Added documentation changes

tripal_core/tripal_core.api.inc

@@ -19,7 +19,15 @@
  * across a missing function that you think should be included go to the sourceforge feature request * page and request it's inclusion in the API. Such feature requests with a working function * definition will be given priority.
  * @}
  */
- 
+
+/** 
+ * @defgroup tripal_schema_api Tripal Schema API
+ * @{
+ * Provides an application programming interface (API) used to describe chado tables to 
+ * drupal/tripal
+ * @}
+ * @ingroup tripal_api
+ */
 require_once "tripal_core.schema.api.inc";
 
 // just a temporary function for debugging

tripal_cv/tripal_cv.api.inc

@@ -1,43 +1,98 @@
 <?php
 
-/*************************************************************************
- * Purpose: To retrieve a chado cv object
- *
- * @params where_options: array(
- *													<column_name> => array(
- *														'type' => <type of column: INT/STRING>,
- *														'value' => <the vlaue you want to filter on>,
- *														'exact' => <if TRUE use =; if FALSE use ~>,
- *													)
- *				)
- * @return chado cv object with all fields from the chado cv table
+/**
+ * @defgroup tripal_cv_api Controlled Vocabulary Module API
+ * @ingroup tripal_api
+ * @ingroup tripal_cv
+ * Provides an application programming interface (API) to controlled vocabularies
  */
-function tripal_cv_get_cv ($where_options) {
-	$previous_db = tripal_db_set_active('chado');
-
-	$where= array();
-	//generate the where clause from supplied options
-	// the key is the column name
-	foreach ($where_options as $key => $val_array) {
-		if (preg_match('/INT/', $val_array['type'])) {
-			$where[] = $key."=".$val_array['value'];
-		} else {
-			if ($val_array['exact']) { $operator='='; }
-			else { $operator='~'; }
-			$where[] = $key.$operator."'".$val_array['value']."'";
-		}
-	}
-	
-  $r = db_fetch_object(db_query(
-    "SELECT * FROM cv WHERE ".implode(' AND ',$where)
-  ));
-  
-  tripal_db_set_active($previous_db);
 
-  return $r;
+/**
+ * Purpose: To retrieve a chado controlled vocabulary object
+ *
+ * @param $select_values
+ *   An array meant to uniquely select a given controlled vocabulary
+ *
+ * @return
+ *   Chado controlled vocabulary object
+ *
+ * The controlled vocabulary is selected using tripal_core_chado select and as such the
+ * $select_values array parameter meant to uniquely identify the controlled vocab to be 
+ * returned follows the same form as when using tripal_core_chado_select directly.
+ *
+ * Example Usage:
+ * @code
+    $select_values = array(
+      'name' => 'feature_property'
+    );
+    $cv_object = tripal_cv_get_cv($select_values);
+ * @endcode
+ *  The above code selects the feature_property cv and returns the following object:
+ * @code
+    $cv_object = stdClass Object ( 
+      [cv_id] => 13
+      [name] => feature_property
+      [definition] => 
+    ); 
+ * @endcode
+ *
+ * @ingroup tripal_cv_api
+ */
+function tripal_cv_get_cv ($select_values) {
+/**
+  $columns = array(
+    'cv_id', 
+    'name', 
+    'definition', 
+  );
+  $results = tripal_core_chado_select('cv', $columns, $select_values);
+  if (sizeof($results) == 1) {
+    return $results[0];
+  } elseif (empty($results)) {
+    watchdog('tripal_cv', 
+      'tripal_cv_get_cv: No cv matches criteria values:%values',
+      array('%values' => print_r($select_values, TRUE)),
+      WATCHDOG_WARNING
+    );
+    return FALSE;
+  } else {
+    watchdog('tripal_cv', 
+      'tripal_cv_get_cv: 2+ cvs match criteria values:%values',
+      array('%values' => print_r($select_values, TRUE)),
+      WATCHDOG_WARNING
+    );
+  }
+*/  
 }
-/*************************************************************************
- * return the cv object for the specified CV name
+
+// Purpose: To retrieve a chado cv object
+// @param $where_options 
+//   @code
+//        array(
+//													<column_name> => array(
+//														'type' => <type of column: INT/STRING>,
+//														'value' => <the vlaue you want to filter on>,
+//														'exact' => <if TRUE use =; if FALSE use ~>,
+//													)
+//				)
+// @endcode
+//
+// @return 
+//   Chado cv object with all fields from the chado cv table
+//
+// @ingroup tripal_cv_api
+//
+//function tripal_cv_get_cv ($where_options)
+
+/**
+ *
+ *
+ * @param $name
+ *  The name of the cv to be returned
+ * @return 
+ *   The cv object for the specified CV name
+ *
+ * @ingroup tripal_cv_api 
  */
 function tripal_cv_get_cv_by_name ($name) {
 	$previous_db = tripal_db_set_active('chado');	
@@ -46,8 +101,11 @@ function tripal_cv_get_cv_by_name ($name) {
 
   return $r;
 }
-/*************************************************************************
+
+/**
  * return the cv object for the specified CV id
+ *
+ * @ingroup tripal_cv_api
  */
 function tripal_cv_get_cv_by_id ($cv_id) {
 	$previous_db = tripal_db_set_active('chado');	
@@ -56,11 +114,15 @@ function tripal_cv_get_cv_by_id ($cv_id) {
 
   return $r;
 }
-/*************************************************************************
+
+/**
  * Purpose: Create an options array to be used in a form element
  *   which provides a list of all chado cvs
  *
- * @return an array(cv_id => name) for each cv in the chado cv table
+ * @return 
+ *   An array(cv_id => name) for each cv in the chado cv table
+ *
+ * @ingroup tripal_cv_api
  */
 function tripal_cv_get_cv_options() {
 
@@ -79,49 +141,106 @@ function tripal_cv_get_cv_options() {
 
 }
 
-/*************************************************************************
- * Purpose: To retrieve a chado cvterm object
- *
- * @params where_options: array(
- *													<column_name> => array(
- *														'type' => <type of column: INT/STRING>,
- *														'value' => <the vlaue you want to filter on>,
- *														'exact' => <if TRUE use =; if FALSE use ~>,
- *													)
- *				)
- * @return chado cvterm object with all fields from the chado cvterm table
+/**
+ * Purpose: To retrieve a chado controlled vocabulary term object
+ *
+ * @param $select_values
+ *   An array meant to uniquely select a given controlled vocabulary term
+ *
+ * @return
+ *   Chado controlled vocabulary term object
+ *
+ * The controlled vocabulary term is selected using tripal_core_chado select and as such the
+ * $select_values array parameter meant to uniquely identify the controlled vocab term to be 
+ * returned follows the same form as when using tripal_core_chado_select directly.
+ *
+ * Example Usage:
+ * @code
+    $select_values = array(
+      'name' => 'synonym',
+      'cv_id' => array(
+        'name' => 'feature_property'
+      )
+    );
+    $cvterm_object = tripal_cv_get_cvterm($select_values);
+ * @endcode
+ *  The above code selects the synonym cvterm from the feature_proeprty cv and returns 
+ *  the following object:
+ * @code
+    $cvterm_object = stdClass Object ( 
+      [cvterm_id] => 2099
+      [name] => synonym
+      [definition] => Historic community symbol, may have originally been symbol []
+      [is_obsolete] => 0
+      [is_relationshiptype] => 1
+      [cv_cv_id] => 13
+      [cv_name] => feature_property
+      [cv_definition] => 
+      [dbreference_dbxref_id] => 2581
+      [dbreference_accession] => synonym
+      [dbreference_description] => 
+      [dbreference_version] => 
+      [dbreference_db_db_id] => 49
+      [dbreference_db_name] => SOFP
+      [dbreference_db_description] => 
+      [dbreference_db_urlprefix] => 
+      [dbreference_db_url] => 
+    ); 
+ * @endcode
+ *
+ * @ingroup tripal_cv_api
  */
-function tripal_cv_get_cvterm ($where_options) {
-	$previous_db = tripal_db_set_active('chado');
-
-	$where= array();
-	//generate the where clause from supplied options
-	// the key is the column name
-	foreach ($where_options as $key => $val_array) {
-		if (preg_match('/INT/', $val_array['type'])) {
-			$where[] = $key."=".$val_array['value'];
-		} else {
-			if ($val_array['exact']) { $operator='='; }
-			else { $operator='~'; }
-			$where[] = $key.$operator."'".$val_array['value']."'";
-		}
-	}
-	
-  $r = db_fetch_object(db_query(
-    "SELECT * FROM cvterm WHERE ".implode(' AND ',$where)
-  ));
-  
-  tripal_db_set_active($previous_db);
-
-  return $r;
+function tripal_cv_get_cvterm ($select_values) {
+/**
+  $columns = array(
+    'cvterm_id', 
+    'cv_id', 
+    'name', 
+    'definition', 
+    'dbxref_id', 
+    'is_obsolete', 
+    'is_relationshiptype'
+  );
+  $results = tripal_core_chado_select('cvterm', $columns, $select_values);
+  if (sizeof($results) == 1) {
+    // Add cv
+    $cvterm = tripal_cv_add_cv_to_object(array('cv_id'=>$results[0]->cv_id),$results[0],array());
+    unset($cvterm->cv_id);
+    
+    // Add dbxref
+    $cvterm = tripal_db_add_dbxref_to_object(array('dbxref_id'=>$cvterm->dbxref_id),$cvterm,array());
+    unset($cvterm->dbxref_id);
+    
+    return $cvterm;
+  } elseif (empty($results)) {
+    watchdog('tripal_cv', 
+      'tripal_cv_get_cvterm: No cvterm matches criteria values:%values',
+      array('%values' => print_r($select_values, TRUE)),
+      WATCHDOG_WARNING
+    );
+    return FALSE;
+  } else {
+    watchdog('tripal_cv', 
+      'tripal_cv_get_cvterm: 2+ cvterms match criteria values:%values',
+      array('%values' => print_r($select_values, TRUE)),
+      WATCHDOG_WARNING
+    );
+  }
+*/  
 }
 
-/*************************************************************************
+/**
  * Purpose: Retrieve a chado cvterm object with a given name
  *
- * @params name: the cvterm.name
- * @params cv_id: the cv_id of the term you are looking for
- * @return cvterm object
+ * @param $name
+ *   the cvterm.name
+ * @param $cv_id
+ *   the cv_id of the term you are looking for
+ *
+ * @return 
+ *   cvterm object
+ *
+ * @ingroup tripal_cv_api
  */
 function tripal_cv_get_cvterm_by_name ($name, $cv_id=0) {
 
@@ -140,14 +259,19 @@ function tripal_cv_get_cvterm_by_name ($name, $cv_id=0) {
   return $r;
   
 }
-/*************************************************************************
+
+/**
  * Purpose: Create an options array to be used in a form element
  *   which provides a list of all chado cvterms
  * 
- * @params cv_id: the chado cv_id
+ * @param $cv_id 
+ *   The chado cv_id;
  *   only cvterms with the supplied cv_id will be returned
- * @return an array(cvterm_id => name) 
+ * @return 
+ *   An array(cvterm_id => name) 
  *   for each cvterm in the chado cvterm table where cv_id=that supplied
+ *
+ * @ingroup tripal_cv_api
  */
 function tripal_cv_get_cvterm_options($cv_id = 0) {
 
@@ -172,17 +296,15 @@ function tripal_cv_get_cvterm_options($cv_id = 0) {
 
 }
 
-/****************************************************************************
- * @section Chado Table Descriptions
- ****************************************************************************/
-
-/****************************************************************************
+/**
  * Implements hook_chado_cvterm_schema()
  * Purpose: To add descriptions and foreign keys to default table description
  * Note: This array will be merged with the array from all other implementations
  *
  * @return
  *    Array describing the cvterm table
+ *
+ * @ingroup tripal_schema_api 
  */
 function tripal_stock_chado_cvterm_schema() {
   $description = array();

tripal_db/tripal_db.api.inc

@@ -1,10 +1,83 @@
 <?php
 
-/*************************************************************************
+/**
+ * @defgroup tripal_db_api External Database Module API
+ * @ingroup tripal_api
+ * @ingroup tripal_db
+ * Provides an application programming interface (API) to manage databases
+ */
+
+/**
+ * Purpose: To retrieve a chado database object
+ *
+ * @param $select_values
+ *   An array meant to uniquely select a given database
+ *
+ * @return
+ *   Chado database object
+ *
+ * The database is selected using tripal_core_chado select and as such the
+ * $select_values array parameter meant to uniquely identify the database to be 
+ * returned follows the same form as when using tripal_core_chado_select directly.
+ *
+ * Example Usage:
+ * @code
+    $select_values = array(
+      'name' => 'SOFP'
+    );
+    $db_object = tripal_db_get_db($select_values);
+ * @endcode
+ *  The above code selects the SOFP db and returns the following object:
+ * @code
+    $db_object = stdClass Object ( 
+      [db_id] => 49
+      [name] => SOFP
+      [description] => 
+      [urlprefix] => 
+      [url] =>     
+    ); 
+ * @endcode
+ *
+ * @ingroup tripal_db_api
+ */
+function tripal_db_get_db ($select_values) {
+/**
+  $columns = array(
+    'db_id', 
+    'name', 
+    'description',
+    'urlprefix',
+    'url'
+  );
+  $results = tripal_core_chado_select('db', $columns, $select_values);
+  if (sizeof($results) == 1) {
+    return $results[0];
+  } elseif (empty($results)) {
+    watchdog('tripal_cdb', 
+      'tripal_db_get_db: No db matches criteria values:%values',
+      array('%values' => print_r($select_values, TRUE)),
+      WATCHDOG_WARNING
+    );
+    return FALSE;
+  } else {
+    watchdog('tripal_db', 
+      'tripal_db_get_db: 2+ dbs match criteria values:%values',
+      array('%values' => print_r($select_values, TRUE)),
+      WATCHDOG_WARNING
+    );
+  }
+*/  
+}
+
+/**
  * Purpose: To retrieve a chado db object
  *
- * @params db.db_id
- * @return chado db object with all fields from the chado db table
+ * @param $db_id
+ *   db.db_id
+ * @return 
+ *   Chado db object with all fields from the chado db table
+ *
+ * @ingroup tripal_db_api
  */
 function tripal_db_get_db_by_db_id ($db_id) {
 
@@ -17,11 +90,15 @@ function tripal_db_get_db_by_db_id ($db_id) {
   return $r;
 }
 
-/*************************************************************************
+/**
  * Purpose: To retrieve a chado db object
  *
- * @params db.name
- * @return chado db object with all fields from the chado db table
+ * @param $name
+ *   db.name
+ * @return 
+ *   chado db object with all fields from the chado db table
+ *
+ * @ingroup tripal_db_api
  */
 function tripal_db_get_db_by_name ($name) {
 
@@ -34,48 +111,27 @@ function tripal_db_get_db_by_name ($name) {
   return $r;
 }
 
-/*************************************************************************
- * Purpose: To retrieve a chado db object
- *
- * @params where_options: array(
- *													<column_name> => array(
- *														'type' => <type of column: INT/STRING>,
- *														'value' => <the vlaue you want to filter on>,
- *														'exact' => <if TRUE use =; if FALSE use ~>,
- *													)
- *				)
- * @return chado db object with all fields from the chado db table
- */
-function tripal_db_get_db ($where_options) {
-	$previous_db = tripal_db_set_active('chado');
-
-	$where= array();
-	//generate the where clause from supplied options
-	// the key is the column name
-	foreach ($where_options as $key => $val_array) {
-		if (preg_match('/INT/', $val_array['type'])) {
-			$where[] = $key."=".$val_array['value'];
-		} else {
-			if ($val_array['exact']) { $operator='='; }
-			else { $operator='~'; }
-			$where[] = $key.$operator."'".$val_array['value']."'";
-		}
-	}
-	
-  $r = db_fetch_object(db_query(
-    "SELECT * FROM db WHERE ".implode(' AND ',$where)
-  ));
-  
-  tripal_db_set_active($previous_db);
+// Purpose: To retrieve a chado db object
+//
+// @params where_options: array(
+//													<column_name> => array(
+//														'type' => <type of column: INT/**STRING>,
+//														'value' => <the vlaue you want to filter on>,
+//														'exact' => <if TRUE use =; if FALSE use ~>,
+//													)
+//				)
+// @return chado db object with all fields from the chado db table
+//
+//function tripal_db_get_db ($where_options) {
 
-  return $r;
-}
-
-/*************************************************************************
+/**
  * Purpose: Create an options array to be used in a form element
  *   which provides a list of all chado dbs
  *
- * @return an array(db_id => name) for each db in the chado db table
+ * @return 
+ *   An array(db_id => name) for each db in the chado db table
+ *
+ * @ingroup tripal_db_api
  */
 function tripal_db_get_db_options() {
 
@@ -94,49 +150,102 @@ function tripal_db_get_db_options() {
 
 }
 
-/*************************************************************************
- * Purpose: To retrieve a chado dbxref object
- *
- * @params where_options: array(
- *													<column_name> => array(
- *														'type' => <type of column: INT/STRING>,
- *														'value' => <the vlaue you want to filter on>,
- *														'exact' => <if TRUE use =; if FALSE use ~>,
- *													)
- *				)
- * @return chado dbxref object with all fields from the chado dbxref table
- */
-function tripal_db_get_dbxref ($where_options) {
-	$previous_db = tripal_db_set_active('chado');
+// Purpose: To retrieve a chado dbxref object
+//
+// @param where_options: array(
+//													<column_name> => array(
+//														'type' => <type of column: INT/**STRING>,
+//														'value' => <the vlaue you want to filter on>,
+//														'exact' => <if TRUE use =; if FALSE use ~>,
+//													)
+//				)
+// @return chado dbxref object with all fields from the chado dbxref table
+//
+//function tripal_db_get_dbxref ($where_options) {
 
-	$where= array();
-	//generate the where clause from supplied options
-	// the key is the column name
-	foreach ($where_options as $key => $val_array) {
-		if (preg_match('/INT/', $val_array['type'])) {
-			$where[] = $key."=".$val_array['value'];
-		} else {
-			if ($val_array['exact']) { $operator='='; }
-			else { $operator='~'; }
-			$where[] = $key.$operator."'".$val_array['value']."'";
-		}
-	}
-	
-  $r = db_fetch_object(db_query(
-    "SELECT * FROM dbxref WHERE ".implode(' AND ',$where)
-  ));
-  
-  tripal_db_set_active($previous_db);
+/**
+ * Purpose: To retrieve a chado database reference object
+ *
+ * @param $select_values
+ *   An array meant to uniquely select a given database reference
+ *
+ * @return
+ *   Chado database reference object
+ *
+ * The database reference is selected using tripal_core_chado select and as such the
+ * $select_values array parameter meant to uniquely identify the database reference to be 
+ * returned follows the same form as when using tripal_core_chado_select directly.
+ *
+ * Example Usage:
+ * @code
+    $select_values = array(
+      'accession' => 'synonym',
+      'db_id' => array(
+        'name' => 'SOFP'
+      )
+    );
+    $dbxref_object = tripal_db_get_dbxref($select_values);
+ * @endcode
+ *  The above code selects the synonym database reference and returns the following object:
+ * @code
+    $dbxref_object = stdClass Object ( 
+      [dbxref_id] => 2581
+      [accession] => synonym
+      [description] => 
+      [version] => 
+      [db_db_id] => 49
+      [db_name] => SOFP
+      [db_description] => 
+      [db_urlprefix] => 
+      [db_url] =>     
+    ); 
+ * @endcode
+ *
+ * @ingroup tripal_db_api
+ */
+function tripal_db_get_dbxref ($select_values) {
+/**
+  $columns = array(
+    'dbxref_id',
+    'db_id', 
+    'accession', 
+    'description',
+    'version'
+  );
+  $results = tripal_core_chado_select('dbxref', $columns, $select_values);
+  if (sizeof($results) == 1) {
+    $dbxref = tripal_db_add_db_to_object(array('db_id' => $results[0]->db_id), $results[0], array());
+    unset($dbxref->db_id);
 
-  return $r;
+    return $dbxref;
+  } elseif (empty($results)) {
+    watchdog('tripal_db', 
+      'tripal_db_get_dbxref: No dbxref matches criteria values:%values',
+      array('%values' => print_r($select_values, TRUE)),
+      WATCHDOG_WARNING
+    );
+    return FALSE;
+  } else {
+    watchdog('tripal_db', 
+      'tripal_db_get_dbxref: 2+ dbxrefs match criteria values:%values',
+      array('%values' => print_r($select_values, TRUE)),
+      WATCHDOG_WARNING
+    );
+  }
+  */
 }
 
-/*************************************************************************
+/**
  * Purpose: To retrieve a chado dbxref object with a given accession
  *
- * @params dbxref.accession
- * @params dbxref.db_id
- * @return chado dbxref object with all fields from the chado dbxref table
+ * @param $accession
+ *   dbxref.accession
+ * @param $db_id
+ *   dbxref.db_id
+ * @return 
+ *   chado dbxref object with all fields from the chado dbxref table
+ *
+ * @ingroup tripal_db_api
  */
 function tripal_db_get_dbxref_by_accession ($accession, $db_id=0) {
 
@@ -159,17 +268,15 @@ function tripal_db_get_dbxref_by_accession ($accession, $db_id=0) {
   return $r;
 }
 
-/****************************************************************************
- * @section Chado Table Descriptions
- ****************************************************************************/
-
-/****************************************************************************
+/**
  * Implements hook_chado_dbxref_schema()
  * Purpose: To add descriptions and foreign keys to default table description
  * Note: This array will be merged with the array from all other implementations
  *
  * @return
  *    Array describing the dbxref table
+ *
+ * @ingroup tripal_schema_api
  */
 function tripal_stock_chado_dbxref_schema() {
   $description = array();

tripal_feature/fasta_loader.php

@@ -5,12 +5,12 @@
  * @{
  * Provides fasta loading functionality. Creates features based on their specification in a fasta file.
  * @}
+ * @ingroup tripal_feature
  */
  
 /**
  *
  *
- * @ingroup tripal_feature
  * @ingroup fasta_loader
  */
 function tripal_feature_fasta_load_form (){
@@ -200,7 +200,6 @@ function tripal_feature_fasta_load_form (){
 /**
  *
  *
- * @ingroup tripal_feature
  * @ingroup fasta_loader
  */
 function tripal_feature_fasta_load_form_validate($form, &$form_state){
@@ -272,7 +271,6 @@ function tripal_feature_fasta_load_form_validate($form, &$form_state){
 /**
  *
  *
- * @ingroup tripal_feature
  * @ingroup fasta_loader
  */
 function tripal_feature_fasta_load_form_submit ($form, &$form_state){
@@ -301,7 +299,6 @@ function tripal_feature_fasta_load_form_submit ($form, &$form_state){
 /**
  *
  *
- * @ingroup tripal_feature
  * @ingroup fasta_loader
  */
 function tripal_feature_load_fasta($dfile, $organism_id, $type,
@@ -381,7 +378,6 @@ function tripal_feature_load_fasta($dfile, $organism_id, $type,
 /**
  *
  *
- * @ingroup tripal_feature
  * @ingroup fasta_loader
  */
 function tripal_feature_fasta_loader_insert_feature($name,$uname,$db_id,$accession,

tripal_feature/gff_loader.php

@@ -5,6 +5,7 @@
  * @{
  * Provides gff3 loading functionality. Creates features based on their specification in a GFF3 file.
  * @}
+ * @ingroup tripal_feature
  */
 // TODO: The rank column on the feature_relationship table needs to be used to
 //       make sure the ordering of CDS (exons) is correct.
@@ -14,7 +15,6 @@
 /**
  *
  *
- * @ingroup tripal_feature
  * @ingroup gff3_loader
  */
 function tripal_core_gff3_load_form (){
@@ -136,7 +136,6 @@ function tripal_core_gff3_load_form (){
 /**
  *
  *
- * @ingroup tripal_feature
  * @ingroup gff3_loader
  */
 function tripal_core_gff3_load_form_validate ($form, &$form_state){
@@ -169,7 +168,6 @@ function tripal_core_gff3_load_form_validate ($form, &$form_state){
 
 /**
  *
- * @ingroup tripal_feature
  * @ingroup gff3_loader
  */
 function tripal_core_gff3_load_form_submit ($form, &$form_state){
@@ -206,7 +204,6 @@ function tripal_core_gff3_load_form_submit ($form, &$form_state){
 /**
  *
  *
- * @ingroup tripal_feature
  * @ingroup gff3_loader
  */
 function tripal_core_load_gff3($gff_file, $organism_id,$analysis_id,$add_only =0, 
@@ -467,7 +464,6 @@ function tripal_core_load_gff3($gff_file, $organism_id,$analysis_id,$add_only =0
 /**
  *
  *
- * @ingroup tripal_feature
  * @ingroup gff3_loader
  */
 function tripal_core_load_gff3_parents($feature,$cvterm,$parents,$gff_features,$organism_id){
@@ -522,7 +518,6 @@ function tripal_core_load_gff3_parents($feature,$cvterm,$parents,$gff_features,$
 /**
  *
  *
- * @ingroup tripal_feature
  * @ingroup gff3_loader
  */
 function tripal_core_load_gff3_dbxref($feature,$dbxrefs){
@@ -595,7 +590,6 @@ function tripal_core_load_gff3_dbxref($feature,$dbxrefs){
 /**
  *
  *
- * @ingroup tripal_feature
  * @ingroup gff3_loader
  */
 function tripal_core_load_gff3_alias($feature,$aliases){
@@ -696,7 +690,6 @@ function tripal_core_load_gff3_alias($feature,$aliases){
 /**
  *
  *
- * @ingroup tripal_feature
  * @ingroup gff3_loader
  */
 function tripal_core_load_gff3_feature($organism,$analysis_id,$cvterm,$uniquename,$name,
@@ -765,7 +758,6 @@ function tripal_core_load_gff3_feature($organism,$analysis_id,$cvterm,$uniquenam
 /**
  *
  *
- * @ingroup tripal_feature
  * @ingroup gff3_loader
  */
 function tripal_core_load_gff3_featureloc($feature,$organism,$landmark,$fmin,