Documention: Small tweaks to the documentation to get the defn groups to display properly in the api site

tripal_analysis/api/tripal_analysis.api.inc

@@ -1,24 +1,25 @@
 <?php
 
 /**
- * @file
- * API functions relating to Analysis'
- *
  * @defgroup tripal_analysis_api Analysis Module API
  * @ingroup tripal_api
+ * @{
+ * API functions relating to Analysis'
+ * @}
  */
+
 /**
- * Register tripal_analysis sub-modules
+ * Register tripal_analysis_api sub-modules
  *
  * @param $modulename
  *  The name of the module to be registered as a tripal analysis submodule
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_analysis_api
  */
-function tripal_analysis_register_child($modulename) {
-  $sql = "SELECT * FROM {tripal_analysis} WHERE modulename = :modname";
+function tripal_analysis_api_register_child($modulename) {
+  $sql = "SELECT * FROM {tripal_analysis_api} WHERE modulename = :modname";
   if (!db_query($sql, array(':modname' => $modulename))->fetchField()) {
-    $sql = "INSERT INTO {tripal_analysis} (modulename) VALUES (:modname)";
+    $sql = "INSERT INTO {tripal_analysis_api} (modulename) VALUES (:modname)";
     db_query($sql, array(':modname' => $modulename));
   }
 }
@@ -29,11 +30,11 @@ function tripal_analysis_register_child($modulename) {
  * @param $modulename
  *  The name of the module to un-register
  *
- * @ingroup tripal_analysis
+ * @ingroup tripal_analysis_api
  */
-function tripal_analysis_unregister_child($modulename) {
-  if (db_table_exists('tripal_analysis')) {
-      $sql = "DELETE FROM {tripal_analysis} WHERE modulename = :modname";
+function tripal_analysis_api_unregister_child($modulename) {
+  if (db_table_exists('tripal_analysis_api')) {
+      $sql = "DELETE FROM {tripal_analysis_api} WHERE modulename = :modname";
       db_query($sql, array(':modname' => $modulename));
   }
 }
@@ -50,9 +51,9 @@ function tripal_analysis_unregister_child($modulename) {
  * @return
  *    An analysis chado variable with the specified properties expanded
  *
- * @ingroup tripal_analysis_api
+ * @ingroup tripal_analysis_api_api
  */
-function tripal_analysis_get_property($analysis_id, $property, $cvname = 'tripal') {
+function tripal_analysis_api_get_property($analysis_id, $property, $cvname = 'tripal') {
   return tripal_core_get_property('analysis', $analysis_id, $property, $cvname);
 }
 
@@ -73,9 +74,9 @@ function tripal_analysis_get_property($analysis_id, $property, $cvname = 'tripal
  * @return
  *   True of success, False otherwise
  *
- * @ingroup tripal_analysis_api
+ * @ingroup tripal_analysis_api_api
  */
-function tripal_analysis_insert_property($analysis_id, $property, $value, $update_if_present = 0, $cvname = 'tripal') {
+function tripal_analysis_api_insert_property($analysis_id, $property, $value, $update_if_present = 0, $cvname = 'tripal') {
     return tripal_core_insert_property('analysis', $analysis_id, $property, $cvname, $value, $update_if_present);
 }
 
@@ -99,9 +100,9 @@ function tripal_analysis_insert_property($analysis_id, $property, $value, $updat
  * @return
  *   True of success, False otherwise
  *
- * @ingroup tripal_analysis_api
+ * @ingroup tripal_analysis_api_api
  */
-function tripal_analysis_update_property($analysis_id, $property, $value, $insert_if_missing = 0, $cvname = 'tripal') {
+function tripal_analysis_api_update_property($analysis_id, $property, $value, $insert_if_missing = 0, $cvname = 'tripal') {
   return tripal_core_update_property('analysis', $analysis_id, $property, $cvname, $value, $insert_if_missing);
 }
 
@@ -121,9 +122,9 @@ function tripal_analysis_update_property($analysis_id, $property, $value, $inser
  * @return
  *   True of success, False otherwise
  *
- * @ingroup tripal_analysis_api
+ * @ingroup tripal_analysis_api_api
  */
-function tripal_analysis_delete_property($analysis_id, $property, $cvname = 'tripal') {
+function tripal_analysis_api_delete_property($analysis_id, $property, $cvname = 'tripal') {
   return tripal_core_delete_property('analysis', $analysis_id, $property, $cvname);
 }
 
@@ -136,9 +137,9 @@ function tripal_analysis_delete_property($analysis_id, $property, $cvname = 'tri
  * @return
  *   node of analysis on success, null otherwise
  *
- * @ingroup tripal_analysis_api
+ * @ingroup tripal_analysis_api_api
  */
-function tripal_analysis_get_node($analysis_id) {
+function tripal_analysis_api_get_node($analysis_id) {
   $sql = "SELECT *
            FROM {chado_analysis} CA
               INNER JOIN {node} N on CA.nid = N.nid

tripal_analysis/tripal_analysis.module

@@ -1,17 +1,11 @@
 <?php
 
 /**
- * @file
- * Contains all the main hook implementations for the tripal_analysis module
- *
  * @defgroup tripal_analysis Analysis Module
  * @ingroup tripal_modules
  * @{
  * Provides functions for managing chado analysis' including creating details pages for each one
- *
  * @}
- *
- *
  */
 
 require_once 'api/tripal_analysis.api.inc';
@@ -161,7 +155,7 @@ function tripal_analysis_theme($existing, $type, $theme, $path) {
       'variables' =>  array(NULL),
       'path' => "$path/theme",
     ),
-    
+
     // tripal_feature theme
     'tripal_feature_analyses' => array(
       'template' => 'tripal_feature_analyses',
@@ -233,7 +227,7 @@ function tripal_analysis_views_api() {
 
 /**
  * Implementation of hook_form_alter()
- * 
+ *
  * @param $form
  * @param $form_state
  * @param $form_id

tripal_bulk_loader/api/tripal_bulk_loader.api.templates.inc

@@ -1,10 +1,10 @@
 <?php
 /**
- * @file
- * All functions in this file provide an API to administrative management of bulk loader templates
- *
  * @defgroup tripal_bulk_loader_api Tripal Bulk Loader Module API
  * @ingroup tripal_api
+ * @{
+ * All functions in this file provide an API to administrative management of bulk loader templates
+ * @}
  */
 
 /**

tripal_bulk_loader/tripal_bulk_loader.module

@@ -1,11 +1,11 @@
 <?php
 
 /**
- * @file
- * The functions for the Tripal bulk loader.
- *
  * @defgroup tripal_bulk_loader Tripal Bulk Loader Module
  * @ingroup tripal_modules
+ * @{
+ * Functions implementing the Tripal Generic tab-delimited chado data loader
+ * @}
  */
 
 // Loader

tripal_contact/api/tripal_contact.api.inc

@@ -1,10 +1,10 @@
 <?php
 /**
- * @file
- * Provides an application programming interface (API) to manage libraries
- *
- * @defgroup tripal_contact_api contact Module API
+ * @defgroup tripal_contact_api Contact Module API
  * @ingroup tripal_api
+ * @{
+ * Provides an application programming interface (API) to manage chado contacts
+ * @}
  */
 
 /**
@@ -90,7 +90,7 @@ function tripal_contact_delete_property($contact_id, $property) {
 
 /**
  * Adds a contact to the Chado contact table
- * 
+ *
  * @param $name
  *   The name of the contact
  * @param $description
@@ -101,28 +101,28 @@ function tripal_contact_delete_property($contact_id, $property) {
  *   An associative array containing a list of key value pairs for the properites.
  *   The key's must be valid terms in the tripal_contact vocabulary (e.g. Affiliation,
  *   Address, etc).
- *   
+ *
  * @return
- *   On success, an array is returned containing the fields of the contact 
- *   record including the newly added contact_id. On failure, FALSE is 
+ *   On success, an array is returned containing the fields of the contact
+ *   record including the newly added contact_id. On failure, FALSE is
  *   returned
- *   
+ *
  * @ingroup tripal_contact_api
- * 
+ *
  */
 function tripal_contact_add_contact($name, $description, $type, $properties) {
 
-  // check to see if this contact name already exists.    
+  // check to see if this contact name already exists.
   $values =  array('name' => $name);
   $options = array('statement_name' => 'sel_contact_na');
   $contact = tripal_core_chado_select('contact', array('contact_id'), $values, $options);
-  
-  if (count($contact) == 0) {    
+
+  if (count($contact) == 0) {
     $cvterm = tripal_cv_get_cvterm_by_name($type, NULL, 'tripal_contact');
     if (!$cvterm) {
       watchdog('tripal_contact',"Cannot find contact type '%type'",
         array('%type' => $type), WATCHDOG_ERROR);
-      return FALSE;  
+      return FALSE;
     }
     $values =  array(
       'name' => $name,
@@ -133,26 +133,26 @@ function tripal_contact_add_contact($name, $description, $type, $properties) {
     $contact = tripal_core_chado_insert('contact', $values, $options);
     if (!$contact) {
       watchdog('tripal_contact','Could not add the contact', array(), WATCHDOG_ERROR);
-      return FALSE; 
+      return FALSE;
     }
   }
   else {
     $contact = (array) $contact[0];
   }
- 
+
   // add the description property. We don't store this in the contact.description
-  // field because it is only 255 characters long and may not be enough  
+  // field because it is only 255 characters long and may not be enough
   if ($description) {
     tripal_contact_insert_property($contact['contact_id'], 'contact_description', $description, TRUE);
   }
-    
+
   // add in the other properties provided
   foreach ($properties as $key => $value) {
     $success = tripal_contact_insert_property($contact['contact_id'], $key,$value, TRUE);
     if (!$success) {
       watchdog('tripal_contact',"Could not add the contact property '%prop'", array('%prop' => $key), WATCHDOG_ERROR);
-      return FALSE;  
-    }  
+      return FALSE;
+    }
   }
-  return $contact; 
+  return $contact;
 }

tripal_contact/tripal_contact.module

@@ -1,19 +1,5 @@
 <?php
 
-/**
- *  @file
- * This file contains the basic functions needed for this drupal module.
- * The drupal tripal_contact module maps directly to the chado X module.
- *
- * For documentation regarding the Chado X module:
- * @see http://gmod.org/wiki/Chado_General_Module
- */
-
-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');
-
 /**
  * @defgroup tripal_contact Contact Module
  * @ingroup tripal_modules
@@ -27,8 +13,12 @@ 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
@@ -105,7 +95,7 @@ function tripal_contact_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 0
   );
-  
+
   $items['admin/tripal/chado/tripal_contact/sync'] = array(
     'title' => ' Sync',
     'description' => 'Create pages on this site for libraries stored in Chado',
@@ -147,7 +137,7 @@ function tripal_contact_menu() {
  */
 function tripal_contact_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
-  
+
   $items = array(
     'node__chado_contact' => array(
       'template' => 'node--chado-generic',
@@ -221,7 +211,7 @@ function tripal_contact_block_view($delta = '') {
       case 'contbase':
         $block['subject'] = t('Details');
         $block['content'] = array(
-          '#theme' => 'tripal_contact_base', 
+          '#theme' => 'tripal_contact_base',
           '#nodes' => $node,
           '#title' => '',
         );
@@ -229,7 +219,7 @@ function tripal_contact_block_view($delta = '') {
       case 'contprops':
         $block['subject'] = t('Properties');
         $block['content'] = array(
-          '#theme' => 'tripal_contact_properties', 
+          '#theme' => 'tripal_contact_properties',
           '#nodes' => $node,
           '#title' => '',
         );
@@ -237,7 +227,7 @@ function tripal_contact_block_view($delta = '') {
       case 'contrels':
         $block['subject'] = t('Relationships');
         $block['content'] = array(
-          '#theme' => 'tripal_contact_relationships', 
+          '#theme' => 'tripal_contact_relationships',
           '#nodes' => $node,
           '#title' => '',
         );
@@ -245,7 +235,7 @@ function tripal_contact_block_view($delta = '') {
       case 'contpubs':
         $block['subject'] = t('Publications');
         $block['content'] = array(
-          '#theme' => 'tripal_contact_publications', 
+          '#theme' => 'tripal_contact_publications',
           '#nodes' => $node,
           '#title' => '',
         );

tripal_core/api/tripal_core.chado_general.api.inc

@@ -4,9 +4,6 @@ require_once "tripal_core.schema_v1.2.api.inc";
 require_once "tripal_core.schema_v1.11.api.inc";
 
 /**
- * @file
- * Chado API
- *
  * @defgroup tripal_chado_api Chado API
  * @ingroup tripal_core_api
  * @{

tripal_core/api/tripal_core.chado_nodes.api.inc

@@ -1,7 +1,6 @@
 <?php
 
 /**
- * @file
  * @defgroup tripal_chado_node_api Chado Node API
  * @ingroup tripal_chado_api
  * @{
@@ -11,6 +10,22 @@
  * similar. This API aims to abstract much of the common functionality in order to make
  * it easier for new Tripal modules to implement drupal node types and to centralize the
  * maintenance effort as much as possible.
+ *
+ * A generic sync form has been created. See tripal_core_chado_node_sync_form() for
+ * instructions on how to implement this form in your module.
+ *
+ * Many of the base chado tables also have associated prop, _dbxref and _relationship
+ * tables. Generic mini-forms have been created to help you handle these forms. To
+ * implement this functionality you call the mini-form from your module node form and
+ * then call the associated update functions from both your hook_insert and hook_update.
+ * The functions of interest are as follows:
+ *   - chado_node_properties_form() and chado_node_properties_form_update_properties()
+ *     to provide an interface for adding/removing properties
+ *   - tripal_core_additional_dbxrefs_form() and tripal_core_additional_dbxrefs_form_update_dbxrefs()
+ *     to provide an interface for adding/removing additional database references
+ *   - tripal_core_relationships_form() and tripal_core_relationships_form_update_relationships()
+ *     to provide an interface for adding/removing relationships between chado records
+ *     from your base table
  * @}
  */
 

tripal_core/api/tripal_core.chado_query.api.inc

@@ -1,7 +1,6 @@
 <?php
 
 /**
- * @file
  * @defgroup tripal_chado_query_api Chado Query API
  * @ingroup tripal_chado_api
  * @{

tripal_core/api/tripal_core.chado_schema.api.inc

@@ -1,7 +1,6 @@
 <?php
 
 /**
- * @file
  * @defgroup tripal_chado_schema_api Chado Query API
  * @ingroup tripal_chado_api
  * @{

tripal_core/api/tripal_core.chado_variables.api.inc

@@ -1,7 +1,6 @@
 <?php
 
 /**
- * @file
  * @defgroup tripal_chado_variables_api Chado Variables API
  * @ingroup tripal_chado_api
  * @{

tripal_core/api/tripal_core.custom_tables.api.inc

@@ -1,8 +1,5 @@
 <?php
 /**
- * @file
- * Contains functions for the Custom Tables API
-
  * @defgroup tripal_custom_tables_api Custom Tables API
  * @ingroup tripal_core_api
  * @{
@@ -11,7 +8,7 @@
  */
 
 /**
- * Edits a custom table in the chado database. It supports 
+ * Edits a custom table in the chado database. It supports
  * using the Drupal Schema API array.
  *
  * @param $table_id
@@ -39,11 +36,11 @@ function tripal_core_edit_custom_table($table_id, $table_name, $schema, $skip_cr
   $sql = "SELECT * FROM {tripal_custom_tables} WHERE table_id = :table_id";
   $results = db_query($sql, array(':table_id' => $table_id));
   $custom_table = $results->fetchObject();
-  
+
   // if the user changed the table name, we want to drop the old one and force
   // creation of the new one.
   if ($custom_table->table_name != $table_name) {
-    chado_query("DROP TABLE %s", $custom_table->table_name);  
+    chado_query("DROP TABLE %s", $custom_table->table_name);
     $skip_creation = 0; // we want to create the table
   }
 
@@ -93,7 +90,7 @@ function tripal_core_edit_custom_table($table_id, $table_name, $schema, $skip_cr
  *   A Drupal-style Schema API definition of the table
  * @param $skip_creation
  *   Set as TRUE to skip dropping and re-creation of the table if it already
- *   exists.  This is useful if the table was already created through another 
+ *   exists.  This is useful if the table was already created through another
  *   means and you simply want to make Tripal aware of the table schema.  If the
  *   table does not exist it will be created.
  *
@@ -106,17 +103,17 @@ function tripal_core_create_custom_table($table, $schema, $skip_creation = 1) {
   global $databases;
   $created = 0;
   $recreated = 0;
-  
+
   // see if the table entry already exists in the tripal_custom_tables table.
   $sql = "SELECT * FROM {tripal_custom_tables} WHERE table_name = :table_name";
   $results = db_query($sql, array(':table_name' => $table));
   $centry = $results->fetchObject();
-  
+
   // check to see if the table already exists in the chado schema
-  $exists = chado_table_exists($table); 
-  
+  $exists = chado_table_exists($table);
+
   // if the table does not exist then create it
-  if (!$exists) { 
+  if (!$exists) {
     try {
       $ret = db_create_table('chado.' . $table, $schema);
       $created = 1;
@@ -126,15 +123,15 @@ function tripal_core_create_custom_table($table, $schema, $skip_creation = 1) {
       watchdog('tripal_core', "Error adding custom table: @message", array('@message' => $error), WATCHDOG_ERROR);
       drupal_set_message("Could not add custom table. $error.", "error");
       return FALSE;
-    }    
-  }  
+    }
+  }
 
   // if the table exists in Chado and in our custom table and
-  // skip creation is turned off then drop and re-create the table 
-  if ($exists and is_object($centry) and !$skip_creation) {    
-    
-    // drop the table we'll recreate it with the new schema    
-    try {      
+  // skip creation is turned off then drop and re-create the table
+  if ($exists and is_object($centry) and !$skip_creation) {
+
+    // drop the table we'll recreate it with the new schema
+    try {
       chado_query('DROP TABLE {' . $table . '}');
       db_create_table('chado.' . $table, $schema);
       $recreated = 1;
@@ -162,24 +159,24 @@ function tripal_core_create_custom_table($table, $schema, $skip_creation = 1) {
   if (!$success) {
     watchdog('tripal_core', "Error adding custom table %table_name.",
       array('%table_name' => $table), WATCHDOG_ERROR);
-    drupal_set_message(t("Could not add custom table %table_name. 
-      Please check the schema array.", array('%table_name' => $table)), 'error');      
+    drupal_set_message(t("Could not add custom table %table_name.
+      Please check the schema array.", array('%table_name' => $table)), 'error');
     return FALSE;
   }
-  
-  
+
+
   // now add any foreign key constraints
   if (!$skip_creation and array_key_exists('foreign keys', $schema)) {
-    
+
     // iterate through the foreign keys and add each one
     $fkeys = $schema['foreign keys'];
     foreach ($fkeys as $fktable => $fkdetails) {
       $relations = $fkdetails['columns'];
       foreach ($relations as $left => $right) {
         $sql = '
-          ALTER TABLE {' . $table . '} 
-            ADD CONSTRAINT ' . $table . '_' . $left . '_fkey FOREIGN KEY (' . $left . ') 
-            REFERENCES  {' . $fktable . '} (' . $right . ') 
+          ALTER TABLE {' . $table . '}
+            ADD CONSTRAINT ' . $table . '_' . $left . '_fkey FOREIGN KEY (' . $left . ')
+            REFERENCES  {' . $fktable . '} (' . $right . ')
             ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
         ';
         try {
@@ -189,13 +186,13 @@ function tripal_core_create_custom_table($table, $schema, $skip_creation = 1) {
           $error = $e->getMessage();
           watchdog('tripal_core', "Error, could not add foreign key contraint to custom table: %error",
             array('%error' => $error), WATCHDOG_ERROR);
-          drupal_set_message("Could not add foreign key contraint to table: $error", 'error');      
-          return FALSE;          
+          drupal_set_message("Could not add foreign key contraint to table: $error", 'error');
+          return FALSE;
         }
       }
     }
   }
-  
+
   if ($created) {
     drupal_set_message("Custom table created successfully.", 'status');
   }

tripal_core/api/tripal_core.files.api.inc

@@ -1,27 +1,20 @@
-<?php 
+<?php
 /**
- * @file
- * The Tripal Files API
- *
- * This file provides the API to help Tripal modules to storing files
- * in a consistent directory strcuture.
- *
- * @defgroup tripal_files_api  Files API
+ * @defgroup tripal_files_api Files API
  * @ingroup tripal_core_api
  * @{
  * Provides an application programming interface (API) for managing files within
  * the Tripal data directory structure.
- *
  * @}
  *
  */
- 
+
 /**
  * This function is a substitute for Drupal 6's file_directory_path()
  * function which no longer exists in Drupal 7.  However, the function
  * call is useful because it's more intitutive. So this wrapper was created
- * to mimic the behavior of the old function.  
- * 
+ * to mimic the behavior of the old function.
+ *
  * @return
  *   the public directory where tripal files are housed: sites/default/files/tripal
  */
@@ -59,7 +52,7 @@ function tripal_create_moddir($module_name) {
 /**
  * This function creates directories inside of the module's
  * Data directory.
- * 
+ *
  * @param $module_name
  * @param $path
  */
@@ -67,7 +60,7 @@ function tripal_create_mod_subdir($module_name, $path) {
 
   // make sure the module data directory exists
   tripal_create_moddir($module_name);
-  
+
   // now make sure the sub dir exists
   $sub_dir = tripal_file_directory_path() . $module_name . $path;
   if (!file_prepare_directory($sub_dir, FILE_CREATE_DIRECTORY | FILE_MODIFY_PERMISSIONS)) {
@@ -87,7 +80,7 @@ function tripal_create_mod_subdir($module_name, $path) {
  *
  * @returns
  *   The path within the Drupal installation where the data directory resides
- *   
+ *
  * @ingroup tripal_files_api
  */
 function tripal_get_moddir($module_name) {

tripal_core/api/tripal_core.jobs.api.inc

@@ -1,8 +1,5 @@
 <?php
 /**
- * @file
- * Contains functions related to the Tripal Jobs API
- *
  * @defgroup tripal_jobs_api Jobs API
  * @ingroup tripal_core_api
  * @{
@@ -21,7 +18,7 @@
  * 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.
- * @} 
+ * @}
  */
 
 /**
@@ -68,7 +65,7 @@ function tripal_add_job($job_name, $modulename, $callback, $arguments, $uid, $pr
   if (is_array($arguments)) {
     $args = serialize($arguments);
   }
-  
+
   $record = new stdClass();
   $record->job_name = $job_name;
   $record->modulename = $modulename;
@@ -190,14 +187,14 @@ function tripal_jobs_get_end_time($job) {
  */
 function tripal_jobs_rerun($job_id, $goto_jobs_page = TRUE) {
   global $user;
-  
+
   $user_id = $user->uid;
 
   $sql = "SELECT * FROM {tripal_jobs} WHERE job_id = :job_id";
   $results = db_query($sql, array(':job_id' => $job_id));
-  $job = $results->fetchObject(); 
+  $job = $results->fetchObject();
   // arguments for jobs used to be stored as plain string with a double colon
-  // separating them.  But as of Tripal v2.0 the arguments are stored as 
+  // separating them.  But as of Tripal v2.0 the arguments are stored as
   // a serialized array.  To be backwards compatible, we should check for serialization
   // and if not then we will use the old style
   $args = unserialize($job->arguments);
@@ -295,7 +292,7 @@ function tripal_jobs_launch($do_parallel = 0, $job_id = NULL) {
     // Add the job_id as the last item in the list of arguments. All
     // callback functions should support this argument.
     $callback = $job->callback;
-    
+
     // arguments for jobs used to be stored as plain string with a double colon
     // separating them.  But as of Tripal v2.0 the arguments are stored as
     // a serialized array.  To be backwards compatible, we should check for serialization

tripal_core/api/tripal_core.mviews.api.inc

@@ -1,8 +1,5 @@
 <?php
 /**
- * @file
- * Contains functions for the Materialized Views API
-
  * @defgroup tripal_mviews_api Materalized Views API
  * @ingroup tripal_core_api
  * @{
@@ -72,7 +69,7 @@ function tripal_add_legacy_mview($name, $modulename, $mv_table, $mv_specs, $inde
         $field = trim($field);
         $index .= "CREATE INDEX idx_${mv_table}_${field} ON $mv_table ($field);";
       }
-    } 
+    }
   }
 
   // add the table to the database
@@ -100,19 +97,19 @@ function tripal_add_legacy_mview($name, $modulename, $mv_table, $mv_specs, $inde
  *   The name of the module submitting the materialized view (e.g. 'tripal_library')
  * @param $mv_schema
  *   If using the newer Schema API array to define the materialized view then
- *   this variable should contain the array or a string representation of the 
+ *   this variable should contain the array or a string representation of the
  *   array.
  * @param $query
  *   The SQL query that loads the materialized view with data
  * @param $comment
- *   A string containing a description of the materialized view 
- *   
+ *   A string containing a description of the materialized view
+ *
  * @ingroup tripal_mviews_api
  */
 function tripal_add_mview($name, $modulename, $schema_arr, $query, $comment = NULL) {
-  
+
   $mv_table = $schema_arr['table'];
-  
+
   if (!$mv_table) {
      watchdog('tripal_core', 'Must have a table name when creating an mview.', array(), WATCHDOG_ERROR);
      return NULL;
@@ -135,7 +132,7 @@ function tripal_add_mview($name, $modulename, $schema_arr, $query, $comment = NU
     if (chado_table_exists($mv_table)) {
       $sql = 'DROP TABLE {' . $mv_table . '}';
       chado_query($sql);
-    }   
+    }
     // create the table
     if (!tripal_core_create_custom_table ($mv_table, $schema_arr, 0)) {
       drupal_set_message(t("Could not create the materialized view. Check Drupal error report logs."), 'error');
@@ -200,14 +197,14 @@ function tripal_edit_mview($mview_id, $name, $modulename, $mv_table, $mv_specs,
   // get the view before we update and check to see if the table structure has
   // changed. IF so, then we want to drop and recreate the table. If not, then
   // just save the updated SQL.
-  $create_table = 1;  
+  $create_table = 1;
   $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = :mview_id";
   $results = db_query($sql, array(':mview_id' => $mview_id));
-  $mview = $results->fetchObject();  
-  if ($mview->mv_schema == $mv_schema and $mview->mv_table == $mv_table and 
-     $mview->mv_specs == $mv_specs and $mview->indexed == $indexed and 
+  $mview = $results->fetchObject();
+  if ($mview->mv_schema == $mv_schema and $mview->mv_table == $mv_table and
+     $mview->mv_specs == $mv_specs and $mview->indexed == $indexed and
      $mview->special_index == $special_index) {
-    // nothing has changed so simpy update the SQL and other fields 
+    // nothing has changed so simpy update the SQL and other fields
     $create_table = 0;
   }
   else {
@@ -219,7 +216,7 @@ function tripal_edit_mview($mview_id, $name, $modulename, $mv_table, $mv_specs,
     $record->query = $query;
     $record->special_index = $special_index;
   }
-  
+
   // if we are going to create the table then we must first drop it if it exists
   if ($create_table) {
     $previous_db = tripal_db_set_active('chado');  // use chado database
@@ -248,7 +245,7 @@ function tripal_edit_mview($mview_id, $name, $modulename, $mv_table, $mv_specs,
 
     // re-create the table differently depending on if it the traditional method
     // or the Drupal Schema API method
-    if ($create_table and $mv_schema) {     
+    if ($create_table and $mv_schema) {
       if (!tripal_core_create_custom_table($mv_table, $schema_arr, 0)) {
         drupal_set_message(t("Could not create the materialized view. Check Drupal error report logs."));
       }
@@ -260,11 +257,11 @@ function tripal_edit_mview($mview_id, $name, $modulename, $mv_table, $mv_specs,
       $sql = "CREATE TABLE {$mv_table} ($mv_specs); $index";
       $results = chado_query($sql);
       if ($results) {
-        drupal_set_message(t("View '%name' created.  All records cleared. Please re-populate the view.", 
+        drupal_set_message(t("View '%name' created.  All records cleared. Please re-populate the view.",
           array('%name' => $name)));
       }
       else {
-        drupal_set_message(t("Failed to create the materialized view table: '%mv_table'", 
+        drupal_set_message(t("Failed to create the materialized view table: '%mv_table'",
           array('%mv_table' => $mv_table)), 'error');
       }
     }
@@ -273,12 +270,12 @@ function tripal_edit_mview($mview_id, $name, $modulename, $mv_table, $mv_specs,
       if ($query != $mview->query) {
         $message .= "Please repopulate the view to use updated query.";
       }
-      drupal_set_message(t($message, array('%name' => $name)));  
+      drupal_set_message(t($message, array('%name' => $name)));
     }
   }
   else {
-    drupal_set_message(t("Failed to update the materialized view: '%mv_table'", 
-      array('%mv_table' => $mv_table)), 'error');  
+    drupal_set_message(t("Failed to update the materialized view: '%mv_table'",
+      array('%mv_table' => $mv_table)), 'error');
   }
 }
 
@@ -320,7 +317,7 @@ function tripal_mviews_get_mview_id($view_name) {
  */
 function tripal_mviews_action($op, $mview_id, $redirect = FALSE) {
   global $user;
-  
+
   if (!$mview_id) {
     return '';
   }
@@ -336,17 +333,17 @@ function tripal_mviews_action($op, $mview_id, $redirect = FALSE) {
     tripal_add_job("Populate materialized view '$mview->name'", 'tripal_core',
        'tripal_update_mview', $args, $user->uid);
   }
-  
+
   // if op is to delete then do so
   if ($op == 'delete') {
-    
+
     // remove the mview from the tripal_mviews table
     $sql = "DELETE FROM {tripal_mviews} WHERE mview_id = $mview_id";
     db_query($sql);
-    
+
     // does the table already exist?
     $mview_exists = db_table_exists('chado.' . $mview->mv_table);
-    
+
     // drop the table from chado if it exists
     if ($mview_exists) {
       $sql = "DROP TABLE {" . $mview->mv_table . "}";
@@ -375,17 +372,17 @@ function tripal_update_mview($mview_id) {
   $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = :mview_id ";
   $results = db_query($sql, array(':mview_id' => $mview_id));
   $mview = $results->fetchObject();
-  if ($mview) {    
+  if ($mview) {
     // execute the query inside a transaction so that it doesn't destroy existing data
     // that may leave parts of the site unfunctional
     $transaction = db_transaction();
     try {
       $previous_db = tripal_db_set_active('chado');  // use chado database
       $success = db_query("DELETE FROM {" . $mview->mv_table . "}");
-      $success = db_query("INSERT INTO {" . $mview->mv_table . "} ($mview->query)");    
+      $success = db_query("INSERT INTO {" . $mview->mv_table . "} ($mview->query)");
       tripal_db_set_active($previous_db);  // now use drupal database
       // if success get the number of results and update the table record
-      if ($success) { 
+      if ($success) {
         $sql = "SELECT count(*) as cnt FROM {" . $mview->mv_table . "}";
         $results = chado_query($sql);
         $count = $results->fetchObject();
@@ -395,7 +392,7 @@ function tripal_update_mview($mview_id) {
         $record->status = "Populated with " . number_format($count->cnt) . " rows";
         drupal_write_record('tripal_mviews', $record, 'mview_id');
       }
-      // if not success then throw an error 
+      // if not success then throw an error
       else {
         throw new Exception("ERROR populating the materialized view ". $mview->mv_table . ". See Drupal's recent log entries for details.");
       }

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

@@ -1,23 +1,14 @@
 <?php
-/* @file: This file contains default schema definitions for all chado v1.11 tables
- *        to be used by other function. Specifically these functions are used
- *        by the tripal_core select/insert/update API functions and by
- *        the Tripal Views module.
- *
- *        These schema definitions can be augmented by anohter modules
- *        (specifically to add missing definitions) by implementing
- *        hook_chado_schema_v1_11_<table name>().
- *
+/**
  * @defgroup tripal_schema_v1_11_api Chado v1.11 Schema API
- * @ingroup tripal_core_api
+ * @ingroup tripal_chado_schema_api
  * @{
  * Provides an application programming interface (API) for describing Chado tables.
  * 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
- * relationships are needed to for Tripal Views.  Therefore, FK relationships
- * have been added to the schema defintitions below.
+ * Because Drupal 6 does not handle foreign key (FK) relationships, which are needed to
+ * for Tripal Views, they have been added to the schema defintitions below.
  *
  * The functions provided in this documentation should not be called as is, but if you need
  * the Drupal-style array definition for any table, use the following function
@@ -30,6 +21,9 @@
  * Chado and uses the Drupal hook infrastructure to call the appropriate
  * hook function to retrieve the table schema.
  *
+ * If you need to augment these schema definitions within your own module, you need to
+ * implement the hook_chado_schema_v1_11_[table name]() hook where [table name] is the
+ * name of the chado table whose schema definition you want to augment.
  * @}
  */
 

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

@@ -1,23 +1,14 @@
 <?php
-/* @file: This file contains default schema definitions for all chado v1.2 tables
- *        to be used by other function. Specifically these functions are used
- *        by the tripal_core select/insert/update API functions and by
- *        the Tripal Views module.
- *
- *        These schema definitions can be augmented by another modules
- *        (specifically to add missing definitions) by implementing
- *        hook_chado_schema_v1_2_<table name>().
- *
+/**
  * @defgroup tripal_schema_v1_2_api Chado v1.2 Schema API
- * @ingroup tripal_core_api
+ * @ingroup tripal_chado_schema_api
  * @{
  * Provides an application programming interface (API) for describing Chado tables.
  * 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 
- * relationships are needed to for Tripal Views.  Therefore, FK relationships
- * have been added to the schema defintitions below.
+ * Because Drupal 6 does not handle foreign key (FK) relationships, which are needed to
+ * for Tripal Views, they have been added to the schema defintitions below.
  *
  * The functions provided in this documentation should not be called as is, but if you need
  * the Drupal-style array definition for any table, use the following function
@@ -26,10 +17,13 @@
  *   $table_desc = tripal_core_get_chado_table_schema($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.
  *
+ * If you need to augment these schema definitions within your own module, you need to
+ * implement the hook_chado_schema_v1_2_[table name]() hook where [table name] is the
+ * name of the chado table whose schema definition you want to augment.
  * @}
  */
 
@@ -14178,6 +14172,6 @@ function tripal_core_chado_get_v1_2_tables() {
     'synonym',
     'tableinfo',
     'treatment'
-   );  
+   );
    return $tables;
 }

tripal_core/tripal_core.module

@@ -29,11 +29,18 @@
  /**
  * @defgroup tripal_core_api Core Module API
  * @ingroup tripal_api
+ * @{
+ * Functions providing support for all Tripal modules.
+ * @}
  */
 
 /**
  * @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.
+ * @}
  */
 
 // APPLICATION PROGRAMMER INTERFACE -------------

tripal_cv/api/tripal_cv.api.inc

@@ -1,10 +1,7 @@
 <?php
 
 /**
- * @file
- * Controlled Vocabulary API
- *
- * @defgroup tripal_cv_api CV Module API
+ * @defgroup tripal_cv_api Ccontrolled Vocabulary API
  * @ingroup tripal_api
  * This module provides a set of functions to simplify working with
  * controlled vocabularies.  Most of the API functions deal with retrieving
@@ -158,11 +155,11 @@ function tripal_cv_get_cv_id($cv_name) {
 }
 
 /**
- * Create an options array to be used in a form element which provides a 
+ * Create an options array to be used in a form element which provides a
  * list of all chado cvs
  *
  * NOTE: This function is deprecated as of Tripal v1.0
- * 
+ *
  * @return
  *   An array(cv_id => name) for each cv in the chado cv table
  *
@@ -197,7 +194,7 @@ function tripal_cv_get_cvterm_by_id($cvterm_id) {
   }
   $values = array('cvterm_id' => $cvterm_id);
   $options = array('statement_name' => 'sel_cvterm_id');
-  $r = tripal_core_chado_select('cvterm', array('*'), $values, $options);  
+  $r = tripal_core_chado_select('cvterm', array('*'), $values, $options);
   if (!$r) {
     return FALSE;
   }
@@ -284,7 +281,7 @@ function tripal_cv_get_cvterm_by_synonym($synonym, $cv_id = NULL, $cv_name = 'tr
   $statement = "sel_cvtermsynonym_sy";
   if ($cv_id) {
     $values['cvterm_id'] = array('cv_id' => $cv_id);
-    $statement = "sel_cvtermsynonym_sycv";    
+    $statement = "sel_cvtermsynonym_sycv";
   }
   if ($cv_name) {
     $values['cvterm_id'] = array('cv_id' => array('name' => $cv_name));
@@ -295,7 +292,7 @@ function tripal_cv_get_cvterm_by_synonym($synonym, $cv_id = NULL, $cv_name = 'tr
     'case_insensitive_columns' => array('name')
   );
   $synonym = tripal_core_chado_select('cvtermsynonym', array('cvterm_id'), $values, $options);
-  
+
   // if the synonym doens't exist or more than one record is returned then return false
   if (count($synonym) == 0) {
     return FALSE;
@@ -303,12 +300,12 @@ function tripal_cv_get_cvterm_by_synonym($synonym, $cv_id = NULL, $cv_name = 'tr
   if (count($synonym) > 1) {
     return FALSE;
   }
-  
+
   // get the cvterm
   $values = array('cvterm_id' => $synonym[0]->cvterm_id);
   $options = array('statement_name' => 'sel_cvterm_id');
   $cvterm = tripal_core_chado_select('cvterm', array('*'), $values, $options);
-  return $cvterm[0]; 
+  return $cvterm[0];
 }
 /**
  * Create an options array to be used in a form element
@@ -361,17 +358,17 @@ function tripal_cv_update_cvtermpath($cvid, $job_id = NULL) {
   // first get the controlled vocabulary name:
   $sql = "SELECT * FROM {cv} WHERE cv_id = :cv_id";
   $cv = chado_query($sql, array(':cv_id' => $cvid))->fetchObject();
-  
+
   print "\nUpdating cvtermpath for $cv->name...\n";
-  
+
   $previous = tripal_db_set_active('chado');
   try {
     $sql = "SELECT * FROM fill_cvtermpath(:name)";
     db_query($sql, array(':name' => $cv->name));
-    tripal_db_set_active($previous); 
+    tripal_db_set_active($previous);
   }
   catch (Exception $e) {
-    tripal_db_set_active($previous);  
+    tripal_db_set_active($previous);
     $error = $e->getMessage();
     watchdog('tripal_cv', "Could not fill cvtermpath table: @error", array('@error' => $error), WATCHDOG_ERROR);
     return FALSE;
@@ -395,20 +392,20 @@ function tripal_cv_update_cvtermpath($cvid, $job_id = NULL) {
  * @ingroup tripal_cv_api
  */
 function tripal_cv_add_cv($name, $definition) {
-  
+
   // insert/update values
   $ins_values = array(
     'name'       => $name,
     'definition' => $definition
   );
-  
+
   // see if the CV (default-namespace) exists already in the database
   $sel_values = array('name' => $name);
   $sel_options = array('statement_name' => 'sel_cv_na');
   $results = tripal_core_chado_select('cv', array('*'), $sel_values, $sel_options);
 
   // if it does not exists then add it
-  if (count($results) == 0) {    
+  if (count($results) == 0) {
     $ins_options = array('statement_name' => 'ins_cv_nade');
     $success = tripal_core_chado_insert('cv', $ins_values, $ins_options);
     if (!$success) {
@@ -474,9 +471,9 @@ function tripal_cv_add_cv($name, $definition) {
  *
  * @ingroup tripal_cv_api
  */
-function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship = 0, 
+function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship = 0,
   $update = 1, $dbname = 'internal') {
-      
+
   // get the term properties
   $id = $term['id'];
   $name = '';
@@ -484,17 +481,17 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
   $definition = '';
   $is_obsolete = 0;
   $accession = '';
-  
+
   if (array_key_exists('name', $term)) {
-    $name = $term['name'];  
+    $name = $term['name'];
   }
   else {
-    $name = $id;  
+    $name = $id;
   }
 
   if (array_key_exists('namespace', $term)) {
     $cvname = $term['namespace'];
-  } 
+  }
   else {
     $cvname = $defaultcv;
   }
@@ -509,7 +506,7 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
     if (strcmp($is_obsolete, 'true') == 0) {
       $is_obsolete = 1;
     }
-  }  
+  }
   if (!$name and !$id) {
     watchdog('tripal_cv', "Cannot find cvterm without 'id' or 'name'", NULL, WATCHDOG_WARNING);
     return 0;
@@ -517,27 +514,27 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
   if (!$id) {
     $id = $name;
   }
-  
+
   // get the accession and the database from the cvterm id
   if ($dbname) {
     $accession = $id;
   }
-  
+
   if (preg_match('/^.+?:.*$/', $id)) {
     $accession = preg_replace('/^.+?:(.*)$/', '\1', $id);
     $dbname = preg_replace('/^(.+?):.*$/', '\1', $id);
   }
-  
+
   // check that we have a database name, give a different message if it's a relationship
   if ($is_relationship and !$dbname) {
     watchdog('tripal_cv', "A database name is not provided for this relationship term: $id", NULL, WATCHDOG_WARNING);
-    return 0; 
+    return 0;
   }
   if (!$is_relationship and !$dbname) {
     watchdog('tripal_cv', "A database identifier is missing from the term: $id", NULL, WATCHDOG_WARNING);
     return 0;
   }
-  
+
   // make sure the CV name exists
   $cv = tripal_cv_get_cv_by_name($cvname);
   if (!$cv) {
@@ -552,16 +549,16 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
   // here for easy reference below.  Because CV terms can change their names
   // but accessions don't change, the following SQL finds cvterms based on
   // their accession rather than the name
-  $cvtermsql = "     
-    SELECT CVT.name, CVT.cvterm_id, CV.cv_id, CV.name as cvname, 
-      DB.name as dbname, DB.db_id, DBX.accession 
+  $cvtermsql = "
+    SELECT CVT.name, CVT.cvterm_id, CV.cv_id, CV.name as cvname,
+      DB.name as dbname, DB.db_id, DBX.accession
     FROM {cvterm} CVT
       INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
       INNER JOIN {db} DB on DBX.db_id = DB.db_id
       INNER JOIN {cv} CV on CV.cv_id = CVT.cv_id
     WHERE DBX.accession = :accession and DB.name = :name
-  ";    
-  
+  ";
+
   // add the database. The function will just return the DB object if the
   // database already exists.
   $db = tripal_db_get_db_by_name($dbname);
@@ -584,25 +581,25 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
   );
   $options = array('statement_name' => 'sel_cvterm_c1');
   $result = tripal_core_chado_select('cvterm', array('*'), $values, $options);
-  
+
   // if the constraint is met then let's check it to see if
   // the database name matches the one we have been provided
   if (count($result) == 1) {
     $cvterm = $result[0];
-    
+
     // get the dbxref record
     $values = array('dbxref_id' => $cvterm->dbxref_id);
     $options = array('statement_name' => 'sel_dbxref_id');
     $result = tripal_core_chado_select('dbxref', array('*'), $values, $options);
     $dbxref = $result[0];
-    
+
     // get the db
     $values = array('db_id' => $dbxref->db_id);
     $options = array('statement_name' => 'sel_db_id');
     $result = tripal_core_chado_select('db', array('*'), $values, $options);
     $db_check = $result[0];
-    
-    // the database name for this existing term does not match that of the 
+
+    // the database name for this existing term does not match that of the
     // one provided to this function.  The CV name matches otherwise we
     // wouldn't have made it this far. So, let's swap the database for
     // this term
@@ -611,19 +608,19 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
       // look to see if the correct dbxref record already exists for this database
       $values = array(
         'db_id' => $db->db_id,
-        'accession' => $accession,       
+        'accession' => $accession,
       );
       $options = array('statement_name' => 'sel_dbxref_idac');
       $result = tripal_core_chado_select('dbxref', array('*'), $values, $options);
 
-      // if we already have a good dbxref then we want to update our cvterm 
+      // if we already have a good dbxref then we want to update our cvterm
       // to use this dbxref
       if (count($result) > 0) {
         $dbxref = $result[0];
         $match = array('cvterm_id' => $cvterm->cvterm_id);
         $values = array('dbxref_id' => $dbxref->dbxref_id);
         $options = array('statement_name' => 'upd_cvterm_db');
-        $success = tripal_core_chado_update('cvterm', $match, $values, $options); 
+        $success = tripal_core_chado_update('cvterm', $match, $values, $options);
         if (!$success) {
           watchdog('tripal_cv', "Failed to correct the dbxref id for the cvterm " .
             "'$name' (id: $accession), for database $dbname", NULL, WATCHDOG_WARNING);
@@ -631,20 +628,20 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
         }
       }
       // if we don't have the record then we want to delete our cvterm and let the code
-      // below recreate it with the correct info 
-      else {          
+      // below recreate it with the correct info
+      else {
         $match = array('cvterm_id' => $cvterm->cvterm_id);
         $options = array('statement_name' => 'del_cvterm_cv');
         tripal_core_chado_delete('cvterm', $match, $options);
-      }      
+      }
     }
-    
-    // check that the accession matches.  Sometimes an OBO can define the same term 
+
+    // check that the accession matches.  Sometimes an OBO can define the same term
     // multiple times but with different accessions.  If this is the case we
     // can't do an insert or it will violate the constraint in the cvterm table.
     // so we'll need to add the record to the cvterm_dbxref table instead
     if ($dbxref->accession != $accession) {
-      
+
       // get/add the dbxref fort his term
       $dbxref_new =  tripal_db_add_dbxref($db->db_id, $accession);
       if (!$dbxref_new) {
@@ -652,17 +649,17 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
           "$name (id: $accession), for database $dbname", NULL, WATCHDOG_WARNING);
         return 0;
       }
-      
+
       // check to see if the cvterm_dbxref record already exists
       $values = array(
         'cvterm_id' => $cvterm->cvterm_id,
         'dbxref_id' => $dbxref_new->dbxref_id,
         'is_for_definition' => 1,
       );
-      $options = array('statement_name' => 'sel_cvtermdbxref_cvdbis');      
+      $options = array('statement_name' => 'sel_cvtermdbxref_cvdbis');
       $result = tripal_core_chado_select('cvterm_dbxref', array('*'), $values, $options);
-      
-      // if the cvterm_dbxref record does not exists then add it 
+
+      // if the cvterm_dbxref record does not exists then add it
       if (count($result)==0) {
         $options = array(
           'statement_name' => 'ins_cvtermdbxref_cvdbis',
@@ -670,21 +667,21 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
         );
         $success = tripal_core_chado_insert('cvterm_dbxref', $values, $options);
         if (!$success) {
-          watchdog('tripal_cv', "Failed to find or insert the cvterm_dbxref record for a " . 
+          watchdog('tripal_cv', "Failed to find or insert the cvterm_dbxref record for a " .
             "duplicated cvterm:  $name (id: $accession), for database $dbname", NULL, WATCHDOG_WARNING);
           return 0;
         }
-      }        
+      }
       // get the original cvterm with the same name and return that.
       $result = chado_query($cvtermsql, array(':accession' => $dbxref->accession, ':name' => $dbname));
       $cvterm = $result->fetchObject();
       return $cvterm;
     }
-    
-    // continue on, we've fixed the record if the db_id did not match, 
+
+    // continue on, we've fixed the record if the db_id did not match,
     // we can now perform and updated if we need to.
   }
-  
+
   // get the CVterm record
   $result = chado_query($cvtermsql, array(':accession' => $accession, ':name' => $dbname));
   $cvterm = $result->fetchObject();
@@ -697,13 +694,13 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
         "$name (id: $accession), for database $dbname", NULL, WATCHDOG_WARNING);
       return 0;
     }
-    
+
     // check to see if the dbxref already has an entry in the cvterm table
     // this is the second constraint in the cvterm table
     $values = array('dbxref_id' => $dbxref->dbxref_id);
     $options = array('statement_name' => 'sel_cvterm_db');
     $check = tripal_core_chado_select('cvterm', array('cvterm_id'), $values, $options);
-    if (count($check) == 0) {      
+    if (count($check) == 0) {
       // now add the cvterm
       $ins_values = array(
         'cv_id'                => $cv->cv_id,
@@ -711,7 +708,7 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
         'definition'           => $definition,
         'dbxref_id'            => $dbxref->dbxref_id,
         'is_obsolete'          => $is_obsolete,
-        'is_relationshiptype'  => $is_relationship, 
+        'is_relationshiptype'  => $is_relationship,
       );
       $ins_options = array('statement_name' => 'ins_cvterm_all');
       $success = tripal_core_chado_insert('cvterm', $ins_values, $ins_options);
@@ -726,32 +723,32 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
         }
       }
     }
-    // this dbxref already exists in the cvterm table 
+    // this dbxref already exists in the cvterm table
     else {
       watchdog('tripal_cv', "The dbxref already exists for another cvterm record: $name (cv: " . $cvname . " db: $dbname)", NULL, WATCHDOG_WARNING);
       return 0;
-    } 
+    }
     $result = chado_query($cvtermsql, array(':accession' => $accession, ':name' => $dbname));
     $cvterm = $result->fetchObject();
   }
   // upate the cvterm
-  elseif ($update) { 
+  elseif ($update) {
     $match = array('cvterm_id' => $cvterm->cvterm_id);
     $upd_values = array(
       'name'                => $name,
       'definition'          => $definition,
       'is_obsolete'         => $is_obsolete,
-      'is_relationshiptype' => $is_relationship, 
+      'is_relationshiptype' => $is_relationship,
     );
     $upd_options = array('statement_name' => 'upd_cvterm_nadeisis');
-    $success = tripal_core_chado_update('cvterm', $match, $upd_values, $upd_options);    
+    $success = tripal_core_chado_update('cvterm', $match, $upd_values, $upd_options);
     if (!$success) {
       watchdog('tripal_cv', "Failed to update the term: $name", NULL, WATCHDOG_WARNING);
       return 0;
     }
     $result = chado_query($cvtermsql, array(':accession' => $accession, ':name' => $dbname));
     $cvterm = $result->fetchObject();
-  } 
+  }
   else {
      // do nothing, we have the cvterm but we don't want to update
   }
@@ -769,7 +766,7 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
  * this is the first time the ontology has been provided to Tripal
  * then it will be added to the database and will be assigned a
  * unique OBO ID.
- * 
+ *
  * @param $obo_id
  *   If the ontology is already loaded into the Tripal tables then
  *   use this argument to specify the unique ID for the ontology
@@ -782,11 +779,11 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
  *   use this argument to provide the URL.
  * @param $obo_file
  *   If the OBO is housed on the local file system of the server then
- *   use this argument to specify the full path.  
- *   
+ *   use this argument to specify the full path.
+ *
  * @return
  *   returns the job_id of the submitted job or FALSE if the job was not added
- *   
+ *
  * @ingroup tripal_cv_api
  */
 
@@ -796,7 +793,7 @@ function tripal_cv_submit_obo_job($obo_id = NULL, $obo_name = NULL, $obo_url = N
   if ($obo_id) {
     $sql = "SELECT * FROM {tripal_cv_obo} WHERE obo_id = :obo_id";
     $obo = db_query($sql, array(':obo_id' => $obo_id))->fetchObject();
-        
+
     $args = array($obo_id);
     return tripal_add_job("Load OBO $obo->name", 'tripal_cv',
        "tripal_cv_load_obo_v1_2_id", $args, $user->uid);
@@ -818,15 +815,15 @@ function tripal_cv_submit_obo_job($obo_id = NULL, $obo_name = NULL, $obo_url = N
 
 /**
  * Add the obo to the tripal_cv_obo table in the Drupal database
- * 
+ *
  * @param $name
  * The human readable name of this ontology
  * @param $path
  * The file path or URL of the ontology
- * 
+ *
  * @return
  * Returns the ontology ID
- * 
+ *
  * @ingroup tripal_cv_api
  */
 function tripal_cv_add_obo_ref($name, $path) {
@@ -834,35 +831,35 @@ function tripal_cv_add_obo_ref($name, $path) {
   $record->name = $name;
   $record->path = $path;
   drupal_write_record('tripal_cv_obo', $record);
-  return $record->obo_id;  
+  return $record->obo_id;
 }
 
 /**
  * This function is intended to be used in autocomplete forms
  * for searching for CV terms that begin with the provided string
- * 
+ *
  * @param $cv_id
  * The CV ID in which to search for the term
  * @param $string
  * The string to search for
- * 
+ *
  * @return
  * A json array of terms that begin with the provided string
- *  
+ *
  * @ingroup tripal_cv_api
  */
 function tripal_cv_cvterm_name_autocomplete($cv_id, $string = '') {
   $sql = "
-    SELECT cvterm_id, name 
-    FROM {cvterm} 
-    WHERE cv_id = :cv_id and name like :name 
-    ORDER by name 
+    SELECT cvterm_id, name
+    FROM {cvterm}
+    WHERE cv_id = :cv_id and name like :name
+    ORDER by name
     LIMIT 25 OFFSET 0
   ";
   $results = chado_query($sql, array(':cv_id' => $cv_id, ':name' => $string . '%'));
   $items = array();
   foreach ($results as $term) {
      $items[$term->name] = $term->name;
-  }  
-  drupal_json_output($items);   
+  }
+  drupal_json_output($items);
 }

tripal_cv/tripal_cv.module

@@ -1,5 +1,14 @@
 <?php
 
+/**
+ * @defgroup tripal_cv Controlled Vocabulary Module
+ * @ingroup tripal_modules
+ * @{
+ * Provides functions for managing chado controlled vocabularies which are used ubiquitously
+ * throughout chado.
+ * @}
+ */
+
 require_once "includes/charts.inc";
 require_once "includes/trees.inc";
 require_once "includes/obo_loader.inc";
@@ -13,11 +22,6 @@ require_once "includes/tripal_cv_admin.inc";
 
 require_once "api/tripal_cv.schema.api.inc";
 
-/**
- * @defgroup tripal_cv CV Module
- * @ingroup tripal_modules
- */
-
 /**
  * Implements hook_init().
  * Adds CSS and JS needed for this modules rendered content
@@ -75,7 +79,7 @@ function tripal_cv_menu() {
     'access arguments' => array('administer controlled vocabularies'),
     'type' => MENU_CALLBACK,
   );
-  
+
   $items['admin/tripal/loaders/obo_loader'] = array(
     'title' => 'Load Ontology',
     'description' => 'Load an Ontology into chado as a controlled vocabulary.',

tripal_db/api/tripal_db.api.inc

@@ -1,11 +1,12 @@
 <?php
 
 /**
- * @file
- * Provides an application programming interface (API) to manage references to external databases
- *
- * @defgroup tripal_db_api DB Module API
+
+ * @defgroup tripal_db_api Database Reference API
  * @ingroup tripal_api
+ * @{
+ * Provides an application programming interface (API) to manage references to external databases
+ * @}
  */
 
 /**

tripal_db/tripal_db.module

@@ -4,8 +4,15 @@ require_once "api/tripal_db.api.inc";
 require_once "includes/tripal_db.admin.inc";
 
 /**
- * @defgroup tripal_db DB Module
+ * @defgroup tripal_db Database Reference Module
  * @ingroup tripal_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,
+ * you might have a feature record in your site which is also in the NCBI website and by
+ * adding a database refrence to your feature, an automatic link to the content at NCBI
+ * is created.
+ * @}
  */
 
 /**

tripal_feature/api/tripal_feature.api.inc

@@ -1,10 +1,10 @@
 <?php
 /**
- * @file
- * Provides an application programming interface (API) for working with features
- *
- * @defgroup tripal_feature_api Feature Module API
+ * @defgroup tripal_feature_api Feature API
  * @ingroup tripal_api
+ * @{
+ * Provides an application programming interface (API) for working with features
+ * @}
  */
 
 /**
@@ -111,7 +111,7 @@ function tripal_feature_analysis_insert_property($analysis_id = NULL, $feature_i
   if (!$success) {
      watchdog('tripal_feature',
       'tripal_feature_analysis_insert_property: Failed to insert analysis feature property',
-       array(), WATCHDOG_WARNING);  
+       array(), WATCHDOG_WARNING);
      return FALSE;
   }
   return $success;
@@ -437,7 +437,7 @@ function tripal_feature_reverse_complement($sequence) {
   return strtoupper($seq);
 }
 /**
- * Retrieves the sequence for a feature.  
+ * Retrieves the sequence for a feature.
  *
  * @param $feature_id
  *   The feature_id of the feature for which the sequence will be retrieved
@@ -450,11 +450,11 @@ function tripal_feature_reverse_complement($sequence) {
  *   Set to '1' if the sequence should be obtained from the parent to which
  *   this feature is aligned.
  * @param $aggregate
- *   Set to '1' if the sequence should only contain sub features, excluding 
+ *   Set to '1' if the sequence should only contain sub features, excluding
  *   intra sub feature sequence.  For example, set this option to obtain just
  *   the coding sequence of an mRNA.
  * @param $output_format
- *   The type of format.  Valid formats include 'fasta_html', 'fasta_txt' and 
+ *   The type of format.  Valid formats include 'fasta_html', 'fasta_txt' and
  *   'raw'.  The format 'fasta_txt' outputs line
  *   breaks as <br> tags and the entire return value is in a <span> tag
  *   with a fixed-width font definition.  'fasta_txt' outputs line breaks with
@@ -464,38 +464,38 @@ function tripal_feature_reverse_complement($sequence) {
  * @param $upstream
  *   An integer specifing the number of upstream bases to include in the output
  * @param $downstream
- *   An integer specifying the number of downstream bases to include in the 
+ *   An integer specifying the number of downstream bases to include in the
  *   output.
  * @param $sub_features
- *   Only include sub features (or child features) of the types provided in the array 
+ *   Only include sub features (or child features) of the types provided in the array
  * @param $relationship
  *   If a relationship name is provided (e.g. sequence_of) then any sequences that
  *   are in relationships of this type with matched sequences are also included
  * @param $rel_part
  *   If a relationship is provided in the preceeding argument then the rel_part
- *   must be either 'object' or 'subject' to indicate which side of the 
+ *   must be either 'object' or 'subject' to indicate which side of the
  *   relationship the matched features belong
- *      
+ *
  * @return
  *   The DNA/protein sequence formated as requested.
  *
  * @ingroup tripal_feature_api
  */
-function tripal_feature_get_formatted_sequence($feature_id, $feature_name, 
+function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
   $num_bases_per_line, $derive_from_parent, $aggregate, $output_format,
   $upstream, $downstream, $sub_features = array(), $relationship = '', $rel_part = '') {
-  
+
   // to speed things up we need to make sure we have a persistent connection
-  $connection = tripal_db_persistent_chado(); 
-  
+  $connection = tripal_db_persistent_chado();
+
   if (!$upstream) {
      $upstream = 0;
   }
   if (!$downstream) {
      $downstream = 0;
   }
-  
-  if ($rel_part == "object" or $rel_part == "subject") { 
+
+  if ($rel_part == "object" or $rel_part == "subject") {
     if ($rel_part == "subject") {
       $psql = '
         PREPARE feature_rel_get_object (int, text) AS
@@ -506,17 +506,17 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
           INNER JOIN feature FO              ON FO.feature_id   = FR.object_id
           INNER JOIN cvterm CVTO             ON CVTO.cvterm_id  = FO.type_id
           INNER JOIN organism O              ON O.organism_id   = FO.organism_id
-        WHERE 
+        WHERE
           FS.feature_id = $1 AND
           CVTFR.name    = $2
-      ';  
+      ';
       $status = tripal_core_chado_prepare('feature_rel_get_object', $psql, array('int', 'text'));
       if (!$status) {
-        watchdog('tripal_feature', "init: not able to prepare SQL statement '%name'", 
+        watchdog('tripal_feature', "init: not able to prepare SQL statement '%name'",
           array('%name' => 'feature_by_subject'), 'WATCHDOG ERROR');
-      }    
+      }
       $sql = "EXECUTE feature_rel_get_object(:feature_id, :relationship)";
-      $features = chado_query($sql, array(':feature_id' => $feature_id, ':relationship' => $relationship)); 
+      $features = chado_query($sql, array(':feature_id' => $feature_id, ':relationship' => $relationship));
     }
     if ($rel_part == "object") {
       $psql = '
@@ -528,20 +528,20 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
           INNER JOIN feature FS              ON FS.feature_id   = FR.subject_id
           INNER JOIN cvterm CVTO             ON CVTO.cvterm_id  = FS.type_id
           INNER JOIN organism O              ON O.organism_id   = FS.organism_id
-        WHERE 
+        WHERE
           FO.feature_id = $1 AND
           CVTFR.name    = $2
       ';
       $status = tripal_core_chado_prepare('feature_rel_get_subject', $psql, array('int', 'text'));
       if (!$status) {
-        watchdog('tripal_feature', "init: not able to prepare SQL statement '%name'", 
+        watchdog('tripal_feature', "init: not able to prepare SQL statement '%name'",
           array('%name' => 'feature_by_object'), 'WATCHDOG ERROR');
       }
       $sql = "EXECUTE feature_rel_get_subject(:feature_id, :relationship)";
-      $features = chado_query($sql, array(':feature_id' => $feature_id, ':relationship' => $relationship));     
+      $features = chado_query($sql, array(':feature_id' => $feature_id, ':relationship' => $relationship));
     }
     $sequences = '';
-    while ($feature = $features->fetchObject()) {  
+    while ($feature = $features->fetchObject()) {
 
       // recurse and get the sequences for these in the relationship
       if ($rel_part == "subject") {
@@ -550,99 +550,99 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
       if ($rel_part == "object") {
         $defline = "$feature->uniquename $feature->feature_type ($feature->genus $feature->species), $relationship, $feature_name";
       }
-      $sequences .= tripal_feature_get_formatted_sequence($feature->feature_id, $defline, 
+      $sequences .= tripal_feature_get_formatted_sequence($feature->feature_id, $defline,
         $num_bases_per_line, $derive_from_parent, $aggregate, $output_format,
-        $upstream, $downstream, $sub_features, '', '');  
-    }  
-    return $sequences;  
+        $upstream, $downstream, $sub_features, '', '');
+    }
+    return $sequences;
   }
-  
+
   // prepare statements we'll need to use later
   if (!tripal_core_is_sql_prepared('sequence_by_parent')) {
     // prepare the queries we're going to use later during the render phase
     // This SQL statement uses conditionals in the select clause to handle
     // cases cases where the alignment is in the reverse direction and when
-    // the upstream and downstream extensions go beyond the lenght of the 
+    // the upstream and downstream extensions go beyond the lenght of the
     // parent sequence.
     $psql ='
-      PREPARE sequence_by_parent (int, int, int) AS 
+      PREPARE sequence_by_parent (int, int, int) AS
       SELECT srcname, srcfeature_id, strand, srctypename, typename,
-        fmin, fmax, upstream, downstream, adjfmin, adjfmax, 
+        fmin, fmax, upstream, downstream, adjfmin, adjfmax,
         substring(residues from (adjfmin + 1) for (upstream + (fmax - fmin) + downstream))  as residues,
         genus, species
       FROM (
         SELECT
-          OF.name srcname, FL.srcfeature_id, FL.strand, 
+          OF.name srcname, FL.srcfeature_id, FL.strand,
           OCVT.name as srctypename, SCVT.name as typename,
           FL.fmin, FL.fmax, OO.genus, OO.species,
-          CASE 
-            WHEN FL.strand >= 0 THEN 
-              CASE 
+          CASE
+            WHEN FL.strand >= 0 THEN
+              CASE
                  WHEN FL.fmin - $1 <= 0 THEN 0
                  ELSE FL.fmin - $1
               END
             WHEN FL.strand < 0 THEN
-              CASE 
+              CASE
                  WHEN FL.fmin - $2 <= 0 THEN 0
                  ELSE FL.fmin - $2
-              END                   
-          END as adjfmin,                                                                
-          CASE 
+              END
+          END as adjfmin,
+          CASE
             WHEN FL.strand >= 0 THEN
-              CASE 
-                WHEN FL.fmax + $2 > OF.seqlen THEN OF.seqlen 
+              CASE
+                WHEN FL.fmax + $2 > OF.seqlen THEN OF.seqlen
                 ELSE FL.fmax + $2
               END
             WHEN FL.strand < 0 THEN
               CASE
                 WHEN FL.fmax + $1 > OF.seqlen THEN OF.seqlen
-                ELSE FL.fmax + $1   
-              END               
-          END as adjfmax,                     
-          CASE 
-            WHEN FL.strand >= 0 THEN 
-              CASE 
+                ELSE FL.fmax + $1
+              END
+          END as adjfmax,
+          CASE
+            WHEN FL.strand >= 0 THEN
+              CASE
                  WHEN FL.fmin - $1 <= 0 THEN FL.fmin
                  ELSE $1
               END
             ELSE
-              CASE 
+              CASE
                  WHEN FL.fmax + $1 > OF.seqlen THEN OF.seqlen - FL.fmax
                  ELSE $1
-              END                   
-          END as upstream,                
-          CASE 
-            WHEN FL.strand >= 0 THEN 
-              CASE 
+              END
+          END as upstream,
+          CASE
+            WHEN FL.strand >= 0 THEN
+              CASE
                  WHEN FL.fmax + $2 > OF.seqlen THEN OF.seqlen - FL.fmax
                  ELSE $2
               END
             ELSE
-              CASE 
+              CASE
                  WHEN FL.fmin - $2 <= 0 THEN FL.fmin
                  ELSE $2
-              END                   
-          END as downstream,  
-          OF.residues                                                     
-        FROM {featureloc} FL 
+              END
+          END as downstream,
+          OF.residues
+        FROM {featureloc} FL
           INNER JOIN {feature} SF   on FL.feature_id    = SF.feature_id
           INNER JOIN {cvterm}  SCVT on SF.type_id       = SCVT.cvterm_id
-          INNER JOIN {feature} OF   on FL.srcfeature_id = OF.feature_id                
+          INNER JOIN {feature} OF   on FL.srcfeature_id = OF.feature_id
           INNER JOIN {cvterm}  OCVT on OF.type_id       = OCVT.cvterm_id
           INNER JOIN {organism} OO  on OF.organism_id   = OO.organism_id
         WHERE SF.feature_id = $3 and NOT (OF.residues = \'\' or OF.residues IS NULL)) as tbl1
-    ';              
+    ';
     $status = tripal_core_chado_prepare('sequence_by_parent', $psql, array('int', 'int', 'int'));
     if (!$status) {
-      watchdog('tripal_feature', 
-        "init: not able to prepare SQL statement '%name'", 
+      watchdog('tripal_feature',
+        "init: not able to prepare SQL statement '%name'",
         array('%name' => 'sequence_by_parent'), 'WATCHDOG ERROR');
     }
-    
+
     // this query is meant to get all of the sub features of any given
     // feature (arg #1) and order them as they appear on the reference
     // feature (arg #2).
-    $psql ='PREPARE sub_features (int, int) AS 
+    $psql ='PREPARE sub_features (int, int) AS
             SELECT SF.feature_id, CVT.name as type_name, SF.type_id
             FROM {feature_relationship} FR
               INNER JOIN {feature} SF on SF.feature_id = FR.subject_id
@@ -650,50 +650,50 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
               INNER JOIN {featureloc} FL on FL.feature_id = FR.subject_id
               INNER JOIN {feature} PF on PF.feature_id = FL.srcfeature_id
             WHERE FR.object_id = $1 and PF.feature_id = $2
-            ORDER BY FL.fmin ASC';            
+            ORDER BY FL.fmin ASC';
     $status = tripal_core_chado_prepare('sub_features', $psql, array('int', 'int'));
     if (!$status) {
-      watchdog('tripal_views_handler_field_sequence', 
-        "init: not able to prepare SQL statement '%name'", 
+      watchdog('tripal_views_handler_field_sequence',
+        "init: not able to prepare SQL statement '%name'",
         array('%name' => 'ssub_features'), 'WATCHDOG ERROR');
     }
-    $psql ='PREPARE count_sub_features (int, int) AS 
+    $psql ='PREPARE count_sub_features (int, int) AS
             SELECT count(*) as num_children
             FROM {feature_relationship} FR
               INNER JOIN {feature} SF on SF.feature_id = FR.subject_id
               INNER JOIN {cvterm} CVT on CVT.cvterm_id = SF.type_id
               INNER JOIN {featureloc} FL on FL.feature_id = FR.subject_id
               INNER JOIN {feature} PF on PF.feature_id = FL.srcfeature_id
-            WHERE FR.object_id = $1 and PF.feature_id = $2';            
+            WHERE FR.object_id = $1 and PF.feature_id = $2';
     $status = tripal_core_chado_prepare('count_sub_features', $psql, array('int', 'int'));
     if (!$status) {
-      watchdog('tripal_views_handler_field_sequence', 
-        "init: not able to prepare SQL statement '%name'", 
+      watchdog('tripal_views_handler_field_sequence',
+        "init: not able to prepare SQL statement '%name'",
         array('%name' => 'count_sub_features'), 'WATCHDOG ERROR');
     }
   }
-    
+
   // if we need to get the sequence from the parent then do so now.
-  if ($derive_from_parent) {                  
-    
+  if ($derive_from_parent) {
+
     // execute the query to get the sequence from the parent
     $sql = "EXECUTE sequence_by_parent (:upstream, :downstream, :feature_id)";
     $parents = chado_query($sql, array(':uptream' => $upstream, ':downstream' => $downstream, ':feature_id' => $feature_id));
 
-    while ($parent = $parents->fetchObject()) {  
+    while ($parent = $parents->fetchObject()) {
       $seq = '';  // initialize the sequence for each parent
 
       // if we are to aggregate then we will ignore the feature returned
       // by the query above and rebuild it using the sub features
       if ($aggregate) {
-        
+
         // now get the sub features that are located on the parent.
         $sql = "EXECUTE sub_features (:feature_id, :srcfeature_id)";
         $children = chado_query($sql, array(':feature_id' => $feature_id, ':srcfeature_id' => $parent->srcfeature_id));
         $sql = "EXECUTE count_sub_features (:feature_id, :srcfeature_id)";
         $sub_features = chado_query($sql, array(':feature_id' => $feature_id, ':srcfeature_id' => $parent->srcfeature_id));
         $num_children = $sub_features->fetchObject();
-               
+
         // iterate through the sub features and concat their sequences. They
         // should already be in order.
         $types = array();
@@ -705,20 +705,20 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
           if (count($sub_features) > 0 and !in_array($child->type_name, $sub_features)) {
              continue;
           }
-        
+
           // keep up with the types
           if (!in_array($child->type_name, $types)) {
             $types[] = $child->type_name;
           }
-          
+
           $sql = "EXECUTE sequence_by_parent (:upstream, %d, :feature_id)";
 
-          // if the first sub feature we need to include the upstream bases. first check if 
+          // if the first sub feature we need to include the upstream bases. first check if
           // the feature is in the foward direction or the reverse.
           if ($i == 0 and $parent->strand >= 0) {  // forward direction
             // -------------------------- ref
-            //    ....---->  ---->        
-            //     up    1       2         
+            //    ....---->  ---->
+            //     up    1       2
             $q = chado_query($sql, array(':upstream' => $upstream, ':downstream' => 0, ':feature_id' => $child->feature_id));
           }
           elseif ($i == 0 and $parent->strand < 0) { // reverse direction
@@ -727,7 +727,7 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
             //    down  1       2
             $q = chado_query($sql, array(':upstream' => 0, ':downstream' => $downstream, ':feature_id' => $child->feature_id));
           }
-                    
+
           // Next, if the last sub feature we need to include the downstream bases. first check if
           // the feature is in teh forward direction or the reverse
           if ($i == $num_children->num_children - 1 and $parent->strand >= 0) {  // forward direction
@@ -742,38 +742,38 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
             //          1       2  up
             $q = chado_query($sql, array(':upstream' => $upstream, ':downstream' => 0, ':feature_id' => $child->feature_id));
           }
-          
+
           // for internal sub features we don't want upstream or downstream bases
-          else {         
+          else {
             $sql = "EXECUTE sequence_by_parent (%d, %d, %d)";
             $q = chado_query($sql, array(':upstream' => 0, ':downstream' => 0, ':feature_id' => $child->feature_id));
           }
-          
+
           while ($subseq = $q->fetchObject()) {
-            // concatenate the sequences of all the sub features            
+            // concatenate the sequences of all the sub features
             if ($subseq->srcfeature_id == $parent->srcfeature_id) {
-              $seq .= $subseq->residues;   
+              $seq .= $subseq->residues;
             }
-          }                 
+          }
           $i++;
-        } 
-      } 
+        }
+      }
       // if this isn't an aggregate then use the parent residues
       else {
          $seq = $parent->residues;
       }
-                            
+
       // get the reverse compliment if feature is on the reverse strand
       $dir = 'forward';
       if ($parent->strand < 0) {
         $seq = tripal_feature_reverse_complement($seq);
         $dir = 'reverse';
       }
-      
+
       // now format for display
       if ($output_format == 'fasta_html') {
          $seq = wordwrap($seq, $num_bases_per_line, "<br>", TRUE);
-      } 
+      }
       elseif ($output_format == 'fasta_txt') {
          $seq = wordwrap($seq, $num_bases_per_line, "\r\n", TRUE);
       }
@@ -788,19 +788,19 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
          $residues .= "Includes " . $parent->downstream . " bases downstream.  ";
       }
       if (!$seq) {
-        
+
         if ($output_format == 'fasta_html') {
-          $residues .= "No sequence available.</br>"; 
-        } 
+          $residues .= "No sequence available.</br>";
+        }
         else {
-          $residues .= "No sequence available.\r\n"; 
-        }         
+          $residues .= "No sequence available.\r\n";
+        }
       }
       else {
         if ($output_format == 'fasta_html') {
           $residues .= "<br>";
         }
-        $residues .= "\r\n" . $seq . "\r\n";          
+        $residues .= "\r\n" . $seq . "\r\n";
         if ($output_format == 'fasta_html') {
           $residues .= "<br>";
         }
@@ -810,18 +810,18 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
   // if we are not getting the sequence from the parent sequence then
   // use what comes through from the feature record
   else {
-    $sql = "SELECT * FROM {feature} F WHERE feature_id = :feature_id"; 
+    $sql = "SELECT * FROM {feature} F WHERE feature_id = :feature_id";
     $values = chado_query($sql, array(':feature_id' => $feature_id))->fetchObject();
     $residues = $values->residues;
     if ($output_format == 'fasta_html') {
-       $residues = wordwrap($residues, $num_bases_per_line, "<br>", TRUE);  
-    } 
+       $residues = wordwrap($residues, $num_bases_per_line, "<br>", TRUE);
+    }
     elseif ($output_format == 'fasta_txt') {
-       $residues = wordwrap($residues, $num_bases_per_line, "\r\n", TRUE);  
+       $residues = wordwrap($residues, $num_bases_per_line, "\r\n", TRUE);
     }
     $residues = ">$feature_name\r\n$residues\r\n";
   }
-  
+
   // format the residues for display
   if ($residues and $num_bases_per_line) {
     if ($output_format == 'fasta_html') {
@@ -837,34 +837,34 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
  * This function adds an entry to the feature_dbxref table.
   *
  * @param $feature_id
- *   The numeric feature_if of the feature 
+ *   The numeric feature_if of the feature
  * @param $dbname
  *   The name of the database to which the term belongs
  * @param accession
- *   The accession of the term   
- *    
+ *   The accession of the term
+ *
  * @return
  *   TRUE on success. FALSE on failure.
  *
  * @ingroup tripal_feature_api
  */
 function tripal_feature_add_dbxref($feature_id, $dbname, $accession) {
-   
+
   // make sure the db exists. If it doesn't, then add it
   $values = array('name' => $dbname);
   $options = array('statement_name' => 'sel_db_na');
   $db = tripal_core_chado_select('db', array('db_id'), $values, $options);
-  if (!$db or count($db) == 0) {    
+  if (!$db or count($db) == 0) {
     $options = array('statement_name' => 'ins_db_na');
     $success = tripal_core_chado_insert('db', $values, $options);
       if (!$success) {
-      watchdog('tripal_feature', 'tripal_feature_add_dbxref: The feature dbxref entry for feature, %feature_id, " . 
-        "could not be added because the database, %dbname, does not exist and cannot be added.', 
+      watchdog('tripal_feature', 'tripal_feature_add_dbxref: The feature dbxref entry for feature, %feature_id, " .
+        "could not be added because the database, %dbname, does not exist and cannot be added.',
         array('%feature_id' => $feature_id, '%dbname' => $dbname), WATCHDOG_WARNING);
       return FALSE;
     }
   }
-  
+
   // first make sure that the record doesn't already exist
   $values = array(
     'dbxref_id' => array(
@@ -877,13 +877,13 @@ function tripal_feature_add_dbxref($feature_id, $dbname, $accession) {
   );
   $options = array('statement_name' => 'sel_featuredbxref_dbfe');
   $xref = tripal_core_chado_select('feature_dbxref', array('feature_dbxref_id'), $values, $options);
-  if (count($xref) == 0) {    
+  if (count($xref) == 0) {
     // if the record doesn't exist then add it.
     $options = array('statement_name' => 'ins_featuredbxref_dbfe');
     $success = tripal_core_chado_insert('feature_dbxref', $values, $options);
     if (!$success) {
-      watchdog('tripal_feature', 'tripal_feature_add_dbxref: The feature dbxref entry for feature, %feature_id, ' . 
-        'could not be added: %db:%accession.', array('%feature_id' => $feature_id, '%db' => $dbname, 
+      watchdog('tripal_feature', 'tripal_feature_add_dbxref: The feature dbxref entry for feature, %feature_id, ' .
+        'could not be added: %db:%accession.', array('%feature_id' => $feature_id, '%db' => $dbname,
         '%accession' => $accession), WATCHDOG_WARNING);
       return FALSE;
     }
@@ -895,34 +895,34 @@ function tripal_feature_add_dbxref($feature_id, $dbname, $accession) {
  * This function adds an entry to the feature_cvterm table.
   *
  * @param $feature_id
- *   The numeric feature_if of the feature 
+ *   The numeric feature_if of the feature
  * @param $cvname
  *   The name of the controlled vocabulary to which the term belongs
  * @param cvterm
- *   The name of the cvterm  
- *    
+ *   The name of the cvterm
+ *
  * @return
  *   TRUE on success. FALSE on failure.
  *
  * @ingroup tripal_feature_api
  */
 function tripal_feature_add_cvterm($feature_id, $cvname, $cvterm) {
-   
+
   // make sure the cv exists. If it doesn't, then add it
   $values = array('name' => $cvname);
   $options = array('statement_name' => 'sel_cv_na');
   $cv = tripal_core_chado_select('cv', array('cv_id'), $values, $options);
-  if (!$cv or count($cv) == 0) {    
+  if (!$cv or count($cv) == 0) {
     $options = array('statement_name' => 'ins_cv_na');
     $success = tripal_core_chado_insert('cv', $values, $options);
       if (!$success) {
-      watchdog('tripal_feature', 'tripal_feature_add_cvterm: The feature cvterm entry for feature, %feature_id, " . 
-        "could not be added because the CV, %cvname, does not exist and cannot be added.', 
+      watchdog('tripal_feature', 'tripal_feature_add_cvterm: The feature cvterm entry for feature, %feature_id, " .
+        "could not be added because the CV, %cvname, does not exist and cannot be added.',
         array('%feature_id' => $feature_id, '%cvname' => $cvname), WATCHDOG_WARNING);
       return FALSE;
     }
   }
-  
+
   // first make sure that the record doesn't already exist
   $values = array(
     'cvterm_id' => array(
@@ -936,12 +936,12 @@ function tripal_feature_add_cvterm($feature_id, $cvname, $cvterm) {
   );
   $options = array('statement_name' => 'sel_featuredcvterm_cvfepu');
   $xref = tripal_core_chado_select('feature_cvterm', array('feature_cvterm_id'), $values, $options);
-  if (count($xref) == 0) {    
+  if (count($xref) == 0) {
     // if the record doesn't exist then add it.
     $options = array('statement_name' => 'ins_featurecvterm_cvfepu');
     $success = tripal_core_chado_insert('feature_cvterm', $values, $options);
     if (!$success) {
-      watchdog('tripal_feature', 'tripal_feature_add_cvterm: The feature cvterm entry for feature, %feature_id, ' . 
+      watchdog('tripal_feature', 'tripal_feature_add_cvterm: The feature cvterm entry for feature, %feature_id, ' .
         'could not be added: %cvterm.', array('%feature_id' => $feature_id, '%cvterm' => $cvterm), WATCHDOG_WARNING);
       return FALSE;
     }

tripal_feature/tripal_feature.module

@@ -1,10 +1,5 @@
 <?php
 
-/**
- * @file
- * @todo Add file header description
- */
-
 /**
  * @defgroup tripal_feature Feature Module
  * @ingroup tripal_modules

tripal_featuremap/api/tripal_featuremap.api.inc

@@ -1,5 +1,13 @@
 <?php
 
+/**
+ * @defgroup tripal_featuremap_api Feature Map API
+ * @ingroup tripal_api
+ * @{
+ * Provides an application programming interface (API) to manage chado feature maps
+ * @}
+ */
+
 /**
  * Retrieve properties of a given type for a given featuremap
  *
@@ -117,7 +125,7 @@ function tripal_featuremap_add_featuremap_dbxref($featuremap_id, $featuremap_dbx
 
   // make sure our database already exists
   $db = tripal_db_add_db($dbname);
-   
+
   // get the database cross-reference
   $dbxvalues = array(
     'accession' => $accession,

tripal_genetic/tripal_genetic.module

@@ -1,15 +1,11 @@
 <?php
 
 /**
- *  @file
- * This file contains the basic functions needed for this drupal module.
- * The drupal tripal_genetic module maps directly to the chado X module.
- *
- * For documentation regarding the Chado X module:
- * @see http://gmod.org/wiki/Chado_General_Module
- *
  * @defgroup tripal_genetic Genetic Module
  * @ingroup tripal_modules
+ * @{
+ * Provides functions for managing chado genetic data
+ * @}
  */
 
 require('api/tripal_genetic.api.inc');
@@ -77,7 +73,7 @@ function tripal_genetic_views_api() {
  */
 function tripal_genetic_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
-    
+
   $items = array(
     'tripal_feature_genotypes' => array(
       'variables' => array('node' => NULL),
@@ -104,7 +100,7 @@ function tripal_genetic_theme($existing, $type, $theme, $path) {
  * @ingroup tripal_genetic
  */
 function tripal_genetic_node_view($node, $view_mode, $langcode) {
-  
+
   if ($node->type == 'chado_feature') {
     if ($view_mode == 'full') {
       // the tripal_natural_diversity module provides a tripal_feature_nd_genotype

tripal_library/api/tripal_library.api.inc

@@ -1,10 +1,10 @@
 <?php
 /**
- * @file
- * Provides an application programming interface (API) to manage libraries
- *
- * @defgroup tripal_library_api Library Module API
+ * @defgroup tripal_library_api Library API
  * @ingroup tripal_api
+ * @{
+ * Provides an application programming interface (API) to manage libraries
+ * @}
  */
 
 /**

tripal_natural_diversity/tripal_natural_diversity.module

@@ -5,15 +5,11 @@ require_once('theme/tripal_natural_diversity.theme.inc');
 require_once('includes/tripal_natural_diversity.schema.inc');
 require_once('includes/tripal_natural_diversity.admin.inc');
 /**
- *  @file
- * This file contains the basic functions needed for this drupal module.
- * The drupal tripal_natural_diversity module maps directly to the chado X module.
- *
- * For documentation regarding the Chado X module:
- * @see http://gmod.org/wiki/Chado_General_Module
- *
  * @defgroup tripal_natural_diversity Natural Diversity Module
  * @ingroup tripal_modules
+ * @{
+ * Provides functions for managing chado natural diversity data
+ * @}
  */
 
 /**
@@ -77,7 +73,7 @@ function tripal_natural_diversity_views_api() {
  */
 function tripal_natural_diversity_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
-  
+
   $items = array(
     // tripal_feature templates
     'tripal_feature_nd_genotypes' => array(
@@ -159,7 +155,7 @@ function tripal_natural_diversity_node_view($node, $view_mode, $langcode) {
       if ($view_mode == 'full') {
         // the tripal_genetic module provides a tripal_feature_genotype
         // template. if the tripal_genetic content is present get rid of it as this
-        // module superceeds it.      
+        // module superceeds it.
         if (array_key_exists('tripal_feature_genotypes', $node->content)) {
           unset($node->content['tripal_feature_genotypes']);
         }

tripal_organism/api/tripal_organism.api.inc

@@ -1,11 +1,11 @@
 <?php
 
 /**
- * @file
- * Provides an application programming interface (API) to manage organisms
- *
- * @defgroup tripal_library_api Organism Module API
+ * @defgroup tripal_library_api Organism API
  * @ingroup tripal_api
+ * @{
+ * Provides an application programming interface (API) to manage organisms
+ * @}
  */
 
 /**
@@ -69,29 +69,29 @@ function tripal_organism_get_synced() {
 }
 
 /**
- * 
+ *
  * @param $organism
  * @param $nid
  */
 function tripal_organism_get_image_url($organism, $nid = NULL) {
   $url = '';
-  
+
   // first look for an image with the genus/species name.  This is old-style tripal
   // and we keep it for backwards compatibility.  If we don't find that file
   // then look for the image with the node ID in the name. If we don't find that then
-  // no image tag is generated  
+  // no image tag is generated
   $base_path = realpath('.');
   $image_dir = tripal_get_moddir('tripal_organism') . "/images";
   $image_name =  $organism->genus . "_" . $organism->species . ".jpg";
 
-  if (file_exists("$base_path/$image_dir/$image_name")) { 
-    $url = file_create_url("$image_dir/$image_name"); 
-  } 
+  if (file_exists("$base_path/$image_dir/$image_name")) {
+    $url = file_create_url("$image_dir/$image_name");
+  }
   else {
      $image_name = $nid . ".jpg";
-     if (file_exists("$base_path/$image_dir/$image_name")) { 
-       $url = file_create_url("$image_dir/$image_name"); 
-     }  
-  } 
+     if (file_exists("$base_path/$image_dir/$image_name")) {
+       $url = file_create_url("$image_dir/$image_name");
+     }
+  }
   return $url;
 }

tripal_organism/tripal_organism.module

@@ -8,6 +8,9 @@ require_once "includes/tripal_organism.chado_node.inc";
  * @file
  * @defgroup tripal_organism Organism Module
  * @ingroup tripal_modules
+ * @{
+ * Provides functions for managing chado organisms including creating details pages for each one
+ * @}
  */
 
 /**
@@ -88,7 +91,7 @@ function tripal_organism_menu() {
     'access arguments' => array('adminster tripal organism'),
     'type' => MENU_NORMAL_ITEM,
   );
-  
+
   $items['admin/tripal/chado/tripal_organism/help'] = array(
     'title' => 'Help',
     'description' => "A description of the Tripal Organism module including a short description of it's usage.",
@@ -98,7 +101,7 @@ function tripal_organism_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 10
   );
-  
+
   $items['admin/tripal/chado/tripal_organism/configuration'] = array(
     'title' => 'Settings',
     'description' => 'Manage integration of Chado organisms including associated features',
@@ -118,7 +121,7 @@ function tripal_organism_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 2
   );
-  
+
   $items['admin/tripal/chado/tripal_organism/views/organisms/enable'] = array(
     'title' => 'Enable Organism Administrative View',
     'page callback' => 'tripal_views_admin_enable_view',
@@ -126,7 +129,7 @@ function tripal_organism_menu() {
     'access arguments' => array('administer tripal organism'),
     'type' => MENU_CALLBACK,
   );
-  
+
 
   return $items;
 }

tripal_phenotype/tripal_phenotype.module

@@ -1,15 +1,11 @@
 <?php
 
 /**
- *  @file
- * This file contains the basic functions needed for this drupal module.
- * The drupal tripal_phenotype module maps directly to the chado X module.
- *
- * For documentation regarding the Chado X module:
- * @see http://gmod.org/wiki/Chado_General_Module
- *
  * @defgroup tripal_phenotype Phenotype Module
  * @ingroup tripal_modules
+ * @{
+ * Provides functions for managing chado phenotype data
+ * @}
  */
 
 /**

tripal_project/api/tripal_project.api.inc

@@ -7,6 +7,9 @@
 /**
  * @defgroup tripal_project_api Project Module API
  * @ingroup tripal_api
+ * @{
+ * Provides an application programming interface (API) to manage projects
+ * @}
  */
 
 /**

tripal_project/tripal_project.module

@@ -5,15 +5,11 @@ require('includes/tripal_project.admin.inc');
 require('includes/tripal_project.chado_node.inc');
 
 /**
- *  @file
- * This file contains the basic functions needed for this drupal module.
- * The drupal tripal_project module maps directly to the chado general module.
- *
- * For documentation regarding the Chado General module:
- * @see http://gmod.org/wiki/Chado_General_Module
- *
  * @defgroup tripal_project Project Module
  * @ingroup tripal_modules
+ * @{
+ * Provides functions for managing chado projects including creating details pages for each one
+ * @}
  */
 
 /**
@@ -74,7 +70,7 @@ function tripal_project_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 0
   );
-  
+
   $items['admin/tripal/chado/tripal_project/views/projects/enable'] = array(
     'title' => 'Enable Project Administrative View',
     'page callback' => 'tripal_views_admin_enable_view',

tripal_pub/api/tripal_pub.api.inc

@@ -1,10 +1,10 @@
 <?php
 /**
- * @file
- * The Tripal Pub API
- *
  * @defgroup tripal_pub_api Publication Module API
  * @ingroup tripal_api
+ * @{
+ * Provides an application programming interface (API) to manage chado publications
+ * @}
  */
 
 /*
@@ -112,7 +112,7 @@ function tripal_pub_update_publications($do_contact = FALSE, $dbxref = NULL, $db
         INNER JOIN pub_dbxref PDBX ON P.pub_id = PDBX.pub_id
         INNER JOIN dbxref DBX      ON DBX.dbxref_id = PDBX.dbxref_id
         INNER JOIN db DB           ON DB.db_id = DBX.db_id
-    "; 
+    ";
     $args = array();
     if ($dbxref and preg_match('/^(.*?):(.*?)$/', $dbxref, $matches)) {
       $dbname = $matches[1];
@@ -127,18 +127,18 @@ function tripal_pub_update_publications($do_contact = FALSE, $dbxref = NULL, $db
     }
     $sql .= "ORDER BY DB.name, P.pub_id";
     $results = chado_query($sql, $args);
-  
+
     $num_to_retrieve = 100;
     $i = 0;                 // count the number of IDs. When we hit $num_to_retrieve we'll do the query
     $curr_db = '';          // keeps track of the current current database
     $ids = array();         // the list of IDs for the database
     $search = array();      // the search array passed to the search function
-  
+
     // iterate through the pub IDs
     while ($pub = $results->fetchObject()) {
       $accession = $pub->accession;
       $remote_db = $pub->db_name;
-  
+
       // here we need to only update publications for databases we support
       $supported_dbs = variable_get('tripal_pub_supported_dbs', array());
       if(!in_array($remote_db, $supported_dbs)) {
@@ -158,14 +158,14 @@ function tripal_pub_update_publications($do_contact = FALSE, $dbxref = NULL, $db
       );
       $pubs = tripal_pub_get_remote_search_results($remote_db, $search, 1, 0);
       tripal_pub_add_publications($pubs, $do_contact, TRUE);
-  
+
       $i++;
     }
-  
+
     // sync the newly added publications with Drupal
     print "Syncing publications with Drupal...\n";
     tripal_pub_sync_pubs();
-  
+
     // if the caller wants to create contacts then we should sync them
     if ($do_contact) {
       print "Syncing contacts with Drupal...\n";
@@ -249,14 +249,14 @@ function tripal_pub_import_publications_by_import_id($import_id, $job_id = NULL)
 function tripal_pub_import_publications($report_email = FALSE, $do_update = FALSE) {
   $num_to_retrieve = 100;
   $page = 0;
-  
+
   print "\nNOTE: Loading of publications is performed using a database transaction. \n" .
       "If the load fails or is terminated prematurely then the entire set of \n" .
       "insertions/updates is rolled back and will not be found in the database\n\n";
-  
+
   // start the transaction
   $transaction = db_transaction();
-  
+
   try {
     // get all of the loaders
     $args = array();
@@ -284,13 +284,13 @@ function tripal_pub_import_publications($report_email = FALSE, $do_update = FALS
       // our requested numer of records.  This means we've hit the end
       while (count($pubs) == $num_to_retrieve);
     }
-    
+
     // sync the newly added publications with Drupal. If the user
     // requested a report then we don't want to print any syncing information
     // so pass 'FALSE' to the sync call
     print "Syncing publications with Drupal...\n";
     tripal_pub_sync_pubs();
-  
+
     // iterate through each of the reports and generate a final report with HTML links
     $HTML_report = '';
     if ($report_email) {
@@ -315,7 +315,7 @@ function tripal_pub_import_publications($report_email = FALSE, $do_update = FALS
       );
       drupal_mail('tripal_pub', 'import_report', $report_email, language_default(), $params, $site_email, TRUE);
     }
-  
+
     // if any of the importers wanted to create contacts from the authors then sync them
     if($do_contact) {
       print "Syncing contacts with Drupal...\n";
@@ -343,13 +343,13 @@ function tripal_pub_import_by_dbxref($pub_dbxref, $do_contact = FALSE, $do_updat
   print "\nNOTE: Loading of publications is performed using a database transaction. \n" .
       "If the load fails or is terminated prematurely then the entire set of \n" .
       "insertions/updates is rolled back and will not be found in the database\n\n";
-  
+
   $transaction = db_transaction();
   try {
     if(preg_match('/^(.*?):(.*?)$/', $pub_dbxref, $matches)) {
       $dbname = $matches[1];
       $accession = $matches[2];
-  
+
       $criteria = array(
         'num_criteria' => 1,
         'remote_db' => $dbname,
@@ -373,7 +373,7 @@ function tripal_pub_import_by_dbxref($pub_dbxref, $do_contact = FALSE, $do_updat
     // sync the newly added publications with Drupal
     print "Syncing publications with Drupal...\n";
     tripal_pub_sync_pubs();
-  
+
     // if any of the importers wanted to create contacts from the authors then sync them
     if($do_contact) {
       print "Syncing contacts with Drupal...\n";
@@ -387,11 +387,11 @@ function tripal_pub_import_by_dbxref($pub_dbxref, $do_contact = FALSE, $do_updat
         print "FAILED: Rolling back database changes...\n";
       return;
   }
-   
+
   print "Done.\n";
 }
 /**
- * 
+ *
  * @param $pubs
  * @param $do_contact
  * @param $update
@@ -402,13 +402,13 @@ function tripal_pub_add_publications($pubs, $do_contact, $update = FALSE) {
   $report['inserted'] = array();
   $report['skipped'] = array();
   $total_pubs = count($pubs);
-  
+
   // iterate through the publications and add each one
   $i = 1;
   foreach ($pubs as $pub) {
     $memory = number_format(memory_get_usage()) . " bytes";
     print "Processing $i of $total_pubs. Memory usage: $memory.\r";
-     
+
     // add the publication to Chado
     $action = '';
     $pub_id = tripal_pub_add_publication($pub, $action, $do_contact, $update);
@@ -475,7 +475,7 @@ function tripal_pub_add_pub_dbxref($pub_id, $pub_dbxref) {
 
   // make sure our database already exists
   $db = tripal_db_add_db($dbname);
-   
+
   // get the database cross-reference
   $dbxvalues = array(
     'accession' => $accession,
@@ -673,7 +673,7 @@ function tripal_pub_get_pub_by_uniquename($name) {
  */
 function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE, $update_if_exists = FALSE) {
   $pub_id = 0;
-  
+
   if (!is_array($pub_details)) {
     return FALSE;
   }
@@ -717,7 +717,7 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
     }
     elseif (count($results) > 1) {
       watchdog('tripal_pub', "The publication with the same title, type and year is present multiple times. Cannot ".
-        "determine which to use.  Title: '%title'. Type: '%type'. Year: '%year'", 
+        "determine which to use.  Title: '%title'. Type: '%type'. Year: '%year'",
       array('%title' => $pub_details['Title'], '%type' => $pub_details['Publication Type'], '%year' => $pub_details['Year']), WATCHDOG_ERROR);
       $action = 'error';
       return FALSE;
@@ -788,13 +788,13 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
   // is an update.  The only thing we don't want to remove are the 'Publication Dbxref'
   if ($update_if_exists) {
     $sql = "
-      DELETE FROM {pubprop} 
-      WHERE 
-        pub_id = :pub_id AND 
+      DELETE FROM {pubprop}
+      WHERE
+        pub_id = :pub_id AND
         NOT type_id in (
           SELECT cvterm_id
-          FROM {cvterm} 
-          WHERE name = 'Publication Dbxref' 
+          FROM {cvterm}
+          WHERE name = 'Publication Dbxref'
         )
     ";
     chado_query($sql, array(':pub_id' => $pub_id));
@@ -825,7 +825,7 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
     $key == 'Year' or $key == 'Pages') {
       continue;
     }
-     
+
     $success = 0;
     if (is_array($value)) {
       foreach ($value as $subkey => $subvalue) {
@@ -889,7 +889,7 @@ function tripal_pub_add_authors($pub_id, $authors, $do_contact) {
       $type = 'Collective';
     }
     $name = trim($name);
-     
+
     // add an entry to the pubauthors table
     $values = array(
       'pub_id' => $pub_id,
@@ -1010,17 +1010,17 @@ function tripal_pub_delete_property($pub_id, $property) {
 
 
 /**
- * This function generates an array suitable for use with the 
+ * This function generates an array suitable for use with the
  * tripal_pub_create_citation function for any publication
  * already stored in the Chado tables.
- *  
+ *
  * @param $pub_id
  *   The publication ID
  * @param $skip_existing
  *   Set to TRUE to skip publications that already have a citation
- *   in the pubprop table.  Set to FALSE to generate a citation 
+ *   in the pubprop table.  Set to FALSE to generate a citation
  *   regardless if the citation already exists.
- *   
+ *
  * @return
  *   An array suitable for the trpial_pub_create_citation function. On
  *   failure returns FALSE.
@@ -1074,7 +1074,7 @@ function tripal_pub_get_publication_array($pub_id, $skip_existing = TRUE) {
   // get the citation
   // ---------------------------------
   $values = array(
-    'pub_id' => $pub->pub_id, 
+    'pub_id' => $pub->pub_id,
     'type_id' => array(
       'name' => 'Citation',
     ),
@@ -1091,13 +1091,13 @@ function tripal_pub_get_publication_array($pub_id, $skip_existing = TRUE) {
       // skip this publication, it already has a citation
       return FALSE;
     }
-  }  
+  }
 
   // ---------------------------------
   // get the publication types
   // ---------------------------------
   $values = array(
-    'pub_id' => $pub->pub_id, 
+    'pub_id' => $pub->pub_id,
     'type_id' => array(
       'name' => 'Publication Type',
     ),
@@ -1114,7 +1114,7 @@ function tripal_pub_get_publication_array($pub_id, $skip_existing = TRUE) {
   // get the authors list
   // ---------------------------------
   $values = array(
-    'pub_id' => $pub->pub_id, 
+    'pub_id' => $pub->pub_id,
     'type_id' => array(
       'name' => 'Authors',
     ),
@@ -1132,8 +1132,8 @@ function tripal_pub_get_publication_array($pub_id, $skip_existing = TRUE) {
   // if there is no 'Author's property then try to retreive authors from the pubauthor table
   else {
     $sql = "
-      SELECT string_agg(surname || ' ' || givennames, ', ') 
-      FROM {pubauthor} 
+      SELECT string_agg(surname || ' ' || givennames, ', ')
+      FROM {pubauthor}
       WHERE pub_id = :pub_id
       GROUP BY pub_id
     ";
@@ -1176,25 +1176,25 @@ function tripal_pub_get_publication_array($pub_id, $skip_existing = TRUE) {
     'Media Alias',
     'Original Title');
   foreach ($props AS $prop) {
-    $sql = 
-      "SELECT value FROM {pubprop} 
-       WHERE type_id = 
-         (SELECT cvterm_id 
-          FROM {cvterm} 
-          WHERE name = :cvtname AND cv_id = 
-            (SELECT cv_id 
-             FROM {cv} 
+    $sql =
+      "SELECT value FROM {pubprop}
+       WHERE type_id =
+         (SELECT cvterm_id
+          FROM {cvterm}
+          WHERE name = :cvtname AND cv_id =
+            (SELECT cv_id
+             FROM {cv}
              WHERE name = 'tripal_pub'
             )
-         ) 
+         )
        AND pub_id = :pub_id
     ";
     $val = trim(chado_query($sql, array(':cvtname' => $prop, ':pub_id' => $pub->pub_id))->fetchField());
     if ($val) {
       $pub_array[$prop] =$val;
-    } 
+    }
   }
-  return $pub_array;  
+  return $pub_array;
 }
 
 
@@ -1202,34 +1202,34 @@ function tripal_pub_get_publication_array($pub_id, $skip_existing = TRUE) {
  * This function generates citations for publications.  It requires
  * an array structure with keys being the terms in the Tripal
  * publication ontology.  This function is intended to be used
- * for any function that needs to generate a citation. 
- * 
+ * for any function that needs to generate a citation.
+ *
  * @param $pub
  *   An array structure containing publication details where the keys
- *   are the publication ontology term names and values are the 
+ *   are the publication ontology term names and values are the
  *   corresponding details.  The pub array can contain the following
- *   keys with corresponding values:   
+ *   keys with corresponding values:
  *     - Publication Type:  an array of publication types. a publication can have more than one type
  *     - Authors: a  string containing all of the authors of a publication
  *     - Journal Name:  a string containing the journal name
  *     - Journal Abbreviation: a string containing the journal name abbreviation
  *     - Series Name: a string containing the series (e.g. conference proceedings) name
- *     - Series Abbreviation: a string containing the series name abbreviation     
+ *     - Series Abbreviation: a string containing the series name abbreviation
  *     - Volume: the serives volume number
  *     - Issue: the series issue number
  *     - Pages: the page numbers for the publication
  *     - Publication Date:  A date in the format "Year Month Day"
- *      
+ *
  * @return
  *   A text string containing the citation
  */
 function tripal_pub_create_citation($pub) {
   $citation = '';
   $pub_type = '';
-  
+
   // An article may have more than one publication type. For example,
   // a publication type can be 'Journal Article' but also a 'Clinical Trial'.
-  // Therefore, we need to select the type that makes most sense for 
+  // Therefore, we need to select the type that makes most sense for
   // construction of the citation. Here we'll iterate through them all
   // and select the one that matches best.
   if(is_array($pub['Publication Type'])) {
@@ -1237,19 +1237,19 @@ function tripal_pub_create_citation($pub) {
       if ($ptype == 'Journal Article' ) {
         $pub_type = $ptype;
         break;
-      } 
-      else if ($ptype == 'Conference Proceedings'){ 
+      }
+      else if ($ptype == 'Conference Proceedings'){
         $pub_type = $ptype;
         break;
-      } 
+      }
       else if ($ptype == 'Book') {
         $pub_type = $ptype;
         break;
-      } 
+      }
       else if ($ptype == 'Letter') {
         $pub_type = $ptype;
         break;
-      } 
+      }
       else if ($ptype == 'Book Chapter') {
         $pub_type = $ptype;
         break;
@@ -1257,24 +1257,24 @@ function tripal_pub_create_citation($pub) {
       else if ($ptype == "Research Support, Non-U.S. Gov't") {
         $pub_type = $ptype;
         // we don't break because if the article is also a Journal Article
-        // we prefer that type 
+        // we prefer that type
       }
     }
     if (!$pub_type) {
-      watchdog('tripal_pub', "Cannot generate citation for publication type: %types", 
+      watchdog('tripal_pub', "Cannot generate citation for publication type: %types",
         array('%types' => print_r($pub['Publication Type'], TRUE)), WATCHDOG_ERROR);
       return FALSE;
     }
   }
   else {
     $pub_type = $pub['Publication Type'];
-  }    
+  }
   //----------------------
   // Journal Article
   //----------------------
   if ($pub_type == 'Journal Article') {
     $citation = $pub['Authors'] . '. ' . $pub['Title'] .  '. ';
-  
+
     if (array_key_exists('Journal Name', $pub)) {
       $citation .= $pub['Journal Name'] . '. ';
     }
@@ -1282,7 +1282,7 @@ function tripal_pub_create_citation($pub) {
       $citation .= $pub['Journal Abbreviation'] . '. ';
     }
     elseif (array_key_exists('Series Name', $pub)) {
-      $citation .= $pub['Series Name'] . '. ';  
+      $citation .= $pub['Series Name'] . '. ';
     }
     elseif (array_key_exists('Series Abbreviation', $pub)) {
       $citation .= $pub['Series Abbreviation'] . '. ';
@@ -1315,7 +1315,7 @@ function tripal_pub_create_citation($pub) {
   //----------------------
   elseif ($pub_type == "Research Support, Non-U.S. Gov't") {
     $citation = $pub['Authors'] . '. ' . $pub['Title'] .  '. ';
-  
+
     if (array_key_exists('Journal Name', $pub)) {
       $citation .= $pub['Journal Name'] . '. ';
     }
@@ -1332,7 +1332,7 @@ function tripal_pub_create_citation($pub) {
   //----------------------
   elseif ($pub_type == 'Letter') {
     $citation = $pub['Authors'] . '. ' . $pub['Title'] .  '. ';
-  
+
     if (array_key_exists('Journal Name', $pub)) {
       $citation .= $pub['Journal Name'] . '. ';
     }
@@ -1340,7 +1340,7 @@ function tripal_pub_create_citation($pub) {
       $citation .= $pub['Journal Abbreviation'] . '. ';
     }
     elseif (array_key_exists('Series Name', $pub)) {
-      $citation .= $pub['Series Name'] . '. ';  
+      $citation .= $pub['Series Name'] . '. ';
     }
     elseif (array_key_exists('Series Abbreviation', $pub)) {
       $citation .= $pub['Series Abbreviation'] . '. ';
@@ -1372,25 +1372,25 @@ function tripal_pub_create_citation($pub) {
   // Book
   //----------------------
   elseif ($pub_type == 'Book') {
-  
+
   }
   //----------------------
   // Book Chapter
   //----------------------
   elseif ($pub_type == 'Book Chapter') {
-    
+
   }
   //----------------------
   // Conference Proceedings
   //----------------------
   elseif ($pub_type == 'Conference Proceedings') {
     $citation = $pub['Authors'] . '. ' . $pub['Title'] .  '. ';
-  
+
     if (array_key_exists('Conference Name', $pub)) {
       $citation .= $pub['Conference Name'] . '. ';
     }
     elseif (array_key_exists('Series Name', $pub)) {
-      $citation .= $pub['Series Name'] . '. ';  
+      $citation .= $pub['Series Name'] . '. ';
     }
     elseif (array_key_exists('Series Abbreviation', $pub)) {
       $citation .= $pub['Series Abbreviation'] . '. ';

tripal_pub/tripal_pub.module

@@ -11,12 +11,14 @@ require_once "includes/importers/tripal_pub.PMID.inc";
 require_once "includes/importers/tripal_pub.AGL.inc";
 
 /**
- * @file
- *
+ * @defgroup tripal_pub Publication Module
+ * @ingroup tripal_modules
+ * @{
  * The Tripal Publication module allows you to search the PubMed databse for academic articles,
- * that relate to user specified tpoic\s. As well, it allows management of publications so that
+ * 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.
+ * @}
  */
 
 
@@ -96,7 +98,7 @@ function tripal_pub_menu() {
     'weight' => 2
   );
   return $items;
-  
+
   $items['admin/tripal/chado/tripal_pub/citation'] = array(
     'title' => 'Citations',
     'description' => 'Update publication citations',
@@ -106,7 +108,7 @@ function tripal_pub_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 1
   );
-  
+
   $items['admin/tripal/chado/tripal_pub/import_list'] = array(
     'title' => t('Importers'),
     'description' => t('List all publication importers'),
@@ -115,7 +117,7 @@ function tripal_pub_menu() {
     'type' => MENU_LOCAL_TASK,
     'weight' => 0
   );
-  
+
   // add a second link for the importer on the data loaders page
   $items['admin/tripal/loaders/pub_import'] = array(
     'title' => 'Publications Importers',
@@ -124,7 +126,7 @@ function tripal_pub_menu() {
     'access arguments' => array('administer tripal pubs'),
     'type' => MENU_NORMAL_ITEM,
   );
-  
+
   $items['admin/tripal/chado/tripal_pub/import/new'] = array(
     'title' => t('Add an Importer'),
     'description' => t('Add a new publication importer.'),
@@ -146,7 +148,7 @@ function tripal_pub_menu() {
     'access arguments' => array('administer tripal pubs'),
     'type ' => MENU_CALLBACK,
   );
-  
+
   $items['admin/tripal/chado/tripal_pub/import/submit/%'] = array(
     'page callback' => 'tripal_pub_importer_submit_job',
     'page arguments' => array(6),
@@ -205,7 +207,7 @@ function tripal_pub_menu() {
  */
 function tripal_pub_theme($existing, $type, $theme, $path) {
   $core_path = drupal_get_path('module', 'tripal_core');
-  
+
   $items = array(
     'node__chado_pub' => array(
       'template' => 'node--chado-generic',
@@ -279,7 +281,7 @@ function tripal_pub_theme($existing, $type, $theme, $path) {
     'tripal_pub_search_setup_form_elements' => array(
       'render element' => 'form',
     ),
-    
+
     // teaser
     'tripal_pub_teaser' => array(
       'variables' => array('node' => NULL),
@@ -402,7 +404,7 @@ function tripal_pub_form_alter(&$form, &$form_state, $form_id) {
 }
 
 /**
- * 
+ *
  * @param $callback
  * @param $args
  */
@@ -414,7 +416,7 @@ function tripal_pub_job_describe_args($callback, $args) {
     $qargs = array(':import_id' => $args[0]);
     $sql = "SELECT * FROM {tripal_pub_import} WHERE pub_import_id = :import_id ";
     $import = db_query($sql, $qargs)->fetchObject();
-    
+
     $new_args['Importer'] = $import->name;
   }
   return $new_args;

tripal_stock/api/tripal_stock.api.inc

@@ -7,6 +7,9 @@
 /**
  * @defgroup tripal_stock_api Stock Module API
  * @ingroup tripal_api
+ * @{
+ * Provides an application programming interface (API) to manage stocks
+ * @}
  */
 
 /**

tripal_views/api/tripal_views.api.inc

@@ -3,9 +3,14 @@
 /**
  * @file
  * API functions for Tripal Views Integration
- *
+ */
+
+ /**
  * @defgroup tripal_views_api Tripal Views Module API
  * @ingroup tripal_api
+ * @{
+ * Provides functions for Tripal Views Integrations
+ * @}
  */
 
 /**

tripal_views/tripal_views.module

@@ -1,5 +1,13 @@
 <?php
 
+/**
+ * @defgroup tripal_views Tripal Views Module
+ * @ingroup tripal_modules
+ * @{
+ * Provides functions for integrating chado with Drupal Views.
+ * @}
+ */
+
 require_once "tripal_views.views.inc";
 
 require_once "includes/tripal_views_integration.inc";