Merge branch '6.x-tripal_views_setup_ahah_helper-og' of git.drupal.org:sandbox/spficklin/1337878 into 6.x-tripal_views_setup_ahah_helper-og

base/tripal_core/mviews.php

@@ -179,7 +179,7 @@ function tripal_mview_report ($mview_id) {
    // create a table with each row containig stats for
    // an individual job in the results set.
 
-   $return_url = url("admin/tripal/tripal_mviews/");
+   $return_url = url("admin/tripal/views/mviews/");
 
    $output .= "<p><a href=\"$return_url\">Return to table of materialized views.</a></p>";
    $output .= "<br />";
@@ -240,9 +240,9 @@ function tripal_mview_report ($mview_id) {
 
    // build the URLs using the url function so we can handle installations where
    // clean URLs are or are not used
-   $update_url = url("admin/tripal/tripal_mviews/action/update/$mview->mview_id");
-   $delete_url = url("admin/tripal/tripal_mviews/action/delete/$mview->mview_id");
-   $edit_url = url("admin/tripal/tripal_mviews/edit/$mview->mview_id");
+   $update_url = url("admin/tripal/views/mviews/action/update/$mview->mview_id");
+   $delete_url = url("admin/tripal/views/mviews/action/delete/$mview->mview_id");
+   $edit_url = url("admin/tripal/views/mviews/edit/$mview->mview_id");
 
    $output .= "<tr><th>Actions</th>".
               "<td> <a href='$update_url'>Update</a>, ".
@@ -279,9 +279,9 @@ function tripal_mviews_report () {
       }
 	  // build the URLs using the url function so we can handle installations where
 	  // clean URLs are or are not used
-	  $view_url = url("admin/tripal/tripal_mview/$mview->mview_id");
-	  $update_url = url("admin/tripal/tripal_mviews/action/update/$mview->mview_id");
-	  $delete_url = url("admin/tripal/tripal_mviews/action/delete/$mview->mview_id");
+	  $view_url   = url("admin/tripal/views/mviews/report/$mview->mview_id");
+	  $update_url = url("admin/tripal/views/mviews/action/update/$mview->mview_id");
+	  $delete_url = url("admin/tripal/views/mviews/action/delete/$mview->mview_id");
 	  // create the row for the table
       $output .= "  <tr>";
       $output .= "    <td><a href='$view_url'>View</a>&nbsp".
@@ -291,7 +291,7 @@ function tripal_mviews_report () {
                  "    <td><a href='$delete_url'>Delete</a></td>".
                  "  </tr>";
    }
-   $new_url = url("admin/tripal/tripal_mviews/new");
+   $new_url = url("admin/tripal/views/mviews/new");
    $output .= "</table>";
    $output .= "<br />";
    $output .= "<p><a href=\"$new_url\">Create a new materialized view.</a></p>";
@@ -411,7 +411,7 @@ function tripal_mviews_form(&$form_state = NULL,$mview_id = NULL){
      '#executes_submit_callback' => TRUE,
    );
 
-   $form['#redirect'] = 'admin/tripal/tripal_mviews';
+   $form['#redirect'] = 'admin/tripal/views/mviews';
    return $form;
 }
 /**

base/tripal_core/tripal_core.info

@@ -5,3 +5,5 @@ core = 6.x
 project = tripal_core
 package = Tripal
 version = 6.x-0.3.1b
+
+dependencies = views

base/tripal_core/tripal_core.install

@@ -100,6 +100,141 @@ function tripal_core_get_schemas (){
       'primary key' => array('mview_id'),
   );
 
+	$schema['tripal_views_integration'] = array(
+		'description' => 'contains the setupes, their materialized view id and base table name that was used.',
+		'fields' => array(
+			'setup_id' => array(
+				'description' => 'the id of the setup',
+				'type' => 'serial',
+				'unsigned' => TRUE,
+				'not null' => TRUE,
+			),
+			'mview_id' => array(
+				'description' => 'the materialized view used for this setup',
+				'type' => 'int',
+				'unsigned' => TRUE,
+			),
+			'chado_table_name' => array(
+				'description' => 'the base table name to be used when using this setup',
+				'type' => 'varchar',
+				'length' => 255,
+				'not null' => TRUE,
+				'default' => '',
+			),
+			'name' => array(
+				'description' => 'Human readable name of this setup',
+				'type' => 'varchar',
+				'length' => 255,
+				'not null' => TRUE,
+				'default' => '',
+			),
+			'description' => array(
+				'description' => 'description of this row',
+				'type' => 'varchar',
+				'length' => 255,
+				'not null' => TRUE,
+				'default' => '',
+			),
+		),
+		'unique_keys' => array(
+			'setup_id' => array('setup_id'),
+		),
+		'primary key' => array('setup_id'),
+	);
+
+	$schema['tripal_mviews_join'] = array(
+		'description' => 'which materialzed views and chado tables to join in a given setup',
+		'fields' => array(
+		  'mview_join_id' => array(
+				'description' => 'the id of the join',
+					'type' => 'serial',
+					'unsigned' => TRUE,
+					'not null' => TRUE,
+		  ),
+			'setup_id' => array(
+				'description' => 'tripal setup id from tripal_views_integration 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)',
+				'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',
+				'type' => 'varchar',
+				'length' => '255',
+				'not null' => TRUE,
+				'default' => '',
+			),
+			'chado_column' => array(
+				'description' => 'chado table (above) column to join on materialized view in this serach',
+				'type' => 'varchar',
+				'length' => '255',
+				'not null' => TRUE,
+				'default' => '',
+	    ),
+		),
+		'unique_keys' => array(
+			'setup_id' => array('mview_join_id'),
+		),
+		'primary key' => array('mview_join_id'),
+	);
+
+	$schema['tripal_views_handlers'] = array(
+		'description' => 'in formation for views: column and views handler name',
+		'fields' => array(
+			'handler_id' => array(
+				'description' => 'the id of the handler',
+					'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,
+			),
+			'column_name' => array(
+				'description' => '',
+				'type' => 'varchar',
+				'length' => '255',
+				'not null' => TRUE,
+				'default' => '',
+			),
+			'handler_filter' => array(
+				'description' => 'identifier of the handler filter to be used for this column',
+				'type' => 'varchar',
+				'length' => '255',
+				'not null' => TRUE,
+				'default' => '',
+			),
+			'handler_field' => array(
+				'description' => 'identifier of the handler field to be used for this column',
+				'type' => 'varchar',
+				'length' => '255',
+				'not null' => TRUE,
+				'default' => '',
+	    ),
+		),
+		'unique_keys' => array(
+				'setup_id' => array('handler_id'),
+	  ),
+		'primary key' => array('handler_id'),
+	);
+	return $schema;
   return $schema;
 }
 ?>

base/tripal_core/tripal_core.module

@@ -4,6 +4,7 @@ require_once "jobs.php";
 require_once "mviews.php";
 require_once "cvterms.php";
 require_once "chado_install.php";
+require_once "tripal_views_integration.inc";
 
 require_once "tripal_core.api.inc";
 
@@ -85,7 +86,6 @@ function tripal_core_menu() {
       'file' => 'system.admin.inc',
       'file path' => drupal_get_path('module', 'system'),
    );
-
    $items['admin/tripal/tripal_jobs'] = array(
      'title' => 'Jobs',
      'description' => 'Jobs managed by Tripal',
@@ -117,66 +117,124 @@ function tripal_core_menu() {
      'access arguments' => array('access administration pages'),
      'type' => MENU_CALLBACK,
    );
-   $items['admin/tripal/tripal_mview/%'] = array(
-     'title' => 'Materialized View',
-     'description' => 'Materialized views are used to improve speed of large or complex queries.',
-     'page callback' => 'tripal_mview_report',
-     'page arguments' => array(3),
+   $items['tripal_toggle_box_menu/%/%/%'] = array(
+     'title' => t('Libraries'),
+     'page callback' => 'tripal_toggle_box_menu',
+     'page arguments' => array(1,2,3),
      'access arguments' => array('access administration pages'),
+     'type' => MENU_CALLBACK | MENU_LINKS_TO_PARENT 
+   );
+   $items['admin/tripal/chado_1_11_install'] = array(
+     'title' => 'Install Chado v1.11',
+     'description' => 'Installs Chado version 1.11 inside the current Drupal database',
+     'page callback' => 'drupal_get_form',
+     'page arguments' => array('tripal_core_chado_v1_11_load_form'),
+     'access arguments' => array('access administration pages'),
+     'type' => MENU_NORMAL_ITEM,
+   );
+
+   $items['admin/tripal/views'] = array(
+     'title' => t('Views'),
+     'description' => 'Management of Materialized Views & Integration with Drupal Views',
+     'page callback' => 'tripal_core_views_description_page',
+     'access arguments' => array('administer site configuration'),
      'type' => MENU_NORMAL_ITEM,
    );
-   $items['admin/tripal/tripal_mviews'] = array(
-     'title' => 'Materialized Views',
+   $items['admin/tripal/views/mviews'] = array(
+     'title' => 'MViews',
      'description' => 'Materialized views are used to improve speed of large or complex queries.',
      'page callback' => 'tripal_mviews_report',
      'access arguments' => array('access administration pages'),
      'type' => MENU_NORMAL_ITEM,
    );
-   $items['admin/tripal/tripal_mviews/new'] = array(
-     'title' => 'Create View',
+   $items['admin/tripal/views/mviews/report/%'] = array(
+     'title' => 'Materialized View',
+     'description' => 'Materialized views are used to improve speed of large or complex queries.',
+     'page callback' => 'tripal_mview_report',
+     'page arguments' => array(5),
+     'access arguments' => array('access administration pages'),
+     'type' => MENU_NORMAL_ITEM,
+   );
+   $items['admin/tripal/views/mviews/new'] = array(
+     'title' => 'Create MView',
      'description' => 'Materialized views are used to improve speed of large or complex queries.',
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_mviews_form'),
      'access arguments' => array('access administration pages'),
      'type' => MENU_NORMAL_ITEM,
    );
-   $items['admin/tripal/tripal_mviews/edit/%'] = array(
-     'title' => 'Edit View',
+   $items['admin/tripal/views/mviews/edit/%'] = array(
+     'title' => 'Edit MView',
      'page callback' => 'drupal_get_form',
-     'page arguments' => array('tripal_mviews_form',4),
+     'page arguments' => array('tripal_mviews_form',5),
      'access arguments' => array('access administration pages'),
      'type' => MENU_NORMAL_ITEM,
    );
-   $items['admin/tripal/tripal_mviews/action/%/%'] = array(
-     'title' => 'Create View',
+   $items['admin/tripal/views/mviews/action/%/%'] = array(
+     'title' => 'Create MView',
      'description' => 'Materialized views are used to improve speed of large or complex queries.',
      'page callback' => 'tripal_mviews_action',
-     'page arguments' => array(4,5),
+     'page arguments' => array(5,6),
      'access arguments' => array('access administration pages'),
      'type' => MENU_CALLBACK,
    );
+	$items['admin/tripal/views/integration'] = array(
+    'title' => t('Drupal Views Integration'),
+    'description' => t('Allows you to select existing materialized views and provide details for integration with Drupal Views.'),
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_core_views_integration_admin_form'),
+    'access arguments' => array('manage tripal_views_integration'),
+    'type' => MENU_NORMAL_ITEM,
+	);
+	$items['admin/tripal/views/integration/mviews'] = array(
+    'title' => t('Integrated MViews'),
+    'description' => t('Allows you to select existing materialized views and provide details for integration with Drupal Views.'),
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_core_views_integration_admin_form'),
+    'access arguments' => array('manage tripal_views_integration'),
+    'type' => MENU_NORMAL_ITEM,
+	);
 
-   $items['tripal_toggle_box_menu/%/%/%'] = array(
-     'title' => t('Libraries'),
-     'page callback' => 'tripal_toggle_box_menu',
-     'page arguments' => array(1,2,3),
-     'access arguments' => array('access administration pages'),
-     'type' => MENU_CALLBACK | MENU_LINKS_TO_PARENT 
-   );
-   $items['admin/tripal/chado_1_11_install'] = array(
-     'title' => 'Install Chado v1.11',
-     'description' => 'Installs Chado version 1.11 inside the current Drupal database',
+	//page to actually create setup->mview->chado table relationships
+	$items['admin/tripal/views/integration/mviews/new'] = array(
+     'title' => 'Add an MView',
      'page callback' => 'drupal_get_form',
-     'page arguments' => array('tripal_core_chado_v1_11_load_form'),
-     'access arguments' => array('access administration pages'),
+     'page arguments' => array('tripal_core_views_integration_new_setup_form'),
+     'access arguments' => array('manage tripal_views_integration'), //TODO: figure out the proper permissions arguments
      'type' => MENU_NORMAL_ITEM,
-   );
+	);
 
+	$items['admin/tripal/views/integration/chado'] = array(
+    'title' => t('Integrated Chado Table'),
+    'description' => t('Tripal Views Setups settings page, allows you to select and create materialized views and chado tables to use for searches.'),
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_core_views_integration_admin_form'),
+    'access arguments' => array('manage tripal_views_integration'),
+    'type' => MENU_NORMAL_ITEM,
+	);
+	$items['admin/tripal/views/integration/chado/new'] = array(
+     'title' => 'Add a Chado table',
+     '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
+     'type' => MENU_NORMAL_ITEM,
+	);
   return $items;
 }
 
 
-
+/**
+ *  Set the permission types that the chado module uses.  Essentially we
+ *  want permissionis that protect creation, editing and deleting of chado
+ *  data objects
+ *
+ * @ingroup tripal_core
+ */
+function tripal_core_perm(){
+   return array(
+      'manage tripal_views_integration',
+   );
+}
 /**
  *
  *
@@ -233,6 +291,10 @@ function tripal_core_theme () {
          'arguments' => array('job_id'=> null),
          'template' => 'tripal_core_job_view',
       ),
+	  'tripal_core_views_integration_new_setup_form' => array(
+         'arguments' => array('form' => NULL),
+         'template'  => 'tripal_views_integration_fields_form',
+	   ),
    );
 }
 /**
@@ -258,3 +320,4 @@ function tripal_core_load_gff3($gff_file, $organism_id,$analysis_id,$add_only =0
    tripal_feature_load_gff3($gff_file, $organism_id,$analysis_id,$add_only, 
       $update, $refresh, $remove, $job);
 }
+

base/tripal_core/tripal_core.views.inc

@@ -280,4 +280,144 @@ function tripal_core_add_node_ids_to_view (&$view) {
 	} //end of case for stock NID
 		
 	return $view;
-}
+}
+/**
+ *
+ * @ingroup tripal_core
+ */
+
+function tripal_core_views_data(){   
+
+    $tvi_query = db_query('SELECT * FROM tripal_views_integration');
+
+    //tvi = tripal_views_integration
+    while($tvi_row = db_fetch_object($tvi_query)){
+
+      //ids we'll use for queries
+      $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';"));
+
+      //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(
+        'group' => t($tvi_row->name),
+        'title' => t($tvi_row->name),
+        'help'  => t($tvi_row->description),
+      );
+
+      //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),
+           'help' => t("**"),
+           'field' => array(
+              'handler' => 'views_handler_field',
+              'click sortable' => TRUE,
+           ),
+           'sort' => array(
+              'handler' => 'views_handler_sort',
+           ),
+           'filter' => array(
+              'handler' => 'views_handler_filter_string',
+           ),
+           '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,
+        );
+
+        // 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'";
+        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,
+           );
+        }
+      }
+    }
+
+    return $data;
+}
+/**
+ *
+ * @ingroup tripal_core
+ */
+function tripal_core_views_data_alter(&$data) {
+    $tvi_query = db_query('SELECT * FROM tripal_views_integration');
+
+    //tvi = tripal_views_integration
+    while($tvi_row = db_fetch_object($tvi_query)){
+
+      //ids we'll use for queries
+      $mview_id = $tvi_row->mview_id;
+      $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';"));
+
+      // 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;      
+ 
+        // 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,
+        );
+
+        // 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.  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'";
+        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,
+           );
+
+           // 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",
+           	'left_field' => 'nid',
+           	'field' => 'nid',
+           );
+        }
+      }
+    }
+
+    return $data;
+}

base/tripal_views_integration/includes/tripal_views_integration.admin.inc → base/tripal_core/tripal_views_integration.inc

@@ -7,17 +7,20 @@
  *
  * @ingroup tripal_views_integration
  */
-function tripal_views_integration_module_description_page() {
+function tripal_core_views_description_page() {
 
-  $text .= '<h3>Tripal Views Integration Administrative Tools Quick Links:</h3>';
+  $text .= '<h3>Tripal Views Quick Links:</h3>';
   $text .= "<ul>
-             <li><a href=\"".url("admin/tripal/tripal_views_integration/list") . "\">List of integrated views</a></li>
-             <li><a href=\"".url("admin/tripal/tripal_views_integration/new"). "\">Setup integration of a materialized view</a></li>
+             <li><a href=\"".url("admin/tripal/views/mviews") . "\">List of Materialized Views (MViews)</a></li>
+             <li><a href=\"".url("admin/tripal/views/mviews/new") . "\">Create a new MViews</a></li>
+             <li><a href=\"".url("admin/tripal/views/integration/mviews") . "\">List of integrated MViews</a></li>
+             <li><a href=\"".url("admin/tripal/views/integration/mviews/new"). "\">Integrate a MView</a></li>
+             <li><a href=\"".url("admin/tripal/views/integration/chado"). "\">List of integrated Chado tables</a></li>
+             <li><a href=\"".url("admin/tripal/views/integration/chado/new"). "\">Integrate a Chado tables</a></li>
            </ul>";
-  #             <li><a href=\"".url("admin/tripal/tripal_feature/aggregate"). "\">Feature Relationship Aggegators</a></li>
 
-  $text .= '<h3>Module Description:</h3>';
-  $text .= '<p>This module provides an interface for integrating <a href="http://drupal.org/project/views">Drupal Views</a>
+  $text .= '<h3>Views Integartion Description:</h3>';
+  $text .= '<p>Tripal Views provides an interface for integrating <a href="http://drupal.org/project/views">Drupal Views</a>
             with Tripal materialized views.  This will allow site administrators to create custom queries for the materialized views
             and in turn provide custom content pages, custom blocks and custom search forms. The forms allow a site administrator
             to select a materialized view and associate other Chado tables on which the view can join.  Usage of this module requires
@@ -25,22 +28,19 @@ function tripal_views_integration_module_description_page() {
             </p>';
 
   $text .= '<h3>Setup Instructions:</h3>';
-  $text .= '<p>After installation of the feature module.  The following tasks should be performed
+  $text .= '<p>After installation of the Tripal core module.  The following tasks should be performed
             <ol>
-              <li><b>Install Drupal Views</b>: The <a href="http://drupal.org/project/views">Drupal Views</a> module
-                must first be installed before this module can be used.  If you are reading this page then you must have
-                Drupal Views installed</li>
               <li><b>Set Permissions</b>: To allow access to site administrators for this module, simply
                <a href="'.url('admin/user/permissions').'">assign permissions</a> to the appropriate user roles for the
                permission type "manage tripal_views_integration". </li>
             </ol>
             </p>';
   $text .= '<h3>Usage Instructions:</h3>';
-  $text .= "<p>To use this module follow these steps:
+  $text .= "<p>To use Tripal Views integration follow these steps:
             <ol>
-               <li><b>Identify or create a materialized view:</b> Using the <a href=\"".url("admin/tripal/tripal_mviews") . "\">
+               <li><b>Identify or create a materialized view:</b> Using the <a href=\"".url("admin/tripal/views/mviews") . "\">
                  Tripal materialized View</a> interface, identify the view you would like to integrate or create a new one.</li>
-               <li><b>Setup the Views Integration</b>: Navigate to the <a href=\"".url("admin/tripal/tripal_views_integration/new") . "\">
+               <li><b>Setup the Views Integration</b>: Navigate to the <a href=\"".url("admin/tripal/views/integration/mviews/new") . "\">
                  Tripal views integration setup page</a> to integrate the selected materialized view.  Provide a  user friendly name
                  and description to help you remember the purpose for integrating the view.  Next, select the view you want to integrate
                  from the provided select box.  If your materialized view has fields that can join with other Chado tables, you may
@@ -49,26 +49,18 @@ function tripal_views_integration_module_description_page() {
                <li><b>Create custom pages/block/search form</b>:  After saving setup information from step 2 above, you will be redirected to the
                  Drupal Views interface</a> where you can create a custom page, block or search form.</li>
                <li><b>Review your integrated views</b>:  A page providing a
-                 <a href=\"".url("admin/tripal/tripal_views_integration/list") . "\">list of all integrated views</a> is provided. You may
+                 <a href=\"".url("admin/tripal/views/integration/mviews/list") . "\">list of all integrated views</a> is provided. You may
                  view this page to see all integrated views, but also to remove any unwanted integrations.</li>
             </ol>
          
             </p>";
-  $text .= '<h3>Features of this Module:</h3>';
-  $text .= '<p>This module provides the following functionality
-            <ul>
-              <li>A dynamic form for integration of an existing materialized view with Drupal Views.  This form allows the site
-                  administrator to select an existing view and indicate Chado tables on which the fields may join.</li>
-            </ul>
-            
-            </p>';
   return $text;
 }
 /**
  *
  * @ingroup tripal_views_integration
  */
-function tripal_views_integration_admin_form(){
+function tripal_core_views_integration_admin_form(){
 
   $form = array();
 
@@ -103,14 +95,9 @@ function tripal_views_integration_admin_form(){
     '#value' => t('Remove'),
   );
 
-  $form['cancel'] = array(
-    '#type' => 'markup',
-    '#value' => l(t('Cancel '), 'admin/tripal/'),
-  );
-
   $form['new'] = array(
     '#type' => 'markup',
-    '#value' => l(t(' New'), 'admin/tripal/tripal_views_integration/new'),
+    '#value' => l(t(' Add a New MView'), 'admin/tripal/views/integration/mviews/new'),
   );
 
   return $form;
@@ -120,7 +107,7 @@ function tripal_views_integration_admin_form(){
  *
  * @ingroup tripal_views_integration
  */
-function tripal_views_integration_admin_form_submit($form, &$form_state){
+function tripal_core_views_integration_admin_form_submit($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_handlers WHERE setup_id = $value;");
@@ -131,7 +118,7 @@ function tripal_views_integration_admin_form_submit($form, &$form_state){
  * @ingroup tripal_views_integration
  */
 
-function tripal_views_integration_new_setup_form(&$form_state){
+function tripal_core_views_integration_new_setup_form(&$form_state){
 
   $form = array();
 
@@ -222,8 +209,8 @@ function tripal_views_integration_new_setup_form(&$form_state){
     $chado_tables = tripal_core_get_chado_tables();
     $chado_tables = array_merge(array('',), $chado_tables);
 
-    $handlers_filters = array('', 'hello' , 'world');
-    $handlers_fields = array('', 'foo', 'bar');
+    $handlers_filters = array('<default>');
+    $handlers_fields = array('<default>');
     $form['view_setup_table']["instructions"] = array(
          '#type' => 'markup',
          '#value' => "Select an optional table to which the fields of the materialized view can join.  If a field does not need to join you may leave the selection blank.",
@@ -341,7 +328,7 @@ function tripal_views_integration_new_setup_form(&$form_state){
  *
  * @ingroup tripal_views_integration
  */
-function tripal_views_integration_new_setup_form_validate($form, &$form_state){
+function tripal_core_views_integration_new_setup_form_validate($form, &$form_state){
   $name_array = explode(" ", $form_state['values']['row_name']);
   if(count($name_array) > 1){
     form_set_error($form_state['values']['row_name'], 'Name must be ONE word only.');
@@ -352,13 +339,13 @@ function tripal_views_integration_new_setup_form_validate($form, &$form_state){
  *
  * @ingroup tripal_views_integration
  */
-function tripal_views_integration_new_setup_form_submit($form, &$form_state){
+function tripal_core_views_integration_new_setup_form_submit($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'],
+  	 'description' => $form_state['values']['row_description'],
   );
 
   drupal_write_record('tripal_views_integration', $tripal_views_integration_record);

base/tripal_core/tripal_views_integration_fields_form.tpl.php

@@ -0,0 +1,50 @@
+<style type="text/css">
+
+#tripal-core-views-integration-new-setup-form  .fields-new-row, .field-headers {
+   dislay: block;
+   margin: 0px;
+   border-bottom-style: solid;
+   border-bottom-width: 1px;
+}
+#tripal-core-views-integration-new-setup-form .form-item {
+   margin: 0px 0px 5px 0px;
+}
+#tripal-core-views-integration-new-setup-form .column-id, .fields-column-join,.fields-column-join-column, .fields-filter-handler, .fields-field-handler {
+   display: inline-block;
+   margin: 0px;
+   vertical-align: top;
+}
+#tripal-core-views-integration-new-setup-form  .field-headers {
+   font-weight: bold;
+}
+#tripal-core-views-integration-new-setup-form  .field-headers div {
+   display: inline-block;
+   margin: 0px;
+   vertical-align: top;
+}
+#tripal-core-views-integration-new-setup-form .column-name {
+
+}
+#tripal-core-views-integration-new-setup-form .column-type {
+   font-style: italic;
+}
+#tripal-core-views-integration-new-setup-form .column-id {
+   width: 15%;
+}
+#tripal-core-views-integration-new-setup-form .fields-column-join {
+   width: 30%;
+}
+#tripal-core-views-integration-new-setup-form .fields-column-join-column {
+   width: 30%;
+}
+#tripal-core-views-integration-new-setup-form .fields-filter-handler {
+   width: 10%;
+}
+#tripal-core-views-integration-new-setup-form .fields-field-handler {
+   width: 10%;
+}
+
+</style>
+
+<?php print drupal_render($form); ?>
+

base/tripal_views_integration/README.patches.txt

@@ -1,20 +0,0 @@
-This README lists all patches that were used in developement of tripal_views_integration.
-
-------------------------------------------------------
-These are the patches needed to ahah_helper module:
-Submit issue reported and solved here:
-http://drupal.org/node/1231140
-The original patch location:
-http://drupal.org/files/issues/1231140.ahah_helper.form-submit-handler.patch
-The patch file alexgl used:
-patches/1231140.ahah_helper.form-submit-handler.patch
-Usage:
-1. Find the global or local path to this module and substitue in the command below for*path_to_tripal_views_integration*
-2. Navigate to the folder of contrib module ahah_helper and run:
-ahah_helper$ patch -p1 < *path_to_tripal_views_integration*/patches/1231140.ahah_helper.form-submit-handler.patch
-
-(alternatively you can just copy the patch file to the ahah_helper folder and run the command without *path_to_tripal_views_integration*)
-NOTE: we have to use patch -p1 command, since this is a git patch, and the ahah_helper folder most likely will not be
-	git inintialized. -p0 will not work. If folder is not git initialized then 'git apply -v *patchname*' will do nothing.
------------------------------------------------------
-

base/tripal_views_integration/patches/1231140.ahah_helper.form-submit-handler.patch

@@ -1,18 +0,0 @@
-diff --git a/ahah_helper.module b/ahah_helper.module
-index dfd222a..32d5c5d 100644
---- a/ahah_helper.module
-+++ b/ahah_helper.module
-@@ -132,6 +132,13 @@ function ahah_helper_generic_submit($form, &$form_state) {
-  */
- function ahah_helper_real_submit($form, &$form_state) {
-   unset($form_state['storage']);
-+
-+  // Call FormAPI's standard submit handler for the form.
-+  $form_id = $form['form_id']['#value'];
-+  $function = $form_id . '_submit';
-+  if (function_exists($function)) {
-+    $function($form, &$form_state);
-+  }
- }
- 
- /**

base/tripal_views_integration/tripal_views_integration.info

@@ -1,9 +0,0 @@
-name = Tripal Views Integration
-description = Tripal module that integrates materialized views with Drupal views to enable custom pages, queries and search forms.
-core = 6.x
-package = Tripal
-
-dependencies[] = tripal_core
-dependencies[] = ahah_helper
-dependencies[] = views
-

base/tripal_views_integration/tripal_views_integration.install

@@ -1,155 +0,0 @@
-<?php
-function tripal_views_integration_schema(){
-	$schema = array();
-	$schema['tripal_views_integration'] = array(
-		'description' => 'contains the setupes, their materialized view id and base table name that was used.',
-		'fields' => array(
-			'setup_id' => array(
-				'description' => 'the id of the setup',
-				'type' => 'serial',
-				'unsigned' => TRUE,
-				'not null' => TRUE,
-			),
-			'mview_id' => array(
-				'description' => 'the materialized view used for this setup',
-				'type' => 'int',
-				'unsigned' => TRUE,
-			),
-			'chado_table_name' => array(
-				'description' => 'the base table name to be used when using this setup',
-				'type' => 'varchar',
-				'length' => 255,
-				'not null' => TRUE,
-				'default' => '',
-			),
-			'name' => array(
-				'description' => 'Human readable name of this setup',
-				'type' => 'varchar',
-				'length' => 255,
-				'not null' => TRUE,
-				'default' => '',
-			),
-			'description' => array(
-				'description' => 'description of this row',
-				'type' => 'varchar',
-				'length' => 255,
-				'not null' => TRUE,
-				'default' => '',
-			),
-		),
-		'unique_keys' => array(
-			'setup_id' => array('setup_id'),
-		),
-		'primary key' => array('setup_id'),
-	);
-	$schema['tripal_mviews_join'] = array(
-		'description' => 'which materialzed views and chado tables to join in a given setup',
-		'fields' => array(
-		  'mview_join_id' => array(
-				'description' => 'the id of the join',
-					'type' => 'serial',
-					'unsigned' => TRUE,
-					'not null' => TRUE,
-		  ),
-			'setup_id' => array(
-				'description' => 'tripal setup id from tripal_views_integration 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)',
-				'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',
-				'type' => 'varchar',
-				'length' => '255',
-				'not null' => TRUE,
-				'default' => '',
-			),
-			'chado_column' => array(
-				'description' => 'chado table (above) column to join on materialized view in this serach',
-				'type' => 'varchar',
-				'length' => '255',
-				'not null' => TRUE,
-				'default' => '',
-	    ),
-		),
-		'unique_keys' => array(
-			'setup_id' => array('mview_join_id'),
-		),
-		'primary key' => array('mview_join_id'),
-	);
-	$schema['tripal_views_handlers'] = array(
-		'description' => 'in formation for views: column and views handler name',
-		'fields' => array(
-			'handler_id' => array(
-				'description' => 'the id of the handler',
-					'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,
-			),
-			'column_name' => array(
-				'description' => '',
-				'type' => 'varchar',
-				'length' => '255',
-				'not null' => TRUE,
-				'default' => '',
-			),
-			'handler_filter' => array(
-				'description' => 'identifier of the handler filter to be used for this column',
-				'type' => 'varchar',
-				'length' => '255',
-				'not null' => TRUE,
-				'default' => '',
-			),
-			'handler_field' => array(
-				'description' => 'identifier of the handler field to be used for this column',
-				'type' => 'varchar',
-				'length' => '255',
-				'not null' => TRUE,
-				'default' => '',
-	    ),
-		),
-		'unique_keys' => array(
-				'setup_id' => array('handler_id'),
-	  ),
-		'primary key' => array('handler_id'),
-	);
-	return $schema;
-}
-
-function tripal_views_integration_install(){
-	drupal_install_schema('tripal_views_integration');
-}
-
-function tripal_views_integration_uninstall(){
-	drupal_uninstall_schema('tripal_views_integration');
-}
-
-
-/*
- * NOTE: when updating schema for this module's tables
- * follow api of schema module, otherwise on uninstall
- * the tables will not be removed correctly
- *
- */
-
-

base/tripal_views_integration/tripal_views_integration.module

@@ -1,81 +0,0 @@
-<?php
-
-require_once 'includes/tripal_views_integration.admin.inc';
-
-/**
- * Implements hook_views_api()
- *
- * Purpose: Essentially this hook tells drupal that there is views support for
- *  for this module which then includes tripal_db.views.inc where all the
- *  views integration code is
- *
- * @ingroup tripal_views_integration
- */ 
-function tripal_views_integration_views_api() {
-   return array(
-      'api' => 2.0,
-   );
-}
-
-/**
- *
- * @ingroup tripal_views_integration
- */
-function tripal_views_integration_menu(){
-	$items = array();
-
-   $items['admin/tripal/tripal_views_integration'] = array(
-     'title' => t('Views Integration'),
-     'description' => 'Basic Description of Tripal Views Integration Module',
-     'page callback' => 'tripal_views_integration_module_description_page',
-     'access arguments' => array('administer site configuration'),
-     'type' => MENU_NORMAL_ITEM,
-   );
-
-	$items['admin/tripal/tripal_views_integration/list'] = array(
-    'title' => t('List of Integrated Views'),
-    'description' => t('Tripal Views Setups settings page, allows you to select and create materialized views and chado tables to use for searches.'),
-    'page callback' => 'drupal_get_form',
-    'page arguments' => array('tripal_views_integration_admin_form'),
-    'access arguments' => array('manage tripal_views_integration'),
-    'type' => MENU_NORMAL_ITEM,
-	);
-
-	//page to actually create setup->mview->chado table relationships
-	$items['admin/tripal/tripal_views_integration/new'] = array(
-     'title' => 'Integrate a Materialized View',
-     'page callback' => 'drupal_get_form',
-     'page arguments' => array('tripal_views_integration_new_setup_form'),
-     'access arguments' => array('manage tripal_views_integration'), //TODO: figure out the proper permissions arguments
-     'type' => MENU_NORMAL_ITEM,
-	);
-
-	return $items;
-}
-/**
- *  Set the permission types that the chado module uses.  Essentially we
- *  want permissionis that protect creation, editing and deleting of chado
- *  data objects
- *
- * @ingroup tripal_views_integration
- */
-function tripal_views_integration_perm(){
-   return array(
-      'manage tripal_views_integration',
-   );
-}
-/**
- *
- * @ingroup tripal_views_integration
- */
-function tripal_views_integration_theme(){
-	$theme = array();
-
-	$theme['tripal_views_integration_new_setup_form'] = array(
-      'arguments' => array('form' => NULL),
-      'template'  => 'tripal_views_integration_fields_form',
-	);
-
-	return $theme;
-}
-

base/tripal_views_integration/tripal_views_integration.views.inc

@@ -1,140 +0,0 @@
-  <?php
-/**
- *
- * @ingroup tripal_views_integration
- */
-function tripal_views_integration_views_data(){   
-
-    $tvi_query = db_query('SELECT * FROM tripal_views_integration');
-
-    //tvi = tripal_views_integration
-    while($tvi_row = db_fetch_object($tvi_query)){
-
-      //ids we'll use for queries
-      $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';"));
-
-      //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(
-        'group' => t($tvi_row->name),
-        'title' => t($tvi_row->name),
-        'help'  => t($tvi_row->description),
-      );
-
-      //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),
-           'help' => t("**"),
-           'field' => array(
-              'handler' => 'views_handler_field',
-              'click sortable' => TRUE,
-           ),
-           'sort' => array(
-              'handler' => 'views_handler_sort',
-           ),
-           'filter' => array(
-              'handler' => 'views_handler_filter_string',
-           ),
-           '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,
-        );
-
-        // 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'";
-        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,
-           );
-        }
-      }
-    }
-
-    return $data;
-}
-/**      $setup_id = $tvi_row->setup_id;
- *
- * @ingroup tripal_views_integration
- */
-function tripal_views_integration_views_data_alter(&$data) {
-    $tvi_query = db_query('SELECT * FROM tripal_views_integration');
-
-    //tvi = tripal_views_integration
-    while($tvi_row = db_fetch_object($tvi_query)){
-
-      //ids we'll use for queries
-      $mview_id = $tvi_row->mview_id;
-      $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';"));
-
-      // 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;      
- 
-        // 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,
-        );
-
-        // 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.  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'";
-        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,
-           );
-
-           // 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",
-           	'left_field' => 'nid',
-           	'field' => 'nid',
-           );
-        }
-      }
-    }
-
-    return $data;
-}

base/tripal_views_integration/tripal_views_integration_fields_form.tpl.php

@@ -1,50 +0,0 @@
-<style type="text/css">
-
-#tripal-views-integration-new-setup-form  .fields-new-row, .field-headers {
-   dislay: block;
-   margin: 0px;
-   border-bottom-style: solid;
-   border-bottom-width: 1px;
-}
-#tripal-views-integration-new-setup-form .form-item {
-   margin: 0px 0px 5px 0px;
-}
-#tripal-views-integration-new-setup-form .column-id, .fields-column-join,.fields-column-join-column, .fields-filter-handler, .fields-field-handler {
-   display: inline-block;
-   margin: 0px;
-   vertical-align: top;
-}
-#tripal-views-integration-new-setup-form  .field-headers {
-   font-weight: bold;
-}
-#tripal-views-integration-new-setup-form  .field-headers div {
-   display: inline-block;
-   margin: 0px;
-   vertical-align: top;
-}
-#tripal-views-integration-new-setup-form .column-name {
-
-}
-#tripal-views-integration-new-setup-form .column-type {
-   font-style: italic;
-}
-#tripal-views-integration-new-setup-form .column-id {
-   width: 25%;
-}
-#tripal-views-integration-new-setup-form .fields-column-join {
-   width: 25%;
-}
-#tripal-views-integration-new-setup-form .fields-column-join-column {
-   width: 25%;
-}
-#tripal-views-integration-new-setup-form .fields-filter-handler {
-   width: 10%;
-}
-#tripal-views-integration-new-setup-form .fields-field-handler {
-   width: 10%;
-}
-
-</style>
-
-<?php print drupal_render($form); ?>
-

extensions/tripal_search_unigene/tripal_search_unigene.module

@@ -4,15 +4,15 @@
 
 /*************************************************************************
  * tripal_search_unigene_init
- */ 
+ */
 function tripal_search_unigene_init(){
-	drupal_add_css(drupal_get_path('theme', 'tripal_search_unigene').'/theme/css/tripal_search_unigene.css');
-	drupal_add_js(drupal_get_path('theme', 'tripal_search_unigene').'/theme/js/tripal_search_unigene.js');
+	drupal_add_css(drupal_get_path('module', 'tripal_search_unigene').'/theme/css/tripal_search_unigene.css');
+	drupal_add_js(drupal_get_path('module', 'tripal_search_unigene').'/theme/js/tripal_search_unigene.js');
 }
 
 /*************************************************************************
  * tripal_search_unigene_views_api
- */ 
+ */
 function tripal_search_unigene_views_api() {
    return array(
       'api' => 2.0,