API: Changed chado_get_[table] naming to [table]_retrieve naming

tripal_analysis/api/tripal_analysis.DEPRECATED.inc

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- * This function has been replaced by chado_get_analysis().
+ * This function has been replaced by analysis_retrieve().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

tripal_analysis/api/tripal_analysis.api.inc

@@ -70,7 +70,7 @@ function tripal_analysis_unregister_child($modulename) {
  *
  * @ingroup tripal_analysis_api
  */
-function chado_get_analysis($identifier, $options) {
+function analysis_retrieve($identifier, $options) {
 
   // Set Defaults
   if (!isset($options['include_fk'])) {
@@ -126,7 +126,7 @@ function chado_get_analysis($identifier, $options) {
     tripal_report_error(
       'tripal_analysis_api',
       TRIPAL_ERROR,
-      "chado_get_analysis: The identifiers you passed in were not unique. You passed in %identifier.",
+      "analysis_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
       )
@@ -138,7 +138,7 @@ function chado_get_analysis($identifier, $options) {
     tripal_report_error(
       'tripal_analysis_api',
       TRIPAL_ERROR,
-      "chado_get_analysis: chado_generate_var() failed to return a analysis based on the identifiers
+      "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 chado_get_cv().
+ * This function has been replaced by cv_retrieve().
  *
- * @see chado_get_cv().
+ * @see 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' => 'chado_get_cv'
+      '%new_function' => 'cv_retrieve'
     )
   );
 
-  return chado_get_cv($select_values);
+  return cv_retrieve($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 chado_get_cv().
+ * This function has been replaced by cv_retrieve().
  *
- * @see chado_get_cv().
+ * @see 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' => 'chado_get_cv'
+      '%new_function' => 'cv_retrieve'
     )
   );
 
-  return chado_get_cv(array('name' => $name));
+  return 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 chado_get_cv().
+ * This function has been replaced by cv_retrieve().
  *
- * @see chado_get_cv().
+ * @see 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' => 'chado_get_cv'
+      '%new_function' => 'cv_retrieve'
     )
   );
 
-  return chado_get_cv(array('cv_id' => $id));
+  return 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 chado_get_cv().
+ * This function has been replaced by cv_retrieve().
  *
- * @see chado_get_cv().
+ * @see 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' => 'chado_get_cv'
+      '%new_function' => 'cv_retrieve'
     )
   );
 
-  $cv = chado_get_cv(array('name' => $cv_name));
+  $cv = cv_retrieve(array('name' => $cv_name));
   if (isset($cv->cv_id)) {
     return $cv->cv_id;
   }
@@ -123,9 +123,9 @@ function tripal_cv_get_cv_options() {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by chado_get_cvterm().
+ * This function has been replaced by cvterm_retrieve().
  *
- * @see chado_get_cvterm().
+ * @see cvterm_retrieve().
  */
 function tripal_cv_get_cvterm_by_id($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' => 'chado_get_cvterm'
+      '%new_function' => 'cvterm_retrieve'
     )
   );
 
-  return chado_get_cvterm(array('cvterm_id' => $cvterm_id));
+  return 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 chado_get_cvterm().
+ * This function has been replaced by cvterm_retrieve().
  *
- * @see chado_get_cvterm().
+ * @see 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' => 'chado_get_cvterm'
+      '%new_function' => 'cvterm_retrieve'
     )
   );
 
@@ -171,15 +171,15 @@ function tripal_cv_get_cvterm_by_name($name, $cv_id = NULL, $cv_name = 'tripal')
     );
   }
 
-  return chado_get_cvterm($identifiers);
+  return cvterm_retrieve($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 chado_get_cvterm().
+ * This function has been replaced by cvterm_retrieve().
  *
- * @see chado_get_cvterm().
+ * @see 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' => 'chado_get_cvterm'
+      '%new_function' => 'cvterm_retrieve'
     )
   );
 
-  return chado_get_cvterm(array(
+  return 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 chado_get_cv($identifiers, $options = array()) {
+function cv_retrieve($identifiers, $options = array()) {
 
   // Set Defaults
   if (!isset($options['include_fk'])) {
@@ -57,7 +57,7 @@ function chado_get_cv($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_cv_api',
       TRIPAL_ERROR,
-      "chado_get_cv: The identifier passed in is expected to be an array with the key
+      "cv_retrieve: The identifier passed in is expected to be an array with the key
         matching a column name in the cv table (ie: cv_id or name). You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
@@ -68,7 +68,7 @@ function chado_get_cv($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_cv_api',
       TRIPAL_ERROR,
-      "chado_get_cv: You did not pass in anything to identify the cv you want. The identifier
+      "cv_retrieve: You did not pass in anything to identify the cv you want. The identifier
         is expected to be an array with the key matching a column name in the cv table
         (ie: cv_id or name). You passed in %identifier.",
       array(
@@ -89,7 +89,7 @@ function chado_get_cv($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_cv_api',
       TRIPAL_ERROR,
-      "chado_get_cv: The identifiers you passed in were not unique. You passed in %identifier.",
+      "cv_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
       )
@@ -101,7 +101,7 @@ function chado_get_cv($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_cv_api',
       TRIPAL_ERROR,
-      "chado_get_cv: chado_generate_var() failed to return a cv based on the identifiers
+      "cv_retrieve: chado_generate_var() failed to return a cv based on the identifiers
         you passed in. You should check that your identifiers are correct, as well as, look
         for a chado_generate_var error for additional clues. You passed in %identifier.",
       array(
@@ -168,7 +168,7 @@ function cv_get_select_options() {
  *
  * @ingroup tripal_cv_api
  */
-function chado_get_cvterm($identifiers, $options = array()) {
+function cvterm_retrieve($identifiers, $options = array()) {
 
   // Set Defaults
   if (!isset($options['include_fk'])) {
@@ -181,7 +181,7 @@ function chado_get_cvterm($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_cv_api',
       TRIPAL_ERROR,
-      "chado_get_cvterm: The identifier passed in is expected to be an array with the key
+      "cvterm_retrieve: The identifier passed in is expected to be an array with the key
         matching a column name in the cvterm table (ie: cvterm_id or name). You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
@@ -192,7 +192,7 @@ function chado_get_cvterm($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_cv_api',
       TRIPAL_ERROR,
-      "chado_get_cvterm: You did not pass in anything to identify the cvterm you want. The identifier
+      "cvterm_retrieve: You did not pass in anything to identify the cvterm you want. The identifier
         is expected to be an array with the key matching a column name in the cvterm table
         (ie: cvterm_id or name). You passed in %identifier.",
       array(
@@ -257,7 +257,7 @@ function chado_get_cvterm($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_cv_api',
       TRIPAL_ERROR,
-      "chado_get_cvterm: The identifiers you passed in were not unique. You passed in %identifier.",
+      "cvterm_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
       )
@@ -269,7 +269,7 @@ function chado_get_cvterm($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_cv_api',
       TRIPAL_ERROR,
-      "chado_get_cvterm: chado_generate_var() failed to return a cvterm based on the identifiers
+      "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 chado_get_db().
+ * This function has been replaced by db_retrieve().
  *
- * @see chado_get_db().
+ * @see 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' => 'chado_get_db'
+      '%new_function' => 'db_retrieve'
     )
   );
 
-  return chado_get_db($select_values);
+  return db_retrieve($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 chado_get_db().
+ * This function has been replaced by db_retrieve().
  *
- * @see chado_get_db().
+ * @see 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' => 'chado_get_db'
+      '%new_function' => 'db_retrieve'
     )
   );
 
-  return chado_get_db(array('db_id' => $db_id));
+  return 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 chado_get_db().
+ * This function has been replaced by db_retrieve().
  *
- * @see chado_get_db().
+ * @see 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' => 'chado_get_db'
+      '%new_function' => 'db_retrieve'
     )
   );
 
-  return chado_get_db(array('name' => $name));
+  return 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 chado_get_db().
+ * This function has been replaced by db_retrieve().
  *
- * @see chado_get_dbxref().
+ * @see 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' => 'chado_get_dbxref'
+      '%new_function' => 'dbxref_retrieve'
     )
   );
 
-  return chado_get_dbxref($select_values);
+  return dbxref_retrieve($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 chado_get_db().
+ * This function has been replaced by db_retrieve().
  *
- * @see chado_get_dbxref().
+ * @see 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' => 'chado_get_dbxref'
+      '%new_function' => 'dbxref_retrieve'
     )
   );
 
@@ -141,7 +141,7 @@ function tripal_db_get_dbxref_by_accession($accession, $db_id=0) {
       'db_id' => $db_id
     );
   }
-  return chado_get_dbxref($identifiers);
+  return dbxref_retrieve($identifiers);
 }
 
 /**

tripal_db/api/tripal_db.api.inc

@@ -54,7 +54,7 @@
  *
  * @ingroup tripal_db_api
  */
-function chado_get_db($identifiers, $options = array()) {
+function db_retrieve($identifiers, $options = array()) {
 
   // Set Defaults
   if (!isset($options['include_fk'])) {
@@ -67,7 +67,7 @@ function chado_get_db($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_db_api',
       TRIPAL_ERROR,
-      "chado_get_db: The identifier passed in is expected to be an array with the key
+      "db_retrieve: The identifier passed in is expected to be an array with the key
         matching a column name in the db table (ie: db_id or name). You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
@@ -78,7 +78,7 @@ function chado_get_db($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_db_api',
       TRIPAL_ERROR,
-      "chado_get_db: You did not pass in anything to identify the db you want. The identifier
+      "db_retrieve: You did not pass in anything to identify the db you want. The identifier
         is expected to be an array with the key matching a column name in the db table
         (ie: db_id or name). You passed in %identifier.",
       array(
@@ -99,7 +99,7 @@ function chado_get_db($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_db_api',
       TRIPAL_ERROR,
-      "chado_get_db: The identifiers you passed in were not unique. You passed in %identifier.",
+      "db_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
       )
@@ -111,7 +111,7 @@ function chado_get_db($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_db_api',
       TRIPAL_ERROR,
-      "chado_get_db: chado_generate_var() failed to return a db based on the identifiers
+      "db_retrieve: chado_generate_var() failed to return a db based on the identifiers
         you passed in. You should check that your identifiers are correct, as well as, look
         for a chado_generate_var error for additional clues. You passed in %identifier.",
       array(
@@ -200,7 +200,7 @@ function db_get_select_options() {
  *
  * @ingroup tripal_db_api
  */
-function chado_get_dbxref($identifiers, $options = array()) {
+function dbxref_retrieve($identifiers, $options = array()) {
 
   // Set Defaults
   if (!isset($options['include_fk'])) {
@@ -213,7 +213,7 @@ function chado_get_dbxref($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_db_api',
       TRIPAL_ERROR,
-      "chado_get_dbxref: The identifier passed in is expected to be an array with the key
+      "dbxref_retrieve: The identifier passed in is expected to be an array with the key
         matching a column name in the dbxref table (ie: dbxref_id or name). You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
@@ -224,7 +224,7 @@ function chado_get_dbxref($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_db_api',
       TRIPAL_ERROR,
-      "chado_get_dbxref: You did not pass in anything to identify the dbxref you want. The identifier
+      "dbxref_retrieve: You did not pass in anything to identify the dbxref you want. The identifier
         is expected to be an array with the key matching a column name in the dbxref table
         (ie: dbxref_id or name). You passed in %identifier.",
       array(
@@ -254,7 +254,7 @@ function chado_get_dbxref($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_db_api',
       TRIPAL_ERROR,
-      "chado_get_dbxref: The identifiers you passed in were not unique. You passed in %identifier.",
+      "dbxref_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
       )
@@ -266,7 +266,7 @@ function chado_get_dbxref($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_db_api',
       TRIPAL_ERROR,
-      "chado_get_dbxref: chado_generate_var() failed to return a dbxref based on the identifiers
+      "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(

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 chado_get_organism().
+ * This function has been replaced by organism_retrieve().
  *
- * @see chado_get_organism().
+ * @see 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' => 'chado_get_organism'
+      '%new_function' => 'organism_retrieve'
     )
   );
 
-  return chado_get_organism(array('nid' => $nid));
+  return 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 chado_get_organism().
+ * This function has been replaced by organism_retrieve().
  *
- * @see chado_get_organism().
+ * @see 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' => 'chado_get_organism'
+      '%new_function' => 'organism_retrieve'
     )
   );
 
-  return chado_get_organism(array('organism_id' => $organism_id));
+  return organism_retrieve(array('organism_id' => $organism_id));
 }
 
 /**

tripal_organism/api/tripal_organism.api.inc

@@ -39,7 +39,7 @@
  *
  * @ingroup tripal_organism_api
  */
-function chado_get_organism($identifiers, $options = array()) {
+function organism_retrieve($identifiers, $options = array()) {
 
   // Set Defaults
   if (!isset($options['include_fk'])) {
@@ -52,7 +52,7 @@ function chado_get_organism($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_organism_api',
       TRIPAL_ERROR,
-      "chado_get_organism: The identifier passed in is expected to be an array with the key
+      "organism_retrieve: The identifier passed in is expected to be an array with the key
         matching a column name in the organism table (ie: organism_id or name). You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
@@ -63,7 +63,7 @@ function chado_get_organism($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_organism_api',
       TRIPAL_ERROR,
-      "chado_get_organism: You did not pass in anything to identify the organism you want. The identifier
+      "organism_retrieve: You did not pass in anything to identify the organism you want. The identifier
         is expected to be an array with the key matching a column name in the organism table
         (ie: organism_id or name). You passed in %identifier.",
       array(
@@ -95,7 +95,7 @@ function chado_get_organism($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_organism_api',
       TRIPAL_ERROR,
-      "chado_get_organism: The identifiers you passed in were not unique. You passed in %identifier.",
+      "organism_retrieve: The identifiers you passed in were not unique. You passed in %identifier.",
       array(
         '%identifier'=> print_r($identifiers, TRUE)
       )
@@ -107,7 +107,7 @@ function chado_get_organism($identifiers, $options = array()) {
     tripal_report_error(
       'tripal_organism_api',
       TRIPAL_ERROR,
-      "chado_get_organism: chado_generate_var() failed to return a organism based on the identifiers
+      "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 chado_get_stock().
+ * This function has been replaced by stock_retrieve().
  *
- * @see chado_get_stock().
+ * @see 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' => 'chado_get_stock'
+      '%new_function' => 'stock_retrieve'
     )
   );
 
-  return chado_get_stock(array('nid' => $nid));
+  return 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 chado_get_stock().
+ * This function has been replaced by stock_retrieve().
  *
- * @see chado_get_stock().
+ * @see 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' => 'chado_get_stock'
+      '%new_function' => 'stock_retrieve'
     )
   );
 
-  return chado_get_stock(array('stock_id' => $stock_id));
+  return 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 chado_get_multiple_stocks().
+ * This function has been replaced by stock_retrieve_multiple().
  *
- * @see chado_get_multiple_stocks().
+ * @see 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 chado_get_multiple_stocks().
+ * This function has been replaced by stock_retrieve_multiple().
  *
- * @see chado_get_multiple_stocks().
+ * @see 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' => 'chado_get_multiple_stocks'
+      '%new_function' => 'stock_retrieve_multiple'
     )
   );
 
-  return chado_get_multiple_stocks($values);
+  return stock_retrieve_multiple($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 chado_get_stock().
+ * This function has been replaced by stock_retrieve().
  *
- * @see chado_get_stock().
+ * @see 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' => 'chado_get_stock'
+      '%new_function' => 'stock_retrieve'
     )
   );
 
   $stock_values['property'] = $stockprop_values;
-  return chado_get_multiple_stocks($stock_values);
+  return 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 chado_get_stock().
+ * This function has been replaced by 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, $stock_values)
  * @return
  *   An array of stock node objects
  *
- * @see chado_get_stock().
+ * @see stock_retrieve().
  */
 function tripal_stock_get_stock_by_name_identifier($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' => 'chado_get_stock'
+      '%new_function' => 'stock_retrieve'
     )
   );
 

tripal_stock/api/tripal_stock.api.inc

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