Cleaned up a few functions which weren't actually the same as in Tripal 1.x and added a little bit more doc

tripal_core/api/tripal_core.DEPRECATED.inc

@@ -7,14 +7,16 @@
 /**
  * @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- * This function has been replaced by @see chado_get_id_from_nid().
+ * This function has been replaced by chado_get_id_from_nid().
+ *
+ * @see chado_get_id_from_nid()
  */
-function chado_get_id_for_node($table, $nid) {
+function chado_get_id_for_node($table, $node) {
 
   tripal_report_error(
     'tripal_api',
     TRIPAL_NOTICE,
-    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    "DEPRECATED: %old_function has been replaced with %new_function. The arguments have been changed slightly (ie: $nid instead of $node). Please update your code.",
     array(
       '%old_function'=>'chado_get_id_for_node',
       '%new_function' => 'chado_get_id_from_nid'
@@ -22,13 +24,15 @@ function chado_get_id_for_node($table, $nid) {
   );
 
   //New API Function
-  return chado_get_id_from_nid($table, $nid);
+  return chado_get_id_from_nid($table, $node->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- * This function has been replaced by @see chado_get_nid_from_id().
+ * This function has been replaced by chado_get_nid_from_id().
+ *
+ * @see chado_get_nid_from_id().
  */
 function chado_get_node_id($table, $id) {
 
@@ -49,7 +53,9 @@ function chado_get_node_id($table, $id) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_cleanup_orphaned_nodes().
+ * This function has been replaced by chado_cleanup_orphaned_nodes().
+ *
+ * @see chado_cleanup_orphaned_nodes().
  */
 function tripal_core_chado_node_cleanup_orphaned($table, $job_id = NULL) {
 
@@ -70,7 +76,9 @@ function tripal_core_chado_node_cleanup_orphaned($table, $job_id = NULL) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_add_node_form_dbxrefs().
+ * This function has been replaced by chado_add_node_form_dbxrefs().
+ *
+ * @see chado_add_node_form_dbxrefs().
  */
 function chado_node_additional_dbxrefs_form(&$form, &$form_state, $details) {
 
@@ -91,7 +99,9 @@ function chado_node_additional_dbxrefs_form(&$form, &$form_state, $details) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_retrieve_node_form_dbxrefs().
+ * This function has been replaced by chado_retrieve_node_form_dbxrefs().
+ *
+ * @see chado_retrieve_node_form_dbxrefs().
  */
 function chado_node_additional_dbxrefs_form_retreive($node) {
 
@@ -112,7 +122,9 @@ function chado_node_additional_dbxrefs_form_retreive($node) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_update_node_form_dbxrefs().
+ * This function has been replaced by chado_update_node_form_dbxrefs().
+ *
+ * @see chado_update_node_form_dbxrefs().
  */
 function chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details, $retrieved_dbxrefs = FALSE) {
 
@@ -133,7 +145,9 @@ function chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details, $ret
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_add_node_form_properties().
+ * This function has been replaced by chado_add_node_form_properties().
+ *
+ * @see chado_add_node_form_properties().
  */
 function chado_node_properties_form($form, $form_state, $details) {
 
@@ -154,7 +168,9 @@ function chado_node_properties_form($form, $form_state, $details) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_retrieve_node_form_properties().
+ * This function has been replaced by chado_retrieve_node_form_properties().
+ *
+ * @see chado_retrieve_node_form_properties().
  */
 function chado_node_properties_form_retreive($node) {
 
@@ -175,7 +191,9 @@ function chado_node_properties_form_retreive($node) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_update_node_form_properties().
+ * This function has been replaced by chado_update_node_form_properties().
+ *
+ * @see chado_update_node_form_properties().
  */
 function chado_node_properties_form_update_properties($node, $details, $retrieved_properties = FALSE) {
 
@@ -196,7 +214,9 @@ function chado_node_properties_form_update_properties($node, $details, $retrieve
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_add_node_form_relationships().
+ * This function has been replaced by chado_add_node_form_relationships().
+ *
+ * @see chado_add_node_form_relationships().
  */
 function chado_node_relationships_form(&$form, &$form_state, $details) {
 
@@ -217,7 +237,9 @@ function chado_node_relationships_form(&$form, &$form_state, $details) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_retrieve_node_form_relationships().
+ * This function has been replaced by chado_retrieve_node_form_relationships().
+ *
+ * @see chado_retrieve_node_form_relationships().
  */
 function chado_node_relationships_form_retreive($node) {
 
@@ -238,7 +260,9 @@ function chado_node_relationships_form_retreive($node) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_update_node_form_relationships().
+ * This function has been replaced by chado_update_node_form_relationships().
+ *
+ * @see chado_update_node_form_relationships().
  */
 function chado_node_relationships_form_update_relationships($node, $details, $retrieved_relationships = FALSE) {
 
@@ -259,7 +283,9 @@ function chado_node_relationships_form_update_relationships($node, $details, $re
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_node_sync_form().
+ * This function has been replaced by chado_node_sync_form().
+ *
+ * @see chado_node_sync_form().
  */
 function tripal_core_chado_node_sync_form($form, &$form_state) {
 
@@ -280,7 +306,9 @@ function tripal_core_chado_node_sync_form($form, &$form_state) {
 /**
  * @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 @see chado_node_sync_records().
+ * This function has been replaced by chado_node_sync_records().
+ *
+ * @see chado_node_sync_records().
  */
 function tripal_core_chado_node_sync_records($base_table, $max_sync = FALSE, $organism_id = FALSE,
     $types = array(), $ids = array(), $job_id = NULL) {
@@ -320,7 +348,9 @@ function tripal_core_is_tripal_node_type() {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_schema_get_foreign_key().
+ * This function has been replaced by chado_schema_get_foreign_key().
+ *
+ * @see chado_schema_get_foreign_key().
  */
 function tripal_core_chado_get_foreign_key($table_desc, $field, $values, $options = NULL) {
 
@@ -341,7 +371,9 @@ function tripal_core_chado_get_foreign_key($table_desc, $field, $values, $option
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_delete_record().
+ * This function has been replaced by chado_delete_record().
+ *
+ * @see chado_delete_record().
  */
 function tripal_core_chado_delete($table, $match, $options = NULL) {
 
@@ -362,7 +394,9 @@ function tripal_core_chado_delete($table, $match, $options = NULL) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_expand_var().
+ * This function has been replaced by chado_expand_var().
+ *
+ * @see chado_expand_var().
  */
 function tripal_core_expand_chado_vars($object, $type, $to_expand, $table_options = array()) {
 
@@ -383,7 +417,9 @@ function tripal_core_expand_chado_vars($object, $type, $to_expand, $table_option
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_generate_var().
+ * This function has been replaced by chado_generate_var().
+ *
+ * @see chado_generate_var().
  */
 function tripal_core_generate_chado_var($table, $values, $base_options = array()) {
 
@@ -404,7 +440,9 @@ function tripal_core_generate_chado_var($table, $values, $base_options = array()
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_insert_record().
+ * This function has been replaced by chado_insert_record().
+ *
+ * @see chado_insert_record().
  */
 function tripal_core_chado_insert($table, $values, $options = array()) {
 
@@ -425,7 +463,9 @@ function tripal_core_chado_insert($table, $values, $options = array()) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_select_record();
+ * This function has been replaced by chado_select_record().
+ *
+ * @see chado_select_record().
  */
 function tripal_core_chado_select($table, $columns, $values, $options = NULL) {
   tripal_report_error(
@@ -445,7 +485,9 @@ function tripal_core_chado_select($table, $columns, $values, $options = NULL) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_update_record();
+ * This function has been replaced by chado_update_record().
+ *
+ * @see chado_update_record().
  */
 function tripal_core_chado_update($table, $match, $values, $options = NULL) {
   tripal_report_error(
@@ -465,7 +507,9 @@ function tripal_core_chado_update($table, $match, $values, $options = NULL) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see tripal_create_files_dir();
+ * This function has been replaced by tripal_create_files_dir().
+ *
+ * @see tripal_create_files_dir().
  */
 function tripal_create_moddir($module_name) {
   tripal_report_error(
@@ -485,7 +529,9 @@ function tripal_create_moddir($module_name) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see tripal_create_files_dir();
+ * This function has been replaced by tripal_create_files_dir().
+ *
+ * @see tripal_create_files_dir().
  */
 function tripal_create_mod_subdir($module_name, $path) {
   tripal_report_error(
@@ -505,7 +551,10 @@ function tripal_create_mod_subdir($module_name, $path) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see tripal_create_files_dir().
+ * This function has been replaced by tripal_create_files_dir().
+ *
+ * @see tripal_create_files_dir().
+ * @todo Remove. This was not in Tripal 1.x.
  */
 function tripal_file_directory_path() {
   tripal_report_error(
@@ -525,7 +574,9 @@ function tripal_file_directory_path() {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see tripal_get_files_dir().
+ * This function has been replaced by tripal_get_files_dir().
+ *
+ * @see tripal_get_files_dir().
  */
 function tripal_get_moddir($module_name) {
   tripal_report_error(
@@ -545,7 +596,9 @@ function tripal_get_moddir($module_name) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see tripal_cancel_job().
+ * This function has been replaced by tripal_cancel_job().
+ *
+ * @see tripal_cancel_job().
  */
 function tripal_jobs_cancel($job_id, $redirect = TRUE) {
   tripal_report_error(
@@ -565,7 +618,9 @@ function tripal_jobs_cancel($job_id, $redirect = TRUE) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see tripal_get_active_jobs().
+ * This function has been replaced by tripal_get_active_jobs().
+ *
+ * @see tripal_get_active_jobs().
  */
 function tripal_get_module_active_jobs($modulename) {
   tripal_report_error(
@@ -585,7 +640,9 @@ function tripal_get_module_active_jobs($modulename) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see tripal_get_job_end().
+ * This function has been replaced by tripal_get_job_end().
+ *
+ * @see tripal_get_job_end().
  */
 function tripal_jobs_get_end_time($job) {
   tripal_report_error(
@@ -605,7 +662,9 @@ function tripal_jobs_get_end_time($job) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see tripal_get_job_start().
+ * This function has been replaced by tripal_get_job_start().
+ *
+ * @see tripal_get_job_start().
  */
 function tripal_jobs_get_start_time($job) {
   tripal_report_error(
@@ -625,7 +684,9 @@ function tripal_jobs_get_start_time($job) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see tripal_get_job_submit_date().
+ * This function has been replaced by tripal_get_job_submit_date().
+ *
+ * @see tripal_get_job_submit_date().
  */
 function tripal_jobs_get_submit_date($job) {
   tripal_report_error(
@@ -645,7 +706,9 @@ function tripal_jobs_get_submit_date($job) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see tripal_is_job_running().
+ * This function has been replaced by tripal_is_job_running().
+ *
+ * @see tripal_is_job_running().
  */
 function tripal_jobs_check_running() {
   tripal_report_error(
@@ -665,7 +728,9 @@ function tripal_jobs_check_running() {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see tripal_launch_job().
+ * This function has been replaced by tripal_launch_job().
+ *
+ * @see tripal_launch_job().
  */
 function tripal_jobs_launch($do_parallel = 0, $job_id = NULL) {
   tripal_report_error(
@@ -685,7 +750,9 @@ function tripal_jobs_launch($do_parallel = 0, $job_id = NULL) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see tripal_rerun_job().
+ * This function has been replaced by tripal_rerun_job().
+ *
+ * @see tripal_rerun_job().
  */
 function tripal_jobs_rerun($job_id, $goto_jobs_page = TRUE) {
   tripal_report_error(
@@ -705,7 +772,9 @@ function tripal_jobs_rerun($job_id, $goto_jobs_page = TRUE) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see tripal_set_job_progress().
+ * This function has been replaced by tripal_set_job_progress().
+ *
+ * @see tripal_set_job_progress().
  */
 function tripal_job_set_progress($job_id, $percentage) {
   tripal_report_error(
@@ -725,7 +794,9 @@ function tripal_job_set_progress($job_id, $percentage) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see tripal_update_mview().
+ * This function has been replaced by tripal_update_mview().
+ *
+ * @see tripal_update_mview().
  */
 function tripal_mviews_action($op, $mview_id, $redirect = FALSE) {
 
@@ -781,7 +852,9 @@ function tripal_add_legacy_mview($name, $modulename, $mv_table, $mv_specs, $inde
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see tripal_populate_mview();
+ * This function has been replaced by tripal_populate_mview().
+ *
+ * @see tripal_populate_mview().
  */
 function tripal_update_mview($mview_id) {
   tripal_report_error(
@@ -802,6 +875,8 @@ function tripal_update_mview($mview_id) {
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
  * This function is considered to be no easier to use than chado_delete_record directly
+ * chado_delete_record().
+ *
  * @see chado_delete_record().
  */
 function tripal_core_delete_property_by_id($basetable, $property_id) {
@@ -830,7 +905,9 @@ function tripal_core_delete_property_by_id($basetable, $property_id) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_delete_property().
+ * This function has been replaced by chado_delete_property().
+ *
+ * @see chado_delete_property().
  */
 function tripal_core_delete_property($basetable, $record_id, $property, $cv_name) {
   tripal_report_error(
@@ -850,7 +927,9 @@ function tripal_core_delete_property($basetable, $record_id, $property, $cv_name
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_get_property().
+ * This function has been replaced by chado_get_property().
+ *
+ * @see chado_get_property().
  */
 function tripal_core_get_property($basetable, $record_id, $property, $cv_name) {
   tripal_report_error(
@@ -870,15 +949,39 @@ function tripal_core_get_property($basetable, $record_id, $property, $cv_name) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_get_table_max_rank().
+ * This function has been replaced by chado_get_table_max_rank().
+ *
+ * @see chado_get_table_max_rank().
+ */
+function tripal_get_max_chado_rank($tablename, $where_options) {
+  tripal_report_error(
+    'tripal_api',
+    TRIPAL_NOTICE,
+    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    array(
+      '%old_function'=>'tripal_get_max_chado_rank',
+      '%new_function' => 'chado_get_table_max_rank'
+    )
+  );
+
+  //New API Function
+  return chado_get_table_max_rank($tablename, $where_options);
+}
+
+/**
+ * @deprecated Restructured API to make naming more readable and consistent.
+ * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
+ * This function has been replaced by chado_get_table_max_rank().
+ *
+ * @see chado_get_table_max_rank().
  */
-function tripal_core_get_max_chado_rank($tablename, $where_options) {
+function get_max_chado_rank($tablename, $where_options) {
   tripal_report_error(
     'tripal_api',
     TRIPAL_NOTICE,
     "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
     array(
-      '%old_function'=>'tripal_core_get_max_chado_rank',
+      '%old_function'=>'get_max_chado_rank',
       '%new_function' => 'chado_get_table_max_rank'
     )
   );
@@ -887,10 +990,13 @@ function tripal_core_get_max_chado_rank($tablename, $where_options) {
   return chado_get_table_max_rank($tablename, $where_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 @see chado_insert_property().
+ * This function has been replaced by chado_insert_property().
+ *
+ * @see chado_insert_property().
  */
 function tripal_core_insert_property($basetable, $record_id, $property,
 $cv_name, $value, $update_if_present = 0) {
@@ -911,7 +1017,9 @@ $cv_name, $value, $update_if_present = 0) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_update_property().
+ * This function has been replaced by chado_update_property().
+ *
+ * @see chado_update_property().
  */
 function tripal_core_update_property_by_id($basetable, $record_id, $property,
 $cv_name, $value) {
@@ -933,7 +1041,9 @@ $cv_name, $value) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_update_property().
+ * This function has been replaced by chado_update_property().
+ *
+ * @see chado_update_property().
  */
 function tripal_core_update_property($basetable, $record_id, $property,
 $cv_name, $value, $insert_if_missing = 0) {
@@ -954,13 +1064,17 @@ $cv_name, $value, $insert_if_missing = 0) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_create_custom_table().
+ * This function has been replaced by chado_create_custom_table().
+ *
+ * @see chado_create_custom_table().
  */
-function tripal_core_create_custom_table($table, $schema, $skip_creation = 1) {
+function tripal_core_create_custom_table(&$ret, $table, $schema, $skip_creation = 1) {
   tripal_report_error(
     'tripal_api',
     TRIPAL_NOTICE,
-    "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
+    "DEPRECATED: %old_function has been replaced with %new_function. Note that $ret has
+      been removed from the paramters since this is not longer used in Drupal 7.
+      Please update your code.",
     array(
       '%old_function'=>'tripal_core_create_custom_table',
       '%new_function' => 'chado_create_custom_table'
@@ -974,7 +1088,9 @@ function tripal_core_create_custom_table($table, $schema, $skip_creation = 1) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_edit_custom_table().
+ * This function has been replaced by chado_edit_custom_table().
+ *
+ * @see chado_edit_custom_table().
  */
 function tripal_core_edit_custom_table($table_id, $table_name, $schema, $skip_creation = 1) {
   tripal_report_error(
@@ -994,7 +1110,9 @@ function tripal_core_edit_custom_table($table_id, $table_name, $schema, $skip_cr
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_get_custom_table_id().
+ * This function has been replaced by chado_get_custom_table_id().
+ *
+ * @see chado_get_custom_table_id().
  */
 function tripal_custom_tables_get_table_id($table_name) {
   tripal_report_error(
@@ -1014,7 +1132,9 @@ function tripal_custom_tables_get_table_id($table_name) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_get_custom_table_schema().
+ * This function has been replaced by chado_get_custom_table_schema().
+ *
+ * @see chado_get_custom_table_schema().
  */
 function tripal_get_chado_custom_schema($table) {
   tripal_report_error(
@@ -1034,7 +1154,9 @@ function tripal_get_chado_custom_schema($table) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_is_installed().
+ * This function has been replaced by chado_is_installed().
+ *
+ * @see chado_is_installed().
  */
 function tripal_core_is_chado_installed() {
   tripal_report_error(
@@ -1054,7 +1176,9 @@ function tripal_core_is_chado_installed() {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_get_schema().
+ * This function has been replaced by chado_get_schema().
+ *
+ * @see chado_get_schema().
  */
 function tripal_core_get_chado_table_schema($table) {
   tripal_report_error(
@@ -1074,7 +1198,9 @@ function tripal_core_get_chado_table_schema($table) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_get_version().
+ * This function has been replaced by chado_get_version().
+ *
+ * @see chado_get_version().
  */
 function tripal_core_get_chado_version($exact = FALSE, $warn_if_unsupported = FALSE) {
   tripal_report_error(
@@ -1094,7 +1220,9 @@ function tripal_core_get_chado_version($exact = FALSE, $warn_if_unsupported = FA
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_set_active().
+ * This function has been replaced by chado_set_active().
+ *
+ * @see chado_set_active().
  */
 function tripal_db_set_active($dbname  = 'default') {
   tripal_report_error(
@@ -1114,7 +1242,9 @@ function tripal_db_set_active($dbname  = 'default') {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_is_local().
+ * This function has been replaced by chado_is_local().
+ *
+ * @see chado_is_local().
  */
 function tripal_core_is_chado_local() {
   tripal_report_error(
@@ -1134,7 +1264,9 @@ function tripal_core_is_chado_local() {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_get_table_names().
+ * This function has been replaced by chado_get_table_names().
+ *
+ * @see chado_get_table_names().
  */
 function tripal_core_get_chado_tables($include_custom = NULL) {
   tripal_report_error(
@@ -1154,7 +1286,9 @@ function tripal_core_get_chado_tables($include_custom = NULL) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_is_local().
+ * This function has been replaced by chado_is_local().
+ *
+ * @see chado_is_local().
  */
 function tripal_core_chado_schema_exists() {
   tripal_report_error(
@@ -1174,7 +1308,9 @@ function tripal_core_chado_schema_exists() {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see chado_dbschema_exists().
+ * This function has been replaced by chado_dbschema_exists().
+ *
+ * @see chado_dbschema_exists().
  */
 function tripal_core_schema_exists($schema) {
   tripal_report_error(
@@ -1194,7 +1330,9 @@ function tripal_core_schema_exists($schema) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see tripal_set_admin_message().
+ * This function has been replaced by tripal_set_admin_message().
+ *
+ * @see tripal_set_admin_message().
  *
 function theme_tripal_admin_message($variables) {
   tripal_report_error(
@@ -1215,7 +1353,10 @@ function theme_tripal_admin_message($variables) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by @see tripal_report_error().
+ * This function has been replaced by tripal_report_error().
+ *
+ * @see tripal_report_error().
+ * @todo Remove. This was not in Tripal 1.x.
  */
 function tripal_core_report_error($type, $severity, $message, $variables = array(), $options = array()) {