Core: some documentation changes

tripal_core/api/tripal_core.chado_nodes.api.inc

@@ -21,35 +21,14 @@
  * 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 +331,7 @@ 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

@@ -1395,7 +1395,7 @@ 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/tripal_core.module

@@ -74,7 +74,7 @@ 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