Merge branch '6.x-0.4-dev' into 6.x-1482618-API_for_default_views_integration

base/tripal_core/mviews.php

@@ -102,7 +102,7 @@ function tripal_mviews_get_mview_id ($view_name){
 *
 * @ingroup tripal_core
 */
-function tripal_mviews_action ($op,$mview_id){
+function tripal_mviews_action ($op,$mview_id,$redirect=0){
    global $user;
    $args = array("$mview_id");
    
@@ -133,7 +133,9 @@ function tripal_mviews_action ($op,$mview_id){
       }
       tripal_db_set_active($previous_db);  // now use drupal database
    }
-   drupal_goto("admin/tripal/views/mviews");
+   if($redirect){
+      drupal_goto("admin/tripal/mviews");
+   }
 }
 /**
 * Update a Materialized View
@@ -179,7 +181,7 @@ 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/views/mviews/");
+   $return_url = url("admin/tripal/mviews/");
 
    $output .= "<p><a href=\"$return_url\">Return to table of materialized views.</a></p>";
    $output .= "<br />";
@@ -240,9 +242,9 @@ function tripal_mview_report ($mview_id) {
 
    // build the URLs using the url function so we can handle installations where
    // clean URLs are or are not used
-   $update_url = url("admin/tripal/views/mviews/action/update/$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");
+   $update_url = url("admin/tripal/mviews/action/update/$mview->mview_id");
+   $delete_url = url("admin/tripal/mviews/action/delete/$mview->mview_id");
+   $edit_url = url("admin/tripal/mviews/edit/$mview->mview_id");
 
    $output .= "<tr><th>Actions</th>".
               "<td> <a href='$update_url'>Update</a>, ".
@@ -271,16 +273,16 @@ function tripal_mviews_report () {
          $update = 'Not yet populated';
       }
       $rows[] = array(
-         l('View',"admin/tripal/views/mviews/report/$mview->mview_id") ." | ".
-            l('Update',"admin/tripal/views/mviews/action/update/$mview->mview_id"),
+         l('View',"admin/tripal/mviews/report/$mview->mview_id") ." | ".
+            l('Update',"admin/tripal/mviews/action/update/$mview->mview_id"),
          $mview->name,
          $update,
-         l('Delete',"admin/tripal/views/mviews/action/delete/$mview->mview_id"),
+         l('Delete',"admin/tripal/mviews/action/delete/$mview->mview_id"),
       );
    }
    $rows[] = array(
       'data' => array( 
-         array('data' => l('Create a new materialized view.',"admin/tripal/views/mviews/new"), 
+         array('data' => l('Create a new materialized view.',"admin/tripal/mviews/new"), 
                'colspan' => 4),
          )
    );
@@ -400,7 +402,7 @@ function tripal_mviews_form(&$form_state = NULL,$mview_id = NULL){
      '#executes_submit_callback' => TRUE,
    );
 
-   $form['#redirect'] = 'admin/tripal/views/mviews';
+   $form['#redirect'] = 'admin/tripal/mviews';
    return $form;
 }
 /**

base/tripal_core/tripal_core.info

@@ -4,8 +4,5 @@ description = The core module for the Tripal package that integrates Drupal and
 core = 6.x
 project = tripal_core
 package = Tripal
-version = 6.x-0.3.1b
+version = 6.x-0.4
 
-dependencies[] = views
-dependencies[] = ahah_helper
-dependencies[] = views_data_export

base/tripal_core/tripal_core.install

@@ -60,10 +60,6 @@ function tripal_core_get_schemas (){
    foreach ($temp as $table => $arr){ 
       $schema[$table] = $arr; 
    }
-   $temp = tripal_core_views_schema();
-   foreach ($temp as $table => $arr){ 
-      $schema[$table] = $arr; 
-   } 
 
 	return $schema;
 }
@@ -131,169 +127,4 @@ function tripal_core_jobs_schema(){
    );
    return $schema;
 }
-/************************************************************************
-* 
-*
-* @ingroup tripal_core
-*/
-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(
-				'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,
-			),
-			'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,
-				'default' => '',
-			),
-			'name' => array(
-				'description' => 'Human readable name of this setup',
-				'type' => 'varchar',
-				'length' => 255,
-				'not null' => TRUE,
-				'default' => '',
-			),
-			'comment' => array(
-				'description' => 'add notes about this views setup',
-				'type' => 'text',
-				'size' => 'normal',
-				'not null' => FALSE,
-				'default' => '',
-			),
-		),
-		'unique_keys' => array(
-			'setup_id' => array('setup_id'),
-		),
-		'primary key' => array('setup_id'),
-	);
-
-	$schema['tripal_views_join'] = array(
-		'description' => 'coordinate the joining of tables',
-		'fields' => array(
-		  'view_join_id' => array(
-				'description' => 'the id of the join',
-				'type' => 'serial',
-				'unsigned' => TRUE,
-				'not null' => TRUE,
-		  ),
-			'setup_id' => array(
-				'description' => 'setup id from tripal_views table',
-				'type' => 'int',
-				'unsigned' => TRUE,
-				'not null'=> TRUE,
-			),
-			'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' => '',
-			),
-			'left_table' => array(
-				'description' => 'the table on which to perform a left join',
-				'type' => 'varchar',
-				'length' => '255',
-				'not null' => TRUE,
-				'default' => '',
-			),
-			'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('view_join_id'),
-		),
-		'primary key' => array('view_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' => 'setup id from the tripal_views table',
-				'type' => 'int',
-				'unsigned' => TRUE,
-				'not null'=> TRUE,
-			),
-			'column_name' => array(
-				'description' => '',
-				'type' => 'varchar',
-				'length' => '255',
-				'not null' => TRUE,
-				'default' => '',
-			),
-			'handler_type' => array(
-				'description' => 'identifies the type of hander (e.g. field, filter, sort, argument, relationship, etc.)',
-				'type' => 'varchar',
-				'length' => '50',
-				'not null' => TRUE,
-				'default' => '',
-			),
-			'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'),
-	   ),
-		'primary key' => array('handler_id'),
-	);
-
-   return $schema;
-}
-/************************************************************************
-* 
-*
-* @ingroup tripal_core
-*/
-function tripal_core_update_6000(){
-   $schema = tripal_core_views_schema();
-   $ret = array();
-   foreach ($schema as $name => $table) {
-      db_create_table($ret, $name, $table);
-   }   
-   return $ret;
-}
-
 ?>

base/tripal_core/tripal_core.module

@@ -4,10 +4,8 @@ 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";
-require_once "tripal_core.views.inc";
+
 
 /**
  * @defgroup tripal_modules Tripal Modules
@@ -137,30 +135,24 @@ function tripal_core_menu() {
    );
  
 
-   // Views Integration
-   $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/views/mviews'] = array(
+   // Materialized Views 
+
+   $items['admin/tripal/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/views/mviews/report/%'] = array(
+   $items['admin/tripal/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),
+     'page arguments' => array(4),
      'access arguments' => array('access administration pages'),
      'type' => MENU_NORMAL_ITEM,
    );
-   $items['admin/tripal/views/mviews/new'] = array(
+   $items['admin/tripal/mviews/new'] = array(
      'title' => 'Create MView',
      'description' => 'Materialized views are used to improve speed of large or complex queries.',
      'page callback' => 'drupal_get_form',
@@ -168,53 +160,21 @@ function tripal_core_menu() {
      'access arguments' => array('access administration pages'),
      'type' => MENU_CALLBACK,
    );
-   $items['admin/tripal/views/mviews/edit/%'] = array(
+   $items['admin/tripal/mviews/edit/%'] = array(
      'title' => 'Edit MView',
      'page callback' => 'drupal_get_form',
-     'page arguments' => array('tripal_mviews_form',5),
+     'page arguments' => array('tripal_mviews_form',4),
      'access arguments' => array('access administration pages'),
      'type' => MENU_NORMAL_ITEM,
    );
-   $items['admin/tripal/views/mviews/action/%/%'] = array(
+   $items['admin/tripal/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(5,6),
+     'page arguments' => array(4,5,"1"),
      'access arguments' => array('access administration pages'),
      'type' => MENU_CALLBACK,
    );
- 	$items['admin/tripal/views/integration'] = array(
-     'title' => t('Views Integration'),
-     'description' => t('Allows you to select existing materialized views and provide details for integration with Drupal Views.'),
-     'page callback' => 'tripal_core_views_integration_setup_list',
-     'access arguments' => array('manage tripal_views_integration'),
-     'type' => MENU_NORMAL_ITEM,
- 	);
-
-
-	$items['admin/tripal/views/integration/new'] = array(
-     'title' => 'Integrate Views',
-     'page callback' => 'drupal_get_form',
-     'page arguments' => array('tripal_core_views_integration_form'),
-     'access arguments' => array('manage tripal_views_integration'), //TODO: figure out the proper permissions arguments
-     'type' => MENU_CALLBACK,
-	);
-	
-	$items['admin/tripal/views/integration/edit/%'] = array(
-     'title' => 'Edit Views Integration',
-     'page callback' => 'drupal_get_form',
-     'page arguments' => array('tripal_core_views_integration_form',5),
-     'access arguments' => array('manage tripal_views_integration'), //TODO: figure out the proper permissions arguments
-     'type' => MENU_CALLBACK,
-	);
-
-	$items['admin/tripal/views/integration/delete/%'] = array(
-     'title' => 'Delete Views Integration',
-     'page callback' => 'tripal_core_views_integration_delete',
-     'page arguments' => array(5),
-     'access arguments' => array('manage tripal_views_integration'), //TODO: figure out the proper permissions arguments
-     'type' => MENU_CALLBACK,
-	);
   return $items;
 }
 
@@ -228,7 +188,6 @@ function tripal_core_menu() {
  */
 function tripal_core_perm(){
    return array(
-      'manage tripal_views_integration',
    );
 }
 /**
@@ -261,21 +220,6 @@ function tripal_core_is_chado_installed(){
    return false;
 }
 
-/**
- * Implements hook_views_api()
- *
- * Purpose: Essentially this hook tells drupal that there is views support for
- *  for this module which then includes tripal_core.views.inc where all the
- *  views integration code is
- *
- * @ingroup tripal_core
- */
-function tripal_core_views_api() {
-   return array(
-      'api' => 2.0,
-   );
-}
-
 
 /**
  *
@@ -287,14 +231,6 @@ function tripal_core_theme () {
          'arguments' => array('job_id'=> null),
          'template' => 'tripal_core_job_view',
       ),
-	   'tripal_core_views_integration_form' => array(
-         'arguments' => array('form' => NULL),
-         'template'  => 'tripal_views_integration_fields_form',
-	   ),
-	   'tripal_core_views_data_export_download_form' => array(
-         'arguments' => array('form' => NULL),
-         'template'  => 'tripal_core_views_data_export_download_form',
-	   ),
    );
 }
 /**

base/tripal_core/tripal_views_integration_fields_form.tpl.php

@@ -1,66 +0,0 @@
-<style type="text/css">
-
-#tripal-core-views-integration-form  .fields-new-row, .field-headers {
-   dislay: block;
-   margin: 0px;
-   border-bottom-style: solid;
-   border-bottom-width: 1px;
-}
-#tripal-core-views-integration-form .form-item {
-   margin: 0px 0px 5px 0px;
-}
-#tripal-core-views-integration-form .column-id, .column-form-fields, .column-one, .column-two {
-   display: inline-block;
-   margin: 0px;
-   vertical-align: top;
-   //border: 1px solid #000;
-}
-#tripal-core-views-integration-form  .field-headers {
-   font-weight: bold;
-}
-#tripal-core-views-integration-form  .field-headers div {
-   display: inline-block;
-   margin: 0px;
-   vertical-align: top;
-}
-#tripal-core-views-integration-form .column-name {
-   font-weight: bold;
-}
-#tripal-core-views-integration-form .column-type {
-   font-style: italic;
-}
-#tripal-core-views-integration-form .column-id {
-   width: 20%;
-   height: 50px;
-}
-#tripal-core-views-integration-form  .fields-new-row {
-   padding-bottom: 10px;
-   margin-bottom: 5px;
-   padding-top: 10px;
-}
-#tripal-core-views-integration-form .column-form-fields {
-   //border: 3px solid #f00;
-}
-#tripal-core-views-integration-form .column-one {
-   margin-left: 15px;
-}
-#tripal-core-views-integration-form .column-two {
-   margin-left: 15px;
-}
-#tripal-core-views-integration-form .fields-column-join {
-
-}
-#tripal-core-views-integration-form .fields-column-join-column {
-
-}
-#tripal-core-views-integration-form .fields-filter-handler {
-
-}
-#tripal-core-views-integration-form .fields-field-handler {
-
-}
-
-</style>
-
-<?php print drupal_render($form); ?>
-

base/tripal_core/views_data_export/plugins/tripal_core_plugin_style_export_fasta.inc~

@@ -1,56 +0,0 @@
-<?php
-/**
- * @file
- * Plugin include file for export style plugin.
- */
-
-/**
- * Generalized style plugin for export plugins.
- *
- * @ingroup views_style_plugins
- */
-class tripal_core_plugin_style_export_fasta extends views_data_export_plugin_style_export {
-
-  /**
-   * Set options fields and default values.
-   *
-   * @return
-   * An array of options information.
-   */
-  function option_definition() {
-    $options = parent::option_definition();
-
-  
-    return $options;
-  }
-
-  /**
-   * Options form mini callback.
-   *
-   * @param $form
-   * Form array to add additional fields to.
-   * @param $form_state
-   * State of the form.
-   * @return
-   * None.
-   */
-  function options_form(&$form, &$form_state) {
-    parent::options_form($form, $form_state);
-
-    $form['defline_fields'] = array(
-      '#prefix' => '<div><div id="edit-options-newline-replacement">',
-      '#suffix' => '</div></div>',
-      '#type' => 'textfield',
-      '#title' => t('Defenition line fields'),
-      '#default_value' => $this->options['defline_fields'],
-      '#description' => t("This field controls the information present in the definition ".
-         "line for each sequence. Any of the fields in the view can be used in the ".
-         "definition line.  To discover these fields, add the feature residues as the ".
-         "last field in the view.  Then edit the field and click the checkbox \"Rewrite ".
-         "the output of this field\".  In the replacement patterns section are the ".
-         "field replacement tokens that can be used in this field. You may include any ".
-         "additional text to separte or qualify these fields.  Only fields that have not ".
-         "been excluded from the display will appear"),
-    );
-  }
-}

base/tripal_core/views_data_export/theme/tripal_core_views_data_export.theme.inc~

@@ -1,17 +0,0 @@
-<?php
-
-function template_preprocess_views_data_export_fasta_body(&$vars) {
-   _views_data_export_header_shared_preprocess($vars);
-   _views_data_export_body_shared_preprocess($vars);
-   $defline_tpl = $vars['options']['defline_fields'];
-
-   // iterate through the rows and replace the field tokens with values
-   // to generate the definition line
-   foreach ($vars['themed_rows'] as $i => $fields) {
-      $defline = $defline_tpl;
-      foreach ($fields as $key => $value) {
-         $defline = preg_replace("/\[$key\]/",$value,$defline);
-      }
-      $vars['themed_rows'][$i]['defline'] = $defline;
-   }
-}

base/tripal_core/views_data_export/theme/views-data-export-fasta-body.tpl.php~

@@ -1,19 +0,0 @@
-<?php
-//print_r($themed_rows);
-print $defline;
-foreach ($themed_rows as $index => $fields){
-   $defline = array();
-   $residues = '';
-   foreach ($fields as $key => $value){
-     if(strcmp($key,'residues')==0){
-        $residues = wordwrap($value, 60, "\r\n", true);
-     } 
-     if($strcmp($key,'defline')==0){
-        $defline = $value;
-     }
-   }
-   print ">$defline\r\n";
-   print "$residues\r\n";
-}
-
-

base/tripal_core/views_data_export/theme/views-data-export-fasta-footer.tpl.php~

@@ -1,5 +0,0 @@
-<?php
-
-/**
- * CSV files don't really have a footer.
- */

base/tripal_core/views_data_export/theme/views-data-export-fasta-header.tpl.php~

@@ -1,6 +0,0 @@
-<?php
-
-// Print out header row, if option was selected.
-if ($options['header']) {
-  print implode($separator, $header) . "\r\n";
-}

base/tripal_views/tripal_views.info

@@ -0,0 +1,10 @@
+name = Tripal Views
+description = This module provides integration with Drupal Views. Other Tripal modules may have an optional dependency with this module and once enabled Views support becomes active for those modules.  This module provides a way to integrate Materialized Views and Chado Tables with Views. It also integrates the Views Data Export module to allow for downloads of Views into Excel, CSV and FASTA formats.
+core = 6.x
+project = tripal_core
+package = Tripal
+version = 6.x-0.4
+
+dependencies[] = views
+dependencies[] = ahah_helper
+dependencies[] = views_data_export

base/tripal_views/tripal_views.install

@@ -0,0 +1,206 @@
+<?php
+
+/************************************************************************
+*  Implementation of hook_install();
+* 
+* @ingroup tripal_views
+*/
+function tripal_views_install(){
+
+   // create the module's data directory
+   tripal_create_moddir('tripal_views');
+
+  // create the tables that manage materialized views and jobs
+  drupal_install_schema('tripal_views');
+
+}
+
+/************************************************************************
+* Implementation of hook_schema().
+*
+* @ingroup tripal_views
+*/
+function tripal_views_schema() {
+   $schema = tripal_views_get_schemas();
+   return $schema;
+}
+/************************************************************************
+* Implementation of hook_uninstall()
+*
+* @ingroup tripal_views
+*/
+function tripal_views_uninstall(){
+   drupal_uninstall_schema('tripal_views');
+}
+
+/************************************************************************
+* This function simply defines all tables needed for the module to work
+* correctly.  By putting the table definitions in a separate function we
+* can easily provide the entire list for hook_install or individual
+* tables for an update.
+*
+* @ingroup tripal_views
+*/
+function tripal_views_get_schemas (){  
+   $schema = array();
+
+   $temp = tripal_views_views_schema();
+   foreach ($temp as $table => $arr){ 
+      $schema[$table] = $arr; 
+   } 
+
+	return $schema;
+}
+
+/************************************************************************
+* 
+*
+* @ingroup tripal_views
+*/
+function tripal_views_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(
+				'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,
+			),
+			'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,
+				'default' => '',
+			),
+			'name' => array(
+				'description' => 'Human readable name of this setup',
+				'type' => 'varchar',
+				'length' => 255,
+				'not null' => TRUE,
+				'default' => '',
+			),
+			'comment' => array(
+				'description' => 'add notes about this views setup',
+				'type' => 'text',
+				'size' => 'normal',
+				'not null' => FALSE,
+				'default' => '',
+			),
+		),
+		'unique_keys' => array(
+			'setup_id' => array('setup_id'),
+		),
+		'primary key' => array('setup_id'),
+	);
+
+	$schema['tripal_views_join'] = array(
+		'description' => 'coordinate the joining of tables',
+		'fields' => array(
+		  'view_join_id' => array(
+				'description' => 'the id of the join',
+				'type' => 'serial',
+				'unsigned' => TRUE,
+				'not null' => TRUE,
+		  ),
+			'setup_id' => array(
+				'description' => 'setup id from tripal_views table',
+				'type' => 'int',
+				'unsigned' => TRUE,
+				'not null'=> TRUE,
+			),
+			'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' => '',
+			),
+			'left_table' => array(
+				'description' => 'the table on which to perform a left join',
+				'type' => 'varchar',
+				'length' => '255',
+				'not null' => TRUE,
+				'default' => '',
+			),
+			'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('view_join_id'),
+		),
+		'primary key' => array('view_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' => 'setup id from the tripal_views table',
+				'type' => 'int',
+				'unsigned' => TRUE,
+				'not null'=> TRUE,
+			),
+			'column_name' => array(
+				'description' => '',
+				'type' => 'varchar',
+				'length' => '255',
+				'not null' => TRUE,
+				'default' => '',
+			),
+			'handler_type' => array(
+				'description' => 'identifies the type of hander (e.g. field, filter, sort, argument, relationship, etc.)',
+				'type' => 'varchar',
+				'length' => '50',
+				'not null' => TRUE,
+				'default' => '',
+			),
+			'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'),
+	   ),
+		'primary key' => array('handler_id'),
+	);
+
+   return $schema;
+}
+?>

base/tripal_views/tripal_views.module

@@ -0,0 +1,98 @@
+<?php
+
+require_once "tripal_views_integration.inc";
+require_once "tripal_views.views.inc";
+
+/**
+ *
+ *
+ * @ingroup tripal_views
+ */
+function tripal_views_menu() {
+   $items = array();
+   
+   $items['admin/tripal/views'] = array(
+     'title' => t('Views Integration'),
+     'description' => 'Integration with Drupal Views',
+     'page callback' => 'tripal_views_description_page',
+     'access arguments' => array('administer site configuration'),
+     'type' => MENU_NORMAL_ITEM,
+   );
+
+ 	$items['admin/tripal/views/integration'] = array(
+     'title' => t('Views Integration'),
+     'description' => t('Allows you to select existing materialized views and provide details for integration with Drupal Views.'),
+     'page callback' => 'tripal_views_integration_setup_list',
+     'access arguments' => array('manage tripal_views_integration'),
+     'type' => MENU_NORMAL_ITEM,
+ 	);
+
+
+	$items['admin/tripal/views/integration/new'] = array(
+     'title' => 'Integrate Views',
+     'page callback' => 'drupal_get_form',
+     'page arguments' => array('tripal_views_integration_form'),
+     'access arguments' => array('manage tripal_views_integration'), //TODO: figure out the proper permissions arguments
+     'type' => MENU_CALLBACK,
+	);
+	
+	$items['admin/tripal/views/integration/edit/%'] = array(
+     'title' => 'Edit Views Integration',
+     'page callback' => 'drupal_get_form',
+     'page arguments' => array('tripal_views_integration_form',5),
+     'access arguments' => array('manage tripal_views_integration'), //TODO: figure out the proper permissions arguments
+     'type' => MENU_CALLBACK,
+	);
+
+	$items['admin/tripal/views/integration/delete/%'] = array(
+     'title' => 'Delete Views Integration',
+     'page callback' => 'tripal_views_integration_delete',
+     'page arguments' => array(5),
+     'access arguments' => array('manage tripal_views_integration'), //TODO: figure out the proper permissions arguments
+     'type' => MENU_CALLBACK,
+	);
+
+   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
+ */
+function tripal_views_perm(){
+   return array(
+      'manage tripal_views_integration',
+   );
+}
+/**
+ * Implements hook_views_api()
+ *
+ * Purpose: Essentially this hook tells drupal that there is views support for
+ *  for this module which then includes tripal_views.views.inc where all the
+ *  views integration code is
+ *
+ * @ingroup tripal_views
+ */
+function tripal_views_views_api() {
+   return array(
+      'api' => 2.0,
+   );
+}
+/**
+ *
+ * @ingroup tripal_views
+ */
+function tripal_views_theme () {
+   return array(
+	   'tripal_views_integration_form' => array(
+         'arguments' => array('form' => NULL),
+         'template'  => 'tripal_views_integration_fields_form',
+	   ),
+	   'tripal_views_data_export_download_form' => array(
+         'arguments' => array('form' => NULL),
+         'template'  => 'tripal_views_data_export_download_form',
+	   ),
+   );
+}

base/tripal_core/tripal_core.views.inc → base/tripal_views/tripal_views.views.inc

@@ -53,13 +53,13 @@ include('tripal_views.api.inc');
  * @return
  *   An array of handler definitions
  *
- * @ingroup tripal_core
+ * @ingroup tripal_views
  */
-function tripal_core_views_handlers() {
+function tripal_views_views_handlers() {
 
  return array(
    'info' => array(
-     'path' => drupal_get_path('module', 'tripal_core') . '/views/handlers',
+     'path' => drupal_get_path('module', 'tripal_views') . '/views/handlers',
    ),
    'handlers' => array(
    
@@ -181,13 +181,13 @@ function tripal_core_views_handlers() {
  *
  * @todo add if !<chado/drupal same db> around NID portion
  *
- * @ingroup tripal_core
+ * @ingroup tripal_views
  */
-function tripal_core_views_pre_render	(&$view) {
+function tripal_views_views_pre_render	(&$view) {
 		
 		//Add Node IDs in to every table that needs them
-		// @see file: tripal_core.views.inc
-		tripal_core_add_node_ids_to_view ($view);
+		// @see file: tripal_views.views.inc
+		tripal_views_add_node_ids_to_view ($view);
 		
 }
 
@@ -206,9 +206,9 @@ function tripal_core_views_pre_render	(&$view) {
  *
  * @return the views object with nids added to the result array
  *
- * @ingroup tripal_core
+ * @ingroup tripal_views
  */
-function tripal_core_add_node_ids_to_view (&$view) {
+function tripal_views_add_node_ids_to_view (&$view) {
 	
 	//-----Analysis----------------------------------------------
 	if (!empty($view->field['analysis_nid'])) {
@@ -369,10 +369,10 @@ function tripal_core_add_node_ids_to_view (&$view) {
 }
 /**
  *
- * @ingroup tripal_core
+ * @ingroup tripal_views
  */
 
-function tripal_core_views_data(){   
+function tripal_views_views_data(){   
   
    // Define Global Fields -------------
    // Filter handler that lets the admin say: 
@@ -488,9 +488,9 @@ function tripal_core_views_data(){
 }
 /**
  *
- * @ingroup tripal_core
+ * @ingroup tripal_views
  */
-function tripal_core_views_data_alter(&$data) {
+function tripal_views_views_data_alter(&$data) {
     $tvi_query = db_query('SELECT * FROM {tripal_views}');
 
     // iterate through the views that we manage
@@ -548,15 +548,15 @@ function tripal_core_views_data_alter(&$data) {
 /**
  * Implementation of hook_views_plugins().
  */
-function tripal_core_views_plugins() {
-  $tc_path = drupal_get_path('module', 'tripal_core');
+function tripal_views_views_plugins() {
+  $tc_path = drupal_get_path('module', 'tripal_views');
 
   $style_defaults = array(
     'path' => $tc_path . '/views_data_export/plugins',
     'parent' => 'views_data_export',
     'theme' => 'views_data_export',
     'theme path' => $tc_path . '/views_data_export/theme',
-    'theme file' => 'tripal_core_views_data_export.theme.inc',
+    'theme file' => 'tripal_views_data_export.theme.inc',
     'uses row plugin' => FALSE,
     'uses fields' => TRUE,
     'uses options' => TRUE,
@@ -569,7 +569,7 @@ function tripal_core_views_plugins() {
       'views_data_export_fasta' => array(
         'title' => t('FASTA file'),
         'help' => t('Display results in FASTA format. All fields in results are on the definition line while the feature.residues field must be present .'),
-        'handler' => 'tripal_core_plugin_style_export_fasta',
+        'handler' => 'tripal_views_plugin_style_export_fasta',
         // Views Data Export element that will be used to set additional headers when serving the feed.
         'export headers' => array('Content-type: text/plain; charset=utf-8'),
         // Views Data Export element mostly used for creating some additional classes and template names.
@@ -590,14 +590,14 @@ function tripal_core_views_plugins() {
 /**
  * Implementation of hook_views_pre_view().
  */
-function tripal_core_views_pre_view(&$view,&$display_id,&$args){
-   $form = drupal_get_form('tripal_core_views_data_export_download_form',$view,$display_id,$args);
+function tripal_views_views_pre_view(&$view,&$display_id,&$args){
+   $form = drupal_get_form('tripal_views_data_export_download_form',$view,$display_id,$args);
    $view->attachment_after = $form;
 }
 /**
  * 
  */
-function tripal_core_views_data_export_download_form(&$form_state, $view,$display_id,$args){
+function tripal_views_data_export_download_form(&$form_state, $view,$display_id,$args){
    $form = array();
    $urls = array();
 
@@ -656,7 +656,7 @@ function tripal_core_views_data_export_download_form(&$form_state, $view,$displa
 /**
  * 
  */
-function tripal_core_views_data_export_download_form_submit($form, &$form_state){
+function tripal_views_data_export_download_form_submit($form, &$form_state){
    $urls = $form_state['storage']['urls'];
    $display_id = $form_state['values']['file_type'];
    drupal_goto($urls[$display_id]['path'],$urls[$display_id]['query']);

base/tripal_core/tripal_views_integration.inc → base/tripal_views/tripal_views_integration.inc

@@ -8,19 +8,15 @@
  *
  * @ingroup tripal_views_integration
  */
-function tripal_core_views_description_page() {
+function tripal_views_description_page() {
 
   $text .= '<h3>Tripal Views Quick Links:</h3>';
   $text .= "<ul>
-             <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>
+             <li><a href=\"".url("admin/tripal/views/integration/mviews") . "\">List of integrated tables</a></li>
+             <li><a href=\"".url("admin/tripal/views/integration/mviews/new"). "\">Integrate a new table</a></li>
            </ul>";
 
-  $text .= '<h3>Views Integartion Description:</h3>';
+  $text .= '<h3>Views Integration 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
@@ -61,7 +57,7 @@ function tripal_core_views_description_page() {
  *
  * @ingroup tripal_views_integration
  */
-function tripal_core_views_integration_setup_list(){
+function tripal_views_integration_setup_list(){
 
    $header = array('', 'Drupal Views Type Name', 'Table Name', 'Is Mview', 'Comment','');
    $rows = array();
@@ -106,7 +102,7 @@ function tripal_core_views_integration_setup_list(){
  *
  * @ingroup tripal_views_integration
  */
-function tripal_core_views_integration_delete($setup_id){
+function tripal_views_integration_delete($setup_id){
   db_query("DELETE FROM {tripal_views} WHERE setup_id = %d",$setup_id);
   db_query("DELETE FROM {tripal_views_handlers} WHERE setup_id = %d",$setup_id);
   db_query("DELETE FROM {tripal_views_join} WHERE setup_id = %d",$setup_id);
@@ -117,7 +113,7 @@ function tripal_core_views_integration_delete($setup_id){
  *
  * @ingroup tripal_views_integration
  */
-function tripal_core_views_integration_form(&$form_state, $setup_id = NULL){
+function tripal_views_integration_form(&$form_state, $setup_id = NULL){
   
    $form = array();
    $data = array();
@@ -226,10 +222,7 @@ function tripal_core_views_integration_form(&$form_state, $setup_id = NULL){
     '#maxlength' => 128,
     '#description' => 'Provide the view type name.  This is the name that will appear in '.
                       'the Drupal Views interface when adding a new view.  The view type name '.
-                      'must be unique.  You may use the a materialized view or Chado table '.
-                      'multiple times as the base table for different type names.  This allows '.
-                      'for differetn handlers to be '.
-                      'applied to the same table in different ways.',
+                      'must be unique.',
     '#required' => TRUE,   
   );
   
@@ -299,7 +292,7 @@ function tripal_core_views_integration_form(&$form_state, $setup_id = NULL){
     $chado_join_tables = array_merge(array('Select a Join Table',), $chado_join_tables);
 
     // get list of all handlers
-    $all_handlers = tripal_core_views_integration_discover_handlers();
+    $all_handlers = tripal_views_integration_discover_handlers();
     $handlers_fields = array();
     $handlers_filters = array();
     $handlers_sort = array();
@@ -554,7 +547,7 @@ function tripal_core_views_integration_form(&$form_state, $setup_id = NULL){
  *
  * @ingroup tripal_views_integration
  */
-function tripal_core_views_integration_form_validate($form, &$form_state){
+function tripal_views_integration_form_validate($form, &$form_state){
   $name_array = explode(" ", $form_state['values']['row_name']);
   $mview_id = $form_state['values']['mview_id'];
   $table_name = $form_state['values']['table_name'];
@@ -574,7 +567,7 @@ function tripal_core_views_integration_form_validate($form, &$form_state){
  *
  * @ingroup tripal_views_integration
  */
-function tripal_core_views_integration_form_submit($form, &$form_state){
+function tripal_views_integration_form_submit($form, &$form_state){
    $name = $form_state['values']['row_name'];
    $mview_id = $form_state['values']['mview_id'];
    $table_name = $form_state['values']['table_name'];
@@ -684,7 +677,7 @@ function tripal_core_views_integration_form_submit($form, &$form_state){
  *
  * @ingroup tripal_views_integration
  */
-function tripal_core_views_integration_discover_handlers() {
+function tripal_views_integration_discover_handlers() {
 
    $handlers = array();
 
@@ -701,7 +694,7 @@ function tripal_core_views_integration_discover_handlers() {
    }
 
    // these handlers are hard coded because I could not
-   // get the views_views_handlers() function to be called
+   // get the views_handlers() function to be called
    // in the code above.  However, we will be creating
    // Chado wrappers for many of these and once that work
    // is done these will no longer be needed.

base/tripal_views/tripal_views_integration_fields_form.tpl.php

@@ -0,0 +1,66 @@
+<style type="text/css">
+
+#tripal-views-integration-form  .fields-new-row, .field-headers {
+   dislay: block;
+   margin: 0px;
+   border-bottom-style: solid;
+   border-bottom-width: 1px;
+}
+#tripal-views-integration-form .form-item {
+   margin: 0px 0px 5px 0px;
+}
+#tripal-views-integration-form .column-id, .column-form-fields, .column-one, .column-two {
+   display: inline-block;
+   margin: 0px;
+   vertical-align: top;
+   //border: 1px solid #000;
+}
+#tripal-views-integration-form  .field-headers {
+   font-weight: bold;
+}
+#tripal-views-integration-form  .field-headers div {
+   display: inline-block;
+   margin: 0px;
+   vertical-align: top;
+}
+#tripal-views-integration-form .column-name {
+   font-weight: bold;
+}
+#tripal-views-integration-form .column-type {
+   font-style: italic;
+}
+#tripal-views-integration-form .column-id {
+   width: 20%;
+   height: 50px;
+}
+#tripal-views-integration-form  .fields-new-row {
+   padding-bottom: 10px;
+   margin-bottom: 5px;
+   padding-top: 10px;
+}
+#tripal-views-integration-form .column-form-fields {
+   //border: 3px solid #f00;
+}
+#tripal-views-integration-form .column-one {
+   margin-left: 15px;
+}
+#tripal-views-integration-form .column-two {
+   margin-left: 15px;
+}
+#tripal-views-integration-form .fields-column-join {
+
+}
+#tripal-views-integration-form .fields-column-join-column {
+
+}
+#tripal-views-integration-form .fields-filter-handler {
+
+}
+#tripal-views-integration-form .fields-field-handler {
+
+}
+
+</style>
+
+<?php print drupal_render($form); ?>
+

base/tripal_core/views_data_export/plugins/tripal_core_plugin_style_export_fasta.inc → base/tripal_views/views_data_export/plugins/tripal_views_plugin_style_export_fasta.inc

@@ -9,7 +9,7 @@
  *
  * @ingroup views_style_plugins
  */
-class tripal_core_plugin_style_export_fasta extends views_data_export_plugin_style_export {
+class tripal_views_plugin_style_export_fasta extends views_data_export_plugin_style_export {
 
   /**
    * Set options fields and default values.
@@ -42,6 +42,7 @@ class tripal_core_plugin_style_export_fasta extends views_data_export_plugin_sty
       '#suffix' => '</div></div>',
       '#type' => 'textfield',
       '#title' => t('Defenition line fields'),
+      '#required' => TRUE,
       '#default_value' => $this->options['defline_fields'],
       '#description' => t("This field controls the information present in the definition ".
          "line for each sequence. Any of the fields in the view can be used in the ".