tripal/tripal_core/tripal_core.module

<?php

require_once "jobs.php";
require_once "mviews.php";
require_once "cvterms.php";
require_once "chado_install.php";
require_once "bulk_loader.php";

require_once "tripal_core.api.inc";

/**
 * @defgroup tripal_core Core Tripal Module
 * @{
 * Provides basic functions for interacting with chado
 * @}
 */
 
/**
 *
 *
 * @ingroup tripal_core
 */
function tripal_core_init(){
   // the two lines below are necessary to ensure that the search_path
   // variable is always set.  In the case where a view needs to query the
   // chado schema when it is local to the Drupal database.  Otherwise the
   // search_path isn't set.  When tripal_db_set_active is called it
   // automatically sets the serach path if chado is local to the 
   // Drupal database
   $previous = tripal_db_set_active('chado');
   tripal_db_set_active($previous);

   // create the 'tripal' controlled volcabulary in chado but only if it doesn't already exist, and
   // only if the chado database is present.
   if(tripal_core_is_chado_installed()){
      $previous_db = tripal_db_set_active('chado');  // use chado database
      if(!db_fetch_object(db_query("SELECT * FROM {cv} WHERE name = 'tripal'"))){
         $results = db_query("INSERT INTO {cv} (name,definition) ".
    	                     "VALUES ('tripal','Terms used by Tripal for modules to manage data such as that stored in property tables like featureprop, analysisprop, etc')");
      } 
      if(!db_fetch_object(db_query("SELECT * FROM {db} WHERE name = 'tripal'"))){
         $results = db_query("INSERT INTO {db} (name,description) ". 
	                        "VALUES ('tripal','Used as a database placeholder for tripal defined objects such as tripal cvterms')");
      }  
      tripal_db_set_active($previous_db);  // now use drupal database
   }

   // the tripal themeing uses rounded corners. We could use CSS but IE8 doesn't supprt
   // rouneded corners so we will use the JQuery method.
   drupal_add_js (drupal_get_path('theme', 'tripal').'/js/jquery-corners-0.3/jquery.corners.min.js');
}

/**
 *
 *
 * @ingroup tripal_core
 */
function tripal_create_moddir($module_name){
   // make the data directory for this module
   $data_dir = file_directory_path() . "/tripal/$module_name";
   if(!file_check_directory($data_dir,FILE_CREATE_DIRECTORY|FILE_MODIFY_PERMISSIONS)){
      $message = "Cannot create directory $data_dir. This module may not ".
                 "behave correctly without this directory.  Please  create ".
                 "the directory manually or fix the problem and reinstall.";
      drupal_set_message($message,'error');      
      watchdog('tripal_core',$message,array(),WATCHDOG_ERROR);
   }
}

/**
 *
 *
 * @ingroup tripal_core
 */
function tripal_get_moddir($module_name){
   $data_dir = file_directory_path() . "/tripal/$module_name";
   return $data_dir;
}

/**
 *
 *
 * @ingroup tripal_core
 */
function tripal_core_menu() {
   $items = array();
   
   // Triapl setting groups
   $items['admin/tripal'] = array(
      'title' => 'Tripal Management',
      'description' => "Manage the behavior or Tripal and its various modules.",
      'position' => 'right',
      'weight' => -5,
      'page callback' => 'system_admin_menu_block_page',
      'access arguments' => array('administer site configuration'),
      'file' => 'system.admin.inc',
      'file path' => drupal_get_path('module', 'system'),
   );

   // the administative settings menu
/*   $items['admin/tripal/tripal_core'] = array(
     'title' => 'Tripal core settings',
     'description' => 'Tripal Settings',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_core_admin'),
     'access arguments' => array('access administration pages'),
     'type' => MENU_NORMAL_ITEM,
   );
 */
   $items['admin/tripal/tripal_jobs'] = array(
     'title' => 'Jobs',
     'description' => 'Jobs managed by Tripal',
     'page callback' => 'tripal_jobs_report',
     'access arguments' => array('access administration pages'),
     'type' => MENU_NORMAL_ITEM,
   );
   $items['admin/tripal/tripal_jobs/cancel/%'] = array(
     'title' => 'Jobs',
     'description' => 'Cancel a pending job',
     'page callback' => 'tripal_jobs_cancel',
     'page arguments' => array(4),
     'access arguments' => array('access administration pages'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/tripal_jobs/rerun/%'] = array(
     'title' => 'Jobs',
     'description' => 'Re-run an existing job.',
     'page callback' => 'tripal_jobs_rerun',
     'page arguments' => array(4),
     'access arguments' => array('access administration pages'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/tripal_jobs/view/%'] = array(
     'title' => 'Jobs Details',
     'description' => 'View job details.',
     'page callback' => 'tripal_jobs_view',
     'page arguments' => array(4),
     '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),
     'access arguments' => array('access administration pages'),
     'type' => MENU_NORMAL_ITEM,
   );
   $items['admin/tripal/tripal_mviews'] = array(
     'title' => 'Materialized Views',
     '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',
     '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',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_mviews_form',4),
     'access arguments' => array('access administration pages'),
     'type' => MENU_NORMAL_ITEM,
   );
   $items['admin/tripal/tripal_mviews/action/%/%'] = array(
     'title' => 'Create View',
     'description' => 'Materialized views are used to improve speed of large or complex queries.',
     'page callback' => 'tripal_mviews_action',
     'page arguments' => array(4,5),
     'access arguments' => array('access administration pages'),
     'type' => MENU_CALLBACK,
   );

   $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/bulk_load/create'] = array(
     'title' => 'Create Bulk Loader',
     'description' => 'Create a bulk loader template for loading data into Chado',
     'page callback' => 'tripal_core_bulk_loader_create',
     'access arguments' => array('access administration pages'),
     'type' => MENU_NORMAL_ITEM,
   );

   $items['admin/tripal/bulk_load/step2_get_type/%'] = array(
     'title' => 'Create Bulk Loader',
     'description' => 'Create a bulk loader template for loading data into Chado',
     'page callback' => 'tripal_core_bulk_loader_ahah_step2_feature_type',
     'page arguments' => array(4),
     'access arguments' => array('access administration pages'),
     'type' => MENU_CALLBACK,
   );

   $items['test2'] = array(
     'title' => 'test',
     'description' => 'test',
     'page callback' => 'tripal_core_chado_insert_test',
     'access arguments' => array('access administration pages'),
     'type' => MENU_CALLBACK,
   );

  return $items;
}

/**
 *
 *
 * @ingroup tripal_core
 */
function tripal_core_admin () {


   $form['chado_feature_data_url'] = array (
      '#title'       => t('URL for data files'),
      '#type'        => t('textfield'),
      '#description' => t("This is the base URL location (without a leading forward slash)  for where files (e.g. blast .xml files) related to each feature are stored. All files available for download or parsing that a feature needs for display should be located in this base directory."), 
      '#required'    => TRUE,
      '#default_value' => variable_get('chado_feature_data_url','sites/default/files/data'),
   );
   
   return system_settings_form($form);
}

/**
 * Set the Tripal Database
 *
 * The tripal_db_set_active function is used to prevent namespace collisions
 * when chado and drupal are installed in the same database but in different
 * schemas.  It is also used for backwards compatibility with older versions
 * of tripal or in cases where chado is located outside of the Drupal database.
 *
 * @ingroup tripal_core
 */
function tripal_db_set_active($dbname){
   global $db_url, $db_type;
   $chado_exists = 0;

   // only postgres can support search paths.  So if this is MysQL then
   // just run the normal tripal_db_set_active function.
   if(strcmp($db_type,'pgsql')==0){

      // if the 'chado' database is in the $db_url variable then chado is 
      // not in the same Drupal database
      if(is_array($db_url)){ 
         if(isset($db_url[$dbname])){
            return db_set_active($dbname);
         } 
      }

      // check to make sure the chado schema exists
      $sql = "select nspname from pg_catalog.pg_namespace where nspname = 'chado'";
      if(db_fetch_object(db_query($sql))){
         $chado_exists = 1;
      }

      // here we make the assumption that the default database schema is
      // 'public'.  This will most likely always be the case but if not,
      // then this code will break
      if($chado_exists && strcmp($dbname,'chado')==0){
         db_query("set search_path to %s",'chado,public');  
         return 'public,chado';
      } 
      elseif($chado_exists) {
         db_query("set search_path to %s",'public,chado');  
         return 'chado,public';
      }
      else {
         return db_set_active($dbname);
      }
   }
   else return db_set_active($dbname);
}

/**
 *
 *
 * @ingroup tripal_core
 */
function tripal_core_is_chado_installed(){
   global $db_url, $db_type;

   // first check if chado is in the db_url of the 
   // settings.php file
   if(is_array($db_url)){ 
      if(isset($db_url['chado'])){
         return true;
      } 
   }
   // check to make sure the chado schema exists
   $sql = "select nspname from pg_catalog.pg_namespace where nspname = 'chado'";
   if(db_fetch_object(db_query($sql))){
      return true;
   }
   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,
   );
}

/**
 * Purpose: Get max rank for a given set of criteria
 *   This function was developed with the many property tables in chado in mind
 *
 * @param $tablename
 *    The name of the chado table you want to select the max rank from this table must contain a 
 *    rank column of type integer
 * @param $where_options
 *   where options should include the id and type for that table to correctly
 *     group a set of records together where the only difference are the value and rank
 * @code 
 *  array(
 *													<column_name> => array(
 *														'type' => <type of column: INT/STRING>,
 *														'value' => <the value you want to filter on>,
 *														'exact' => <if TRUE use =; if FALSE use ~>,
 *													)
 *				)
 * @endcode
 * @return the maximum rank
 *
 * @ingroup tripal_core
 */
function tripal_get_max_chado_rank ($tablename, $where_options) {

	$where= array();
	//generate the where clause from supplied options
	// the key is the column name
	foreach ($where_options as $key => $val_array) {
		if (preg_match('/INT/', $val_array['type'])) {
			$where[] = $key."=".$val_array['value'];
		} else {
			if ($val_array['exact']) { $operator='='; }
			else { $operator='~'; }
			$where[] = $key.$operator."'".$val_array['value']."'";
		}
	}
	
  $previous_db = tripal_db_set_active('chado');
  $result = db_fetch_object(db_query(
    "SELECT max(rank) as max_rank, count(rank) as count FROM %s WHERE %s",
    $tablename,
    implode(' AND ',$where)
  ));
  tripal_db_set_active($previous_db);
	//drupal_set_message("Max Rank Query=SELECT max(rank) as max_rank, count(rank) as count FROM ".$tablename." WHERE ".implode(' AND ',$where));
	if ($result->count > 0) {
	  return $result->max_rank;
	} else {
		return -1;
	}
}

function tripal_core_theme () {
   return array(      
      'tripal_core_job_view' => array (
         'arguments' => array('job_id'=> null),
         'template' => 'tripal_core_job_view',
      ),
   );
}