updated core update,select,insert and delete to use Drupal style placeholders. had to remove code for prepared statements. the db module now supports adding/editing and deleting of databases

tripal_core/api/tripal_core_chado.api.inc

@@ -299,14 +299,6 @@ function tripal_core_chado_insert($table, $values, $options = array()) {
  *  An associative array containing the values for updating.
  * @param $options
  *  An array of options such as:
- *  - statement_name: the name of the prepared statement to use. If the statement
- *     has not yet been prepared it will be prepared automatically. On subsequent
- *     calls with the same statement_name only an execute on the previously
- *     prepared statement will occur.
- *  - is_prepared: TRUE or FALSE. Whether or not the statement is prepared. By
- *     default if the statement is not prepared it will be automatically.
- *     However to avoid this check, which requires a database query you can
- *     set this value to true and the check will not be performed.
  *  - return_record: by default, the function will return the TRUE if the record
  *     was succesfully updated.  However, set this option to TRUE to return the
  *     record that was updated.  The returned record will have the fields provided
@@ -381,14 +373,7 @@ function tripal_core_chado_update($table, $match, $values, $options = NULL) {
   if (!is_array($options)) {
     $options = array();
   }
-/*  
-  if (!array_key_exists('is_prepared', $options)) {
-    $options['is_prepared'] = FALSE;
-  }
-  if (!array_key_exists('statement_name', $options)) {
-    $options['statement_name'] = FALSE;
-  }
-*/  
+
   if (!array_key_exists('return_record', $options)) {
     $options['return_record'] = FALSE;
   }
@@ -396,28 +381,6 @@ function tripal_core_chado_update($table, $match, $values, $options = NULL) {
   $update_values = array();   // contains the values to be updated
   $update_matches = array();  // contains the values for the where clause
 
-/*  
-  // Determine plan of action
-  if ($options['statement_name']) {
-    // we have a prepared statment (or want to create one) so set $prepared = TRUE
-    $prepared = TRUE;
-
-    // we need to get a persistent connection.  If one exists this function
-    // will not recreate it, but if not it will create one and store it in
-    // a Drupal variable for reuse later.
-    $connection = tripal_db_persistent_chado();
-
-    // if we cannot get a connection the abandon the prepared statement
-    if (!$connection ) {
-       $prepared = FALSE;
-       unset($options['statement_name']);
-    }
-  }
-  else {
-    //print "NO STATEMENT (update): $table\n";
-    //debug_print_backtrace();
-  }
-*/  
 
   // get the table description
   $table_desc = tripal_core_get_chado_table_schema($table);
@@ -446,21 +409,8 @@ function tripal_core_chado_update($table, $match, $values, $options = NULL) {
 
   // get the values needed for matching in the SQL statement
   foreach ($match as $field => $value) {
-    if (is_array($value)) {
-      $foreign_options = array();
-/*      
-      if ($options['statement_name']) {
-        // add the fk relationship info to the prepared statement name so that
-        // we can prepare the selects run by the recrusive tripal_core_chado_get_foreign_key
-        // function.
-        $fk_sname = "fk_" . $table . "_" . $field;
-        foreach ($value as $k => $v) {
-          $fk_sname .= substr($k, 0, 2);
-        }
-        $foreign_options['statement_name'] = $fk_sname;
-      }
-*/      
-      $results = tripal_core_chado_get_foreign_key($table_desc, $field, $value, $foreign_options);
+    if (is_array($value)) {   
+      $results = tripal_core_chado_get_foreign_key($table_desc, $field, $value);
       if (sizeof($results) > 1) {
         watchdog('tripal_core', 'tripal_core_chado_update: When trying to find record to update, too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value, TRUE)), WATCHDOG_ERROR);
       }
@@ -480,19 +430,7 @@ function tripal_core_chado_update($table, $match, $values, $options = NULL) {
   foreach ($values as $field => $value) {
     if (is_array($value)) {
       $foreign_options = array();
-      // select the value from the foreign key relationship for this value
-/*      
-      if ($options['statement_name']) {
-        // add the fk relationship info to the prepared statement name so that
-        // we can prepare the selects run by the recrusive tripal_core_chado_get_foreign_key
-        // function.
-        $fk_sname = "fk_" . $table . "_" . $field;
-        foreach ($value as $k => $v) {
-          $fk_sname .= substr($k, 0, 2);
-        }
-        $foreign_options['statement_name'] = $fk_sname;
-      }
-*/      
+      // select the value from the foreign key relationship for this value   
       $results = tripal_core_chado_get_foreign_key($table_desc, $field, $value, $foreign_options);
       if (sizeof($results) > 1) {
         watchdog('tripal_core', 'tripal_core_chado_update: When trying to find update values, 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);
@@ -511,171 +449,32 @@ function tripal_core_chado_update($table, $match, $values, $options = NULL) {
 
   // now build the SQL statement
   $sql  = 'UPDATE {' . $table . '} SET ';
-  $psql = 'UPDATE {' . $table . '} SET ';
-  $uargs = array();
-  $idatatypes = array();
-  $pvalues = array();
-  $ivalues = array();
-  $i = 1;
-  foreach ($update_values as $field => $value) {
-
-    if (strcasecmp($table_desc['fields'][$field]['type'], 'serial')==0 OR
-        strcasecmp($table_desc['fields'][$field]['type'], 'int')==0 OR
-        strcasecmp($table_desc['fields'][$field]['type'], 'integer')==0) {
-      if (strcmp($value, '__NULL__') == 0) {
-        $sql .= " $field = %s, ";
-        $ivalues[] = 'NULL';
-        $pvalues[] = '%s';
-        $uargs[] = 'NULL';
-      }
-      else {
-        $sql .= " $field = %d, ";
-        $ivalues[] = $value;
-        $pvalues[] = '%d';
-        $uargs[] = $value;
-      }
-      $idatatypes[] = 'int';
-
-    }
-    elseif (strcasecmp($table_desc['fields'][$field]['type'], 'boolean')==0) {
-      $sql .= " $field = %s, ";
-      $pvalues[] = '%s';
-      if (strcmp($value, '__NULL__')==0) {
-        $ivalues[] = 'NULL';
-        $uargs[] = 'NULL';
-      }
-      else {
-        $ivalues[] = $value;
-        $uargs[] = $value;
-      }
-      $idatatypes[] = 'bool';
-    }
-    elseif (strcasecmp($table_desc['fields'][$field]['type'], 'float')==0) {
-      $sql .= " $field = %s, ";
-      $pvalues[] = '%s';
-      if (strcmp($value, '__NULL__')==0) {
-        $ivalues[] = 'NULL';
-        $uargs[] = 'NULL';
-      }
-      else {
-        $ivalues[] = $value;
-        $uargs[] = $value;
-      }
-      $idatatypes[] = 'numeric';
+  $args = array();        // arguments passed to chado_query
+  foreach ($update_values as $field => $value) {    
+    if (strcmp($value, '__NULL__') == 0) {
+      $sql .= " $field = NULL, ";
     }
     else {
-      if (strcmp($value, '__NULL__') == 0) {
-        $sql .= " $field = %s, ";
-        $ivalues[] = 'NULL';
-        $uargs[] = 'NULL';
-        $pvalues[] = '%s';
-      }
-      else {
-        $sql .= " $field = '%s', ";
-        $ivalues[] = $value;
-        $uargs[] = $value;
-        $pvalues[] = "'%s'";
-      }
-      $idatatypes[] = 'text';
-    }
-    $psql .= "$field = \$" . $i . ", ";
-    $i++;
+      $sql .= " $field = :$field, ";
+      $args[":$field"] = $value;
+    }    
   }
   $sql = drupal_substr($sql, 0, -2);  // get rid of the trailing comma & space
-  $psql = drupal_substr($psql, 0, -2);  // get rid of the trailing comma & space
 
   $sql .= " WHERE ";
-  $psql .= " WHERE ";
   foreach ($update_matches as $field => $value) {
-
-    if (strcasecmp($table_desc['fields'][$field]['type'], 'serial')==0 OR
-        strcasecmp($table_desc['fields'][$field]['type'], 'int')==0 OR
-        strcasecmp($table_desc['fields'][$field]['type'], 'integer')==0) {
-      if (strcmp($value, '__NULL__')==0) {
-        $sql .= " $field = %s AND ";
-        $ivalues[] = 'NULL';
-        $uargs[] = 'NULL';
-        $pvalues[] = '%s';
-      }
-      else {
-        $sql .= " $field = %d AND ";
-        $ivalues[] = $value;
-        $uargs[] = $value;
-        $pvalues[] = '%s';
-      }
-      $idatatypes[] = 'int';
-    }
-    elseif (strcasecmp($table_desc['fields'][$field]['type'], 'boolean')==0) {
-      $sql .= " $field = %s AND ";
-      $pvalues[] = '%s';
-      if (strcmp($value, '__NULL__')==0) {
-        $ivalues[] = 'NULL';
-        $uargs[] = 'NULL';
-      }
-      else {
-        $ivalues[] = $value;
-        $uargs[] = $value;
-      }
-      $idatatypes[] = 'bool';
-    }
-    elseif (strcasecmp($table_desc['fields'][$field]['type'], 'float')==0) {
-      $sql .= " $field = %s AND ";
-      $pvalues[] = '%s';
-      if (strcmp($value, '__NULL__')==0) {
-        $ivalues[] = 'NULL';
-        $uargs[] = 'NULL';
-      }
-      else {
-        $ivalues[] = $value;
-        $uargs[] = $value;
-      }
-      $idatatypes[] = 'numeric';
+    if (strcmp($value, '__NULL__')==0) {
+      $sql .= " $field = NULL AND ";
     }
     else {
-      if (strcmp($value, '__NULL__')==0) {
-        $sql .= " $field = %s AND ";
-        $ivalues[] = 'NULL';
-        $uargs[] = 'NULL';
-        $pvalues[] = '%s';
-      }
-      else {
-        $sql .= " $field = '%s' AND ";
-        $ivalues[] = $value;
-        $uargs[] = $value;
-        $pvalues[] = "'%s'";
-      }
-      $idatatypes[] = 'text';
-    }
-    $psql .= "$field = \$" . $i . " AND ";
-    $i++;
+      $sql .= " $field = :$field AND ";
+      $args[":$field"] = $value;
+    }    
   }
   $sql = drupal_substr($sql, 0, -4);  // get rid of the trailing 'AND'
-  $psql = drupal_substr($psql, 0, -4);  // get rid of the trailing 'AND'
 
-  // finish constructing the prepared SQL statement
-//  $psql =  "PREPARE " . $options['statement_name'] . " (" . implode(', ', $idatatypes) . ") AS " . $psql;
+  $result = chado_query($sql, $args);
 
-  // finally perform the update.  If successful, return the updated record
-/*  
-  if ($prepared) {
-    // if this is the first time we've run this query
-    // then we need to do the prepare, otherwise just execute
-    if ($options['is_prepared'] != TRUE and !tripal_core_is_sql_prepared($options['statement_name'])) {
-      $status = chado_query($psql);
-      if (!$status) {
-        watchdog('tripal_core', "tripal_core_chado_update: not able to prepare '%name' statement for: %sql",
-          array('%name' => $options['statement_name'], '%sql' => $sql), WATCHDOG_ERROR);
-        return FALSE;
-      }
-    }
-    $sql = "EXECUTE " . $options['statement_name'] . "(" . implode(", ", $pvalues) . ")";
-    $result = chado_query($sql, $ivalues);
-  }
-  // if it's not a prepared statement then insert normally
-  else {
-*/  
-    $result = chado_query($sql, $uargs);
-//  }
   // if we have a result then add primary keys to return array
   if ($options['return_record'] == TRUE and $result) {
     // only if we have a single result do we want to add the primary keys to the values
@@ -713,15 +512,7 @@ function tripal_core_chado_update($table, $match, $values, $options = NULL) {
  * @param $match
  *  An associative array containing the values for locating a record to update.
  * @param $options
- *  An array of options such as:
- *  - statement_name: the name of the prepared statement to use. If the statement
- *     has not yet been prepared it will be prepared automatically. On subsequent
- *     calls with the same statement_name only an execute on the previously
- *     prepared statement will occur.
- *  - is_prepared: TRUE or FALSE. Whether or not the statement is prepared. By
- *     default if the statement is not prepared it will be automatically.
- *     However to avoid this check, which requires a database query you can
- *     set this value to true and the check will not be performed.
+ *  Currently there are no options
  * @return
  *   On success this function returns TRUE. On failure, it returns FALSE.
  *
@@ -751,7 +542,7 @@ function tripal_core_chado_update($table, $match, $values, $options = NULL) {
      'is_obsolete' => 0
    ),
  );
- *   $result = tripal_core_chado_update('feature',$umatch,$uvalues);
+ *   $result = tripal_core_chado_update('feature', $umatch, $uvalues);
  * @endcode
  * The above code species that a feature with a given uniquename, organism_id,
  * and type_id (the unique constraint for the feature table) will be deleted.
@@ -781,35 +572,7 @@ function tripal_core_chado_delete($table, $match, $options = NULL) {
   if (!is_array($options)) {
     $options = array();
   }
-/*  
-  if (!array_key_exists('is_prepared', $options)) {
-    $options['is_prepared'] = FALSE;
-  }
-  if (!array_key_exists('statement_name', $options)) {
-    $options['statement_name'] = FALSE;
-  }
 
-  // Determine plan of action
-  if ($options['statement_name']) {
-    // we have a prepared statment (or want to create one) so set $prepared = TRUE
-    $prepared = TRUE;
-
-    // we need to get a persistent connection.  If one exists this function
-    // will not recreate it, but if not it will create one and store it in
-    // a Drupal variable for reuse later.
-    $connection = tripal_db_persistent_chado();
-
-    // if we cannot get a connection the abandon the prepared statement
-    if (!$connection ) {
-       $prepared = FALSE;
-       unset($options['statement_name']);
-    }
-  }
-  else {
-    //print "NO STATEMENT (update): $table\n";
-    //debug_print_backtrace();
-  }
-*/
   $delete_matches = array();  // contains the values for the where clause
 
   // get the table description
@@ -844,118 +607,36 @@ function tripal_core_chado_delete($table, $match, $options = NULL) {
 
   // now build the SQL statement
   $sql = 'DELETE FROM {' . $table . '} WHERE ';
-  $psql = $sql;
-  $uargs = array();
-  $idatatypes = array();
-  $pvalues = array();
-  $ivalues = array();
-  $dargs = array();
-  $void_prepared = 0;
-  $i = 1;
+  $args = array();
   foreach ($delete_matches as $field => $value) {
-
     // if we have an array values then this is an "IN" clasue.
     // we cannot use prepared statements with these
+    
     if (count($value) > 1) {
-      $sql .= "$field IN (" . db_placeholders($value, 'varchar') . ") AND ";
+      $sql .= "$field IN (";
+      $index = 0;
       foreach ($value as $v) {
-        $dargs[] = $v;
+      	$sql .= ":$field" . $index . ", ";
+        $args[":$field" . $index] = $v;
+        $index++;
       }
-      $void_prepared = 1;
-      continue;
+      $sql = drupal_substr($sql, 0, -2); // get rid of trailing ', '
+      $sql .= ") AND ";
     }
-
-    if (strcasecmp($table_desc['fields'][$field]['type'], 'serial') == 0 OR
-        strcasecmp($table_desc['fields'][$field]['type'], 'int') == 0 OR
-        strcasecmp($table_desc['fields'][$field]['type'], 'integer') == 0) {
+    else {
       if (strcmp($value, '__NULL__') == 0) {
         $sql .= " $field = NULL AND ";
-        $ivalues[] = 'NULL';
-        $pvalues[] = '%s';
-        $uargs[] = 'NULL';
-      }
-      else {
-        $sql .= " $field = %d AND ";
-        $ivalues[] = $value;
-        $pvalues[] = '%d';
-        $uargs[] = $value;
-      }
-      $idatatypes[] = 'int';
-    }
-    elseif (strcasecmp($table_desc['fields'][$field]['type'], 'boolean')==0) {
-      $sql .= " $field = %s AND ";
-      $pvalues[] = '%s';
-      if (strcmp($value, '__NULL__')==0) {
-        $ivalues[] = 'NULL';
-        $uargs[] = 'NULL';
       }
       else {
-        $ivalues[] = $value;
-        $uargs[] = $value;
+        $sql .= " $field = :$field AND ";
+        $args[":$field"] = $value;
       }
-      $idatatypes[] = 'bool';
-    }
-    elseif (strcasecmp($table_desc['fields'][$field]['type'], 'float')==0) {
-      $sql .= " $field = %s AND ";
-      $pvalues[] = '%s';
-      if (strcmp($value, '__NULL__')==0) {
-        $ivalues[] = 'NULL';
-        $uargs[] = 'NULL';
-      }
-      else {
-        $ivalues[] = $value;
-        $uargs[] = $value;
-      }
-      $idatatypes[] = 'numeric';
     }
-    else {
-      if (strcmp($value, '__NULL__')==0) {
-        $sql .= " $field = %s AND ";
-        $ivalues[] = 'NULL';
-        $uargs[] = 'NULL';
-        $pvalues[] = '%s';
-      }
-      else {
-        $sql .= " $field = '%s' AND ";
-        $ivalues[] = $value;
-        $uargs[] = $value;
-        $pvalues[] = "'%s'";
-      }
-      $idatatypes[] = 'text';
-    }
-    array_push($dargs, $value);
-    $psql .= "$field = \$" . $i . " AND ";
-    $i++;
   }
   $sql = drupal_substr($sql, 0, -4);  // get rid of the trailing 'AND'
-  $psql = drupal_substr($psql, 0, -4);  // get rid of the trailing 'AND'
-
-  // finish constructing the prepared SQL statement
-//  $psql =  "PREPARE " . $options['statement_name'] . " (" . implode(', ', $idatatypes) . ") AS " . $psql;
-/*
-  // finally perform the update.  If successful, return the updated record
-  if ($prepared and !$void_prepared) {
-    // if this is the first time we've run this query
-    // then we need to do the prepare, otherwise just execute
-    if ($options['is_prepared'] != TRUE and
-    !tripal_core_is_sql_prepared($options['statement_name'])) {
-      $status = chado_query($psql);
-      if (!$status) {
-        watchdog('tripal_core', "tripal_core_chado_delete: not able to prepare '%name' statement for: %sql", array('%name' => $options['statement_name'], '%sql' => $sql), WATCHDOG_ERROR);
-        return FALSE;
-      }
-    }
-    $sql = "EXECUTE " . $options['statement_name'] . "(" . implode(", ", $pvalues) . ")";
-    $resource = chado_query($sql, $ivalues);
-  }
-  // if it's not a prepared statement then insert normally
-  else {
-*/  
-    $resource = chado_query($sql, $uargs);
-//  }
 
   // finally perform the delete.  If successful, return the updated record
-  $result = chado_query($sql, $dargs);
+  $result = chado_query($sql, $args);
   if ($result) {
     return TRUE;
   }
@@ -1332,10 +1013,11 @@ function tripal_core_chado_select($table, $columns, $values, $options = NULL) {
         $sql .= "$field IN (";
         $index = 0;
         foreach ($value as $v) {
-        	$sql .= ':' . $field . $index . ', ';
-          $args[':' . $field . $index] = $v;
+        	$sql .= ":$field" . $index . ', ';
+          $args[":$field" . $index] = $v;
+          $index++;
         }
-        $sql = substr($sql, -2, 0); // remove trailing ', '
+        $sql = drupal_substr($sql, 0, -2); // remove trailing ', '
         $sql .= ") AND ";
       }
       // if we have a null value then we need an IS NULL in our where statement

tripal_db/includes/tripal_db.admin.inc

@@ -25,7 +25,7 @@ function tripal_db_select_form() {
  * 
  * @ingroup tripal_db
  */
-function tripal_db_db_edit_form($form, $form_state) {
+function tripal_db_db_edit_form($form, &$form_state) {
   
 	// get the dbid if form was submitted via AJAX
 	$dbid = 0;
@@ -54,24 +54,15 @@ function tripal_db_db_edit_form($form, $form_state) {
       'event'    => 'change',
       'method'   => 'replace',
     ),
-    '#suffix' => '<div id="db-edit-div"></div>',
-    '#default_value' => $dbid,
+    '#default_value' => $dbid,    
   );
+  
       
-  // if we don't have a db_id then we can safetly return the form
+  // if we don't have a db_id then we can  return the form, otherwise
+  // add in the other fields
   if ($dbid) {
-  	  	
-    // if we are here because of an AJAX calback, that means the database select
-    // box was changed and the form is being rebuilt on an AJAX call not on a
-    // form validation error.  Therefore, we want to provide the dbid  
-    if (array_key_exists('triggering_element', $form_state) and 
-        $form_statte['triggerming_element']['#ajax']['callback'] = tripal_db_edit_form_ajax) {
-	    tripal_db_add_db_form_fields($form, $form_state, $dbid);
-    }
-    else {
-    	tripal_db_add_db_form_fields($form, $form_state);
-    }
-	  
+    tripal_db_add_db_form_fields($form, $form_state, $dbid);
+    	  
 	  $form['update'] = array(
 	    '#type'         => 'submit',
 	    '#value'        => t('Update'),
@@ -83,6 +74,15 @@ function tripal_db_db_edit_form($form, $form_state) {
       '#weight'       => 6,
     );
   }
+  else {
+  	// if we don't have a dbid then this is the first time the form has
+  	// benn loaded and we need to create the div where ajax replacement elements get stored
+  	$form['div_replace'] = array(
+  	  '#type' => 'item',
+  	  '#prefix' => '<div id="db-edit-div">',
+  	  '#suffix' => '</div>',
+  	);
+  }
   return $form;
 }
 /**
@@ -118,23 +118,17 @@ function tripal_db_add_db_form_fields(&$form, $form_state, $dbid = NULL) {
   $default_desc      = '';
   $default_url       = '';
   $default_urlprefix = '';
-      
-  // get the default values from the databae first  
+        
+  // get the default values from the database first  
   if ($dbid) {
     $values = array('db_id' => $dbid);
-    $db = tripal_core_chado_select('db', array('*'), $values);    
-    $default_db        = $db[0]->name;
-    $default_desc      = $db[0]->description;
-    $default_url       = $db[0]->url;
-    $default_urlprefix = $db[0]->urlprefix;  
-  }    
-  // set the default value to the form_state if those exist
-  elseif (array_key_exists('values', $form_state)) {
-    $default_db        = array_key_exists('name', $form_state['values'])        ? $form_state['values']['name']        : $default_db;
-    $default_desc      = array_key_exists('description', $form_state['values']) ? $form_state['values']['description'] : $default_desc;
-    $default_url       = array_key_exists('url', $form_state['values'])         ? $form_state['values']['url']         : $default_url;
-    $default_urlprefix = array_key_exists('urlprefix', $form_state['values'])   ? $form_state['values']['urlprefix']   : $default_urlprefix;      
-  }     
+    $result = tripal_core_chado_select('db', array('*'), $values);
+    $db = $result[0]; 
+    $default_db = $db->name;
+    $default_desc = $db->description;
+    $default_url = $db->url;
+    $default_urlprefix = $db->urlprefix;   
+  }   
     
   // add a fieldset for the Drupal Schema API
   $form['fields'] = array(
@@ -149,7 +143,6 @@ function tripal_db_add_db_form_fields(&$form, $form_state, $dbid = NULL) {
     '#description'   => t('Please enter the name for this external database.'),
     '#required'      => TRUE,
     '#default_value' => $default_db,
-    '#weight'        => 1,
     '#maxlength'     => 255,
   );
 
@@ -158,7 +151,6 @@ function tripal_db_add_db_form_fields(&$form, $form_state, $dbid = NULL) {
     '#title'         => t('Description'),
     '#description'   => t('Please enter a description for this database'),
     '#default_value' => $default_desc,
-    '#weight'        => 2,
     '#maxlength'     => 255,
   );
   $form['fields']['url']= array(
@@ -166,7 +158,6 @@ function tripal_db_add_db_form_fields(&$form, $form_state, $dbid = NULL) {
     '#title'         => t('URL'),
     '#description'   => t('Please enter the web address for this database.'),
     '#default_value' => $default_url,
-    '#weight'        => 3,
     '#maxlength'     => 255,
   );
   $form['fields']['urlprefix']= array(
@@ -174,10 +165,8 @@ function tripal_db_add_db_form_fields(&$form, $form_state, $dbid = NULL) {
     '#title'         => t('URL prefix'),
     '#description'   => t('Tripal can provide links to external databases when accession numbers or unique identifiers are known.  Typically, a database will provide a unique web address for each accession and the accession usually is the last component of the page address.  Please enter the web address, minus the accession number for this database.  When an accession number is present, Tripal will combine this web address with the accession and provide a link to the external site.'),
     '#default_value' => $default_urlprefix,
-    '#weight'        => 4,
     '#maxlength'     => 255,
   );
-
   return $form;
 }
 
@@ -209,10 +198,11 @@ function tripal_db_db_edit_form_validate($form, &$form_state) {
  * @ingroup tripal_db
  */
 function tripal_db_form_fields_validate($form, &$form_state) {
-  $name =  trim($form_state['values']['name']);
-  $desc =  trim($form_state['values']['description']);
-  $url  =  trim($form_state['values']['url']);
-  $urlp =  trim($form_state['values']['urlprefix']);
+  $name =  array_key_exists('name', $form_state['values'])        ? trim($form_state['values']['name']) : '';
+  $desc =  array_key_exists('description', $form_state['values']) ? trim($form_state['values']['description']) : '';
+  $url  =  array_key_exists('url', $form_state['values'])         ? trim($form_state['values']['url']) : '';
+  $urlp =  array_key_exists('urlprefix', $form_state['values'])   ? trim($form_state['values']['urlprefix']) : '';  
+  $dbid =  array_key_exists('dbid', $form_state['values'])        ? trim($form_state['values']['dbid']) : '';
  
   // make sure the database name is unique
   $values = array('name' => $name);
@@ -230,10 +220,10 @@ function tripal_db_form_fields_validate($form, &$form_state) {
  */
 function tripal_db_db_add_form_submit($form, &$form_state) {
 
-  $name =  trim($form_state['values']['name']);
-  $desc =  trim($form_state['values']['description']);
-  $url  =  trim($form_state['values']['url']);
-  $urlp =  trim($form_state['values']['urlprefix']);
+  $name =  array_key_exists('name', $form_state['values'])        ? trim($form_state['values']['name']) : '';
+  $desc =  array_key_exists('description', $form_state['values']) ? trim($form_state['values']['description']) : '';
+  $url  =  array_key_exists('url', $form_state['values'])         ? trim($form_state['values']['url']) : '';
+  $urlp =  array_key_exists('urlprefix', $form_state['values'])   ? trim($form_state['values']['urlprefix']) : '';  
 
   $values = array(
     'name' => $name,
@@ -259,11 +249,11 @@ function tripal_db_db_add_form_submit($form, &$form_state) {
  */
 function tripal_db_db_edit_form_submit($form, &$form_state) {
 
-  $name =  trim($form_state['values']['name']);
-  $desc =  trim($form_state['values']['description']);
-  $url  =  trim($form_state['values']['url']);
-  $urlp =  trim($form_state['values']['urlprefix']);
-  $dbid =  trim($form_state['values']['dbid']);
+  $name =  array_key_exists('name', $form_state['values'])        ? trim($form_state['values']['name']) : '';
+  $desc =  array_key_exists('description', $form_state['values']) ? trim($form_state['values']['description']) : '';
+  $url  =  array_key_exists('url', $form_state['values'])         ? trim($form_state['values']['url']) : '';
+  $urlp =  array_key_exists('urlprefix', $form_state['values'])   ? trim($form_state['values']['urlprefix']) : '';  
+  $dbid =  array_key_exists('dbid', $form_state['values'])        ? trim($form_state['values']['dbid']) : '';
   $op   =  trim($form_state['values']['op']);
 
   $values = array(
@@ -272,6 +262,7 @@ function tripal_db_db_edit_form_submit($form, &$form_state) {
     'url' => $url,
     'urlprefix' => $urlp,
   );
+
   if (strcmp($op, 'Update')==0) {      
     $match = array('db_id' => $dbid);
     $success = tripal_core_chado_update('db', $match, $values);
@@ -298,6 +289,27 @@ function tripal_db_db_edit_form_submit($form, &$form_state) {
  * @ingroup tripal_db
  */
 function tripal_db_edit_form_ajax($form, $form_state) {
-	unset($form['dbid']);	
-  return $form;
+	
+	$elements = array();
+	
+	// add in the form fields and the buttons	
+	if (array_key_exists('dbid', $form_state['values'])) {
+		$elements['fields'] = $form['fields'];
+		$elements['update'] = $form['update'];
+		$elements['delete'] = $form['delete'];
+	}
+	
+	 // add back in the db-edit-div that is used for the next round of AJAX
+  $elements['fields']['#prefix'] =  '<div id="db-edit-div">';
+  $elements['fields']['#suffix'] =  '</div">';
+  
+  // reset the values for the fields to the defaults
+  $elements['fields']['name']['#value']        = $elements['fields']['name']['#default_value'];
+  $elements['fields']['description']['#value'] = $elements['fields']['description']['#default_value'];
+  $elements['fields']['url']['#value']         = $elements['fields']['url']['#default_value'];
+  $elements['fields']['urlprefix']['#value']   = $elements['fields']['urlprefix']['#default_value'];
+	
+	//drupal_set_message('<pre>' . print_r($elements, TRUE) . '</pre>', "status");
+	
+  return $elements;
 }