Changed Chado API to use array for indicating status of Chado as it was slowing down loaders the previous way

tripal_analysis/tripal_analysis.install

@@ -25,7 +25,7 @@ function tripal_analysis_requirements($phase) {
   $requirements = array();
   if ($phase == 'install') {
     // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
+    if (!$GLOBALS["chado_is_installed"]) {
       $requirements ['tripal_analysis'] = array(
             'title' => "tripal_analysis",
             'value' => "ERROR: Chado most be installed before this module can be enabled",

tripal_bulk_loader/tripal_bulk_loader.install

@@ -270,7 +270,7 @@ function tripal_bulk_loader_requirements($phase) {
   $requirements = array();
   if ($phase == 'install') {
     // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
+    if (!$GLOBALS["chado_is_installed"]) {
       $requirements ['tripal_bulk_loader'] = array(
             'title' => "tripal_bulk_loader",
             'value' => "ERROR: Chado most be installed before this module can be enabled",

tripal_contact/tripal_contact.install

@@ -32,7 +32,7 @@ function tripal_contact_requirements($phase) {
   $requirements = array();
   if ($phase == 'install') {
     // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
+    if (!$GLOBALS["chado_is_installed"]) {
       $requirements ['tripal_contact'] = array(
         'title' => "tripal_contact",
         'value' => "ERROR: Chado most be installed before this module can be enabled",

tripal_core/api/tripal_core_chado.api.inc

@@ -301,12 +301,9 @@ function tripal_core_chado_insert($table, $values, $options = array()) {
         }
         // now check the constraint
         if (tripal_core_chado_select($table, $ukselect_cols, $ukselect_vals)) {
-          tripal_core_report_error(
-            'tripal_core',
-            TRIPAL_ERROR,
+          tripal_core_report_error('tripal_core', TRIPAL_ERROR,
             "tripal_core_chado_insert; Cannot insert duplicate record into $table table: !values",
-            array('!values' => print_r($values, TRUE)),
-            array('print' => $print_errors)
+            array('!values' => print_r($values, TRUE)), array('print' => $print_errors)
           );
           return FALSE;
         }
@@ -317,11 +314,9 @@ function tripal_core_chado_insert($table, $values, $options = array()) {
     if (array_key_exists('primary key', $table_desc)) {
       $pkey = $table_desc['primary key'][0];
       if (array_key_exists($pkey, $insert_values)) {
-        $coptions = array('statement_name' => 'pqsel_' . $table . '_' . $pkey);
+        $coptions = array();
         if (tripal_core_chado_select($table, array($pkey), array($pkey => $insert_values[$pkey]), $coptions)) {
-          tripal_core_report_error(
-            'tripal_core',
-            TRIPAL_ERROR,
+          tripal_core_report_error('tripal_core', TRIPAL_ERROR,
             'tripal_core_chado_insert; Cannot insert duplicate primary key into !table table: !values',
             array('!table' => $table, '!values' => print_r($values, TRUE)),
             array('print' => $print_errors)
@@ -559,7 +554,7 @@ function tripal_core_chado_update($table, $match, $values, $options = NULL) {
         $columns[] = $field;
         $stmt_suffix .= substr($field, 0, 2);
       }
-      $options2 = array('statement_name' => 'sel_' . $table . '_' . $stmt_suffix);
+      $options2 = array();
       $results = tripal_core_chado_select($table, $columns, $match, $options2);
       if (count($results) > 0) {
         foreach ($results as $index => $pkey) {
@@ -574,18 +569,14 @@ function tripal_core_chado_update($table, $match, $values, $options = NULL) {
     if (is_array($value)) {
       $results = tripal_core_chado_get_foreign_key($table_desc, $field, $value);
       if (sizeof($results) > 1) {
-        tripal_core_report_error(
-          'tripal_core',
-          TRIPAL_ERROR,
+        tripal_core_report_error('tripal_core', TRIPAL_ERROR,
           'tripal_core_chado_update: When trying to find record to update, too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)',
           array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)),
           array('print' => $print_errors)
         );
       }
       elseif (sizeof($results) < 1) {
-        tripal_core_report_error(
-          'tripal_core',
-          TRIPAL_DEBUG,
+        tripal_core_report_error('tripal_core',TRIPAL_DEBUG,
           'tripal_core_chado_update: When trying to find record to update, no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)',
           array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)),
           array('print' => $print_errors)
@@ -875,14 +866,6 @@ function tripal_core_chado_delete($table, $match, $options = NULL) {
  *     An associative array containing the column names of the table as keys
  *     and the type of sort (i.e. ASC, DESC) as the values.  The results in the
  *     query will be sorted by the key values in the direction listed by the value
- *  - statement_name: the name of the prepared statement to use. If the statement
- *     has not yet been prepared it will be prepared automatically. On subsequent
- *     calls with the same statement_name only an execute on the previously
- *     prepared statement will occur.
- *  - is_prepared: TRUE or FALSE. Whether or not the statement is prepared. By
- *     default if the statement is not prepared it will be automatically.
- *     However to avoid this check, which requires a database query you can
- *     set this value to true and the check will not be performed.
  *  - is_duplicate: TRUE or FALSE.  Checks the values submited to see if
  *     they violate any of the unique constraints. If so, the record
  *     is returned, if not, FALSE is returned.
@@ -892,8 +875,7 @@ function tripal_core_chado_delete($table, $match, $options = NULL) {
  *     should specify the number of records to return and 'element' is a
  *     unique integer to differentiate between pagers when more than one
  *     appear on a page.  The 'element' should start with zero and increment by
- *     one for each pager.  The pager currently does not work with prepared queries
- *     (when using the -statement_name option).
+ *     one for each pager.  
  *
  * @return
  *  An array of results, FALSE if the query was not executed
@@ -922,7 +904,6 @@ function tripal_core_chado_delete($table, $match, $options = NULL) {
  *      ),
  *   );
  *   $options = array(
- *     'statement_name' => 'sel_feature_genus_species_cvname'
  *     'order_by' => array(
  *        'name' => 'ASC'
  *     ),
@@ -1091,17 +1072,12 @@ function tripal_core_chado_select($table, $columns, $values, $options = NULL) {
         // and there is no default value then we cannot check if the record
         // is a duplicate so return FALSE
         else {
-          tripal_core_report_error(
-            'tripal_core',
-            TRIPAL_ERROR,
+          tripal_core_report_error('tripal_core', TRIPAL_ERROR,
             'tripal_core_chado_select: There is no value for %field thus we cannot check if this record is unique',
-            array('%field' => $field),
-            array('print' => $print_errors)
-          );
+            array('%field' => $field), array('print' => $print_errors));
           return FALSE;
         }
       }
-      $new_options['statement_name'] = $uq_sname;
 
       $results = tripal_core_chado_select($table, $new_columns, $new_values, $new_options);
       // if we have a duplicate record then return the results
@@ -1367,7 +1343,7 @@ function tripal_core_chado_get_foreign_key($table_desc, $field, $values, $option
     // TODO: what do we do if we get to this point and we have a fk
     // relationship expected but we don't have any definition for one in the
     // table schema??
-    $version = tripal_core_get_chado_version(TRUE);
+    $version = $GLOBALS["chado_version"];
     $message = t("There is no foreign key relationship defined for " . $field . " .
        To define a foreign key relationship, determine the table this foreign
        key referrs to (<foreign table>) and then implement
@@ -1839,14 +1815,7 @@ function tripal_core_expand_chado_vars($object, $type, $to_expand, $table_option
           }
 
           // generate a new object for this table using the FK values in the base table.
-          // if a prepared statement is provided generate a new statement_name so that
-          // we don't conflict when we recurse.
           $new_options = $table_options;
-/*
-          if (array_key_exists('statement_name', $table_options)) {
-             $new_options['statement_name'] = "exp_" . $foreign_table . "_" . substr($left, 0, 2) . substr($right, 0, 2);
-          }
-*/
           $foreign_object = tripal_core_generate_chado_var($foreign_table, array($left => $object->{$right}), $new_options);
 
           // if the generation of the object was successful, update the base object to include it.
@@ -2133,8 +2102,7 @@ function chado_query_range($query, $args, $from, $count) {
  * @ingroup tripal_chado_api
  */
 function chado_query($sql, $args = array()) {
-
-  $is_local = tripal_core_is_chado_local();
+  $is_local = $GLOBALS["chado_is_local"];
 
   // Args should be an array
   if (!is_array($args)) {
@@ -2143,6 +2111,7 @@ function chado_query($sql, $args = array()) {
       array('%value' => $args, '%query' => $sql)
     );
     $args = array($args);
+    return FALSE;
   }
 
   // if Chado is local to the database then prefix the Chado table
@@ -2168,7 +2137,7 @@ function chado_query($sql, $args = array()) {
   // switch to another database
   else {
     $previous_db = tripal_db_set_active('chado') ;
-    $results = db_query($sql);
+    $results = db_query($sql, $args);
     tripal_db_set_active($previous_db);
   }
 
@@ -2322,7 +2291,7 @@ $cv_name, $value, $update_if_present = 0) {
     'name' => $property,
   );
 
-  $options = array('statement_name' => 'sel_cvterm_cv');
+  $options = array();
   $term = tripal_core_chado_select('cvterm', array('cvterm_id'), $values, $options);
   if (!$term or count($term) == 0) {
     watchdog('tripal_core', "Cannot find property '%prop_name'.",
@@ -2347,7 +2316,7 @@ $cv_name, $value, $update_if_present = 0) {
     'rank' => $rank,
   );
 
-  $options = array('statement_name' => 'ins_' . $basetable . 'prop_' . substr($fkcol, 0, 2) . 'tyvara');
+  $options = array();
   $result = tripal_core_chado_insert($basetable . 'prop', $values, $options);
   return $result;
 }
@@ -2591,34 +2560,7 @@ function chado_table_exists($table) {
   }
   return TRUE;
 }
-/**
- * Check that the Chado schema exists within the local database
- *
- * @return
- *   TRUE/FALSE depending upon whether it exists
- */
-function tripal_core_chado_schema_exists() {
 
-  // This is postgresql-specific code to check the existence of the chado schema
-  // @coder-ignore: acting on pg_catalog schema rather then drupal schema therefore, table prefixing does not apply
-  $sql = "
-    SELECT nspname
-    FROM pg_namespace
-    WHERE
-      has_schema_privilege(nspname, 'USAGE') AND
-      nspname = 'chado'
-  ";
-  $results = db_query($sql);
-  $name = $results->fetchObject();
-  if ($name) {
-    variable_set('chado_schema_exists', FALSE);
-    return TRUE;
-  }
-  else {
-    variable_set('chado_schema_exists', TRUE);
-    return FALSE;
-  }
-}
 /**
  * Check that any given schema exists
  *
@@ -2665,10 +2607,9 @@ function tripal_core_schema_exists($schema) {
  * @ingroup tripal_core_api
  */
 function tripal_core_get_chado_tables($include_custom = NULL) {
-
-
+ 
   // first get the chado version that is installed
-  $v = tripal_core_get_chado_version();
+  $v = $GLOBALS["chado_version"];
 
   $tables = array();
   if ($v == '1.2') {
@@ -2698,18 +2639,34 @@ function tripal_core_get_chado_tables($include_custom = NULL) {
   return $tables;
 }
 /**
- * Sets a Drupal variable with the current version of Chado.  This variable
- * can then be queried later using the tripal_core_get_chado_Version
+ * Returns the version number of the currently installed Chado instance.
+ * It can return the real or effective version.  Note, this function
+ * is executed in the hook_init() of the tripal_core module which then
+ * sets the $GLOBAL['exact_chado_version'] and $GLOBAL['chado_version'] 
+ * variable.  You can access these variables rather than calling this function.
+ *
+ * @param $exact
+ *   Set this argument to 1 to retrieve the exact version that is installed.
+ *   Otherwise, this function will set the version to the nearest 'tenth'.
+ *   Chado versioning numbers in the hundreds represent changes to the
+ *   software and not the schema.  Changes in the tenth's represent changes
+ *   in the schema.
+ *
+ * @param $warn_if_unsupported
+ *   If the currently installed version of Chado is not supported by Tripal
+ *   this generates a Drupal warning.
  *
  * @returns
  *   The version of Chado
  *
  * @ingroup tripal_core_api
  */
-function tripal_core_set_chado_version() {
+function tripal_core_get_chado_version($exact = FALSE, $warn_if_unsupported = FALSE) {
+  
   global $databases;
+  $version = '';
   $is_local = 0;
-
+  
   // check that Chado is installed if not return 'uninstalled as the version'
   $chado_exists = tripal_core_chado_schema_exists();
   if (!$chado_exists) {
@@ -2720,6 +2677,7 @@ function tripal_core_set_chado_version() {
       // return uninstalled as the version
       return 'not installed';
     }
+    $is_local = 0;
     $previous_db = tripal_db_set_active('chado');
     $prop_exists = db_table_exists('chadoprop');
     tripal_db_set_active($previous_db);
@@ -2728,66 +2686,40 @@ function tripal_core_set_chado_version() {
     $is_local = 1;
     $prop_exists = db_table_exists('chado.chadoprop');
   }
-
+  
   // if the table doesn't exist then we don't know what version but we know
   // it must be 1.11 or older.
   if (!$prop_exists) {
-    return "1.11 or older";
-  }
-
-  $sql = "
-    SELECT value
-    FROM {chadoprop} CP
-      INNER JOIN {cvterm} CVT on CVT.cvterm_id = CP.type_id
-      INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
-    WHERE CV.name = 'chado_properties' and CVT.name = 'version'
-  ";
-  if (!$is_local) {
-    $previous_db = tripal_db_set_active('chado');
-    $results = db_query($sql);
-    tripal_db_set_active($previous_db);
-  }
-  else {
-    $results = chado_query($sql);
-  }
-  $v = $results->fetchObject();
-
-  // if we don't have a version in the chadoprop table then it must be
-  // v1.11 or older
-  if (!$v) {
-    variable_set('chado_version', "1.11 or older");
-    return "1.11 or older";
+    $version = "1.11 or older";
+  }
+  else {  
+    $sql = "
+      SELECT value
+      FROM {chadoprop} CP
+        INNER JOIN {cvterm} CVT on CVT.cvterm_id = CP.type_id
+        INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
+      WHERE CV.name = 'chado_properties' and CVT.name = 'version'
+    ";
+    if (!$is_local) {
+      $previous_db = tripal_db_set_active('chado');
+      $results = db_query($sql);
+      tripal_db_set_active($previous_db);
+    }
+    else {
+      $results = chado_query($sql);
+    }
+    $v = $results->fetchObject();
+    
+    // if we don't have a version in the chadoprop table then it must be
+    // v1.11 or older
+    if (!$v) {
+      $version =  "1.11 or older";
+    }  
+    $version =  $v->value;
   }
-
-  variable_set('chado_version', $v->value);
-  return $v->value;
-}
-/**
- * Returns the version number of the currently installed Chado instance.
- * It can return the real or effective version.
- *
- * @param $exact
- *   Set this argument to 1 to retrieve the exact version that is installed.
- *   Otherwise, this function will set the version to the nearest 'tenth'.
- *   Chado versioning numbers in the hundreds represent changes to the
- *   software and not the schema.  Changes in the tenth's represent changes
- *   in the schema.
- *
- * @param $warn_if_unsupported
- *   If the currently installed version of Chado is not supported by Tripal
- *   the generatea a Drupal warning.
- *
- * @returns
- *   The version of Chado
- *
- * @ingroup tripal_core_api
- */
-function tripal_core_get_chado_version($exact = FALSE, $warn_if_unsupported = FALSE) {
-  // first get the chado version that is installed
-//  $exact_version = variable_get('chado_version', '');
-//  if (!$exact_version) {
-    $exact_version = tripal_core_set_chado_version();
-//  }
+  
+  // next get the exact Chado version that is installed
+  $exact_version = $version;
 
   // Tripal only supports v1.11 or newer.. really this is the same as v1.1
   // but at the time the v1.11 schema API was written we didn't know that so
@@ -2832,7 +2764,7 @@ function tripal_core_get_chado_version($exact = FALSE, $warn_if_unsupported = FA
 function tripal_core_get_chado_table_schema($table) {
 
   // first get the chado version that is installed
-  $v = tripal_core_get_chado_version();
+  $v = $GLOBALS["chado_version"];
 
   // get the table array from the proper chado schema
   $v = preg_replace("/\./", "_", $v); // reformat version for hook name
@@ -2958,7 +2890,34 @@ function tripal_core_clean_orphaned_nodes($table, $job_id) {
 
   return '';
 }
+/**
+ * Check that the Chado schema exists within the local database
+ *
+ * @return
+ *   TRUE/FALSE depending upon whether it exists
+ */
+function tripal_core_chado_schema_exists() {
 
+  // This is postgresql-specific code to check the existence of the chado schema
+  // @coder-ignore: acting on pg_catalog schema rather then drupal schema therefore, table prefixing does not apply
+  $sql = "
+    SELECT nspname
+    FROM pg_namespace
+    WHERE
+      has_schema_privilege(nspname, 'USAGE') AND
+      nspname = 'chado'
+  ";
+  $results = db_query($sql);
+  $name = $results->fetchObject();
+  if ($name) {
+    variable_set('chado_schema_exists', FALSE);
+    return TRUE;
+  }
+  else {
+    variable_set('chado_schema_exists', TRUE);
+    return FALSE;
+  }
+}
 /**
  * Check whether chado is installed (either in the same or a different database)
  *
@@ -2989,18 +2948,15 @@ function tripal_core_is_chado_installed() {
  * @ingroup tripal_chado_api
  */
 function tripal_core_is_chado_local() {
-  global $db_url, $db_type;
+  global $databases, $db_type;
 
-  $is_installed = tripal_core_is_chado_installed();
-  if ($is_installed) {
-    if (is_array($db_url)) {
-      if (isset($db_url['chado'])) {
-        return FALSE;
-      }
-    }
-    return TRUE;
+  // first check if chado is in the $databases variable of the settings.php file
+  if (array_key_exists('chado', $databases)) {
+    return FALSE;
   }
-  return FALSE;
+  
+  // check to make sure the chado schema exists
+  return tripal_core_chado_schema_exists();
 }
 
 /**
@@ -3035,7 +2991,6 @@ function tripal_core_is_tripal_node_type($chado_table) {
 function tripal_db_set_active($dbname  = 'default') {
   global $databases, $active_db;
 
-  $chado_exists = variable_get('chado_schema_exists', FALSE);
   if ($dbname ) {
     if ($dbname == 'chado') {
       db_query('set search_path to chado,public');

tripal_core/includes/chado_install.inc

@@ -13,7 +13,7 @@
 function tripal_core_chado_load_form() {
 
   // we want to force the version of Chado to be set properly
-  $real_version = tripal_core_set_chado_version();
+  $real_version = tripal_core_get_chado_version(TRUE);
 
   // get the effective version.  Pass true as second argument
   // to warn the user if the current version is not compatible

tripal_core/tripal_core.drush.inc

@@ -305,7 +305,7 @@ function drush_tripal_core_tripal_update_mview() {
  * Returns the current version of chado
  */
 function drush_tripal_core_tripal_chado_version() {
-  $version = tripal_core_get_chado_version();
+  $version = $GLOBALS["exact_chado_version"];
   drush_print('Current Chado Version: ' . $version);
 }
 

tripal_core/tripal_core.module

@@ -36,8 +36,6 @@
  * @ingroup tripal_modules
  */
 
-
-
 require_once "api/tripal_core_chado.api.inc";
 require_once "api/tripal_core_files.api.inc";
 require_once "api/tripal_core_ahah.api.inc";
@@ -51,6 +49,7 @@ require_once "includes/custom_tables.inc";
 require_once "includes/chado_install.inc";
 require_once "includes/form_elements.inc";
 
+
 /**
  * Implements hook_init().
  * Used to set the search_path, create default content and set default variables.
@@ -64,13 +63,22 @@ function tripal_core_init() {
   drupal_add_js(drupal_get_path('module', 'tripal_core') . '/theme/js/tripal.js');
   drupal_add_css(drupal_get_path('module', 'tripal_core') . '/theme/css/tripal.css');
 
-
+  // these global variables are meant to be accessed by all Tripal
+  // modules to find the chado version installed and if Chado is local.
+  // these variables are stored as globals rather than using the drupal_set_variable
+  // functions because the Drupal functions make databaes queries and for long
+  // running loaders we don't want those queries repeatedly.
+  $GLOBALS["chado_is_installed"]  = tripal_core_is_chado_installed();
+  if ($GLOBALS["chado_is_installed"]) {
+    $GLOBALS["chado_is_local"]      = tripal_core_is_chado_local();
+    $GLOBALS["chado_version"]       = tripal_core_get_chado_version();
+    $GLOBALS["exact_chado_version"] = tripal_core_get_chado_version(TRUE);
+  }
+  
+  
   // create the 'tripal' controlled volcabulary in chado but only if it doesn't already exist, and
   // only if the chado database is present.
-  if (tripal_core_is_chado_installed()) {
-
-    // make sure the current version of chado is set
-    tripal_core_set_chado_version();
+  if ($GLOBALS["chado_is_installed"]) {
 
     // if the Tripal cv is missing then add
     $results = chado_query("SELECT * FROM {cv} WHERE name = 'tripal'");
@@ -94,7 +102,6 @@ function tripal_core_init() {
   }
 
   // add some variables for all javasript to use for building URLs
-  global $base_url;
   $theme_dir = drupal_get_path('theme', 'tripal');
   $clean_urls = variable_get('clean_url', 0);
   drupal_add_js(

tripal_cv/tripal_cv.install

@@ -26,7 +26,7 @@ function tripal_cv_requirements($phase) {
   $requirements = array();
   if ($phase == 'install') {
     // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
+    if (!$GLOBALS["chado_is_installed"]) {
       $requirements ['tripal_cv'] = array(
         'title' => "tripal_cv",
         'value' => "ERROR: Chado most be installed before this module can be enabled",

tripal_db/tripal_db.install

@@ -26,7 +26,7 @@ function tripal_db_requirements($phase) {
   $requirements = array();
   if ($phase == 'install') {
     // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
+    if (!$GLOBALS["chado_is_installed"]) {
       $requirements ['tripal_db'] = array(
           'title' => "tripal_db",
           'value' => "ERROR: Chado most be installed before this module can be enabled",

tripal_feature/includes/gff_loader.inc → tripal_feature/includes/tripal_feature.gff_loader.inc

@@ -567,12 +567,10 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
               'genus' => $org_matches[1],
               'species' => $org_matches[2],
             ); 
-            $options = array('statement_name' => 'sel_organism_gesp');
-            $org = tripal_core_chado_select('organism', array("*"), $values, $options);
+            $org = tripal_core_chado_select('organism', array("*"), $values);
             if (count($org) == 0) {
               if ($create_organism) {
-                $options = array('statement_name' => 'ins_organism_gesp');
-                $feature_organism = (object) tripal_core_chado_insert('organism', $values, $options);
+                $feature_organism = (object) tripal_core_chado_insert('organism', $values);
                 if (!$feature_organism) {
                   watchdog('T_gff3_loader', "Could not add the organism, '%org', from line %line. Skipping this line. ",
                     array('%org' => $attr_organism, '%line' => $line_num), WATCHDOG_ERROR); 
@@ -661,14 +659,12 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
           'uniquename'  => $landmark,
         );      
         $columns = array('count(*) as num_landmarks');
-        $options = array('statement_name' => 'sel_feature_numland');
         if ($landmark_type) {
           $select['type_id'] = array(
             'name' => $landmark_type,
           );
-          $options = array('statement_name' => 'sel_feature_numlandty');
         }      
-        $count = tripal_core_chado_select('feature', $columns, $select, $options);        
+        $count = tripal_core_chado_select('feature', $columns, $select);        
         if (!$count or count($count) == 0 or $count[0]->num_landmarks == 0) {        
           // now look for the landmark using the name rather than uniquename.
           $select = array(
@@ -676,14 +672,12 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
             'name'  => $landmark,
           );
           $columns = array('count(*) as num_landmarks');
-          $options = array('statement_name' => 'sel_feature_numlandna');              
           if ($landmark_type) {
             $select['type_id'] = array(
               'name' => $landmark_type,
             );
-            $options = array('statement_name' => 'sel_feature_numlandnaty');
           }
-          $count = tripal_core_chado_select('feature', $columns, $select, $options); 
+          $count = tripal_core_chado_select('feature', $columns, $select); 
           if (!$count or count($count) == 0 or $count[0]->num_landmarks == 0) {
             watchdog('T_gff3_loader', "The landmark '%landmark' cannot be found for this organism (%species) " .
                   "Please add the landmark and then retry the import of this GFF3 " .
@@ -730,7 +724,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
         $feature = tripal_feature_load_gff3_feature($feature_organism, $analysis_id, $cvterm,
           $attr_uniquename, $attr_name, $residues, $attr_is_analysis,
           $attr_is_obsolete, $add_only, $score);  
-     
+
         if ($feature) {
           
           // add a record for this feature to the tripal_gff_temp table for
@@ -742,12 +736,10 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
             'uniquename' => $feature->uniquename
           );
           // make sure this record doesn't already exist in oru temp table
-          $options = array('statement_name' => 'sel_tripalgfftemp_all');
-          $results = tripal_core_chado_select('tripal_gff_temp', array('*'), $values, $options);
+          $results = tripal_core_chado_select('tripal_gff_temp', array('*'), $values);
   
           if (count($results) == 0) {
-            $options = array('statement_name' => 'ins_tripalgfftemp');
-            $result = tripal_core_chado_insert('tripal_gff_temp', $values, $options);
+            $result = tripal_core_chado_insert('tripal_gff_temp', $values);
             if (!$result) {
               watchdog('T_gff3_loader', "Cound not save record in temporary table, Cannot continue.", array(), WATCHDOG_ERROR);
               exit;
@@ -760,11 +752,11 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
               $landmark, $fmin, $fmax, $strand, $phase, $attr_fmin_partial,
               $attr_fmax_partial, $attr_residue_info, $attr_locgroup);
           }
-
+          
           // add any aliases for this feature
           if (array_key_exists('Alias', $tags)) {
             tripal_feature_load_gff3_alias($feature, $tags['Alias']);
-          }      
+          }
           // add any dbxrefs for this feature
           if (array_key_exists('Dbxref', $tags)) {
             tripal_feature_load_gff3_dbxref($feature, $tags['Dbxref']);
@@ -772,11 +764,12 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
           // add any ontology terms for this feature
           if (array_key_exists('Ontology_term', $tags)) {
             tripal_feature_load_gff3_ontology($feature, $tags['Ontology_term']);
-          }       
+          }
           // add parent relationships
           if (array_key_exists('Parent', $tags)) {
             tripal_feature_load_gff3_parents($feature, $cvterm, $tags['Parent'], $feature_organism->organism_id, $fmin);
-          }               
+          }
+          
           // add target relationships
           if (array_key_exists('Target', $tags)) {
             tripal_feature_load_gff3_target($feature, $tags, $target_organism_id, $target_type, $create_target, $attr_locgroup);          
@@ -830,21 +823,12 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
       $parents = chado_query($sql);
       
       // build and prepare the SQL for selecting the children relationship
-      $sql = "";
-  
-      $sql = "
-        PREPARE sel_gffchildren (int) AS 
+      $sel_gffchildren_sql = "
         SELECT DISTINCT FR.feature_relationship_id, FL.fmin, FR.rank
         FROM {feature_relationship} FR
           INNER JOIN {featureloc} FL on FL.feature_id = FR.subject_id
-        WHERE FR.object_id = \$1 ORDER BY FL.fmin ASC
+        WHERE FR.object_id = :feature_id ORDER BY FL.fmin ASC
       ";            
-      $success = chado_query('sel_gffchildren', $sql);
-      if (!$success) {
-        watchdog("T_gff3_loader", "Cannot prepare statement 'sel_gffchildren' and cannot set children ranks.", 
-           array(), WATCHDOG_WARNING);
-        return 0;  
-      }
       
       // now set the rank of any parent/child relationships.  The order is based
       // on the fmin.  The start rank is 1.  This allows features with other
@@ -854,7 +838,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
         
         // get the children
         if ($connection) {      
-          $result = chado_query('EXECUTE sel_gffchildren (:feature_id)', array(':feature_id' => $parent->feature_id));
+          $result = chado_query($sel_gffchildren_sql, array(':feature_id' => $parent->feature_id));
         }
         else {
           $result = chado_query($sql, array(':feature_id' => $parent->feature_id));
@@ -878,19 +862,17 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
         $rank = -1;
         foreach ($children as $child) {
           $match = array('feature_relationship_id' => $child->feature_relationship_id);
-          $options = array('statement_name' => 'upd_featurerelationship_rank');      
           $values = array('rank' => $rank);      
-          tripal_core_chado_update('feature_relationship', $match, $values, $options);
+          tripal_core_chado_update('feature_relationship', $match, $values);
           $rank--;
         }
         // now set the rank correctly. The rank should start at 0.
         $rank = 0;
         foreach ($children as $child) {
           $match = array('feature_relationship_id' => $child->feature_relationship_id);
-          $options = array('statement_name' => 'upd_featurerelationship_rank');      
           $values = array('rank' => $rank); 
           //print "Was: " . $child->rank . " now $rank ($parent->strand)\n"     ;
-          tripal_core_chado_update('feature_relationship', $match, $values, $options);
+          tripal_core_chado_update('feature_relationship', $match, $values);
           $rank++;
         }
       }
@@ -924,8 +906,7 @@ function tripal_feature_load_gff3_derives_from($feature, $subject, $organism) {
     'organism_id' => $organism->organism_id,
     'uniquename' => $subject,
   );
-  $options = array('statement_name' => 'sel_tripalgfftemp_orun');
-  $result = tripal_core_chado_select('tripal_gff_temp', array('type_name'), $values, $options);   
+  $result = tripal_core_chado_select('tripal_gff_temp', array('type_name'), $values);   
   if (count($result) == 0) {
     watchdog("T_gff3_loader", "Cannot find subject type for feature in 'derives_from' relationship: %subject", array('%subject' => $subject), WATCHDOG_WARNING);
      return ''; 
@@ -943,8 +924,7 @@ function tripal_feature_load_gff3_derives_from($feature, $subject, $organism) {
       ),
     ),      
   );
-  $options = array('statement_name' => 'sel_feature_orunty');
-  $sfeature = tripal_core_chado_select('feature', array('feature_id'), $match, $options);
+  $sfeature = tripal_core_chado_select('feature', array('feature_id'), $match);
   if (count($sfeature)==0) {
     watchdog('T_gff3_loader', "Could not add 'Derives_from' relationship " .
       "for %uniquename and %subject.  Subject feature, '%subject', " .
@@ -964,15 +944,13 @@ function tripal_feature_load_gff3_derives_from($feature, $subject, $organism) {
     ),
     'rank' => 0
   );
-  $options = array('statement_name' => 'sel_featurerelationship_objectid_subjectid_typeid_rank');
-  $rel = tripal_core_chado_select('feature_relationship', array('*'), $values, $options);
+  $rel = tripal_core_chado_select('feature_relationship', array('*'), $values);
   if (count($rel) > 0) {
     return;
   }
 
   // finally insert the relationship if it doesn't exist
-  $options = array('statement_name' => 'ins_featurerelationship_objectid_subjectid_typeid_rank');
-  $ret = tripal_core_chado_insert('feature_relationship', $values, $options);
+  $ret = tripal_core_chado_insert('feature_relationship', $values);
   if (!$ret) {
     watchdog("T_gff3_loader", "Could not add 'Derives_from' relationship for $feature->uniquename and $subject", 
       array(), WATCHDOG_WARNING);
@@ -990,20 +968,13 @@ function tripal_feature_load_gff3_parents($feature, $cvterm, $parents, $organism
   $rel_type = 'part_of';
 
   // prepare these SQL statements that will be used repeatedly.
-  $psql = "
-    PREPARE sel_cvterm_cvname_cvtname_synonym (text, text, text) AS
+  $cvterm_sql = "
     SELECT CVT.cvterm_id
     FROM {cvterm} CVT
       INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
       LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id
-    WHERE cv.name = $1 and (CVT.name = $2 or CVTS.synonym = $3)
+    WHERE cv.name = :cvname and (CVT.name = :name or CVTS.synonym = :synonym)
   ";
-  $status = chado_query($psql);
-  if (!$status) {
-     watchdog("T_gff3_loader", "Cannot prepare statement 'sel_cvterm_cvname_cvtname_synonym' for ontology term", 
-       array(), WATCHDOG_WARNING);
-     return '';
-  }
 
   // iterate through the parents in the list
   foreach ($parents as $parent) {
@@ -1012,8 +983,7 @@ function tripal_feature_load_gff3_parents($feature, $cvterm, $parents, $organism
       'organism_id' => $organism_id,
       'uniquename' => $parent,
     );
-    $options = array('statement_name' => 'sel_tripalgfftemp_orun');
-    $result = tripal_core_chado_select('tripal_gff_temp', array('type_name'), $values, $options);    
+    $result = tripal_core_chado_select('tripal_gff_temp', array('type_name'), $values);    
     if (count($result) == 0) {
       watchdog("T_gff3_loader", "Cannot find parent: %parent", array('%parent' => $parent), WATCHDOG_WARNING);
        return '';  
@@ -1021,17 +991,14 @@ function tripal_feature_load_gff3_parents($feature, $cvterm, $parents, $organism
     $parent_type = $result[0]->type_name;
 
     // try to find the parent
-    $parentcvterm = chado_query("EXECUTE sel_cvterm_cvname_cvtname_synonym (:cvname, :name, :synonym)", 
-      array(':cvname' => 'sequence', ':name' => $parent_type, ':synonym' => $parent_type))->fetchObject();
-    $relcvterm = chado_query("EXECUTE sel_cvterm_cvname_cvtname_synonym (:cvname, :name, :synonym)", 
-      array(':cvname' => 'relationship', ':name' => $rel_type, ':synonym' => $rel_type))->fetchObject();
+    $parentcvterm = chado_query($cvterm_sql, array(':cvname' => 'sequence', ':name' => $parent_type, ':synonym' => $parent_type))->fetchObject();
+    $relcvterm = chado_query($cvterm_sql, array(':cvname' => 'relationship', ':name' => $rel_type, ':synonym' => $rel_type))->fetchObject();
     $values = array(
         'organism_id' => $organism_id,
         'uniquename' => $parent,
         'type_id' => $parentcvterm->cvterm_id,
     );
-    $options = array('statement_name' => 'sel_feature_orunty');
-    $result = tripal_core_chado_select('feature', array('feature_id'), $values, $options);
+    $result = tripal_core_chado_select('feature', array('feature_id'), $values);
     $parent_feature = $result[0];
 
     // if the parent exists then add the relationship otherwise print error and skip
@@ -1043,20 +1010,18 @@ function tripal_feature_load_gff3_parents($feature, $cvterm, $parents, $organism
         'subject_id' => $feature->feature_id,
         'type_id' => $relcvterm->cvterm_id,
       );
-      $options = array('statement_name' => 'sel_featurerelationship_objectid_subjectid_typeid');
-      $rel = tripal_core_chado_select('feature_relationship', array('*'), $values, $options);
+      $rel = tripal_core_chado_select('feature_relationship', array('*'), $values);
 
       if (count($rel) > 0) {
       }
       else {
         // the relationship doesn't already exist, so add it.
         $values = array(
-           'subject_id' => $feature->feature_id,
-           'object_id'  => $parent_feature->feature_id,
-           'type_id' => $relcvterm->cvterm_id,
+          'subject_id' => $feature->feature_id,
+          'object_id'  => $parent_feature->feature_id,
+          'type_id' => $relcvterm->cvterm_id,
         );
-        $options = array('statement_name' => 'ins_featurerelationship_subjectid_objectid_typeid');
-        $result = tripal_core_chado_insert('feature_relationship', $values, $options);
+        $result = tripal_core_chado_insert('feature_relationship', $values);
         if (!$result) {
           watchdog("T_gff3_loader", "Failed to insert feature relationship '$uname' ($type) $rel_type '$parent' ($parent_type)", 
             array(), WATCHDOG_WARNING);
@@ -1091,23 +1056,20 @@ function tripal_feature_load_gff3_dbxref($feature, $dbxrefs) {
     // can't be found then look for the name as is.  If it still can't be found
     // the create the database
     $values = array('name' => "DB:$dbname");
-    $options = array('statement_name' => 'sel_db_name');
-    $db = tripal_core_chado_select('db', array('db_id'), $values, $options);
+    $db = tripal_core_chado_select('db', array('db_id'), $values);
     if (count($db) == 0) {
       $values = array('name' => "$dbname");
-      $db = tripal_core_chado_select('db', array('db_id'), $values, $options);
+      $db = tripal_core_chado_select('db', array('db_id'), $values);
     }
     if (count($db) == 0) {
       $values = array(
         'name' => $dbname,
         'description' => 'Added automatically by the GFF loader'
       );
-      $options = array('statement_name' => 'ins_db_name');
-      $success = tripal_core_chado_insert('db', $values, $options);
+      $success = tripal_core_chado_insert('db', $values);
       if ($success) {
         $values = array('name' => "$dbname");
-        $options = array('statement_name' => 'sel_db_name');        
-        $db = tripal_core_chado_select('db', array('db_id'), $values, $options);
+        $db = tripal_core_chado_select('db', array('db_id'), $values);
       }
       else {
         watchdog("T_gff3_loader", "Cannot find or add the database $dbname", array(), WATCHDOG_WARNING);
@@ -1121,8 +1083,7 @@ function tripal_feature_load_gff3_dbxref($feature, $dbxrefs) {
       'accession' => $accession, 
       'db_id' => $db->db_id
     );
-    $options = array('statement_name' => 'sel_dbxref_accession_dbid');
-    $dbxref = tripal_core_chado_select('dbxref', array('dbxref_id'), $values, $options);
+    $dbxref = tripal_core_chado_select('dbxref', array('dbxref_id'), $values);
 
     // if the accession doesn't exist then we want to add it
     if (sizeof($dbxref) == 0) {
@@ -1131,14 +1092,12 @@ function tripal_feature_load_gff3_dbxref($feature, $dbxrefs) {
         'accession' => $accession, 
         'version' => ''
       );
-      $options = array('statement_name' => 'ins_dbxref_dbid_accession_version');
-      $ret = tripal_core_chado_insert('dbxref', $values, $options);
+      $ret = tripal_core_chado_insert('dbxref', $values);
       $values = array(
         'accession' => $accession, 
         'db_id' => $db->db_id
       );
-      $options = array('statement_name' => 'sel_dbxref_accession_dbid');
-      $dbxref = tripal_core_chado_select('dbxref', array('dbxref_id'), $values, $options);
+      $dbxref = tripal_core_chado_select('dbxref', array('dbxref_id'), $values);
     }
     $dbxref = $dbxref[0];
 
@@ -1147,8 +1106,7 @@ function tripal_feature_load_gff3_dbxref($feature, $dbxrefs) {
       'dbxref_id' => $dbxref->dbxref_id, 
       'feature_id' => $feature->feature_id
     );
-    $options = array('statement_name' => 'sel_featuredbxref_dbxrefid_featureid');
-    $fdbx = tripal_core_chado_select('feature_dbxref', array('feature_dbxref_id'), $values, $options);
+    $fdbx = tripal_core_chado_select('feature_dbxref', array('feature_dbxref_id'), $values);
 
     // now associate this feature with the database reference if it doesn't
     // already exist
@@ -1157,8 +1115,7 @@ function tripal_feature_load_gff3_dbxref($feature, $dbxrefs) {
         'dbxref_id' => $dbxref->dbxref_id,
         'feature_id' => $feature->feature_id
       );
-      $options = array('statement_name' => 'ins_featuredbxref_dbxrefid_featureid');
-      $success = tripal_core_chado_insert('feature_dbxref', $values, $options);
+      $success = tripal_core_chado_insert('feature_dbxref', $values);
       if (!$success) {
         watchdog("T_gff3_loader", "Failed to insert Dbxref: $dbname:$accession", array(), WATCHDOG_WARNING);
         return 0;
@@ -1183,11 +1140,10 @@ function tripal_feature_load_gff3_ontology($feature, $dbxrefs) {
     $accession = $ref[1];
 
     // first look for the database name
-    $options = array('statement_name' => 'sel_db_name');
-    $db = tripal_core_chado_select('db', array('db_id'), array('name' => "DB:$dbname"), $options);
+    $db = tripal_core_chado_select('db', array('db_id'), array('name' => "DB:$dbname"));
     if (sizeof($db) == 0) {
       // now look for the name without the 'DB:' prefix.
-      $db = tripal_core_chado_select('db', array('db_id'), array('name' => "$dbname"), $options);
+      $db = tripal_core_chado_select('db', array('db_id'), array('name' => "$dbname"));
       if (sizeof($db) == 0) {
         watchdog("T_gff3_loader", "Database, $dbname, is not present. Cannot associate term: $dbname:$accession", array(), WATCHDOG_WARNING);
         return 0;
@@ -1196,9 +1152,8 @@ function tripal_feature_load_gff3_ontology($feature, $dbxrefs) {
     $db = $db[0];
 
     // now check to see if the accession exists
-    $options = array('statement_name' => 'sel_dbxref_accession_dbid');
     $dbxref = tripal_core_chado_select('dbxref', array('dbxref_id'), 
-      array('accession' => $accession, 'db_id' => $db->db_id), $options);
+      array('accession' => $accession, 'db_id' => $db->db_id));
     if (sizeof($dbxref) == 0) {
       watchdog("T_gff3_loader", "Accession, $accession is missing for reference: $dbname:$accession", array(), WATCHDOG_WARNING);
       return 0;
@@ -1206,14 +1161,12 @@ function tripal_feature_load_gff3_ontology($feature, $dbxrefs) {
     $dbxref = $dbxref[0];
 
     // now check to see if the cvterm exists
-    $options = array('statement_name' => 'sel_cvterm_dbxrefid');
     $cvterm = tripal_core_chado_select('cvterm', array('cvterm_id'), array(
-       'dbxref_id' => $dbxref->dbxref_id), $options);
+       'dbxref_id' => $dbxref->dbxref_id));
     // if it doesn't exist in the cvterm table, look for an alternate id
     if (sizeof($cvterm) == 0) {
-      $options = array('statement_name' => 'sel_cvtermdbxref_dbxrefid');
       $cvterm = tripal_core_chado_select('cvterm_dbxref', array('cvterm_id'), array(
-        'dbxref_id' => $dbxref->dbxref_id), $options);
+        'dbxref_id' => $dbxref->dbxref_id));
       if (sizeof($cvterm) == 0) {
         watchdog("T_gff3_loader", "CV Term is missing for reference: $dbname:$accession", array(), WATCHDOG_WARNING);
         return 0;
@@ -1223,10 +1176,8 @@ function tripal_feature_load_gff3_ontology($feature, $dbxrefs) {
 
 
     // check to see if this feature cvterm already exists
-    $options = array('statement_name' => 'sel_featurecvterm_cvtermid_featureid');
     $fcvt = tripal_core_chado_select('feature_cvterm', array('feature_cvterm_id'),
-      array('cvterm_id' => $cvterm->cvterm_id, 'feature_id' => $feature->feature_id),
-      $options);
+      array('cvterm_id' => $cvterm->cvterm_id, 'feature_id' => $feature->feature_id));
 
     // now associate this feature with the cvterm if it doesn't already exist
     if (sizeof($fcvt)==0) {
@@ -1237,8 +1188,7 @@ function tripal_feature_load_gff3_ontology($feature, $dbxrefs) {
           'uniquename' => 'null',
         ),
       );
-      $options = array('statement_name' => 'ins_featurecvterm_cvtermid_featureid_pubid');
-      $success = tripal_core_chado_insert('feature_cvterm', $values, $options);
+      $success = tripal_core_chado_insert('feature_cvterm', $values);
 
       if (!$success) {
         watchdog("T_gff3_loader", "Failed to insert ontology term: $dbname:$accession", array(), WATCHDOG_WARNING);
@@ -1257,8 +1207,7 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
 
   // make sure we have a 'synonym_type' vocabulary
   $select = array('name' => 'synonym_type');
-  $options = array('statement_name' => 'sel_cv_name');  
-  $results = tripal_core_chado_select('cv', array('*'), $select, $options);
+  $results = tripal_core_chado_select('cv', array('*'), $select);
   
   if (count($results) == 0) {
     // insert the 'synonym_type' vocabulary
@@ -1266,15 +1215,13 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
       'name' => 'synonym_type',
       'definition' => 'vocabulary for synonym types',
     );
-    $options = array('statement_name' => 'ins_cv_name_definition');
-    $success = tripal_core_chado_insert('cv', $values, $options);
+    $success = tripal_core_chado_insert('cv', $values);
     if (!$success) {
       watchdog("T_gff3_loader", "Failed to add the synonyms type vocabulary", array(), WATCHDOG_WARNING);
       return 0;
     }
     // now that we've added the cv we need to get the record
-    $options = array('statement_name' => 'sel_cv_name');
-    $results = tripal_core_chado_select('cv', array('*'), $select, $options);
+    $results = tripal_core_chado_select('cv', array('*'), $select);
     if (count($results) > 0) {
       $syncv = $results[0];
     }
@@ -1290,8 +1237,7 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
         'name' => 'synonym_type'
      ),
   );
-  $options = array('statement_name' => 'sel_cvterm_name_cvid');
-  $result = tripal_core_chado_select('cvterm', array('*'), $select, $options);  
+  $result = tripal_core_chado_select('cvterm', array('*'), $select);  
   if (count($result) == 0) {
     $term = array(
       'name' => 'exact',
@@ -1299,7 +1245,6 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
       'definition' => '',
       'is_obsolete' => 0,
     );
-    // TODO: fix the function so it uses prepared statements    
     $syntype = tripal_cv_add_cvterm($term, $syncv->name, 0, 1);
     if (!$syntype) {
       watchdog("T_gff3_loader", "Cannot add synonym type: internal:$type", array(), WATCHDOG_WARNING);
@@ -1319,22 +1264,19 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
        'name' => $alias,
        'type_id' => $syntype->cvterm_id,
     );
-    $options = array('statement_name' => 'sel_synonym_name_typeid');
-    $result = tripal_core_chado_select('synonym', array('*'), $select, $options);    
+    $result = tripal_core_chado_select('synonym', array('*'), $select);    
     if (count($result) == 0) {
       $values = array(
          'name' => $alias,
          'type_id' => $syntype->cvterm_id,
          'synonym_sgml' => '',
       );
-      $options = array('statement_name' => 'ins_synonym_name_typeid_synonymsgml');
-      $success = tripal_core_chado_insert('synonym', $values, $options);
+      $success = tripal_core_chado_insert('synonym', $values);
       if (!$success) {
         watchdog("T_gff3_loader", "Cannot add alias $alias to synonym table", array(), WATCHDOG_WARNING);
         return 0;
       }
-      $options = array('statement_name' => 'sel_synonym_name_typeid');
-      $result = tripal_core_chado_select('synonym', array('*'), $select, $options);
+      $result = tripal_core_chado_select('synonym', array('*'), $select);
       $synonym = $result[0];
     }
     else {
@@ -1343,20 +1285,18 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
 
     // check to see if we have a NULL publication in the pub table.  If not,
     // then add one.
-    // @coder-ignore: non-drupal schema thus table prefixing does not apply
     $select = array('uniquename' => 'null');
-    $options = array('statement_name' => 'sel_pub_uniquename');
-    $result = tripal_core_chado_select('pub', array('*'), $select, $options);    
+    $result = tripal_core_chado_select('pub', array('*'), $select);    
     if (count($result) == 0) {
       // prepare the statement
-      $psql = "
-        PREPARE ins_pub_uniquename_typeid (text, text) AS
-        INSERT INTO {pub} (uniquename,type_id) VALUES ('%s',
-        (SELECT cvterm_id
-        FROM {cvterm} CVT
-          INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
-          INNER JOIN {db} DB on DB.db_id = DBX.db_id
-        WHERE CVT.name = $1 and DB.name = $2)
+      $pub_sql = "
+        INSERT INTO {pub} (uniquename,type_id) 
+        VALUES (:uname,
+          (SELECT cvterm_id
+           FROM {cvterm} CVT
+             INNER JOIN {dbxref} DBX ON DBX.dbxref_id = CVT.dbxref_id
+             INNER JOIN {db} DB      ON DB.db_id      = DBX.db_id
+           WHERE CVT.name = :type_id))
       ";
       $status = chado_query($psql);
       if (!$status) {
@@ -1365,14 +1305,12 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
       } 
 
       // insert the null pub 
-      $result = chado_query("EXECUTE ins_pub_uniquename_typeid (:uname, :type_id)", 
-        array(':uname' => 'null', ':type_id' => 'null'))->fetchObject();
+      $result = chado_query($pub_sql, array(':uname' => 'null', ':type_id' => 'null'))->fetchObject();
       if (!$result) {
         watchdog("T_gff3_loader", "Cannot add null publication needed for setup of alias", array(), WATCHDOG_WARNING);
         return 0;
       }
-      $options = array('statement_name' => 'sel_pub_uniquename');
-      $result = tripal_core_chado_select('pub', array('*'), $select, $options);
+      $result = tripal_core_chado_select('pub', array('*'), $select);
       $pub = $result[0];
     }
     else {
@@ -1387,16 +1325,14 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
        'pub_id' => $pub->pub_id,
     );
     $columns = array('feature_synonym_id');
-    $options = array('statement_name' => 'sel_featuresynonym_syfepu');
-    $result = tripal_core_chado_select('feature_synonym', $columns, $values, $options);
+    $result = tripal_core_chado_select('feature_synonym', $columns, $values);
     if (count($result) == 0) {      
       $values = array(
          'synonym_id' => $synonym->synonym_id,
          'feature_id' => $feature->feature_id,
          'pub_id' => $pub->pub_id,
       );  
-      $ins_options = array('statement_name' => 'ins_featuresynonym_syfepu');
-      $success = tripal_core_chado_insert('feature_synonym', $values, $ins_options);   
+      $success = tripal_core_chado_insert('feature_synonym', $values);   
      
       if (!$success) {
         watchdog("T_gff3_loader", "Cannot add alias $alias to feature synonym table", array(), WATCHDOG_WARNING);
@@ -1422,9 +1358,8 @@ function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uni
      'uniquename' => $uniquename,
      'type_id' => $cvterm->cvterm_id
   );
-  $options = array('statement_name' => 'sel_feature_orunty');
   $columns = array('feature_id', 'name', 'uniquename', 'seqlen', 'organism_id', 'type_id');
-  $result = tripal_core_chado_select('feature', $columns, $fselect, $options);
+  $result = tripal_core_chado_select('feature', $columns, $fselect);
   if (count($result) > 0) {
     $feature = $result[0];
   }
@@ -1455,8 +1390,7 @@ function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uni
        'is_analysis' => $is_analysis,
        'is_obsolete' => $is_obsolete,
     );
-    $options = array('statement_name' => 'ins_feature_all');
-    $result = tripal_core_chado_insert('feature', $values, $options);
+    $result = tripal_core_chado_insert('feature', $values);
     if (!$result) {
       watchdog("T_gff3_loader", "Failed to insert feature '$uniquename' ($cvterm->name)", array(), WATCHDOG_WARNING);
       return 0;
@@ -1476,8 +1410,7 @@ function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uni
       'uniquename' => $uniquename,
       'type_id' => $cvterm->cvterm_id,
     );
-    $options = array('statement_name' => 'upd_feature');
-    $result = tripal_core_chado_update('feature', $match, $values, $options);
+    $result = tripal_core_chado_update('feature', $match, $values);
     if (!$result) {
       watchdog("T_gff3_loader", "Failed to update feature '$uniquename' ($cvterm->name)", array(), WATCHDOG_WARNING);
       return 0;
@@ -1490,9 +1423,8 @@ function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uni
   }
 
   // get the newly added feature
-  $options = array('statement_name' => 'sel_feature_orunty');
   $columns = array('feature_id', 'name', 'uniquename', 'seqlen', 'organism_id', 'type_id');
-  $result = tripal_core_chado_select('feature', $columns, $fselect, $options);  
+  $result = tripal_core_chado_select('feature', $columns, $fselect);  
   $feature = $result[0];
 
   // add the analysisfeature entry to the analysisfeature table if it doesn't already exist
@@ -1500,18 +1432,13 @@ function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uni
     'analysis_id' => $analysis_id,
     'feature_id' => $feature->feature_id
   );
-  $options = array('statement_name' => 'sel_analysisfeature_analysisid_featureid');
-  $afeature = tripal_core_chado_select('analysisfeature', array('analysisfeature_id'), $af_values, $options);
+  $afeature = tripal_core_chado_select('analysisfeature', array('analysisfeature_id'), $af_values);
   if (count($afeature)==0) {
     // if a score is available then set that to be the significance field
     if (strcmp($score, '.') != 0) {
       $af_values['significance'] = $score;
-      $options = array('statement_name' => 'ins_analysisfeature_analysisid_featureid_significance');
     } 
-    else {
-      $options = array('statement_name' => 'ins_analysisfeature_analysisid_featureid');
-    }
-    if (!tripal_core_chado_insert('analysisfeature', $af_values, $options)) {
+    if (!tripal_core_chado_insert('analysisfeature', $af_values)) {
       watchdog("T_gff3_loader", "Could not add analysisfeature record: $analysis_id, $feature->feature_id", array(), WATCHDOG_WARNING);
     }    
   }
@@ -1525,8 +1452,7 @@ function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uni
       $new_vals['significance'] = '__NULL__';
     }
     if (!$add_only) {
-      $options = array('statement_name' => 'upd_analysisfeature');
-      $ret = tripal_core_chado_update('analysisfeature', $af_values, $new_vals, $options);
+      $ret = tripal_core_chado_update('analysisfeature', $af_values, $new_vals);
       if (!$ret) {
         watchdog("T_gff3_loader", "Could not update analysisfeature record: $analysis_id, $feature->feature_id", array(), WATCHDOG_WARNING);
       }
@@ -1549,12 +1475,10 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
     'organism_id' => $landmark_organism_id ? $landmark_organism_id : $organism->organism_id,
     'uniquename' => $landmark,
   );
-  $options = array('statement_name' => 'sel_feature_orun');
   if ($landmark_type_id) {
     $select['type_id'] = $landmark_type_id;
-    $options = array('statement_name' => 'sel_feature_orunty');
   }  
-  $results = tripal_core_chado_select('feature', array('feature_id'), $select, $options);
+  $results = tripal_core_chado_select('feature', array('feature_id'), $select);
 
   $srcfeature = '';
   if (count($results)==0) {
@@ -1564,19 +1488,16 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
       'organism_id' => $landmark_organism_id ? $landmark_organism_id : $organism->organism_id,
       'name' => $landmark,
     );
-    $options = array('statement_name' => 'sel_feature_orna');    
     if ($landmark_type_id) {
       $select['type_id'] = $landmark_type_id;
-      $options = array('statement_name' => 'sel_feature_ornaty');
     } 
-    $results = tripal_core_chado_select('feature', array('feature_id'), $select, $options);
+    $results = tripal_core_chado_select('feature', array('feature_id'), $select);
     if (count($results) == 0) {
        // if the landmark is the target feature in a matched alignment then try one more time to
        // find it by querying any feature with the same uniquename. If we find one then use it.
        if ($landmark_is_target) {
          $select = array('uniquename' => $landmark);
-         $options = array('statement_name' => 'sel_feature_un');
-         $results = tripal_core_chado_select('feature', array('feature_id'), $select, $options);
+         $results = tripal_core_chado_select('feature', array('feature_id'), $select);
          if (count($results) == 1) {
            $srcfeature = $results[0]; 
          }
@@ -1592,8 +1513,7 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
               'uniquename' => $landmark,
               'type_id' => $landmark_type_id
             );
-            $options = array('statement_name' => 'ins_feature_ornaunty');
-            $results = tripal_core_chado_insert('feature', $values, $options);
+            $results = tripal_core_chado_insert('feature', $values);
             if (!$results) {
               watchdog("T_gff3_loader", "Cannot find landmark feature: '%landmark', nor could it be inserted", 
                 array('%landmark' => $landmark), WATCHDOG_WARNING);
@@ -1639,7 +1559,6 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
   $exists = 0;
   $select = array('feature_id' => $feature->feature_id);
   $options = array(
-    'statement_name' => 'sel_featureloc_fe',
     'order_by' => array(
        'rank' => 'ASC'
     ),
@@ -1654,9 +1573,8 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
       continue;
     }    
     $select = array('feature_id' => $featureloc->srcfeature_id);
-    $options = array('statement_name' => 'sel_feature_fe');
     $columns = array('feature_id', 'name');
-    $locsfeature = tripal_core_chado_select('feature', $columns, $select, $options);   
+    $locsfeature = tripal_core_chado_select('feature', $columns, $select);   
     
     // the source feature name and at least the fmin and fmax must be the same
     // for an update of the featureloc, otherwise we'll insert a new record.
@@ -1675,8 +1593,7 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
          $values['strand'] = $strand;
       }
       if (count($values) > 0) {
-        $options = array('statement_name' => 'upd_featureloc_all');
-        tripal_core_chado_update('featureloc', $match, $values, $options);
+        tripal_core_chado_update('featureloc', $match, $values);
       }
     }
     $rank = $featureloc->rank + 1;
@@ -1708,12 +1625,10 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
        'locgroup'        => $locgroup,
        'rank'            => $rank 
     );
-    $options = array('statement_name' => 'ins_featureloc_all');
     if ($phase) {
       $values['phase'] = $phase;
-      $options = array('statement_name' => 'ins_featureloc_allphase');
     }    
-    $success = tripal_core_chado_insert('featureloc', $values, $options);
+    $success = tripal_core_chado_insert('featureloc', $values);
     if (!$success) {
       watchdog("T_gff3_loader", "Failed to insert featureloc", array(), WATCHDOG_WARNING);
       exit;
@@ -1736,8 +1651,7 @@ function tripal_feature_load_gff3_property($feature, $property, $value) {
         'name' => 'feature_property',
      ),
   );
-  $options = array('statement_name' => 'sel_cvterm_name_cvid');
-  $result = tripal_core_chado_select('cvterm', array('*'), $select, $options);
+  $result = tripal_core_chado_select('cvterm', array('*'), $select);
 
   // if we don't have a property like this already, then add it otherwise, just return
   if (count($result) == 0) {
@@ -1768,7 +1682,6 @@ function tripal_feature_load_gff3_property($feature, $property, $value) {
      'type_id' => $cvterm->cvterm_id,
   );
   $options = array(
-    'statement_name' => 'sel_featureprop_featureid_typeid',
     'order_by' => array(
       'rank' => 'ASC',
     ),
@@ -1789,8 +1702,7 @@ function tripal_feature_load_gff3_property($feature, $property, $value) {
        'value' => $value,
        'rank' => $rank,
     );
-    $options = array('statement_name' => 'ins_featureprop_all');
-    $result = tripal_core_chado_insert('featureprop', $values, $options);
+    $result = tripal_core_chado_insert('featureprop', $values);
     if (!$result) {
       watchdog("T_gff3_loader", "cannot add featureprop, $property", array(), WATCHDOG_WARNING);
     }
@@ -1803,17 +1715,10 @@ function tripal_feature_load_gff3_property($feature, $property, $value) {
 function tripal_feature_load_gff3_fasta($fh, $interval, &$num_read, &$intv_read, &$line_num) {
   print "Loading FASTA sequences\n";
   $residues = '';
-  $sql = " 
-    PREPARE sel_gfftemp_un (text) AS
+  $sel_gfftemp_un_sql = " 
     SELECT feature_id FROM tripal_gff_temp
-    WHERE uniquename = $1
+    WHERE uniquename = :uname
   ";
-  $status = tripal_core_chado_prepare('sel_gfftemp_un', $sql, array('text'));
-  if (!$status) {
-   watchdog('T_gff3_loader', 'Cannot prepare statement \'sel_gfftemp_un\'.', 
-     array(), WATCHDOG_ERROR);
-   return '';  
-  }
   $id = NULL;
   
   // iterate through the remaining lines of the file
@@ -1841,8 +1746,7 @@ function tripal_feature_load_gff3_fasta($fh, $interval, &$num_read, &$intv_read,
       // just finished.     
              
       if ($id) {
-        $sql = "EXECUTE sel_gfftemp_un('%s')";
-        $result = tripal_core_chado_execute_prepared('sel_gfftemp_un', $sql, array($id));
+        $result = chado_query($sel_gfftemp_un_sql, array(':uname' => $id));
         if (!$result) {
           watchdog('T_gff3_loader', 'Cannot find feature to assign FASTA sequence: %uname', 
              array('%uname' => $id), WATCHDOG_WARNING); 
@@ -1852,8 +1756,7 @@ function tripal_feature_load_gff3_fasta($fh, $interval, &$num_read, &$intv_read,
           $feature = $result->fetchObject();    
           $values = array('residues' => $residues);
           $match = array('feature_id' => $feature->feature_id);
-          $options = array('statement_name' => 'upd_feature_re');
-          tripal_core_chado_update('feature', $match, $values, $options);
+          tripal_core_chado_update('feature', $match, $values);
         }
       }
       // get the feature ID for this ID from the tripal_gff_temp table
@@ -1865,8 +1768,7 @@ function tripal_feature_load_gff3_fasta($fh, $interval, &$num_read, &$intv_read,
     }
   } 
   // add in the last sequence
-  $sql = "EXECUTE sel_gfftemp_un('%s')";
-  $result = tripal_core_chado_execute_prepared('sel_gfftemp_un', $sql, array($id));
+  $result = chado_query($sel_gfftemp_un_sql, array(':uname' => $id));
   if (!$result) {
     watchdog('T_gff3_loader', 'Cannot find feature to assign FASTA sequence: %uname', 
        array('%uname' => $id), WATCHDOG_WARNING); 
@@ -1876,8 +1778,7 @@ function tripal_feature_load_gff3_fasta($fh, $interval, &$num_read, &$intv_read,
     $feature = $result->fetchObject();    
     $values = array('residues' => $residues);
     $match = array('feature_id' => $feature->feature_id);
-    $options = array('statement_name' => 'upd_feature_re');
-    tripal_core_chado_update('feature', $match, $values, $options);
+    tripal_core_chado_update('feature', $match, $values);
   } 
 }
 
@@ -1932,8 +1833,7 @@ function tripal_feature_load_gff3_target($feature, $tags, $target_organism_id, $
           'genus' => $matches[1],
           'species' => $matches[2],
         );
-        $options = array('statement_name' => 'sel_organism_gesp');
-        $torganism = tripal_core_chado_select('organism', array('organism_id'), $values, $options);
+        $torganism = tripal_core_chado_select('organism', array('organism_id'), $values);
         if (count($torganism) == 1) {
           $t_organism_id = $torganism[0]->organism_id;
         }
@@ -1961,8 +1861,7 @@ function tripal_feature_load_gff3_target($feature, $tags, $target_organism_id, $
            'name' => 'sequence',
         )
       );
-      $options = array('statement_name' => 'sel_cvterm_nacv');
-      $type = tripal_core_chado_select('cvterm', array('cvterm_id'), $values, $options);
+      $type = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);
       if (count($type) == 1) {
         $t_type_id = $type[0]->cvterm_id;
       }
@@ -1979,8 +1878,7 @@ function tripal_feature_load_gff3_target($feature, $tags, $target_organism_id, $
            'name' => 'sequence',
         )
       );
-      $options = array('statement_name' => 'sel_cvterm_nacv');
-      $type = tripal_core_chado_select('cvterm', array('cvterm_id'), $values, $options);
+      $type = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);
       if (count($type) == 1) {
         $t_type_id = $type[0]->cvterm_id;
       }

tripal_feature/tripal_feature.install

@@ -25,7 +25,7 @@ function tripal_feature_requirements($phase) {
   $requirements = array();
   if ($phase == 'install') {
     // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
+    if (!$GLOBALS["chado_is_installed"]) {
       $requirements ['tripal_feature'] = array(
           'title' => "t ripal_feature",
           'value' => "ERROR: Chado most be installed before this module can be enabled",

tripal_feature/tripal_feature.module

@@ -14,14 +14,16 @@
  */
 
 require_once "api/tripal_feature.api.inc";
+require_once "api/tripal_feature.schema.api.inc";
+
 require_once "includes/tripal_feature.admin.inc";
 require_once "includes/tripal_feature.sync_features.inc";
-require_once "includes/fasta_loader.inc";
-require_once "includes/gff_loader.inc";
-require_once "includes/seq_extract.inc";
-require_once "includes/tripal_feature-delete.inc";
+require_once "includes/tripal_feature.fasta_loader.inc";
+require_once "includes/tripal_feature.gff_loader.inc";
+require_once "includes/tripal_feature.seq_extract.inc";
+require_once "includes/tripal_feature.delete.inc";
 require_once "includes/tripal_feature.form.inc";
-require_once "api/tripal_feature.schema.api.inc";
+
 
 /**
  *

tripal_featuremap/tripal_featuremap.install

@@ -25,7 +25,7 @@ function tripal_featuremap_requirements($phase) {
   $requirements = array();
   if ($phase == 'install') {
     // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
+    if (!$GLOBALS["chado_is_installed"]) {
       $requirements ['tripal_featuremap'] = array(
         'title' => "tripal_featuremap",
         'value' => "ERROR: Chado most be installed before this module can be enabled",

tripal_library/tripal_library.install

@@ -25,7 +25,7 @@ function tripal_library_requirements($phase) {
   $requirements = array();
   if ($phase == 'install') {
     // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
+    if (!$GLOBALS["chado_is_installed"]) {
       $requirements ['tripal_library'] = array(
         'title' => "tripal_library",
         'value' => "ERROR: Chado most be installed before this module can be enabled",

tripal_natural_diversity/tripal_natural_diversity.install

@@ -25,7 +25,7 @@ function tripal_natural_diversity_requirements($phase) {
   $requirements = array();
   if ($phase == 'install') {
     // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
+    if (!$GLOBALS["chado_is_installed"]) {
       $requirements ['tripal_natural_diversity'] = array(
         'title' => "tripal_natural_diversity",
         'value' => "ERROR: Chado most be installed before this module can be enabled",

tripal_organism/tripal_organism.install

@@ -98,7 +98,7 @@ function tripal_organism_requirements($phase) {
   $requirements = array();
   if ($phase == 'install') {
     // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
+    if (!$GLOBALS["chado_is_installed"]) {
       $requirements ['tripal_organism'] = array(
             'title' => "tripal_organism",
             'value' => "ERROR: Chado most be installed before this module can be enabled",

tripal_project/tripal_project.install

@@ -32,7 +32,7 @@ function tripal_project_requirements($phase) {
   $requirements = array();
   if ($phase == 'install') {
     // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
+    if (!$GLOBALS["chado_is_installed"]) {
       $requirements ['tripal_project'] = array(
         'title' => "tripal_project",
         'value' => "ERROR: Chado most be installed before this module can be enabled",

tripal_pub/tripal_pub.install

@@ -31,7 +31,7 @@ function tripal_pub_requirements($phase) {
   $requirements = array();
   if ($phase == 'install') {
     // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
+    if (!$GLOBALS["chado_is_installed"]) {
       $requirements ['tripal_pub'] = array(
         'title' => "tripal_pub",
         'value' => "ERROR: Chado most be installed before this module can be enabled",

tripal_stock/tripal_stock.install

@@ -28,7 +28,7 @@ function tripal_stock_requirements($phase) {
   $requirements = array();
   if ($phase == 'install') {
     // make sure chado is installed
-    if (!tripal_core_is_chado_installed()) {
+    if (!$GLOBALS["chado_is_installed"]) {
       $requirements ['tripal_stock'] = array(
         'title' => "tripal_stock",
         'value' => "ERROR: Chado most be installed before this module can be enabled",

tripal_views/tripal_views.install

@@ -380,7 +380,7 @@ function tripal_views_requirements($phase) {
   $requirements = array();
   if ($phase == 'install') {
     // make sure chado is installed
-    $version = tripal_core_set_chado_version();
+    $version = tripal_get_set_chado_version(TRUE);
     if ($version == 'not installed') {
       $requirements ['tripal_views'] = array(
             'title' => "tripal_views",