Added tripal_db_persistent_chado(), tripal_db_release_persistent_chado(). Also tripal_core_chado_insert() now uses prepared statements :)

tripal_core/tripal_core.api.inc

@@ -108,120 +108,180 @@ require_once "tripal_core.schema.api.inc";
 *
 * @ingroup tripal_chado_api
 */
-function tripal_core_chado_insert($table,$values){
-   $insert_values = array();
-   
-   // get the table description
-   $table_desc = module_invoke_all('chado_'.$table.'_schema');
-   if (empty($table_desc)) {
-   	watchdog('tripal_core', 'tripal_core_chado_insert: There is no table description for !table_name', array('!table_name' => $table), WATCHDOG_WARNING);       
-   }
-
-   // iterate through the values array and create a new 'insert_values' array
-   // that has all the values needed for insert with all foreign relationsihps
-   // resolved.
-   foreach($values as $field => $value){
-      if(is_array($value)){
-         // select the value from the foreign key relationship for this value
-         $results = tripal_core_chado_get_foreign_key($table_desc,$field,$value);
-         if (sizeof($results) > 1) {
-           watchdog('tripal_core', 'tripal_core_chado_insert: Too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value,TRUE)), WATCHDOG_ERROR);         
-         } elseif (sizeof($results) < 1) {
-           //watchdog('tripal_core', 'tripal_core_chado_insert: no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value,TRUE)), WATCHDOG_ERROR);
-         } else {
-           $insert_values[$field] = $results[0];
-         }
-      }  
-      else {
-         $insert_values[$field] = $value;
+function tripal_core_chado_insert($table, $values, $options = array()){
+  $chado_db = tripal_db_persistent_chado();
+  
+  // Determine plan of action
+  if ($options['statement_name']) {
+    $prepared = TRUE;
+    if ($options['prepare']) {
+      $build_sql = TRUE;
+    } else {
+      $build_sql = FALSE;
+    }  
+  } else {
+    $build_sql = TRUE;
+  }
+  
+  // get the table description
+  $table_desc = module_invoke_all('chado_'.$table.'_schema');
+  if (empty($table_desc)) {
+    watchdog('tripal_core', 'tripal_core_chado_insert: There is no table description for !table_name', array('!table_name' => $table), WATCHDOG_WARNING);       
+  }
+  
+  // iterate through the values array and create a new 'insert_values' array
+  // that has all the values needed for insert with all foreign relationsihps
+  // resolved.
+  $insert_values = array();
+  foreach($values as $field => $value){
+    if(is_array($value)){
+       // select the value from the foreign key relationship for this value
+       $results = tripal_core_chado_get_foreign_key($table_desc,$field,$value);
+       if (sizeof($results) > 1) {
+         watchdog('tripal_core', 'tripal_core_chado_insert: Too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value,TRUE)), WATCHDOG_ERROR);         
+       } elseif (sizeof($results) < 1) {
+         //watchdog('tripal_core', 'tripal_core_chado_insert: no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value,TRUE)), WATCHDOG_ERROR);
+       } else {
+         $insert_values[$field] = $results[0];
+       }
+    }  
+    else {
+       $insert_values[$field] = $value;
+    }
+  }
+  
+  // check for violation of any unique constraints
+  $ukeys = $table_desc['unique keys'];
+  $ukselect_cols = array();
+  $ukselect_vals = array();
+  if ($ukeys) {
+   foreach($ukeys as $name => $fields){
+      foreach($fields as $index => $field){
+         // build the arrays for performing a select that will check the contraint
+         array_push($ukselect_cols,$field);
+         $ukselect_vals[$field] = $insert_values[$field];
       }
-   }
-
-   // check for violation of any unique constraints
-   $ukeys = $table_desc['unique keys'];
-   $ukselect_cols = array();
-   $ukselect_vals = array();
-   if ($ukeys) {
-     foreach($ukeys as $name => $fields){
-        foreach($fields as $index => $field){
-           // build the arrays for performing a select that will check the contraint
-           array_push($ukselect_cols,$field);
-           $ukselect_vals[$field] = $insert_values[$field];
-        }
-        // now check the constraint
-        if(tripal_core_chado_select($table,$ukselect_cols,$ukselect_vals)){
-           watchdog('tripal_core',"tripal_core_chado_insert: Cannot insert duplicate record into $table table: " . print_r($values,1),array(),'WATCHDOG_ERROR');
-           return false;
-        }
-     }
-   }
-
-   // if trying to insert a field that is the primary key, make sure it also is unique
-   $pkey = $table_desc['primary key'][0];
-   if($insert_values[$pkey]){
-      if(tripal_core_chado_select($table,array($pkey),array($pkey => $insert_values[$pkey]))){
-         watchdog('tripal_core',"tripal_core_chado_insert: Cannot insert duplicate primary key into $table table: " . print_r($values,1),array(),'WATCHDOG_ERROR');
+      // now check the constraint
+      if(tripal_core_chado_select($table,$ukselect_cols,$ukselect_vals)){
+         watchdog('tripal_core',"tripal_core_chado_insert: Cannot insert duplicate record into $table table: " . print_r($values,1),array(),'WATCHDOG_ERROR');
          return false;
       }
    }
+  }
+  
+  // if trying to insert a field that is the primary key, make sure it also is unique
+  $pkey = $table_desc['primary key'][0];
+  if($insert_values[$pkey]){
+    if(tripal_core_chado_select($table,array($pkey),array($pkey => $insert_values[$pkey]))){
+       watchdog('tripal_core',"tripal_core_chado_insert: Cannot insert duplicate primary key into $table table: " . print_r($values,1),array(),'WATCHDOG_ERROR');
+       return false;
+    }
+  }
+  
+  // make sure required fields have a value
+  $fields = $table_desc['fields'];
+  if (!is_array($fields)) {
+   $fields = array();
+   watchdog('tripal_core',"tripal_core_chado_insert: %table not defined in tripal schema api", array('%table' => $table), 'WATCHDOG WARNING');
+  }
+  foreach($fields as $field => $def){
+    // a field is considered missing if it cannot be null and there is no default
+    // value for it or it is of type 'serial'
+    if($def['not null'] == 1 and !array_key_exists($field,$insert_values) and !isset($def['default']) and strcmp($def['type'],serial)!=0){
+       watchdog('tripal_core',"tripal_core_chado_insert: Field $table.$field cannot be null: " . print_r($values,1),array(),'WATCHDOG_ERROR');
+       return false;
+    }
+  }
+  
+  // Now build the insert SQL statement
+  $ifields = array();
+  $ivalues = array();
+  $itypes = array();
+  $iplaceholders = array();
+  $i = 1;
+  foreach ($insert_values as $field => $value){
+    array_push($ifields,$field);
+    array_push($ivalues,$value);
+    array_push($iplaceholders,'$'.$i);
+    $i++;
+    if(strcmp($value,'__NULL__')==0){
+       array_push($itypes,"NULL");
+    } 
+    elseif(strcmp($fields[$field]['type'],'serial')==0 or 
+       strcmp($fields[$field]['type'],'int')==0){
+       array_push($itypes,"%d");
+    } 
+    else {
+       array_push($itypes,"'%s'");
+    }
+  }
 
-   // make sure required fields have a value
-   $fields = $table_desc['fields'];
-   if (!is_array($fields)) {
-   	 $fields = array();
-   	 watchdog('tripal_core',"tripal_core_chado_insert: %table not defined in tripal schema api", array('%table' => $table), 'WATCHDOG WARNING');
-   }
-   foreach($fields as $field => $def){
-      // a field is considered missing if it cannot be null and there is no default
-      // value for it or it is of type 'serial'
-      if($def['not null'] == 1 and !array_key_exists($field,$insert_values) and !isset($def['default']) and strcmp($def['type'],serial)!=0){
-         watchdog('tripal_core',"tripal_core_chado_insert: Field $table.$field cannot be null: " . print_r($values,1),array(),'WATCHDOG_ERROR');
-         return false;
+  if ($build_sql) {   
+    // prepare the statement
+    if ($prepared) {
+      $sql = "INSERT INTO {$table} (" . implode(", ",$ifields) . ") VALUES (". implode(", ",$iplaceholders) .")";
+      
+      $previous_db = tripal_db_set_active('chado');
+      $status = pg_prepare($chado_db, $options['statement_name'], $sql);
+      tripal_db_set_active($previous_db);
+      
+      if (!$status) {
+        watchdog('tripal_core',"tripal_core_chado_insert: not able to prepare '%name' statement for: %sql", array('%name' => $options['statement_name'], '%sql' => $sql), 'WATCHDOG ERROR');
+        return FALSE;
       }
-   }
-
-   // Now build the insert SQL statement
-   $ifields = array();
-   $ivalues = array();
-   $itypes = array();
-   foreach ($insert_values as $field => $value){
-      array_push($ifields,$field);
-      array_push($ivalues,$value);
-      if(strcmp($value,'__NULL__')==0){
-         array_push($itypes,"NULL");
-      } 
-      elseif(strcmp($fields[$field]['type'],'serial')==0 or 
-         strcmp($fields[$field]['type'],'int')==0){
-         array_push($itypes,"%d");
-      } 
-      else {
-         array_push($itypes,"'%s'");
+    } else {
+      $sql = "INSERT INTO {$table} (" . implode(", ",$ifields) . ") VALUES (". implode(", ",$itypes) .")";
+    }
+    
+  }
+    
+  // finally perform the insert. 
+  if ($prepared) {
+    
+      $previous_db = tripal_db_set_active('chado');
+      $result = pg_execute($chado_db, $options['statement_name'], $ivalues);
+      tripal_db_set_active($previous_db);
+      if ($result) {
+        // add primary keys to values before return
+        $primary_key = array();
+        if (!is_array($table_desc['primary key'])) {
+          $table_desc['primary key'] = array();
+          watchdog('tripal_core',"tripal_core_chado_insert: %table not defined in tripal schema api", array('%table' => $table), 'WATCHDOG WARNING');
+        }
+        foreach ($table_desc['primary key'] as $field) {
+          $value = db_last_insert_id($table, $field);
+          $values[$field] = $value;
+        }
+        return $values;
+      } else {
+        watchdog('tripal_core',"tripal_core_chado_insert: not able to execute prepared statement '%name' with values: %values", array('%name' => $options['statement_name'], '%values' => print_r($values,1)), 'WATCHDOG ERROR');
+        return FALSE;
       }
-   }
-   $sql = "INSERT INTO {$table} (" . implode(", ",$ifields) . ") VALUES (". implode(", ",$itypes) .")";
 
-   // finally perform the insert. 
-   $previous_db = tripal_db_set_active('chado');  // use chado database
-   $result = db_query($sql,$ivalues);
-   tripal_db_set_active($previous_db);  // now use drupal database 
-   if($result){
+  } else {
+    $previous_db = tripal_db_set_active('chado');  // use chado database
+    $result = db_query($sql,$ivalues);
+    tripal_db_set_active($previous_db);  // now use drupal database 
+    if($result){
       // add primary keys to values before return
       $primary_key = array();
       if (!is_array($table_desc['primary key'])) {
-      	$table_desc['primary key'] = array();
-      	watchdog('tripal_core',"tripal_core_chado_insert: %table not defined in tripal schema api", array('%table' => $table), 'WATCHDOG WARNING');
+        $table_desc['primary key'] = array();
+        watchdog('tripal_core',"tripal_core_chado_insert: %table not defined in tripal schema api", array('%table' => $table), 'WATCHDOG WARNING');
       }
       foreach ($table_desc['primary key'] as $field) {
         $value = db_last_insert_id($table, $field);
         $values[$field] = $value;
       }
       return $values;
-   } 
-   else {
+    } 
+    else {
       watchdog('tripal_core',"tripal_core_chado_insert: Cannot insert record into $table table: " . print_r($values,1),array(),'WATCHDOG_ERROR');
       return false;
-   }
-   return false;
+    }
+  }
+  
+  return false;
 }
 
 /**
@@ -595,7 +655,7 @@ function tripal_core_chado_select($table,$columns,$values,$options = null){
               'case_insensitive_columns' => $options['case_insensitive_columns']
             );
             $results = tripal_core_chado_get_foreign_key($table_desc,$field,$value, $foreign_options);
-            if (count($results) ==0) {
+            if (sizeof($results) < 1) {
               // foreign key records are required
               // thus if none matched then return false and alert the admin through watchdog
               //watchdog('tripal_core', 
@@ -759,12 +819,10 @@ function tripal_core_chado_get_foreign_key($table_desc,$field,$values, $options
                $select_cols = array($right);
                $result = tripal_core_chado_select($table,$select_cols,$values, $options);
                $fields = array();
-               if(count($result) > 0){
-                  foreach ($result as $obj) {
-                    $fields[] = $obj->$right;
-                  }
-                  return $fields;
+               foreach ($result as $obj) {
+                 $fields[] = $obj->$right;
                }
+               return $fields;
             }
          }
       } 
@@ -1361,22 +1419,19 @@ function chado_get_node_id ($table, $id) {
  *   The base table for which the property should be retrieved. Thus to retrieve a property
  *   for a feature the basetable=feature and property is retrieved from featureprop
  * @param $record_id
- *   The foriegn key field of the base table. This should be in integer.
+ *   The primary key of the basetable to retrieve properties for. This should be in integer.
  * @param $property
  *   The cvterm name describing the type of properties to be retrieved
  * @param $cv_name
  *   The name of the cv that the above cvterm is part of
  *
  * @return
- *   An array in the same format as that generated by the function
- *   tripal_core_generate_chado_var().  If only one record is returned it
- *   is a single object.  If more than one record is returned then it is an array
- *   of objects
+ *   A chado variable with the specified properties expanded
  *
  * @ingroup tripal_chado_api
  */
 function tripal_core_get_property($basetable, $record_id, $property, $cv_name){
-  
+
    // get the foreign key for this property table
    $table_desc = module_invoke_all('chado_'.$basetable.'prop_schema');
    $fkcol = key($table_desc['foreign keys'][$basetable]['columns']);
@@ -1392,7 +1447,6 @@ function tripal_core_get_property($basetable, $record_id, $property, $cv_name){
          'is_obsolete' => 0
       ),
    );
-
    $results = tripal_core_generate_chado_var($basetable.'prop',$values);
    $results = tripal_core_expand_chado_vars($results,'field',$basetable.'prop.value');
    return $results;
@@ -1407,7 +1461,7 @@ function tripal_core_get_property($basetable, $record_id, $property, $cv_name){
  *   The base table for which the property should be inserted. Thus to insert a property
  *   for a feature the basetable=feature and property is inserted into featureprop
  * @param $record_id
- *   The foriegn key field of the base table. This should be in integer. 
+ *   The primary key of the basetable to insert a property for. This should be in integer.
  * @param $property
  *   The cvterm name describing the type of properties to be inserted
  * @param $cv_name
@@ -1430,25 +1484,17 @@ function tripal_core_insert_property($basetable, $record_id, $property,
    // first see if the property already exists, if the user want's to update
    // then we can do that, but otherwise we want to increment the rank and
    // insert
-   $props = tripal_core_get_property($basetable,$record_id,$property,$cv_name);
-   if(!is_array($props)) { 
-    $props = array($props); 
-   }   
+   $prop = tripal_core_get_property($basetable,$record_id,$property,$cv_name);
    $rank = 0;
-   if(count($props)>0){       
+   if(count($prop)>0){ 
       if($update_if_present){
-         return tripal_core_update_property($basetable, $record_id, $property, $cv_name, $value) ;
+         return tripal_core_update_property($basetable,$record_id,$property,$cv_name,$value) ;
       } else {
-         // iterate through the properties returned and check to see if the
-         // property with this value already exists if not, get the largest rank
-         // and insert the same property but with this new value
-         foreach($props as $p){
+         // iterate through the properties returned and get the largest rank
+         foreach($prop as $p){
             if($p->rank > $rank){
                $rank = $p->rank;
             }
-            if(strcmp($p->value,$value)==0){
-               return TRUE;
-            }
          }
          // now add 1 to the rank
          $rank++;
@@ -1745,6 +1791,47 @@ function tripal_db_set_active($dbname){
    }
    else return db_set_active($dbname);
 }
+
+/**
+ * Instantiate or Return a persistent chado connection
+ *
+ * NOTE: cannot use $active_db since a new connection is created each time 
+ * db_set_active() is called
+ *
+ * @return
+ *   A postgresql connection object which can be used by pg_prepare, pg_execute, etc.
+ */
+function tripal_db_persistent_chado () {
+  global $db_url;
+  
+  // get connection if it already exists
+  $connection = variable_get('tripal_perisistent_chado',NULL);
+  
+  if ($connection) {
+    return $connection;
+  
+  // Otherwise we need to set it
+  } else {
+    if (is_array($db_url) && isset($db_url['chado'])) {
+      $connection = db_connect($db_url['chado']);
+      variable_set('tripal_perisistent_chado', $connection); 
+    } else {
+      $connection = db_connect($db_url);
+      variable_set('tripal_perisistent_chado', $connection); 
+    }
+    
+    return $connection;
+  }
+  return FALSE;
+}
+
+/**
+ * Release a persistent chado connection
+ */
+function tripal_db_release_persistent_chado () {
+  variable_del('tripal_perisistent_chado');
+}
+
 /**
  * Purpose: Get max rank for a given set of criteria
  *   This function was developed with the many property tables in chado in mind
@@ -1797,40 +1884,3 @@ function tripal_get_max_chado_rank ($tablename, $where_options) {
 		return -1;
 	}
 }
-/**
- * Add a new table to the Chado schema. This function is simply a wrapper for
- * the db_create_table() function of Drupal, but ensures the table is created
- * inside the Chado schema rather than the Drupal schema.
- *
- * @param $ret
- *   Array to which query results will be added.
- * @param $table
- *   The name of the table to create.
- * @param $schema 
- *   A Drupal-style Schema API definition of the table
- *
- * @return 
- *   A database query result resource for the new table, or FALSE if table was not constructed.
- *
- * @ingroup tripal_core_api
- */
-function tripal_create_chado_table (&$ret,$table,$schema) {
-   $ret = array();
-   
-   $previous_db = tripal_db_set_active('chado');  // use chado database
-   db_create_table($ret,$table,$schema);
-   tripal_db_set_active($previous_db);  // now use drupal database
-   
-   // if the table creation was succesful then add an entry
-   // in the tripal_custom_table
-   if($ret){
-      $record = new stdClass();
-      $record->table_name = $table;
-      $record->schema = serialize($schema);
-      $success = drupal_write_record('tripal_custom_tables',$record);
-      if(!$success){
-         drupal_set_message($message,"Error adding custom table: $table");   
-      }
-   }
-   return $ret;
-}