module.
+ *
+ * @ingroup tripal_contact
+ */
 function tripal_contact_add_cvterms() {
 
 }
 
 /**
  * Implementation of hook_schema().
+ *
+ * @ingroup tripal_contact
  */
 function tripal_contact_schema() {
   $schema['chado_contact'] = array(
@@ -138,9 +155,11 @@ function tripal_contact_schema() {
   return $schema;
 }
 
-
-/*
+/**
+ * Add any custom tables needed by this module.
+ * - Contactprop: keep track of properties of contact
  *
+ * @ingroup tripal_contact
  */
 function tripal_contact_add_custom_tables(){
   $schema = array (
@@ -206,9 +225,12 @@ function tripal_contact_add_custom_tables(){
 
 /**
  * This is the required update for tripal_contact when upgrading from Drupal core API 6.x.
+ *
+ * @ingroup tripal_contact
  */
 function tripal_contact_update_7000() {
 
   tripal_contact_add_cvs();
   tripal_contact_add_cvterms();
+
 }

tripal_contact/tripal_contact.module

@@ -1,4 +1,10 @@
 <?php
+/**
+ * @file
+ * Functions related to general module functionality.
+ *
+ * @ingroup tripal_contact
+ */
 
 /**
  * @defgroup tripal_contact Contact Module
@@ -8,44 +14,37 @@
  * @}
  */
 
-require('api/tripal_contact.api.inc');
-require('theme/tripal_contact.theme.inc');
-require('includes/tripal_contact.admin.inc');
-require('includes/tripal_contact.chado_node.inc');
+require 'api/tripal_contact.api.inc';
+
+require 'theme/tripal_contact.theme.inc';
+
+require 'includes/tripal_contact.admin.inc';
+require 'includes/tripal_contact.chado_node.inc';
 
 /**
- * Implements hook_views_api()
- * Purpose: Essentially this hook tells drupal that there is views support for
- *  for this module which then includes tripal_contact.views.inc where all the
- *  views integration code is
+ * Implements hook_views_api().
+ * Essentially this hook tells drupal that there is views support for
+ * for this module which then includes tripal_contact.views.inc where all the
+ * views integration code is.
  *
  * @ingroup tripal_contact
  */
 function tripal_contact_views_api() {
   return array(
-      'api' => 2.0,
+      'api' => 3.0,
   );
 }
 
 /**
- *
- * @ingroup tripal_contact
- */
-function tripal_contact_init() {
-
-}
-
-
-
-/**
- * Tripal-contact-Menu
- *
- * Implemets hook_menu(): Adds menu items for the tripal_contact module menu. This section
+ * Implemets hook_menu().
+ * Adds menu items for the tripal_contact module menu. This section
  * gives the outline for the main menu of the Tripal-contact module
  *
  * @return
  *   An array of menu items that is visible within the Drupal Menu, returned as soon
  *   as the program is ran
+ *
+ * @ingroup tripal_contact
  */
 function tripal_contact_menu() {
 
@@ -103,12 +102,13 @@ function tripal_contact_menu() {
 }
 
 /**
- * Implements hook_theme(): Register themeing functions for this module
- *
+ * Implements hook_theme().
+ * Register themeing functions for this module
  *
  * @return
  *   An array of themeing functions to register
  *
+ * @ingroup tripal_contact
  */
 function tripal_contact_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
@@ -153,7 +153,10 @@ function tripal_contact_theme($existing, $type, $theme, $path) {
   );
   return $items;
 }
+
 /**
+ * Implements hook_block_info().
+ *
  * @ingroup tripal_contact
  */
 function tripal_contact_block_info() {
@@ -172,7 +175,9 @@ function tripal_contact_block_info() {
 
   return $blocks;
 }
+
 /**
+ * Implements hook_block_view().
  * @ingroup tripal_contact
  */
 function tripal_contact_block_view($delta = '') {
@@ -222,7 +227,9 @@ function tripal_contact_block_view($delta = '') {
 }
 
 /**
- * Implement hook_perm().
+ * Implement hook_permissions().
+ *
+ * @ingroup tripal_contact
  */
 function tripal_contact_permissions() {
   return array(
@@ -249,15 +256,10 @@ function tripal_contact_permissions() {
   );
 }
 
-
-
-
 /**
- * Implementation of hook_form_alter()
+ * Implementation of hook_form_alter().
  *
- * @param $form
- * @param $form_state
- * @param $form_id
+ * @ingroup tripal_contact
  */
 function tripal_contact_form_alter(&$form, &$form_state, $form_id) {
   // turn of preview button for insert/updates

tripal_contact/tripal_contact.views_default.inc

@@ -1,7 +1,15 @@
 <?php
+/**
+ * @file
+ * Define default views for contacts.
+ *
+ * @ingroup tripal_contact
+ */
 
 /**
+ * Implements hook_views_default_views().
  *
+ * @ingroup tripal_contact
  */
 function tripal_contact_views_default_views() {
   $views = array();
@@ -13,7 +21,9 @@ function tripal_contact_views_default_views() {
 }
 
 /**
+ * Define the default view for contact administration.
  *
+ * @ingroup tripal_contact
  */
 function tripal_contact_defaultview_admin_contacts() {
 
@@ -204,4 +214,4 @@ function tripal_contact_defaultview_admin_contacts() {
   $handler->display->display_options['filters']['type_id']['expose']['max_length'] = 40;
   */
   return $view;
-}
+}

tripal_core/api/get_FKs.php

@@ -1,22 +1,24 @@
 <?php
-// This script will add FK relatinsions to an existing schema API array for each 
-// Chado table.  It requires Chado is installed in a 'chado' schema of 
-// the drupal database.  It also requires existing schema hooks for 
-// version of Chado.  The goal is to use the output of this script to 
-// update the existing schema hooks.  Redirect the output of this script to 
-// a file and then replace the existing schema API include file (e.g. 
-// tripal_core.schema_v1.2.api.inc).  Be sure to check it before replacing
-
-// this script requires a single argument (-v) which is the Chado version
-//
-// example usage in drupal directory root:
-//
-// php ./sites/all/modules/tripal/tripal_core/api/get_FKs.php -v 1.11 > \
-//   ./sites/all/modules/tripal/tripal_core/apitripal_core.schema_v1.11.api.inc.new
-//
-// php ./sites/all/modules/tripal/tripal_core/api/get_FKs.php -v 1.2 > \
-//   ./sites/all/modules/tripal/tripal_core/api/tripal_core.schema_v1.2.api.inc.new
-
+/**
+ * @file
+ * This script will add FK relatinsions to an existing schema API array for each
+ * Chado table.  It requires Chado is installed in a 'chado' schema of
+ * the drupal database.  It also requires existing schema hooks for
+ * version of Chado.  The goal is to use the output of this script to
+ * update the existing schema hooks.  Redirect the output of this script to
+ * a file and then replace the existing schema API include file (e.g.
+ * tripal_core.schema_v1.2.api.inc).  Be sure to check it before replacing
+ *
+ * This script requires a single argument (-v) which is the Chado version.
+ *
+ * Example usage in drupal directory root:
+ *
+ * php ./sites/all/modules/tripal/tripal_core/api/get_FKs.php -v 1.11 > \
+ *   ./sites/all/modules/tripal/tripal_core/apitripal_core.schema_v1.11.api.inc.new
+ *
+ * php ./sites/all/modules/tripal/tripal_core/api/get_FKs.php -v 1.2 > \
+ *   ./sites/all/modules/tripal/tripal_core/api/tripal_core.schema_v1.2.api.inc.new
+ */
 
 $arguments = getopt("v:");
 
@@ -35,27 +37,28 @@ if (isset($arguments['v'])) {
 }
 
 /**
- *
+ * This function does the actual work of determining the foreign key relationships from
+ * the database and creating the schema file.
  */
 function get_chado_fk_relationships($version) {
 
   // convert the version to a form suitable for function names
   $v = $version;
   $v = preg_replace("/\./","_",$v);
- 
-  $tables = tripal_core_get_chado_tables(); 
+
+  $tables = tripal_core_get_chado_tables();
   $sql ="
     SELECT
-        tc.constraint_name, tc.table_name, kcu.column_name, 
+        tc.constraint_name, tc.table_name, kcu.column_name,
         ccu.table_name AS foreign_table_name,
-        ccu.column_name AS foreign_column_name 
-    FROM 
-        information_schema.table_constraints AS tc 
+        ccu.column_name AS foreign_column_name
+    FROM
+        information_schema.table_constraints AS tc
         JOIN information_schema.key_column_usage AS kcu ON tc.constraint_name = kcu.constraint_name
         JOIN information_schema.constraint_column_usage AS ccu ON ccu.constraint_name = tc.constraint_name
     WHERE constraint_type = 'FOREIGN KEY' AND tc.table_name=:table_name
   ";
-    
+
   // iterate through the tables and get the foreign keys
   print "<?php
 /* @file: This file contains default schema definitions for all chado v$version tables
@@ -73,7 +76,7 @@ function get_chado_fk_relationships($version) {
  * This API consists of a set of functions, one for each table in Chado.  Each
  * function simply returns a Drupal style array that defines the table.
  *
- * Because Drupal 6 does not handle foreign key (FK) relationships, however FK 
+ * Because Drupal 6 does not handle foreign key (FK) relationships, however FK
  * relationships are needed to for Tripal Views.  Therefore, FK relationships
  * have been added to the schema defintitions below.
  *
@@ -84,8 +87,8 @@ function get_chado_fk_relationships($version) {
  *   \$table_desc = tripal_core_get_chado_table_schema(\$table)
  *
  * where the variable \$table contains the name of the table you want to
- * retireve.  The tripal_core_get_chado_table_schema function determines the appropriate version of 
- * Chado and uses the Drupal hook infrastructure to call the appropriate 
+ * retireve.  The tripal_core_get_chado_table_schema function determines the appropriate version of
+ * Chado and uses the Drupal hook infrastructure to call the appropriate
  * hook function to retrieve the table schema.
  *
  * @}
@@ -98,15 +101,15 @@ function get_chado_fk_relationships($version) {
 
     // get the existing table array
     $table_arr = tripal_core_get_chado_table_schema($table);
-    
+
     if (empty($table_arr)) {
        print "ERROR: empty table definition $table\n";
        continue;
     }
-    
+
     // add the table name to the array
     $table_arr['table'] = $table;
-    
+
     // get the foreign keys and add them to the array
     $fks = db_query($sql, array(':table_name' => $table));
     foreach ($fks as $fk) {
@@ -116,23 +119,23 @@ function get_chado_fk_relationships($version) {
     }
     $tables_def[] = $table_arr;
   }
-  
+
   // now add in the referring tables and print
   foreach ($tables_def as $table_arr) {
     $table = $table_arr['table'];
-    
+
     // add in the referring tables
     $table_referring = array_unique($reffering[$table]);
     $table_arr['referring_tables'] = $table_referring;
-      
+
     // reformat the array to be more legible
     $arr = var_export($table_arr, 1);
     $arr = preg_replace("/\n\s+array/","array", $arr); // move array( to previous line
     $arr = preg_replace("/\n/","\n  ", $arr); // add indentation
     $arr = preg_replace("/true/","TRUE", $arr); // add indentation
     $arr = preg_replace("/false/","FALSE", $arr); // add indentation
-    $arr = preg_replace("/array \(/","array(", $arr); // add indentation      
-      
+    $arr = preg_replace("/array \(/","array(", $arr); // add indentation
+
       // print out the new Schema API function for this table
 print "/**
  * Implements hook_chado_schema_v".$v."_".$table."()

tripal_core/api/tripal_core.chado_general.api.inc

@@ -1,13 +1,18 @@
 <?php
+/**
+ * @file
+ * Provides an application programming interface (API) to manage data withing the Chado database.
+ */
 
-require_once "tripal_core.schema_v1.2.api.inc";
-require_once "tripal_core.schema_v1.11.api.inc";
+require_once 'tripal_core.schema_v1.2.api.inc';
+require_once 'tripal_core.schema_v1.11.api.inc';
 
 /**
  * @defgroup tripal_chado_api Chado API
  * @ingroup tripal_core_api
  * @{
  * Provides an application programming interface (API) to manage data withing the Chado database.
+ *
  * This includes functions for selecting, inserting, updating and deleting records
  * in Chado tables.  The functions will ensure proper integrity contraints are met
  * for inserts and updates.

tripal_core/api/tripal_core.chado_nodes.api.inc

@@ -1,4 +1,8 @@
 <?php
+/**
+ * @file
+ * API to handle much of the common functionality implemented when creating a drupal node type.
+ */
 
 /**
  * @defgroup tripal_chado_node_api Chado Node API
@@ -21,35 +25,14 @@
  * The functions of interest are as follows:
  *   - chado_add_node_form_properties() and chado_update_node_form_properties()
  *     to provide an interface for adding/removing properties
- *   - tripal_core_additional_dbxrefs_form() and tripal_core_additional_dbxrefs_form_update_dbxrefs()
+ *   - chado_add_node_form_dbxrefs() and chado_update_node_form_dbxrefs()
  *     to provide an interface for adding/removing additional database references
- *   - tripal_core_relationships_form() and tripal_core_relationships_form_update_relationships()
+ *   - chado_add_node_form_relationships() and chado_update_node_form_relationships()
  *     to provide an interface for adding/removing relationships between chado records
  *     from your base table
  * @}
  */
 
-/**
- * Determine whether a given chado table is directly linked to a node
- *
- * @param $chado_table
- *   The name of a chado table to check (ie: feature)
- * @return
- *   TRUE if it is linked to a node and FALSE otherwise
- *
- * @ingroup tripal_chado_node_api
- *
-function tripal_core_is_tripal_node_type($chado_table) {
-  $linking_table = 'chado_' . $chado_table;
-  if (db_table_exists($linking_table)) {
-    return TRUE;
-  }
-  else {
-    return FALSE;
-  }
-}
-*/
-
 /**
  * Sync'ing chado records with Drupal by creating nodes
  *
@@ -352,7 +335,7 @@ function chado_node_sync_form($form, &$form_state) {
 /**
  * Generic Sync Form Submit
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_node_sync_form_submit($form, $form_state) {
 

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

@@ -356,7 +356,7 @@ function chado_add_node_form_dbxrefs(&$form, &$form_state, $details) {
  * Validate the user input for creating a new dbxref
  * Called by the add button in chado_add_node_form_dbxrefs
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_add_node_form_dbxrefs_add_button_validate($form, &$form_state) {
 
@@ -385,7 +385,7 @@ 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_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_add_node_form_dbxrefs_add_button_submit(&$form, &$form_state) {
 
@@ -416,7 +416,7 @@ 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_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_add_node_form_dbxrefs_remove_button_validate($form, $form_state) {
   // No Validation needed for remove
@@ -426,7 +426,7 @@ function chado_add_node_form_dbxrefs_remove_button_validate($form, $form_state)
  * Remove the correct dbxref from the form
  * Called by the many remove buttons in chado_add_node_form_dbxrefs
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_add_node_form_dbxrefs_remove_button_submit(&$form, &$form_state) {
 
@@ -450,7 +450,7 @@ function chado_add_node_form_dbxrefs_remove_button_submit(&$form, &$form_state)
 /**
  * Ajax function which returns the section of the form to be re-rendered
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_add_node_form_dbxrefs_ajax_update($form, $form_state) {
   return $form['addtl_dbxrefs']['dbxref_table'];
@@ -472,7 +472,7 @@ function chado_add_node_form_dbxrefs_ajax_update($form, $form_state) {
  *   ),
  * );
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_add_node_form_dbxrefs_create_dbxref_formstate_array($form, &$form_state) {
 

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

@@ -723,7 +723,7 @@ function chado_add_node_form_properties(&$form, &$form_state, $details) {
  * Validate the user input for creating a new property
  * Called by the add button in chado_add_node_form_properties
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_update_node_form_properties_add_button_validate($form, &$form_state) {
 
@@ -752,7 +752,7 @@ function chado_update_node_form_properties_add_button_validate($form, &$form_sta
  * Create an array of properties in the form state. This array will then be
  * used to rebuild the form in subsequent builds
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_add_node_form_properties_add_button_submit(&$form, &$form_state) {
 
@@ -795,7 +795,7 @@ 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_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_add_node_form_properties_remove_button_validate($form, $form_state) {
   // No Validation needed for remove
@@ -805,7 +805,7 @@ function chado_add_node_form_properties_remove_button_validate($form, $form_stat
  * Remove the correct property from the form
  * Called by the many remove buttons in chado_add_node_form_properties
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_add_node_form_properties_remove_button_submit(&$form, &$form_state) {
 
@@ -828,6 +828,8 @@ function chado_add_node_form_properties_remove_button_submit(&$form, &$form_stat
 
 /**
  * Ajax function which returns the section of the form to be re-rendered
+ *
+ * @ingroup tripal_core
  */
 function chado_add_node_form_properties_ajax_update($form, $form_state) {
   return $form['properties']['property_table'];
@@ -849,7 +851,7 @@ function chado_add_node_form_properties_ajax_update($form, $form_state) {
  *   ),
  * );
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_add_node_form_properties_create_property_formstate_array($form, &$form_state) {
 

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

@@ -419,7 +419,7 @@ function chado_add_node_form_relationships(&$form, &$form_state, $details) {
  * Validate the user input for creating a new relationship
  * Called by the add button in chado_add_node_form_relationships
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_add_node_form_relationships_add_button_validate($form, &$form_state) {
 
@@ -524,7 +524,7 @@ 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_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_add_node_form_relationships_add_button_submit(&$form, &$form_state) {
 
@@ -575,7 +575,7 @@ function chado_add_node_form_relationships_add_button_submit(&$form, &$form_stat
  *
  * Called by the many remove buttons in chado_add_node_form_relationships
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_add_node_form_relationships_form_remove_button_validate($form, $form_state) {
   // No Validation needed for remove
@@ -585,7 +585,7 @@ function chado_add_node_form_relationships_form_remove_button_validate($form, $f
  * Remove the correct relationship from the form
  * Called by the many remove buttons in chado_add_node_form_relationships
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_add_node_form_relationships_remove_button_submit(&$form, &$form_state) {
 
@@ -609,7 +609,7 @@ function chado_add_node_form_relationships_remove_button_submit(&$form, &$form_s
 /**
  * Ajax function which returns the section of the form to be re-rendered
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_add_node_form_relationships_ajax_update($form, $form_state) {
   return $form['relationships']['relationship_table'];
@@ -631,7 +631,7 @@ function chado_add_node_form_relationships_ajax_update($form, $form_state) {
  *   ),
  * );
  *
- * @ingroup tripal_chado_node_api
+ * @ingroup tripal_core
  */
 function chado_add_node_form_relationships_create_relationship_formstate_array($form, &$form_state) {
 
@@ -838,6 +838,8 @@ function chado_update_node_form_relationships($node, $details, $retrieved_relati
  *
  * @param $string
  *    The part of the string already typed in the textfield
+ *
+ * @ingroup tripal_core
  */
 function chado_add_node_form_relationships_name_to_id_callback($base_table, $name_field, $string) {
   $matches = array();

tripal_core/api/tripal_core.chado_query.api.inc

@@ -1,4 +1,9 @@
 <?php
+/**
+ * @file
+ * Provides an API for querying of chado including inserting, updating, deleting and
+ * selecting from chado.
+ */
 
 /**
  * @defgroup tripal_chado_query_api Chado Query API
@@ -1395,7 +1400,7 @@ function chado_pager_query($query, $args, $limit, $element, $count_query = '') {
  * species.  The cvterm is also specified using its foreign key and the cv_id
  * for the cvterm is nested as well.
  *
- * @ingroup tripal_chado_query_api
+ * @ingroup tripal_core
  */
 function chado_schema_get_foreign_key($table_desc, $field, $values, $options = NULL) {
 

tripal_core/api/tripal_core.chado_variables.api.inc

@@ -1,4 +1,8 @@
 <?php
+/**
+ * @file
+ * This API generates objects containing the full details of a record(s) in chado.
+ */
 
 /**
  * @defgroup tripal_chado_variables_api Chado Variables API

tripal_core/api/tripal_core.custom_tables.api.inc

@@ -1,4 +1,9 @@
 <?php
+/**
+ * @file
+ * Provides an API to manage custom tables in Chado.
+ */
+
 /**
  * @defgroup tripal_custom_tables_api Custom Tables API
  * @ingroup tripal_core_api

tripal_core/api/tripal_core.files.api.inc

@@ -1,4 +1,10 @@
 <?php
+/**
+ * @file
+ * Provides an application programming interface (API) for managing files within
+ * the Tripal data directory structure.
+ */
+
 /**
  * @defgroup tripal_files_api Files API
  * @ingroup tripal_core_api
@@ -19,6 +25,8 @@
  *   the name of the module being installed
  * @param $path
  *   Optional sub-path to create
+ *
+ * @ingroup tripal_files_api
  */
 function tripal_create_files_dir($module_name, $path = FALSE) {
 

tripal_core/api/tripal_core.jobs.api.inc

@@ -1,4 +1,10 @@
 <?php
+/**
+ * @file
+ * Tripal offers a job management subsystem for managing tasks that may require an extended period of time for
+ * completion.
+ */
+
 /**
  * @defgroup tripal_jobs_api Jobs API
  * @ingroup tripal_core_api

tripal_core/api/tripal_core.mviews.api.inc

@@ -1,4 +1,9 @@
 <?php
+/**
+ * @file
+ * Provides an application programming interface (API) to manage materialized views in Chado.
+ */
+
 /**
  * @defgroup tripal_mviews_api Materalized Views API
  * @ingroup tripal_core_api
@@ -314,7 +319,7 @@ function tripal_mviews_get_mview_id($view_name) {
  * @param $redirect
  *   TRUE/FALSE depending on whether you want to redirect the user to admin/tripal/mviews
  *
- * @ingroup tripal_core
+ * @ingroup tripal_mviews_api
  */
 function tripal_add_populate_mview($mview_id, $redirect = FALSE) {
   global $user;
@@ -349,7 +354,7 @@ function tripal_add_populate_mview($mview_id, $redirect = FALSE) {
  * @param $redirect
  *   TRUE/FALSE depending on whether you want to redirect the user to admin/tripal/mviews
  *
- * @ingroup tripal_core
+ * @ingroup tripal_mviews_api
  */
 function tripal_delete_mview($mview_id, $redirect = FALSE) {
   global $user;
@@ -436,4 +441,4 @@ function tripal_populate_mview($mview_id) {
     print "Done.\n";
     return TRUE;
   }
-}
+}

tripal_core/api/tripal_core.schema_v1.11.api.inc

@@ -1,4 +1,9 @@
 <?php
+/**
+ * @file
+ * Describes the chado tables in version 1.11
+ */
+
 /**
  * @defgroup tripal_schema_v1_11_api Chado v1.11 Schema API
  * @ingroup tripal_chado_schema_api

tripal_core/api/tripal_core.schema_v1.2.api.inc

@@ -1,4 +1,9 @@
 <?php
+/**
+ * @file
+ * Describes the chado tables in version 1.2
+ */
+
 /**
  * @defgroup tripal_schema_v1_2_api Chado v1.2 Schema API
  * @ingroup tripal_chado_schema_api

tripal_core/includes/chado_install.inc

@@ -1,5 +1,4 @@
 <?php
-
 /**
  * @file
  * Functions to install chado schema through Drupal
@@ -59,7 +58,7 @@ function tripal_core_chado_load_form() {
 }
 
 /**
- * Submit Load Chado Schema 1.11 Form
+ * Submit Load Chado Schema Form
  *
  * @ingroup tripal_core
  */

tripal_core/includes/custom_tables.inc

@@ -1,15 +1,25 @@
 <?php
-
 /**
  * @file
  * Contains functions for creating, editing and deleting custom tables
  * on the Tripal website.
  *
+ * @ingroup tripal_custom_tables
+ */
+
+/**
+ * @defgroup tripal_custom_tables Custom Chado Tables
  * @ingroup tripal_core
+ * @{
+ * Contains functions for creating, editing and deleting custom tables
+ * on the Tripal website.
+ * @}
  */
 
 /**
- * Provides a landing page for tripal jobs admin
+ * Provides a landing page for administrating custom tables.
+ *
+ * @ingroup tripal_custom_tables
  */
 function tripal_custom_table_admin_view() {
   $output = '';
@@ -42,20 +52,22 @@ function tripal_custom_table_admin_view() {
 }
 
 /**
+ * Renders the tripal_custom_tables_form.
  *
+ * @ingroup tripal_custom_tables
  */
 function tripal_custom_table_new_page() {
   $output = drupal_render(drupal_get_form('tripal_custom_tables_form'));
   return $output;
-
 }
+
 /**
  * A template function which returns markup to display details for the custom table
  *
  * @param $table_id
  *  The unique ID of the custom table
  *
- * @ingroup tripal_core
+ * @ingroup tripal_custom_tables
  */
 function tripal_custom_table_view($table_id) {
 
@@ -101,7 +113,7 @@ function tripal_custom_table_view($table_id) {
 /**
  * A template function to render a listing of all Custom tables
  *
- * @ingroup tripal_core
+ * @ingroup tripal_custom_tables
  */
 function tripal_custom_tables_list() {
   $header = array('', 'Table Name', 'Description');
@@ -140,7 +152,7 @@ function tripal_custom_tables_list() {
 }
 
 /**
- * A Form to Create/Edit a Custom table
+ * A Form to Create/Edit a Custom table.
  *
  * @param $form_state
  *   The current state of the form (Form API)
@@ -150,7 +162,7 @@ function tripal_custom_tables_list() {
  * @return
  *   A form array (Form API)
  *
- * @ingroup tripal_core
+ * @ingroup tripal_custom_tables
  */
 function tripal_custom_tables_form($form, &$form_state = NULL, $table_id = NULL) {
 
@@ -287,10 +299,10 @@ array (
 }
 
 /**
- * Validate the Create/Edit custom table form
- * Implements hook_form_validate().
+ * Implements hook_validate().
+ * Validate the Create/Edit custom table form.
  *
- * @ingroup tripal_core
+ * @ingroup tripal_custom_tables
  */
 function tripal_custom_tables_form_validate($form, &$form_state) {
   $action = $form_state['values']['action'];
@@ -344,7 +356,7 @@ function tripal_custom_tables_form_validate($form, &$form_state) {
  * Submit the Create/Edit Custom table form
  * Implements hook_form_submit().
  *
- * @ingroup tripal_core
+ * @ingroup tripal_custom_tables
  */
 function tripal_custom_tables_form_submit($form, &$form_state) {
 
@@ -376,6 +388,7 @@ function tripal_custom_tables_form_submit($form, &$form_state) {
 
   return '';
 }
+
 /**
  * Does the specified action for the specified custom table
  *
@@ -386,7 +399,7 @@ function tripal_custom_tables_form_submit($form, &$form_state) {
  * @param $redirect
  *   TRUE/FALSE depending on whether you want to redirect the user to admin/tripal/custom_tables
  *
- * @ingroup tripal_core
+ * @ingroup tripal_custom_tables
  */
 function tripal_custom_tables_action($op, $table_id, $redirect = FALSE) {
   global $user;

tripal_core/includes/form_elements.inc

@@ -1,12 +1,13 @@
 <?php
-
 /**
  * @file
- * Form elements used for tripal views
+ * Form elements used Various places in Tripal
  */
 
 /**
- * Register form elements
+ * Register form elements.
+ *
+ * @ingroup tripal_core
  */
 function tripal_core_element_info() {
   $elements = array();
@@ -32,8 +33,9 @@ function tripal_core_element_info() {
 }
 
 /**
- * Upload File and keep track of previously uploaded files
- * Form element description
+ * Upload File and keep track of previously uploaded files.
+ *
+ * @ingroup tripal_core
  */
 function expand_file_upload_combo($element, $form_state, $complete_form) {
 
@@ -76,9 +78,10 @@ function expand_file_upload_combo($element, $form_state, $complete_form) {
   return $element;
 }
 
-
 /**
- * Theme the file upload combo form element
+ * Theme the file upload combo form element.
+ *
+ * @ingroup tripal_core
  */
 function theme_file_upload_combo($variables) {
   $element = $variables['element'];
@@ -93,9 +96,10 @@ function theme_file_upload_combo($variables) {
   return $output;
 }
 
-
 /**
- * Validate all content passed into the file upload combo form element
+ * Validate all content passed into the file upload combo form element.
+ *
+ * @ingroup tripal_core
  */
 function file_upload_combo_value_callback($element, $input = FALSE, &$form_state) {
   $values = array();
@@ -151,7 +155,9 @@ function file_upload_combo_value_callback($element, $input = FALSE, &$form_state
 }
 
 /**
- * Form element description
+ * Retrieve Sequence bases form element.
+ *
+ * @ingroup tripal_core
  */
 function expand_sequence_combo($element, $form_state, $complete_form) {
 
@@ -189,7 +195,9 @@ 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
+ * D7 @todo: test/fix this callback.
+ *
+ * @ingroup tripal_core
  */
 function sequence_combo_value_callback($element, $input = FALSE, &$form_state) {
   $upstream = $form['values'][$element['#name']]['upstream'];
@@ -212,7 +220,9 @@ function sequence_combo_value_callback($element, $input = FALSE, &$form_state) {
 }
 
 /**
- * Theme the file sequence form element
+ * Theme the file sequence form element.
+ *
+ * @ingroup tripal_core
  */
 function theme_sequence_combo($variables) {
   $element = $variables['element'];

tripal_core/includes/jobs.inc

@@ -1,13 +1,21 @@
 <?php
-
 /**
  * @file
  * Contains functions related to the display of Tripal jobs in a Tripal website.
- *
+ */
+
+/**
+ * @defgroup tripal_jobs Jobs
+ * @ingroup tripal_core
+ * @{
+ * Contains functions related to the display of Tripal jobs in a Tripal website.
+ * @}
  */
 
 /**
  * Provides a landing page for tripal jobs admin
+ *
+ * @ingroup tripal_jobs
  */
 function tripal_jobs_admin_view() {
   $output = '';
@@ -40,7 +48,8 @@ function tripal_jobs_admin_view() {
 
 /**
  * NO LONGER USED: REPLACED BY VIEW
- * @ingroup tripal_core
+ *
+ * @ingroup tripal_jobs
  */
 function tripal_jobs_report_form($form, &$form_state = NULL) {
   $form = array();
@@ -87,9 +96,11 @@ function tripal_jobs_report_form($form, &$form_state = NULL) {
   );
   return $form;
 }
+
 /**
+ * NO LONGER USED: REPLACED BY VIEW
  *
- * @ingroup tripal_core
+ * @ingroup tripal_jobs
  */
 function tripal_jobs_report_form_submit($form, &$form_state = NULL) {
 
@@ -105,7 +116,7 @@ function tripal_jobs_report_form_submit($form, &$form_state = NULL) {
  * @return
  *   The HTML to be rendered which describes the job report
  *
- * @ingroup tripal_core
+ * @ingroup tripal_jobs
  */
 function tripal_jobs_report() {
 
@@ -213,6 +224,7 @@ function tripal_jobs_report() {
   $output .= theme('pager');
   return $output;
 }
+
 /**
  * Returns the HTML code to display a given job
  *
@@ -222,6 +234,8 @@ function tripal_jobs_report() {
  * @return
  *   The HTML describing the indicated job
  * @ingroup tripal_core
+ *
+ * @ingroup tripal_jobs
  */
 function tripal_jobs_view($job_id) {
   // get the job record
@@ -305,5 +319,3 @@ function tripal_jobs_view($job_id) {
   $output .= theme_table($table);
   return $output;
 }
-
-

tripal_core/includes/mviews.inc

@@ -1,13 +1,23 @@
 <?php
-
 /**
  * @file
  * Contains functions for viewing and editing of Materialized Views
  * on a Tripal website.
  */
 
+/**
+ * @defgroup tripal_mviews Tripal Materialized Views
+ * @ingroup tripal_core
+ * @{
+ * Contains functions for viewing and editing of Materialized Views
+ * on a Tripal website.
+ * @}
+ */
+
 /**
  * Provides a landing page for tripal jobs admin
+ *
+ * @ingroup tripal_mviews
  */
 function tripal_mview_admin_view() {
   $output = '';
@@ -39,14 +49,13 @@ function tripal_mview_admin_view() {
   return $output;
 }
 
-
 /**
  * A template function which returns markup to display details for the current materialized view
  *
  * @param $mview_id
  *  The unique ID of the materialized view to render
  *
- * @ingroup tripal_core
+ * @ingroup tripal_mviews
  */
 function tripal_mview_report($mview_id) {
 
@@ -120,7 +129,7 @@ function tripal_mview_report($mview_id) {
 /**
  * A template function to render a listing of all Materialized Views
  *
- * @ingroup tripal_core
+ * @ingroup tripal_mviews
  */
 function tripal_mviews_report() {
   $header = array('', 'MView Name', 'Last Update', 'Status', 'Description', '');
@@ -190,7 +199,7 @@ function tripal_mviews_report() {
  * @return
  *   A form array (Form API)
  *
- * @ingroup tripal_core
+ * @ingroup tripal_mviews
  */
 function tripal_mviews_form($form, &$form_state = NULL, $mview_id = NULL) {
   if (!$mview_id) {
@@ -434,7 +443,7 @@ function tripal_mviews_form($form, &$form_state = NULL, $mview_id = NULL) {
  * Validate the Create/Edit Materialized View Form
  * Implements hook_form_validate().
  *
- * @ingroup tripal_core
+ * @ingroup tripal_mviews
  */
 function tripal_mviews_form_validate($form, &$form_state) {
   $action = $form_state['values']['action'];
@@ -494,7 +503,7 @@ function tripal_mviews_form_validate($form, &$form_state) {
  * Submit the Create/Edit Materialized View Form
  * Implements hook_form_submit().
  *
- * @ingroup tripal_core
+ * @ingroup tripal_mviews
  */
 function tripal_mviews_form_submit($form, &$form_state) {
 
@@ -536,4 +545,4 @@ function tripal_mviews_form_submit($form, &$form_state) {
   }
 
   return '';
-}
+}

tripal_core/tripal_core.drush.inc

@@ -1,15 +1,23 @@
 <?php
-
 /**
  * @file
  * Contains function relating to drush-integration of this module.
  */
 
+/**
+ * @defgroup tripal_drush Tripal Drush Integration
+ * @{
+ * Contains function relating to drush-integration of various tripal modules.
+ * @}
+ */
+
 /**
  * Describes each drush command implemented by the module
  *
  * @return
  *   The first line of description when executing the help for a given command
+ *
+ * @ingroup tripal_drush
  */
 function tripal_core_drush_help($command) {
   switch ($command) {
@@ -39,6 +47,8 @@ function tripal_core_drush_help($command) {
  *
  * @return
  *   And array of command descriptions
+ *
+ * @ingroup tripal_drush
  */
 function tripal_core_drush_command() {
   $items = array();
@@ -169,8 +179,9 @@ function tripal_core_drush_command() {
 }
 
 /**
+ * Set the user to run a drush job.
  *
- * @param $username
+ * @ingroup tripal_drush
  */
 function drush_tripal_core_set_user($username) {
   if ($username) {
@@ -195,6 +206,8 @@ function drush_tripal_core_set_user($username) {
  * Executes jobs in the Tripal Jobs Queue
  *
  * NOTE: The following code is executed when drush 'trpjob-run' or 'drush tripal-launch-jobs' is called
+ *
+ * @ingroup tripal_drush
  */
 function drush_tripal_core_tripal_jobs_launch($username) {
   $parallel = drush_get_option('parallel');
@@ -220,6 +233,8 @@ function drush_tripal_core_tripal_jobs_launch($username) {
  * Executes jobs in the Tripal Jobs Queue
  *
  * NOTE: The following code is executed when drush 'trpjob-run' or 'drush tripal-launch-jobs' is called
+ *
+ * @ingroup tripal_drush
  */
 function drush_tripal_core_tripal_jobs_rerun($username, $job_id) {
 
@@ -233,6 +248,8 @@ function drush_tripal_core_tripal_jobs_rerun($username, $job_id) {
  * Prints details about the current running job
  *
  * NOTE: The following code is executed when 'drush trpjob-curr' or 'drush tripal-current-job' is called
+ *
+ * @ingroup tripal_drush
  */
 function drush_tripal_core_tripal_jobs_current() {
   $sql =  "
@@ -269,6 +286,8 @@ function drush_tripal_core_tripal_jobs_current() {
  *   The name of the table storing the materialized view (tripal_mview.mv_table)
  *
  * Note: Either $mview_id OR $table_name is required
+ *
+ * @ingroup tripal_drush
  */
 function drush_tripal_core_tripal_update_mview() {
   $mview_id = drush_get_option('mview_id');
@@ -303,6 +322,8 @@ function drush_tripal_core_tripal_update_mview() {
 
 /**
  * Returns the current version of chado
+ *
+ * @ingroup tripal_drush
  */
 function drush_tripal_core_tripal_chado_version() {
   $version = $GLOBALS["exact_chado_version"];
@@ -314,6 +335,8 @@ function drush_tripal_core_tripal_chado_version() {
  *
  * @param $table_name
  *  The name of the table to return the description of
+ *
+ * @ingroup tripal_drush
  */
 function drush_tripal_core_tripal_chadotable_desc($table_name) {
   $section = drush_get_option('section');
@@ -334,6 +357,8 @@ function drush_tripal_core_tripal_chadotable_desc($table_name) {
  *
  * @param $module
  *  The name of a module with nodes associated with it. For example, feature
+ *
+ * @ingroup tripal_drush
  */
 function drush_tripal_core_tripal_node_sync($module) {
   switch ($module) {
@@ -366,7 +391,9 @@ function drush_tripal_core_tripal_node_sync($module) {
  *
  * @param $module
  *  The name of a module with nodes associated with it. For example, feature
+ *
+ * @ingroup tripal_drush
  */
 function drush_tripal_core_tripal_node_clean($module) {
   chado_cleanup_orphaned_nodes($module, 0);
-}
+}

tripal_core/tripal_core.install

@@ -1,5 +1,4 @@
 <?php
-
 /**
  * @file
  * Contains functions used to install/uninstall tripal_core.

tripal_core/tripal_core.module

@@ -45,36 +45,37 @@
 
 // APPLICATION PROGRAMMER INTERFACE -------------
 // Chado API
-require_once "api/tripal_core.chado_general.api.inc";
+require_once 'api/tripal_core.chado_general.api.inc';
 require_once 'api/tripal_core.chado_query.api.inc';
 require_once 'api/tripal_core.chado_variables.api.inc';
 require_once 'api/tripal_core.chado_schema.api.inc';
-require_once "api/tripal_core.chado_nodes.api.inc";
-require_once "api/tripal_core.chado_nodes.properties.api.inc";
-require_once "api/tripal_core.chado_nodes.dbxrefs.api.inc";
-require_once "api/tripal_core.chado_nodes.relationships.api.inc";
+require_once 'api/tripal_core.chado_nodes.api.inc';
+require_once 'api/tripal_core.chado_nodes.properties.api.inc';
+require_once 'api/tripal_core.chado_nodes.dbxrefs.api.inc';
+require_once 'api/tripal_core.chado_nodes.relationships.api.inc';
 
 // Table API
-require_once "api/tripal_core.custom_tables.api.inc";
-require_once "api/tripal_core.mviews.api.inc";
+require_once 'api/tripal_core.custom_tables.api.inc';
+require_once 'api/tripal_core.mviews.api.inc';
 
 // Miscellaneous API
-require_once "api/tripal_core.files.api.inc";
-require_once "api/tripal_core.jobs.api.inc";
+require_once 'api/tripal_core.files.api.inc';
+require_once 'api/tripal_core.jobs.api.inc';
 
 require_once 'api/tripal_core.DEPRECATED.inc';
 
 // INCLUDES -------------------------------------
-require_once "includes/jobs.inc";
-require_once "includes/mviews.inc";
-require_once "includes/custom_tables.inc";
-require_once "includes/chado_install.inc";
-require_once "includes/form_elements.inc";
+require_once 'includes/jobs.inc';
+require_once 'includes/mviews.inc';
+require_once 'includes/custom_tables.inc';
+require_once 'includes/chado_install.inc';
+require_once 'includes/form_elements.inc';
 
 tripal_core_set_globals();
 /**
  * This function is used to set the global Chado variables
- * @ingroup tripal_chado_api
+ *
+ * @ingroup tripal_core
  */
 function tripal_core_set_globals() {
   // these global variables are meant to be accessed by all Tripal

tripal_core/tripal_core.views.inc

@@ -1,8 +1,14 @@
 <?php
+/**
+ * @file
+ * Integrates many of the core database tables with drupal views
+ */
 
 /**
  * Describe various Tripal Core systems to Views
- *   for the creation of administrative views
+ *   for the creation of administrative views.
+ *
+ * @ingroup tripal_core
  */
 function tripal_core_views_data() {
   $data = array();
@@ -26,6 +32,8 @@ function tripal_core_views_data() {
  *   Previously generated tripal_core views data array
  * return
  *   $data array with job management system described
+ *
+ * @ingroup tripal_core
  */
 function tripal_core_views_data_jobs($data) {
 
@@ -287,6 +295,8 @@ function tripal_core_views_data_jobs($data) {
  *   Previously generated tripal_core views data array
  * return
  *   $data array with custom tables management described
+ *
+ * @ingroup tripal_core
  */
 function tripal_core_views_data_custom_tables($data) {
 
@@ -362,6 +372,8 @@ function tripal_core_views_data_custom_tables($data) {
  *   Previously generated tripal_core views data array
  * return
  *   $data array with custom tables management described
+ *
+ * @ingroup tripal_core
  */
 function tripal_core_views_data_mviews($data) {
 
@@ -604,4 +616,4 @@ function tripal_core_views_data_mviews($data) {
   );
 
   return $data;
-}
+}

tripal_core/tripal_core.views_default.inc

@@ -1,7 +1,13 @@
 <?php
+/**
+ * @file
+ * Describes core default views
+ */
 
 /**
+ * Describes core default views
  *
+ * @ingroup tripal_core
  */
 function tripal_core_views_default_views() {
   $views = array();
@@ -18,6 +24,11 @@ function tripal_core_views_default_views() {
   return $views;
 }
 
+/**
+ * Describes the jobs administration view.
+ *
+ * @ingroup tripal_core
+ */
 function tripal_core_admin_defaultview_jobs() {
 
   $view = new view();
@@ -290,6 +301,11 @@ function tripal_core_admin_defaultview_jobs() {
   return $view;
 }
 
+/**
+ * Describes the custom tables administration view.
+ *
+ * @ingroup tripal_core
+ */
 function tripal_core_admin_defaultview_custom_tables() {
 
   $view = new view();
@@ -407,6 +423,11 @@ function tripal_core_admin_defaultview_custom_tables() {
   return $view;
 }
 
+/**
+ * Describes the materialized views administration view.
+ *
+ * @ingroup tripal_core
+ */
 function tripal_core_admin_defaultview_mviews() {
 
   $view = new view();
@@ -667,4 +688,4 @@ function tripal_core_admin_defaultview_mviews() {
   $handler->display->display_options['tab_options']['weight'] = '0';
 
   return $view;
-}
+}