tripal/base/tripal_views_setup/tripal_views_setup.module

<?php

require_once 'includes/tripal_views_setup.admin.inc';

function tripal_views_setup_menu(){
	$items = array();
	
	//parents admin page TODO: figure out what to do here: add / remove searches
	$items['admin/tripal/tripal_views_setup'] = array(
	  'title' => t('Tripal Views Setups'),
	  '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_setup_admin_form'),
	  'access arguments' => array('access administration pages'),
	  'type' => MENU_NORMAL_ITEM,
	);
	
	//page to actually create searche->mview->chado table relationships
 	$items['admin/tripal/tripal_views_setup_new'] = array(
		 'title' => 'Create New Views Setup',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_views_setup_new_search_form'),
     'access arguments' => array('access administration pages'), //TODO: figure out the proper permissions arguments
     'type' => MENU_NORMAL_ITEM,
 	);
	
	return $items;
}

function tripal_views_setup_theme(){
	$theme = array();
	
	$theme['tripal_views_setup_form'] = array(
		'arguments' => array('form' => NULL,),
	);
	
	$theme['tripal_views_setup_admin_form'] = array(
		'arguments' => array(),
	);
	
	return $theme;
}


function theme_tripal_views_setup_admin_form($form){
	$header = array(
		theme('table_select_header_cell'),//using previously empty field
		array('data' => t('Setup ID'), 'field' => 'setup_id', 'sort' => 'asc'),
    array('data' => t('MView ID'), 'field' => 'mview_id'),
    array('data' => t('Base Table Name'), 'field' => 'base_table_name'),
  );
	
	if(!empty($form['checkboses']['#options'])) {
		foreach (element_children($form['uid']) as $key) {
			$rows[] = array(
				drupal_render($form['checkboxes'][$key]),
				drupal_render($form['setup_id'][$key]),
				drupal_render($form['mview_id'][$key]),
				drupal_render($form['base_table_name'][$key]),
			);
		}
	}
	else {
		$row[] = array(array('data' => '<div class="error">click link above to add entries</div>', 'colspan' => 4));
	}
	
	$output .= theme('table', $header, $rows);
	
	$output .= drupal_render($form);
	return $output;
	
}