Quick doc clean-up

tripal_contact/tripal_contact.module

@@ -4,12 +4,7 @@
  * @defgroup tripal_contact Contact Module
  * @ingroup tripal_modules
  * @{
- * Currently this module only provides support for integration with Drupal
- * views and some support for querying using the Tripal Core API.
- *
- * This module needs further development to support full management of
- * contact information within Chado, and full definitions for foreign
- * key relationships in Chado.
+ * Integrates the Chado Contact module with Drupal Nodes & Views
  * @}
  */
 

tripal_feature/tripal_feature.module

@@ -4,7 +4,7 @@
  * @defgroup tripal_feature Feature Module
  * @ingroup tripal_modules
  * @{
- * Provides functions for managing chado features including creating details pages for each feature
+ * Integrates the Chado Sequence module with Drupal Nodes & Views
  * @}
  */
 
@@ -135,7 +135,7 @@ function tripal_feature_menu() {
     'access arguments' => array('access chado_feature content'),
     'type' => MENU_LOCAL_TASK,
   );
-  
+
   // the administative settings menu
   $items['admin/tripal/chado/tripal_feature'] = array(
     'title' => 'Features',

tripal_featuremap/tripal_featuremap.module

@@ -4,7 +4,7 @@
  * @defgroup tripal_featuremap Feature Map Module
  * @ingroup tripal_modules
  * @{
- * Provides functions for managing chado maps including creating details pages for each map
+ * Integrates the Chado Map module with Drupal Nodes & Views
  * @}
  */
 
@@ -116,7 +116,7 @@ function tripal_featuremap_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 2
   );
-  
+
   $items['admin/tripal/chado/tripal_featuremap/sync'] = array(
     'title' => ' Sync',
     'description' => 'Sync featuremaps from Chado with Drupal',

tripal_library/tripal_library.module

@@ -4,7 +4,7 @@
  * @defgroup tripal_library Library Module
  * @ingroup tripal_modules
  * @{
- * Provides functions for managing chado libraries including creating details pages for each library
+ * Integrates the Chado Library module with Drupal Nodes & Views
  * @}
  */
 
@@ -130,7 +130,7 @@ function tripal_library_views_api() {
  */
 function tripal_library_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
-  
+
   $items = array(
     'node__chado_library' => array(
       'template' => 'node--chado-generic',
@@ -175,28 +175,28 @@ function tripal_library_theme($existing, $type, $theme, $path) {
       'variables' =>  array(NULL),
       'path' => "$path/theme",
     ),
-    
+
     // teaser
     'tripal_library_teaser' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_library.teaser',
       'path' => "$path/theme/tripal_library",
     ),
-    
+
     // tripal_organism templates
     'tripal_organism_libraries' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_organism.libraries',
       'path' => "$path/theme/tripal_organism",
     ),
-    
+
     // tripal_feature templates
     'tripal_feature_libraries' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_feature.libraries',
       'path' => "$path/theme/tripal_feature",
     ),
-    
+
   );
   return $items;
 }

tripal_organism/tripal_organism.module

@@ -8,7 +8,7 @@ require_once "includes/tripal_organism.chado_node.inc";
  * @defgroup tripal_organism Organism Module
  * @ingroup tripal_modules
  * @{
- * Provides functions for managing chado organisms including creating details pages for each one
+ * Integrates the Chado Organism module with Drupal Nodes & Views
  * @}
  */
 

tripal_project/tripal_project.module

@@ -8,7 +8,7 @@ require('includes/tripal_project.chado_node.inc');
  * @defgroup tripal_project Project Module
  * @ingroup tripal_modules
  * @{
- * Provides functions for managing chado projects including creating details pages for each one
+ * Integrates the Chado Project tables with Drupal Nodes & Views
  * @}
  */
 

tripal_pub/tripal_pub.module

@@ -14,7 +14,10 @@ require_once "includes/importers/tripal_pub.AGL.inc";
  * @defgroup tripal_pub Publication Module
  * @ingroup tripal_modules
  * @{
- * The Tripal Publication module allows you to search the PubMed databse for academic articles,
+ * Integrates the Chado Publication module with Drupal Nodes & Views, as well as, provides
+ * the ability to import publication from PubMed
+ *
+ * The Tripal Publication module allows you to search the PubMed database for academic articles,
  * that relate to user specified topic\s. As well, it allows management of publications so that
  * a user can enter specified details regarding a desired publication. This allows all of the important
  * information that is unique to a Academic Publication to be stored for access.

tripal_stock/tripal_stock.module

@@ -9,7 +9,7 @@
  * @defgroup tripal_stock Stock Module
  * @ingroup tripal_modules
  * @{
- * Provides functions for managing chado stocks including creating details pages for each stock
+ * Integrates the Chado Stock module with Drupal Nodes & Views
  *
  * The Tripal Stock Module provides functionality for adding, editing, deleting and accessing chado
  * stocks. The stock module was designed to store information about stock collections in a
@@ -46,7 +46,7 @@ function tripal_stock_menu() {
     'access arguments' => array('access chado_stock content'),
     'type' => MENU_LOCAL_TASK,
   );
-  
+
   //Administrative settings menu-----------------
   $items['admin/tripal/chado/tripal_stock'] = array(
     'title' => 'Stocks',
@@ -229,7 +229,7 @@ function tripal_stock_views_api() {
  */
 function tripal_stock_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
-  
+
   $items = array(
 
     // property edit forms function templates
@@ -245,7 +245,7 @@ function tripal_stock_theme($existing, $type, $theme, $path) {
       'variables' => array('form'),
       'function' => 'theme_tripal_stock_edit_ALL_relationships_form',
     ),
-    
+
     // tripal_stock templates
     'node__chado_stock' => array(
       'template' => 'node--chado-generic',
@@ -475,11 +475,11 @@ function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
     foreach ($orelationships as $relationship) {
       $rel = new stdClass();
       $rel->record = $relationship;
-       
+
       // get the relationship and child types
       $rel_type = t(preg_replace('/_/', " ", $relationship->type_id->name));
       $child_type = $relationship->subject_id->type_id->name;
-       
+
       // get the node id of the subject
       $sql = "SELECT nid FROM {chado_stock} WHERE stock_id = :stock_id";
       $n = db_query($sql, array(':stock_id' => $relationship->subject_id->stock_id))->fetchObject();
@@ -504,14 +504,14 @@ function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
       $rel->record = $relationship;
       $rel_type = t(preg_replace('/_/', " ", $relationship->type_id->name));
       $parent_type = $relationship->object_id->type_id->name;
-       
+
       // get the node id of the subject
       $sql = "SELECT nid FROM {chado_stock} WHERE stock_id = :stock_id";
       $n = db_query($sql, array(':stock_id' => $relationship->object_id->stock_id))->fetchObject();
       if ($n) {
         $rel->record->nid = $n->nid;
       }
-       
+
       if (!array_key_exists($rel_type, $relationships['subject'])) {
         $relationships['subject'][$rel_type] = array();
       }

tripal_views/tripal_views.views.inc

@@ -6,37 +6,37 @@ include('views/handlers/tripal_views_handler_area_action_links.inc');
 /**
  * @file
  * Tripal Views Integration
- *
- * @defgroup views Views Integration
- * @{
- * Provide rules for formatting and composition of fields
- * @}
- *
+ */
+
+/**
  * @defgroup views_handlers Views Integration Handlers
  * @ingroup views
  * @{
  * Provide rules for formatting and composition of fields
  * @}
- *
+ */
+/**
  * @defgroup views_field_handlers Views Field Handlers
  * @ingroup views_handlers
  * @{
  * Provide rules for formatting and composition of fields
  * @}
- *
- *
+ */
+/**
  * @defgroup views_filter_handlers Views Filter Handlers
  * @ingroup views_handlers
  * @{
  * Provide the ability to filter based on specified data
  * @}
- *
+ */
+/**
  * @defgroup views_sort_handlers Views Sort Handlers
  * @ingroup views_handlers
  * @{
  * Provide methods describing how specific data should be sorted
  * @}
- *
+ */
+/**
  * @defgroup views_argument_handlers Views Arguement Handlers
  * @ingroup views_handlers
  * @{