Converted old API functions to new functions

tripal_analysis/api/tripal_analysis.api.inc

@@ -61,7 +61,7 @@ function tripal_analysis_api_unregister_child($modulename) {
  * @ingroup tripal_analysis_api
  */
 function tripal_analysis_api_get_property($analysis_id, $property, $cvname = 'tripal') {
-  return tripal_core_get_property('analysis', $analysis_id, $property, $cvname);
+  return chado_get_property('analysis', $analysis_id, $property, $cvname);
 }
 
 /**
@@ -84,7 +84,7 @@ function tripal_analysis_api_get_property($analysis_id, $property, $cvname = 'tr
  * @ingroup tripal_analysis_api
  */
 function tripal_analysis_api_insert_property($analysis_id, $property, $value, $update_if_present = 0, $cvname = 'tripal') {
-    return tripal_core_insert_property('analysis', $analysis_id, $property, $cvname, $value, $update_if_present);
+    return chado_insert_property('analysis', $analysis_id, $property, $cvname, $value, $update_if_present);
 }
 
 /**
@@ -110,7 +110,7 @@ function tripal_analysis_api_insert_property($analysis_id, $property, $value, $u
  * @ingroup tripal_analysis_api
  */
 function tripal_analysis_api_update_property($analysis_id, $property, $value, $insert_if_missing = 0, $cvname = 'tripal') {
-  return tripal_core_update_property('analysis', $analysis_id, $property, $cvname, $value, $insert_if_missing);
+  return chado_update_property('analysis', $analysis_id, $property, $cvname, $value, $insert_if_missing);
 }
 
 /**
@@ -132,7 +132,7 @@ function tripal_analysis_api_update_property($analysis_id, $property, $value, $i
  * @ingroup tripal_analysis_api
  */
 function tripal_analysis_api_delete_property($analysis_id, $property, $cvname = 'tripal') {
-  return tripal_core_delete_property('analysis', $analysis_id, $property, $cvname);
+  return chado_delete_property('analysis', $analysis_id, $property, $cvname);
 }
 
 /**

tripal_analysis/api/tripal_analysis.schema.api.inc

@@ -3,9 +3,9 @@
 /**
  * Implements hook_chado_schema_v1_11_analysisfeatureprop()
  * Purpose: To describe the structure of 'analysisfeatureprop' to tripal
- * @see tripal_core_chado_insert()
- * @see tripal_core_chado_update()
- * @see tripal_core_chado_select()
+ * @see chado_insert_record()
+ * @see chado_update_record()
+ * @see chado_select_record()
  *
  * @return
  *    An array describing the 'analysisfeatureprop' table

tripal_analysis/includes/tripal_analysis.chado_node.inc

@@ -74,7 +74,7 @@ function chado_analysis_form($node, &$form_state) {
   // if we are editing an existing node then the analysis is already part of the node
   if (property_exists($node, 'analysis')) {
     $analysis = $node->analysis;
-    $analysis = tripal_core_expand_chado_vars($analysis, 'field', 'analysis.description');
+    $analysis = chado_expand_var($analysis, 'field', 'analysis.description');
     $analysis_id = $analysis->analysis_id;
 
     // get form defaults
@@ -241,7 +241,7 @@ function chado_analysis_form($node, &$form_state) {
     'fieldset_title' => 'Properties',
     'additional_instructions' => $instructions
   );
-  chado_node_properties_form($form, $form_state, $details);
+  chado_add_node_form_properties($form, $form_state, $details);
 
   return $form;
 }
@@ -292,13 +292,13 @@ function tripal_analysis_validate($node, $form, &$form_state) {
 
     // get the existing node
     $values = array('analysis_id' => $node->analysis_id);
-    $result = tripal_core_chado_select('analysis', array('*'), $values);
+    $result = chado_select_record('analysis', array('*'), $values);
     $analysis = $result[0];
 
     // if the name has changed make sure it doesn't conflict with an existing name
     if ($analysis->name != $node->analysisname) {
       $values = array('name' => $node->analysisname);
-      $result = tripal_core_chado_select('analysis', array('analysis_id'), $values);
+      $result = chado_select_record('analysis', array('analysis_id'), $values);
       if ($result and count($result) > 0) {
         form_set_error('analysisname', 'Cannot update the analysis with this analysis name. An analysis with this name already exists.');
         return;
@@ -314,7 +314,7 @@ function tripal_analysis_validate($node, $form, &$form_state) {
         'programversion' => $node->programversion,
         'sourcename' => $node->sourcename,
       );
-      $result = tripal_core_chado_select('analysis', array('analysis_id'), $values);
+      $result = chado_select_record('analysis', array('analysis_id'), $values);
       if ($result and count($result) > 0) {
         if ($analysis->program != $node->program) {
           $field = 'program';
@@ -338,7 +338,7 @@ function tripal_analysis_validate($node, $form, &$form_state) {
       'programversion' => $node->programversion,
       'sourcename' => $node->sourcename,
     );
-    $analysis = tripal_core_chado_select('analysis', array('analysis_id'), $values);
+    $analysis = chado_select_record('analysis', array('analysis_id'), $values);
     if ($analysis and count($analysis) > 0) {
       form_set_error('program', 'Cannot add the analysis with this program,
         program version and source name. An analysis with these values already exists.');
@@ -349,7 +349,7 @@ function tripal_analysis_validate($node, $form, &$form_state) {
     // for the analysis table but we use the analysis name for the Drupal node
     // title, so it should be unique
     $values = array('name' => $node->analysisname);
-    $result = tripal_core_chado_select('analysis', array('analysis_id'), $values);
+    $result = chado_select_record('analysis', array('analysis_id'), $values);
     if ($result and count($result) > 0) {
       form_set_error('analysisname', 'Cannot add the analysis with this analysis name. An analysis with this name already exists.');
       return;
@@ -400,10 +400,10 @@ function chado_analysis_insert($node) {
       'sourceuri'      => $node->sourceuri,
       'timeexecuted'   => $timestamp
     );
-    $analysis = tripal_core_chado_insert('analysis', $values);
+    $analysis = chado_insert_record('analysis', $values);
     if (!$analysis) {
       drupal_set_message(t('Unable to add analysis.', 'warning'));
-      tripal_core_report_error('tripal_analysis', TRIPAL_ERROR, 'Insert analysis: Unable to create analysis where values:%values',
+      tripal_report_error('tripal_analysis', TRIPAL_ERROR, 'Insert analysis: Unable to create analysis where values:%values',
         array('%values' => print_r($values, TRUE)));
       return;
     }
@@ -416,7 +416,7 @@ function chado_analysis_insert($node) {
       'foreignkey_name' => 'analysis_id',
       'foreignkey_value' => $analysis_id
     );
-    chado_node_properties_form_update_properties($node, $details);
+    chado_update_node_form_properties($node, $details);
   }
   else {
     $analysis_id = $node->analysis_id;
@@ -424,7 +424,7 @@ function chado_analysis_insert($node) {
 
   // Make sure the entry for this analysis doesn't already exist in the
   // chado_analysis table if it doesn't exist then we want to add it.
-  $check_org_id = chado_get_id_for_node('analysis', $node->nid);
+  $check_org_id = chado_get_id_from_nid('analysis', $node->nid);
   if (!$check_org_id) {
     $record = new stdClass();
     $record->nid = $node->nid;
@@ -446,7 +446,7 @@ function chado_analysis_insert($node) {
  * @ingroup tripal_analysis
  */
 function chado_analysis_delete($node) {
-  $analysis_id = chado_get_id_for_node('analysis', $node->nid);
+  $analysis_id = chado_get_id_from_nid('analysis', $node->nid);
 
   // if we don't have an analysis id for this node then this isn't a node of
   // type chado_analysis or the entry in the chado_analysis table was lost.
@@ -490,7 +490,7 @@ function chado_analysis_update($node) {
   $timestamp = $month . '/' . $day . '/' . $year;
 
   // update the record in Chado
-  $analysis_id = chado_get_id_for_node('analysis', $node->nid);
+  $analysis_id = chado_get_id_from_nid('analysis', $node->nid);
   $match = array(
     'analysis_id' => $node->analysis_id,
   );
@@ -506,10 +506,10 @@ function chado_analysis_update($node) {
     'timeexecuted'   => $timestamp,
     'analysis_id'    => $analysis_id
   );
-  $status = tripal_core_chado_update('analysis', $match, $values);
+  $status = chado_update_record('analysis', $match, $values);
   if (!$status) {
     drupal_set_message(t('Unable to update analysis.', 'warning'));
-    tripal_core_report_error('tripal_analysis', TRIPAL_ERROR, 'Update analysis: Unable to update analysis where values: %values',
+    tripal_report_error('tripal_analysis', TRIPAL_ERROR, 'Update analysis: Unable to update analysis where values: %values',
     array('%values' => print_r($values, TRUE)));
   }
 
@@ -521,7 +521,7 @@ function chado_analysis_update($node) {
     'foreignkey_name' => 'analysis_id',
     'foreignkey_value' => $analysis_id
   );
-  chado_node_properties_form_update_properties($node, $details);
+  chado_update_node_form_properties($node, $details);
 }
 
 /**
@@ -535,14 +535,14 @@ function chado_analysis_load($nodes) {
 
   foreach ($nodes as $nid => $node) {
     // find the analysis and add in the details
-    $analysis_id = chado_get_id_for_node('analysis', $nid);
+    $analysis_id = chado_get_id_from_nid('analysis', $nid);
 
     // build the analysis variable
     $values = array('analysis_id' => $analysis_id);
-    $analysis = tripal_core_generate_chado_var('analysis', $values);
+    $analysis = chado_generate_var('analysis', $values);
 
     // add in the description field
-    $analysis = tripal_core_expand_chado_vars($analysis, 'field', 'analysis.description');
+    $analysis = chado_expand_var($analysis, 'field', 'analysis.description');
     $nodes[$nid]->analysis = $analysis;
   }
 }

tripal_analysis/includes/tripal_analysis_privacy.inc

@@ -85,7 +85,7 @@ function tripal_analysis_set_feature_permission($analysis_id, $nid) {
   foreach ($feature_nids AS $fnid) {
     if ($idx_iterations % $interval == 0) {
       $percentage = (int) ($idx_iterations / ($counter + 1) * 100);
-      tripal_job_set_progress($job_id, $percentage);
+      tripal_set_job_progress($job_id, $percentage);
       print $percentage . "% ";
     }
 

tripal_analysis/tripal_analysis.install

@@ -51,7 +51,7 @@ function tripal_analysis_requirements($phase) {
 function tripal_analysis_install() {
 
   // create the module's data directory
-  tripal_create_moddir('tripal_analysis');
+  tripal_create_files_dir('tripal_analysis');
 
   // we may need the analysisfeatureprop table if it doesn't already exist
   tripal_analysis_create_analysisfeatureprop();

tripal_bulk_loader/includes/tripal_bulk_loader.admin.templates.inc

@@ -329,7 +329,7 @@ function tripal_bulk_loader_modify_template_base_form($form, &$form_state = NULL
               // so we need to get it.
               $fk_priority = $form_state['storage']['record2priority'][$field['foreign key']];
               $fk_table = $form_state['storage']['template'][$fk_priority]['table'];
-              $tbl_description = tripal_core_get_chado_table_schema($table_array['table']);
+              $tbl_description = chado_get_schema($table_array['table']);
               foreach ($tbl_description['foreign keys'] as $key_table => $key_array) {
                 foreach ($key_array['columns'] as $left_field => $right_field) {
                   if ($key_table == $fk_table and $left_field == $field['field']) {
@@ -849,7 +849,7 @@ function tripal_bulk_loader_edit_template_record_form($form, $form_state) {
   }
 
   // Tables and default table
-  $tables = tripal_core_get_chado_tables(TRUE);
+  $tables = chado_get_table_names(TRUE);
   if (isset($form_state['values']['chado_table'])) {
     $table = $form_state['values']['chado_table'];
   }
@@ -1135,7 +1135,7 @@ function tripal_bulk_loader_edit_template_record_form_submit($form, &$form_state
     }
     else {
       drupal_set_message(t('Unable to Save Template!'), 'error');
-      tripal_core_report_error('T_bulk_loader',
+      tripal_report_error('T_bulk_loader',
         TRIPAL_ERROR,
         'Unable to save bulk loader template: %template',
         array('%template' => print_r($form_state['storage']['template'], TRUE))
@@ -1529,7 +1529,7 @@ function tripal_bulk_loader_template_field_form_default_values($mode, &$form_sta
   }
 
   // Chado Tables and default table
-  $tables = tripal_core_get_chado_tables(TRUE);
+  $tables = chado_get_table_names(TRUE);
   if (isset($form_state['values']['chado_table'])) {
     if (!preg_match('/^' . current($tables) . '$/', $form_state['values']['chado_table'])) {
       $table = $form_state['values']['chado_table'];
@@ -1550,7 +1550,7 @@ function tripal_bulk_loader_template_field_form_default_values($mode, &$form_sta
 
   // Chado fields
   $chado_fields = array();
-  $table_description = tripal_core_get_chado_table_schema($table);
+  $table_description = chado_get_schema($table);
   foreach ($table_description['fields'] as $field_name => $field_array) {
     $chado_fields[$field_name] = $field_name;
   }
@@ -1670,7 +1670,7 @@ function tripal_bulk_loader_template_field_form_default_values($mode, &$form_sta
         }
       }
       // now add in the remaining fields of the referring record's table.
-      $fk_description = tripal_core_get_chado_table_schema($fk_table);
+      $fk_description = chado_get_schema($fk_table);
       foreach ($fk_description['fields'] as $fk_field_name => $fk_farray) {
         // don't include the FK field it's included above
         if (in_array('Foreign Key', $ref_chado_fields)) {
@@ -2216,7 +2216,7 @@ function tripal_bulk_loader_template_field_form_submit($form, &$form_state) {
     }
     else {
       drupal_set_message(t('Unable to Save Template!'), 'error');
-      tripal_core_report_error('T_bulk_loader',
+      tripal_report_error('T_bulk_loader',
         TRIPAL_ERROR,
         'Unable to save bulk loader template: %template',
         array('%template' => print_r($form_state['storage']['template'], TRUE))

tripal_bulk_loader/includes/tripal_bulk_loader.loader.inc

@@ -86,7 +86,7 @@ function tripal_bulk_loader_add_loader_job_form_submit($form, $form_state) {
     }
   }
   elseif (preg_match('/Re-Submit Job/', $form_state['values']['op'])) {
-    tripal_jobs_rerun($form_state['values']['job_id']);
+    tripal_rerun_job($form_state['values']['job_id']);
     $success = db_update('tripal_bulk_loader')->fields(array(
         'job_status' => 'Submitted to Queue'
       ))->condition('nid',$form_state['values']['nid'])->execute();
@@ -95,7 +95,7 @@ function tripal_bulk_loader_add_loader_job_form_submit($form, $form_state) {
     $success = db_update('tripal_bulk_loader')->fields(array(
         'job_status' => 'Job Cancelled'
       ))->condition('nid',$form_state['values']['nid'])->execute();
-    tripal_jobs_cancel($form_state['values']['job_id']);
+    tripal_cancel_job($form_state['values']['job_id']);
   }
   elseif (preg_match('/Revert/', $form_state['values']['op'])) {
 
@@ -230,7 +230,7 @@ function tripal_bulk_loader_load_data($nid, $job_id) {
         // out what field we're joining on.  For templates created using a
         // previous version it was assumed that the FK field was always the field to join
         if (!array_key_exists('foreign field', $field_array)) {
-          $tbl_description = tripal_core_get_chado_table_schema($record_array['table']);
+          $tbl_description = chado_get_schema($record_array['table']);
           foreach ($tbl_description['foreign keys'] as $key_table => $key_array) {
             if ($key_table == $fk_table) {
               foreach ($key_array['columns'] as $left_field => $right_field) {
@@ -392,7 +392,7 @@ function tripal_bulk_loader_load_data($nid, $job_id) {
         // and had a group percentage of 50% then the job progress would be
         // (2*100 + 50%) / 3 = 250%/3 = 83%
         $job_progress = round(((($group_index - 1) * 100) + $group_progress) / $total_num_groups);
-        tripal_job_set_progress($node->job_id, $job_progress);
+        tripal_set_job_progress($node->job_id, $job_progress);
       }
 
       $data = $default_data;
@@ -503,7 +503,7 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
   }
 
   // get the table description
-  $table_desc = tripal_core_get_chado_table_schema($table);
+  $table_desc = chado_get_schema($table);
   if (!$table_desc) {
     $msg = "Tripal does not know about the table named '%table'. If this is a custom table,
       please define it first";
@@ -610,7 +610,7 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
      $table_data['select_if_duplicate'] == 1 or
      $table_data['update_if_duplicate'] == 1) {
     $options = array('is_duplicate' => TRUE, 'print_errors' => TRUE);
-    $duplicate = tripal_core_chado_select($table, array_keys($table_desc['fields']), $values, $options);
+    $duplicate = chado_select_record($table, array_keys($table_desc['fields']), $values, $options);
 
     // if this is a duplicate then substitute the values in the table_data array so
     // that for future records that may depend on this one, they can get the values needed
@@ -662,7 +662,7 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
     else {
       $options = array();
     }
-    // Skip tripal_core_chado_insert() built-in validation?
+    // Skip chado_insert_record() built-in validation?
     if (variable_get('tripal_bulk_loader_skip_validation', FALSE)) {
       $options['skip_validation'] = TRUE;
     }
@@ -697,17 +697,17 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
       }
       if (!empty($match)) {
         // Now we need to check if it already exists via a select
-        $results = tripal_core_chado_select($table, array_keys($table_desc['fields']), $match, array('print_errors' => TRUE));
+        $results = chado_select_record($table, array_keys($table_desc['fields']), $match, array('print_errors' => TRUE));
         // If not then insert
         if (empty($results)) {
           $options['statement_name'] = 'ins_'.$options['statement_name'];
           $options['print_errors'] = TRUE;
-          $record = tripal_core_chado_insert($table, $values, $options);
+          $record = chado_insert_record($table, $values, $options);
         }
         else {
           $options['return_record'] = TRUE;
           $options['print_errors'] = TRUE;
-          $record = tripal_core_chado_update($table, $match, $values, $options);
+          $record = chado_update_record($table, $match, $values, $options);
         }
       }
       else {
@@ -722,7 +722,7 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
     }
     else {
       $options['print_errors'] = TRUE;
-      $record = tripal_core_chado_insert($table, $values, $options);
+      $record = chado_insert_record($table, $values, $options);
     }
 
     // if the insert was not successful
@@ -790,7 +790,7 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
     // get the matches for this select
     $matches = array();
     if (is_array($values) and count($values) > 0) {
-      $matches = tripal_core_chado_select($table, array_keys($table_desc['fields']), $values, array('print_errors' => TRUE));
+      $matches = chado_select_record($table, array_keys($table_desc['fields']), $values, array('print_errors' => TRUE));
     }
     // if the record doesn't exist and it's not optional then generate an error
     if (count($matches) == 0) {
@@ -913,7 +913,7 @@ function tripal_bulk_loader_add_foreignkey_to_values($table_array, $values, $dat
 
       // if the field in the Referral records is in a FK relationship with
       // this field then we can simply keep the value we have
-      $tbl_description = tripal_core_get_chado_table_schema($table_array['table']);
+      $tbl_description = chado_get_schema($table_array['table']);
       if ($tbl_description and
           array_key_exists('foreign keys', $tbl_description) and
           array_key_exists($foreign_table, $tbl_description['foreign keys']) and
@@ -928,7 +928,7 @@ function tripal_bulk_loader_add_foreignkey_to_values($table_array, $values, $dat
       else {
         // if the current value of the referral records is a non-array then this
         // is the primary key, we can use it to select the value we need.
-        $fk_description = tripal_core_get_chado_table_schema($foreign_table);
+        $fk_description = chado_get_schema($foreign_table);
         if (!is_array($foreign_values)) {
           // if we have a value then use it to get the field we need
           if ($foreign_values) {
@@ -936,7 +936,7 @@ function tripal_bulk_loader_add_foreignkey_to_values($table_array, $values, $dat
             $columns = array($foreign_field);
             $options = array('statement_name' => 'pk_' . $foreign_table);
             $options['print_errors'] = TRUE;
-            $record  = tripal_core_chado_select($foreign_table, $columns, $fvalues, $options);
+            $record  = chado_select_record($foreign_table, $columns, $fvalues, $options);
             if ($record) {
               $values[$field] = $record[0]->$foreign_field;
             }
@@ -957,7 +957,7 @@ function tripal_bulk_loader_add_foreignkey_to_values($table_array, $values, $dat
           $columns = array($foreign_field);
           $options = array('statement_name' => 'blk_' . $nid . $priority . $foreign_table);
           $options['print_errors'] = TRUE;
-          $record  = tripal_core_chado_select($foreign_table, $columns, $fvalues, $options);
+          $record  = chado_select_record($foreign_table, $columns, $fvalues, $options);
           if ($record) {
             $values[$field] = $record[0]->$foreign_field;
           }
@@ -1174,7 +1174,7 @@ function tripal_bulk_loader_throw_error($msg, $args, $severity) {
     unset($options['print']);
   }
 
-  tripal_core_report_error(
+  tripal_report_error(
     'tripal_bulk',
     $severity,
     $msg,

tripal_bulk_loader/tripal_bulk_loader.drush.inc

@@ -130,7 +130,7 @@ function drush_tripal_bulk_loader_tripal_loader_view ($nid) {
 function drush_tripal_bulk_loader_tripal_loader_cancel ($nid) {
   $node = node_load($nid);
   db_query("UPDATE {tripal_bulk_loader} SET job_status='%s' WHERE nid=%d", 'Job Cancelled', $node->nid);
-  tripal_jobs_cancel($node->job_id,FALSE);
+  tripal_cancel_job($node->job_id,FALSE);
 }
 
 /**
@@ -146,7 +146,7 @@ function drush_tripal_bulk_loader_tripal_loader_submit ($nid) {
 
   if ($node->job_id) {
     //Re-submit Tripal Job
-    tripal_jobs_rerun($node->job_id);
+    tripal_rerun_job($node->job_id);
     db_query("UPDATE {tripal_bulk_loader} SET job_status='%s' WHERE nid=%d", 'Submitted to Queue', $nid);
   }
   else {

tripal_bulk_loader/tripal_bulk_loader.module

@@ -405,7 +405,7 @@ function tripal_bulk_loader_progess_file_get_progress($job_id, $update_progress
 
       // update the progress of the job
       if ($update_progress AND ($percent != 0 OR $percent != 100)) {
-        tripal_job_set_progress($job_id, round($total_percent, 0));
+        tripal_set_job_progress($job_id, round($total_percent, 0));
       }
     }
   }

tripal_contact/api/tripal_contact.api.inc

@@ -21,7 +21,7 @@
  * @ingroup tripal_contact_api
  */
 function tripal_contact_get_property($contact_id, $property) {
-  return tripal_core_get_property('contact', $contact_id, $property, 'tripal_contact');
+  return chado_get_property('contact', $contact_id, $property, 'tripal_contact');
 }
 
 /**
@@ -42,7 +42,7 @@ function tripal_contact_get_property($contact_id, $property) {
  * @ingroup tripal_contact_api
  */
 function tripal_contact_insert_property($contact_id, $property, $value, $update_if_present = 0) {
-  return tripal_core_insert_property('contact', $contact_id, $property, 'tripal_contact', $value, $update_if_present);
+  return chado_insert_property('contact', $contact_id, $property, 'tripal_contact', $value, $update_if_present);
 }
 
 /**
@@ -66,7 +66,7 @@ function tripal_contact_insert_property($contact_id, $property, $value, $update_
  * @ingroup tripal_contact_api
  */
 function tripal_contact_update_property($contact_id, $property, $value, $insert_if_missing = 0) {
-  return tripal_core_update_property('contact', $contact_id, $property, 'tripal_contact', $value, $insert_if_missing);
+  return chado_update_property('contact', $contact_id, $property, 'tripal_contact', $value, $insert_if_missing);
 }
 /**
  * Delete a given property
@@ -85,7 +85,7 @@ function tripal_contact_update_property($contact_id, $property, $value, $insert_
  * @ingroup tripal_contact_api
  */
 function tripal_contact_delete_property($contact_id, $property) {
-  return tripal_core_delete_property('contact', $contact_id, $property, 'tripal_contact');
+  return chado_delete_property('contact', $contact_id, $property, 'tripal_contact');
 }
 
 /**
@@ -115,12 +115,12 @@ function tripal_contact_add_contact($name, $description, $type, $properties) {
   // check to see if this contact name already exists.
   $values =  array('name' => $name);
   $options = array('statement_name' => 'sel_contact_na');
-  $contact = tripal_core_chado_select('contact', array('contact_id'), $values, $options);
+  $contact = chado_select_record('contact', array('contact_id'), $values, $options);
 
   if (count($contact) == 0) {
     $cvterm = tripal_cv_get_cvterm_by_name($type, NULL, 'tripal_contact');
     if (!$cvterm) {
-      tripal_core_report_error('tripal_contact', TRIPAL_ERROR, "Cannot find contact type '%type'",
+      tripal_report_error('tripal_contact', TRIPAL_ERROR, "Cannot find contact type '%type'",
         array('%type' => $type));
       return FALSE;
     }
@@ -130,9 +130,9 @@ function tripal_contact_add_contact($name, $description, $type, $properties) {
       'type_id' => $cvterm->cvterm_id,
     );
     $options = array('statement_name' => 'ins_contact_nadety');
-    $contact = tripal_core_chado_insert('contact', $values, $options);
+    $contact = chado_insert_record('contact', $values, $options);
     if (!$contact) {
-      tripal_core_report_error('tripal_contact', TRIPAL_ERROR, 'Could not add the contact', array());
+      tripal_report_error('tripal_contact', TRIPAL_ERROR, 'Could not add the contact', array());
       return FALSE;
     }
   }
@@ -150,7 +150,7 @@ function tripal_contact_add_contact($name, $description, $type, $properties) {
   foreach ($properties as $key => $value) {
     $success = tripal_contact_insert_property($contact['contact_id'], $key,$value, TRUE);
     if (!$success) {
-      tripal_core_report_error('tripal_contact', TRIPAL_ERROR,
+      tripal_report_error('tripal_contact', TRIPAL_ERROR,
         "Could not add the contact property '%prop'", array('%prop' => $key));
       return FALSE;
     }

tripal_contact/includes/tripal_contact.chado_node.inc

@@ -195,17 +195,17 @@ function chado_contact_form(&$node, $form_state) {
     'cv_name' => 'tripal_contact',
     'select_options' => $select_options
   );
-  chado_node_properties_form($form, $form_state, $details);
+  chado_add_node_form_properties($form, $form_state, $details);
 
   // RELATIONSHIPS FORM
   //---------------------------------------------
   // We want to use the contact_relationship_types cv if there are any terms available
   // and if not, to default to the relationship ontology
-  $cv_result = tripal_core_chado_select('cv',array('cv_id'),array('name' => 'contact_relationship_types'));
+  $cv_result = chado_select_record('cv',array('cv_id'),array('name' => 'contact_relationship_types'));
   $cv_id = $cv_result[0]->cv_id;
   $select_options = tripal_cv_get_cvterm_options($cv_id);
   if (empty($select_options)) {
-    $cv_result = tripal_core_chado_select('cv',array('cv_id'),array('name' => 'relationship'));
+    $cv_result = chado_select_record('cv',array('cv_id'),array('name' => 'relationship'));
     $cv_id = $cv_result[0]->cv_id;
     $select_options = tripal_cv_get_cvterm_options($cv_id);
   }
@@ -222,7 +222,7 @@ function chado_contact_form(&$node, $form_state) {
     'select_options' => $select_options
   );
   // Adds the form elements to your current form
-  chado_node_relationships_form($form, $form_state, $details);
+  chado_add_node_form_relationships($form, $form_state, $details);
 
   return $form;
 }
@@ -252,13 +252,13 @@ function chado_contact_validate($node, $form, &$form_state) {
   if (property_exists($node, 'nid')) {
     // get the existing node
     $values = array('contact_id' => $node->contact_id);
-    $result = tripal_core_chado_select('contact', array('*'), $values);
+    $result = chado_select_record('contact', array('*'), $values);
     $contact = $result[0];
 
     // if the name has changed make sure it doesn't conflict with an existing name
     if ($contact->name != $node->contactname) {
       $values = array('name' => $node->contactname);
-      $result = tripal_core_chado_select('contact', array('contact_id'), $values);
+      $result = chado_select_record('contact', array('contact_id'), $values);
       if ($result and count($result) > 0) {
         form_set_error('contactname', 'Cannot update the contact with this contact name. A contact with this name already exists.');
         return;
@@ -271,7 +271,7 @@ function chado_contact_validate($node, $form, &$form_state) {
     $values = array(
       'name' => $node->contactname,
     );
-    $contact = tripal_core_chado_select('contact', array('contact_id'), $values);
+    $contact = chado_select_record('contact', array('contact_id'), $values);
     if ($contact and count($contact) > 0) {
       form_set_error('contactname', 'Cannot add the contact with this name. A contact with these values already exists.');
       return;
@@ -356,10 +356,10 @@ function chado_contact_insert($node) {
       'description'    => '',
       'type_id'        => $node->type_id,
     );
-    $contact = tripal_core_chado_insert('contact', $values);
+    $contact = chado_insert_record('contact', $values);
     if (!$contact) {
       drupal_set_message(t('Unable to add contact.', 'warning'));
-      tripal_core_report_error('tripal_contact', TRIPAL_ERROR, 
+      tripal_report_error('tripal_contact', TRIPAL_ERROR, 
         'Insert contact: Unable to create contact where values: %values',
         array('%values' => print_r($values, TRUE)));
       return;
@@ -367,7 +367,7 @@ function chado_contact_insert($node) {
     $contact_id = $contact['contact_id'];
 
       // Add the description property
-    $properties = chado_node_properties_form_retreive($node);
+    $properties = chado_retrieve_node_form_properties($node);
     $contact_descrip_id = tripal_cv_get_cvterm_by_name('contact_description', NULL, 'tripal_contact');
     $properties[$contact_descrip_id->cvterm_id][0] = $node->description;
 
@@ -378,14 +378,14 @@ function chado_contact_insert($node) {
       'foreignkey_name' => 'contact_id',
       'foreignkey_value' => $contact_id
     );
-    chado_node_properties_form_update_properties($node, $details, $properties);
+    chado_update_node_form_properties($node, $details, $properties);
 
     // * Relationships Form *
     $details = array(
       'relationship_table' => 'contact_relationship',  // name of the _relationship table
       'foreignkey_value' => $contact_id                // value of the contact_id key
     );
-    chado_node_relationships_form_update_relationships($node, $details);
+    chado_update_node_form_relationships($node, $details);
   }
   else {
     $contact_id = $node->contact_id;
@@ -393,7 +393,7 @@ function chado_contact_insert($node) {
 
   // Make sure the entry for this contact doesn't already exist in the
   // chado_contact table if it doesn't exist then we want to add it.
-  $check_org_id = chado_get_id_for_node('contact', $node->nid);
+  $check_org_id = chado_get_id_from_nid('contact', $node->nid);
   if (!$check_org_id) {
     $record = new stdClass();
     $record->nid = $node->nid;
@@ -422,7 +422,7 @@ function chado_contact_update($node) {
   $node->contactname          = trim($node->contactname);
   $node->description    = trim($node->description);
 
-  $contact_id = chado_get_id_for_node('contact', $node->nid) ;
+  $contact_id = chado_get_id_from_nid('contact', $node->nid) ;
 
   // update the contact record
   $match = array(
@@ -433,16 +433,16 @@ function chado_contact_update($node) {
     'description' => '',
     'type_id' => $node->type_id
   );
-  $status = tripal_core_chado_update('contact', $match, $values);
+  $status = chado_update_record('contact', $match, $values);
   if (!$status) {
     drupal_set_message("Error updating contact", "error");
-    tripal_core_report_error('tripal_contact', TRIPAL_ERROR, 
+    tripal_report_error('tripal_contact', TRIPAL_ERROR, 
       "Error updating contact", array());
     return;
   }
 
   // Add the description property
-  $properties = chado_node_properties_form_retreive($node);
+  $properties = chado_retrieve_node_form_properties($node);
   $contact_descrip_id = tripal_cv_get_cvterm_by_name('contact_description', NULL, 'tripal_contact');
   $properties[$contact_descrip_id->cvterm_id][0] = $node->description;
 
@@ -454,14 +454,14 @@ function chado_contact_update($node) {
     'foreignkey_name' => 'contact_id',
     'foreignkey_value' => $contact_id
   );
-  chado_node_properties_form_update_properties($node, $details, $properties);
+  chado_update_node_form_properties($node, $details, $properties);
 
   // * Relationships Form *
   $details = array(
     'relationship_table' => 'contact_relationship',  // name of the _relationship table
     'foreignkey_value' => $contact_id                // value of the contact_id key
   );
-  chado_node_relationships_form_update_relationships($node, $details);
+  chado_update_node_form_relationships($node, $details);
 }
 
 
@@ -480,11 +480,11 @@ function chado_contact_load($nodes) {
 
   foreach ($nodes as $nid => $node) {
     // find the contact and add in the details
-    $contact_id = chado_get_id_for_node('contact', $nid);
+    $contact_id = chado_get_id_from_nid('contact', $nid);
 
     // get the contact
     $values = array('contact_id' => $contact_id);
-    $contact = tripal_core_generate_chado_var('contact', $values);
+    $contact = chado_generate_var('contact', $values);
 
     // get the contact description from the contactprop table and replace
     // the contact.description field with this one (we don't use the contact.description
@@ -499,9 +499,9 @@ function chado_contact_load($nodes) {
       'return_array' => 1,
       'include_fk' => array('type_id' => 1),
     );
-    $description = tripal_core_generate_chado_var('contactprop', $values, $options);
+    $description = chado_generate_var('contactprop', $values, $options);
     if (count($description) == 1) {
-      $description = tripal_core_expand_chado_vars($description, 'field', 'contactprop.value');
+      $description = chado_expand_var($description, 'field', 'contactprop.value');
       $contact->description = $description[0]->value;
     }
 
@@ -522,7 +522,7 @@ function chado_contact_load($nodes) {
  */
 function chado_contact_delete(&$node) {
 
-  $contact_id = chado_get_id_for_node('contact', $node->nid);
+  $contact_id = chado_get_id_from_nid('contact', $node->nid);
 
   // if we don't have a contact id for this node then this isn't a node of
   // type chado_contact or the entry in the chado_contact table was lost.

tripal_contact/theme/tripal_contact.theme.inc

@@ -22,7 +22,7 @@ function tripal_contact_preprocess_tripal_contact_relationships(&$variables) {
       ),
     ),
   );
-  $contact = tripal_core_expand_chado_vars($contact, 'table', 'contact_relationship', $options);
+  $contact = chado_expand_var($contact, 'table', 'contact_relationship', $options);
 
   // get the subject relationships
   $srelationships = $contact->contact_relationship->subject_id;

tripal_contact/tripal_contact.install

@@ -49,7 +49,7 @@ function tripal_contact_requirements($phase) {
 function tripal_contact_install() {
 
   // create the module's data directory
-  tripal_create_moddir('tripal_contact');
+  tripal_create_files_dir('tripal_contact');
 
   // add the contactprop table to Chado
   tripal_contact_add_custom_tables();
@@ -201,7 +201,7 @@ function tripal_contact_add_custom_tables(){
       ),
     ),
   );
-  tripal_core_create_custom_table('contactprop', $schema, TRUE);
+  chado_create_custom_table('contactprop', $schema, TRUE);
 }
 
 /**

tripal_core/api/tripal_core.files.api.inc

@@ -12,9 +12,8 @@
 /**
  * This function is typically used in the '.install' file for a Tripal module
  * Each module should call this function during installation to create
- * the module data directory which is sites/default/files/tripal/[module_name]
- * for default Drupal settings.  This directory can then be used by the module
- * for storing files.
+ * the module data directory which is sites/default/files/tripal/[module_name].
+ * This directory can then be used by the module for storing files.
  *
  * @param $module_name
  *   the name of the module being installed
@@ -36,21 +35,23 @@ function tripal_create_files_dir($module_name, $path = FALSE) {
       tripal_report_error('tripal_core', TRIPAL_ERROR, $message, array());
     }
   }
-
-  // make sure the module data directory exists
-  tripal_create_files_dir($module_name);
-
-  // now make sure the sub dir exists
-  $sub_dir = tripal_get_files_dir() . $module_name . $path;
-  if (!file_prepare_directory($sub_dir, FILE_CREATE_DIRECTORY | FILE_MODIFY_PERMISSIONS)) {
-    $message = "Cannot create directory $sub_dir. ";
-    drupal_set_message(check_plain(t($message)), 'error');
-    tripal_report_error('tripal_core', TRIPAL_ERROR, $message, array());
+  else {
+    // make sure the module data directory exists, we make a recursive call
+    // but without the path
+    tripal_create_files_dir($module_name);
+  
+    // now make sure the sub dir exists
+    $sub_dir = tripal_get_files_dir() . $module_name . $path;
+    if (!file_prepare_directory($sub_dir, FILE_CREATE_DIRECTORY | FILE_MODIFY_PERMISSIONS)) {
+      $message = "Cannot create directory $sub_dir. ";
+      drupal_set_message(check_plain(t($message)), 'error');
+      tripal_report_error('tripal_core', TRIPAL_ERROR, $message, array());
+    }
   }
 }
 
 /**
- * Each Tripal module has a unique data directory which was creatd using the
+ * Each Tripal module has a unique data directory which was created using the
  * tripal_create_files_dir function during installation.  This function
  * retrieves the directory path.
  *

tripal_cv/api/tripal_cv.api.inc

@@ -54,18 +54,18 @@ function tripal_cv_get_cv($select_values) {
     'name',
     'definition',
   );
-  $results = tripal_core_chado_select('cv', $columns, $select_values);
+  $results = chado_select_record('cv', $columns, $select_values);
   if (sizeof($results) == 1) {
     return $results[0];
   }
   elseif (empty($results)) {
-    tripal_core_report_error('tripal_cv', TRIPAL_WARNING,
+    tripal_report_error('tripal_cv', TRIPAL_WARNING,
       'tripal_cv_get_cv: No cv matches criteria values:%values',
       array('%values' => print_r($select_values, TRUE)));
     return FALSE;
   }
   else {
-    tripal_core_report_error('tripal_cv', TRIPAL_WARNING,
+    tripal_report_error('tripal_cv', TRIPAL_WARNING,
       'tripal_cv_get_cv: 2+ cvs match criteria values:%values',
       array('%values' => print_r($select_values, TRUE)));
   }
@@ -103,7 +103,7 @@ function tripal_cv_get_cv($select_values) {
  */
 function tripal_cv_get_cv_by_name($name) {
 
-  $r = tripal_core_chado_select('cv', array('*'), array('name' => $name));
+  $r = chado_select_record('cv', array('*'), array('name' => $name));
 
   return $r[0];
 }
@@ -124,7 +124,7 @@ function tripal_cv_get_cv_by_name($name) {
  */
 function tripal_cv_get_cv_by_id($cv_id) {
 
-  $r = tripal_core_chado_select('cv', array('*'), array('cv_id' => $cv_id));
+  $r = chado_select_record('cv', array('*'), array('cv_id' => $cv_id));
 
   return $r;
 }
@@ -163,7 +163,7 @@ function tripal_cv_get_cv_id($cv_name) {
  */
 function tripal_cv_get_cv_options() {
 
-  $results = tripal_core_chado_select('cv', array('cv_id', 'name'), array());
+  $results = chado_select_record('cv', array('cv_id', 'name'), array());
 
   $options = array();
   foreach ($results as $r) {
@@ -190,7 +190,7 @@ function tripal_cv_get_cvterm_by_id($cvterm_id) {
   }
   $values = array('cvterm_id' => $cvterm_id);
   $options = array('statement_name' => 'sel_cvterm_id');
-  $r = tripal_core_chado_select('cvterm', array('*'), $values, $options);
+  $r = chado_select_record('cvterm', array('*'), $values, $options);
   if (!$r) {
     return FALSE;
   }
@@ -221,7 +221,7 @@ function tripal_cv_get_cvterm_by_name($name, $cv_id = NULL, $cv_name = 'tripal')
     $options = array(
       'case_insensitive_columns' => array('name')
     );
-    $r = tripal_core_chado_select('cvterm', array('*'), $values, $options);
+    $r = chado_select_record('cvterm', array('*'), $values, $options);
   }
   elseif ($cv_name) {
     $values = array(
@@ -231,19 +231,19 @@ function tripal_cv_get_cvterm_by_name($name, $cv_id = NULL, $cv_name = 'tripal')
       ),
     );
     $options = array('case_insensitive_columns' => array('name'));
-    $r = tripal_core_chado_select('cvterm', array('*'), $values, $options);
+    $r = chado_select_record('cvterm', array('*'), $values, $options);
   }
   else {
     $values = array('name' => $name);
     $options = array('case_insensitive_columns' => array('name'));
-    $r = tripal_core_chado_select('cvterm', array('*'), $values, $options);
+    $r = chado_select_record('cvterm', array('*'), $values, $options);
   }
 
   if (!$r) {
     return FALSE;
   }
   if (count($r) > 1) {
-    tripal_core_report_error('tripal_cv', TRIPAL_ERROR, 
+    tripal_report_error('tripal_cv', TRIPAL_ERROR, 
       "Cannot find a unique term for the term '%name' in the vocabulary '%cv'. Multiple entries exist for this name",
       array('%name' => $name, '%cv' => $cv_name ? $cv_name : $cv_id));
     return FALSE;
@@ -288,7 +288,7 @@ function tripal_cv_get_cvterm_by_synonym($synonym, $cv_id = NULL, $cv_name = 'tr
     'statement_name' => $statement,
     'case_insensitive_columns' => array('name')
   );
-  $synonym = tripal_core_chado_select('cvtermsynonym', array('cvterm_id'), $values, $options);
+  $synonym = chado_select_record('cvtermsynonym', array('cvterm_id'), $values, $options);
 
   // if the synonym doens't exist or more than one record is returned then return false
   if (count($synonym) == 0) {
@@ -301,7 +301,7 @@ function tripal_cv_get_cvterm_by_synonym($synonym, $cv_id = NULL, $cv_name = 'tr
   // get the cvterm
   $values = array('cvterm_id' => $synonym[0]->cvterm_id);
   $options = array('statement_name' => 'sel_cvterm_id');
-  $cvterm = tripal_core_chado_select('cvterm', array('*'), $values, $options);
+  $cvterm = chado_select_record('cvterm', array('*'), $values, $options);
   return $cvterm[0];
 }
 /**
@@ -320,10 +320,10 @@ function tripal_cv_get_cvterm_by_synonym($synonym, $cv_id = NULL, $cv_name = 'tr
 function tripal_cv_get_cvterm_options($cv_id = 0) {
 
   if ($cv_id > 0) {
-    $results = tripal_core_chado_select('cvterm', array('cvterm_id', 'name'), array('cv_id' => $cv_id));
+    $results = chado_select_record('cvterm', array('cvterm_id', 'name'), array('cv_id' => $cv_id));
   }
   else {
-    $results = tripal_core_chado_select('cvterm', array('cvterm_id', 'name'), array());
+    $results = chado_select_record('cvterm', array('cvterm_id', 'name'), array());
   }
 
   $options = array();
@@ -358,16 +358,16 @@ function tripal_cv_update_cvtermpath($cvid, $job_id = NULL) {
 
   print "\nUpdating cvtermpath for $cv->name...\n";
 
-  $previous = tripal_db_set_active('chado');
+  $previous = chado_set_active('chado');
   try {
     $sql = "SELECT * FROM fill_cvtermpath(:name)";
     db_query($sql, array(':name' => $cv->name));
-    tripal_db_set_active($previous);
+    chado_set_active($previous);
   }
   catch (Exception $e) {
-    tripal_db_set_active($previous);
+    chado_set_active($previous);
     $error = $e->getMessage();
-    tripal_core_report_error('tripal_cv', TRIPAL_ERROR, "Could not fill cvtermpath table: @error", array('@error' => $error));
+    tripal_report_error('tripal_cv', TRIPAL_ERROR, "Could not fill cvtermpath table: @error", array('@error' => $error));
     return FALSE;
   }
 
@@ -399,27 +399,27 @@ function tripal_cv_add_cv($name, $definition) {
   // see if the CV (default-namespace) exists already in the database
   $sel_values = array('name' => $name);
   $sel_options = array('statement_name' => 'sel_cv_na');
-  $results = tripal_core_chado_select('cv', array('*'), $sel_values, $sel_options);
+  $results = chado_select_record('cv', array('*'), $sel_values, $sel_options);
 
   // if it does not exists then add it
   if (count($results) == 0) {
     $ins_options = array('statement_name' => 'ins_cv_nade');
-    $success = tripal_core_chado_insert('cv', $ins_values, $ins_options);
+    $success = chado_insert_record('cv', $ins_values, $ins_options);
     if (!$success) {
-      tripal_core_report_error('tripal_cv', TRIPAL_WARNING, "Failed to create the CV record", NULL);
+      tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to create the CV record", NULL);
       return FALSE;
     }
-    $results = tripal_core_chado_select('cv', array('*'), $sel_values, $sel_options);
+    $results = chado_select_record('cv', array('*'), $sel_values, $sel_options);
   }
   // if it already exists then do an update
   else {
     $upd_options = array('statement_name' => 'upd_cv_nade');
-    $success = tripal_core_chado_update('cv', $sel_values, $ins_values, $upd_options);
+    $success = chado_update_record('cv', $sel_values, $ins_values, $upd_options);
     if (!$success) {
-      tripal_core_report_error('tripal_cv', TRIPAL_WARNING, "Failed to update the CV record", NULL);
+      tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to update the CV record", NULL);
       return FALSE;
     }
-    $results = tripal_core_chado_select('cv', array('*'), $sel_values, $sel_options);
+    $results = chado_select_record('cv', array('*'), $sel_values, $sel_options);
   }
 
   // return the cv object
@@ -505,7 +505,7 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
     }
   }
   if (!$name and !$id) {
-    tripal_core_report_error('tripal_cv', TRIPAL_WARNING, "Cannot find cvterm without 'id' or 'name'", NULL);
+    tripal_report_error('tripal_cv', TRIPAL_WARNING, "Cannot find cvterm without 'id' or 'name'", NULL);
     return 0;
   }
   if (!$id) {
@@ -524,11 +524,11 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
 
   // check that we have a database name, give a different message if it's a relationship
   if ($is_relationship and !$dbname) {
-    tripal_core_report_error('tripal_cv', TRIPAL_WARNING, "A database name is not provided for this relationship term: $id", NULL);
+    tripal_report_error('tripal_cv', TRIPAL_WARNING, "A database name is not provided for this relationship term: $id", NULL);
     return 0;
   }
   if (!$is_relationship and !$dbname) {
-    tripal_core_report_error('tripal_cv', TRIPAL_WARNING, "A database identifier is missing from the term: $id", NULL);
+    tripal_report_error('tripal_cv', TRIPAL_WARNING, "A database identifier is missing from the term: $id", NULL);
     return 0;
   }
 
@@ -538,7 +538,7 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
     $cv = tripal_cv_add_cv($cvname, '');
   }
   if (!$cv) {
-    tripal_core_report_error('tripal_cv', TRIPAL_WARNING, "Cannot find namespace '$cvname' when adding/updating $id", NULL);
+    tripal_report_error('tripal_cv', TRIPAL_WARNING, "Cannot find namespace '$cvname' when adding/updating $id", NULL);
     return 0;
   }
 
@@ -563,7 +563,7 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
     $db = tripal_db_add_db($dbname);
   }
   if (!$db) {
-    tripal_core_report_error('tripal_cv', TRIPAL_WARNING, "Cannot find database '$dbname' in Chado.", NULL);
+    tripal_report_error('tripal_cv', TRIPAL_WARNING, "Cannot find database '$dbname' in Chado.", NULL);
     return 0;
   }
 
@@ -577,7 +577,7 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
     ),
   );
   $options = array('statement_name' => 'sel_cvterm_c1');
-  $result = tripal_core_chado_select('cvterm', array('*'), $values, $options);
+  $result = chado_select_record('cvterm', array('*'), $values, $options);
 
   // if the constraint is met then let's check it to see if
   // the database name matches the one we have been provided
@@ -587,13 +587,13 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
     // get the dbxref record
     $values = array('dbxref_id' => $cvterm->dbxref_id);
     $options = array('statement_name' => 'sel_dbxref_id');
-    $result = tripal_core_chado_select('dbxref', array('*'), $values, $options);
+    $result = chado_select_record('dbxref', array('*'), $values, $options);
     $dbxref = $result[0];
 
     // get the db
     $values = array('db_id' => $dbxref->db_id);
     $options = array('statement_name' => 'sel_db_id');
-    $result = tripal_core_chado_select('db', array('*'), $values, $options);
+    $result = chado_select_record('db', array('*'), $values, $options);
     $db_check = $result[0];
 
     // the database name for this existing term does not match that of the
@@ -608,7 +608,7 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
         'accession' => $accession,
       );
       $options = array('statement_name' => 'sel_dbxref_idac');
-      $result = tripal_core_chado_select('dbxref', array('*'), $values, $options);
+      $result = chado_select_record('dbxref', array('*'), $values, $options);
 
       // if we already have a good dbxref then we want to update our cvterm
       // to use this dbxref
@@ -617,9 +617,9 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
         $match = array('cvterm_id' => $cvterm->cvterm_id);
         $values = array('dbxref_id' => $dbxref->dbxref_id);
         $options = array('statement_name' => 'upd_cvterm_db');
-        $success = tripal_core_chado_update('cvterm', $match, $values, $options);
+        $success = chado_update_record('cvterm', $match, $values, $options);
         if (!$success) {
-          tripal_core_report_error('tripal_cv', TRIPAL_WARNING, "Failed to correct the dbxref id for the cvterm " .
+          tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to correct the dbxref id for the cvterm " .
             "'$name' (id: $accession), for database $dbname", NULL);
           return 0;
         }
@@ -629,7 +629,7 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
       else {
         $match = array('cvterm_id' => $cvterm->cvterm_id);
         $options = array('statement_name' => 'del_cvterm_cv');
-        tripal_core_chado_delete('cvterm', $match, $options);
+        chado_delete_record('cvterm', $match, $options);
       }
     }
 
@@ -642,7 +642,7 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
       // get/add the dbxref fort his term
       $dbxref_new =  tripal_db_add_dbxref($db->db_id, $accession);
       if (!$dbxref_new) {
-        tripal_core_report_error('tripal_cv', TRIPAL_WARNING, "Failed to find or insert the dbxref record for cvterm, " .
+        tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to find or insert the dbxref record for cvterm, " .
           "$name (id: $accession), for database $dbname", NULL);
         return 0;
       }
@@ -654,7 +654,7 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
         'is_for_definition' => 1,
       );
       $options = array('statement_name' => 'sel_cvtermdbxref_cvdbis');
-      $result = tripal_core_chado_select('cvterm_dbxref', array('*'), $values, $options);
+      $result = chado_select_record('cvterm_dbxref', array('*'), $values, $options);
 
       // if the cvterm_dbxref record does not exists then add it
       if (count($result)==0) {
@@ -662,9 +662,9 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
           'statement_name' => 'ins_cvtermdbxref_cvdbis',
           'return_record' => FALSE,
         );
-        $success = tripal_core_chado_insert('cvterm_dbxref', $values, $options);
+        $success = chado_insert_record('cvterm_dbxref', $values, $options);
         if (!$success) {
-          tripal_core_report_error('tripal_cv', TRIPAL_WARNING, "Failed to find or insert the cvterm_dbxref record for a " .
+          tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to find or insert the cvterm_dbxref record for a " .
             "duplicated cvterm:  $name (id: $accession), for database $dbname", NULL);
           return 0;
         }
@@ -687,7 +687,7 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
     // check to see if the dbxref exists if not, add it
     $dbxref =  tripal_db_add_dbxref($db->db_id, $accession);
     if (!$dbxref) {
-      tripal_core_report_error('tripal_cv', TRIPAL_WARNING, "Failed to find or insert the dbxref record for cvterm, " .
+      tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to find or insert the dbxref record for cvterm, " .
         "$name (id: $accession), for database $dbname", NULL);
       return 0;
     }
@@ -696,7 +696,7 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
     // this is the second constraint in the cvterm table
     $values = array('dbxref_id' => $dbxref->dbxref_id);
     $options = array('statement_name' => 'sel_cvterm_db');
-    $check = tripal_core_chado_select('cvterm', array('cvterm_id'), $values, $options);
+    $check = chado_select_record('cvterm', array('cvterm_id'), $values, $options);
     if (count($check) == 0) {
       // now add the cvterm
       $ins_values = array(
@@ -708,21 +708,21 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
         'is_relationshiptype'  => $is_relationship,
       );
       $ins_options = array('statement_name' => 'ins_cvterm_all');
-      $success = tripal_core_chado_insert('cvterm', $ins_values, $ins_options);
+      $success = chado_insert_record('cvterm', $ins_values, $ins_options);
       if (!$success) {
         if (!$is_relationship) {
-          tripal_core_report_error('tripal_cv', TRIPAL_WARNING, "Failed to insert the term: $name ($dbname)", NULL);
+          tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to insert the term: $name ($dbname)", NULL);
           return 0;
         }
         else {
-          tripal_core_report_error('tripal_cv', TRIPAL_WARNING, "Failed to insert the relationship term: $name (cv: " . $cvname . " db: $dbname)", NULL);
+          tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to insert the relationship term: $name (cv: " . $cvname . " db: $dbname)", NULL);
           return 0;
         }
       }
     }
     // this dbxref already exists in the cvterm table
     else {
-      tripal_core_report_error('tripal_cv', TRIPAL_WARNING, "The dbxref already exists for another cvterm record: $name (cv: " . $cvname . " db: $dbname)", NULL);
+      tripal_report_error('tripal_cv', TRIPAL_WARNING, "The dbxref already exists for another cvterm record: $name (cv: " . $cvname . " db: $dbname)", NULL);
       return 0;
     }
     $result = chado_query($cvtermsql, array(':accession' => $accession, ':name' => $dbname));
@@ -738,9 +738,9 @@ function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship =
       'is_relationshiptype' => $is_relationship,
     );
     $upd_options = array('statement_name' => 'upd_cvterm_nadeisis');
-    $success = tripal_core_chado_update('cvterm', $match, $upd_values, $upd_options);
+    $success = chado_update_record('cvterm', $match, $upd_values, $upd_options);
     if (!$success) {
-      tripal_core_report_error('tripal_cv', TRIPAL_WARNING, "Failed to update the term: $name", NULL);
+      tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to update the term: $name", NULL);
       return 0;
     }
     $result = chado_query($cvtermsql, array(':accession' => $accession, ':name' => $dbname));

tripal_cv/api/tripal_cv.schema.api.inc

@@ -3,9 +3,9 @@
 /**
  * Implements hook_chado_schema_v1_2_tripal_obo_temp()
  * Purpose: To describe the structure of 'tripal_obo_temp' to tripal
- * @see tripal_core_chado_insert()
- * @see tripal_core_chado_update()
- * @see tripal_core_chado_select()
+ * @see chado_insert_record()
+ * @see chado_update_record()
+ * @see chado_select_record()
  *
  * @return
  *    An array describing the 'tripal_obo_temp' table

tripal_cv/includes/cv_form.inc

@@ -102,7 +102,7 @@ function tripal_cv_add_cv_form_fields(&$form, $form_state, $cv_id = NULL) {
 
   if ($cv_id) {
     $values = array('cv_id' => $cv_id);
-    $result = tripal_core_chado_select('cv', array('*'), $values);
+    $result = chado_select_record('cv', array('*'), $values);
     $cv = $result[0];
     $default_name = $cv->name;
     $default_desc = $cv->definition;
@@ -169,7 +169,7 @@ function tripal_cv_form_fields_validate($form, &$form_state) {
 
   // make sure the cv name is unique
   $values = array('name' => $name);
-  $results = tripal_core_chado_select('cv', array('cv_id'), $values);
+  $results = chado_select_record('cv', array('cv_id'), $values);
   if (count($results) > 0 and $results[0]->cv_id != $cv_id) {
     form_set_error('name', 'The vocabulary name must be unique');
   }
@@ -188,7 +188,7 @@ function tripal_cv_cv_add_form_submit($form, &$form_state) {
     'name' => $name,
     'definition' => $desc,
   );
-  $success = tripal_core_chado_insert('cv', $values);
+  $success = chado_insert_record('cv', $values);
   if ($success) {
     drupal_set_message(t("Controlled vocabulary added"));
   }
@@ -213,7 +213,7 @@ function tripal_cv_cv_edit_form_submit($form, &$form_state) {
   );
   if (strcmp($op, 'Update')==0) {
     $match = array('cv_id' => $cv_id);
-    $success = tripal_core_chado_update('cv', $match, $values);
+    $success = chado_update_record('cv', $match, $values);
     if ($success) {
       drupal_set_message(t("Controlled vocabulary updated"));
     }
@@ -223,7 +223,7 @@ function tripal_cv_cv_edit_form_submit($form, &$form_state) {
   }
   if (strcmp($op, 'Delete')==0) {
     $match = array('cv_id' => $cv_id);
-    $success = tripal_core_chado_delete('cv', $match);
+    $success = chado_delete_record('cv', $match);
     if ($success) {
       drupal_set_message(t("Controlled vocabulary deleted"));
     }

tripal_cv/includes/cvterm_form.inc

@@ -181,7 +181,7 @@ function tripal_cv_add_cvterm_form_fields(&$form, $form_state, $cv_id = 0, $cvte
   // get default values
   if ($cvterm_name) {
     $values = array('cv_id' => $cv_id, 'name' => $cvterm_name);
-    $cvterm = tripal_core_generate_chado_var('cvterm', $values);
+    $cvterm = chado_generate_var('cvterm', $values);
     $name = $cvterm->name;
     $definition = $cvterm->definition;
     $is_relationship = $cvterm->is_relationshiptype;
@@ -227,7 +227,7 @@ function tripal_cv_add_cvterm_form_fields(&$form, $form_state, $cv_id = 0, $cvte
   $values = array();
   $columns = array('db_id', 'name');
   $options = array('order_by' => array('name' => 'ASC'));
-  $results = tripal_core_chado_select('db', $columns, $values, $options);
+  $results = chado_select_record('db', $columns, $values, $options);
   $dbs = array();
   $dbs[] = '';
   foreach ($results as $db) {
@@ -274,7 +274,7 @@ function tripal_cv_cvterm_edit_form_validate($form, &$form_state) {
   // make sure the cv term name is unique for this vocabulary
   if ($step == 1) {
     $values = array('name' => $name, 'cv_id' => $cv_id);
-    $results = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);
+    $results = chado_select_record('cvterm', array('cvterm_id'), $values);
     foreach ($results as $r) {
       if ($r->cvterm_id != $cvterm_id) {
         form_set_error('name', 'The term name must be unique for this vocabulary. Another term with this name already exists.');
@@ -294,28 +294,28 @@ function tripal_cv_cvterm_add_form_validate($form, &$form_state) {
   $accession = array_key_exists('accession', $form_state['values']) ? $form_state['values']['accession'] : '';
 
   $values = array('cv_id' => $cv_id);
-  $results = tripal_core_chado_select('cv', array('name'), $values);
+  $results = chado_select_record('cv', array('name'), $values);
   if (!$results or count($results) == 0) {
     form_set_error('cv_id', 'The controlled vocabulary does not exist');
   }
 
   // make sure the DB exists
   $values = array('db_id' => $db_id);
-  $results = tripal_core_chado_select('db', array('name'), $values);
+  $results = chado_select_record('db', array('name'), $values);
   if (!$results or count($results) == 0) {
     form_set_error('db_id', 'The database name does not exist');
   }
 
   // make sure the cv term name is unique for this vocabulary
   $values = array('name' => $name, 'cv_id' => $cv_id);
-  $results = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);
+  $results = chado_select_record('cvterm', array('cvterm_id'), $values);
   if (count($results) > 0) {
     form_set_error('name', 'The term name must be unique for this vocabulary. Another term with this name already exists.');
   }
 
   // make sure this accession is unique for the database
   $values = array('accession' => $accession, 'db_id' => $db_id);
-  $results = tripal_core_chado_select('dbxref', array('dbxref_id'), $values);
+  $results = chado_select_record('dbxref', array('dbxref_id'), $values);
   if (count($results) > 0 ) {
     form_set_error('accession', 'The accession is not uniuqe for this vocabulary\'s database.');
   }
@@ -352,7 +352,7 @@ function tripal_cv_cvterm_edit_form_submit($form, &$form_state) {
 
       // get the original cvterm_id
       $values = array('name' => $name, 'cv_id' => $cv_id);
-      $results = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);
+      $results = chado_select_record('cvterm', array('cvterm_id'), $values);
       $cvterm = $results[0];
 
       $form_state['storage']['cv_id'] = $cv_id;
@@ -367,12 +367,12 @@ function tripal_cv_cvterm_edit_form_submit($form, &$form_state) {
       if ($op == 'Update') {
         // get the cv
         $values = array('cv_id' => $cv_id);
-        $results = tripal_core_chado_select('cv', array('name'), $values);
+        $results = chado_select_record('cv', array('name'), $values);
         $cv = $results[0];
 
         // get the db
         $values = array('db_id' => $db_id);
-        $results = tripal_core_chado_select('db', array('name'), $values);
+        $results = chado_select_record('db', array('name'), $values);
         $db = $results[0];
 
         // now add the term
@@ -394,7 +394,7 @@ function tripal_cv_cvterm_edit_form_submit($form, &$form_state) {
       }
       if ($op == 'Delete') {
         $values = array('cvterm_id' => $cvterm_id);
-        $success = tripal_core_chado_delete('cvterm', $values);
+        $success = chado_delete_record('cvterm', $values);
         if ($success) {
           drupal_set_message('Term deleted successfully.');
         }
@@ -423,12 +423,12 @@ function tripal_cv_cvterm_add_form_submit($form, &$form_state) {
 
   // get the database
   $values = array('db_id' => $db_id);
-  $results = tripal_core_chado_select('db', array('name'), $values);
+  $results = chado_select_record('db', array('name'), $values);
   $db = $results[0];
 
   // get the cv
   $values = array('cv_id' => $cv_id);
-  $results = tripal_core_chado_select('cv', array('name'), $values);
+  $results = chado_select_record('cv', array('name'), $values);
   $cv = $results[0];
 
   // now add the term

tripal_cv/includes/obo_loader.inc

@@ -280,7 +280,7 @@ function tripal_cv_load_obo_v1_2($file, $jobid = NULL, &$newcvs) {
  */
 function tripal_cv_obo_quiterror($message) {
 
-  tripal_core_report_error("T_obo_loader", TRIPAL_ERROR, $message, array());
+  tripal_report_error("T_obo_loader", TRIPAL_ERROR, $message, array());
   exit;
 
 }
@@ -312,7 +312,7 @@ function tripal_cv_obo_load_typedefs($defaultcv, $newcvs, $default_db, $jobid) {
     // update the job status every interval
     if ($jobid and $i % $interval == 0) {
       $complete = ($i / $count) * 33.33333333;
-      tripal_job_set_progress($jobid, intval($complete + 33.33333333));
+      tripal_set_job_progress($jobid, intval($complete + 33.33333333));
       printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));
     }
 
@@ -328,7 +328,7 @@ function tripal_cv_obo_load_typedefs($defaultcv, $newcvs, $default_db, $jobid) {
     else {
       $complete = 33.33333333;
     }
-    tripal_job_set_progress($jobid, intval($complete + 33.33333333));
+    tripal_set_job_progress($jobid, intval($complete + 33.33333333));
     printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));
   }
   return 1;
@@ -368,7 +368,7 @@ function tripal_cv_obo_process_terms($defaultcv, $jobid = NULL, &$newcvs, $defau
     // update the job status every interval
     if ($jobid and $i % $interval == 0) {
       $complete = ($i / $count) * 33.33333333;
-      tripal_job_set_progress($jobid, intval($complete + 66.666666));
+      tripal_set_job_progress($jobid, intval($complete + 66.666666));
       printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));
     }
 
@@ -388,7 +388,7 @@ function tripal_cv_obo_process_terms($defaultcv, $jobid = NULL, &$newcvs, $defau
     else {
       $complete = 33.33333333;
     }
-    tripal_job_set_progress($jobid, intval($complete + 66.666666));
+    tripal_set_job_progress($jobid, intval($complete + 66.666666));
     printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));
   }
 
@@ -621,13 +621,13 @@ function tripal_cv_obo_add_relationship($cvterm, $defaultcv, $rel,
     'object_id'  => $objcvterm->cvterm_id
   );
   $options = array('statement_name' => 'sel_cvtermrelationship_tysuob');
-  $result = tripal_core_chado_select('cvterm_relationship', array('*'), $values, $options);
+  $result = chado_select_record('cvterm_relationship', array('*'), $values, $options);
   if (count($result) == 0) {
     $options = array(
       'statement_name' => 'ins_cvtermrelationship_tysuob',
       'return_record' => FALSE
     );
-    $success = tripal_core_chado_insert('cvterm_relationship', $values, $options);
+    $success = chado_insert_record('cvterm_relationship', $values, $options);
     if (!$success) {
       tripal_cv_obo_quiterror("Cannot add term relationship: '$cvterm->name' $rel '$objcvterm->name'");
     }
@@ -643,7 +643,7 @@ function tripal_cv_obo_add_relationship($cvterm, $defaultcv, $rel,
 function tripal_cv_obo_get_term($id) {
   $values = array('id' => $id);
   $options = array('statement_name' => 'sel_tripalobotemp_id');
-  $result = tripal_core_chado_select('tripal_obo_temp', array('stanza'), $values, $options);
+  $result = chado_select_record('tripal_obo_temp', array('stanza'), $values, $options);
   if (count($result) == 0) {
     return FALSE;
   }
@@ -679,7 +679,7 @@ function tripal_cv_obo_add_synonyms($term, $cvterm) {
         ),
       );
       $options = array('statement_name' => 'sel_cvterm_nacv', 'is_updlicate' => 1);
-      $results = tripal_core_chado_select('cvterm', array('*'), $values, $options);
+      $results = chado_select_record('cvterm', array('*'), $values, $options);
 
       // if it doesn't exist then add it
       if (!$results) {
@@ -705,7 +705,7 @@ function tripal_cv_obo_add_synonyms($term, $cvterm) {
         'synonym' => $def
       );
       $options = array('statement_name' => 'sel_cvtermsynonym_cvsy');
-      $results = tripal_core_chado_select('cvtermsynonym', array('*'), $values, $options);
+      $results = chado_select_record('cvtermsynonym', array('*'), $values, $options);
       if (count($results) == 0) {
         $values = array(
           'cvterm_id' => $cvterm->cvterm_id,
@@ -716,7 +716,7 @@ function tripal_cv_obo_add_synonyms($term, $cvterm) {
           'statement_name' => 'ins_cvtermsynonym_cvsy',
           'return_record' => FALSE
         );
-        $success = tripal_core_chado_insert('cvtermsynonym', $values, $options);
+        $success = chado_insert_record('cvtermsynonym', $values, $options);
         if (!$success) {
           tripal_cv_obo_quiterror("Failed to insert the synonym for term: $name ($def)");
         }
@@ -775,7 +775,7 @@ function tripal_cv_obo_parse($obo_file, &$header, $jobid) {
     if ($jobid and $intv_read >= $interval) {
       $percent = sprintf("%.2f", ($num_read / $filesize) * 100);
       print "Parsing Line $line_num (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
-      tripal_job_set_progress($jobid, intval(($num_read / $filesize) * 33.33333333));
+      tripal_set_job_progress($jobid, intval(($num_read / $filesize) * 33.33333333));
       $intv_read = 0;
     }
 
@@ -806,9 +806,9 @@ function tripal_cv_obo_parse($obo_file, &$header, $jobid) {
           'type' => $type,
         );
         $options = array('statement_name' => 'ins_tripalobotemp_all');
-        $success = tripal_core_chado_insert('tripal_obo_temp', $values, $options);
+        $success = chado_insert_record('tripal_obo_temp', $values, $options);
         if (!$success) {
-          tripal_core_report_error('T_obo_loader', "ERROR: Cannot insert stanza into temporary table.", array(), 'error');
+          tripal_report_error('T_obo_loader', "ERROR: Cannot insert stanza into temporary table.", array(), 'error');
           exit;
         }
 
@@ -855,14 +855,14 @@ function tripal_cv_obo_parse($obo_file, &$header, $jobid) {
       'type' => $type,
     );
     $options = array('statement_name' => 'ins_tripalobotemp_all');
-    tripal_core_chado_insert('tripal_obo_temp', $values, $options);
+    chado_insert_record('tripal_obo_temp', $values, $options);
     if (!$success) {
-      tripal_core_report_error('T_obo_loader', "ERROR: Cannot insert stanza into temporary table.", array(), 'error');
+      tripal_report_error('T_obo_loader', "ERROR: Cannot insert stanza into temporary table.", array(), 'error');
       exit;
     }
     $percent = sprintf("%.2f", ($num_read / $filesize) * 100);
     print "Parsing Line $line_num (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
-    tripal_job_set_progress($jobid, intval(($num_read / $filesize) * 33.33333333));
+    tripal_set_job_progress($jobid, intval(($num_read / $filesize) * 33.33333333));
   }
   return $default_db;
 }
@@ -881,7 +881,7 @@ function tripal_cv_obo_add_cvterm_dbxref($cvterm, $xref) {
 
   if (!$accession) {
     tripal_cv_obo_quiterror();
-    tripal_core_report_error("T_obo_loader", TRIPAL_WARNING, "Cannot add a dbxref without an accession: '$xref'", NULL);
+    tripal_report_error("T_obo_loader", TRIPAL_WARNING, "Cannot add a dbxref without an accession: '$xref'", NULL);
     return FALSE;
   }
 
@@ -909,13 +909,13 @@ function tripal_cv_obo_add_cvterm_dbxref($cvterm, $xref) {
     'dbxref_id' => $dbxref->dbxref_id,
   );
   $options = array('statement_name' => 'sel_cvtermdbxref_cvdb');
-  $result = tripal_core_chado_select('cvterm_dbxref', array('*'), $values, $options);
+  $result = chado_select_record('cvterm_dbxref', array('*'), $values, $options);
   if (count($result) == 0) {
     $ins_options = array(
       'statement_name' => 'ins_cvtermdbxref_cvdb',
       'return_record' => FALSE
     );
-    $result = tripal_core_chado_insert('cvterm_dbxref', $values, $ins_options);
+    $result = chado_insert_record('cvterm_dbxref', $values, $ins_options);
     if (!$result) {
       tripal_cv_obo_quiterror("Cannot add cvterm_dbxref: $xref");
       return FALSE;
@@ -943,7 +943,7 @@ function tripal_cv_obo_add_cvterm_prop($cvterm, $property, $value, $rank) {
     'cv_id' => $cv->cv_id,
   );
   $options = array('statement_name' => 'sel_cvterm_nacv_na');
-  $results = tripal_core_chado_select('cvterm', array('*'), $values, $options);
+  $results = chado_select_record('cvterm', array('*'), $values, $options);
   if (count($results) == 0) {
     $term = array(
       'name' => $property,
@@ -965,7 +965,7 @@ function tripal_cv_obo_add_cvterm_prop($cvterm, $property, $value, $rank) {
   if ($rank == 0) {
     $values = array('cvterm_id' => $cvterm->cvterm_id);
     $options = array('statement_name' => 'del_cvtermprop_cv');
-    $success = tripal_core_chado_delete('cvtermprop', $values, $options);
+    $success = chado_delete_record('cvtermprop', $values, $options);
     if (!$success) {
        tripal_cv_obo_quiterror("Could not remove existing properties to update property $property for term\n");
        return FALSE;
@@ -983,7 +983,7 @@ function tripal_cv_obo_add_cvterm_prop($cvterm, $property, $value, $rank) {
     'statement_name' => 'ins_cvtermprop_cvtyvara',
     'return_record' => FALSE,
   );
-  $result = tripal_core_chado_insert('cvtermprop', $values, $options);
+  $result = chado_insert_record('cvtermprop', $values, $options);
   if (!$result) {
     tripal_cv_obo_quiterror("Could not add property $property for term\n");
     return FALSE;
@@ -1004,7 +1004,7 @@ function tripal_cv_obo_add_dbxref($db_id, $accession, $version='', $description=
     'accession' => $accession,
   );
   $options = array('statement_name' => 'sel_dbxref_idac');
-  $result = tripal_core_chado_select('dbxref', array('dbxref_id'), $values, $options);
+  $result = chado_select_record('dbxref', array('dbxref_id'), $values, $options);
   if (count($result) == 0) {
     $ins_values = array(
       'db_id'       => $db_id,
@@ -1016,12 +1016,12 @@ function tripal_cv_obo_add_dbxref($db_id, $accession, $version='', $description=
       'statement_name' => 'ins_dbxref_idacvede',
       'return_record' => FALSE
     );
-    $result = tripal_core_chado_insert('dbxref', $ins_values, $ins_options);
+    $result = chado_insert_record('dbxref', $ins_values, $ins_options);
     if (!$result) {
       tripal_cv_obo_quiterror("Failed to insert the dbxref record $accession");
       return FALSE;
     }
-    $result = tripal_core_chado_select('dbxref', array('dbxref_id'), $values, $options);
+    $result = chado_select_record('dbxref', array('dbxref_id'), $values, $options);
   }
   return $result[0];
 }

tripal_cv/tripal_cv.install

@@ -44,7 +44,7 @@ function tripal_cv_requirements($phase) {
 function tripal_cv_install() {
 
   // create the module's data directory
-  tripal_create_moddir('tripal_cv');
+  tripal_create_files_dir('tripal_cv');
 
   // add the cv_root_mview
   tripal_cv_add_cv_root_mview();

tripal_cv/tripal_cv.module

@@ -308,14 +308,14 @@ function tripal_cv_form_alter(&$form, &$form_state, $form_id) {
  *
  * @ingroup tripal_db
  */
-function tripal_cv_theme() {
-  $theme_path = drupal_get_path('module', 'tripal_cv') . '/theme';
-  $items = array(
-    'tripal_cv_admin' => array(
-      'template' => 'tripal_cv_admin',
-      'arguments' =>  array(NULL),
-      'path' => $theme_path,
-    ),
+function tripal_cv_theme($existing, $type, $theme, $path) {
+ 
+ $items = array(
+    'tripal_cv_help' => array(
+      'template' => 'tripal_cv_help',
+      'variables' =>  array(NULL),
+      'path' => "$path/theme/"
+    )
   );
 
   return $items;

tripal_db/api/tripal_db.api.inc

@@ -51,18 +51,18 @@ function tripal_db_get_db($select_values) {
     'urlprefix',
     'url'
   );
-  $results = tripal_core_chado_select('db', $columns, $select_values);
+  $results = chado_select_record('db', $columns, $select_values);
   if (sizeof($results) == 1) {
     return $results[0];
   }
   elseif (empty($results)) {
-    tripal_core_report_error('tripal_db', TRIPAL_WARNING,
+    tripal_report_error('tripal_db', TRIPAL_WARNING,
       'tripal_db_get_db: No db matches criteria values:%values',
       array('%values' => print_r($select_values, TRUE)));
     return FALSE;
   }
   else {
-    tripal_core_report_error('tripal_db', TRIPAL_WARNING,
+    tripal_report_error('tripal_db', TRIPAL_WARNING,
       'tripal_db_get_db: 2+ dbs match criteria values:%values',
       array('%values' => print_r($select_values, TRUE)));
   }
@@ -100,7 +100,7 @@ function tripal_db_get_db_by_name($name) {
   $values = array('name' => $name);
   $options = array('statement_name' => 'sel_db_na');
 
-  $db = tripal_core_chado_select('db', array('*'), $values, $options);
+  $db = chado_select_record('db', array('*'), $values, $options);
   if (count($db) == 1) {
     return $db[0];
   }
@@ -209,7 +209,7 @@ function tripal_db_get_dbxref($select_values) {
     'description',
     'version'
   );
-  $results = tripal_core_chado_select('dbxref', $columns, $select_values);
+  $results = chado_select_record('dbxref', $columns, $select_values);
   if (sizeof($results) == 1) {
     $dbxref = tripal_db_add_db_to_object(array('db_id' => $results[0]->db_id), $results[0], array());
     unset($dbxref->db_id);
@@ -217,13 +217,13 @@ function tripal_db_get_dbxref($select_values) {
     return $dbxref;
   }
   elseif (empty($results)) {
-    tripal_core_report_error('tripal_db', TRIPAL_WARNING,
+    tripal_report_error('tripal_db', TRIPAL_WARNING,
       'tripal_db_get_dbxref: No dbxref matches criteria values:%values',
       array('%values' => print_r($select_values, TRUE)));
     return FALSE;
   }
   else {
-    tripal_core_report_error('tripal_db', TRIPAL_WARNING,
+    tripal_report_error('tripal_db', TRIPAL_WARNING,
       'tripal_db_get_dbxref: 2+ dbxrefs match criteria values:%values',
       array('%values' => print_r($select_values, TRUE)));
   }
@@ -294,27 +294,27 @@ function tripal_db_add_db($dbname, $description = '', $url = '',
   // get the database record if it already exists
   $sel_values = array('name' => $dbname);
   $sel_options = array('statement_name' => 'sel_db_na');
-  $result = tripal_core_chado_select('db', array('*'), $sel_values, $sel_options);
+  $result = chado_select_record('db', array('*'), $sel_values, $sel_options);
 
   // if it does not exists then add it
   if (count($result) == 0) {
     $ins_options = array('statement_name' => 'ins_db_nadeurur');
-    $success = tripal_core_chado_insert('db', $ins_values, $ins_options);
+    $success = chado_insert_record('db', $ins_values, $ins_options);
     if (!$success) {
-      tripal_core_report_error('tripal_db', TRIPAL_WARNING, "Cannot create db '$dbname'.", NULL);
+      tripal_report_error('tripal_db', TRIPAL_WARNING, "Cannot create db '$dbname'.", NULL);
       return 0;
     }
-    $result = tripal_core_chado_select('db', array('*'), $sel_values, $sel_options);
+    $result = chado_select_record('db', array('*'), $sel_values, $sel_options);
   }
   // if it exists and update is enabled the do the update
   elseif ($update) {
     $upd_options = array('statement_name' => 'upd_db_nadeurur');
-    $success = tripal_core_chado_update('db', $sel_values, $ins_values, $upd_options);
+    $success = chado_update_record('db', $sel_values, $ins_values, $upd_options);
     if (!$success) {
-      tripal_core_report_error('tripal_db', TRIPAL_WARNING, "Cannot update db '$dbname'.", NULL);
+      tripal_report_error('tripal_db', TRIPAL_WARNING, "Cannot update db '$dbname'.", NULL);
       return 0;
     }
-    $result = tripal_core_chado_select('db', array('*'), $sel_values, $sel_options);
+    $result = chado_select_record('db', array('*'), $sel_values, $sel_options);
   }
 
   // return the database object
@@ -340,16 +340,16 @@ function tripal_db_add_dbxref($db_id, $accession, $version = '', $description =
     'accession' => $accession,
     'version' => $version
   );
-  $result = tripal_core_chado_select('dbxref', array('*'), $sel_values);
+  $result = chado_select_record('dbxref', array('*'), $sel_values);
 
   // if it doesn't already exist then add it
   if (!$result) {
-    $success = tripal_core_chado_insert('dbxref', $ins_values);
+    $success = chado_insert_record('dbxref', $ins_values);
     if (!$success) {
-      tripal_core_report_error('tripal_cv', TRIPAL_WARNING, "Failed to insert the dbxref record $accession", NULL);
+      tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to insert the dbxref record $accession", NULL);
       return 0;
     }
-    $result = tripal_core_chado_select('dbxref', array('*'), $sel_values);
+    $result = chado_select_record('dbxref', array('*'), $sel_values);
   }
 
   if (isset($result[0])) {
@@ -370,16 +370,16 @@ function tripal_db_add_dbxref_link($linking_table, $dbxref_id, $foreignkey_name,
     $foreignkey_name => $foreignkey_id
   );
 
-  $result = tripal_core_chado_select($linking_table, array('*'), $values);
+  $result = chado_select_record($linking_table, array('*'), $values);
 
   // if it doesn't already exist then add it
   if (!$result) {
-    $success = tripal_core_chado_insert($linking_table, $values);
+    $success = chado_insert_record($linking_table, $values);
     if (!$success) {
-      tripal_core_report_error('tripal_db', TRIPAL_WARNING, "Failed to insert the $linking_table record $accession", NULL);
+      tripal_report_error('tripal_db', TRIPAL_WARNING, "Failed to insert the $linking_table record $accession", NULL);
       return 0;
     }
-    $result = tripal_core_chado_select($linking_table, array('*'), $values);
+    $result = chado_select_record($linking_table, array('*'), $values);
   }
 
   if (isset($result[0])) {

tripal_db/includes/tripal_db.admin.inc

@@ -145,7 +145,7 @@ function tripal_db_add_db_form_fields(&$form, $form_state, $dbid = NULL) {
   // get the default values from the database first
   if ($dbid) {
     $values = array('db_id' => $dbid);
-    $result = tripal_core_chado_select('db', array('*'), $values);
+    $result = chado_select_record('db', array('*'), $values);
     $db = $result[0];
     $default_db = $db->name;
     $default_desc = $db->description;
@@ -229,7 +229,7 @@ function tripal_db_form_fields_validate($form, &$form_state) {
 
   // make sure the database name is unique
   $values = array('name' => $name);
-  $results = tripal_core_chado_select('db', array('db_id'), $values);
+  $results = chado_select_record('db', array('db_id'), $values);
   if (count($results) > 0 and $results[0]->db_id != $dbid) {
     form_set_error('name', 'The database name must be unique');
   }
@@ -254,7 +254,7 @@ function tripal_db_db_add_form_submit($form, &$form_state) {
     'url' => $url,
     'urlprefix' => $urlp,
   );
-  $success = tripal_core_chado_insert('db', $values);
+  $success = chado_insert_record('db', $values);
   if ($success) {
     drupal_set_message(t("External database added"));
   }
@@ -288,7 +288,7 @@ function tripal_db_db_edit_form_submit($form, &$form_state) {
 
   if (strcmp($op, 'Update')==0) {
     $match = array('db_id' => $dbid);
-    $success = tripal_core_chado_update('db', $match, $values);
+    $success = chado_update_record('db', $match, $values);
     if ($success) {
       drupal_set_message(t("External database updated"));
     }
@@ -298,7 +298,7 @@ function tripal_db_db_edit_form_submit($form, &$form_state) {
   }
   if (strcmp($op, 'Delete')==0) {
     $match = array('db_id' => $dbid);
-    $success = tripal_core_chado_delete('db', $match);
+    $success = chado_delete_record('db', $match);
     if ($success) {
       drupal_set_message(t("External database deleted"));
     }

tripal_db/tripal_db.info

@@ -7,4 +7,3 @@ version = 7.x-2.0a
 configure = admin/tripal/chado/tripal_db
 
 dependencies[] = tripal_core
-dependencies[] = tripal_views

tripal_db/tripal_db.install

@@ -45,7 +45,7 @@ function tripal_db_requirements($phase) {
 function tripal_db_install() {
 
   // create the module's data directory
-  tripal_create_moddir('tripal_db');
+  tripal_create_files_dir('tripal_db');
 
 }
 

tripal_db/tripal_db.module

@@ -132,14 +132,14 @@ function tripal_db_views_api() {
  *
  * @ingroup tripal_db
  */
-function tripal_db_theme() {
-  $theme_path = drupal_get_path('module', 'tripal_db') . '/theme';
-  $items = array(
-    'tripal_db_admin' => array(
-      'template' => 'tripal_db_admin',
-      'arguments' =>  array(NULL),
-      'path' => $theme_path,
-    ),
+function tripal_db_theme($existing, $type, $theme, $path) {
+ 
+ $items = array(
+    'tripal_db_help' => array(
+      'template' => 'tripal_db_help',
+      'variables' =>  array(NULL),
+      'path' => "$path/theme/"
+    )
   );
   return $items;
 }

tripal_example/includes/tripal_example.chado_node.inc

@@ -114,7 +114,7 @@ function chado_example_form($node, &$form_state) {
   // if we are editing an existing node then the example is already part of the node
   if (property_exists($node, 'example')) {
     // $example = $node->example;
-    // $example = tripal_core_expand_chado_vars($example, 'field', 'example.residues');
+    // $example = chado_expand_var($example, 'field', 'example.residues');
     // $example_id   = $example->example_id;
     // $uniquename   = $example->uniquename;
 
@@ -150,7 +150,7 @@ function chado_example_form($node, &$form_state) {
     'cv_name' => 'example_property_types'   // the cv.name of the cv governing exampleprop.type_id
   );
   // Adds the form elements to your current form
-  chado_node_properties_form($form, $form_state, $details);
+  chado_add_node_form_properties($form, $form_state, $details);
 
   // ADDITIONAL DBXREFS FORM
   //---------------------------------------------
@@ -162,7 +162,7 @@ function chado_example_form($node, &$form_state) {
     'base_key_value' => $example_id       // the value of example_id for this record
   );
   // Adds the form elements to your current form
-  chado_node_additional_dbxrefs_form($form, $form_state, $details);
+  chado_add_node_form_dbxrefs($form, $form_state, $details);
 
   // RELATIONSHIPS FORM
   //---------------------------------------------
@@ -177,7 +177,7 @@ function chado_example_form($node, &$form_state) {
     'cv_name' => 'example_relationship_types'         // the cv.name of the cv governing example_relationship.type_id
   );
   // Adds the form elements to your current form
-  chado_node_relationships_form($form, $form_state, $details);
+  chado_add_node_form_relationships($form, $form_state, $details);
 
   // return the form
   return $form;
@@ -258,10 +258,10 @@ function chado_example_insert($node) {
     //  'uniquename' => $node->uniquename,
     //  'residues' => $residues,
     //);
-    //$example = tripal_core_chado_select('example', array('*'), $values);
+    //$example = chado_select_record('example', array('*'), $values);
     //if (!$example) {
     //  drupal_set_message(t('Unable to add example.'), 'warning');
-    //  tripal_core_report_error('tripal_example', TRIPAL_WARNING, 'Insert example: Unable to create example where values: %values',
+    //  tripal_report_error('tripal_example', TRIPAL_WARNING, 'Insert example: Unable to create example where values: %values',
     //    array('%values' => print_r($values, TRUE)));
     //  return;
     //}
@@ -281,7 +281,7 @@ function chado_example_insert($node) {
       //   'foreignkey_name' => 'example_id',   // the name of the key in your base table
       //   'foreignkey_value' => $example_id    // the value of the example_id key
       // );
-      // chado_node_properties_form_update_properties($node, $details);
+      // chado_update_node_form_properties($node, $details);
 
       // * Additional DBxrefs Form *
       // If you implemented the dbxrefs form in chado_example_form then you need to
@@ -291,7 +291,7 @@ function chado_example_insert($node) {
       //   'foreignkey_name' => 'example_id',     // the name of the key in your base table
       //   'foreignkey_value' => $example_id      // the value of the example_id key
       // );
-      // chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
+      // chado_update_node_form_dbxrefs($node, $details);
 
       // * Relationships Form *
       // If you implemented the relationships form in chado_example_form then you need to
@@ -300,7 +300,7 @@ function chado_example_insert($node) {
       //   'relationship_table' => 'example_relationship',  // name of the _relationship table
       //   'foreignkey_value' => $example_id                // value of the example_id key
       // );
-      // chado_node_relationships_form_update_relationships($node, $details);
+      // chado_update_node_form_relationships($node, $details);
     }
   }
   else {
@@ -310,7 +310,7 @@ function chado_example_insert($node) {
 
   // Make sure the entry for this example doesn't already exist in the
   // chado_example table if it doesn't exist then we want to add it.
-  // $check_org_id = chado_get_id_for_node('example', $node->nid);
+  // $check_org_id = chado_get_id_from_nid('example', $node->nid);
   //if (!$check_org_id) {
   //  $record = new stdClass();
   //  $record->nid = $node->nid;
@@ -334,7 +334,7 @@ function chado_example_update($node) {
   // be sure to always trim text fields
   // $node->uniquename   = trim($node->uniquename);
 
-  // use the tripal_core_chado_update() function to update the record
+  // use the chado_update_record() function to update the record
   //$match = array(
   //'example_id' => $example_id,
   //);
@@ -342,11 +342,11 @@ function chado_example_update($node) {
   //  'uniquename' => $node->uniquename,
   //);
   //$options = array('return_record' => TRUE);
-  //$status = tripal_core_chado_update('example', $match, $values, $options);
+  //$status = chado_update_record('example', $match, $values, $options);
 
   //if (!$status) {
   //  drupal_set_message(t('Unable to update example.'), 'warning');
-  //  tripal_core_report_error('tripal_example', TRIPAL_WARNING, 'Update example: Unable to update example where values: %values',
+  //  tripal_report_error('tripal_example', TRIPAL_WARNING, 'Update example: Unable to update example where values: %values',
   //    array('%values' => print_r($values, TRUE)));
   //}
 
@@ -359,7 +359,7 @@ function chado_example_update($node) {
   //   'foreignkey_name' => 'example_id',   // the name of the key in your base table
   //   'foreignkey_value' => $example_id    // the value of the example_id key
   // );
-  // chado_node_properties_form_update_properties($node, $details);
+  // chado_update_node_form_properties($node, $details);
 
   // * Additional DBxrefs Form *
   // If you implemented the dbxrefs form in chado_example_form then you need to
@@ -369,7 +369,7 @@ function chado_example_update($node) {
   //   'foreignkey_name' => 'example_id',     // the name of the key in your base table
   //   'foreignkey_value' => $example_id      // the value of the example_id key
   // );
-  // chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
+  // chado_update_node_form_dbxrefs($node, $details);
 
   // * Relationships Form *
   // If you implemented the relationships form in chado_example_form then you need to
@@ -378,7 +378,7 @@ function chado_example_update($node) {
   //   'relationship_table' => 'example_relationship',  // name of the _relationship table
   //   'foreignkey_value' => $example_id                // value of the example_id key
   // );
-  // chado_node_relationships_form_update_relationships($node, $details);
+  // chado_update_node_form_relationships($node, $details);
 
 }
 /**
@@ -394,7 +394,7 @@ function chado_example_update($node) {
 function chado_example_delete($node) {
 
   // get the example id from the node
-  //$example_id  = chado_get_id_for_node('example', $node->nid);
+  //$example_id  = chado_get_id_from_nid('example', $node->nid);
 
   // if we don't have a example id for this node then this isn't a node of
   // type chado_example or the entry in the chado_example table was lost.
@@ -435,21 +435,21 @@ function chado_example_load($nodes) {
   // them all
   foreach ($nodes as $nid => $node) {
     // find the example and add in the details
-    //$example_id = chado_get_id_for_node('example', $nid);
+    //$example_id = chado_get_id_from_nid('example', $nid);
 
-    // build the example variable by using the tripal_core_generate_chado_var() function
+    // build the example variable by using the chado_generate_var() function
     //$values = array('example_id' => $example_id);
-    //$example = tripal_core_generate_chado_var('example', $values);
+    //$example = chado_generate_var('example', $values);
 
     // for fields in the table that are of type 'text' you may want to include those
     // by default, the tripal_core_generate_chado_var does not include text fields as
     // they may be very large and including a large text field can slow the page load.
     // If you know a text field will never be large and it is important for the
     // other functions that will see the node to have access to a field you can
-    // include it here using the tripal_core_expand_chado_vars() function.  In most
+    // include it here using the chado_expand_var() function.  In most
     // cases it is probably best to let the end-user decide if text fields should
     // be included by using this function in the templates.
-    //$example = tripal_core_expand_chado_vars($example, 'field', 'example.residues');
+    //$example = chado_expand_var($example, 'field', 'example.residues');
 
     // add the new example object to this node.
     //$nodes[$nid]->example = $example;

tripal_feature/api/tripal_feature.api.inc

@@ -39,7 +39,7 @@ function tripal_feature_analysis_get_property($analysis_id = NULL, $feature_id =
   // check that the incoming arguments are correct
   if (($analysis_id and !$feature_id) or
     (!$analysis_id and $feature_id)) {
-      tripal_core_report_error('tripal_feature', TRIPAL_WARNING,
+      tripal_report_error('tripal_feature', TRIPAL_WARNING,
       'tripal_feature_analysis_get_property: Both an analysis ID and feature ID should be specified',
       array());
   }
@@ -48,12 +48,12 @@ function tripal_feature_analysis_get_property($analysis_id = NULL, $feature_id =
   if (!$analysisfeature_id) {
     $columns = array('analysisfeature_id');
     $values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id);
-    $result = tripal_core_chado_select('analysisfeature', $columns, $values);
+    $result = chado_select_record('analysisfeature', $columns, $values);
     $analysisfeature_id = $result[0]->analysisfeature_id;
   }
 
   // get the property.
-  return tripal_core_get_property('analysisfeature', $analysisfeature_id, $property, $cv_name);
+  return chado_get_property('analysisfeature', $analysisfeature_id, $property, $cv_name);
 }
 
 /**
@@ -92,7 +92,7 @@ function tripal_feature_analysis_insert_property($analysis_id = NULL, $feature_i
   // check that the incoming arguments are correct
   if (($analysis_id and !$feature_id) or
       (!$analysis_id and $feature_id)) {
-    tripal_core_report_error('tripal_feature', TRIPAL_WARNING,
+    tripal_report_error('tripal_feature', TRIPAL_WARNING,
       'tripal_feature_analysis_insert_property: Both an analysis ID and feature ID should be specified',
       array());
   }
@@ -101,15 +101,15 @@ function tripal_feature_analysis_insert_property($analysis_id = NULL, $feature_i
   if (!$analysisfeature_id) {
     $columns = array('analysisfeature_id');
     $values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id);
-    $result = tripal_core_chado_select('analysisfeature', $columns, $values);
+    $result = chado_select_record('analysisfeature', $columns, $values);
     $analysisfeature_id = $result[0]->analysisfeature_id;
   }
 
   // insert the property.
-  $success = tripal_core_insert_property('analysisfeature', $analysisfeature_id,
+  $success = chado_insert_property('analysisfeature', $analysisfeature_id,
     $property, $cv_name, $value, $update_if_present);
   if (!$success) {
-     tripal_core_report_error('tripal_feature', TRIPAL_WARNING,
+     tripal_report_error('tripal_feature', TRIPAL_WARNING,
       'tripal_feature_analysis_insert_property: Failed to insert analysis feature property',
        array());
      return FALSE;
@@ -160,7 +160,7 @@ function tripal_feature_analysis_update_property($analysis_id = NULL, $feature_i
   // check that the incoming arguments are correct
   if (($analysis_id and !$feature_id) or
     (!$analysis_id and $feature_id)) {
-      tripal_core_report_error('tripal_feature', TRIPAL_WARNING,
+      tripal_report_error('tripal_feature', TRIPAL_WARNING,
       'tripal_feature_analysis_update_property: Both an analysis ID and feature ID should be specified',
       array());
   }
@@ -169,12 +169,12 @@ function tripal_feature_analysis_update_property($analysis_id = NULL, $feature_i
   if (!$analysisfeature_id) {
     $columns = array('analysisfeature_id');
     $values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id);
-    $result = tripal_core_chado_select('analysisfeature', $columns, $values);
+    $result = chado_select_record('analysisfeature', $columns, $values);
     $analysisfeature_id = $result[0]->analysisfeature_id;
   }
 
   // update the property.
-  return tripal_core_update_property('analysisfeature', $analysisfeature_id, $property, $cv_name, $value, $insert_if_missing);
+  return chado_update_property('analysisfeature', $analysisfeature_id, $property, $cv_name, $value, $insert_if_missing);
 }
 
 /**
@@ -199,7 +199,7 @@ function tripal_feature_analysis_update_property_by_id($analysisfeatureprop_id,
   $property, $value, $cv_name = 'tripal') {
 
     // update the property.
-    return tripal_core_update_property_by_id('analysisfeature',
+    return chado_update_propertyID('analysisfeature',
       $analysisfeatureprop_id, $property, $cv_name, $value);
 }
 /**
@@ -239,7 +239,7 @@ function tripal_feature_analysis_delete_property($analysis_id = NULL, $feature_i
   // check that the incoming arguments are correct
   if (($analysis_id and !$feature_id) or
     (!$analysis_id and $feature_id)) {
-      tripal_core_report_error('tripal_feature', TRIPAL_WARNING,
+      tripal_report_error('tripal_feature', TRIPAL_WARNING,
       'tripal_feature_analysis_delete_property: Both an analysis ID and feature ID should be specified',
         array());
   }
@@ -248,12 +248,12 @@ function tripal_feature_analysis_delete_property($analysis_id = NULL, $feature_i
   if (!$analysisfeature_id) {
     $columns = array('analysisfeature_id');
     $values = array('analysis_id' => $analysis_id, 'feature_id' => $feature_id);
-    $result = tripal_core_chado_select('analysisfeature', $columns, $values);
+    $result = chado_select_record('analysisfeature', $columns, $values);
     $analysisfeature_id = $result[0]->analysisfeature_id;
   }
 
   // get the property.
-  return tripal_core_delete_property('analysisfeature', $analysisfeature_id, $property, $cv_name);
+  return chado_delete_property('analysisfeature', $analysisfeature_id, $property, $cv_name);
 }
 /**
  * Delete a property using the analysisfeatureprop_id
@@ -268,7 +268,7 @@ function tripal_feature_analysis_delete_property($analysis_id = NULL, $feature_i
  */
 function tripal_feature_analysis_delete_property_by_id($analysisfeatureprop_id) {
   // get the property.
-  return tripal_core_delete_property_by_id('analysisfeature', $analysisfeatureprop_id);
+  return chado_delete_propertyID('analysisfeature', $analysisfeatureprop_id);
 }
 /**
  * Retrieve properties of a given type for a given feature
@@ -287,7 +287,7 @@ function tripal_feature_analysis_delete_property_by_id($analysisfeatureprop_id)
  * @ingroup tripal_feature_api
  */
 function tripal_feature_get_property($feature_id, $property, $cv_name='tripal') {
-  return tripal_core_get_property('feature', $feature_id, $property, $cv_name);
+  return chado_get_property('feature', $feature_id, $property, $cv_name);
 }
 
 /**
@@ -312,7 +312,7 @@ function tripal_feature_get_property($feature_id, $property, $cv_name='tripal')
  */
 function tripal_feature_insert_property($feature_id, $property, $value,
   $update_if_present = 0, $cv_name = 'tripal') {
-  return tripal_core_insert_property('feature', $feature_id, $property,
+  return chado_insert_property('feature', $feature_id, $property,
     $cv_name, $value, $update_if_present);
 }
 /**
@@ -341,7 +341,7 @@ function tripal_feature_insert_property($feature_id, $property, $value,
  */
 function tripal_feature_update_property($feature_id, $property,
   $value, $insert_if_missing = 0, $cv_name = 'tripal') {
-    return tripal_core_update_property('feature', $feature_id, $property, $cv_name, $value, $insert_if_missing);
+    return chado_update_property('feature', $feature_id, $property, $cv_name, $value, $insert_if_missing);
 }
 
 /**
@@ -364,7 +364,7 @@ function tripal_feature_update_property($feature_id, $property,
  */
 function tripal_feature_update_property_by_id($featureprop_id, $property,
   $value, $cv_name = 'tripal') {
-    return tripal_core_update_property_by_id('feature', $featureprop_id, $property, $cv_name, $value);
+    return chado_update_propertyID('feature', $featureprop_id, $property, $cv_name, $value);
 }
 
 /**
@@ -388,7 +388,7 @@ function tripal_feature_update_property_by_id($featureprop_id, $property,
  * @ingroup tripal_feature_api
  */
 function tripal_feature_delete_property($feature_id, $property, $cv_name='tripal') {
-  return tripal_core_delete_property('feature', $feature_id, $property, $cv_name);
+  return chado_delete_property('feature', $feature_id, $property, $cv_name);
 }
 /**
  * Delete a given feature property using the featureprop_id
@@ -402,7 +402,7 @@ function tripal_feature_delete_property($feature_id, $property, $cv_name='tripal
  * @ingroup tripal_feature_api
  */
 function tripal_feature_delete_property_by_id($featureprop_id) {
-  return tripal_core_delete_property_by_id('feature', $featureprop_id);
+  return chado_delete_propertyID('feature', $featureprop_id);
 }
 
 /**
@@ -512,7 +512,7 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
       ';
       $status = tripal_core_chado_prepare('feature_rel_get_object', $psql, array('int', 'text'));
       if (!$status) {
-        tripal_core_report_error('tripal_feature', TRIPAL_ERROR, "init: not able to prepare SQL statement '%name'",
+        tripal_report_error('tripal_feature', TRIPAL_ERROR, "init: not able to prepare SQL statement '%name'",
           array('%name' => 'feature_by_subject'));
       }
       $sql = "EXECUTE feature_rel_get_object(:feature_id, :relationship)";
@@ -534,7 +534,7 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
       ';
       $status = tripal_core_chado_prepare('feature_rel_get_subject', $psql, array('int', 'text'));
       if (!$status) {
-        tripal_core_report_error('tripal_feature', TRIPAL_ERROR, "init: not able to prepare SQL statement '%name'",
+        tripal_report_error('tripal_feature', TRIPAL_ERROR, "init: not able to prepare SQL statement '%name'",
           array('%name' => 'feature_by_object'));
       }
       $sql = "EXECUTE feature_rel_get_subject(:feature_id, :relationship)";
@@ -634,7 +634,7 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
     ';
     $status = tripal_core_chado_prepare('sequence_by_parent', $psql, array('int', 'int', 'int'));
     if (!$status) {
-      tripal_core_report_error('tripal_feature', TRIPAL_ERROR,
+      tripal_report_error('tripal_feature', TRIPAL_ERROR,
         "init: not able to prepare SQL statement '%name'",
         array('%name' => 'sequence_by_parent'));
     }
@@ -653,7 +653,7 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
             ORDER BY FL.fmin ASC';
     $status = tripal_core_chado_prepare('sub_features', $psql, array('int', 'int'));
     if (!$status) {
-      tripal_core_report_error('tripal_feature', TRIPAL_ERROR,
+      tripal_report_error('tripal_feature', TRIPAL_ERROR,
         "init: not able to prepare SQL statement '%name'",
         array('%name' => 'ssub_features'));
     }
@@ -667,7 +667,7 @@ function tripal_feature_get_formatted_sequence($feature_id, $feature_name,
             WHERE FR.object_id = $1 and PF.feature_id = $2';
     $status = tripal_core_chado_prepare('count_sub_features', $psql, array('int', 'int'));
     if (!$status) {
-      tripal_core_report_error('tripal_feature', TRIPAL_ERROR,
+      tripal_report_error('tripal_feature', TRIPAL_ERROR,
         "init: not able to prepare SQL statement '%name'",
         array('%name' => 'count_sub_features'));
     }
@@ -853,12 +853,12 @@ function tripal_feature_add_dbxref($feature_id, $dbname, $accession) {
   // make sure the db exists. If it doesn't, then add it
   $values = array('name' => $dbname);
   $options = array('statement_name' => 'sel_db_na');
-  $db = tripal_core_chado_select('db', array('db_id'), $values, $options);
+  $db = chado_select_record('db', array('db_id'), $values, $options);
   if (!$db or count($db) == 0) {
     $options = array('statement_name' => 'ins_db_na');
-    $success = tripal_core_chado_insert('db', $values, $options);
+    $success = chado_insert_record('db', $values, $options);
       if (!$success) {
-      tripal_core_report_error('tripal_feature', TRIPAL_WARNING, 'tripal_feature_add_dbxref: The feature dbxref entry for feature, %feature_id, " .
+      tripal_report_error('tripal_feature', TRIPAL_WARNING, 'tripal_feature_add_dbxref: The feature dbxref entry for feature, %feature_id, " .
         "could not be added because the database, %dbname, does not exist and cannot be added.',
         array('%feature_id' => $feature_id, '%dbname' => $dbname));
       return FALSE;
@@ -876,13 +876,13 @@ function tripal_feature_add_dbxref($feature_id, $dbname, $accession) {
     'feature_id' => $feature_id,
   );
   $options = array('statement_name' => 'sel_featuredbxref_dbfe');
-  $xref = tripal_core_chado_select('feature_dbxref', array('feature_dbxref_id'), $values, $options);
+  $xref = chado_select_record('feature_dbxref', array('feature_dbxref_id'), $values, $options);
   if (count($xref) == 0) {
     // if the record doesn't exist then add it.
     $options = array('statement_name' => 'ins_featuredbxref_dbfe');
-    $success = tripal_core_chado_insert('feature_dbxref', $values, $options);
+    $success = chado_insert_record('feature_dbxref', $values, $options);
     if (!$success) {
-      tripal_core_report_error('tripal_feature', TRIPAL_WARNING, 'tripal_feature_add_dbxref: The feature dbxref entry for feature, %feature_id, ' .
+      tripal_report_error('tripal_feature', TRIPAL_WARNING, 'tripal_feature_add_dbxref: The feature dbxref entry for feature, %feature_id, ' .
         'could not be added: %db:%accession.', array('%feature_id' => $feature_id, '%db' => $dbname,
         '%accession' => $accession));
       return FALSE;
@@ -911,12 +911,12 @@ function tripal_feature_add_cvterm($feature_id, $cvname, $cvterm) {
   // make sure the cv exists. If it doesn't, then add it
   $values = array('name' => $cvname);
   $options = array('statement_name' => 'sel_cv_na');
-  $cv = tripal_core_chado_select('cv', array('cv_id'), $values, $options);
+  $cv = chado_select_record('cv', array('cv_id'), $values, $options);
   if (!$cv or count($cv) == 0) {
     $options = array('statement_name' => 'ins_cv_na');
-    $success = tripal_core_chado_insert('cv', $values, $options);
+    $success = chado_insert_record('cv', $values, $options);
       if (!$success) {
-      tripal_core_report_error('tripal_feature', TRIPAL_WARNING, 'tripal_feature_add_cvterm: The feature cvterm entry for feature, %feature_id, " .
+      tripal_report_error('tripal_feature', TRIPAL_WARNING, 'tripal_feature_add_cvterm: The feature cvterm entry for feature, %feature_id, " .
         "could not be added because the CV, %cvname, does not exist and cannot be added.',
         array('%feature_id' => $feature_id, '%cvname' => $cvname));
       return FALSE;
@@ -935,13 +935,13 @@ function tripal_feature_add_cvterm($feature_id, $cvname, $cvterm) {
     'pub_id' => 1,
   );
   $options = array('statement_name' => 'sel_featuredcvterm_cvfepu');
-  $xref = tripal_core_chado_select('feature_cvterm', array('feature_cvterm_id'), $values, $options);
+  $xref = chado_select_record('feature_cvterm', array('feature_cvterm_id'), $values, $options);
   if (count($xref) == 0) {
     // if the record doesn't exist then add it.
     $options = array('statement_name' => 'ins_featurecvterm_cvfepu');
-    $success = tripal_core_chado_insert('feature_cvterm', $values, $options);
+    $success = chado_insert_record('feature_cvterm', $values, $options);
     if (!$success) {
-      tripal_core_report_error('tripal_feature', TRIPAL_WARNING, 'tripal_feature_add_cvterm: The feature cvterm entry for feature, %feature_id, ' .
+      tripal_report_error('tripal_feature', TRIPAL_WARNING, 'tripal_feature_add_cvterm: The feature cvterm entry for feature, %feature_id, ' .
         'could not be added: %cvterm.', array('%feature_id' => $feature_id, '%cvterm' => $cvterm));
       return FALSE;
     }

tripal_feature/api/tripal_feature.schema.api.inc

@@ -3,9 +3,9 @@
 /**
  * Implements hook_chado_schema_v1_2_tripal_gff_temp()
  * Purpose: To describe the structure of 'tripal_gff_temp' to tripal
- * @see tripal_core_chado_insert()
- * @see tripal_core_chado_update()
- * @see tripal_core_chado_select()
+ * @see chado_insert_record()
+ * @see chado_update_record()
+ * @see chado_select_record()
  *
  * @return
  *    An array describing the 'tripal_gff_temp' table

tripal_feature/includes/tripal_feature.admin.inc

@@ -433,7 +433,7 @@ function tripal_features_set_taxonomy($max_sync = 0, $job_id = NULL) {
 
   // update the job status every 1% features
   if ($job_id and $i % $interval == 0) {
-    tripal_job_set_progress($job_id, intval(($i/$count)*100));
+    tripal_set_job_progress($job_id, intval(($i/$count)*100));
   }
   print "$i of $count: ";
   $node = db_query($nsql, array(':nid' => $chado_feature->nid))->fetchObject();

tripal_feature/includes/tripal_feature.chado_node.inc

@@ -71,7 +71,7 @@ function chado_feature_form($node, &$form_state) {
   // if we are editing an existing node then the feature is already part of the node
   if (property_exists($node, 'feature')) {
     $feature = $node->feature;
-    $feature = tripal_core_expand_chado_vars($feature, 'field', 'feature.residues');
+    $feature = chado_expand_var($feature, 'field', 'feature.residues');
     $feature_id   = $feature->feature_id;
     $uniquename   = $feature->uniquename;
     $fname        = $feature->name;
@@ -89,7 +89,7 @@ function chado_feature_form($node, &$form_state) {
     // get synonyms from the database if we don't already have them
     if (!$synonyms) {
       $options = array('return_array' => 1);
-      $feature = tripal_core_expand_chado_vars($feature, 'table', 'feature_synonym', $options);
+      $feature = chado_expand_var($feature, 'table', 'feature_synonym', $options);
       $feature_synonyms = (isset($feature->feature_synonym)) ? $feature->feature_synonym : array();
       foreach ($feature_synonyms as $index => $synonym) {
         $synonyms .= $synonym->synonym_id->name . "\n";
@@ -142,7 +142,7 @@ function chado_feature_form($node, &$form_state) {
   );
   // get the sequence ontology CV ID
   $values = array('name' => 'sequence');
-  $cv = tripal_core_chado_select('cv', array('cv_id'), $values);
+  $cv = chado_select_record('cv', array('cv_id'), $values);
   $cv_id = $cv[0]->cv_id;
 
   $form['feature_type'] = array(
@@ -220,7 +220,7 @@ function chado_feature_form($node, &$form_state) {
     'cv_name' => 'feature_property'         // the cv.name of the cv governing featureprop.type_id
   );
   // Adds the form elements to your current form
-  chado_node_properties_form($form, $form_state, $details);
+  chado_add_node_form_properties($form, $form_state, $details);
 
   // ADDITIONAL DBXREFS FORM
   //---------------------------------------------
@@ -230,7 +230,7 @@ function chado_feature_form($node, &$form_state) {
     'base_key_value' => $feature_id       // the value of feature_id for this record
   );
   // Adds the form elements to your current form
-  chado_node_additional_dbxrefs_form($form, $form_state, $details);
+  chado_add_node_form_dbxrefs($form, $form_state, $details);
 
   return $form;
 }
@@ -402,7 +402,7 @@ function chado_feature_insert($node) {
     ),
     'name' => $node->feature_type
   );
-  $type = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);
+  $type = chado_select_record('cvterm', array('cvterm_id'), $values);
 
   $feature_id = '';
 
@@ -420,10 +420,10 @@ function chado_feature_insert($node) {
       'type_id' => $type[0]->cvterm_id,
       'md5checksum' => md5($residues)
     );
-    $feature = tripal_core_chado_insert('feature', $values);
+    $feature = chado_insert_record('feature', $values);
     if (!$feature) {
       drupal_set_message(t('Unable to add feature.'), 'warning');
-      tripal_core_report_error('tripal_feature', TRIPAL_WARNING, 'Insert feature: Unable to create feature where values: %values',
+      tripal_report_error('tripal_feature', TRIPAL_WARNING, 'Insert feature: Unable to create feature where values: %values',
       array('%values' => print_r($values, TRUE)));
       return;
     }
@@ -439,7 +439,7 @@ function chado_feature_insert($node) {
       'foreignkey_name' => 'feature_id',   // the name of the key in your base table
       'foreignkey_value' => $feature_id    // the value of the feature_id key
     );
-    chado_node_properties_form_update_properties($node, $details);
+    chado_update_node_form_properties($node, $details);
 
     // * Additional DBxrefs Form *
     $details = array(
@@ -447,7 +447,7 @@ function chado_feature_insert($node) {
       'foreignkey_name' => 'feature_id',     // the name of the key in your base table
       'foreignkey_value' => $feature_id      // the value of the feature_id key
     );
-    chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
+    chado_update_node_form_dbxrefs($node, $details);
 
   }
   else {
@@ -456,7 +456,7 @@ function chado_feature_insert($node) {
 
   // Make sure the entry for this feature doesn't already exist in the
   // chado_feature table if it doesn't exist then we want to add it.
-  $check_org_id = chado_get_id_for_node('feature', $node->nid);
+  $check_org_id = chado_get_id_from_nid('feature', $node->nid);
   if (!$check_org_id) {
     $record = new stdClass();
     $record->nid = $node->nid;
@@ -492,9 +492,9 @@ function chado_feature_update($node) {
     ),
     'name' => $node->feature_type
   );
-  $type = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);
+  $type = chado_select_record('cvterm', array('cvterm_id'), $values);
 
-  $feature_id = chado_get_id_for_node('feature', $node->nid) ;
+  $feature_id = chado_get_id_from_nid('feature', $node->nid) ;
 
   if (sizeof($type) > 0) {
     $match = array(
@@ -511,7 +511,7 @@ function chado_feature_update($node) {
       'md5checksum' => md5($residues)
     );
     $options = array('return_record' => TRUE);
-    $status = tripal_core_chado_update('feature', $match, $values, $options);
+    $status = chado_update_record('feature', $match, $values, $options);
 
     // add the genbank synonyms
     chado_feature_add_synonyms($node->synonyms, $feature_id);
@@ -523,7 +523,7 @@ function chado_feature_update($node) {
       'foreignkey_name' => 'feature_id',   // the name of the key in your base table
       'foreignkey_value' => $feature_id    // the value of the feature_id key
     );
-    chado_node_properties_form_update_properties($node, $details);
+    chado_update_node_form_properties($node, $details);
 
     // * Additional DBxrefs Form *
     $details = array(
@@ -531,12 +531,12 @@ function chado_feature_update($node) {
       'foreignkey_name' => 'feature_id',     // the name of the key in your base table
       'foreignkey_value' => $feature_id      // the value of the feature_id key
     );
-    chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
+    chado_update_node_form_dbxrefs($node, $details);
 
   }
   else {
     drupal_set_message(t('Unable to update feature.'), 'warning');
-    tripal_core_report_error('tripal_feature', TRIPAL_WARNING,
+    tripal_report_error('tripal_feature', TRIPAL_WARNING,
      'Update feature: Unable to update feature where values: %values',
      array('%values' => print_r($values, TRUE))
     );
@@ -551,7 +551,7 @@ function chado_feature_update($node) {
  */
 function chado_feature_delete($node) {
 
-  $feature_id  = chado_get_id_for_node('feature', $node->nid);
+  $feature_id  = chado_get_id_from_nid('feature', $node->nid);
 
   // if we don't have a library id for this node then this isn't a node of
   // type chado_library or the entry in the chado_library table was lost.
@@ -595,7 +595,7 @@ function chado_feature_add_synonyms($synonyms, $feature_id) {
   // remove any old synonyms
   $feature_syn_dsql = "DELETE FROM {feature_synonym} WHERE feature_id = :feature_id";
   if (!chado_query($feature_syn_dsql, array(':feature_id' => $feature_id))) {
-    tripal_core_report_error('tripal_feature', TRIPAL_ERROR, "Could not remove synonyms from feature. ", array());
+    tripal_report_error('tripal_feature', TRIPAL_ERROR, "Could not remove synonyms from feature. ", array());
     return;
   }
 
@@ -626,7 +626,7 @@ function chado_feature_add_synonyms($synonyms, $feature_id) {
           )
       ";
       if (!chado_query($synonym_isql, array(':name' => $syn, ':synonym_sgml' => $syn))) {
-        tripal_core_report_error('tripal_feature', "Could not add synonym. ", array(), TRIPAL_WARNING);
+        tripal_report_error('tripal_feature', "Could not add synonym. ", array(), TRIPAL_WARNING);
         return;
       }
       // now get the synonym we just added
@@ -640,7 +640,7 @@ function chado_feature_add_synonyms($synonyms, $feature_id) {
       VALUES (:synonym_id, :feature_id, :pub_id)";
     $args = array(':synonym_id' => $synonym->synonym_id, ':feature_id' => $feature_id, ':pub_id'=> 1);
     if (!chado_query($feature_syn_isql, $args)) {
-      tripal_core_report_error('tripal_feature', "Could not associate synonym with feature. ", array(), TRIPAL_WARNING);
+      tripal_report_error('tripal_feature', "Could not associate synonym with feature. ", array(), TRIPAL_WARNING);
       return;
     }
   }
@@ -656,11 +656,11 @@ function chado_feature_load($nodes) {
 
   foreach ($nodes as $nid => $node) {
     // find the feature and add in the details
-    $feature_id = chado_get_id_for_node('feature', $nid);
+    $feature_id = chado_get_id_from_nid('feature', $nid);
 
     // build the feature variable
     $values = array('feature_id' => $feature_id);
-    $feature = tripal_core_generate_chado_var('feature', $values);
+    $feature = chado_generate_var('feature', $values);
     $nodes[$nid]->feature = $feature;
 
     // by default, the titles are saved using the unique constraint.  We will
@@ -714,12 +714,12 @@ function tripal_feature_node_presave($node) {
         $uname       = $node->feature->uniquename;
         $type_id     = $node->feature->type_id;
         $values = array('cvterm_id' => $type_id);
-        $ftype = tripal_core_chado_select('cv', array('name'), $values);
+        $ftype = chado_select_record('cv', array('name'), $values);
         $type = $ftype[0]->name;
       }
      
       $values = array('organism_id' => $organism_id);
-      $organism = tripal_core_chado_select('organism', array('genus', 'species'), $values);
+      $organism = chado_select_record('organism', array('genus', 'species'), $values);
       $node->title = "$name, $uname ($type) " . $organism[0]->genus . ' ' . $organism[0]->species;
       
       if ($name == $uname) {
@@ -779,18 +779,18 @@ function tripal_feature_get_feature_url($node, $url_alias = NULL) {
 
   // get the feature
   $values = array('feature_id' => $node->feature_id);
-  $feature = tripal_core_chado_select('feature', array('*'), $values);
+  $feature = chado_select_record('feature', array('*'), $values);
   if (!$feature) {
-    tripal_core_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find feature when setting URL alias for feature: %id", array('%id' => $node->feature_id));
+    tripal_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find feature when setting URL alias for feature: %id", array('%id' => $node->feature_id));
     return FALSE;
   }
   $feature = (object) $feature[0];
 
   // get the organism
   $values = array('organism_id' => $feature->organism_id);
-  $organism  = tripal_core_chado_select('organism', array('*'), $values);
+  $organism  = chado_select_record('organism', array('*'), $values);
   if (!$organism) {
-    tripal_core_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find organism when setting URL alias for feature: %id", array('%id' => $node->feature_id));
+    tripal_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find organism when setting URL alias for feature: %id", array('%id' => $node->feature_id));
     return FALSE;
   }
   $genus = preg_replace('/\s/', '_', strtolower($organism[0]->genus));
@@ -798,9 +798,9 @@ function tripal_feature_get_feature_url($node, $url_alias = NULL) {
 
   // get the type
   $values = array('cvterm_id' => $feature->type_id);
-  $cvterm = tripal_core_chado_select('cvterm', array('name'), $values);
+  $cvterm = chado_select_record('cvterm', array('name'), $values);
   if (!$cvterm) {
-    tripal_core_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find type when setting URL alias for feature: %id", array('%id' => $node->feature_id));
+    tripal_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find type when setting URL alias for feature: %id", array('%id' => $node->feature_id));
     return FALSE;
   }
   $type = preg_replace('/\s/', '_', $cvterm[0]->name);
@@ -816,7 +816,7 @@ function tripal_feature_get_feature_url($node, $url_alias = NULL) {
   // the dst field of the url_alias table is only 128 characters long.
   // if this is the case then simply return the node URL, we can't set this one
   if (strlen($url_alias) > 128) {
-    tripal_core_report_error('trp-seturl', TRIPAL_ERROR, "Cannot set alias longer than 128 characters: %alias.", array('%alias' => $url_alias));
+    tripal_report_error('trp-seturl', TRIPAL_ERROR, "Cannot set alias longer than 128 characters: %alias.", array('%alias' => $url_alias));
     return "node/" . $node->nid;
   }
 

tripal_feature/includes/tripal_feature.delete.inc

@@ -132,9 +132,9 @@ function tripal_feature_delete_features($organism_id, $analysis_id, $seq_type,
     else {
       $match['name'] = $names;
     }
-    $num_deletes = tripal_core_chado_select('feature', array('count(*) as cnt'), $match);
+    $num_deletes = chado_select_record('feature', array('count(*) as cnt'), $match);
     print "Deleting " . $num_deletes[0]->cnt . " features\n";
-    tripal_core_chado_delete('feature', $match);
+    chado_delete_record('feature', $match);
   }
 
   // if the user has provided an analysis_id then handle that separately
@@ -154,9 +154,9 @@ function tripal_feature_delete_features($organism_id, $analysis_id, $seq_type,
         ),
       );
     }
-    $num_deletes = tripal_core_chado_select('feature', array('count(*) as cnt'), $match);
+    $num_deletes = chado_select_record('feature', array('count(*) as cnt'), $match);
     print "Deleting " . $num_deletes[0]->cnt . " features\n";
-    tripal_core_chado_delete('feature', $match);
+    chado_delete_record('feature', $match);
   }
 
   print "Removing orphaned feature pages\n";

tripal_feature/includes/tripal_feature.fasta_loader.inc

@@ -447,20 +447,20 @@ function tripal_feature_load_fasta($dfile, $organism_id, $type,
                WHERE cv.name = :cvname and (CVT.name = :name or CVTS.synonym = :synonym)";
   $cvterm = chado_query($cvtermsql, array(':cvname' => 'sequence', ':name' => $type, ':synonym' => $type))->fetchObject();     
   if (!$cvterm) {
-    tripal_core_report_error("T_fasta_loader", TRIPAL_ERROR, "Cannot find the term type: '%type'", array('%type' => $type));
+    tripal_report_error("T_fasta_loader", TRIPAL_ERROR, "Cannot find the term type: '%type'", array('%type' => $type));
     return 0;
   }
   if ($parent_type) {
     $parentcvterm = chado_query($cvtermsql, array(':cvname' => 'sequence', ':name' => $parent_type, ':synonym' => $parent_type))->fetchObject();
     if (!$parentcvterm) {
-      tripal_core_report_error("T_fasta_loader", TRIPAL_ERROR, "Cannot find the paretne term type: '%type'", array('%type' => $parentcvterm));
+      tripal_report_error("T_fasta_loader", TRIPAL_ERROR, "Cannot find the paretne term type: '%type'", array('%type' => $parentcvterm));
       return 0;
     }
   }
   if ($rel_type) {
     $relcvterm = chado_query($cvtermsql, array(':cvname' => 'relationship', ':name' => $rel_type, ':synonym' => $rel_type))->fetchObject();
     if (!$relcvterm) {
-      tripal_core_report_error("T_fasta_loader", TRIPAL_ERROR, "Cannot find the relationship term type: '%type'", array('%type' => $relcvterm));
+      tripal_report_error("T_fasta_loader", TRIPAL_ERROR, "Cannot find the relationship term type: '%type'", array('%type' => $relcvterm));
       return 0;
     }
   }
@@ -470,7 +470,7 @@ function tripal_feature_load_fasta($dfile, $organism_id, $type,
   //$lines = file($dfile, FILE_SKIP_EMPTY_LINES);
   $fh = fopen($dfile, 'r');
   if (!$fh) {
-    tripal_core_report_error('T_fasta_loader', TRIPAL_ERROR, "cannot open file: %dfile", array('%dfile' => $dfile));
+    tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "cannot open file: %dfile", array('%dfile' => $dfile));
     return 0;
   }
   $filesize = filesize($dfile);
@@ -487,8 +487,8 @@ function tripal_feature_load_fasta($dfile, $organism_id, $type,
   
   // we need to get the table schema to make sure we don't overrun the 
   // size of fields with what our regular expressions retrieve
-  $feature_tbl = tripal_core_get_chado_table_schema('feature');
-  $dbxref_tbl = tripal_core_get_chado_table_schema('dbxref');
+  $feature_tbl = chado_get_schema('feature');
+  $dbxref_tbl = chado_get_schema('dbxref');
 
   //foreach ($lines as $line_num => $line) {  
   while ($line = fgets($fh)) {
@@ -515,10 +515,10 @@ function tripal_feature_load_fasta($dfile, $organism_id, $type,
       // get the feature name
       if ($re_name) {
         if (!preg_match("/$re_name/", $line, $matches)) {
-          tripal_core_report_error('trp-fasta', "ERROR: Regular expression for the feature name finds nothing. Line %line.", array('%line' => $i), 'error');
+          tripal_report_error('trp-fasta', "ERROR: Regular expression for the feature name finds nothing. Line %line.", array('%line' => $i), 'error');
         }
         elseif (strlen($matches[1]) > $feature_tbl['fields']['name']['length']) {
-          tripal_core_report_error('trp-fasta', "WARNING: Regular expression retrieves a value too long for the feature name. Line %line.", array('%line' => $i), 'error');  
+          tripal_report_error('trp-fasta', "WARNING: Regular expression retrieves a value too long for the feature name. Line %line.", array('%line' => $i), 'error');  
         }
         else {
           $name = trim($matches[1]);
@@ -530,14 +530,14 @@ function tripal_feature_load_fasta($dfile, $organism_id, $type,
         if (strcmp($match_type, 'Name')==0) {
           if (preg_match("/^\s*(.*?)[\s\|].*$/", $line, $matches)) {
             if (strlen($matches[1]) > $feature_tbl['fields']['name']['length']) {
-              tripal_core_report_error('trp-fasta', "WARNING: Regular expression retrieves a feature name too long for the feature name. Line %line.", array('%line' => $i), 'error');  
+              tripal_report_error('trp-fasta', "WARNING: Regular expression retrieves a feature name too long for the feature name. Line %line.", array('%line' => $i), 'error');  
             }
             else {
               $name = trim($matches[1]);
             }
           }
           else {
-            tripal_core_report_error('trp-fasta', "ERROR: Cannot find a feature name. Line %line.", array('%line' => $i), 'error');  
+            tripal_report_error('trp-fasta', "ERROR: Cannot find a feature name. Line %line.", array('%line' => $i), 'error');  
           }
         }
       }
@@ -545,7 +545,7 @@ function tripal_feature_load_fasta($dfile, $organism_id, $type,
       // get the feature unique name
       if ($re_uname) {
         if (!preg_match("/$re_uname/", $line, $matches)) {
-          tripal_core_report_error('trp-fasta', "ERROR: Regular expression for the feature unique name finds nothing. Line %line.", array('%line' => $i), 'error');
+          tripal_report_error('trp-fasta', "ERROR: Regular expression for the feature unique name finds nothing. Line %line.", array('%line' => $i), 'error');
         }
         $uname = trim($matches[1]);
       }
@@ -557,14 +557,14 @@ function tripal_feature_load_fasta($dfile, $organism_id, $type,
             $uname = trim($matches[1]);
           }
           else {
-            tripal_core_report_error('trp-fasta', "ERROR: Cannot find a feature unique name. Line %line.", array('%line' => $i), 'error');  
+            tripal_report_error('trp-fasta', "ERROR: Cannot find a feature unique name. Line %line.", array('%line' => $i), 'error');  
           }
         }
       }
       // get the accession
       preg_match("/$re_accession/", $line, $matches);
       if (strlen($matches[1]) > $dbxref_tbl['fields']['accession']['length']) {
-        tripal_core_report_error('trp-fasta', "WARNING: Regular expression retrieves an accession too long for the feature name. Cannot add cross reference. Line %line.", array('%line' => $i), 'warning');  
+        tripal_report_error('trp-fasta', "WARNING: Regular expression retrieves an accession too long for the feature name. Cannot add cross reference. Line %line.", array('%line' => $i), 'warning');  
       }
       else {
         $accession = trim($matches[1]);
@@ -587,7 +587,7 @@ function tripal_feature_load_fasta($dfile, $organism_id, $type,
         else {
           print "Parsing Line $i (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes. Current feature: $uname\r";  
         }
-        tripal_job_set_progress($job, intval(($num_read / $filesize) * 100));
+        tripal_set_job_progress($job, intval(($num_read / $filesize) * 100));
       }
     }
   }
@@ -619,9 +619,9 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
       'type_id' => $cvterm->cvterm_id,    
     );
     $options = array('statement_name' => 'sel_feature_ornaty');
-    $results = tripal_core_chado_select('feature', array('feature_id'), $values, $options);
+    $results = chado_select_record('feature', array('feature_id'), $values, $options);
     if (count($results) > 1) {
-      tripal_core_report_error('T_fasta_loader', "Multiple features exist with the name '%name' of type 
+      tripal_report_error('T_fasta_loader', "Multiple features exist with the name '%name' of type 
                '%type' for the organism.  skipping", array('%name' => $name, '%type' => $type));
       return 0;
     } 
@@ -638,9 +638,9 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
     );
 
     $options = array('statement_name' => 'sel_feature_oruqty');
-    $results = tripal_core_chado_select('feature', array('feature_id'), $values, $options);
+    $results = chado_select_record('feature', array('feature_id'), $values, $options);
     if (count($results) > 1) {
-      tripal_core_report_error('T_fasta_loader', "Multiple features exist with the name '%name' of type 
+      tripal_report_error('T_fasta_loader', "Multiple features exist with the name '%name' of type 
                '%type' for the organism.  skipping", array('%name' => $name, '%type' => $type));
       return 0;
     } 
@@ -650,7 +650,7 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
     
     // if the feature exists but this is an "insert only" method then skip this feature 
     if ($feature and (strcmp($method, 'Insert only')==0)) {
-      tripal_core_report_error('T_fasta_loader', TRIPAL_WARNING, "Feature already exists '%name' ('%uname') while matching on %type. Skipping insert.", 
+      tripal_report_error('T_fasta_loader', TRIPAL_WARNING, "Feature already exists '%name' ('%uname') while matching on %type. Skipping insert.", 
         array('%name' => $name, '%uname' => $uname, '%type' => drupal_strtolower($match_type)));
       return 0;
     } 
@@ -680,9 +680,9 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
       'is_obsolete' => 'FALSE',
     );
     $options = array('statement_name' => 'ins_feature_all');
-    $success = tripal_core_chado_insert('feature', $values, $options);    
+    $success = chado_insert_record('feature', $values, $options);    
     if (!$success) {
-      tripal_core_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to insert feature '%name (%uname)'", 
+      tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to insert feature '%name (%uname)'", 
         array('%name' => $name, '%uname' => $numane));
       return 0;
     }
@@ -694,13 +694,13 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
       'type_id' => $cvterm->cvterm_id,    
     );
     $options = array('statement_name' => 'sel_feature_oruqty');
-    $results = tripal_core_chado_select('feature', array('feature_id'), $values, $options);
+    $results = chado_select_record('feature', array('feature_id'), $values, $options);
     if (count($results) == 1) {
        $inserted = 1;
        $feature = $results[0];
     } 
     else {
-      tripal_core_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to retreive newly inserted feature '%name (%uname)'", 
+      tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to retreive newly inserted feature '%name (%uname)'", 
         array('%name' => $name, '%uname' => $numane));
       return 0;  
     }     
@@ -708,7 +708,7 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
   
   // if we don't have a feature and the user wants to do an update then fail
   if (!$feature and (strcmp($method, 'Update only')==0 or drupal_strcmp($method, 'Insert and update')==0)) {
-    tripal_core_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to find feature '%name' ('%uname') while matching on " . 
+    tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to find feature '%name' ('%uname') while matching on " . 
       drupal_strtolower($match_type), array('%name' => $name, '%uname' => $uname));
     return 0;
   }
@@ -728,9 +728,9 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
           'type_id' => $cvterm->cvterm_id,    
         );    
         $options = array('statement_name' => 'sel_feature_oruqty');
-        $results = tripal_core_chado_select('feature', array('feature_id'), $values, $options);
+        $results = chado_select_record('feature', array('feature_id'), $values, $options);
         if (count($results) > 0) {
-          tripal_core_report_error('T_fasta_loader', "Cannot update the feature '%name' with a uniquename of '%uname' and type of '%type' as it 
+          tripal_report_error('T_fasta_loader', "Cannot update the feature '%name' with a uniquename of '%uname' and type of '%type' as it 
             conflicts with an existing feature with the same uniquename and type.", 
             array('%name' => $name, '%uname' => $uname, '%type' => $type));
           return 0;
@@ -770,9 +770,9 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
       }
       
       // perform the update
-      $success = tripal_core_chado_update('feature', $match, $values, $options);
+      $success = chado_update_record('feature', $match, $values, $options);
       if (!$success) {
-        tripal_core_report_error('T_fasta_loader', TRIPAL_ERROR, 
+        tripal_report_error('T_fasta_loader', TRIPAL_ERROR, 
           "Failed to update feature '%name' ('%name')", 
           array('%name' => $name, '%uiname' => $uname));
         return 0;
@@ -813,9 +813,9 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
         );
         $options = array('statement_name' => 'upd_feature_naresemdisis_unorty'); 
       }
-      $success = tripal_core_chado_update('feature', $match, $values, $options);
+      $success = chado_update_record('feature', $match, $values, $options);
       if (!$success) {
-        tripal_core_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to update feature '%name' ('%name')", 
+        tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to update feature '%name' ('%name')", 
           array('%name' => $name, '%uiname' => $uname));
         return 0;
       }
@@ -830,12 +830,12 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
       'feature_id' => $feature->feature_id,
     );
     $sel_options = array('statement_name' => 'sel_analysisfeature_anfe');
-    $results = tripal_core_chado_select('analysisfeature', array('analysisfeature_id'), $values, $sel_options);
+    $results = chado_select_record('analysisfeature', array('analysisfeature_id'), $values, $sel_options);
     if (count($results) == 0) {
       $ins_options = array('statement_name' => 'ins_analysisfeature_anfe');
-      $success = tripal_core_chado_insert('analysisfeature', $values, $ins_options);      
+      $success = chado_insert_record('analysisfeature', $values, $ins_options);      
       if (!$success) {
-        tripal_core_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to associate analysis and feature '%name' ('%name')", 
+        tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to associate analysis and feature '%name' ('%name')", 
           array('%name' => $name, '%uname' => $uname));
         return 0;  
       }
@@ -850,22 +850,22 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
       'accession' => $accession
     );
     $sel_options = array('statement_name' => 'sel_dbxref_dbac');
-    $results = tripal_core_chado_select('dbxref', array('dbxref_id'), $values, $sel_options);
+    $results = chado_select_record('dbxref', array('dbxref_id'), $values, $sel_options);
     // if the accession doesn't exist then add it
     if (count($results) == 0) {   
       $ins_options = array('statement_name' => 'ins_dbxref_dbac');
-      $results = tripal_core_chado_insert('dbxref', $values, $ins_options);
+      $results = chado_insert_record('dbxref', $values, $ins_options);
       if (!$results) {
-        tripal_core_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to add database accession '%accession'", 
+        tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to add database accession '%accession'", 
           array('%accession' => $accession));
         return 0;
       }
-      $results = tripal_core_chado_select('dbxref', array('dbxref_id'), $values, $sel_options);
+      $results = chado_select_record('dbxref', array('dbxref_id'), $values, $sel_options);
       if (count($results) == 1) {
         $dbxref = $results[0];
       }
       else { 
-        tripal_core_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to retreive newly inserted dbxref '%name (%uname)'", 
+        tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to retreive newly inserted dbxref '%name (%uname)'", 
           array('%name' => $name, '%uname' => $numane));
         return 0;
       }
@@ -880,12 +880,12 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
       'dbxref_id' => $dbxref->dbxref_id
     );
     $sel_options = array('statement_name' => 'sel_featuredbxref_fedb');
-    $results = tripal_core_chado_select('feature_dbxref', array('feature_dbxref_id'), $values, $sel_options);
+    $results = chado_select_record('feature_dbxref', array('feature_dbxref_id'), $values, $sel_options);
     if (count($results) == 0) {  
       $ins_options = array('statement_name' => 'ins_featuredbxref_fedb');
-      $success = tripal_core_chado_insert('feature_dbxref', $values, $ins_options);
+      $success = chado_insert_record('feature_dbxref', $values, $ins_options);
       if (!$success) {
-        tripal_core_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to add associate database accession '%accession' with feature", 
+        tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to add associate database accession '%accession' with feature", 
           array('%accession' => $accession));
         return 0;
       }
@@ -900,9 +900,9 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
       'type_id' => $parentcvterm->cvterm_id,    
     );
     $options = array('statement_name' => 'sel_feature_oruqty');
-    $results = tripal_core_chado_select('feature', array('feature_id'), $values, $options);
+    $results = chado_select_record('feature', array('feature_id'), $values, $options);
     if (count($results) != 1) {
-      tripal_core_report_error('T_fasta_loader', "Cannot find a unique fature for the parent '%parent' of type 
+      tripal_report_error('T_fasta_loader', "Cannot find a unique fature for the parent '%parent' of type 
                '%type' for the feature.", array('%parent' => $parent, '%type' => $parent_type));
       return 0;
     } 
@@ -915,12 +915,12 @@ function tripal_feature_fasta_loader_handle_feature($name, $uname, $db_id, $acce
       'type_id' => $relcvterm->cvterm_id,    
     );
     $sel_options = array('statement_name' => 'sel_featurerelationship_suojty');
-    $results = tripal_core_chado_select('feature_relationship', array('feature_relationship_id'), $values, $sel_options);
+    $results = chado_select_record('feature_relationship', array('feature_relationship_id'), $values, $sel_options);
     if (count($results) == 0) {    
       $ins_options = array('statement_name' => 'ins_featurerelationship_suojty');
-      $success = tripal_core_chado_insert('feature_relationship', $values, $ins_options);
+      $success = chado_insert_record('feature_relationship', $values, $ins_options);
       if (!$success) {
-        tripal_core_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to add associate database accession '%accession' with feature", 
+        tripal_report_error('T_fasta_loader', TRIPAL_ERROR, "Failed to add associate database accession '%accession' with feature", 
           array('%accession' => $accession));
         return 0;
       }

tripal_feature/includes/tripal_feature.gff_loader.inc

@@ -335,7 +335,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
       $dfile = $gff_file;
     }
     if (!file_exists($dfile)) {
-      tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "Cannot find the file: %dfile", 
+      tripal_report_error('T_gff3_loader', TRIPAL_ERROR, "Cannot find the file: %dfile", 
         array('%dfile' => $dfile));
       return 0;
     }
@@ -345,7 +345,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
     //$lines = file($dfile,FILE_SKIP_EMPTY_LINES);
     $fh = fopen($dfile, 'r');
     if (!$fh) {
-      tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "cannot open file: %dfile", 
+      tripal_report_error('T_gff3_loader', TRIPAL_ERROR, "cannot open file: %dfile", 
         array('%dfile' => $dfile));
       return 0;
     }
@@ -356,7 +356,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
     $sql = "SELECT * FROM {cv} WHERE name = :cvname";
     $cv = chado_query($sql, array(':cvname' => 'sequence'))->fetchObject();
     if (!$tripal_core_report_error) {   
-      tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "Cannot find the 'sequence' ontology", 
+      tripal_report_error('T_gff3_loader', TRIPAL_ERROR, "Cannot find the 'sequence' ontology", 
         array());
       return '';
     }
@@ -402,7 +402,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
         $intv_read = 0;
         $percent = sprintf("%.2f", ($num_read / $filesize) * 100);
         print "Parsing Line $line_num (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
-        tripal_job_set_progress($job, intval(($num_read / $filesize) * 100));
+        tripal_set_job_progress($job, intval(($num_read / $filesize) * 100));
       }
         
       // check to see if we have FASTA section, if so then set the variable
@@ -424,7 +424,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
           $result = chado_query($sel_cvterm_sql, array(':cv_id' => $cv->cv_id, ':name' => $landmark_type, ':synonym' => $landmark_type));
           $cvterm = $result->fetchObject();
           if (!$cvterm) {
-            tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, 'cannot find feature type \'%landmark_type\' on line %line_num of the GFF file', 
+            tripal_report_error('T_gff3_loader', TRIPAL_ERROR, 'cannot find feature type \'%landmark_type\' on line %line_num of the GFF file', 
               array('%landmark_type' => $landmark_type, '%line_num' => $line_num));
             return '';
           }
@@ -447,7 +447,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
       // get the columns
       $cols = explode("\t", $line);
       if (sizeof($cols) != 9) {
-        tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, 'improper number of columns on line %line_num', 
+        tripal_report_error('T_gff3_loader', TRIPAL_ERROR, 'improper number of columns on line %line_num', 
           array('%line_num' => $line_num));
         return '';
       }
@@ -489,7 +489,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
   
       $cvterm = $result->fetchObject();
       if (!$cvterm) {
-        tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, 'cannot find feature term \'%type\' on line %line_num of the GFF file', 
+        tripal_report_error('T_gff3_loader', TRIPAL_ERROR, 'cannot find feature term \'%type\' on line %line_num of the GFF file', 
           array('%type' => $type, '%line_num' => $line_num));
         return '';
       }
@@ -520,7 +520,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
           continue;
         }
         if (!preg_match('/^[^\=]+\=.+$/', $attr)) {
-          tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, 'Attribute is not correctly formatted on line %line_num: %attr', 
+          tripal_report_error('T_gff3_loader', TRIPAL_ERROR, 'Attribute is not correctly formatted on line %line_num: %attr', 
             array('%line_num' => $line_num, '%attr' => $attr));
           return '';
         }
@@ -557,18 +557,18 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
               'genus' => $org_matches[1],
               'species' => $org_matches[2],
             ); 
-            $org = tripal_core_chado_select('organism', array("*"), $values);
+            $org = chado_select_record('organism', array("*"), $values);
             if (count($org) == 0) {
               if ($create_organism) {
-                $feature_organism = (object) tripal_core_chado_insert('organism', $values);
+                $feature_organism = (object) chado_insert_record('organism', $values);
                 if (!$feature_organism) {
-                  tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "Could not add the organism, '%org', from line %line. Skipping this line. ",
+                  tripal_report_error('T_gff3_loader', TRIPAL_ERROR, "Could not add the organism, '%org', from line %line. Skipping this line. ",
                     array('%org' => $attr_organism, '%line' => $line_num)); 
                   $skip_feature = 1; 
                 }
               } 
               else {
-                tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "The organism attribute '%org' on line %line does not exist. Skipping this line. ",
+                tripal_report_error('T_gff3_loader', TRIPAL_ERROR, "The organism attribute '%org' on line %line does not exist. Skipping this line. ",
                   array('%org' => $attr_organism, '%line' => $line_num)); 
                 $skip_feature = 1;
               }
@@ -579,7 +579,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
             }
           } 
           else {
-            tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "The organism attribute '%org' on line %line is not properly formated. It " .
+            tripal_report_error('T_gff3_loader', TRIPAL_ERROR, "The organism attribute '%org' on line %line is not properly formated. It " .
               "should be of the form: organism=Genus:species.  Skipping this line.", 
               array('%org' => $attr_organism, '%line' => $line_num));
             $skip_feature = 1;  
@@ -654,7 +654,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
             'name' => $landmark_type,
           );
         }      
-        $count = tripal_core_chado_select('feature', $columns, $select);        
+        $count = chado_select_record('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.
           $select = array(
@@ -667,22 +667,22 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
               'name' => $landmark_type,
             );
           }
-          $count = tripal_core_chado_select('feature', $columns, $select); 
+          $count = chado_select_record('feature', $columns, $select); 
           if (!$count or count($count) == 0 or $count[0]->num_landmarks == 0) {
-            tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "The landmark '%landmark' cannot be found for this organism (%species) " .
+            tripal_report_error('T_gff3_loader', TRIPAL_ERROR, "The landmark '%landmark' cannot be found for this organism (%species) " .
                   "Please add the landmark and then retry the import of this GFF3 " .
                   "file", array('%landmark' => $landmark, '%species' => $organism->genus . " " . $organism->species));
             return '';
           }
           elseif ($count[0]->num_landmarks > 1) {
-            tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "The landmark '%landmark' has more than one entry for this organism (%species) " .
+            tripal_report_error('T_gff3_loader', TRIPAL_ERROR, "The landmark '%landmark' has more than one entry for this organism (%species) " .
                   "Cannot continue", array('%landmark' => $landmark, '%species' => $organism->genus . " " . $organism->species));
             return '';  
           }
   
         }
         if ($count[0]->num_landmarks > 1) {
-          tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "The landmark '%landmark' is not unique for this organism. " .
+          tripal_report_error('T_gff3_loader', TRIPAL_ERROR, "The landmark '%landmark' is not unique for this organism. " .
                 "The features cannot be associated", array('%landmark' => $landmark));
           return '';
         }  
@@ -698,9 +698,9 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
            'uniquename'  => $attr_uniquename,
            'type_id'     => $cvterm->cvterm_id
         );
-        $result = tripal_core_chado_delete('feature', $match);
+        $result = chado_delete_record('feature', $match);
         if (!$result) {
-          tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "cannot delete feature %attr_uniquename", 
+          tripal_report_error('T_gff3_loader', TRIPAL_ERROR, "cannot delete feature %attr_uniquename", 
             array('%attr_uniquename' => $attr_uniquename));
         }
         $feature = 0;
@@ -726,12 +726,12 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
             'uniquename' => $feature->uniquename
           );
           // make sure this record doesn't already exist in oru temp table
-          $results = tripal_core_chado_select('tripal_gff_temp', array('*'), $values);
+          $results = chado_select_record('tripal_gff_temp', array('*'), $values);
   
           if (count($results) == 0) {
-            $result = tripal_core_chado_insert('tripal_gff_temp', $values);
+            $result = chado_insert_record('tripal_gff_temp', $values);
             if (!$result) {
-              tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "Cound not save record in temporary table, Cannot continue.", array());
+              tripal_report_error('T_gff3_loader', TRIPAL_ERROR, "Cound not save record in temporary table, Cannot continue.", array());
               exit;
             }
           }
@@ -862,7 +862,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
         foreach ($children as $child) {
           $match = array('feature_relationship_id' => $child->feature_relationship_id);
           $values = array('rank' => $rank);      
-          tripal_core_chado_update('feature_relationship', $match, $values);
+          chado_update_record('feature_relationship', $match, $values);
           $rank--;
         }
         // now set the rank correctly. The rank should start at 0.
@@ -871,7 +871,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
           $match = array('feature_relationship_id' => $child->feature_relationship_id);
           $values = array('rank' => $rank); 
           //print "Was: " . $child->rank . " now $rank ($parent->strand)\n"     ;
-          tripal_core_chado_update('feature_relationship', $match, $values);
+          chado_update_record('feature_relationship', $match, $values);
           $rank++;
         }
         $i++;
@@ -906,9 +906,9 @@ function tripal_feature_load_gff3_derives_from($feature, $subject, $organism) {
     'organism_id' => $organism->organism_id,
     'uniquename' => $subject,
   );
-  $result = tripal_core_chado_select('tripal_gff_temp', array('type_name'), $values);   
+  $result = chado_select_record('tripal_gff_temp', array('type_name'), $values);   
   if (count($result) == 0) {
-    tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot find subject type for feature in 'derives_from' relationship: %subject", array('%subject' => $subject));
+    tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot find subject type for feature in 'derives_from' relationship: %subject", array('%subject' => $subject));
      return ''; 
   }
   $subject_type = $result[0]->type_name;
@@ -924,9 +924,9 @@ function tripal_feature_load_gff3_derives_from($feature, $subject, $organism) {
       ),
     ),      
   );
-  $sfeature = tripal_core_chado_select('feature', array('feature_id'), $match);
+  $sfeature = chado_select_record('feature', array('feature_id'), $match);
   if (count($sfeature)==0) {
-    tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "Could not add 'Derives_from' relationship " .
+    tripal_report_error('T_gff3_loader', TRIPAL_ERROR, "Could not add 'Derives_from' relationship " .
       "for %uniquename and %subject.  Subject feature, '%subject', " .
       "cannot be found", array('%uniquename' => $feature->uniquename, '%subject' => $subject));
     return;
@@ -944,15 +944,15 @@ function tripal_feature_load_gff3_derives_from($feature, $subject, $organism) {
     ),
     'rank' => 0
   );
-  $rel = tripal_core_chado_select('feature_relationship', array('*'), $values);
+  $rel = chado_select_record('feature_relationship', array('*'), $values);
   if (count($rel) > 0) {
     return;
   }
 
   // finally insert the relationship if it doesn't exist
-  $ret = tripal_core_chado_insert('feature_relationship', $values);
+  $ret = chado_insert_record('feature_relationship', $values);
   if (!$ret) {
-    tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Could not add 'Derives_from' relationship for $feature->uniquename and $subject", 
+    tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Could not add 'Derives_from' relationship for $feature->uniquename and $subject", 
       array());
   }
 }
@@ -983,9 +983,9 @@ function tripal_feature_load_gff3_parents($feature, $cvterm, $parents, $organism
       'organism_id' => $organism_id,
       'uniquename' => $parent,
     );
-    $result = tripal_core_chado_select('tripal_gff_temp', array('type_name'), $values);    
+    $result = chado_select_record('tripal_gff_temp', array('type_name'), $values);    
     if (count($result) == 0) {
-      tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot find parent: %parent", array('%parent' => $parent));
+      tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot find parent: %parent", array('%parent' => $parent));
        return '';  
     }
     $parent_type = $result[0]->type_name;
@@ -998,7 +998,7 @@ function tripal_feature_load_gff3_parents($feature, $cvterm, $parents, $organism
         'uniquename' => $parent,
         'type_id' => $parentcvterm->cvterm_id,
     );
-    $result = tripal_core_chado_select('feature', array('feature_id'), $values);
+    $result = chado_select_record('feature', array('feature_id'), $values);
     $parent_feature = $result[0];
 
     // if the parent exists then add the relationship otherwise print error and skip
@@ -1010,7 +1010,7 @@ function tripal_feature_load_gff3_parents($feature, $cvterm, $parents, $organism
         'subject_id' => $feature->feature_id,
         'type_id' => $relcvterm->cvterm_id,
       );
-      $rel = tripal_core_chado_select('feature_relationship', array('*'), $values);
+      $rel = chado_select_record('feature_relationship', array('*'), $values);
 
       if (count($rel) > 0) {
       }
@@ -1021,15 +1021,15 @@ function tripal_feature_load_gff3_parents($feature, $cvterm, $parents, $organism
           'object_id'  => $parent_feature->feature_id,
           'type_id' => $relcvterm->cvterm_id,
         );
-        $result = tripal_core_chado_insert('feature_relationship', $values);
+        $result = chado_insert_record('feature_relationship', $values);
         if (!$result) {
-          tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to insert feature relationship '$uname' ($type) $rel_type '$parent' ($parent_type)", 
+          tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to insert feature relationship '$uname' ($type) $rel_type '$parent' ($parent_type)", 
             array());
         }
       }
     }
     else {
-      tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot establish relationship '$uname' ($type) $rel_type '$parent' ($parent_type): Cannot find the parent", 
+      tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot establish relationship '$uname' ($type) $rel_type '$parent' ($parent_type): Cannot find the parent", 
         array());      
     }
   }
@@ -1056,23 +1056,23 @@ function tripal_feature_load_gff3_dbxref($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");
-    $db = tripal_core_chado_select('db', array('db_id'), $values);
+    $db = chado_select_record('db', array('db_id'), $values);
     if (count($db) == 0) {
       $values = array('name' => "$dbname");
-      $db = tripal_core_chado_select('db', array('db_id'), $values);
+      $db = chado_select_record('db', array('db_id'), $values);
     }
     if (count($db) == 0) {
       $values = array(
         'name' => $dbname,
         'description' => 'Added automatically by the GFF loader'
       );
-      $success = tripal_core_chado_insert('db', $values);
+      $success = chado_insert_record('db', $values);
       if ($success) {
         $values = array('name' => "$dbname");
-        $db = tripal_core_chado_select('db', array('db_id'), $values);
+        $db = chado_select_record('db', array('db_id'), $values);
       }
       else {
-        tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot find or add the database $dbname", array());
+        tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot find or add the database $dbname", array());
         return 0;
       }
     }
@@ -1083,7 +1083,7 @@ function tripal_feature_load_gff3_dbxref($feature, $dbxrefs) {
       'accession' => $accession, 
       'db_id' => $db->db_id
     );
-    $dbxref = tripal_core_chado_select('dbxref', array('dbxref_id'), $values);
+    $dbxref = chado_select_record('dbxref', array('dbxref_id'), $values);
 
     // if the accession doesn't exist then we want to add it
     if (sizeof($dbxref) == 0) {
@@ -1092,12 +1092,12 @@ function tripal_feature_load_gff3_dbxref($feature, $dbxrefs) {
         'accession' => $accession, 
         'version' => ''
       );
-      $ret = tripal_core_chado_insert('dbxref', $values);
+      $ret = chado_insert_record('dbxref', $values);
       $values = array(
         'accession' => $accession, 
         'db_id' => $db->db_id
       );
-      $dbxref = tripal_core_chado_select('dbxref', array('dbxref_id'), $values);
+      $dbxref = chado_select_record('dbxref', array('dbxref_id'), $values);
     }
     $dbxref = $dbxref[0];
 
@@ -1106,7 +1106,7 @@ function tripal_feature_load_gff3_dbxref($feature, $dbxrefs) {
       'dbxref_id' => $dbxref->dbxref_id, 
       'feature_id' => $feature->feature_id
     );
-    $fdbx = tripal_core_chado_select('feature_dbxref', array('feature_dbxref_id'), $values);
+    $fdbx = chado_select_record('feature_dbxref', array('feature_dbxref_id'), $values);
 
     // now associate this feature with the database reference if it doesn't
     // already exist
@@ -1115,9 +1115,9 @@ function tripal_feature_load_gff3_dbxref($feature, $dbxrefs) {
         'dbxref_id' => $dbxref->dbxref_id,
         'feature_id' => $feature->feature_id
       );
-      $success = tripal_core_chado_insert('feature_dbxref', $values);
+      $success = chado_insert_record('feature_dbxref', $values);
       if (!$success) {
-        tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to insert Dbxref: $dbname:$accession", array());
+        tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to insert Dbxref: $dbname:$accession", array());
         return 0;
       }
     }
@@ -1140,35 +1140,35 @@ function tripal_feature_load_gff3_ontology($feature, $dbxrefs) {
     $accession = $ref[1];
 
     // first look for the database name
-    $db = tripal_core_chado_select('db', array('db_id'), array('name' => "DB:$dbname"));
+    $db = chado_select_record('db', array('db_id'), array('name' => "DB:$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"));
+      $db = chado_select_record('db', array('db_id'), array('name' => "$dbname"));
       if (sizeof($db) == 0) {
-        tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Database, $dbname, is not present. Cannot associate term: $dbname:$accession", array());
+        tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Database, $dbname, is not present. Cannot associate term: $dbname:$accession", array());
         return 0;
       }
     }
     $db = $db[0];
 
     // now check to see if the accession exists
-    $dbxref = tripal_core_chado_select('dbxref', array('dbxref_id'), 
+    $dbxref = chado_select_record('dbxref', array('dbxref_id'), 
       array('accession' => $accession, 'db_id' => $db->db_id));
     if (sizeof($dbxref) == 0) {
-      tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Accession, $accession is missing for reference: $dbname:$accession", array());
+      tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Accession, $accession is missing for reference: $dbname:$accession", array());
       return 0;
     }
     $dbxref = $dbxref[0];
 
     // now check to see if the cvterm exists
-    $cvterm = tripal_core_chado_select('cvterm', array('cvterm_id'), array(
+    $cvterm = chado_select_record('cvterm', array('cvterm_id'), array(
        'dbxref_id' => $dbxref->dbxref_id));
     // if it doesn't exist in the cvterm table, look for an alternate id
     if (sizeof($cvterm) == 0) {
-      $cvterm = tripal_core_chado_select('cvterm_dbxref', array('cvterm_id'), array(
+      $cvterm = chado_select_record('cvterm_dbxref', array('cvterm_id'), array(
         'dbxref_id' => $dbxref->dbxref_id));
       if (sizeof($cvterm) == 0) {
-        tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "CV Term is missing for reference: $dbname:$accession", array());
+        tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "CV Term is missing for reference: $dbname:$accession", array());
         return 0;
       }
     }
@@ -1176,7 +1176,7 @@ function tripal_feature_load_gff3_ontology($feature, $dbxrefs) {
 
 
     // check to see if this feature cvterm already exists
-    $fcvt = tripal_core_chado_select('feature_cvterm', array('feature_cvterm_id'),
+    $fcvt = chado_select_record('feature_cvterm', array('feature_cvterm_id'),
       array('cvterm_id' => $cvterm->cvterm_id, 'feature_id' => $feature->feature_id));
 
     // now associate this feature with the cvterm if it doesn't already exist
@@ -1188,10 +1188,10 @@ function tripal_feature_load_gff3_ontology($feature, $dbxrefs) {
           'uniquename' => 'null',
         ),
       );
-      $success = tripal_core_chado_insert('feature_cvterm', $values);
+      $success = chado_insert_record('feature_cvterm', $values);
 
       if (!$success) {
-        tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to insert ontology term: $dbname:$accession", array());
+        tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to insert ontology term: $dbname:$accession", array());
         return 0;
       }
     }
@@ -1207,7 +1207,7 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
 
   // make sure we have a 'synonym_type' vocabulary
   $select = array('name' => 'synonym_type');
-  $results = tripal_core_chado_select('cv', array('*'), $select);
+  $results = chado_select_record('cv', array('*'), $select);
   
   if (count($results) == 0) {
     // insert the 'synonym_type' vocabulary
@@ -1215,13 +1215,13 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
       'name' => 'synonym_type',
       'definition' => 'vocabulary for synonym types',
     );
-    $success = tripal_core_chado_insert('cv', $values);
+    $success = chado_insert_record('cv', $values);
     if (!$success) {
-      tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to add the synonyms type vocabulary", array());
+      tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to add the synonyms type vocabulary", array());
       return 0;
     }
     // now that we've added the cv we need to get the record
-    $results = tripal_core_chado_select('cv', array('*'), $select);
+    $results = chado_select_record('cv', array('*'), $select);
     if (count($results) > 0) {
       $syncv = $results[0];
     }
@@ -1237,7 +1237,7 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
         'name' => 'synonym_type'
      ),
   );
-  $result = tripal_core_chado_select('cvterm', array('*'), $select);  
+  $result = chado_select_record('cvterm', array('*'), $select);  
   if (count($result) == 0) {
     $term = array(
       'name' => 'exact',
@@ -1247,7 +1247,7 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
     );
     $syntype = tripal_cv_add_cvterm($term, $syncv->name, 0, 1);
     if (!$syntype) {
-      tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot add synonym type: internal:$type", array());
+      tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot add synonym type: internal:$type", array());
       return 0;
     }
   } 
@@ -1264,19 +1264,19 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
        'name' => $alias,
        'type_id' => $syntype->cvterm_id,
     );
-    $result = tripal_core_chado_select('synonym', array('*'), $select);    
+    $result = chado_select_record('synonym', array('*'), $select);    
     if (count($result) == 0) {
       $values = array(
          'name' => $alias,
          'type_id' => $syntype->cvterm_id,
          'synonym_sgml' => '',
       );
-      $success = tripal_core_chado_insert('synonym', $values);
+      $success = chado_insert_record('synonym', $values);
       if (!$success) {
-        tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot add alias $alias to synonym table", array());
+        tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot add alias $alias to synonym table", array());
         return 0;
       }
-      $result = tripal_core_chado_select('synonym', array('*'), $select);
+      $result = chado_select_record('synonym', array('*'), $select);
       $synonym = $result[0];
     }
     else {
@@ -1286,7 +1286,7 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
     // check to see if we have a NULL publication in the pub table.  If not,
     // then add one.
     $select = array('uniquename' => 'null');
-    $result = tripal_core_chado_select('pub', array('*'), $select);    
+    $result = chado_select_record('pub', array('*'), $select);    
     if (count($result) == 0) {
       $pub_sql = "
         INSERT INTO {pub} (uniquename,type_id) 
@@ -1299,17 +1299,17 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
       ";
       $status = chado_query($psql);
       if (!$status) {
-        tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot prepare statement 'ins_pub_uniquename_typeid", array());
+        tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot prepare statement 'ins_pub_uniquename_typeid", array());
         return 0;
       } 
 
       // insert the null pub 
       $result = chado_query($pub_sql, array(':uname' => 'null', ':type_id' => 'null'))->fetchObject();
       if (!$result) {
-        tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot add null publication needed for setup of alias", array());
+        tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot add null publication needed for setup of alias", array());
         return 0;
       }
-      $result = tripal_core_chado_select('pub', array('*'), $select);
+      $result = chado_select_record('pub', array('*'), $select);
       $pub = $result[0];
     }
     else {
@@ -1324,17 +1324,17 @@ function tripal_feature_load_gff3_alias($feature, $aliases) {
        'pub_id' => $pub->pub_id,
     );
     $columns = array('feature_synonym_id');
-    $result = tripal_core_chado_select('feature_synonym', $columns, $values);
+    $result = chado_select_record('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,
       );  
-      $success = tripal_core_chado_insert('feature_synonym', $values);   
+      $success = chado_insert_record('feature_synonym', $values);   
      
       if (!$success) {
-        tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot add alias $alias to feature synonym table", array());
+        tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot add alias $alias to feature synonym table", array());
         return 0;
       }
     }
@@ -1358,7 +1358,7 @@ function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uni
      'type_id' => $cvterm->cvterm_id
   );
   $columns = array('feature_id', 'name', 'uniquename', 'seqlen', 'organism_id', 'type_id');
-  $result = tripal_core_chado_select('feature', $columns, $fselect);
+  $result = chado_select_record('feature', $columns, $fselect);
   if (count($result) > 0) {
     $feature = $result[0];
   }
@@ -1389,9 +1389,9 @@ function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uni
        'is_analysis' => $is_analysis,
        'is_obsolete' => $is_obsolete,
     );
-    $result = tripal_core_chado_insert('feature', $values);
+    $result = chado_insert_record('feature', $values);
     if (!$result) {
-      tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to insert feature '$uniquename' ($cvterm->name)", array());
+      tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to insert feature '$uniquename' ($cvterm->name)", array());
       return 0;
     }
   }
@@ -1409,9 +1409,9 @@ function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uni
       'uniquename' => $uniquename,
       'type_id' => $cvterm->cvterm_id,
     );
-    $result = tripal_core_chado_update('feature', $match, $values);
+    $result = chado_update_record('feature', $match, $values);
     if (!$result) {
-      tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to update feature '$uniquename' ($cvterm->name)", array());
+      tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to update feature '$uniquename' ($cvterm->name)", array());
       return 0;
     }
   }
@@ -1423,7 +1423,7 @@ function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uni
 
   // get the newly added feature
   $columns = array('feature_id', 'name', 'uniquename', 'seqlen', 'organism_id', 'type_id');
-  $result = tripal_core_chado_select('feature', $columns, $fselect);  
+  $result = chado_select_record('feature', $columns, $fselect);  
   $feature = $result[0];
 
   // add the analysisfeature entry to the analysisfeature table if it doesn't already exist
@@ -1431,14 +1431,14 @@ function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uni
     'analysis_id' => $analysis_id,
     'feature_id' => $feature->feature_id
   );
-  $afeature = tripal_core_chado_select('analysisfeature', array('analysisfeature_id'), $af_values);
+  $afeature = chado_select_record('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;
     } 
     if (!tripal_core_chado_insert('analysisfeature', $af_values)) {
-      tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Could not add analysisfeature record: $analysis_id, $feature->feature_id", array());
+      tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Could not add analysisfeature record: $analysis_id, $feature->feature_id", array());
     }    
   }
   else {
@@ -1451,9 +1451,9 @@ function tripal_feature_load_gff3_feature($organism, $analysis_id, $cvterm, $uni
       $new_vals['significance'] = '__NULL__';
     }
     if (!$add_only) {
-      $ret = tripal_core_chado_update('analysisfeature', $af_values, $new_vals);
+      $ret = chado_update_record('analysisfeature', $af_values, $new_vals);
       if (!$ret) {
-        tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Could not update analysisfeature record: $analysis_id, $feature->feature_id", array());
+        tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Could not update analysisfeature record: $analysis_id, $feature->feature_id", array());
       }
     }
   }
@@ -1477,7 +1477,7 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
   if ($landmark_type_id) {
     $select['type_id'] = $landmark_type_id;
   }  
-  $results = tripal_core_chado_select('feature', array('feature_id'), $select);
+  $results = chado_select_record('feature', array('feature_id'), $select);
 
   $srcfeature = '';
   if (count($results)==0) {
@@ -1490,13 +1490,13 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
     if ($landmark_type_id) {
       $select['type_id'] = $landmark_type_id;
     } 
-    $results = tripal_core_chado_select('feature', array('feature_id'), $select);
+    $results = chado_select_record('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);
-         $results = tripal_core_chado_select('feature', array('feature_id'), $select);
+         $results = chado_select_record('feature', array('feature_id'), $select);
          if (count($results) == 1) {
            $srcfeature = $results[0]; 
          }
@@ -1512,9 +1512,9 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
               'uniquename' => $landmark,
               'type_id' => $landmark_type_id
             );
-            $results = tripal_core_chado_insert('feature', $values);
+            $results = chado_insert_record('feature', $values);
             if (!$results) {
-              tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot find landmark feature: '%landmark', nor could it be inserted", 
+              tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot find landmark feature: '%landmark', nor could it be inserted", 
                 array('%landmark' => $landmark));
               return 0;  
             }  
@@ -1522,14 +1522,14 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
             $srcfeature->feature_id = $results['feature_id'];
          } 
          else {
-           tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot find unique landmark feature: '%landmark'.", 
+           tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot find unique landmark feature: '%landmark'.", 
              array('%landmark' => $landmark));
            return 0;
          } 
        }        
     } 
     elseif (count($results) > 1) {
-       tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "multiple landmarks exist with the name: '%landmark'.  Cannot 
+       tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "multiple landmarks exist with the name: '%landmark'.  Cannot 
          resolve which one to use. Cannot add the feature location record", 
          array('%landmark' => $landmark));
        return 0;    
@@ -1539,7 +1539,7 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
     }   
   }
   elseif (count($results) > 1) {
-    tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "multiple landmarks exist with the name: '%landmark'.  Cannot 
+    tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "multiple landmarks exist with the name: '%landmark'.  Cannot 
       resolve which one to use. Cannot add the feature location record", 
       array('%landmark' => $landmark));
     return 0;  
@@ -1563,7 +1563,7 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
     ),
   );
  
-  $locrecs = tripal_core_chado_select('featureloc', array('*'), $select, $options);
+  $locrecs = chado_select_record('featureloc', array('*'), $select, $options);
 
   foreach ($locrecs as $featureloc) {
     // it is possible for the featureloc->srcfeature_id to be NULL. This can happen if the srcfeature
@@ -1573,7 +1573,7 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
     }    
     $select = array('feature_id' => $featureloc->srcfeature_id);
     $columns = array('feature_id', 'name');
-    $locsfeature = tripal_core_chado_select('feature', $columns, $select);   
+    $locsfeature = chado_select_record('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.
@@ -1592,7 +1592,7 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
          $values['strand'] = $strand;
       }
       if (count($values) > 0) {
-        tripal_core_chado_update('featureloc', $match, $values);
+        chado_update_record('featureloc', $match, $values);
       }
     }
     $rank = $featureloc->rank + 1;
@@ -1627,9 +1627,9 @@ function tripal_feature_load_gff3_featureloc($feature, $organism, $landmark, $fm
     if ($phase) {
       $values['phase'] = $phase;
     }    
-    $success = tripal_core_chado_insert('featureloc', $values);
+    $success = chado_insert_record('featureloc', $values);
     if (!$success) {
-      tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to insert featureloc", array());
+      tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Failed to insert featureloc", array());
       exit;
       return 0;
     }
@@ -1650,7 +1650,7 @@ function tripal_feature_load_gff3_property($feature, $property, $value) {
         'name' => 'feature_property',
      ),
   );
-  $result = tripal_core_chado_select('cvterm', array('*'), $select);
+  $result = chado_select_record('cvterm', array('*'), $select);
 
   // if we don't have a property like this already, then add it otherwise, just return
   if (count($result) == 0) {
@@ -1662,7 +1662,7 @@ function tripal_feature_load_gff3_property($feature, $property, $value) {
     );    
     $cvterm = (object) tripal_cv_add_cvterm($term, 'feature_property', 0, 0);
     if (!$cvterm) {
-      tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot add cvterm, $property", array());
+      tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot add cvterm, $property", array());
       return 0;  
     }
   } 
@@ -1685,7 +1685,7 @@ function tripal_feature_load_gff3_property($feature, $property, $value) {
       'rank' => 'ASC',
     ),
   );
-  $results = tripal_core_chado_select('featureprop', array('*'), $select, $options);
+  $results = chado_select_record('featureprop', array('*'), $select, $options);
   foreach ($results as $prop) {
     if (strcmp($prop->value, $value)==0) {
       $add = NULL; // don't add it, it already exists
@@ -1701,9 +1701,9 @@ function tripal_feature_load_gff3_property($feature, $property, $value) {
        'value' => $value,
        'rank' => $rank,
     );
-    $result = tripal_core_chado_insert('featureprop', $values);
+    $result = chado_insert_record('featureprop', $values);
     if (!$result) {
-      tripal_core_report_error("T_gff3_loader", TRIPAL_WARNING, "cannot add featureprop, $property", array());
+      tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "cannot add featureprop, $property", array());
     }
   }
 }
@@ -1733,7 +1733,7 @@ function tripal_feature_load_gff3_fasta($fh, $interval, &$num_read, &$intv_read,
       $intv_read = 0;
       $percent = sprintf("%.2f", ($num_read / $filesize) * 100);
       print "Parsing Line $line_num (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
-      tripal_job_set_progress($job, intval(($num_read / $filesize) * 100));
+      tripal_set_job_progress($job, intval(($num_read / $filesize) * 100));
     }
     
     // if we encounter a definition line then get the name, uniquename,
@@ -1743,9 +1743,9 @@ function tripal_feature_load_gff3_fasta($fh, $interval, &$num_read, &$intv_read,
       // if we are beginning a new sequence then save to the database the last one we just finished.     
       if ($id) {
         $values = array('uniquename' => $id);
-        $result = tripal_core_chado_select('tripal_gff_temp', array('*'), $values); 
+        $result = chado_select_record('tripal_gff_temp', array('*'), $values); 
         if (count($result) == 0) {
-          tripal_core_report_error('T_gff3_loader', TRIPAL_WARNING, 'Cannot find feature to assign FASTA sequence: %uname', 
+          tripal_report_error('T_gff3_loader', TRIPAL_WARNING, 'Cannot find feature to assign FASTA sequence: %uname', 
              array('%uname' => $id));
         }
         else {
@@ -1753,7 +1753,7 @@ function tripal_feature_load_gff3_fasta($fh, $interval, &$num_read, &$intv_read,
           $feature = $result[0];
           $values = array('residues' => $residues);
           $match = array('feature_id' => $feature->feature_id);
-          tripal_core_chado_update('feature', $match, $values);
+          chado_update_record('feature', $match, $values);
         }
       }
       
@@ -1768,9 +1768,9 @@ function tripal_feature_load_gff3_fasta($fh, $interval, &$num_read, &$intv_read,
   
   // add in the last sequence
   $values = array('uniquename' => $id);
-  $result = tripal_core_chado_select('tripal_gff_temp', array('*'), $values); 
+  $result = chado_select_record('tripal_gff_temp', array('*'), $values); 
   if (count($result) == 0) {
-    tripal_core_report_error('T_gff3_loader', TRIPAL_WARNING, 'Cannot find feature to assign FASTA sequence: %uname', 
+    tripal_report_error('T_gff3_loader', TRIPAL_WARNING, 'Cannot find feature to assign FASTA sequence: %uname', 
        array('%uname' => $id));
   }
   else {
@@ -1778,7 +1778,7 @@ function tripal_feature_load_gff3_fasta($fh, $interval, &$num_read, &$intv_read,
     $feature = $result[0];
     $values = array('residues' => $residues);
     $match = array('feature_id' => $feature->feature_id);
-    tripal_core_chado_update('feature', $match, $values);
+    chado_update_record('feature', $match, $values);
   }
 
 }
@@ -1834,18 +1834,18 @@ function tripal_feature_load_gff3_target($feature, $tags, $target_organism_id, $
           'genus' => $matches[1],
           'species' => $matches[2],
         );
-        $torganism = tripal_core_chado_select('organism', array('organism_id'), $values);
+        $torganism = chado_select_record('organism', array('organism_id'), $values);
         if (count($torganism) == 1) {
           $t_organism_id = $torganism[0]->organism_id;
         }
         else {
-          tripal_core_report_error('T_gff3_loader', TRIPAL_WARNING, "Cannot find organism for target %target.", 
+          tripal_report_error('T_gff3_loader', TRIPAL_WARNING, "Cannot find organism for target %target.", 
             array('%target' => $gff_target_organism));
           $t_organism_id = '';                                   
         }
       }
       else {
-        tripal_core_report_error('T_gff3_loader', TRIPAL_WARNING, "The target_organism attribute is improperly formatted: %target. 
+        tripal_report_error('T_gff3_loader', TRIPAL_WARNING, "The target_organism attribute is improperly formatted: %target. 
           It should be target_organism=genus:species.", 
           array('%target' => $gff_target_organism));
         $t_organism_id = '';                
@@ -1862,12 +1862,12 @@ function tripal_feature_load_gff3_target($feature, $tags, $target_organism_id, $
            'name' => 'sequence',
         )
       );
-      $type = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);
+      $type = chado_select_record('cvterm', array('cvterm_id'), $values);
       if (count($type) == 1) {
         $t_type_id = $type[0]->cvterm_id;
       }
       else {
-        tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "The target type does not exist in the sequence ontology: %type. ", 
+        tripal_report_error('T_gff3_loader', TRIPAL_ERROR, "The target type does not exist in the sequence ontology: %type. ", 
           array('%type' => $target_type));
         exit;  
       }
@@ -1881,7 +1881,7 @@ function tripal_feature_load_gff3_target($feature, $tags, $target_organism_id, $
       );
       
       // get the cvterm_id for the target type
-      $type = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);
+      $type = chado_select_record('cvterm', array('cvterm_id'), $values);
       if (count($type) == 1) {
         $t_type_id = $type[0]->cvterm_id;
       }
@@ -1899,7 +1899,7 @@ function tripal_feature_load_gff3_target($feature, $tags, $target_organism_id, $
           $t_type_id = $synonym->cvterm_id;
         }
         else {
-          tripal_core_report_error('T_gff3_loader', TRIPAL_WARNING, "The target_type attribute does not exist in the sequence ontology: %type. ", 
+          tripal_report_error('T_gff3_loader', TRIPAL_WARNING, "The target_type attribute does not exist in the sequence ontology: %type. ", 
             array('%type' => $gff_target_type));
           $t_type_id = '';
         }
@@ -1914,7 +1914,7 @@ function tripal_feature_load_gff3_target($feature, $tags, $target_organism_id, $
   }
   // the target attribute is not correctly formatted
   else {
-    tripal_core_report_error('T_gff3_loader', TRIPAL_ERROR, "Could not add 'Target' alignment as it is improperly formatted:  '%target'",
+    tripal_report_error('T_gff3_loader', TRIPAL_ERROR, "Could not add 'Target' alignment as it is improperly formatted:  '%target'",
       array('%target' => $tags['Target'][0]));            
   }
 }

tripal_feature/theme/tripal_feature.theme.inc

@@ -18,7 +18,7 @@ function tripal_feature_preprocess_tripal_feature_sequence(&$variables) {
     ),
   );
 
-  $feature = tripal_core_expand_chado_vars($feature, 'table', 'featureloc', $options);
+  $feature = chado_expand_var($feature, 'table', 'featureloc', $options);
 
   // because there are two foriegn keys in the featureloc table with the feature table
   // we have to access the records for each by specifying the field name after the table name:
@@ -75,7 +75,7 @@ function tripal_feature_preprocess_tripal_feature_alignments(&$variables) {
       ),
     )
   );
-  $feature = tripal_core_expand_chado_vars($feature, 'table', 'featureloc', $options);
+  $feature = chado_expand_var($feature, 'table', 'featureloc', $options);
 
   // get alignments as child
   $cfeaturelocs = $feature->featureloc->feature_id;
@@ -138,7 +138,7 @@ function tripal_feature_preprocess_tripal_feature_alignments(&$variables) {
   foreach ($mfeaturelocs as $featureloc) {
     // get more information about the right feature
     $select = array('feature_id' => $featureloc->right_srcfeature_id);
-    $rfeature = tripal_core_generate_chado_var('feature', $select);
+    $rfeature = chado_generate_var('feature', $select);
     // now add to the list
     $alignment = new stdClass();
     $alignment->record = $featureloc;
@@ -209,7 +209,7 @@ function tripal_feature_get_feature_relationships($feature) {
       ),
     ),
   );
-  $feature = tripal_core_expand_chado_vars($feature, 'table', 'feature_relationship', $options);
+  $feature = chado_expand_var($feature, 'table', 'feature_relationship', $options);
 
   // get the subject relationships
   $srelationships = $feature->feature_relationship->subject_id;
@@ -224,7 +224,7 @@ function tripal_feature_get_feature_relationships($feature) {
       'feature_id' => 1,
     ),
   );
-  $feature = tripal_core_expand_chado_vars($feature, 'table', 'featureloc', $options);
+  $feature = chado_expand_var($feature, 'table', 'featureloc', $options);
   $cfeaturelocs = $feature->featureloc->feature_id;
   if (!$cfeaturelocs) {
     $cfeaturelocs = array();

tripal_feature/tripal_feature.install

@@ -43,7 +43,7 @@ function tripal_feature_requirements($phase) {
  */
 function tripal_feature_install() {
   // create the module's data directory
-  tripal_create_moddir('tripal_feature');
+  tripal_create_files_dir('tripal_feature');
 
   // add the materialized view
   tripal_feature_add_organism_count_mview();

tripal_feature/tripal_feature.module

@@ -290,7 +290,7 @@ function tripal_feature_theme($existing, $type, $theme, $path) {
     'tripal_feature_help' => array(
       'template' => 'tripal_feature_help',
       'variables' =>  array(NULL),
-      'path' => drupal_get_path('module', 'tripal_feature') . '/theme'
+      'path' => "$path/theme/"
     ),
 
     // template for the organism page
@@ -357,8 +357,8 @@ function tripal_feature_load_featurelocs($feature_id, $side = 'as_parent', $aggr
   while ($loc = $flresults->fetchObject()) {
     // if a drupal node exists for this feature then add the nid to the
     // results object
-    $loc->fnid = chado_get_node_id('feature', $loc->feature_id);
-    $loc->snid = chado_get_node_id('feature', $loc->src_feature_id);
+    $loc->fnid = chado_get_nid_from_id('feature', $loc->feature_id);
+    $loc->snid = chado_get_nid_from_id('feature', $loc->src_feature_id);
     // add the result to the array
     $featurelocs[$i++] = $loc;
   }
@@ -977,7 +977,7 @@ function tripal_feature_job_describe_args($callback, $args) {
   $new_args = array();
   if ($callback == 'tripal_feature_load_fasta') {
     $new_args['FASTA file'] = $args[0];
-    $organism = tripal_core_chado_select('organism', array('genus', 'species'), array('organism_id' => $args[1]));
+    $organism = chado_select_record('organism', array('genus', 'species'), array('organism_id' => $args[1]));
     $new_args['Organism'] = $organism[0]->genus . " " . $organism[0]->species;
     $new_args['Sequence Type'] = $args[2];
     $new_args['Name Match Type'] = $args[14];
@@ -991,7 +991,7 @@ function tripal_feature_job_describe_args($callback, $args) {
 
     // add in the database reference arguments
     if ($args[7]) {
-      $db = tripal_core_chado_select('db', array('name'), array('db_id' => $args[7]));
+      $db = chado_select_record('db', array('name'), array('db_id' => $args[7]));
     }
     $new_args['Database Reference'] = $db[0]->name;
     $new_args['Accession RE'] = $args[6];
@@ -999,13 +999,13 @@ function tripal_feature_job_describe_args($callback, $args) {
 
     // add in the analysis
     if ($args[13]) {
-      $analysis = tripal_core_chado_select('analysis', array('name'), array('analysis_id' => $args[13]));
+      $analysis = chado_select_record('analysis', array('name'), array('analysis_id' => $args[13]));
     }
     $new_args['Analysis'] = $analysis[0]->name;
   }
   if ($callback == 'tripal_feature_delete_features') {
     if ($args[0]) {
-      $organism = tripal_core_chado_select('organism', array('genus', 'species'), array('organism_id' => $args[0]));
+      $organism = chado_select_record('organism', array('genus', 'species'), array('organism_id' => $args[0]));
       $new_args['Organism'] = $organism[0]->genus . " " . $organism[0]->species;
     }
     else {
@@ -1013,7 +1013,7 @@ function tripal_feature_job_describe_args($callback, $args) {
     }
 
     if ($args[1]) {
-      $analysis = tripal_core_chado_select('analysis', array('name'), array('analysis_id' => $args[1]));
+      $analysis = chado_select_record('analysis', array('name'), array('analysis_id' => $args[1]));
       $new_args['Analysis'] = $analysis[0]->name;
     }
     else {
@@ -1028,9 +1028,9 @@ function tripal_feature_job_describe_args($callback, $args) {
   elseif ($callback == 'tripal_feature_load_gff3') {
 
     $new_args['GFF File'] = $args[0];
-    $organism = tripal_core_chado_select('organism', array('genus', 'species'), array('organism_id' => $args[1]));
+    $organism = chado_select_record('organism', array('genus', 'species'), array('organism_id' => $args[1]));
     $new_args['Organism'] = $organism[0]->genus . " " . $organism[0]->species;
-    $analysis = tripal_core_chado_select('analysis', array('name'), array('analysis_id' => $args[2]));
+    $analysis = chado_select_record('analysis', array('name'), array('analysis_id' => $args[2]));
     $new_args['Analysis'] = $analysis[0]->name;
     $new_args['Use a Transaction'] = ($args[7] == 1) ? "Yes" : "No";
     $new_args['Import only new features'] = ($args[3] == 1) ? "Yes" : "No";
@@ -1038,7 +1038,7 @@ function tripal_feature_job_describe_args($callback, $args) {
     $new_args['Import all and replace'] = ($args[5] == 1) ? "Yes" : "No";
     $new_args['Delete features'] = ($args[6] == 1) ? "Yes" : "No";
     if ($args[8]) {
-      $target_organism = tripal_core_chado_select('organism', array('genus', 'species'), array('organism_id' => $args[8]));
+      $target_organism = chado_select_record('organism', array('genus', 'species'), array('organism_id' => $args[8]));
       $new_args['Target organism'] = $target_organism[0]->genus . " " . $target_organism[0]->species;
     }
     else {

tripal_featuremap/api/tripal_featuremap.api.inc

@@ -22,7 +22,7 @@
  * @ingroup tripal_featuremap_api
  */
 function tripal_featuremap_get_property($featuremap_id, $property) {
-  return tripal_core_get_property('featuremap', $featuremap_id, $property, 'featuremap_property');
+  return chado_get_property('featuremap', $featuremap_id, $property, 'featuremap_property');
 }
 
 /**
@@ -43,7 +43,7 @@ function tripal_featuremap_get_property($featuremap_id, $property) {
  * @ingroup tripal_featuremap_api
  */
 function tripal_featuremap_insert_property($featuremap_id, $property, $value, $update_if_present = 0) {
-  return tripal_core_insert_property('featuremap', $featuremap_id, $property, 'featuremap_property', $value, $update_if_present);
+  return chado_insert_property('featuremap', $featuremap_id, $property, 'featuremap_property', $value, $update_if_present);
 }
 
 /**
@@ -67,7 +67,7 @@ function tripal_featuremap_insert_property($featuremap_id, $property, $value, $u
  * @ingroup tripal_featuremap_api
  */
 function tripal_featuremap_update_property($featuremap_id, $property, $value, $insert_if_missing = 0) {
-  return tripal_core_update_property('featuremap', $featuremap_id, $property, 'featuremap_property', $value, $insert_if_missing);
+  return chado_update_property('featuremap', $featuremap_id, $property, 'featuremap_property', $value, $insert_if_missing);
 }
 /**
  * Delete a given property
@@ -86,7 +86,7 @@ function tripal_featuremap_update_property($featuremap_id, $property, $value, $i
  * @ingroup tripal_featuremap_api
  */
 function tripal_featuremap_delete_property($featuremap_id, $property) {
-  return tripal_core_delete_property('featuremap', $featuremap_id, $property, 'featuremap_property');
+  return chado_delete_property('featuremap', $featuremap_id, $property, 'featuremap_property');
 }
 
 /*
@@ -116,7 +116,7 @@ function tripal_featuremap_add_featuremap_dbxref($featuremap_id, $featuremap_dbx
     'featuremap_id' => $featuremap_id,
   );
   $options = array('statement_name' => 'sel_featuremapdbxref_dbpu');
-  $results = tripal_core_chado_select('featuremap_dbxref', array('*'), $values, $options);
+  $results = chado_select_record('featuremap_dbxref', array('*'), $values, $options);
 
   // if the featuremap_dbxref record  exist then we don't need to re-add it.
   if(count($results) > 0) {
@@ -132,7 +132,7 @@ function tripal_featuremap_add_featuremap_dbxref($featuremap_id, $featuremap_dbx
     'db_id' => $db->db_id,
   );
   $dbxoptions = array('statement_name' => 'sel_dbxref_acdb');
-  $results = tripal_core_chado_select('dbxref', array('dbxref_id'), $dbxvalues, $dbxoptions);
+  $results = chado_select_record('dbxref', array('dbxref_id'), $dbxvalues, $dbxoptions);
   // if the accession doesn't exist then add it
   if(count($results) == 0){
     $dbxref = tripal_db_add_dbxref($db->db_id, $accession);
@@ -143,9 +143,9 @@ function tripal_featuremap_add_featuremap_dbxref($featuremap_id, $featuremap_dbx
 
   // now add the record
   $options = array('statement_name' => 'ins_featuremapdbxref_dbpu');
-  $results = tripal_core_chado_insert('featuremap_dbxref', $values, $options);
+  $results = chado_insert_record('featuremap_dbxref', $values, $options);
   if (!$results) {
-    tripal_core_report_error('t_featuremap', TRIPAL_ERROR, "Cannot add map dbxref: %db:%accession.",
+    tripal_report_error('t_featuremap', TRIPAL_ERROR, "Cannot add map dbxref: %db:%accession.",
       array('%db' => $dbname, '%accession' => $accession));
     return FALSE;
   }

tripal_featuremap/includes/tripal_featuremap.chado_node.inc

@@ -57,7 +57,7 @@ function chado_featuremap_form($node, &$form_state) {
   // if we are editing an existing node then the featuremap is already part of the node
   if (property_exists($node, 'featuremap')) {
     $featuremap = $node->featuremap;
-    $featuremap = tripal_core_expand_chado_vars($featuremap, 'field', 'featuremap.description');
+    $featuremap = chado_expand_var($featuremap, 'field', 'featuremap.description');
     $featuremap_id = $featuremap->featuremap_id;
 
     // get form defaults
@@ -110,7 +110,7 @@ function chado_featuremap_form($node, &$form_state) {
   );
   $columns = array('cvterm_id','name');
   $options = array('order_by' => array('name' => 'ASC'));
-  $featuremap_units = tripal_core_chado_select('cvterm', $columns, $values, $options);
+  $featuremap_units = chado_select_record('cvterm', $columns, $values, $options);
   $units = array();
   $units[''] = '';
   foreach($featuremap_units as $unit) {
@@ -136,7 +136,7 @@ function chado_featuremap_form($node, &$form_state) {
     'fieldset_name' => 'Additional Details',
     'additional_instructions' => $instructions
   );
-  chado_node_properties_form($form, $form_state, $details);
+  chado_add_node_form_properties($form, $form_state, $details);
 
   // ADDITIONAL DBXREFS FORM
   //---------------------------------------------
@@ -146,7 +146,7 @@ function chado_featuremap_form($node, &$form_state) {
     'base_key_value' => $featuremap_id       // the value of featuremap_id for this record
   );
   // Adds the form elements to your current form
-  chado_node_additional_dbxrefs_form($form, $form_state, $details);
+  chado_add_node_form_dbxrefs($form, $form_state, $details);
 
   return $form;
 }
@@ -270,19 +270,19 @@ function chado_featuremap_insert($node) {
       'description' => $node->description,
       'unittype_id' => $node->unittype_id
     );
-    $featuremap = tripal_core_chado_insert('featuremap', $values);
+    $featuremap = chado_insert_record('featuremap', $values);
     if(!$featuremap) {
       drupal_set_message(t('Unable to add featuremap.', 'warning'));
-      tripal_core_report_error('tripal_featuremap', TRIPAL_WARNING, 'Unable to create feature map where values: %values',
+      tripal_report_error('tripal_featuremap', TRIPAL_WARNING, 'Unable to create feature map where values: %values',
       array('%values' => print_r($values, TRUE)));
       return;
     }
     $featuremap_id = $featuremap['featuremap_id'];
 
     // now add in the properties
-    $properties = chado_node_properties_form_retreive($node);
+    $properties = chado_retrieve_node_form_properties($node);
     // We need to deal with the 'Map Dbxref' property specially
-    $cvterm = tripal_core_chado_select(
+    $cvterm = chado_select_record(
       'cvterm',
       array('cvterm_id'),
       array('name' => 'Map Dbxref', 'cv_id' => array('name' => 'featuremap_property'))
@@ -293,7 +293,7 @@ function chado_featuremap_insert($node) {
         $featuremap_dbxref = tripal_featuremap_add_featuremap_dbxref($featuremap_id, $value);
         if (!$featuremap_dbxref) {
           drupal_set_message("Error cannot add featuremap cross reference: $value", "error");
-          tripal_core_report_error('t_featuremap', TRIPAL_ERROR, "Error cannot add featuremap cross reference: %ref",
+          tripal_report_error('t_featuremap', TRIPAL_ERROR, "Error cannot add featuremap cross reference: %ref",
           array('%ref' => $value));
         }
       }
@@ -305,7 +305,7 @@ function chado_featuremap_insert($node) {
       'foreignkey_name' => 'featuremap_id',
       'foreignkey_value' => $featuremap_id
     );
-    chado_node_properties_form_update_properties($node, $details, $properties);
+    chado_update_node_form_properties($node, $details, $properties);
 
     // * Additional DBxrefs Form *
     $details = array(
@@ -313,7 +313,7 @@ function chado_featuremap_insert($node) {
       'foreignkey_name' => 'featuremap_id',     // the name of the key in your base table
       'foreignkey_value' => $featuremap_id      // the value of the featuremap_id key
     );
-    chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
+    chado_update_node_form_dbxrefs($node, $details);
 
   }
   else {
@@ -322,7 +322,7 @@ function chado_featuremap_insert($node) {
 
   // Make sure the entry for this featuremap doesn't already exist in the
   // chado_featuremap table if it doesn't exist then we want to add it.
-  $check_org_id = chado_get_id_for_node('featuremap', $node->nid);
+  $check_org_id = chado_get_id_from_nid('featuremap', $node->nid);
   if (!$check_org_id) {
     $record = new stdClass();
     $record->nid = $node->nid;
@@ -341,7 +341,7 @@ function chado_featuremap_update($node) {
   $node->fmapname          = trim($node->fmapname);
   $node->description    = trim($node->description);
 
-  $featuremap_id = chado_get_id_for_node('featuremap', $node->nid) ;
+  $featuremap_id = chado_get_id_from_nid('featuremap', $node->nid) ;
 
   // update the map record
   $match = array(
@@ -352,17 +352,17 @@ function chado_featuremap_update($node) {
     'description' => $node->description,
     'unittype_id' => $node->unittype_id
   );
-  $status = tripal_core_chado_update('featuremap', $match, $values);
+  $status = chado_update_record('featuremap', $match, $values);
   if (!$status) {
     drupal_set_message("Error updating map", "error");
-    tripal_core_report_error('t_featuremap', TRIPAL_ERROR, "Error updating map", array());
+    tripal_report_error('t_featuremap', TRIPAL_ERROR, "Error updating map", array());
     return;
   }
 
   // Update the properties
-  $properties = chado_node_properties_form_retreive($node);
+  $properties = chado_retrieve_node_form_properties($node);
   // We need to deal with the 'Map Dbxref' property specially
-  $cvterm = tripal_core_chado_select(
+  $cvterm = chado_select_record(
     'cvterm',
     array('cvterm_id'),
     array('name' => 'Map Dbxref', 'cv_id' => array('name' => 'featuremap_property'))
@@ -373,7 +373,7 @@ function chado_featuremap_update($node) {
       $featuremap_dbxref = tripal_featuremap_add_featuremap_dbxref($featuremap_id, $value);
       if (!$featuremap_dbxref) {
         drupal_set_message("Error cannot add featuremap cross reference: $value", "error");
-        tripal_core_report_error('t_featuremap', TRIPAL_ERROR, "Error cannot add featuremap cross reference: %ref",
+        tripal_report_error('t_featuremap', TRIPAL_ERROR, "Error cannot add featuremap cross reference: %ref",
         array('%ref' => $value));
       }
     }
@@ -385,7 +385,7 @@ function chado_featuremap_update($node) {
     'foreignkey_name' => 'featuremap_id',
     'foreignkey_value' => $featuremap_id
   );
-  chado_node_properties_form_update_properties($node, $details, $properties);
+  chado_update_node_form_properties($node, $details, $properties);
 
   // * Additional DBxrefs Form *
   $details = array(
@@ -393,7 +393,7 @@ function chado_featuremap_update($node) {
     'foreignkey_name' => 'featuremap_id',     // the name of the key in your base table
     'foreignkey_value' => $featuremap_id      // the value of the featuremap_id key
   );
-  chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
+  chado_update_node_form_dbxrefs($node, $details);
 
 }
 /**
@@ -405,13 +405,13 @@ function chado_featuremap_update($node) {
 function chado_featuremap_load($nodes) {
   foreach ($nodes as $nid => $node) {
     // get the feature details from chado
-    $featuremap_id = chado_get_id_for_node('featuremap', $node->nid);
+    $featuremap_id = chado_get_id_from_nid('featuremap', $node->nid);
 
     $values = array('featuremap_id' => $featuremap_id);
-    $featuremap = tripal_core_generate_chado_var('featuremap', $values);
+    $featuremap = chado_generate_var('featuremap', $values);
 
     // expand the description field as it is needed by the form
-    $featuremap = tripal_core_expand_chado_vars($featuremap, 'field', 'featuremap.description');
+    $featuremap = chado_expand_var($featuremap, 'field', 'featuremap.description');
 
     $nodes[$nid]->featuremap = $featuremap;
   }
@@ -423,7 +423,7 @@ function chado_featuremap_load($nodes) {
  */
 function chado_featuremap_delete(&$node) {
 
-  $featuremap_id = chado_get_id_for_node('featuremap', $node->nid);
+  $featuremap_id = chado_get_id_from_nid('featuremap', $node->nid);
 
   // if we don't have a map id for this node then this isn't a node of
   // type chado_featuremap or the entry in the chado_featuremap table was lost.

tripal_featuremap/tripal_featuremap.install

@@ -43,7 +43,7 @@ function tripal_featuremap_requirements($phase) {
  */
 function tripal_featuremap_install() {
   // create the module's data directory
-  tripal_create_moddir('tripal_featuremap');
+  tripal_create_files_dir('tripal_featuremap');
 
   // add the featuremapprop table to Chado
   tripal_featuremap_add_custom_tables();
@@ -303,7 +303,7 @@ function tripal_featuremap_add_custom_tables(){
       ),
     ),
   );
-  tripal_core_create_custom_table('featuremapprop', $schema, TRUE);
+  chado_create_custom_table('featuremapprop', $schema, TRUE);
 
   // add the featuremap_dbxref table to Chado
   $schema = array (
@@ -355,7 +355,7 @@ function tripal_featuremap_add_custom_tables(){
     ),
     'referring_tables' => NULL,
   );
-  tripal_core_create_custom_table('featuremap_dbxref', $schema, TRUE);
+  chado_create_custom_table('featuremap_dbxref', $schema, TRUE);
 
   $schema = array (
     'table' => 'featureposprop',
@@ -415,5 +415,5 @@ function tripal_featuremap_add_custom_tables(){
       ),
     ),
   );
-  tripal_core_create_custom_table('featureposprop', $schema, TRUE);
+  chado_create_custom_table('featureposprop', $schema, TRUE);
 }

tripal_library/api/tripal_library.api.inc

@@ -21,7 +21,7 @@
  * @ingroup tripal_library_api
  */
 function tripal_library_get_property($library_id, $property) {
-  return tripal_core_get_property('library', $library_id, $property, 'library_property');
+  return chado_get_property('library', $library_id, $property, 'library_property');
 }
 
 /**
@@ -42,7 +42,7 @@ function tripal_library_get_property($library_id, $property) {
  * @ingroup tripal_library_api
  */
 function tripal_library_insert_property($library_id, $property, $value, $update_if_present = 0) {
-  return tripal_core_insert_property('library', $library_id, $property, 'library_property', $value, $update_if_present);
+  return chado_insert_property('library', $library_id, $property, 'library_property', $value, $update_if_present);
 }
 
 /**
@@ -66,7 +66,7 @@ function tripal_library_insert_property($library_id, $property, $value, $update_
  * @ingroup tripal_library_api
  */
 function tripal_library_update_property($library_id, $property, $value, $insert_if_missing = 0) {
-  return tripal_core_update_property('library', $library_id, $property, 'library_property', $value, $insert_if_missing);
+  return chado_update_property('library', $library_id, $property, 'library_property', $value, $insert_if_missing);
 }
 /**
  * Delete a given property
@@ -85,5 +85,5 @@ function tripal_library_update_property($library_id, $property, $value, $insert_
  * @ingroup tripal_library_api
  */
 function tripal_library_delete_property($library_id, $property) {
-  return tripal_core_delete_property('library', $library_id, $property, 'library_property');
+  return chado_delete_property('library', $library_id, $property, 'library_property');
 }

tripal_library/includes/tripal_library.chado_node.inc

@@ -120,7 +120,7 @@ function chado_library_form($node, &$form_state) {
   );
   $columns = array('cvterm_id','name');
   $options = array('order_by' => array('name' => 'ASC'));
-  $lib_types = tripal_core_chado_select('cvterm', $columns, $values, $options);
+  $lib_types = chado_select_record('cvterm', $columns, $values, $options);
   $types = array();
   $types[''] = '';
   foreach($lib_types as $type) {
@@ -168,7 +168,7 @@ function chado_library_form($node, &$form_state) {
   //---------------------------------------------
   // Generate our own select list so we can desclude the description since it has it's
   // own form element above
-  $cv_result = tripal_core_chado_select('cv',array('cv_id'),array('name' => 'library_property'));
+  $cv_result = chado_select_record('cv',array('cv_id'),array('name' => 'library_property'));
   $cv_id = $cv_result[0]->cv_id;
   $select_options = tripal_cv_get_cvterm_options($cv_id);
   $descrip_id = array_search('Library Description', $select_options);
@@ -182,7 +182,7 @@ function chado_library_form($node, &$form_state) {
     'select_options' => $select_options
   );
   // Adds the form elements to your current form
-  chado_node_properties_form($form, $form_state, $details);
+  chado_add_node_form_properties($form, $form_state, $details);
 
   // ADDITIONAL DBXREFS FORM
   //---------------------------------------------
@@ -192,7 +192,7 @@ function chado_library_form($node, &$form_state) {
     'base_key_value' => $library_id       // the value of library_id for this record
   );
   // Adds the form elements to your current form
-  chado_node_additional_dbxrefs_form($form, $form_state, $details);
+  chado_add_node_form_dbxrefs($form, $form_state, $details);
 
   return $form;
 }
@@ -249,7 +249,7 @@ function chado_library_insert($node) {
       'organism_id' => $node->organism_id,
       'type_id' => $node->library_type,
     );
-    $library = tripal_core_chado_insert('library', $values);
+    $library = chado_insert_record('library', $values);
     if (!$library) {
       drupal_set_message(t('Unable to add library.', 'warning'));
       watchdog('tripal_library', 'Insert library: Unable to create library where values: %values',
@@ -260,7 +260,7 @@ function chado_library_insert($node) {
 
     // * Properties Form *
     // add the description property
-    $properties = chado_node_properties_form_retreive($node);
+    $properties = chado_retrieve_node_form_properties($node);
     $descrip_id = tripal_cv_get_cvterm_by_name('Library Description', NULL, 'library_property');
     $properties[$descrip_id->cvterm_id][0] = $node->description;
 
@@ -270,7 +270,7 @@ function chado_library_insert($node) {
       'foreignkey_name' => 'library_id',   // the name of the key in your base table
       'foreignkey_value' => $library_id    // the value of the library_id key
     );
-    chado_node_properties_form_update_properties($node, $details, $properties);
+    chado_update_node_form_properties($node, $details, $properties);
 
     // * Additional DBxrefs Form *
     $details = array(
@@ -278,7 +278,7 @@ function chado_library_insert($node) {
       'foreignkey_name' => 'library_id',     // the name of the key in your base table
       'foreignkey_value' => $library_id      // the value of the library_id key
     );
-    chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
+    chado_update_node_form_dbxrefs($node, $details);
 
   }
   else {
@@ -287,7 +287,7 @@ function chado_library_insert($node) {
 
   // Make sure the entry for this library doesn't already exist in the
   // chado_library table if it doesn't exist then we want to add it.
-  $check_org_id = chado_get_id_for_node('library', $node->nid);
+  $check_org_id = chado_get_id_from_nid('library', $node->nid);
   if (!$check_org_id) {
     $record = new stdClass();
     $record->nid = $node->nid;
@@ -308,7 +308,7 @@ function chado_library_update($node) {
   $node->description = trim($node->description);
 
   // update the library record
-  $library_id = chado_get_id_for_node('library', $node->nid);
+  $library_id = chado_get_id_from_nid('library', $node->nid);
   $match = array(
     'library_id' => $library_id,
   );
@@ -319,7 +319,7 @@ function chado_library_update($node) {
     'organism_id' => $node->organism_id,
     'type_id'     => $node->library_type,
   );
-  $status = tripal_core_chado_update('library', $match, $values);
+  $status = chado_update_record('library', $match, $values);
   if (!$status) {
     drupal_set_message(t('Unable to update library.', 'warning'));
     watchdog('tripal_library', 'Update library: Unable to update library where values: %values',
@@ -328,7 +328,7 @@ function chado_library_update($node) {
 
   // * Properties Form *
   // add the description property
-  $properties = chado_node_properties_form_retreive($node);
+  $properties = chado_retrieve_node_form_properties($node);
   $descrip_id = tripal_cv_get_cvterm_by_name('Library Description', NULL, 'library_property');
   $properties[$descrip_id->cvterm_id][0] = $node->description;
 
@@ -338,7 +338,7 @@ function chado_library_update($node) {
     'foreignkey_name' => 'library_id',   // the name of the key in your base table
     'foreignkey_value' => $library_id    // the value of the library_id key
   );
-  chado_node_properties_form_update_properties($node, $details, $properties);
+  chado_update_node_form_properties($node, $details, $properties);
 
   // * Additional DBxrefs Form *
   $details = array(
@@ -346,7 +346,7 @@ function chado_library_update($node) {
     'foreignkey_name' => 'library_id',     // the name of the key in your base table
     'foreignkey_value' => $library_id      // the value of the library_id key
   );
-  chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
+  chado_update_node_form_dbxrefs($node, $details);
 
 }
 /**
@@ -359,13 +359,13 @@ function chado_library_load($nodes) {
 
   foreach ($nodes as $nid => $node) {
     // get the feature details from chado
-    $library_id = chado_get_id_for_node('library', $node->nid);
+    $library_id = chado_get_id_from_nid('library', $node->nid);
 
     $values = array('library_id' => $library_id);
-    $library = tripal_core_generate_chado_var('library', $values);
+    $library = chado_generate_var('library', $values);
 
     // the uniquename field is a text field so we need to expand it
-    $library = tripal_core_expand_chado_vars($library, 'field', 'library.uniquename');
+    $library = chado_expand_var($library, 'field', 'library.uniquename');
 
     $nodes[$nid]->library = $library;
   }
@@ -377,7 +377,7 @@ function chado_library_load($nodes) {
  */
 function chado_library_delete(&$node) {
 
-  $library_id = chado_get_id_for_node('library', $node->nid);
+  $library_id = chado_get_id_from_nid('library', $node->nid);
 
   // if we don't have a library id for this node then this isn't a node of
   // type chado_library or the entry in the chado_library table was lost.

tripal_library/tripal_library.install

@@ -43,7 +43,7 @@ function tripal_library_requirements($phase) {
 function tripal_library_install() {
 
   // create the module's data directory
-  tripal_create_moddir('tripal_library');
+  tripal_create_files_dir('tripal_library');
 
   // add the materialized view
   tripal_library_add_mview_library_feature_count();
@@ -237,7 +237,7 @@ function tripal_library_update_7000() {
   $values = array(
     'name' => 'library_type'
   );
-  $success = tripal_core_chado_update('cv', $match, $values);
+  $success = chado_update_record('cv', $match, $values);
   if (!$success) {
     throw new DrupalUpdateException('Failed to rename tripal_library_types CV.');
   }
@@ -257,7 +257,7 @@ function tripal_library_update_7000() {
     'cv_id' => $cv->cv_id,
     'name' => 'Library Description',
   );
-  tripal_core_chado_update('cvterm', $match, $values);
+  chado_update_record('cvterm', $match, $values);
   if (!$success) {
     throw new DrupalUpdateException('Failed to move library properties to new library_property CV.');
   }

tripal_natural_diversity/tripal_natural_diversity.install

@@ -42,7 +42,7 @@ function tripal_natural_diversity_requirements($phase) {
 function tripal_natural_diversity_install() {
 
   // create the module's data directory
-  tripal_create_moddir('tripal_natural_diversity');
+  tripal_create_files_dir('tripal_natural_diversity');
 
   // add cvterms
   tripal_natural_diversity_add_cvterms();

tripal_organism/api/tripal_organism.api.inc

@@ -81,7 +81,7 @@ function tripal_organism_get_image_url($organism, $nid = NULL) {
   // then look for the image with the node ID in the name. If we don't find that then
   // no image tag is generated
   $base_path = realpath('.');
-  $image_dir = tripal_get_moddir('tripal_organism') . "/images";
+  $image_dir = tripal_get_files_dir('tripal_organism') . "/images";
   $image_name =  $organism->genus . "_" . $organism->species . ".jpg";
 
   if (file_exists("$base_path/$image_dir/$image_name")) {

tripal_organism/includes/tripal_organism.admin.inc

@@ -124,7 +124,7 @@ function tripal_organism_reindex_features($organism_id = NULL, $job_id = NULL) {
   foreach ($ids as $feature_id) {
     // update the job status every 1% features
     if ($job_id and $i % $interval == 0) {
-      tripal_job_set_progress($job_id , intval(($i/$count)*100));
+      tripal_set_job_progress($job_id , intval(($i/$count)*100));
     }
     $i++;
   }
@@ -169,7 +169,7 @@ function tripal_organism_taxonify_features($organism_id = NULL, $job_id = NULL)
   foreach ($ids as $feature_id) {
     // update the job status every 1% features
     if ($job_id and $i % $interval == 0) {
-      tripal_job_set_progress($job_id, intval(($i/$count)*100));
+      tripal_set_job_progress($job_id, intval(($i/$count)*100));
     }
     $node = db_query($nsql, array(':feature_id' => $feature_id))->fetchObject();
     tripal_feature_set_taxonomy($node, $feature_id);

tripal_organism/includes/tripal_organism.chado_node.inc

@@ -122,7 +122,7 @@ function chado_organism_validate($node, $form, &$form_state) {
     if ($result) {
       form_set_error('genus', t("Update cannot proceed. The organism genus
         '$node->genus' and species '$node->species' is already present in the database."));
-      tripal_core_report_error('tripal_organism', TRIPAL_WARNING,
+      tripal_report_error('tripal_organism', TRIPAL_WARNING,
         'Update organism: genus and species already exists: %values',
         array('%values' => "genus = $node->genus, species = $node->species"));
     }
@@ -133,11 +133,11 @@ function chado_organism_validate($node, $form, &$form_state) {
       'genus' => $node->genus,
       'species' => $node->species,
     );
-    $organism = tripal_core_chado_select('organism', array('organism_id'), $values);
+    $organism = chado_select_record('organism', array('organism_id'), $values);
     if (sizeof($organism) > 0) {
       form_set_error('genus', 'Cannot add the organism with this genus and species.
         The organism already exists.');
-      tripal_core_report_error('tripal_organism', TRIPAL_WARNING,
+      tripal_report_error('tripal_organism', TRIPAL_WARNING,
         'Insert organism: genus and species already exists: %values',
         array('%values' => "genus = $node->genus, species = $node->species"));
     }
@@ -169,10 +169,10 @@ function chado_organism_insert($node) {
       'common_name'  => $node->common_name,
       'comment'      => $node->description
     );
-    $organism = tripal_core_chado_insert('organism', $values);
+    $organism = chado_insert_record('organism', $values);
     if (!$organism) {
       drupal_set_message(t('Unable to add organism.', 'warning'));
-      tripal_core_report_error('tripal_organism', TRIPAL_ERROR, 'Insert Organism: Unable to create organism where values:%values',
+      tripal_report_error('tripal_organism', TRIPAL_ERROR, 'Insert Organism: Unable to create organism where values:%values',
       array('%values' => print_r($values, TRUE)));
       return;
     }
@@ -186,7 +186,7 @@ function chado_organism_insert($node) {
         'foreignkey_name' => 'organism_id',   // the name of the key in your base table
         'foreignkey_value' => $organism_id    // the value of the example_id key
       );
-      chado_node_properties_form_update_properties($node, $details);
+      chado_update_node_form_properties($node, $details);
 
       // * Additional DBxrefs Form *
       $details = array(
@@ -194,7 +194,7 @@ function chado_organism_insert($node) {
         'foreignkey_name' => 'organism_id',     // the name of the key in your base table
         'foreignkey_value' => $organism_id      // the value of the organism_id key
       );
-      chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
+      chado_update_node_form_dbxrefs($node, $details);
 
     }
   }
@@ -204,7 +204,7 @@ function chado_organism_insert($node) {
 
   // Make sure the entry for this organism doesn't already exist in the
   // chado_organism table if it doesn't exist then we want to add it.
-  $check_org_id = chado_get_id_for_node('organism', $node->nid);
+  $check_org_id = chado_get_id_from_nid('organism', $node->nid);
   if (!$check_org_id) {
     $record = new stdClass();
     $record->nid = $node->nid;
@@ -229,7 +229,7 @@ function chado_organism_update($node) {
   $node->common_name  = trim($node->common_name);
   $node->description  = trim($node->description);
 
-  $organism_id = chado_get_id_for_node('organism', $node->nid);
+  $organism_id = chado_get_id_from_nid('organism', $node->nid);
 
   if ($node->revision) {
     // there is no way to handle revisions in Chado but leave
@@ -245,7 +245,7 @@ function chado_organism_update($node) {
     'common_name' => $node->common_name,
     'comment' => $node->description
   );
-  $org_status = tripal_core_chado_update('organism', $match, $values);
+  $org_status = chado_update_record('organism', $match, $values);
 
   // add the image
   chado_organism_add_image($node);
@@ -257,7 +257,7 @@ function chado_organism_update($node) {
     'foreignkey_name' => 'organism_id',   // the name of the key in your base table
     'foreignkey_value' => $organism_id    // the value of the example_id key
   );
-  chado_node_properties_form_update_properties($node, $details);
+  chado_update_node_form_properties($node, $details);
 
   // * Additional DBxrefs Form *
   $details = array(
@@ -265,7 +265,7 @@ function chado_organism_update($node) {
     'foreignkey_name' => 'organism_id',     // the name of the key in your base table
     'foreignkey_value' => $organism_id      // the value of the organism_id key
   );
-  chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
+  chado_update_node_form_dbxrefs($node, $details);
 }
 /**
  * Delete organism from both drupal and chado databases. Check dependency before
@@ -274,7 +274,7 @@ function chado_organism_update($node) {
  * @ingroup tripal_organism
  */
 function chado_organism_delete($node) {
-  $organism_id = chado_get_id_for_node('organism', $node->nid);
+  $organism_id = chado_get_id_from_nid('organism', $node->nid);
 
   // if we don't have an organism id for this node then this isn't a node of
   // type chado_organism or the entry in the chado_organism table was lost.
@@ -301,7 +301,7 @@ function chado_organism_delete($node) {
   $check_stock = chado_query($sql, array(':organism_id' => $organism_id))->fetchObject();
 
   if (!$check_lib && !$check_feature && !$check_stock) {
-    tripal_core_chado_delete('organism', array('organism_id' => $organism_id));
+    chado_delete_record('organism', array('organism_id' => $organism_id));
   }
   else {
     drupal_set_message(t("Warning: other data depends on this organism. The organism page was removed from this site but the organism was removed from Chado."), 'warning');
@@ -321,7 +321,7 @@ function chado_organism_add_image($node) {
   is_uploaded_file($_FILES['files']['tmp_name']['organism_image'])) {
 
     // make sure the destination directory exists
-    $dest = tripal_file_directory_path() . "/tripal_organism/images";
+    $dest = tripal_get_files_dir() . "/tripal_organism/images";
     file_prepare_directory($dest, FILE_CREATE_DIRECTORY);
 
     // now move the file
@@ -355,7 +355,7 @@ function chado_organism_form($node, $form_state) {
     $organism = $node->organism;
 
     // add in the comment since it is a text field and may not be included if too big
-    $organism = tripal_core_expand_chado_vars($organism, 'field', 'organism.comment');
+    $organism = chado_expand_var($organism, 'field', 'organism.comment');
 
     // get form defaults
     $abbreviation   = property_exists($node, 'abbreviation')   ? property_exists($node, 'abbreviation')   : $organism->abbreviation;
@@ -430,7 +430,7 @@ function chado_organism_form($node, $form_state) {
     'cv_name' => 'organism_property'         // the cv.name of the cv governing organismprop.type_id
   );
   // Adds the form elements to your current form
-  chado_node_properties_form($form, $form_state, $details);
+  chado_add_node_form_properties($form, $form_state, $details);
 
   // ADDITIONAL DBXREFS FORM
   //---------------------------------------------
@@ -440,7 +440,7 @@ function chado_organism_form($node, $form_state) {
     'base_key_value' => $organism_id       // the value of organism_id for this record
   );
   // Adds the form elements to your current form
-  chado_node_additional_dbxrefs_form($form, $form_state, $details);
+  chado_add_node_form_dbxrefs($form, $form_state, $details);
 
   return $form;
 }
@@ -455,15 +455,15 @@ function chado_organism_load($nodes) {
 
   foreach ($nodes as $nid => $node) {
     // find the organism and add in the details
-    $organism_id = chado_get_id_for_node('organism', $nid);
+    $organism_id = chado_get_id_from_nid('organism', $nid);
 
     // build the organism variable
     $values = array('organism_id' => $organism_id);
-    $organism = tripal_core_generate_chado_var('organism', $values);
+    $organism = chado_generate_var('organism', $values);
 
 
     // add in the description field
-    $organism = tripal_core_expand_chado_vars($organism, 'field', 'organism.comment');
+    $organism = chado_expand_var($organism, 'field', 'organism.comment');
     $nodes[$nid]->organism = $organism;
   }
 }
@@ -473,6 +473,7 @@ function chado_organism_load($nodes) {
  * @param $node
  */
 function tripal_organism_node_presave($node) {
+ print_r($node->organism);
   switch ($node->type) {
     case 'chado_organism':
       // for a form submission the 'genus' field will be set,

tripal_organism/tripal_organism.install

@@ -27,10 +27,10 @@ function tripal_organism_disable() {
 function tripal_organism_install() {
 
   // create the module's data directory
-  tripal_create_moddir('tripal_organism');
+  tripal_create_files_dir('tripal_organism');
 
   // create the directory where image files will be stored.  We create this
-  tripal_create_mod_subdir('tripal_organism', '/images');
+  tripal_create_files_dir('tripal_organism', '/images');
 
   // cvs & cvterms
   tripal_organism_add_cvs();

tripal_organism/tripal_organism.module

@@ -226,7 +226,7 @@ function tripal_organism_job_describe_args($callback, $args) {
 
   $new_args = array();
   if ($callback == 'tripal_organism_sync_organisms') {
-    $organism = tripal_core_chado_select('organism', array('genus', 'species'), array('organism_id' => $args[0]));
+    $organism = chado_select_record('organism', array('genus', 'species'), array('organism_id' => $args[0]));
     $new_args['Organism'] = $organism[0]->genus . " " . $organism[0]->species;
   }
   return $new_args;

tripal_project/api/tripal_project.api.inc

@@ -26,7 +26,7 @@
  * @ingroup tripal_project_api
  */
 function tripal_project_get_property($project_id, $property) {
-  return tripal_core_get_property('project', $project_id, $property, 'project_property');
+  return chado_get_property('project', $project_id, $property, 'project_property');
 }
 
 /**
@@ -47,7 +47,7 @@ function tripal_project_get_property($project_id, $property) {
  * @ingroup tripal_project_api
  */
 function tripal_project_insert_property($project_id, $property, $value, $update_if_present = 0) {
-  return tripal_core_insert_property('project', $project_id, $property, 'project_property', $value, $update_if_present);
+  return chado_insert_property('project', $project_id, $property, 'project_property', $value, $update_if_present);
 }
 
 /**
@@ -71,7 +71,7 @@ function tripal_project_insert_property($project_id, $property, $value, $update_
  * @ingroup tripal_project_api
  */
 function tripal_project_update_property($project_id, $property, $value, $insert_if_missing = 0) {
-  return tripal_core_update_property('project', $project_id, $property, 'project_property', $value, $insert_if_missing);
+  return chado_update_property('project', $project_id, $property, 'project_property', $value, $insert_if_missing);
 }
 /**
  * Delete a given property
@@ -90,5 +90,5 @@ function tripal_project_update_property($project_id, $property, $value, $insert_
  * @ingroup tripal_project_api
  */
 function tripal_project_delete_property($project_id, $property) {
-  return tripal_core_delete_property('project', $project_id, $property, 'project_property');
+  return chado_delete_property('project', $project_id, $property, 'project_property');
 }

tripal_project/includes/tripal_project.chado_node.inc

@@ -139,7 +139,7 @@ function chado_project_form(&$node, $form_state) {
   // because we want to use the property to replace the project.description field as it is
   // only 255 characters which isn't large enough. We don't want the user to set it
   // as a property even though it will be stored as a property.
-  $cv_result = tripal_core_chado_select('cv',array('cv_id'),array('name' => 'project_property'));
+  $cv_result = chado_select_record('cv',array('cv_id'),array('name' => 'project_property'));
   $cv_id = $cv_result[0]->cv_id;
   $select_options = tripal_cv_get_cvterm_options($cv_id);
   $descrip_id = array_search('Project Description', $select_options);
@@ -154,17 +154,17 @@ function chado_project_form(&$node, $form_state) {
     'additional_instructions' => $instructions,
     'select_options' => $select_options
   );
-  chado_node_properties_form($form, $form_state, $details);
+  chado_add_node_form_properties($form, $form_state, $details);
 
   // RELATIONSHIPS FORM
   //---------------------------------------------
   // We want to use the contact_relationship_types cv if there are any terms available
   // and if not, to default to the relationship ontology
-  $cv_result = tripal_core_chado_select('cv',array('cv_id'),array('name' => 'project_relationship_types'));
+  $cv_result = chado_select_record('cv',array('cv_id'),array('name' => 'project_relationship_types'));
   $cv_id = $cv_result[0]->cv_id;
   $select_options = tripal_cv_get_cvterm_options($cv_id);
   if (empty($select_options)) {
-    $cv_result = tripal_core_chado_select('cv',array('cv_id'),array('name' => 'relationship'));
+    $cv_result = chado_select_record('cv',array('cv_id'),array('name' => 'relationship'));
     $cv_id = $cv_result[0]->cv_id;
     $select_options = tripal_cv_get_cvterm_options($cv_id);
   }
@@ -183,7 +183,7 @@ function chado_project_form(&$node, $form_state) {
     'select_options' => $select_options
   );
   // Adds the form elements to your current form
-  chado_node_relationships_form($form, $form_state, $details);
+  chado_add_node_form_relationships($form, $form_state, $details);
 
   return $form;
 
@@ -246,7 +246,7 @@ function chado_project_insert($node) {
       'name' => $node->title,
       'description' => '',
     );
-    $project = tripal_core_chado_insert('project', $values);
+    $project = chado_insert_record('project', $values);
     if (!$project) {
       drupal_set_message(t('Unable to add project.', 'warning'));
       watchdog('tripal_project', 'Insert project: Unable to create project where values:%values',
@@ -257,7 +257,7 @@ function chado_project_insert($node) {
 
     // * Properties Form *
     // Add the description property
-    $properties = chado_node_properties_form_retreive($node);
+    $properties = chado_retrieve_node_form_properties($node);
     $descrip_id = tripal_cv_get_cvterm_by_name('Project Description', NULL, 'project_property');
     $properties[$descrip_id->cvterm_id][0] = $node->description;
 
@@ -267,14 +267,14 @@ function chado_project_insert($node) {
       'foreignkey_name' => 'project_id',
       'foreignkey_value' => $project_id
     );
-    chado_node_properties_form_update_properties($node, $details, $properties);
+    chado_update_node_form_properties($node, $details, $properties);
 
     // * Relationships Form *
     $details = array(
       'relationship_table' => 'project_relationship',  // name of the _relationship table
       'foreignkey_value' => $project_id                // value of the example_id key
     );
-    chado_node_relationships_form_update_relationships($node, $details);
+    chado_update_node_form_relationships($node, $details);
 
   }
   else {
@@ -283,7 +283,7 @@ function chado_project_insert($node) {
 
   // Make sure the entry for this project doesn't already exist in the
   // chado_project table if it doesn't exist then we want to add it.
-  $check_org_id = chado_get_id_for_node('project', $node->nid);
+  $check_org_id = chado_get_id_from_nid('project', $node->nid);
   if (!$check_org_id) {
     $record = new stdClass();
     $record->nid = $node->nid;
@@ -306,7 +306,7 @@ function chado_project_insert($node) {
  */
 function chado_project_delete($node) {
 
-  $project_id = chado_get_id_for_node('project', $node->nid);
+  $project_id = chado_get_id_from_nid('project', $node->nid);
 
   // if we don't have a project id for this node then this isn't a node of
   // type chado_project or the entry in the chado_project table was lost.
@@ -344,13 +344,13 @@ function chado_project_update($node) {
   $node->description = trim($node->description);
 
   // update the project and the description
-  $project_id = chado_get_id_for_node('project', $node->nid) ;
+  $project_id = chado_get_id_from_nid('project', $node->nid) ;
   $match = array('project_id' => $project_id);
   $values = array(
     'name' => $node->title,
     'description' => '',
   );
-  $status = tripal_core_chado_update('project', $match, $values);
+  $status = chado_update_record('project', $match, $values);
   if (!$status) {
     drupal_set_message(t('Unable to update project.', 'warning'));
     watchdog('tripal_project', 'Update project: Unable to update project where values: %values',
@@ -359,7 +359,7 @@ function chado_project_update($node) {
 
   // * Properties Form *
   // Add the description property
-  $properties = chado_node_properties_form_retreive($node);
+  $properties = chado_retrieve_node_form_properties($node);
   $descrip_id = tripal_cv_get_cvterm_by_name('Project Description', NULL, 'project_property');
   $properties[$descrip_id->cvterm_id][0] = $node->description;
 
@@ -369,14 +369,14 @@ function chado_project_update($node) {
     'foreignkey_name' => 'project_id',
     'foreignkey_value' => $project_id
   );
-  chado_node_properties_form_update_properties($node, $details, $properties);
+  chado_update_node_form_properties($node, $details, $properties);
 
   // * Relationships Form *
   $details = array(
     'relationship_table' => 'project_relationship',  // name of the _relationship table
     'foreignkey_value' => $project_id                // value of the example_id key
   );
-  chado_node_relationships_form_update_relationships($node, $details);
+  chado_update_node_form_relationships($node, $details);
 }
 
 /**
@@ -395,10 +395,10 @@ function chado_project_load($nodes) {
 
   foreach ($nodes as $nid => $node) {
     // get the feature details from chado
-    $project_id = chado_get_id_for_node('project', $node->nid);
+    $project_id = chado_get_id_from_nid('project', $node->nid);
 
     $values = array('project_id' => $project_id);
-    $project = tripal_core_generate_chado_var('project', $values);
+    $project = chado_generate_var('project', $values);
 
     $nodes[$nid]->project = $project;
   }

tripal_project/theme/tripal_project.theme.inc

@@ -18,7 +18,7 @@ function tripal_project_preprocess_tripal_project_relationships(&$variables) {
       'subject_project_id' => 1,
     ),
   );
-  $project = tripal_core_expand_chado_vars($project, 'table', 'project_relationship', $options);
+  $project = chado_expand_var($project, 'table', 'project_relationship', $options);
   
   // get the subject relationships
   $srelationships = $project->project_relationship->subject_project_id;

tripal_project/tripal_project.install

@@ -48,7 +48,7 @@ function tripal_project_requirements($phase) {
 function tripal_project_install() {
 
   // create the module's data directory
-  tripal_create_moddir('tripal_project');
+  tripal_create_files_dir('tripal_project');
 
   tripal_project_add_cvs();
   tripal_project_add_cvterms();
@@ -149,7 +149,7 @@ function tripal_project_update_7000() {
   $values = array(
     'name'  => 'Project Description',
   );
-  tripal_core_chado_update('cvterm', $match, $values);
+  chado_update_record('cvterm', $match, $values);
   if (!$success) {
     throw new DrupalUpdateException('Failed to move project properties to new project_property CV.');
   }

tripal_pub/api/tripal_pub.api.inc

@@ -232,7 +232,7 @@ function tripal_pub_import_publications_by_import_id($import_id, $job_id = NULL)
       print "Syncing contacts with Drupal...\n";
       tripal_contact_sync_contacts();
     }
-    tripal_job_set_progress($job_id, '100');
+    tripal_set_job_progress($job_id, '100');
   }
   catch (Exception $e) {
     print "\n"; // make sure we start errors on new line
@@ -466,7 +466,7 @@ function tripal_pub_add_pub_dbxref($pub_id, $pub_dbxref) {
     'pub_id' => $pub_id,
   );
   $options = array('statement_name' => 'sel_pubdbxref_dbpu');
-  $results = tripal_core_chado_select('pub_dbxref', array('*'), $values, $options);
+  $results = chado_select_record('pub_dbxref', array('*'), $values, $options);
 
   // if the pub_dbxref record  exist then we don't need to re-add it.
   if(count($results) > 0) {
@@ -482,7 +482,7 @@ function tripal_pub_add_pub_dbxref($pub_id, $pub_dbxref) {
     'db_id' => $db->db_id,
   );
   $dbxoptions = array('statement_name' => 'sel_dbxref_acdb');
-  $results = tripal_core_chado_select('dbxref', array('dbxref_id'), $dbxvalues, $dbxoptions);
+  $results = chado_select_record('dbxref', array('dbxref_id'), $dbxvalues, $dbxoptions);
   // if the accession doesn't exist then add it
   if(count($results) == 0){
     $dbxref = tripal_db_add_dbxref($db->db_id, $accession);
@@ -493,9 +493,9 @@ function tripal_pub_add_pub_dbxref($pub_id, $pub_dbxref) {
 
   // now add the record
   $options = array('statement_name' => 'ins_pubdbxref_dbpu');
-  $results = tripal_core_chado_insert('pub_dbxref', $values, $options);
+  $results = chado_insert_record('pub_dbxref', $values, $options);
   if (!$results) {
-    tripal_core_report_error('tripal_pub', TRIPAL_ERROR, "Cannot add publication dbxref: %db:%accession.",
+    tripal_report_error('tripal_pub', TRIPAL_ERROR, "Cannot add publication dbxref: %db:%accession.",
     array('%db' => $dbname, '%accession' => $accession));
     return FALSE;
   }
@@ -535,7 +535,7 @@ function tripal_pub_get_pubs_by_dbxref($pub_dbxref) {
     ),
     );
     $options = array('statement_name' => 'sel_pubdbxref_db');
-    $results = tripal_core_chado_select('pub_dbxref', array('pub_id'), $values, $options);
+    $results = chado_select_record('pub_dbxref', array('pub_id'), $values, $options);
     foreach ($results as $index => $pub) {
       $return[] = $pub->pub_id;
     }
@@ -593,7 +593,7 @@ function tripal_pub_get_pubs_by_title_type_pyear_series($title, $type = NULL, $p
     'statement_name' => 'sel_pub_' . $stmnt_suffix,
     'case_insensitive_columns' => array('title', 'series_name'),
   );
-  $results = tripal_core_chado_select('pub', array('pub_id'), $values, $options);
+  $results = chado_select_record('pub', array('pub_id'), $values, $options);
 
   // iterate through any matches and pull out the pub_id
   foreach ($results as $index => $pub) {
@@ -634,7 +634,7 @@ function tripal_pub_get_pub_by_uniquename($name) {
     'statement_name' => 'sel_pub_un',
     'case_insensitive_columns' => array('uniquename'),
   );
-  $results = tripal_core_chado_select('pub', array('pub_id'), $values, $options);
+  $results = chado_select_record('pub', array('pub_id'), $values, $options);
 
   // iterate through any matches and pull out the pub_id
   foreach ($results as $index => $pub) {
@@ -692,7 +692,7 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
       }
     }
     elseif (count($results) > 1) {
-      tripal_core_report_error('tripal_pub', TRIPAL_ERROR, "There are two publications with this accession: %db:%accession. Cannot determine which to update.",
+      tripal_report_error('tripal_pub', TRIPAL_ERROR, "There are two publications with this accession: %db:%accession. Cannot determine which to update.",
       array('%db' => $dbname, '%accession' => $accession));
       $action = 'error';
       return FALSE;
@@ -708,7 +708,7 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
     if (count($results) == 1) {
       $pub_id = $results[0];
       if ($pub_id and !$update_if_exists) {
-        tripal_core_report_error('tripal_pub', TRIPAL_WARNING, "The publication with the same title, type and year already exists. Skipping. ".
+        tripal_report_error('tripal_pub', TRIPAL_WARNING, "The publication with the same title, type and year already exists. Skipping. ".
           " Title: '%title'. Type: '%type'. Year: '%year'",
           array('%title' => $pub_details['Title'], '%type' => $pub_details['Publication Type'], '%year' => $pub_details['Year']));
         $action = 'skipped';
@@ -716,7 +716,7 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
       }
     }
     elseif (count($results) > 1) {
-      tripal_core_report_error('tripal_pub', TRIPAL_ERROR, "The publication with the same title, type and year is present multiple times. Cannot ".
+      tripal_report_error('tripal_pub', TRIPAL_ERROR, "The publication with the same title, type and year is present multiple times. Cannot ".
         "determine which to use.  Title: '%title'. Type: '%type'. Year: '%year'",
       array('%title' => $pub_details['Title'], '%type' => $pub_details['Publication Type'], '%year' => $pub_details['Year']));
       $action = 'error';
@@ -733,12 +733,12 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
     }
   }
   else {
-    tripal_core_report_error('tripal_pub', TRIPAL_ERROR, "The Publication Type is a required property but is missing", array());
+    tripal_report_error('tripal_pub', TRIPAL_ERROR, "The Publication Type is a required property but is missing", array());
     $action = 'error';
     return FALSE;
   }
   if (!$pub_type) {
-    tripal_core_report_error('tripal_pub', TRIPAL_ERROR, "Cannot find publication type: '%type'",
+    tripal_report_error('tripal_pub', TRIPAL_ERROR, "Cannot find publication type: '%type'",
     array('%type' => $pub_details['Publication Type'][0]));
     $action = 'error';
     return FALSE;
@@ -759,9 +759,9 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
   // if there is no pub_id then we need to do an insert.
   if (!$pub_id) {
     $options = array('statement_name' => 'ins_pub_tivoseispypaunty');
-    $pub = tripal_core_chado_insert('pub', $values, $options);
+    $pub = chado_insert_record('pub', $values, $options);
     if (!$pub) {
-      tripal_core_report_error('tripal_pub', TRIPAL_ERROR, "Cannot insert the publication with title: %title",
+      tripal_report_error('tripal_pub', TRIPAL_ERROR, "Cannot insert the publication with title: %title",
       array('%title' => $pub_details['Title']));
       $action = 'error';
       return FALSE;
@@ -774,9 +774,9 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
   if ($pub_id and $update_if_exists) {
     $match = array('pub_id' => $pub_id);
     $options = array('statement_name' => 'up_pub_tivoseispypaunty');
-    $success = tripal_core_chado_update('pub', $match, $values, $options);
+    $success = chado_update_record('pub', $match, $values, $options);
     if (!$success) {
-      tripal_core_report_error('tripal_pub', TRIPAL_ERROR, "Cannot update the publication with title: %title",
+      tripal_report_error('tripal_pub', TRIPAL_ERROR, "Cannot update the publication with title: %title",
       array('%title' => $pub_details['Title']));
       $action = 'error';
       return FALSE;
@@ -812,7 +812,7 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
       $cvterm = tripal_cv_get_cvterm_by_synonym($key, NULL, 'tripal_pub');
     }
     if (!$cvterm) {
-      tripal_core_report_error('tripal_pub', TRIPAL_ERROR, "Cannot find term: '%prop'. Skipping.", array('%prop' => $key));
+      tripal_report_error('tripal_pub', TRIPAL_ERROR, "Cannot find term: '%prop'. Skipping.", array('%prop' => $key));
       continue;
     }
 
@@ -832,18 +832,18 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
         // if the key is an integer then this array is a simple list and
         // we will insert using the primary key. Otheriwse, use the new key
         if(is_int($subkey)) {
-          $success = tripal_core_insert_property('pub', $pub_id, $key, 'tripal_pub', $subvalue, FALSE);
+          $success = chado_insert_property('pub', $pub_id, $key, 'tripal_pub', $subvalue, FALSE);
         }
         else {
-          $success = tripal_core_insert_property('pub', $pub_id, $subkey, 'tripal_pub', $subvalue, FALSE);
+          $success = chado_insert_property('pub', $pub_id, $subkey, 'tripal_pub', $subvalue, FALSE);
         }
       }
     }
     else {
-      $success = tripal_core_insert_property('pub', $pub_id, $key, 'tripal_pub', $value, TRUE);
+      $success = chado_insert_property('pub', $pub_id, $key, 'tripal_pub', $value, TRUE);
     }
     if (!$success) {
-      tripal_core_report_error('tripal_pub', TRIPAL_ERROR, "Cannot add property '%prop' to publication. Skipping.",
+      tripal_report_error('tripal_pub', TRIPAL_ERROR, "Cannot add property '%prop' to publication. Skipping.",
       array('%prop' => $key));
       continue;
     }
@@ -899,7 +899,7 @@ function tripal_pub_add_authors($pub_id, $authors, $do_contact) {
       'suffix' => $author['Suffix'],
     );
     $options = array('statement_name' => 'ins_pubauthor_idrasugisu');
-    $pubauthor = tripal_core_chado_insert('pubauthor', $values, $options);
+    $pubauthor = chado_insert_record('pubauthor', $values, $options);
 
     // if the user wants us to create a contact for each author then do it.
     if ($do_contact) {
@@ -916,9 +916,9 @@ function tripal_pub_add_authors($pub_id, $authors, $do_contact) {
           'contact_id' => $contact['contact_id'],
         );
         $options = array('statement_name' => 'ins_pubauthorcontact_puco');
-        $pubauthor_contact = tripal_core_chado_insert('pubauthor_contact', $values, $options);
+        $pubauthor_contact = chado_insert_record('pubauthor_contact', $values, $options);
         if (!$pubauthor_contact) {
-          tripal_core_report_error('tripal_pub', TRIPAL_ERROR, "Cannot link pub authro and contact.", array());
+          tripal_report_error('tripal_pub', TRIPAL_ERROR, "Cannot link pub authro and contact.", array());
         }
       }
     }
@@ -940,7 +940,7 @@ function tripal_pub_add_authors($pub_id, $authors, $do_contact) {
  * @ingroup tripal_pub_api
  */
 function tripal_pub_get_property($pub_id, $property) {
-  return tripal_core_get_property('pub', $pub_id, $property, 'tripal_pub');
+  return chado_get_property('pub', $pub_id, $property, 'tripal_pub');
 }
 
 /**
@@ -961,7 +961,7 @@ function tripal_pub_get_property($pub_id, $property) {
  * @ingroup tripal_pub_api
  */
 function tripal_pub_insert_property($pub_id, $property, $value, $update_if_present = 0) {
-  return tripal_core_insert_property('pub', $pub_id, $property, 'tripal_pub', $value, $update_if_present);
+  return chado_insert_property('pub', $pub_id, $property, 'tripal_pub', $value, $update_if_present);
 }
 
 /**
@@ -985,7 +985,7 @@ function tripal_pub_insert_property($pub_id, $property, $value, $update_if_prese
  * @ingroup tripal_pub_api
  */
 function tripal_pub_update_property($pub_id, $property, $value, $insert_if_missing = 0) {
-  return tripal_core_update_property('pub', $pub_id, $property, 'tripal_pub', $value, $insert_if_missing);
+  return chado_update_property('pub', $pub_id, $property, 'tripal_pub', $value, $insert_if_missing);
 }
 /**
  * Delete a given property
@@ -1004,7 +1004,7 @@ function tripal_pub_update_property($pub_id, $property, $value, $insert_if_missi
  * @ingroup tripal_pub_api
  */
 function tripal_pub_delete_property($pub_id, $property) {
-  return tripal_core_delete_property('pub', $pub_id, $property, 'tripal_pub');
+  return chado_delete_property('pub', $pub_id, $property, 'tripal_pub');
 }
 
 
@@ -1034,12 +1034,12 @@ function tripal_pub_get_publication_array($pub_id, $skip_existing = TRUE) {
   // get the publication
   // ---------------------------------
   $values = array('pub_id' => $pub_id);
-  $pub = tripal_core_generate_chado_var('pub', $values);
+  $pub = chado_generate_var('pub', $values);
 
   // expand the title
-  $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.title');
-  $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.volumetitle');
-  $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.uniquename');
+  $pub = chado_expand_var($pub, 'field', 'pub.title');
+  $pub = chado_expand_var($pub, 'field', 'pub.volumetitle');
+  $pub = chado_expand_var($pub, 'field', 'pub.uniquename');
   $pub_array = array();
   if (trim($pub->title)) {
     $pub_array['Title'] = $pub->title;
@@ -1079,11 +1079,11 @@ function tripal_pub_get_publication_array($pub_id, $skip_existing = TRUE) {
       'name' => 'Citation',
     ),
   );
-  $citation = tripal_core_generate_chado_var('pubprop', $values);
+  $citation = chado_generate_var('pubprop', $values);
   if ($citation) {
-    $citation = tripal_core_expand_chado_vars($citation, 'field', 'pubprop.value', $options);
+    $citation = chado_expand_var($citation, 'field', 'pubprop.value', $options);
     if (count($citation) > 1) {
-      tripal_core_report_error('tripal_pub', TRIPAL_ERROR, "Publication has multiple citations already: %pub_id",
+      tripal_report_error('tripal_pub', TRIPAL_ERROR, "Publication has multiple citations already: %pub_id",
       array('%pub_id' => $pubid));
       return FALSE;
     }
@@ -1102,9 +1102,9 @@ function tripal_pub_get_publication_array($pub_id, $skip_existing = TRUE) {
       'name' => 'Publication Type',
     ),
   );
-  $ptypes = tripal_core_generate_chado_var('pubprop', $values, $options);
+  $ptypes = chado_generate_var('pubprop', $values, $options);
   if ($ptypes) {
-    $ptypes = tripal_core_expand_chado_vars($ptypes, 'field', 'pubprop.value', $options);
+    $ptypes = chado_expand_var($ptypes, 'field', 'pubprop.value', $options);
     foreach ($ptypes as $ptype) {
      $pub_array['Publication Type'][] = $ptype->value;
     }
@@ -1119,10 +1119,10 @@ function tripal_pub_get_publication_array($pub_id, $skip_existing = TRUE) {
       'name' => 'Authors',
     ),
   );
-  $authors = tripal_core_generate_chado_var('pubprop', $values);
-  $authors = tripal_core_expand_chado_vars($authors, 'field', 'pubprop.value', $options);
+  $authors = chado_generate_var('pubprop', $values);
+  $authors = chado_expand_var($authors, 'field', 'pubprop.value', $options);
   if (count($authors) > 1) {
-   tripal_core_report_error('tripal_pub', TRIPAL_ERROR, "Publication has multiple author lists. It should have only one list: %pub_id",
+   tripal_report_error('tripal_pub', TRIPAL_ERROR, "Publication has multiple author lists. It should have only one list: %pub_id",
    array('%pub_id' => $pubid));
    return FALSE;
   }
@@ -1261,7 +1261,7 @@ function tripal_pub_create_citation($pub) {
       }
     }
     if (!$pub_type) {
-      tripal_core_report_error('tripal_pub', TRIPAL_ERROR, "Cannot generate citation for publication type: %types",
+      tripal_report_error('tripal_pub', TRIPAL_ERROR, "Cannot generate citation for publication type: %types",
         array('%types' => print_r($pub['Publication Type'], TRUE)));
       return FALSE;
     }

tripal_pub/includes/importers/tripal_pub.PMID.inc

@@ -162,7 +162,7 @@ function tripal_pub_PMID_search_init($search_str, $retmax){
   $rfh = fopen($query_url, "r");
   if (!$rfh) {
     drupal_set_message('Could not perform Pubmed query. Cannot connect to Entrez.', 'error');
-    tripal_core_report_error('tpub_pubmed', TRIPAL_ERROR, "Could not perform Pubmed query. Cannot connect to Entrez.",
+    tripal_report_error('tpub_pubmed', TRIPAL_ERROR, "Could not perform Pubmed query. Cannot connect to Entrez.",
               array());
     return 0;
   }
@@ -241,7 +241,7 @@ $retmod = 'null', $start = 0, $limit = 10, $args = array()){
   $rfh = fopen($fetch_url, "r");
   if (!$rfh) {
     drupal_set_message('ERROR: Could not perform PubMed query.', 'error');
-    tripal_core_report_error('tpub_pubmed', TRIPAL_ERROR, "Could not perform PubMed query: %fetch_url.",
+    tripal_report_error('tpub_pubmed', TRIPAL_ERROR, "Could not perform PubMed query: %fetch_url.",
               array('%fetch_url' => $fetch_url));
     return '';
   }
@@ -285,7 +285,7 @@ function tripal_pub_PMID_parse_pubxml($pub_xml) {
       switch ($element) {
         case 'ERROR':
           $xml->read(); // get the value for this element
-          tripal_core_report_error('tpub_pubmed', TRIPAL_ERROR, "Error: %err", array('%err' => $xml->value));
+          tripal_report_error('tpub_pubmed', TRIPAL_ERROR, "Error: %err", array('%err' => $xml->value));
           break;
         case 'PMID':
           // thre are multiple places where a PMID is present in the XML and
@@ -507,7 +507,7 @@ function tripal_pub_PMID_parse_publication_type($xml, &$pub) {
             // see if this we can find the name using a synonym
             $pub_cvterm = tripal_cv_get_cvterm_by_synonym($value, NULL, 'tripal_pub');
             if (!$pub_cvterm) {
-              tripal_core_report_error('tpub_pubmed', TRIPAL_ERROR, 'Cannot find a valid vocabulary term for the publication type: "%term".',
+              tripal_report_error('tpub_pubmed', TRIPAL_ERROR, 'Cannot find a valid vocabulary term for the publication type: "%term".',
               array('%term' => $value));
             }
           }

tripal_pub/includes/tripal_pub.chado_node.inc

@@ -65,9 +65,9 @@ function chado_pub_form($node, $form_state) {
   // if we are editing an existing node then the pub is already part of the node
   if (property_exists($node, 'pub')) {
     $pub = $node->pub;
-    $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.title');
-    $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.volumetitle');
-    $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.uniquename');
+    $pub = chado_expand_var($pub, 'field', 'pub.title');
+    $pub = chado_expand_var($pub, 'field', 'pub.volumetitle');
+    $pub = chado_expand_var($pub, 'field', 'pub.uniquename');
     $pub_id = $pub->pub_id;
 
     $title       = $pub->title;
@@ -252,17 +252,17 @@ function chado_pub_form($node, $form_state) {
     'cv_name' => 'tripal_pub',
     'select_options' => $select_options,
   );
-  chado_node_properties_form($form, $form_state, $details);
+  chado_add_node_form_properties($form, $form_state, $details);
 
   // RELATIONSHIPS FORM
   //---------------------------------------------
   // We want to use the contact_relationship_types cv if there are any terms available
   // and if not, to default to the relationship ontology
-  $cv_result = tripal_core_chado_select('cv',array('cv_id'),array('name' => 'pub_relationship_types'));
+  $cv_result = chado_select_record('cv',array('cv_id'),array('name' => 'pub_relationship_types'));
   $cv_id = $cv_result[0]->cv_id;
   $select_options = tripal_cv_get_cvterm_options($cv_id);
   if (empty($select_options)) {
-    $cv_result = tripal_core_chado_select('cv',array('cv_id'),array('name' => 'relationship'));
+    $cv_result = chado_select_record('cv',array('cv_id'),array('name' => 'relationship'));
     $cv_id = $cv_result[0]->cv_id;
     $select_options = tripal_cv_get_cvterm_options($cv_id);
   }
@@ -279,7 +279,7 @@ function chado_pub_form($node, $form_state) {
     'select_options' => $select_options
   );
   // Adds the form elements to your current form
-  chado_node_relationships_form($form, $form_state, $details);
+  chado_add_node_form_relationships($form, $form_state, $details);
 
   // ADDITIONAL DBXREFS FORM
   //---------------------------------------------
@@ -289,7 +289,7 @@ function chado_pub_form($node, $form_state) {
     'base_key_value' => $pub_id       // the value of pub_id for this record
   );
   // Adds the form elements to your current form
-  chado_node_additional_dbxrefs_form($form, $form_state, $details);
+  chado_add_node_form_dbxrefs($form, $form_state, $details);
 
   return $form;
 
@@ -328,7 +328,7 @@ function chado_pub_validate($node, $form, &$form_state) {
   // get the type of publication
   $values = array('cvterm_id' => $type_id);
   $options = array('statement_name' => 'sel_pub_ty');
-  $cvterm = tripal_core_chado_select('cvterm', array('name'), $values, $options);
+  $cvterm = chado_select_record('cvterm', array('name'), $values, $options);
   if (count($cvterm) == 0) {
     $message = t('Invalid publication type.');
     form_set_error('type_id', $message);
@@ -391,7 +391,7 @@ function chado_pub_validate($node, $form, &$form_state) {
     $values = array('pub_id' => $pub_id);
     $columns = array('title', 'pyear', 'type_id', 'series_name');
     $options = array('statement_name' => 'sel_pub_id');
-    $pub = tripal_core_chado_select('pub', $columns, $values, $options);
+    $pub = chado_select_record('pub', $columns, $values, $options);
 
     // if the title, type,  year or series_name have changed then check the pub
     // to see if it is a duplicate of another
@@ -569,7 +569,7 @@ function chado_pub_insert($node) {
     $cross_refs = array(); // stores any cross references for this publication
 
     // get the properties from the form
-    $properties = chado_node_properties_form_retreive($node);
+    $properties = chado_retrieve_node_form_properties($node);
 
     // get the list of properties for easy lookup (without doing lots of database queries
     $properties_list = array();
@@ -677,7 +677,7 @@ function chado_pub_insert($node) {
       'publisher'   => substr($publisher, 0, 255),
       'pubplace'    => substr($pubplace, 0, 255),
     );
-    $pub = tripal_core_chado_insert('pub', $values);
+    $pub = chado_insert_record('pub', $values);
     if (!$pub) {
       drupal_set_message("Error inserting publication", "error");
       watchdog('tripal_pub', "Error inserting publication", array(), WATCHDOG_ERROR);
@@ -693,14 +693,14 @@ function chado_pub_insert($node) {
       'foreignkey_name' => 'pub_id',
       'foreignkey_value' => $pub_id
     );
-    chado_node_properties_form_update_properties($node, $details, $properties);
+    chado_update_node_form_properties($node, $details, $properties);
 
     // * Relationships Form *
     $details = array(
       'relationship_table' => 'pub_relationship',  // name of the _relationship table
       'foreignkey_value' => $pub_id                // value of the pub_id key
     );
-    chado_node_relationships_form_update_relationships($node, $details);
+    chado_update_node_form_relationships($node, $details);
 
     // add in any database cross-references
     foreach ($cross_refs as $index => $ref) {
@@ -718,7 +718,7 @@ function chado_pub_insert($node) {
       'foreignkey_name' => 'pub_id',     // the name of the key in your base table
       'foreignkey_value' => $pub_id      // the value of the pub_id key
     );
-    chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
+    chado_update_node_form_dbxrefs($node, $details);
   }
   else {
     $pub_id = $node->pub_id;
@@ -726,7 +726,7 @@ function chado_pub_insert($node) {
 
   // Make sure the entry for this pub doesn't already exist in the
   // chado_pub table if it doesn't exist then we want to add it.
-  $check_org_id = chado_get_id_for_node('pub', $node->nid);
+  $check_org_id = chado_get_id_from_nid('pub', $node->nid);
   if (!$check_org_id) {
     $record = new stdClass();
     $record->nid = $node->nid;
@@ -762,13 +762,13 @@ function chado_pub_update($node) {
   $pub_arr = array();
 
   // get the publication ID for this publication
-  $pub_id = chado_get_id_for_node('pub', $node->nid) ;
+  $pub_id = chado_get_id_from_nid('pub', $node->nid) ;
 
   $properties = array(); // stores all of the properties we need to add
   $cross_refs = array(); // stores any cross references for this publication
 
   // get the properties from the form
-  $properties = chado_node_properties_form_retreive($node);
+  $properties = chado_retrieve_node_form_properties($node);
 
   // get the list of properties for easy lookup (without doing lots of database queries
   $properties_list = array();
@@ -880,7 +880,7 @@ function chado_pub_update($node) {
     'publisher'   => substr($publisher, 0, 255),
     'pubplace'    => substr($pubplace, 0, 255),
   );
-  $status = tripal_core_chado_update('pub', $match, $values);
+  $status = chado_update_record('pub', $match, $values);
   if (!$status) {
     drupal_set_message("Error updating publication", "error");
     watchdog('tripal_pub', "Error updating publication", array(), WATCHDOG_ERROR);
@@ -895,17 +895,17 @@ function chado_pub_update($node) {
     'foreignkey_name' => 'pub_id',
     'foreignkey_value' => $pub_id
   );
-  chado_node_properties_form_update_properties($node, $details, $properties);
+  chado_update_node_form_properties($node, $details, $properties);
 
   // * Relationships Form *
   $details = array(
     'relationship_table' => 'pub_relationship',  // name of the _relationship table
     'foreignkey_value' => $pub_id                // value of the pub_id key
   );
-  chado_node_relationships_form_update_relationships($node, $details);
+  chado_update_node_form_relationships($node, $details);
 
   // add in any database cross-references after first removing
-  tripal_core_chado_delete('pub_dbxref', array('pub_id' => $pub_id));
+  chado_delete_record('pub_dbxref', array('pub_id' => $pub_id));
   foreach ($cross_refs as $index => $ref) {
     $pub_dbxref = tripal_pub_add_pub_dbxref($pub_id, trim($ref));
     if (!$pub_dbxref) {
@@ -921,7 +921,7 @@ function chado_pub_update($node) {
     'foreignkey_name' => 'pub_id',     // the name of the key in your base table
     'foreignkey_value' => $pub_id      // the value of the pub_id key
   );
-  chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
+  chado_update_node_form_dbxrefs($node, $details);
 }
 
 
@@ -940,17 +940,17 @@ function chado_pub_load($nodes) {
 
   foreach ($nodes as $nid => $node) {
     // find the pub and add in the details
-    $pub_id = chado_get_id_for_node('pub', $nid);
+    $pub_id = chado_get_id_from_nid('pub', $nid);
 
     // get the pub
     $values = array('pub_id' => $pub_id);
-    $pub = tripal_core_generate_chado_var('pub', $values);
+    $pub = chado_generate_var('pub', $values);
 
     // expand the 'text' fields as those aren't included by default
     // and they really shouldn't be so large to cause problems
-    $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.title');
-    $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.volumetitle');
-    $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.uniquename');
+    $pub = chado_expand_var($pub, 'field', 'pub.title');
+    $pub = chado_expand_var($pub, 'field', 'pub.volumetitle');
+    $pub = chado_expand_var($pub, 'field', 'pub.uniquename');
 
     // set the URL path
     $nodes[$nid]->path = "pub/$pub_id";
@@ -971,7 +971,7 @@ function chado_pub_load($nodes) {
  */
 function chado_pub_delete(&$node) {
 
-  $pub_id = chado_get_id_for_node('pub', $node->nid);
+  $pub_id = chado_get_id_from_nid('pub', $node->nid);
 
   // if we don't have a pub id for this node then this isn't a node of
   // type chado_pub or the entry in the chado_pub table was lost.
@@ -1076,7 +1076,7 @@ function tripal_pub_node_insert($node) {
   // so the nodeapi function ensures that the URL path is set after insert or update
   // of the node and when the node is loaded if it hasn't yet been set.
   if ($node->type == 'chado_pub') {
-    $pub_id = chado_get_id_for_node('pub', $node->nid);
+    $pub_id = chado_get_id_from_nid('pub', $node->nid);
     tripal_pub_set_pub_url($node, $pub_id);
   }
 }
@@ -1096,7 +1096,7 @@ function tripal_pub_node_load($nodes, $types) {
   if (count(array_intersect(array('chado_pub'), $types))) {
     foreach ($nodes as $nid => $node) {
       if ($node->type == 'chado_pub' and !property_exists($node, 'path')) {
-        $pub_id = chado_get_id_for_node('pub', $node->nid);
+        $pub_id = chado_get_id_from_nid('pub', $node->nid);
         $path = tripal_pub_set_pub_url($node, $pub_id);
       }
     }
@@ -1114,7 +1114,7 @@ function tripal_pub_node_update($node) {
   // so the nodeapi function ensures that the URL path is set after insert or update
   // of the node and when the node is loaded if it hasn't yet been set.
   if ($node->type == 'chado_pub') {
-    $pub_id = chado_get_id_for_node('pub', $node->nid);
+    $pub_id = chado_get_id_from_nid('pub', $node->nid);
     tripal_pub_set_pub_url($node, $pub_id);
   }
 }

tripal_pub/includes/tripal_pub.pub_importers.inc

@@ -76,12 +76,12 @@ function tripal_pub_importer_setup_page($action = 'new', $pub_import_id = NULL)
   
   // make sure the tripal_pub and tripal_contact ontologies are loaded
   $values = array('name' => 'tripal_pub');
-  $tpub_cv = tripal_core_chado_select('cv', array('cv_id'), $values);
+  $tpub_cv = chado_select_record('cv', array('cv_id'), $values);
   if (count($tpub_cv) == 0) {
     drupal_set_message(t('Before importing publications you must first ') . l(t('load the Tripal Pub Ontology'), 'admin/tripal/tripal_cv/obo_loader'), 'error');
   }
   $values = array('name' => 'tripal_contact');
-  $tpub_cv = tripal_core_chado_select('cv', array('cv_id'), $values);
+  $tpub_cv = chado_select_record('cv', array('cv_id'), $values);
   if (count($tpub_cv) == 0) {
     drupal_set_message(t('If you want to create contact pages for authors, you must first ') . l(t('load the Tripal Contact Ontology'), 'admin/tripal/tripal_cv/obo_loader'), 'error');
   }
@@ -313,7 +313,7 @@ function tripal_pub_importer_setup_form($form, &$form_state = NULL, $pub_import_
   $values = array(
     'name' => $supported_dbs,
   );
-  $dbs = tripal_core_chado_select('db', array('*'), $values);
+  $dbs = chado_select_record('db', array('*'), $values);
   foreach ($dbs as $index => $db) {
     $remote_dbs[$db->name] = $db->description;
   };

tripal_pub/includes/tripal_pub.pub_search.inc

@@ -45,8 +45,8 @@ function tripal_pub_search_page() {
           'name' => 'Citation',
         ),
       );
-      $citation_rec = tripal_core_generate_chado_var('pubprop', $values);
-      $citation_rec = tripal_core_expand_chado_vars($citation_rec, 'field', 'pubprop.value');
+      $citation_rec = chado_generate_var('pubprop', $values);
+      $citation_rec = chado_expand_var($citation_rec, 'field', 'pubprop.value');
 
       // if we have the citation then use it, otherwise, just use the title
       $title = htmlspecialchars($pub->title);
@@ -499,7 +499,7 @@ function tripal_pub_get_search_results($search_array, $limit) {
 
     // get the scope type
     $values = array('cvterm_id' => $type_id);
-    $cvterm = tripal_core_chado_select('cvterm', array('name'), $values);
+    $cvterm = chado_select_record('cvterm', array('name'), $values);
     $type_name = '';
     if (count($cvterm) > 0) {
       $type_name = $cvterm[0]->name;

tripal_pub/theme/tripal_pub.theme.inc

@@ -22,7 +22,7 @@ function tripal_pub_preprocess_tripal_pub_relationships(&$variables) {
       ),
     ),
   );
-  $pub = tripal_core_expand_chado_vars($pub, 'table', 'pub_relationship', $options);
+  $pub = chado_expand_var($pub, 'table', 'pub_relationship', $options);
 
   // get the subject relationships
   $srelationships = $pub->pub_relationship->subject_id;

tripal_pub/tripal_pub.install

@@ -49,7 +49,7 @@ function tripal_pub_install() {
   global $base_path;
 
   // create the module's data directory
-  tripal_create_moddir('tripal_pub');
+  tripal_create_files_dir('tripal_pub');
 
   // add loading of the the tripal pub ontology to the job queue
   $obo_path =  drupal_realpath(drupal_get_path('module', 'tripal_pub') . '/files/tpub.obo');
@@ -206,7 +206,7 @@ function tripal_pub_add_custom_tables() {
       ),
     ),
   );
-  tripal_core_create_custom_table('pubauthor_contact', $schema, TRUE);
+  chado_create_custom_table('pubauthor_contact', $schema, TRUE);
 }
 
 /**

tripal_stock/api/tripal_stock.api.inc

@@ -45,7 +45,7 @@ function tripal_stock_get_stock_by_stock_id($stock_id) {
     return node_load($r->nid);
   }
   else {
-    tripal_core_report_error('tripal_stock', TRIPAL_WARNING, 'tripal_stock_get_stock_by_stock_id(!stock_id): no stock with that stock_id is sync\'d with drupal', array('!stock_id' => $stock_id));
+    tripal_report_error('tripal_stock', TRIPAL_WARNING, 'tripal_stock_get_stock_by_stock_id(!stock_id): no stock with that stock_id is sync\'d with drupal', array('!stock_id' => $stock_id));
   }
 
   return 0;
@@ -111,7 +111,7 @@ function tripal_stock_get_all_stocks() {
  */
 function tripal_stock_get_stocks($values) {
 
-  $stock_ids = tripal_core_chado_select('stock', array('stock_id'), $values);
+  $stock_ids = chado_select_record('stock', array('stock_id'), $values);
 
   // Change from stock_ids to nodes-----------------------------------
   $stock_ids = array_filter($stock_ids);
@@ -176,7 +176,7 @@ function tripal_stock_get_stocks_by_stockprop($stockprop_values, $stock_values)
   }
 
   //get stock_ids from stockprop table
-  $stock_ids = tripal_core_chado_select('stockprop', array('stock_id'), $stockprop_values);
+  $stock_ids = chado_select_record('stockprop', array('stock_id'), $stockprop_values);
 
   // Change from stock_ids to nodes-----------------------------------
   $stock_ids = array_filter($stock_ids);
@@ -216,7 +216,7 @@ function tripal_stock_get_stock_by_name_identifier($name, $organism_id) {
   );
 
   // where name_identifier = stock.name-------------------------------
-  $current_stocks = tripal_core_chado_select('stock', array('stock_id'),
+  $current_stocks = chado_select_record('stock', array('stock_id'),
     array(
       'name' => $name,
       'organism_id' => $organism_id,
@@ -231,7 +231,7 @@ function tripal_stock_get_stock_by_name_identifier($name, $organism_id) {
   }
 
   // where name_identifier = stock.uniquename-------------------------------
-  $current_stocks = tripal_core_chado_select('stock', array('stock_id'),
+  $current_stocks = chado_select_record('stock', array('stock_id'),
     array(
       'uniquename' => $name,
       'organism_id' => $organism_id,
@@ -247,7 +247,7 @@ function tripal_stock_get_stock_by_name_identifier($name, $organism_id) {
 
   // where name_identifier = dbxref.accession-------------------------------
   // linked to stock through stock.dbxref
-  $current_stocks = tripal_core_chado_select('stock', array('stock_id'),
+  $current_stocks = chado_select_record('stock', array('stock_id'),
     array(
       'dbxref_id' => array(
         'accession' => $name,
@@ -264,7 +264,7 @@ function tripal_stock_get_stock_by_name_identifier($name, $organism_id) {
   }
 
   // linked to stock through stock_dbxref?
-  $current_stocks = tripal_core_chado_select('stock_dbxref', array('stock_id'),
+  $current_stocks = chado_select_record('stock_dbxref', array('stock_id'),
     array(
       'dbxref_id' => array(
         'accession' => $name,
@@ -285,7 +285,7 @@ function tripal_stock_get_stock_by_name_identifier($name, $organism_id) {
 
   // where name_identifier = stockprop.value-------------------------------
   // where type='synonym'
-  $current_stocks = tripal_core_chado_select('stockprop', array('stock_id'),
+  $current_stocks = chado_select_record('stockprop', array('stock_id'),
     array(
       'stock_id' => array(
         'organism_id' => $organism_id,

tripal_stock/includes/tripal_stock.chado_node.inc

@@ -54,9 +54,9 @@ function chado_stock_load($nodes) {
   $new_nodes = array();
   foreach ($nodes as $nid => $node) {
     // get the stock details from chado
-    $stock_id = chado_get_id_for_node('stock', $node->nid);
+    $stock_id = chado_get_id_from_nid('stock', $node->nid);
     if (empty($stock_id)) {
-      tripal_core_report_error('tripal_stock', TRIPAL_ERROR,
+      tripal_report_error('tripal_stock', TRIPAL_ERROR,
         'Unable to retrieve stock_id for %title (NID = %nid).',
         array('%title' => $node->title, '%nid' => $node->nid)
       );
@@ -65,7 +65,7 @@ function chado_stock_load($nodes) {
 
       // build the variable with all the stock details
       $values = array('stock_id' => $stock_id);
-      $stock = tripal_core_generate_chado_var('stock', $values);
+      $stock = chado_generate_var('stock', $values);
 
       // by default, the titles are saved using the unique constraint.  We will
       // keep it the same, but remove the duplicate name if the unique name and name
@@ -131,7 +131,7 @@ function chado_stock_form($node, $form_state) {
       // Check to see if it's excluded and expand it if so
       if (isset($node->expandable_fields)) {
         if (in_array($field_name, $node->expandable_fields)) {
-          $node = tripal_core_expand_chado_vars($node, 'field', $field_name);
+          $node = chado_expand_var($node, 'field', $field_name);
         }
       }
     }
@@ -303,7 +303,7 @@ function chado_stock_form($node, $form_state) {
     'base_key_value' => $stock_id,
     'cv_id' => variable_get('chado_stock_prop_types_cv', FALSE)
   );
-  chado_node_properties_form($form, $form_state, $details);
+  chado_add_node_form_properties($form, $form_state, $details);
 
   // ADDITIONAL DBXREFS FORM
   //---------------------------------------------
@@ -313,7 +313,7 @@ function chado_stock_form($node, $form_state) {
     'base_foreign_key' => 'stock_id',
     'base_key_value' => $stock_id
   );
-  chado_node_additional_dbxrefs_form($form, $form_state, $details);
+  chado_add_node_form_dbxrefs($form, $form_state, $details);
 
   // RELATIONSHIPS FORM
   //---------------------------------------------
@@ -326,7 +326,7 @@ function chado_stock_form($node, $form_state) {
     'nodetype' => 'stock',
     'cv_id' => variable_get('chado_stock_relationship_cv', 0)
   );
-  chado_node_relationships_form($form, $form_state, $details);
+  chado_add_node_form_relationships($form, $form_state, $details);
 
   return $form;
 }
@@ -479,10 +479,10 @@ function chado_stock_insert($node) {
         if (!tripal_core_chado_select('dbxref', array('dbxref_id'), $values)) {
           $values['description'] = $node->db_description;
           $values['version'] = '1';
-          $dbxref_status = tripal_core_chado_insert('dbxref', $values);
+          $dbxref_status = chado_insert_record('dbxref', $values);
           if (!$dbxref_status) {
             drupal_set_message(t('Unable to add database reference to this stock.'), 'warning');
-            tripal_core_report_error('tripal_stock', TRIPAL_WARNING,
+            tripal_report_error('tripal_stock', TRIPAL_WARNING,
               'Insert Stock: Unable to create dbxref where values:%values',
               array('%values' => print_r($values, TRUE)));
           }
@@ -507,7 +507,7 @@ function chado_stock_insert($node) {
         'description' => $node->stock_description,
         'type_id' => $node->type_id
       );
-      $stock = tripal_core_chado_insert('stock', $values);
+      $stock = chado_insert_record('stock', $values);
     }
     // create a stock without a dbxref
     else {
@@ -518,7 +518,7 @@ function chado_stock_insert($node) {
         'description' => $node->stock_description,
         'type_id'     => $node->type_id
       );
-      $stock = tripal_core_chado_insert('stock', $values);
+      $stock = chado_insert_record('stock', $values);
     }
 
     if (is_array($stock)) {
@@ -538,7 +538,7 @@ function chado_stock_insert($node) {
         'foreignkey_name' => 'stock_id',
         'foreignkey_value' => $stock_id
       );
-      chado_node_properties_form_update_properties($node, $details);
+      chado_update_node_form_properties($node, $details);
 
       // Now add the additional references
       $details = array(
@@ -546,14 +546,14 @@ function chado_stock_insert($node) {
         'foreignkey_name' => 'stock_id',
         'foreignkey_value' => $stock_id
       );
-      chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
+      chado_update_node_form_dbxrefs($node, $details);
 
       // Now add in relationships
       $details = array(
         'relationship_table' => 'stock_relationship',
         'foreignkey_value' => $node->stock_id
       );
-      chado_node_relationships_form_update_relationships($node, $details);
+      chado_update_node_form_relationships($node, $details);
     }
   } //end of adding stock to chado
   else {
@@ -576,7 +576,7 @@ function chado_stock_insert($node) {
   }
   else {
     drupal_set_message(t('Error during stock creation.'), 'error');
-    tripal_core_report_error('tripal_stock', TRIPAL_WARNING,
+    tripal_report_error('tripal_stock', TRIPAL_WARNING,
       'Insert Stock: Unable to create stock where values:%values',
       array('%values' => print_r($values, TRUE)));
     return FALSE;
@@ -610,7 +610,7 @@ function chado_stock_update($node) {
     $dbxref_present = TRUE;
     if ($node->accession) {
       $dbxref_mode = '';
-      $stock = tripal_core_chado_select(
+      $stock = chado_select_record(
         'stock',
         array('dbxref_id', 'type_id'),
         array('stock_id' => $node->stock_id)
@@ -622,7 +622,7 @@ function chado_stock_update($node) {
           'accession' => $node->accession,
           'description' => $node->db_description
         );
-        $dbxref_status = tripal_core_chado_update(
+        $dbxref_status = chado_update_record(
           'dbxref',
           array('dbxref_id' => $stock[0]->dbxref_id),
           $values
@@ -639,7 +639,7 @@ function chado_stock_update($node) {
             'description' => $node->db_description,
             'version' => '1',
           );
-          $dbxref_status = tripal_core_chado_insert(
+          $dbxref_status = chado_insert_record(
             'dbxref',
             $values
           );
@@ -647,7 +647,7 @@ function chado_stock_update($node) {
         }
         else {
           drupal_set_message(t('Unable to find stock to Update'), 'error');
-          tripal_core_report_error('tripal_stock', TRIPAL_ERROR,
+          tripal_report_error('tripal_stock', TRIPAL_ERROR,
             'Stock Update: Unable to find stock to update using values: %values',
             array('%values', print_r($values, TRUE))
           );
@@ -657,7 +657,7 @@ function chado_stock_update($node) {
     }
 
     if (!$dbxref_status) {
-      tripal_core_report_error('tripal_stock', TRIPAL_WARNING,
+      tripal_report_error('tripal_stock', TRIPAL_WARNING,
         'Stock Update: Unable to %mode main stock dbxref with values: %values',
         array('%values' => print_r($values, TRUE), '%mode' => $dbxref_mode));
     }
@@ -679,12 +679,12 @@ function chado_stock_update($node) {
       );
     }
   }
-  $status = tripal_core_chado_update('stock', array('stock_id' => $node->stock_id), $update_values);
+  $status = chado_update_record('stock', array('stock_id' => $node->stock_id), $update_values);
 
 
   if (!$status) {
     drupal_set_message(t('Unable to update stock'), 'error');
-    tripal_core_report_error('tripal_stock', TRIPAL_ERROR,
+    tripal_report_error('tripal_stock', TRIPAL_ERROR,
       'Stock Update: Unable to update stock using match values: %mvalues and update values: %uvalues',
       array('%mvalues' => print_r(array('stock_id' => $node->stock_id), TRUE), '%uvalues' => print_r($update_values, TRUE))
     );
@@ -692,7 +692,7 @@ function chado_stock_update($node) {
   else {
     // set the URL for this stock page
     $values = array('stock_id' => $node->stock_id);
-    $stock = tripal_core_chado_select('stock', array('*'), $values);
+    $stock = chado_select_record('stock', array('*'), $values);
   }
 
   // now update the properties
@@ -704,7 +704,7 @@ function chado_stock_update($node) {
       'foreignkey_name' => 'stock_id',
       'foreignkey_value' => $node->stock_id
     );
-    chado_node_properties_form_update_properties($node, $details);
+    chado_update_node_form_properties($node, $details);
 
   }
 
@@ -715,7 +715,7 @@ function chado_stock_update($node) {
       'foreignkey_name' => 'stock_id',
       'foreignkey_value' => $node->stock_id
     );
-    chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
+    chado_update_node_form_dbxrefs($node, $details);
   }
 
   // now update relationships
@@ -724,7 +724,7 @@ function chado_stock_update($node) {
       'relationship_table' => 'stock_relationship',
       'foreignkey_value' => $node->stock_id
     );
-    chado_node_relationships_form_update_relationships($node, $details);
+    chado_update_node_form_relationships($node, $details);
   }
 }
 
@@ -782,7 +782,7 @@ function tripal_stock_node_presave($node) {
         $uniquename  = $node->uniquename;
         $type_id     = $node->type_id;
         $values = array('cvterm_id' => $node->type_id);
-        $cvterm = tripal_core_chado_select('cvterm', array('name'), $values);
+        $cvterm = chado_select_record('cvterm', array('name'), $values);
         $type = $cvterm[0]->name;
       }
       else {
@@ -792,7 +792,7 @@ function tripal_stock_node_presave($node) {
         $type        = $node->stock->type_id->name;
       }
       $values = array('organism_id' => $organism_id);
-      $organism = tripal_core_chado_select('organism', array('genus','species'), $values);
+      $organism = chado_select_record('organism', array('genus','species'), $values);
       $node->title = "$sname, $uniquename ($type) " . $organism[0]->genus . ' ' . $organism[0]->species;
       if ($name == $uname) {
         $node->title = "$sname ($type) " . $organism[0]->genus . ' ' . $organism[0]->species;

tripal_stock/includes/tripal_stock.sync_stocks.inc

@@ -103,7 +103,7 @@ function tripal_stock_sync_form_submit($form, &$form_state) {
   $job_args = array(0, $organism_id, $stock_types);
 
   if ($organism_id) {
-    $organism = tripal_core_chado_select('organism', array('genus', 'species'), array('organism_id' => $organism_id));
+    $organism = chado_select_record('organism', array('genus', 'species'), array('organism_id' => $organism_id));
     $title = "Sync stocks for " .  $organism[0]->genus . " " . $organism[0]->species;
   }
   else {
@@ -186,7 +186,7 @@ function tripal_stock_set_urls($na = NULL, $job = NULL) {
       db_query('DEALLOCATE "del_url_alias_by_src"');
       db_query('DEALLOCATE "ins_url_alias_nisrds"');
       db_query("ROLLBACK");
-      tripal_core_report_error('trp-seturl', TRIPAL_ERROR, "Failed Removing URL Alias: %src", array('%src' => $src));
+      tripal_report_error('trp-seturl', TRIPAL_ERROR, "Failed Removing URL Alias: %src", array('%src' => $src));
       return;
     }
     $success = db_query("EXECUTE ins_url_alias_nisrds(:src, :dst)", array(':src' => $src, ':dst' => $dst));
@@ -194,14 +194,14 @@ function tripal_stock_set_urls($na = NULL, $job = NULL) {
       db_query('DEALLOCATE "del_url_alias_by_src"');
       db_query('DEALLOCATE "ins_url_alias_nisrds"');
       db_query("ROLLBACK");
-      tripal_core_report_error('trp-seturl', TRIPAL_ERROR, "Failed Adding URL Alias: %dst", array('%dst' => $dst));
+      tripal_report_error('trp-seturl', TRIPAL_ERROR, "Failed Adding URL Alias: %dst", array('%dst' => $dst));
       return;
     }
 
     // update the job status every 1% stocks
     if ($job and $num_set % $num_per_interval == 0) {
       $percent = ($num_set / $num_nodes) * 100;
-      tripal_job_set_progress($job, intval($percent));
+      tripal_set_job_progress($job, intval($percent));
       $percent = sprintf("%.2f", $percent);
       print "Setting URLs (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
 
@@ -209,7 +209,7 @@ function tripal_stock_set_urls($na = NULL, $job = NULL) {
     $num_set++;
   }
   $percent = ($num_set / $num_nodes) * 100;
-  tripal_job_set_progress($job, intval($percent));
+  tripal_set_job_progress($job, intval($percent));
   $percent = sprintf("%.2f", $percent);
   print "Setting URLs (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
   print "\nDone. Set " . number_format($num_set) . " URLs\n";
@@ -245,9 +245,9 @@ function tripal_stock_get_stock_url($node, $url_alias = NULL) {
   // get the stock
   $values = array('stock_id' => $node->stock_id);
   $options = array('statement_name' => 'sel_stock_id');
-  $stock = tripal_core_chado_select('stock', array('*'), $values, $options);
+  $stock = chado_select_record('stock', array('*'), $values, $options);
   if (!$stock) {
-    tripal_core_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find stock when setting URL alias for stock: %id", array('%id' => $node->stock_id));
+    tripal_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find stock when setting URL alias for stock: %id", array('%id' => $node->stock_id));
     return FALSE;
   }
   $stock = (object) $stock[0];
@@ -255,9 +255,9 @@ function tripal_stock_get_stock_url($node, $url_alias = NULL) {
   // get the organism
   $values = array('organism_id' => $stock->organism_id);
   $options = array('statement_name' => 'sel_organism_id');
-  $organism  = tripal_core_chado_select('organism', array('*'), $values, $options);
+  $organism  = chado_select_record('organism', array('*'), $values, $options);
   if (!$organism) {
-    tripal_core_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find organism when setting URL alias for stock: %id", array('%id' => $node->stock_id));
+    tripal_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find organism when setting URL alias for stock: %id", array('%id' => $node->stock_id));
     return FALSE;
   }
   $genus = preg_replace('/\s/', '_', strtolower($organism[0]->genus));
@@ -266,9 +266,9 @@ function tripal_stock_get_stock_url($node, $url_alias = NULL) {
   // get the type
   $values = array('cvterm_id' => $stock->type_id);
   $options = array('statement_name' => 'sel_cvterm_id');
-  $cvterm = tripal_core_chado_select('cvterm', array('name'), $values, $options);
+  $cvterm = chado_select_record('cvterm', array('name'), $values, $options);
   if (!$cvterm) {
-    tripal_core_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find type when setting URL alias for stock: %id", array('%id' => $node->stock_id));
+    tripal_report_error('trp-seturl', TRIPAL_ERROR, "Cannot find type when setting URL alias for stock: %id", array('%id' => $node->stock_id));
     return FALSE;
   }
   $type = preg_replace('/\s/', '_', $cvterm[0]->name);
@@ -284,7 +284,7 @@ function tripal_stock_get_stock_url($node, $url_alias = NULL) {
   // the dst field of the url_alias table is only 128 characters long.
   // if this is the case then simply return the node URL, we can't set this one
   if (strlen($url_alias) > 128) {
-    tripal_core_report_error('trp-seturl', TRIPAL_ERROR, "Cannot set alias longer than 128 characters: %alias.", array('%alias' => $url_alias));
+    tripal_report_error('trp-seturl', TRIPAL_ERROR, "Cannot set alias longer than 128 characters: %alias.", array('%alias' => $url_alias));
     return "node/" . $node->nid;
   }
 

tripal_stock/tripal_stock.install

@@ -44,7 +44,7 @@ function tripal_stock_requirements($phase) {
  */
 function tripal_stock_install() {
   // create the module's data directory
-  tripal_create_moddir('tripal_stock');
+  tripal_create_files_dir('tripal_stock');
 }
 
 /**

tripal_stock/tripal_stock.module

@@ -459,7 +459,7 @@ function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
       ),
     ),
   );
-  $stock = tripal_core_expand_chado_vars($stock, 'table', 'stock_relationship', $options);
+  $stock = chado_expand_var($stock, 'table', 'stock_relationship', $options);
 
   // get the subject relationships
   $srelationships = $stock->stock_relationship->subject_id;

tripal_views/api/tripal_views.api.inc

@@ -289,7 +289,7 @@ function tripal_views_integration_add_entry($defn_array) {
   $no_errors = TRUE;
 
   if (empty($defn_array['table'])) {
-    tripal_core_report_error('tripal_views', TRIPAL_WARNING, 'Recieved integration with no tablename: %defn', array('%defn' => print_r($defn_array,TRUE)));
+    tripal_report_error('tripal_views', TRIPAL_WARNING, 'Recieved integration with no tablename: %defn', array('%defn' => print_r($defn_array,TRUE)));
     $no_errors = FALSE;
     return $no_errors;
   }
@@ -590,7 +590,7 @@ function tripal_views_integration_remove_entry_by_setup_id($setup_id) {
  */
 function tripal_views_integrate_all_chado_tables() {
 
-  $tables = tripal_core_get_chado_tables(TRUE);
+  $tables = chado_get_table_names(TRUE);
 
   $base_tables = array(
     'acquisition', 'analysis', 'assay', 'biomaterial', 'contact', 'cv', 'cvterm',
@@ -631,7 +631,7 @@ function tripal_views_integrate_all_chado_tables() {
 function tripal_views_get_integration_array_for_chado_table($table_name, $base_table = TRUE, $priority = 9) {
 
   // Get the schema for this table (via the chado schema api)
-  $schema = tripal_core_get_chado_table_schema($table_name);
+  $schema = chado_get_schema($table_name);
 
   // Base definition array
   $defn_array = array(
@@ -645,7 +645,7 @@ function tripal_views_get_integration_array_for_chado_table($table_name, $base_t
   );
   // Add fields
   if (!isset($schema['fields'])) {
-    tripal_core_report_error('tripal_views', TRIPAL_NOTICE, 
+    tripal_report_error('tripal_views', TRIPAL_NOTICE, 
       'There are no fields defined for %table in the Chado Schema API.', array('%table' => $table_name));
     return FALSE;
   }
@@ -781,7 +781,7 @@ function tripal_views_get_integration_array_for_chado_table($table_name, $base_t
     foreach ($schema['referring_tables'] as $referring_table) {
 
       // D7 @todo: fix referring_tables in schema to list the keys like foreign keys does
-      $referring_schema = tripal_core_get_chado_table_schema($referring_table);
+      $referring_schema = chado_get_schema($referring_table);
       $referring_schema_fk_columns = $referring_schema['foreign keys'][$table_name]['columns'];
       foreach ($referring_schema_fk_columns as $left_field => $right_field) {
         $defn_array['fields'][$right_field]['joins'][ $referring_table ] = array(
@@ -842,7 +842,7 @@ function tripal_views_clone_integration($table_name, $new_priority = NULL, $temp
   $setup_id = $setup_id->fetchObject();
 
   if (empty($setup_id)) {
-    tripal_core_report_error('tripal_views', TRIPAL_ERROR, 'Unable to clone the setup for %table in order to add the following field to the integration: %field.',
+    tripal_report_error('tripal_views', TRIPAL_ERROR, 'Unable to clone the setup for %table in order to add the following field to the integration: %field.',
       array('%table' => $table_name, '%field' => print_r($field_array,TRUE)));
     return FALSE;
   }

tripal_views/includes/tripal_views_integration.inc

@@ -303,7 +303,7 @@ function tripal_views_integration_form($form, $form_state, $arg) {
   );
 
   // build the form element for the Chado tables
-  $chado_tables = tripal_core_get_chado_tables(TRUE);
+  $chado_tables = chado_get_table_names(TRUE);
   $chado_tables = array_merge(array('Select'), $chado_tables);
   $default = '';
   if ($setup_id) {
@@ -479,7 +479,7 @@ function tripal_views_integration_form($form, $form_state, $arg) {
       $columns = explode(",", $mview->mv_specs);
     }
     else {
-      $table_desc = tripal_core_get_chado_table_schema($table_name);
+      $table_desc = chado_get_schema($table_name);
       if ($table_desc) {
         $fields = $table_desc['fields'];
         // iterate through the columns and build the format
@@ -535,7 +535,7 @@ function tripal_views_integration_form($form, $form_state, $arg) {
     );
 
     // get the list of chado tables to join on
-    $chado_join_tables = tripal_core_get_chado_tables(TRUE);
+    $chado_join_tables = chado_get_table_names(TRUE);
     $chado_join_tables = array_merge(array('Select a Join Table'), $chado_join_tables);
 
     // get list of all handlers
@@ -844,7 +844,7 @@ function tripal_views_integration_form($form, $form_state, $arg) {
     );
 
     $base_field_options = array('Select the Base Column');
-    $table_desc = tripal_core_get_chado_table_schema($table_name);
+    $table_desc = chado_get_schema($table_name);
     foreach ($table_desc['fields'] as $column => $def) {
       $base_field_options[$column] = $column;
     }
@@ -938,7 +938,7 @@ function tripal_views_integration_form($form, $form_state, $arg) {
       $columns = array();
       if ($result->left_table) {
         // get the table description
-        $table_desc = tripal_core_get_chado_table_schema($result->left_table);
+        $table_desc = chado_get_schema($result->left_table);
         foreach ($table_desc['fields'] as $column => $def) {
           $columns[$column] = $column;
         }
@@ -1292,7 +1292,7 @@ function tripal_views_integration_ajax_join_field($form, $form_state) {
     return $form['view_setup_table'][$field]['column-3'][$join_field];
   }
   else {
-    tripal_core_report_error('tripal_views', TRIPAL_ERROR, 
+    tripal_report_error('tripal_views', TRIPAL_ERROR, 
       'Tripal Views Integration Ajax failed due to being unable to determine which row needs updating', array());
     return $form;
   }

tripal_views/tripal_views.install

@@ -33,7 +33,7 @@ function tripal_views_requirements($phase) {
 function tripal_views_install() {
 
   // create the module's data directory
-  tripal_create_moddir('tripal_views');
+  tripal_create_files_dir('tripal_views');
 
   // we want views to pick up our changes
   views_invalidate_cache();

tripal_views/tripal_views.views.inc

@@ -235,7 +235,7 @@ function tripal_views_views_data() {
       $base_table = $tvi_row->table_name;
 
       // get the table description
-      $table_desc = tripal_core_get_chado_table_schema($base_table);
+      $table_desc = chado_get_schema($base_table);
 
       $fields = $table_desc['fields'];
       if (!is_array($fields)) {
@@ -342,7 +342,7 @@ function tripal_views_views_data() {
 
         // warn if deprecated method of relationship addition was used (ie: through handlers)
         if (isset($data[$base_table][$base_field]['relationship'])) {
-          tripal_core_report_error('tripal_views', TRIPAL_NOTICE,
+          tripal_report_error('tripal_views', TRIPAL_NOTICE,
             'DEPRECATED: Currently using tripal_views_handlers to store relationship for %base => %left when you should be using tripal_views_joins.',
             array('%base' => $base_table, '%left' => $left_table));
         }

tripal_views/views/handlers/tripal_views_handler_filter_select_cvterm.inc

@@ -24,7 +24,7 @@ class tripal_views_handler_filter_select_cvterm extends tripal_views_handler_fil
     if (isset($this->options['show_all'])) {
       $cv_id = variable_get('chado_' . $this->view->base_table . '_cv', NULL);
       if ($cv_id) {
-        $results = tripal_core_chado_select('cvterm', array('cvterm_id', 'name'), array('cv_id' => $cv_id));
+        $results = chado_select_record('cvterm', array('cvterm_id', 'name'), array('cv_id' => $cv_id));
         if (empty($results)) {
           $results = array();
         }
@@ -47,7 +47,7 @@ class tripal_views_handler_filter_select_cvterm extends tripal_views_handler_fil
         $resource = chado_query($sql);
         $cvterms = array();
         foreach ($resource as $r) {
-          $results = tripal_core_chado_select('cvterm', array('cvterm_id', 'name'), array('cv_id' => $r->cv_id));
+          $results = chado_select_record('cvterm', array('cvterm_id', 'name'), array('cv_id' => $r->cv_id));
           if (empty($results)) {
             $results = array();
           }