More work on Drupal Views Integration. Added support for new handlers, changed table structure, altered submit code and form

base/tripal_core/tripal_core.install

@@ -49,10 +49,62 @@ function tripal_core_uninstall(){
 * @ingroup tripal_core
 */
 function tripal_core_get_schemas (){  
-  $schema = array();
+   $schema = array();
 
+   // get all the various schema parts and join them together
+   $temp = tripal_core_jobs_schema();
+   foreach ($temp as $table => $arr){ 
+      $schema[$table] = $arr; 
+   }
+   $temp = tripal_core_mviews_schema();
+   foreach ($temp as $table => $arr){ 
+      $schema[$table] = $arr; 
+   }
+   $temp = tripal_core_views_schema();
+   foreach ($temp as $table => $arr){ 
+      $schema[$table] = $arr; 
+   } 
 
-  $schema['tripal_jobs'] = array(
+	return $schema;
+}
+/************************************************************************
+* 
+*
+* @ingroup tripal_core
+*/
+function tripal_core_mviews_schema(){
+   $schema = array();
+   $schema['tripal_mviews'] = array(
+      'fields' => array(
+         'mview_id'      => array('type' => 'serial', 'unsigned' => TRUE, 'not null' => TRUE),
+         'name'          => array('type' => 'varchar','length' => 255, 'not null' => TRUE),
+         'modulename'    => array('type' => 'varchar','length' => 50, 'not null' => TRUE, 'description' => 'The module name that provides the callback for this job'),
+         'mv_table'      => array('type' => 'varchar','length' => 128, 'not null' => TRUE),
+         'mv_specs'      => array('type' => 'text', 'size' => 'normal', 'not null' => TRUE),
+         'indexed'       => array('type' => 'text', 'size' => 'normal', 'not null' => TRUE),
+         'query'         => array('type' => 'text', 'size' => 'normal', 'not null' => TRUE),
+         'special_index' => array('type' => 'text', 'size' => 'normal', 'not null' => FALSE),
+         'last_update'   => array('type' => 'int', 'not null' => FALSE, 'description' => 'UNIX integer time'),
+      ),
+      'indexes' => array(
+         'mview_id' => array('mview_id')
+      ),
+      'unique keys' => array(
+         'mv_table' => array('mv_table'),
+         'mv_name' => array('name'),
+      ),
+      'primary key' => array('mview_id'),
+  );
+  return $schema;
+}
+/************************************************************************
+* 
+*
+* @ingroup tripal_core
+*/
+function tripal_core_jobs_schema(){
+   $schema = array();
+   $schema['tripal_jobs'] = array(
       'fields' => array(
          'job_id' => array('type' => 'serial', 'unsigned' => TRUE, 'not null' => TRUE),
          'uid' => array ('type' => 'int', 'unsigned' => TRUE, 'not null' => TRUE, 'description' => 'The Drupal userid of the submitee'),
@@ -76,41 +128,17 @@ function tripal_core_get_schemas (){
          'job_name' => array('job_name')
       ),
       'primary key' => array('job_id'),
-  );
-
-  $schema['tripal_mviews'] = array(
-      'fields' => array(
-         'mview_id' => array('type' => 'serial', 'unsigned' => TRUE, 'not null' => TRUE),
-         'name' => array('type' => 'varchar','length' => 255, 'not null' => TRUE),
-         'modulename' => array('type' => 'varchar','length' => 50, 'not null' => TRUE, 'description' => 'The module name that provides the callback for this job'),
-         'mv_table' => array('type' => 'varchar','length' => 128, 'not null' => TRUE),
-         'mv_specs' => array('type' => 'text', 'size' => 'normal', 'not null' => TRUE),
-         'indexed' => array('type' => 'text', 'size' => 'normal', 'not null' => TRUE),
-         'query' => array('type' => 'text', 'size' => 'normal', 'not null' => TRUE),
-         'special_index' => array('type' => 'text', 'size' => 'normal', 'not null' => FALSE),
-         'last_update' => array ('type' => 'int', 'not null' => FALSE, 'description' => 'UNIX integer time'),
-      ),
-      'indexes' => array(
-         'mview_id' => array('mview_id')
-      ),
-      'unique keys' => array(
-         'mv_table' => array('mv_table'),
-         'mv_name' => array('name'),
-      ),
-      'primary key' => array('mview_id'),
-  );
-
-   $schema = tripal_core_views_integration_schema();
-
-	return $schema;
+   );
+   return $schema;
 }
 /************************************************************************
 * 
 *
 * @ingroup tripal_core
 */
-function tripal_core_views_integration_schema(){
-	$schema['tripal_views_integration'] = array(
+function tripal_core_views_schema(){
+   $schema = array();
+	$schema['tripal_views'] = array(
 		'description' => 'contains the setupes, their materialized view id and base table name that was used.',
 		'fields' => array(
 			'setup_id' => array(
@@ -124,8 +152,8 @@ function tripal_core_views_integration_schema(){
 				'type' => 'int',
 				'unsigned' => TRUE,
 			),
-			'chado_table_name' => array(
-				'description' => 'the base table name to be used when using this setup',
+			'table_name' => array(
+				'description' => 'the base table name to be used when using this setup. Use this field when not using a materialized view',
 				'type' => 'varchar',
 				'length' => 255,
 				'not null' => TRUE,
@@ -138,11 +166,11 @@ function tripal_core_views_integration_schema(){
 				'not null' => TRUE,
 				'default' => '',
 			),
-			'description' => array(
-				'description' => 'description of this row',
-				'type' => 'varchar',
-				'length' => 255,
-				'not null' => TRUE,
+			'comment' => array(
+				'description' => 'add notes about this views setup',
+				'type' => 'text',
+				'size' => 'normal',
+				'not null' => FALSE,
 				'default' => '',
 			),
 		),
@@ -152,54 +180,54 @@ function tripal_core_views_integration_schema(){
 		'primary key' => array('setup_id'),
 	);
 
-	$schema['tripal_mviews_join'] = array(
-		'description' => 'which materialzed views and chado tables to join in a given setup',
+	$schema['tripal_views_join'] = array(
+		'description' => 'coordinate the joining of tables',
 		'fields' => array(
-		  'mview_join_id' => array(
+		  'view_join_id' => array(
 				'description' => 'the id of the join',
-					'type' => 'serial',
-					'unsigned' => TRUE,
-					'not null' => TRUE,
+				'type' => 'serial',
+				'unsigned' => TRUE,
+				'not null' => TRUE,
 		  ),
 			'setup_id' => array(
-				'description' => 'tripal setup id from tripal_views_integration table',
+				'description' => 'setup id from tripal_views table',
 				'type' => 'int',
 				'unsigned' => TRUE,
 				'not null'=> TRUE,
 			),
-			'view_table' => array(
-					'description' => 'materialized view table name',
-					'type' => 'varchar',
-					'length' => '255',
-					'not null' => TRUE,
-					'default' => '',
-	    ),
-			'view_column' => array(
-				'description' => 'column of materialized view table (mview_table)',
+			'base_table' => array(
+			   'description' => 'the name of the base table',
+				'type' => 'varchar',
+				'length' => '255',
+				'not null' => TRUE,
+				'default' => '',
+	      ),
+			'base_field' => array(
+				'description' => 'the name of the base table column that will be joined',
 				'type' => 'varchar',
 				'length' => '255',
 				'not null' => TRUE,
 				'default' => '',
 			),
-			'chado_table_join' => array(
-				'description' => 'on which chado table to join to materialized view in this serach',
+			'left_table' => array(
+				'description' => 'the table on which to perform a left join',
 				'type' => 'varchar',
 				'length' => '255',
 				'not null' => TRUE,
 				'default' => '',
 			),
-			'chado_column' => array(
-				'description' => 'chado table (above) column to join on materialized view in this serach',
+			'left_field' => array(
+				'description' => 'the column on which to perform a left join',
 				'type' => 'varchar',
 				'length' => '255',
 				'not null' => TRUE,
 				'default' => '',
-	    ),
+	      ),
 		),
 		'unique_keys' => array(
-			'setup_id' => array('mview_join_id'),
+			'setup_id' => array('view_join_id'),
 		),
-		'primary key' => array('mview_join_id'),
+		'primary key' => array('view_join_id'),
 	);
 
 	$schema['tripal_views_handlers'] = array(
@@ -207,15 +235,15 @@ function tripal_core_views_integration_schema(){
 		'fields' => array(
 			'handler_id' => array(
 				'description' => 'the id of the handler',
-					'type' => 'serial',
-					'unsigned' => TRUE,
-					'not null' => TRUE,
-	    ),
+				'type' => 'serial',
+			   'unsigned' => TRUE,
+			   'not null' => TRUE,
+	      ),
 			'setup_id' => array(
-				'description' => 'which setup this is used by from tripal_views_integration table',
-					'type' => 'int',
-					'unsigned' => TRUE,
-					'not null'=> TRUE,
+				'description' => 'setup id from the tripal_views table',
+				'type' => 'int',
+				'unsigned' => TRUE,
+				'not null'=> TRUE,
 			),
 			'column_name' => array(
 				'description' => '',
@@ -224,24 +252,31 @@ function tripal_core_views_integration_schema(){
 				'not null' => TRUE,
 				'default' => '',
 			),
-			'handler_filter' => array(
-				'description' => 'identifier of the handler filter to be used for this column',
+			'handler_type' => array(
+				'description' => 'identifies the type of hander (e.g. field, filter, sort, argument, relationship, etc.)',
 				'type' => 'varchar',
-				'length' => '255',
+				'length' => '50',
 				'not null' => TRUE,
 				'default' => '',
 			),
-			'handler_field' => array(
-				'description' => 'identifier of the handler field to be used for this column',
+			'handler_name' => array(
+				'description' => 'the name of the handler',
 				'type' => 'varchar',
 				'length' => '255',
 				'not null' => TRUE,
 				'default' => '',
-	    ),
+			),
+			'arguments' => array(
+				'description' => 'arguments that may get passed to the handler',
+				'type' => 'text',
+				'size' => 'normal',
+				'not null' => FALSE,
+				'default' => '',
+			),
 		),
 		'unique_keys' => array(
-				'setup_id' => array('handler_id'),
-	  ),
+		   'setup_id' => array('handler_id'),
+	   ),
 		'primary key' => array('handler_id'),
 	);
 
@@ -253,20 +288,12 @@ function tripal_core_views_integration_schema(){
 * @ingroup tripal_core
 */
 function tripal_core_update_6000(){
-   // recreate the materialized view
-   tripal_feature_add_organism_count_mview();
-   $ret = array(
-      '#finished' => 1,
-   );
-   
+   $schema = tripal_core_views_schema();
+   $ret = array();
+   foreach ($schema as $name => $table) {
+      db_create_table($ret, $name, $table);
+   }   
    return $ret;
 }
-/************************************************************************
-* 
-*
-* @ingroup tripal_core
-*/
-function tripal_core_update_6000_views_integration(){
 
-}
 ?>

base/tripal_core/tripal_core.module

@@ -198,7 +198,7 @@ function tripal_core_menu() {
 
 	//page to actually create setup->mview->chado table relationships
 	$items['admin/tripal/views/integration/mviews/new'] = array(
-     'title' => 'Add an MView',
+     'title' => 'Integrate an MView with Drupal Views',
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_core_views_integration_new_setup_form'),
      'access arguments' => array('manage tripal_views_integration'), //TODO: figure out the proper permissions arguments

base/tripal_core/tripal_core.views.inc

@@ -288,7 +288,7 @@ function tripal_core_add_node_ids_to_view (&$view) {
 
 function tripal_core_views_data(){   
 
-    $tvi_query = db_query('SELECT * FROM tripal_views_integration');
+    $tvi_query = db_query('SELECT * FROM {tripal_views}');
 
     //tvi = tripal_views_integration
     while($tvi_row = db_fetch_object($tvi_query)){
@@ -297,70 +297,85 @@ function tripal_core_views_data(){
       $setup_id = $tvi_row->setup_id;
       $mview_id = $tvi_row->mview_id;
 
-      //let's get the name of the table
-      $mview_table = db_fetch_object(db_query("SELECT name, mv_specs FROM {tripal_mviews} WHERE mview_id = '$mview_id';"));
+      //let's get the name of the materialized view
+      $base_table = '';
+      $base_fields = array();
+      if($mview_id){
+         $mview_table = db_fetch_object(db_query("SELECT name, mv_specs FROM {tripal_mviews} WHERE mview_id = '$mview_id';"));
+         $base_table = $mview_table->name;
+
+         // get the columns in this materialized view.  They are separated by commas
+         // where the first word is the column name and the rest is the type
+         $sql = "SELECT mv_specs FROM {tripal_mviews} WHERE mview_id = $mview_id";
+         $mview = db_fetch_object(db_query($sql));
+         $columns = explode(",",$mview->mv_specs);
+         foreach ($columns as $column){
+            $column = trim($column);  // trim trailing and leading spaces
+            preg_match("/^(.*?)\ (.*?)$/",$column,$matches);
+            $column_name = $matches[1];
+            $column_type = $matches[2];
+            $base_fields[] = $column_name;
+         }
+      }
+      else {
+         // TODO: get the non materialized view info and populate these variables
+         //  1) $base_table
+         //  2) $base_fields (an array of just the table field names)
+      }
 
       //use name from above and description from $tvi_row
-      $data[$mview_table->name]['table']['group'] = t('Mview ' . $tvi_row->name);
-      $data[$mview_table->name]['table']['base'] = array(
+      $data[$base_table]['table']['group'] = t($tvi_row->name);
+      $data[$base_table]['table']['base'] = array(
         'group' => t($tvi_row->name),
         'title' => t($tvi_row->name),
-        'help'  => t($tvi_row->description),
+        'help'  => t($tvi_row->comment),
       );
 
-      //let's add fields
-      //tmj = tripal_mviews_join
-      $tmj_query = db_query("SELECT * FROM tripal_mviews_join WHERE setup_id = '$setup_id'");
-      while($tmj_row = db_fetch_object($tmj_query)){
-
-        $column_name = $tmj_row->view_column;
-        $handlers = db_fetch_object(db_query("SELECT handler_filter, handler_field FROM {tripal_views_handlers} WHERE setup_id = '$setup_id' AND column_name = '$column_name';"));
-        //handlers would be used $handlers->handler_filter, $handlers->handler_field etc, thuogh may need to include new ones in this query or do select *
-
-        //let's use handlers we retrieved from above
-        $data[$mview_table->name][$tmj_row->view_column] = array(
-           'title' => t($tmj_row->view_column),
+      // first add the fields
+      foreach ($base_fields as $base_field){
+        $data[$base_table][$base_field] = array(
+           'title' => t($base_field),
            'help' => t("**"),
            'field' => array(
-              'handler' => $handlers->handler_field,
               'click sortable' => TRUE,
            ),
-           'sort' => array(
-              'handler' => 'views_handler_sort',
-           ),
-           'filter' => array(
-              'handler' => $handlers->handler_filter,
-           ),
-           'argument' => array(
-              'handler' => 'views_handler_argument_string',
-           ),
         );
-               
-        $chado_join_table = $tmj_row->chado_table_join;
-        $chado_join_column = $tmj_row->chado_column;
-        $mview_join_column = $tmj_row->view_column;
-        
-        // add recipricol join entries
-        $data["$mview_table->name"]['table']['join']["$chado_join_table"] = array(
-          'left_field' => $chado_join_column,
-          'field' => $mview_join_column,
+     };
+
+     // now add the handlers
+     $sql = "SELECT * FROM {tripal_views_handlers} WHERE setup_id = '$setup_id' AND base_field = '$column_name'";
+     $handlers = db_query($sql);
+     while($handler = db_fetch_object($handlers)){
+        $data[$base_table][$column_name][$handler->hander_type]['handler'] = $handler->handler_name;
+     };
+
+     // now add the joins
+     $joins = db_query("SELECT * FROM {tripal_views_join} WHERE setup_id = '$setup_id'");
+     while($join = db_fetch_object($joins)){               
+        $left_table = $join->left_table;
+        $left_field = $join->left_field;
+        $base_field = $join->base_field;  
+      
+        // add join entry
+        $data[$base_table]['table']['join'][$left_table] = array(
+          'left_field' => $left_field,
+          'field' => $base_field,
         );
 
         // check to see if this table is one that correlates with Drupal nodes
         // if so, there will be a chado_<table_name> table in the Drupal database
         // if there is, then we need to add the linking join information
-        $sql = "SELECT tablename FROM pg_tables WHERE tablename = 'chado_$chado_join_table'";
+        $sql = "SELECT tablename FROM pg_tables WHERE tablename = 'chado_$left_table'";
         if(db_fetch_object(db_query($sql))){
 
            // join the mview to the linker table
-           $data["$mview_table->name"]['table']['join']["chado_$chado_join_table"] = array(
-             'left_field' => $chado_join_column,
-             'field' => $mview_join_column,
+           $data[$base_table]['table']['join']["chado_$left_table"] = array(
+             'left_field' => $left_field,
+             'field' => $base_field,
            );
         }
       }
     }
-
     return $data;
 }
 /**
@@ -368,7 +383,7 @@ function tripal_core_views_data(){
  * @ingroup tripal_core
  */
 function tripal_core_views_data_alter(&$data) {
-    $tvi_query = db_query('SELECT * FROM tripal_views_integration');
+    $tvi_query = db_query('SELECT * FROM {tripal_views}');
 
     //tvi = tripal_views_integration
     while($tvi_row = db_fetch_object($tvi_query)){
@@ -378,21 +393,28 @@ function tripal_core_views_data_alter(&$data) {
       $setup_id = $tvi_row->setup_id;
 
       //let's get the name of the table
-      $mview_table = db_fetch_object(db_query("SELECT name, mv_specs FROM {tripal_mviews} WHERE mview_id = '$mview_id';"));
+      $base_table = '';
+      if($mview_id){
+         $mview_table = db_fetch_object(db_query("SELECT name, mv_specs FROM {tripal_mviews} WHERE mview_id = '$mview_id';"));
+         $base_table = $mview_table->name;
+      }
+      else {
+         // TODO: get the non materialized view info and populate these variables
+         //  1) $base_table
+      }
 
       // iterate through the columns and alter the existing data array for
       // joins to other tables
-      $tmj_query = db_query("SELECT * FROM tripal_mviews_join WHERE setup_id = '$setup_id'");
-      while($tmj_row = db_fetch_object($tmj_query)){
-        
-        $chado_join_table = $tmj_row->chado_table_join;
-        $chado_join_column = $tmj_row->chado_column;
-        $mview_join_column = $tmj_row->view_column;      
+      $joins = db_query("SELECT * FROM {tripal_views_join} WHERE setup_id = '$setup_id'");
+      while($join = db_fetch_object($joins)){                       
+        $left_table = $tmj_row->left_join;
+        $left_field = $tmj_row->left_column;
+        $base_field = $tmj_row->base_column;      
  
         // add the recipricol join entries for each column
-        $data["$chado_join_table"]['table']['join']["$mview_table->name"] = array(
-          'left_field' => $mview_join_column,
-          'field' => $chado_join_column,
+        $data[$left_table]['table']['join'][$base_table] = array(
+          'left_field' => $base_field,
+          'field' => $left_field,
         );
 
         // check to see if this table is one that correlates with Drupal nodes
@@ -400,18 +422,18 @@ function tripal_core_views_data_alter(&$data) {
         // if there is, then we need to add the linking join information.  We did
         // this step in the hook_views_data function above, but now we need 
         // to add the reciprical joins
-        $sql = "SELECT tablename FROM pg_tables WHERE tablename = 'chado_$chado_join_table'";
+        $sql = "SELECT tablename FROM pg_tables WHERE tablename = 'chado_$left_table'";
         if(db_fetch_object(db_query($sql))){
 
            // join the linker table to the mview
-           $data["chado_$chado_join_table"]['table']['join']["$mview_table->name"] = array(
-             'left_field' => $mview_join_column,
-             'field' => $chado_join_column,
+           $data["chado_$left_table"]['table']['join'][$base_table] = array(
+             'left_field' => $base_field,
+             'field' => $left_field,
            );
 
            // Join the node table to the view by way of the chado linker table
-           $data['node']['table']['join']["$mview_table->name"] = array(
-           	'left_table' => "chado_$chado_join_table",
+           $data['node']['table']['join'][$base_table] = array(
+           	'left_table' => "chado_$left_table",
            	'left_field' => 'nid',
            	'field' => 'nid',
            );

base/tripal_core/tripal_views_integration.inc

@@ -67,14 +67,14 @@ function tripal_core_views_integration_admin_form(){
 
   $form['#theme'] = 'tripal';
 
-  $query_results = db_query('SELECT * FROM public.tripal_views_integration;');
+  $query_results = db_query('SELECT * FROM tripal_views');
 
-  $header = array('Setup ID', 'Name', 'Materialized View ID', 'Base Table Name', 'Description');
+  $header = array('Setup ID', 'Name', 'MView ID', 'Table Name', 'Comment');
   $rows = array();
 
   $results = array();
   while($result = db_fetch_object($query_results)){
-    $rows[] = array($result->setup_id, $result->name, $result->mview_id, $result->base_table_name, $result->description,);
+    $rows[] = array($result->setup_id, $result->name, $result->mview_id, $result->base_table_name, $result->comment);
     $results[] = $result;
   }
 
@@ -110,9 +110,9 @@ function tripal_core_views_integration_admin_form(){
  */
 function tripal_core_views_integration_admin_form_submit($form, &$form_state){
   $value = $form['existing_rows']['#options'][$form_state['values']['existing_rows']];
-  db_query("DELETE FROM public.tripal_views_integration WHERE setup_id = $value;");
+  db_query("DELETE FROM public.tripal_views WHERE setup_id = $value;");
   db_query("DELETE FROM public.tripal_views_handlers WHERE setup_id = $value;");
-  db_query("DELETE FROM public.tripal_mviews_join WHERE setup_id = $value;");
+  db_query("DELETE FROM public.tripal_views_join WHERE setup_id = $value;");
 }
 /**
  *
@@ -122,9 +122,7 @@ function tripal_core_views_integration_admin_form_submit($form, &$form_state){
 function tripal_core_views_integration_new_setup_form(&$form_state){
 
   $form = array();
-
   $data = array();
-
   $form['#cache'] = TRUE;
 
   //ahah_helper requires this to register the form with it's module
@@ -132,21 +130,19 @@ function tripal_core_views_integration_new_setup_form(&$form_state){
 
   // field for the name of the
   $form['row_name'] = array(
-    '#title' => t('Name'),
+    '#title' => t('View Type Name'),
     '#type' => 'textfield',
     '#size' => 60,
     '#maxlength' => 128,
-    '#description' => 'Name of the Views Setup',
-    '#required' => TRUE,
+    '#description' => 'Provide the view type name.  This is the name that will appear in the Drupal Views interface when adding a new view.',
+    '#required' => TRUE,   
   );
 
   $form['row_description'] = array(
-    '#title' => t('Description'),
-    '#type' => 'textfield',
-    '#size' => 60,
-    '#maxlength' => 255,
-    '#description' => 'Briefly describe in which view this will be used',
-    '#required' => TRUE,
+    '#title' => t('Comment'),
+    '#type' => 'textarea',
+    '#description' => '(Optional). Provide any details regarding this setup you would like.',
+    '#required' => FALSE,
   );
 
   $mview_query = db_query("SELECT mview_id,name FROM {tripal_mviews} ORDER BY name;");
@@ -169,19 +165,9 @@ function tripal_core_views_integration_new_setup_form(&$form_state){
        'effect' => 'fade',
        'event' => 'change',
        'method' => 'replace',
-  ),
+    ),
   );
 
-  // ignore this for now... we'll come back to it later -- spf
-  //   $form['row_base_table_name'] = array(
-  //      '#title' => t('Base Table Name'),
-  //      '#type' => 'select',
-  //      // '#options' => array('stub'),
-  //      '#options' => tripal_core_get_chado_tables(),
-  //      '#description' => 'Select which chado table to use for this view.',
-  //      '#required' => TRUE,
-  //   );
-
   $form['view_setup_table'] = array(
      '#type' => 'item',
        '#prefix' => '<div id="table-rows-div">',
@@ -222,15 +208,35 @@ function tripal_core_views_integration_new_setup_form(&$form_state){
     $all_handlers = tripal_core_views_integration_discover_handlers();
     $handlers_fields = array();
     $handlers_filters = array();
+    $handlers_sort = array();
+    $handlers_arguments = array();
+    $handlers_join = array();
+    $handlers_rel = array();
     
-    $handlers_fields[] = "Select a Field Handler"; 
-    $handlers_filters[] = "Select a Filter Handler";
+    $handlers_fields[0] = "Select a field handler"; 
+    $handlers_filters[0] = "Select a filter handler";
+    $handlers_sort[0] = "Select a sort handler";
+    $handlers_argument[0] = "Select an argument handler";
+    $handlers_join[0] = "Select a join handler";
+    $handlers_rel[0] = "Select a relationship handler";
     foreach($all_handlers as $handler){
        if(preg_match("/views_handler_field/",$handler)){
-          $handlers_fields[] = $handler;
+          $handlers_fields[$handler] = $handler;
        }
        if(preg_match("/views_handler_filter/",$handler)){
-          $handlers_filters[] = $handler;
+          $handlers_filters[$handler] = $handler;
+       }
+       if(preg_match("/views_handler_sort/",$handler)){
+          $handlers_sort[$handler] = $handler;
+       }
+       if(preg_match("/views_handler_argument/",$handler)){
+          $handlers_argument[$handler] = $handler;
+       }
+       if(preg_match("/views_handler_join/",$handler)){
+          $handlers_join[$handler] = $handler;
+       }
+       if(preg_match("/views_handler_relationship/",$handler)){
+          $handlers_rel[$handler] = $handler;
        }
     }
 
@@ -274,9 +280,12 @@ function tripal_core_views_integration_new_setup_form(&$form_state){
          ),
       );
       
+      $columns = array();
       if($table){
         $table_desc = module_invoke_all('chado_'.$table.'_schema');
-        $columns = array_keys($table_desc['fields']);
+        foreach ($table_desc['fields'] as $column => $def){
+           $columns[$column] = $column;
+        }
       } else {
         $columns = array('Select Join Column');
       }
@@ -299,10 +308,38 @@ function tripal_core_views_integration_new_setup_form(&$form_state){
       $form['view_setup_table']["fields_filter_handler_$mview_id-$i"] = array(
         '#type' => 'select',
         '#prefix' => "<div class=\"fields-filter-handler\">",
-        '#suffix' => "</div></div>",
+        '#suffix' => "</div>",
         '#options' => $handlers_filters,
         '#required' => FALSE,
       );
+      $form['view_setup_table']["fields_sort_handler_$mview_id-$i"] = array(
+        '#type' => 'select',
+        '#prefix' => "<div class=\"fields-sort-handler\">",
+        '#suffix' => "</div>",
+        '#options' => $handlers_sort,
+        '#required' => FALSE,
+      );
+      $form['view_setup_table']["fields_argument_handler_$mview_id-$i"] = array(
+        '#type' => 'select',
+        '#prefix' => "<div class=\"fields-argument-handler\">",
+        '#suffix' => "</div>",
+        '#options' => $handlers_argument,
+        '#required' => FALSE,
+      );
+      $form['view_setup_table']["fields_relationship_handler_$mview_id-$i"] = array(
+        '#type' => 'select',
+        '#prefix' => "<div class=\"fields-relationship-handler\">",
+        '#suffix' => "</div>",
+        '#options' => $handlers_rel,
+        '#required' => FALSE,
+      );
+      $form['view_setup_table']["fields_join_handler_$mview_id-$i"] = array(
+        '#type' => 'select',
+        '#prefix' => "<div class=\"fields-join-handler\">",
+        '#suffix' => "</div></div>",
+        '#options' => $handlers_join,
+        '#required' => FALSE,
+      );
       
       $form['view_setup_table']["fields_end_$i"] = array(
         '#type' => 'markup',
@@ -319,7 +356,7 @@ function tripal_core_views_integration_new_setup_form(&$form_state){
   }
 
   //use this to put values into $form_state['values']
-  $form['data'] = array();
+  $form['data'] = array();   
 
   //need to find out if storing $form['data'][$key]['#value'] = $value <- is an issue
   //since it will give me errors if i try to stare an array instead of $value
@@ -351,37 +388,73 @@ function tripal_core_views_integration_new_setup_form_validate($form, &$form_sta
  * @ingroup tripal_views_integration
  */
 function tripal_core_views_integration_new_setup_form_submit($form, &$form_state){
-  $name = $form_state['values']['row_name'];
-  $mview_id = $form_state['values']['mview_id'];
-  $tripal_views_integration_record = array(
-    'mview_id' => $mview_id,
-    'name' => $name,
-  	 'description' => $form_state['values']['row_description'],
-  );
 
-  drupal_write_record('tripal_views_integration', $tripal_views_integration_record);
+   $name = $form_state['values']['row_name'];
+   $mview_id = $form_state['values']['mview_id'];
+   $table_name = $form_state['values']['table_name'];
 
-  $i = 1;
-  foreach ($form_state['values']['field_types'] as $key => $value){
-    $mview_join_record = array(
-        'setup_id' => $tripal_views_integration_record['setup_id'],
-        'view_table' => $form['mview_id']['#options'][$form_state['values']['mview_id']],
-        'view_column' => $key,
-        'chado_table_join' => $form_state['values']["fields_join_$mview_id-$i"],
-        'chado_column' => $form['view_setup_table']["fields_join_column_$mview_id-$i"]['#options'][$form_state['values']["fields_join_column_$mview_id-$i"]],
-    );
-    drupal_write_record('tripal_mviews_join', $mview_join_record);
-    
-    $handlers_record = array(
-      'setup_id' => $tripal_views_integration_record['setup_id'],
-      'column_name' => $key,//TODO: should we change this to an mview_join_id from tripal_view_join?
-      'handler_filter' => $form['view_setup_table']["fields_filter_handler_$mview_id-$i"]['#options'][$form_state['values']["fields_filter_handler_$mview_id-$i"]],
-    	'handler_field' => $form['view_setup_table']["fields_field_handler_$mview_id-$i"]['#options'][$form_state['values']["fields_field_handler_$mview_id-$i"]],
-    );
-    drupal_write_record('tripal_views_handlers', $handlers_record);
-    $i++;
-  }
+   $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = $mview_id";
+   $mview = db_fetch_object(db_query($sql));
+
+   // If this is for a materialized view then we want to add that record
+   $tripal_views_record = array();
+   if($mview_id){
+      $tripal_views_record = array(
+       'mview_id' => $mview_id,
+       'name' => $name,
+       'comment' => $form_state['values']['row_description'],
+      );
+      if(!drupal_write_record('tripal_views', $tripal_views_record)){
+         drupal_set_message("Failed to add setup.");
+         return;
+      }
+   } 
+   // if not a materialized view then just keep track of the table name
+   if($table_name){
+      $tripal_views_record = array(
+       'table_name' => $table_name,
+       'name' => $name,
+       'comment' => $form_state['values']['row_description'],
+      );
+      drupal_write_record('tripal_views', $tripal_views_record);
+   }
 
+   // iterate through the columns of the form and add
+   // the joins if provided, and the handlers
+   $i = 1;
+   foreach ($form_state['values']['field_types'] as $key => $value){
+
+      // first add the join if it exists
+      $left_table = $form_state['values']["fields_join_$mview_id-$i"];
+      $left_column = $form_state['values']["fields_join_column_$mview_id-$i"];
+
+      if($left_column){
+         $view_join_record = array(
+           'setup_id' => $tripal_views_record['setup_id'],
+           'base_table' => $mview->mv_table,
+           'base_field' => $key,
+           'left_table' => $left_table,
+           'left_field' => $left_column,
+         );
+         drupal_write_record('tripal_views_join', $view_join_record);
+      }
+
+      // add the hanlders
+      $handlers = array('filter','field','sort','argument','join','relationship');
+      foreach($handlers as $handler){
+         $handler_name = $form_state['values']["fields_".$handler."_handler_$mview_id-$i"];
+         if($handler_name){
+            $handler_record = array(
+            'setup_id' => $tripal_views_record['setup_id'],
+            'column_name' => $key, 
+            'handler_type' => $handler,
+            'handler_name' => $handler_name,
+            );
+            drupal_write_record('tripal_views_handlers', $handler_record);
+         }
+      }
+      $i++;
+   }
 }
 
 /**