API: changed [table]_retrieve to chado_[table]_retrieve

tripal_analysis/api/tripal_analysis.DEPRECATED.inc

@@ -95,9 +95,9 @@ function tripal_analysis_delete_property($analysis_id, $property, $cv_name = 'tr
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by analysis_retrieve().
+ * This function has been replaced by chado_analysis_retrieve().
  *
- * @see analysis_retrieve().
+ * @see chado_analysis_retrieve().
  */
 function tripal_analysis_get_node($analysis_id) {
 
@@ -107,9 +107,9 @@ function tripal_analysis_get_node($analysis_id) {
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_analysis_get_node',
-      '%new_function' => 'analysis_retrieve'
+      '%new_function' => 'chado_analysis_retrieve'
     )
   );
 
-  return analysis_retrieve(array('analysis_id' => $analysis_id));
+  return chado_analysis_retrieve(array('analysis_id' => $analysis_id));
 }

tripal_analysis/api/tripal_analysis.api.inc

@@ -70,7 +70,7 @@ function tripal_analysis_unregister_child($modulename) {
  *
  * @ingroup tripal_analysis_api
  */
-function analysis_retrieve($identifier, $options) {
+function chado_analysis_retrieve($identifier, $options) {
 
   // Set Defaults
   if (!isset($options['include_fk'])) {
@@ -126,7 +126,7 @@ function analysis_retrieve($identifier, $options) {
     tripal_report_error(
       'tripal_analysis_api',
       TRIPAL_ERROR,
-      "analysis_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
+      "chado_analysis_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
       )
@@ -138,7 +138,7 @@ function analysis_retrieve($identifier, $options) {
     tripal_report_error(
       'tripal_analysis_api',
       TRIPAL_ERROR,
-      "analysis_retrieve: chado_generate_var() failed to return a analysis based on the identifiers
+      "chado_analysis_retrieve: chado_generate_var() failed to return a analysis based on the identifiers
         you passed in. You should check that your identifiers are correct, as well as, look
         for a chado_generate_var error for additional clues. You passed in %identifier.",
       array(

tripal_cv/api/tripal_cv.DEPRECATED.inc

@@ -7,9 +7,9 @@
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by cv_retrieve().
+ * This function has been replaced by chado_cv_retrieve().
  *
- * @see cv_retrieve().
+ * @see chado_cv_retrieve().
  */
 function tripal_cv_get_cv($select_values) {
 
@@ -19,19 +19,19 @@ function tripal_cv_get_cv($select_values) {
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_cv_get_cv',
-      '%new_function' => 'cv_retrieve'
+      '%new_function' => 'chado_cv_retrieve'
     )
   );
 
-  return cv_retrieve($select_values);
+  return chado_cv_retrieve($select_values);
 }
 
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by cv_retrieve().
+ * This function has been replaced by chado_cv_retrieve().
  *
- * @see cv_retrieve().
+ * @see chado_cv_retrieve().
  */
 function tripal_cv_get_cv_by_name($name) {
 
@@ -41,19 +41,19 @@ function tripal_cv_get_cv_by_name($name) {
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_cv_get_cv_by_name',
-      '%new_function' => 'cv_retrieve'
+      '%new_function' => 'chado_cv_retrieve'
     )
   );
 
-  return cv_retrieve(array('name' => $name));
+  return chado_cv_retrieve(array('name' => $name));
 }
 
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by cv_retrieve().
+ * This function has been replaced by chado_cv_retrieve().
  *
- * @see cv_retrieve().
+ * @see chado_cv_retrieve().
  */
 function tripal_cv_get_cv_by_id($cv_id) {
 
@@ -63,19 +63,19 @@ function tripal_cv_get_cv_by_id($cv_id) {
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_cv_get_cv_by_id',
-      '%new_function' => 'cv_retrieve'
+      '%new_function' => 'chado_cv_retrieve'
     )
   );
 
-  return cv_retrieve(array('cv_id' => $id));
+  return chado_cv_retrieve(array('cv_id' => $id));
 }
 
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by cv_retrieve().
+ * This function has been replaced by chado_cv_retrieve().
  *
- * @see cv_retrieve().
+ * @see chado_cv_retrieve().
  */
 function tripal_cv_get_cv_id($cv_name) {
 
@@ -85,11 +85,11 @@ function tripal_cv_get_cv_id($cv_name) {
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_cv_get_cv_id',
-      '%new_function' => 'cv_retrieve'
+      '%new_function' => 'chado_cv_retrieve'
     )
   );
 
-  $cv = cv_retrieve(array('name' => $cv_name));
+  $cv = chado_cv_retrieve(array('name' => $cv_name));
   if (isset($cv->cv_id)) {
     return $cv->cv_id;
   }
@@ -123,9 +123,9 @@ function tripal_cv_get_cv_options() {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by cvterm_retrieve().
+ * This function has been replaced by chado_cvterm_retrieve().
  *
- * @see cvterm_retrieve().
+ * @see chado_cvterm_retrieve().
  */
 function tripal_cv_get_cvterm_by_id($cvterm_id) {
 
@@ -135,19 +135,19 @@ function tripal_cv_get_cvterm_by_id($cvterm_id) {
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_cv_get_cvterm_by_id',
-      '%new_function' => 'cvterm_retrieve'
+      '%new_function' => 'chado_cvterm_retrieve'
     )
   );
 
-  return cvterm_retrieve(array('cvterm_id' => $cvterm_id));
+  return chado_cvterm_retrieve(array('cvterm_id' => $cvterm_id));
 }
 
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by cvterm_retrieve().
+ * This function has been replaced by chado_cvterm_retrieve().
  *
- * @see cvterm_retrieve().
+ * @see chado_cvterm_retrieve().
  */
 function tripal_cv_get_cvterm_by_name($name, $cv_id = NULL, $cv_name = 'tripal') {
 
@@ -157,7 +157,7 @@ function tripal_cv_get_cvterm_by_name($name, $cv_id = NULL, $cv_name = 'tripal')
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_cv_get_cvterm_by_name',
-      '%new_function' => 'cvterm_retrieve'
+      '%new_function' => 'chado_cvterm_retrieve'
     )
   );
 
@@ -171,15 +171,15 @@ function tripal_cv_get_cvterm_by_name($name, $cv_id = NULL, $cv_name = 'tripal')
     );
   }
 
-  return cvterm_retrieve($identifiers);
+  return chado_cvterm_retrieve($identifiers);
 }
 
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by cvterm_retrieve().
+ * This function has been replaced by chado_cvterm_retrieve().
  *
- * @see cvterm_retrieve().
+ * @see chado_cvterm_retrieve().
  */
 function tripal_cv_get_cvterm_by_synonym($synonym, $cv_id = NULL, $cv_name = 'tripal') {
 
@@ -189,11 +189,11 @@ function tripal_cv_get_cvterm_by_synonym($synonym, $cv_id = NULL, $cv_name = 'tr
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_cv_get_cvterm_by_synonym',
-      '%new_function' => 'cvterm_retrieve'
+      '%new_function' => 'chado_cvterm_retrieve'
     )
   );
 
-  return cvterm_retrieve(array(
+  return chado_cvterm_retrieve(array(
     'synonym' => array(
       'name' => $synonym,
       'cv_id' => $cv_id,

tripal_cv/api/tripal_cv.api.inc

@@ -44,7 +44,7 @@
  *
  * @ingroup tripal_cv_api
  */
-function cv_retrieve($identifiers, $options = array()) {
+function chado_cv_retrieve($identifiers, $options = array()) {
 
   // Set Defaults
   if (!isset($options['include_fk'])) {
@@ -57,7 +57,7 @@ function cv_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_cv_api',
       TRIPAL_ERROR,
-      "cv_retrieve: The identifier passed in is expected to be an array with the key
+      "chado_cv_retrieve: The identifier passed in is expected to be an array with the key
         matching a column name in the cv table (ie: cv_id or name). You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
@@ -68,7 +68,7 @@ function cv_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_cv_api',
       TRIPAL_ERROR,
-      "cv_retrieve: You did not pass in anything to identify the cv you want. The identifier
+      "chado_cv_retrieve: You did not pass in anything to identify the cv you want. The identifier
         is expected to be an array with the key matching a column name in the cv table
         (ie: cv_id or name). You passed in %identifier.",
       array(
@@ -89,7 +89,7 @@ function cv_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_cv_api',
       TRIPAL_ERROR,
-      "cv_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
+      "chado_cv_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
       )
@@ -101,7 +101,7 @@ function cv_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_cv_api',
       TRIPAL_ERROR,
-      "cv_retrieve: chado_generate_var() failed to return a cv based on the identifiers
+      "chado_cv_retrieve: chado_generate_var() failed to return a cv based on the identifiers
         you passed in. You should check that your identifiers are correct, as well as, look
         for a chado_generate_var error for additional clues. You passed in %identifier.",
       array(
@@ -168,7 +168,7 @@ function cv_get_select_options() {
  *
  * @ingroup tripal_cv_api
  */
-function cvterm_retrieve($identifiers, $options = array()) {
+function chado_cvterm_retrieve($identifiers, $options = array()) {
 
   // Set Defaults
   if (!isset($options['include_fk'])) {
@@ -181,7 +181,7 @@ function cvterm_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_cv_api',
       TRIPAL_ERROR,
-      "cvterm_retrieve: The identifier passed in is expected to be an array with the key
+      "chado_cvterm_retrieve: The identifier passed in is expected to be an array with the key
         matching a column name in the cvterm table (ie: cvterm_id or name). You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
@@ -192,7 +192,7 @@ function cvterm_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_cv_api',
       TRIPAL_ERROR,
-      "cvterm_retrieve: You did not pass in anything to identify the cvterm you want. The identifier
+      "chado_cvterm_retrieve: You did not pass in anything to identify the cvterm you want. The identifier
         is expected to be an array with the key matching a column name in the cvterm table
         (ie: cvterm_id or name). You passed in %identifier.",
       array(
@@ -202,17 +202,25 @@ function cvterm_retrieve($identifiers, $options = array()) {
   }
 
   // If synonym was passed in, then process this first before calling chado_generate_var()
-  if (array_key_exists('synonym', $identifiers)) {
-    $sname = $identifiers['synonym']['name'];
+  if (isset($identifier['synonym'])) {
+    $synonym = $identifier['synonym']['name'];
 
-    $values = array('synonym' => $sname);
-    if (array_key_exists('cv_id', $identifiers['synonym'])) {
-      $values['cvterm_id'] = array('cv_id' => $identifiers['synonym']['cv_id']);
+    $values = array(
+       'synonym' => $synonym,
+    );
+    $statement = "sel_cvtermsynonym_sy";
+    if (isset($identifier['synonym']['cv_id'])) {
+      $values['cvterm_id'] = array('cv_id' => $identifier['synonym']['cv_id']);
+      $statement = "sel_cvtermsynonym_sycv";
     }
-    if (array_key_exists('cv_name', $identifiers['synonym'])) {
-      $values['cvterm_id'] = array('cv_id' => array('name' => $identifiers['synonym']['cv_name']));
+    if (isset($identifier['synonym']['cv_name'])) {
+      $values['cvterm_id'] = array('cv_id' => array('name' => $identifier['synonym']['cv_name']));
+      $statement = "sel_cvtermsynonym_sycv";
     }
-    $options = array('case_insensitive_columns' => array('name'));
+    $options = array(
+      'statement_name' => $statement,
+      'case_insensitive_columns' => array('name')
+    );
     $synonym = chado_select_record('cvtermsynonym', array('cvterm_id'), $values, $options);
 
     // if the synonym doens't exist or more than one record is returned then return false
@@ -232,10 +240,16 @@ function cvterm_retrieve($identifiers, $options = array()) {
     unset($identifiers['property']);
     $cvterm = chado_get_record_with_property('cvterm', $property, $identifiers, $options);
   }
+
   // Else we have a simple case and we can just use chado_generate_var to get the cvterm
   else {
+
     // Try to get the cvterm
-    $cvterm = chado_generate_var('cvterm', $identifiers, $options);
+    $cvterm = chado_generate_var(
+      'cvterm',
+      $identifiers,
+      $options
+    );
   }
 
   // Ensure the cvterm is singular. If it's an array then it is not singular
@@ -243,7 +257,7 @@ function cvterm_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_cv_api',
       TRIPAL_ERROR,
-      "cvterm_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
+      "chado_cvterm_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
       )
@@ -255,7 +269,7 @@ function cvterm_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_cv_api',
       TRIPAL_ERROR,
-      "cvterm_retrieve: chado_generate_var() failed to return a cvterm based on the identifiers
+      "chado_cvterm_retrieve: chado_generate_var() failed to return a cvterm based on the identifiers
         you passed in. You should check that your identifiers are correct, as well as, look
         for a chado_generate_var error for additional clues. You passed in %identifier.",
       array(

tripal_db/api/tripal_db.DEPRECATED.inc

@@ -7,9 +7,9 @@
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by db_retrieve().
+ * This function has been replaced by chado_db_retrieve().
  *
- * @see db_retrieve().
+ * @see chado_db_retrieve().
  */
 function tripal_db_get_db($select_values) {
 
@@ -19,19 +19,19 @@ function tripal_db_get_db($select_values) {
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_db_get_db',
-      '%new_function' => 'db_retrieve'
+      '%new_function' => 'chado_db_retrieve'
     )
   );
 
-  return db_retrieve($select_values);
+  return chado_db_retrieve($select_values);
 }
 
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by db_retrieve().
+ * This function has been replaced by chado_db_retrieve().
  *
- * @see db_retrieve().
+ * @see chado_db_retrieve().
  */
 function tripal_db_get_db_by_db_id($db_id) {
 
@@ -41,19 +41,19 @@ function tripal_db_get_db_by_db_id($db_id) {
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_db_get_db_by_db_id',
-      '%new_function' => 'db_retrieve'
+      '%new_function' => 'chado_db_retrieve'
     )
   );
 
-  return db_retrieve(array('db_id' => $db_id));
+  return chado_db_retrieve(array('db_id' => $db_id));
 }
 
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by db_retrieve().
+ * This function has been replaced by chado_db_retrieve().
  *
- * @see db_retrieve().
+ * @see chado_db_retrieve().
  */
 function tripal_db_get_db_by_name($name) {
 
@@ -63,11 +63,11 @@ function tripal_db_get_db_by_name($name) {
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_db_get_db_by_name',
-      '%new_function' => 'db_retrieve'
+      '%new_function' => 'chado_db_retrieve'
     )
   );
 
-  return db_retrieve(array('name' => $name));
+  return chado_db_retrieve(array('name' => $name));
 }
 
 /**
@@ -95,9 +95,9 @@ function tripal_db_get_db_options() {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by db_retrieve().
+ * This function has been replaced by chado_db_retrieve().
  *
- * @see dbxref_retrieve().
+ * @see chado_dbxref_retrieve().
  */
 function tripal_db_get_dbxref($select_values) {
 
@@ -107,19 +107,19 @@ function tripal_db_get_dbxref($select_values) {
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_db_get_dbxref',
-      '%new_function' => 'dbxref_retrieve'
+      '%new_function' => 'chado_dbxref_retrieve'
     )
   );
 
-  return dbxref_retrieve($select_values);
+  return chado_dbxref_retrieve($select_values);
 }
 
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by db_retrieve().
+ * This function has been replaced by chado_db_retrieve().
  *
- * @see dbxref_retrieve().
+ * @see chado_dbxref_retrieve().
  */
 function tripal_db_get_dbxref_by_accession($accession, $db_id=0) {
 
@@ -129,7 +129,7 @@ function tripal_db_get_dbxref_by_accession($accession, $db_id=0) {
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_db_get_dbxref_by_accession',
-      '%new_function' => 'dbxref_retrieve'
+      '%new_function' => 'chado_dbxref_retrieve'
     )
   );
 
@@ -141,7 +141,7 @@ function tripal_db_get_dbxref_by_accession($accession, $db_id=0) {
       'db_id' => $db_id
     );
   }
-  return dbxref_retrieve($identifiers);
+  return chado_dbxref_retrieve($identifiers);
 }
 
 /**

tripal_db/api/tripal_db.api.inc

@@ -54,7 +54,7 @@
  *
  * @ingroup tripal_db_api
  */
-function db_retrieve($identifiers, $options = array()) {
+function chado_db_retrieve($identifiers, $options = array()) {
 
   // Set Defaults
   if (!isset($options['include_fk'])) {
@@ -67,7 +67,7 @@ function db_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_db_api',
       TRIPAL_ERROR,
-      "db_retrieve: The identifier passed in is expected to be an array with the key
+      "chado_db_retrieve: The identifier passed in is expected to be an array with the key
         matching a column name in the db table (ie: db_id or name). You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
@@ -78,7 +78,7 @@ function db_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_db_api',
       TRIPAL_ERROR,
-      "db_retrieve: You did not pass in anything to identify the db you want. The identifier
+      "chado_db_retrieve: You did not pass in anything to identify the db you want. The identifier
         is expected to be an array with the key matching a column name in the db table
         (ie: db_id or name). You passed in %identifier.",
       array(
@@ -99,7 +99,7 @@ function db_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_db_api',
       TRIPAL_ERROR,
-      "db_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
+      "chado_db_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
       )
@@ -111,7 +111,7 @@ function db_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_db_api',
       TRIPAL_ERROR,
-      "db_retrieve: chado_generate_var() failed to return a db based on the identifiers
+      "chado_db_retrieve: chado_generate_var() failed to return a db based on the identifiers
         you passed in. You should check that your identifiers are correct, as well as, look
         for a chado_generate_var error for additional clues. You passed in %identifier.",
       array(
@@ -200,7 +200,7 @@ function db_get_select_options() {
  *
  * @ingroup tripal_db_api
  */
-function dbxref_retrieve($identifiers, $options = array()) {
+function chado_dbxref_retrieve($identifiers, $options = array()) {
 
   // Set Defaults
   if (!isset($options['include_fk'])) {
@@ -213,7 +213,7 @@ function dbxref_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_db_api',
       TRIPAL_ERROR,
-      "dbxref_retrieve: The identifier passed in is expected to be an array with the key
+      "chado_dbxref_retrieve: The identifier passed in is expected to be an array with the key
         matching a column name in the dbxref table (ie: dbxref_id or name). You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
@@ -224,7 +224,7 @@ function dbxref_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_db_api',
       TRIPAL_ERROR,
-      "dbxref_retrieve: You did not pass in anything to identify the dbxref you want. The identifier
+      "chado_dbxref_retrieve: You did not pass in anything to identify the dbxref you want. The identifier
         is expected to be an array with the key matching a column name in the dbxref table
         (ie: dbxref_id or name). You passed in %identifier.",
       array(
@@ -254,7 +254,7 @@ function dbxref_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_db_api',
       TRIPAL_ERROR,
-      "dbxref_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
+      "chado_dbxref_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
       )
@@ -266,7 +266,7 @@ function dbxref_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_db_api',
       TRIPAL_ERROR,
-      "dbxref_retrieve: chado_generate_var() failed to return a dbxref based on the identifiers
+      "chado_dbxref_retrieve: chado_generate_var() failed to return a dbxref based on the identifiers
         you passed in. You should check that your identifiers are correct, as well as, look
         for a chado_generate_var error for additional clues. You passed in %identifier.",
       array(
@@ -413,11 +413,9 @@ function chado_dbxref_insert_record($values) {
  * @param $record_id
  *   The primary key of the basetable to associate the dbxref with. This should be in integer.
  * @param $dbxref
- *   An associative array describing the dbxref. Valid keys include: 
- *     'accession' => the accession for the dbxref, 
- *     'db_name' => the name of the database the dbxref belongs to;
- *     'db_id' => the db_id from the databaes table of Chado. Substitutes for 'db_name'
- *     'dbxref_id' => the dbxref_id of the dbxref to assocaite.  Substitutes for all other keys.
+ *   An associative array describing the dbxref. Valid keys include: 'accession' => the
+ *   accession for the dbxref, 'db_name' => the name of the database the dbxref belongs to;
+ *   'db_id' => the primary key of the database the dbxref belongs to.
  * @param $options
  *   An associative array of options. Valid keys include:
  *    - insert_dbxref: Insert the dbxref if it doesn't already exist. TRUE is the default
@@ -439,8 +437,7 @@ function chado_associate_dbxref($basetable, $record_id, $dbxref, $options = arra
     );
     if (isset($dbxref['db_id'])) {
       $values['db_id'] = $dbxref['db_id'];
-    } 
-    elseif (isset($dbxref['db_name'])) {
+    } elseif (isset($dbxref['db_name'])) {
       $values['db_id'] = array(
         'name' => $dbxref['db_name']
       );

tripal_organism/api/tripal_organism.DEPRECATED.inc

@@ -7,9 +7,9 @@
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by organism_retrieve().
+ * This function has been replaced by chado_organism_retrieve().
  *
- * @see organism_retrieve().
+ * @see chado_organism_retrieve().
  */
 function tripal_organism_get_organism_by_nid($nid) {
 
@@ -19,19 +19,19 @@ function tripal_organism_get_organism_by_nid($nid) {
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_organism_get_organism_by_nid',
-      '%new_function' => 'organism_retrieve'
+      '%new_function' => 'chado_organism_retrieve'
     )
   );
 
-  return organism_retrieve(array('nid' => $nid));
+  return chado_organism_retrieve(array('nid' => $nid));
 }
 
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by organism_retrieve().
+ * This function has been replaced by chado_organism_retrieve().
  *
- * @see organism_retrieve().
+ * @see chado_organism_retrieve().
  */
 function tripal_organism_get_organism_by_organism_id($organism_id) {
 
@@ -41,11 +41,11 @@ function tripal_organism_get_organism_by_organism_id($organism_id) {
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_organism_get_organism_by_organism_id',
-      '%new_function' => 'organism_retrieve'
+      '%new_function' => 'chado_organism_retrieve'
     )
   );
 
-  return organism_retrieve(array('organism_id' => $organism_id));
+  return chado_organism_retrieve(array('organism_id' => $organism_id));
 }
 
 /**

tripal_organism/api/tripal_organism.api.inc

@@ -39,7 +39,7 @@
  *
  * @ingroup tripal_organism_api
  */
-function organism_retrieve($identifiers, $options = array()) {
+function chado_organism_retrieve($identifiers, $options = array()) {
 
   // Set Defaults
   if (!isset($options['include_fk'])) {
@@ -52,7 +52,7 @@ function organism_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_organism_api',
       TRIPAL_ERROR,
-      "organism_retrieve: The identifier passed in is expected to be an array with the key
+      "chado_organism_retrieve: The identifier passed in is expected to be an array with the key
         matching a column name in the organism table (ie: organism_id or name). You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
@@ -63,7 +63,7 @@ function organism_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_organism_api',
       TRIPAL_ERROR,
-      "organism_retrieve: You did not pass in anything to identify the organism you want. The identifier
+      "chado_organism_retrieve: You did not pass in anything to identify the organism you want. The identifier
         is expected to be an array with the key matching a column name in the organism table
         (ie: organism_id or name). You passed in %identifier.",
       array(
@@ -95,7 +95,7 @@ function organism_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_organism_api',
       TRIPAL_ERROR,
-      "organism_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
+      "chado_organism_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
       )
@@ -107,7 +107,7 @@ function organism_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_organism_api',
       TRIPAL_ERROR,
-      "organism_retrieve: chado_generate_var() failed to return a organism based on the identifiers
+      "chado_organism_retrieve: chado_generate_var() failed to return a organism based on the identifiers
         you passed in. You should check that your identifiers are correct, as well as, look
         for a chado_generate_var error for additional clues. You passed in %identifier.",
       array(

tripal_stock/api/tripal_stock.DEPRECATED.inc

@@ -7,9 +7,9 @@
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by stock_retrieve().
+ * This function has been replaced by chado_stock_retrieve().
  *
- * @see stock_retrieve().
+ * @see chado_stock_retrieve().
  */
 function tripal_stock_get_stock_by_nid($nid) {
 
@@ -19,19 +19,19 @@ function tripal_stock_get_stock_by_nid($nid) {
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_stock_get_stock_by_nid',
-      '%new_function' => 'stock_retrieve'
+      '%new_function' => 'chado_stock_retrieve'
     )
   );
 
-  return stock_retrieve(array('nid' => $nid));
+  return chado_stock_retrieve(array('nid' => $nid));
 }
 
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by stock_retrieve().
+ * This function has been replaced by chado_stock_retrieve().
  *
- * @see stock_retrieve().
+ * @see chado_stock_retrieve().
  */
 function tripal_stock_get_stock_by_stock_id($stock_id) {
 
@@ -41,19 +41,19 @@ function tripal_stock_get_stock_by_stock_id($stock_id) {
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_stock_get_stock_by_stock_id',
-      '%new_function' => 'stock_retrieve'
+      '%new_function' => 'chado_stock_retrieve'
     )
   );
 
-  return stock_retrieve(array('stock_id' => $stock_id));
+  return chado_stock_retrieve(array('stock_id' => $stock_id));
 }
 
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by stock_retrieve_multiple().
+ * This function has been replaced by chado_stock_retrieve_multiple().
  *
- * @see stock_retrieve_multiple().
+ * @see chado_stock_retrieve_multiple().
  */
 function tripal_stock_get_all_stocks() {
 
@@ -82,9 +82,9 @@ function tripal_stock_get_all_stocks() {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by stock_retrieve_multiple().
+ * This function has been replaced by chado_stock_retrieve_multiple().
  *
- * @see stock_retrieve_multiple().
+ * @see chado_stock_retrieve_multiple().
  */
 function tripal_stock_get_stocks($values) {
 
@@ -94,19 +94,19 @@ function tripal_stock_get_stocks($values) {
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_stock_get_stocks',
-      '%new_function' => 'stock_retrieve_multiple'
+      '%new_function' => 'chado_stock_retrieve_multiple'
     )
   );
 
-  return stock_retrieve_multiple($values);
+  return chado_stock_retrieve_multiple($values);
 }
 
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by stock_retrieve().
+ * This function has been replaced by chado_stock_retrieve().
  *
- * @see stock_retrieve().
+ * @see chado_stock_retrieve().
  */
 function tripal_stock_get_stocks_by_stockprop($stockprop_values, $stock_values) {
 
@@ -116,18 +116,18 @@ function tripal_stock_get_stocks_by_stockprop($stockprop_values, $stock_values)
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_stock_get_stocks_by_stockprop',
-      '%new_function' => 'stock_retrieve'
+      '%new_function' => 'chado_stock_retrieve'
     )
   );
 
   $stock_values['property'] = $stockprop_values;
-  return stock_retrieve_multiple($stock_values);
+  return chado_stock_retrieve_multiple($stock_values);
 }
 
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by stock_retrieve().
+ * This function has been replaced by chado_stock_retrieve().
  *
  * Return all stocks with a given name identifier
  *  which might match stock.name, stock.uniquename, dbxref.accession,
@@ -141,7 +141,7 @@ function tripal_stock_get_stocks_by_stockprop($stockprop_values, $stock_values)
  * @return
  *   An array of stock node objects
  *
- * @see stock_retrieve().
+ * @see chado_stock_retrieve().
  */
 function tripal_stock_get_stock_by_name_identifier($name, $organism_id) {
 
@@ -151,7 +151,7 @@ function tripal_stock_get_stock_by_name_identifier($name, $organism_id) {
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
       '%old_function'=>'tripal_stock_get_stock_by_name_identifier',
-      '%new_function' => 'stock_retrieve'
+      '%new_function' => 'chado_stock_retrieve'
     )
   );
 

tripal_stock/api/tripal_stock.api.inc

@@ -39,7 +39,7 @@
  *
  * @ingroup tripal_stock_api
  */
-function stock_retrieve($identifiers, $options = array()) {
+function chado_stock_retrieve($identifiers, $options = array()) {
 
   // Set Defaults
   if (!isset($options['include_fk'])) {
@@ -52,7 +52,7 @@ function stock_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_stock_api',
       TRIPAL_ERROR,
-      "stock_retrieve: The identifier passed in is expected to be an array with the key
+      "chado_stock_retrieve: The identifier passed in is expected to be an array with the key
         matching a column name in the stock table (ie: stock_id or name). You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
@@ -63,7 +63,7 @@ function stock_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_stock_api',
       TRIPAL_ERROR,
-      "stock_retrieve: You did not pass in anything to identify the stock you want. The identifier
+      "chado_stock_retrieve: You did not pass in anything to identify the stock you want. The identifier
         is expected to be an array with the key matching a column name in the stock table
         (ie: stock_id or name). You passed in %identifier.",
       array(
@@ -95,7 +95,7 @@ function stock_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_stock_api',
       TRIPAL_ERROR,
-      "stock_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
+      "chado_stock_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
       )
@@ -107,7 +107,7 @@ function stock_retrieve($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_stock_api',
       TRIPAL_ERROR,
-      "stock_retrieve: chado_generate_var() failed to return a stock based on the identifiers
+      "chado_stock_retrieve: chado_generate_var() failed to return a stock based on the identifiers
         you passed in. You should check that your identifiers are correct, as well as, look
         for a chado_generate_var error for additional clues. You passed in %identifier.",
       array(
@@ -139,7 +139,7 @@ function stock_retrieve($identifiers, $options = array()) {
  *
  * @ingroup tripal_stock_api
  */
-function stock_retrieve_multiple($identifiers, $options = array()) {
+function chado_stock_retrieve_multiple($identifiers, $options = array()) {
 
   // Set Defaults
   if (!isset($options['include_fk'])) {
@@ -152,7 +152,7 @@ function stock_retrieve_multiple($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_stock_api',
       TRIPAL_ERROR,
-      "stock_retrieve: The identifier passed in is expected to be an array with the key
+      "chado_stock_retrieve: The identifier passed in is expected to be an array with the key
         matching a column name in the stock table (ie: stock_id or name). You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
@@ -163,7 +163,7 @@ function stock_retrieve_multiple($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_stock_api',
       TRIPAL_ERROR,
-      "stock_retrieve: You did not pass in anything to identify the stock you want. The identifier
+      "chado_stock_retrieve: You did not pass in anything to identify the stock you want. The identifier
         is expected to be an array with the key matching a column name in the stock table
         (ie: stock_id or name). You passed in %identifier.",
       array(
@@ -195,7 +195,7 @@ function stock_retrieve_multiple($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_stock_api',
       TRIPAL_ERROR,
-      "stock_retrieve: chado_generate_var() failed to return a stock based on the identifiers
+      "chado_stock_retrieve: chado_generate_var() failed to return a stock based on the identifiers
         you passed in. You should check that your identifiers are correct, as well as, look
         for a chado_generate_var error for additional clues. You passed in %identifier.",
       array(