tripal/tripal_core/tripal_core.module

<?php
/**
 * @file
 * The Tripal Core module
 */

 /**
 * @defgroup tripal_modules Tripal Modules
 * @{
 * All documented functions for the various Tripal Modules excluding API functions and Views Integration functions.
 * @}
 */

/**
 * @defgroup tripal_api Tripal API
 * @{
 * Provides an application programming interface (API) for Tripal
 *
 * The Tripal API currently provides generic insert/update/select functions for all chado content as
 * well as some module specific functions that insert/update/delete/select specific chado content.
 *
 * This API is currently in its infancy and some necessary functions might be missing. If you find
 * a missing function that you think should be included go to the sourceforge feature request
 * page and request it's inclusion in the API. Such feature requests with a working function
 * definition will be given priority.
 * @}
 */

 /**
 * @defgroup tripal_core_api Core Module API
 * @ingroup tripal_api
 */

/**
 * @defgroup tripal_core Tripal Core Module
 * @ingroup tripal_modules
 */

require_once "api/tripal_core_chado.api.inc";
require_once "api/tripal_core_files.api.inc";
require_once "api/tripal_core_chado_nodes.api.inc";
require_once "api/tripal_core_custom_tables.api.inc";
require_once "api/tripal_core_jobs.api.inc";
require_once "api/tripal_core_mviews.api.inc";
require_once "api/tripal_core_properties.api.inc";
require_once "api/tripal_core.database_references.api.inc";

require_once "includes/jobs.inc";
require_once "includes/mviews.inc";
require_once "includes/custom_tables.inc";
require_once "includes/chado_install.inc";
require_once "includes/form_elements.inc";


tripal_core_set_globals();

/**
 * Implements hook_init().
 * Used to set the search_path, create default content and set default variables.
 *
 * @ingroup tripal_core
 */
function tripal_core_init() {
  global $base_url;

  // add javascript files
  drupal_add_js(drupal_get_path('module', 'tripal_core') . '/theme/js/tripal.js');
  drupal_add_css(drupal_get_path('module', 'tripal_core') . '/theme/css/tripal.css');


  // create the 'tripal' controlled volcabulary in chado but only if it doesn't already exist, and
  // only if the chado database is present.
  if ($GLOBALS["chado_is_installed"]) {

    // if the Tripal cv is missing then add
    $results = chado_query("SELECT * FROM {cv} WHERE name = 'tripal'");
    $tripal_cv = $results->fetchObject();
    if (!$tripal_cv) {
      $results = chado_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 the Tripal db is missing then add it
    $results = chado_query("SELECT * FROM {db} WHERE name = 'tripal'");
    $tripal_db = $results->fetchObject();
    if (!$tripal_db) {
      $results = chado_query(
        "INSERT INTO {db} (name,description) " .
        "VALUES ('tripal', 'Used as a database placeholder for tripal defined objects such as tripal cvterms')"
      );
    }
  }

  // add some variables for all javasript to use for building URLs
  $theme_dir = drupal_get_path('theme', 'tripal');
  $clean_urls = variable_get('clean_url', 0);
  drupal_add_js(
    " var baseurl  = '$base_url';
      var themedir = '$theme_dir';
      var isClean  =  $clean_urls;",
    'inline', 'header');

  // make sure the date time settings are the way Tripal will insert them
  // otherwise PostgreSQL version that may have a different datestyle setting
  // will fail when inserting or updating a date column in a table.
  db_query("SET DATESTYLE TO :style", array(':style' => 'MDY'));

  // If we want AHAH elements on the node forms (e.g. chado_pub form) then we need to include
  // the node.pages file. Otherwise this error message is given:
  //
  // warning: call_user_func_array() expects parameter 1 to be a valid callback,
  // function 'node_form' not found or invalid function name
  // in /var/www/includes/form.inc on line 382.
  module_load_include('inc', 'node', 'node.pages');

}

/**
 * Implements hook_menu().
 * Defines all menu items needed by Tripal Core
 *
 * @ingroup tripal_core
 */
function tripal_core_menu() {
  $items = array();

  // Triapl setting groups
  $items['admin/tripal'] = array(
    'title' => 'Tripal',
    'description' => "Manage the behavior or Tripal and its various modules.",
    'weight' => -8,
    'page callback' => 'system_admin_menu_block_page',
    'access arguments' => array('administer site configuration'),
    'file' => 'system.admin.inc',
    'file path' => drupal_get_path('module', 'system'),
  );
  $items['admin/tripal/schema'] = array(
    'title' => 'Chado Schema',
    'description' => "Tools to extend the chado schema through custom tables & materialized views.",
    'weight' => -2,
    'access arguments' => array('administer site configuration'),
  );
  $items['admin/tripal/chado'] = array(
    'title' => 'Chado Modules',
    'description' => 'Configuration for specific chado data types such as Vocabularies, Features, etc.',
    'access arguments' => array('access administration pages'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => -6
  );
  $items['admin/tripal/loaders'] = array(
    'title' => 'Chado Data Loaders',
    'description' => 'Tools facilitating loading data into the chado database. Includes a generic tab-delimited loader (Bulk Loader).',
    'access arguments' => array('access administration pages'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => -4
  );
  $items['admin/tripal/extension'] = array(
    'title' => 'Extension Modules',
    'description' => 'Configuration for Tripal extension modules.',
    'access arguments' => array('access administration pages'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => 0
  );

  // Tripal Setup
  $items['admin/tripal/setup'] = array(
    'title' => 'Setup Tripal',
    'description' => 'Tools for initial setup of Tripal',
    'access arguments' => array('administer site configuration'),
    'weight' => -8
  );
  $items['admin/tripal/setup/customize'] = array(
    'title' => 'Customize Tripal',
    'description' => 'Information on how to customize tripal',
    'page callback' => 'theme',
    'page arguments' => array('tripal_core_customize'),
    'access arguments' => array('administer site configuration'),
    'weight' => 10
  );
  $items['admin/tripal/setup/chado_install'] = array(
    'title' => 'Install Chado Schema',
    'description' => 'Installs the Chado database tables, views, etc., inside the current Drupal database',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_core_chado_load_form'),
    'access arguments' => array('install chado'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => -10
  );

  // Jobs Management
  $items['admin/tripal/tripal_jobs'] = array(
    'title' => 'Jobs',
    'description' => 'Jobs managed by Tripal',
    'page callback' => 'tripal_jobs_admin_view',
    'access arguments' => array('access administration pages'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => -10
  );
  $items['admin/tripal/tripal_jobs/help'] = array(
    'title' => 'Help',
    'description' => 'Help for the tripal job management system',
    'page callback' => 'theme',
    'page arguments' => array('tripal_core_job_help'),
    'access arguments' => array('access administration pages'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10
  );
  $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_jobs/views/jobs/enable'] = array(
    'title' => 'Enable Jobs Administrative View',
    'page callback' => 'tripal_views_admin_enable_view',
    'page arguments' => array('tripal_core_admin_jobs', 'admin/tripal/tripal_jobs'),
    'access arguments' => array('access administration pages'),
    'type' => MENU_CALLBACK,
  );

  // Materialized Views
  $items['admin/tripal/schema/mviews'] = array(
    'title' => 'Materialized Views',
    'description' => 'Materialized views are used to improve speed of large or complex queries.',
    'page callback' => 'tripal_mview_admin_view',
    'access arguments' => array('access administration pages'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => -10
  );
  $items['admin/tripal/schema/mviews/help'] = array(
    'title' => 'Help',
    'description' => 'Help for the materialized views management system',
    'page callback' => 'theme',
    'page arguments' => array('tripal_core_mviews_help'),
    'access arguments' => array('access administration pages'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10
  );
  /**
  $items['admin/tripal/schema/mviews/list'] = array(
    'title' => 'List Materialized Views',
    'description' => 'A list of existing materialized views with the ability to edit & delete existing materialized views.',
    'page callback' => 'tripal_mviews_report',
    'access arguments' => array('access administration pages'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => -10
  );
  */
  $items['admin/tripal/schema/mviews/report/%'] = array(
    'title' => 'Materialized View',
    'description' => 'Materialized views are used to improve speed of large or complex queries. These are database views as compared to Drupal views.',
    'page callback' => 'tripal_mview_report',
    'page arguments' => array(5),
    'access arguments' => array('access administration pages'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/schema/mviews/new'] = array(
    'title' => 'Create Materialized View',
    'description' => 'Create a new materialized view.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_mviews_form'),
    'access arguments' => array('access administration pages'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/schema/mviews/edit/%'] = array(
    'title' => 'Edit Materialized View',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_mviews_form', 5),
    'access arguments' => array('access administration pages'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/schema/mviews/action/%/%'] = array(
    'title' => 'Create Materialized View',
    'description' => 'Materialized views are used to improve speed of large or complex queries.',
    'page callback' => 'tripal_mviews_action',
    'page arguments' => array(5, 6, "1"),
    'access arguments' => array('access administration pages'),
    'type' => MENU_CALLBACK,
  );

  // Custom Tables
  $items['admin/tripal/schema/custom_tables'] = array(
    'title' => 'Custom Tables',
    'description' => 'Creation of custom tables that are added to Chado database.',
    'page callback' => 'tripal_custom_table_admin_view',
    'access arguments' => array('access administration pages'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => -10
  );
  $items['admin/tripal/schema/custom_tables/help'] = array(
    'title' => 'Help',
    'description' => 'Help for the tripal job management system',
    'page callback' => 'theme',
    'page arguments' => array('tripal_core_job_help'),
    'access arguments' => array('access administration pages'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10
  );
  /**
  $items['admin/tripal/schema/custom_tables/list'] = array(
    'title' => 'List of Custom Tables',
    'description' => 'Provides a list of all custom tables created by Tripal and allows for editing or removing existing custom tables.',
    'page callback' => 'tripal_custom_tables_list',
    'access arguments' => array('access administration pages'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => -10
  );
  */
  $items['admin/tripal/schema/custom_tables/view/%'] = array(
    'title' => 'Custom Tables',
    'description' => 'Custom tables are added to Chado.',
    'page callback' => 'tripal_custom_table_view',
    'page arguments' => array(4),
    'access arguments' => array('access administration pages'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/schema/custom_tables/new'] = array(
    'title' => 'Create Custom Table',
    'description' => 'An interface for creating your own custom tables.',
    'page callback' => 'tripal_custom_table_new_page',
    'access arguments' => array('access administration pages'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/schema/custom_tables/edit/%'] = array(
    'title' => 'Edit Custom Table',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_custom_tables_form', 4),
    'access arguments' => array('access administration pages'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/schema/custom_tables/action/%/%'] = array(
    'title' => 'Create Custom Table',
    'description' => 'Custom tables are added to Chado.',
    'page callback' => 'tripal_custom_tables_action',
    'page arguments' => array(4, 5, "1"),
    'access arguments' => array('access administration pages'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/schema/custom_tables/views/tables/enable'] = array(
    'title' => 'Enable Custom Tables Administrative View',
    'page callback' => 'tripal_views_admin_enable_view',
    'page arguments' => array('tripal_core_admin_custom_table', 'admin/tripal/schema/custom_tables'),
    'access arguments' => array('access administration pages'),
    '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_core
 */
function tripal_core_permission() {
  return array(
    'install chado' => array(
      'title' => t('Install Chado'),
      'description' => t('Allow the user to install or upgrade a Chado database in the existing Drupal database.')
    ),
  );
}

/**
 * Implements hook_theme().
 * Registers template files/functions used by this module.
 *
 * @ingroup tripal_core
 */
function tripal_core_theme($existing, $type, $theme, $path) {
  return array(
    'tripal_core_customize' => array(
      'arguments' => array('job_id' => NULL),
      'template' => 'tripal_core_customize',
      'path' => "$path/theme"
    ),
    'theme_file_upload_combo' => array(
      'render element' => 'element',
    ),
    'theme_sequence_combo' => array(
      'render element' => 'element',
    ),
    'tripal_core_jobs_help' => array(
      'template' => 'tripal_core_jobs_help',
      'variables' =>  array(NULL),
      'path' => "$path/theme"
    ),
    'tripal_core_customtables_help' => array(
      'template' => 'tripal_core_customtables_help',
      'variables' =>  array(NULL),
      'path' => "$path/theme"
    ),

    // form theme
    'tripal_core_properties_form' => array(
      'render element' => 'form',
    ),

    // additional dbxrefs form theme
    'tripal_core_additional_dbxrefs_form_table' => array(
      'function' => 'theme_tripal_core_additional_dbxrefs_form_table',
      'render element' => 'element',
    ),
  );
}

/**
 * Implements hook_job_describe_args().
 * Describes the arguements for the tripal_update_mview job to allow for greater
 * readability in the jobs details pages.
 *
 * @param $callback
 *   The callback of the current tripal job (this is the function that will be executed
 *   when tripal_launch_jobs.php is run.
 * @param $args
 *   An array of arguments passed in when the job was registered.
 *
 * @return
 *   A more readable $args array
 *
 * @ingroup tripal_core
 */
function tripal_core_job_describe_args($callback, $args) {
  $new_args = array();
  if ($callback == 'tripal_update_mview') {
    // get this mview details
    $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = :mview_id ";
    $results = db_query($sql, array(':mview_id' => $args[0]));
    $mview = $results->fetchObject();
    $new_args['View Name'] = $mview->name;
  }

  elseif ($callback == 'tripal_core_install_chado') {
     $new_args['Action'] = $args[0];
  }
  return $new_args;
}

/**
 * this is just a wrapper for backwards compatibility with a naming mistake.
 * it can go away in the future as it only is useful for jobs created by v0.3b
 *
 * @todo remove this function
 */
function tripal_core_load_gff3($gff_file, $organism_id, $analysis_id, $add_only = 0,
  $update = 0, $refresh = 0, $remove = 0, $job = NULL) {

  tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id, $add_only,
    $update, $refresh, $remove, $job);
}

/**
 * Implements hook_coder_ignore().
 * Defines the path to the file (tripal_core.coder_ignores.txt) where ignore rules for coder are stored
 */
function tripal_core_coder_ignore() {
  return array(
    'path' => drupal_get_path('module', 'tripal_core'),
    'line prefix' => drupal_get_path('module', 'tripal_core'),
  );
}

/**
 * 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_organism
 */
function tripal_core_views_api() {
  return array(
    'api' => 3.0,
  );
}