tripal/tripal_core/tripal_core.module

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

/**
 * @defgroup tripal_core Tripal Core Module
 * @ingroup tripal_modules
 * @{
 * Functionality useful for all other Tripal modules including the Tripal jobs, files,
 * materialized views and custom table functions.
 * @}
 */

// APPLICATION PROGRAMMER INTERFACE -------------
// Chado API
require_once 'api/tripal_core.chado_general.api.inc';
require_once 'api/tripal_core.chado_query.api.inc';
require_once 'api/tripal_core.chado_variables.api.inc';
require_once 'api/tripal_core.chado_schema.api.inc';
require_once 'api/tripal_core.chado_nodes.api.inc';
require_once 'api/tripal_core.chado_nodes.title_and_path.inc';
require_once 'api/tripal_core.chado_nodes.properties.api.inc';
require_once 'api/tripal_core.chado_nodes.dbxrefs.api.inc';
require_once 'api/tripal_core.chado_nodes.relationships.api.inc';

// Table API
require_once 'api/tripal_core.custom_tables.api.inc';
require_once 'api/tripal_core.mviews.api.inc';

// Miscellaneous API
require_once 'api/tripal_core.files.api.inc';
require_once 'api/tripal_core.jobs.api.inc';
require_once 'api/tripal_core.tripal.api.inc';
require_once 'api/tripal_core.tripal_variables.api.inc';
require_once 'api/tripal_core.d3js.api.inc';
require_once 'api/tripal_core.DEPRECATED.inc';

// INCLUDES
require_once 'includes/tripal_core.jobs.inc';
require_once 'includes/tripal_core.mviews.inc';
require_once 'includes/tripal_core.custom_tables.inc';
require_once 'includes/tripal_core.chado_install.inc';
require_once 'includes/tripal_core.form_elements.inc';

tripal_core_set_globals();

/**
 * This function is used to set the global Chado variables
 *
 * @ingroup tripal_core
 */
function tripal_core_set_globals() {
  // these global variables are meant to be accessed by all Tripal
  // modules to find the chado version installed and if Chado is local.
  // these variables are stored as globals rather than using the drupal_set_variable
  // functions because the Drupal functions make databaes queries and for long
  // running loaders we don't want those queries repeatedly.
  $GLOBALS["chado_is_installed"]  = chado_is_installed();
  if ($GLOBALS["chado_is_installed"]) {
    $GLOBALS["chado_is_local"]      = chado_is_local();
    $GLOBALS["chado_version"]       = chado_get_version();
    $GLOBALS["exact_chado_version"] = chado_get_version(TRUE);
  }
}

/**
 * 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;

  // 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();

  // Tripal setting groups
  $items['admin/tripal'] = array(
    'title' => 'Tripal',
    'description' => t("Manage the behavior or Tripal and its various modules."),
    'weight' => -8,
    'page callback' => 'system_admin_menu_block_page',
    'access arguments' => array('administer tripal'),
    'file' => 'system.admin.inc',
    'file path' => drupal_get_path('module', 'system'),
  );
  $items['admin/tripal/tripal_jobs'] = array(
    'title' => 'Jobs',
    'description' => t('Jobs managed by Tripal'),
    'page callback' => 'tripal_jobs_admin_view',
    'access arguments' => array('administer tripal'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => 0
  );
  $items['admin/tripal/loaders'] = array(
    'title' => 'Data Loaders',
    'description' => t('Tools facilitating loading data. Includes a generic tab-delimited loader (Bulk Loader).'),
    'access arguments' => array('administer tripal'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => 6
  );
  $items['admin/tripal/storage'] = array(
    'title' => 'Storage Backend',
    'description' => t("Functionality related to data storage and tools to interact with the storage backend."),
    'weight' => 8,
    'access arguments' => array('administer tripal'),
  );
  $items['admin/tripal/chado'] = array(
    'title' => 'Legacy Tripal',
    'description' => t('Tools related to Tripal2 Legacy chado-based node types.'),
    'access arguments' => array('administer tripal'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => 20
  );
  $items['admin/tripal/extension'] = array(
    'title' => 'Extensions',
    'description' => t('Configuration for Tripal extensions.'),
    'access arguments' => array('administer tripal'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => 100
  );
  $items['admin/tripal/extension/import'] = array(
    'title' => 'Import Extensions',
    'description' => 'Provides a list of the available extensions that are registered at the tripal.info site. From this page you can easily import or install extensions to your site.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_core_extensions_form'),
    'access arguments' => array('administer tripal'),
    'type' => MENU_NORMAL_ITEM,
    'file' =>  'includes/tripal_core.extensions.inc',
    'file path' => drupal_get_path('module', 'tripal_core'),
    'weight' => -100,
  );

  // Chado Storage Backend
  $items['admin/tripal/storage/chado'] = array(
    'title' => 'Chado Schema',
    'description' => t("Tools to extend the chado schema through custom tables & materialized views."),
    'weight' => -100,
    'access arguments' => array('administer tripal'),
  );
  $items['admin/tripal/storage/chado/chado_install'] = array(
    'title' => 'Install Chado Schema',
    'description' => t('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' => -100
  );
/*
  $items['admin/tripal/setup/customize'] = array(
    'title' => 'Customize Tripal',
    'description' => t('Information on how to customize tripal'),
    'page callback' => 'theme',
    'page arguments' => array('tripal_core_customize'),
    'access arguments' => array('administer tripal'),
    'weight' => 10
  );
*/

  // Jobs Management
  $items['admin/tripal/tripal_jobs/help'] = array(
    'title' => 'Help',
    'description' => t('Help for the tripal job management system'),
    'page callback' => 'theme',
    'page arguments' => array('tripal_core_job_help'),
    'access arguments' => array('administer tripal'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10
  );
  $items['admin/tripal/tripal_jobs/cancel/%'] = array(
    'title' => 'Jobs',
    'description' => t('Cancel a pending job'),
    'page callback' => 'tripal_cancel_job',
    'page arguments' => array(4),
    'access arguments' => array('administer tripal'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/tripal_jobs/rerun/%'] = array(
    'title' => 'Jobs',
    'description' => t('Re-run an existing job.'),
    'page callback' => 'tripal_rerun_job',
    'page arguments' => array(4),
    'access arguments' => array('administer tripal'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/tripal_jobs/view/%'] = array(
    'title' => 'Jobs Details',
    'description' => t('View job details.'),
    'page callback' => 'tripal_jobs_view',
    'page arguments' => array(4),
    'access arguments' => array('administer tripal'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/tripal_jobs/views/jobs/enable'] = array(
    'title' => 'Enable Jobs Administrative View',
    'page callback' => 'tripal_enable_view',
    'page arguments' => array('tripal_core_admin_jobs', 'admin/tripal/tripal_jobs'),
    'access arguments' => array('administer tripal'),
    'type' => MENU_CALLBACK,
  );

  // Materialized Views
  $items['admin/tripal/storage/chado/mviews'] = array(
    'title' => 'Materialized Views',
    'description' => t('Materialized views are used to improve speed of large or complex queries.'),
    'page callback' => 'tripal_mview_admin_view',
    'access arguments' => array('administer tripal'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => -10
  );
  $items['admin/tripal/storage/chado/mviews/help'] = array(
    'title' => 'Help',
    'description' => t('Help for the materialized views management system'),
    'page callback' => 'theme',
    'page arguments' => array('tripal_core_mviews_help'),
    'access arguments' => array('administer tripal'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10
  );
  $items['admin/tripal/storage/chado/mviews/report/%'] = array(
    'title' => 'Materialized View',
    'description' => t('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('administer tripal'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/storage/chado/mviews/new'] = array(
    'title' => 'Create Materialized View',
    'description' => t('Create a new materialized view.'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_mviews_form'),
    'access arguments' => array('administer tripal'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/storage/chado/mviews/edit/%'] = array(
    'title' => 'Edit Materialized View',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_mviews_form', 5),
    'access arguments' => array('administer tripal'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/storage/chado/mviews/update/%'] = array(
    'title' => 'Create Materialized View',
    'description' => t('Materialized views are used to improve speed of large or complex queries.'),
    'page callback' => 'tripal_mviews_add_populate_job',
    'page arguments' => array(5),
    'access arguments' => array('administer tripal'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/storage/chado/mviews/delete/%'] = array(
    'title' => 'Create Materialized View',
    'description' => t('Materialized views are used to improve speed of large or complex queries.'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_mviews_delete_form', 5),
    'access arguments' => array('administer tripal'),
    'type' => MENU_CALLBACK,
  );
  // TODO: complete the code for exporting and importing of MViews.
  // Need to address security issues of sharing SQL.
  $items['admin/tripal/storage/chado/mviews/import'] = array(
    'title' => 'Import MView',
    'description' => 'Import a materialized view from another Tripal instance.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_mviews_import_form'),
    'access arguments' => array('administer tripal'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/storage/chado/mviews/%tblid/export'] = array(
    'title' => 'Export MView',
    'description' => 'Export a materialized view for use by another Tripal instance.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_mviews_export_form', 5),
    'access arguments' => array('administer tripal'),
    'type' => MENU_CALLBACK,
  );

  // Custom Tables
  $items['admin/tripal/storage/chado/custom_tables'] = array(
    'title' => 'Custom Tables',
    'description' => t('Creation of custom tables that are added to Chado database.'),
    'page callback' => 'tripal_custom_table_admin_view',
    'access arguments' => array('administer tripal'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => -10
  );
  $items['admin/tripal/storage/chado/custom_tables/help'] = array(
    'title' => 'Help',
    'description' => t('Help for the tripal job management system'),
    'page callback' => 'theme',
    'page arguments' => array('tripal_core_job_help'),
    'access arguments' => array('administer tripal'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10
  );
  $items['admin/tripal/storage/chado/custom_tables/view/%'] = array(
    'title' => 'Custom Tables',
    'description' => t('Custom tables are added to Chado.'),
    'page callback' => 'tripal_custom_table_view',
    'page arguments' => array(5),
    'access arguments' => array('administer tripal'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/storage/chado/custom_tables/new'] = array(
    'title' => 'Create Custom Table',
    'description' => t('An interface for creating your own custom tables.'),
    'page callback' => 'tripal_custom_table_new_page',
    'access arguments' => array('administer tripal'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/storage/chado/custom_tables/edit/%'] = array(
    'title' => 'Edit Custom Table',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_custom_tables_form', 5),
    'access arguments' => array('administer tripal'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/storage/chado/custom_tables/delete/%'] = array(
    'title' => 'Create Custom Table',
    'description' => t('Custom tables are added to Chado.'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_custom_tables_delete_form', 5),
    'access arguments' => array('administer tripal'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/storage/chado/custom_tables/views/tables/enable'] = array(
    'title' => 'Enable Custom Tables Administrative View',
    'page callback' => 'tripal_enable_view',
    'page arguments' => array('tripal_core_admin_custom_table', 'admin/tripal/storage/chado/custom_tables'),
    'access arguments' => array('administer tripal'),
    'type' => MENU_CALLBACK,
  );

  // Relationshi API autocomplete callback
  $items['tripal_ajax/relationship_nodeform/%/%/name_to_id'] = array(
    'page callback' => 'chado_add_node_form_relationships_name_to_id_callback',
    'page arguments' => array(2,3),
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK
  );

  // The node's TOC tab
  $items['node/%node/tripal_toc'] = array(
    'title' => 'TOC',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_core_node_toc_form', 1),
    'access callback' => 'tripal_core_access_node_toc_form',
    'access arguments' => array(1),
    'type' => MENU_LOCAL_TASK,
    'file' => '/includes/tripal_core.toc.inc',
  );

  // Web Services API callbacks.
//   $items['ws/chado/v0.1'] = array(
//     'title' => 'Tripal Web Services API v0.1',
//     'page callback' => 'tripal_core_chado_hal_api',
//     'access arguments' => array('access content'),
//     'type' => MENU_CALLBACK,
//     'file' => '/includes/tripal_core.ws_hal.inc',
//   );

  return $items;
}

/**
 * An access wrapper function for editing the TOC
 *
 * @param $node
 *   A node object
 * @return
 *   Returns TRUE if the node is a Tripal-based node and the user hass
 *   the 'administer tripal' role.
 */
function tripal_core_access_node_toc_form($node) {
  $types = module_invoke_all('node_info');
  if (array_key_exists($node->type, $types) and
      array_key_exists('chado_node_api', $types[$node->type])) {
    return user_access('administer tripal');
  }
  return FALSE;
}

/**
 * Implements hook_permission().
 *
 * 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.')
    ),
    'administer tripal' => array(
      'title' => t('Administer Tripal'),
      'description' => t('Allow the user to access administrative pages of Tripal.')
    ),
    'view dev helps' => array(
      'title' => t('View Developer Hints'),
      'description' => t('Tripal will provide blue shaded boxes that provide
          instructions for how to customize or setup specific pages on a
          site.  This permission should be enabled for developers. But can
          be disabled once developers are accustomed to these hints.'),
      'restrict access' => TRUE,
    ),
    'view ids' => array(
      'title' => t('View Internal IDs'),
      'description' => t('On content pages Tripal will typically provide
          a table of information pulled from the Chado database but the
          primary key IDs for that data is typically not shown.  The
          default Tripal templates can show the primary key ID inside of a
          blue shaded table row if this permission is enabled. This can
          be useful for site developers who might want these IDs when working
          with the underlying database.'),
      'restrict access' => TRUE,
    )
  );
}

/**
 * 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/templates"
    ),
    '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' => "$path/theme/templates"
    ),
    'tripal_core_customtables_help' => array(
      'template' => 'tripal_core_customtables_help',
      'variables' =>  array(NULL),
      'path' => "$path/theme/templates"
    ),

    // Chado Node API Themes
    // --------------------------------
    // Properties Node Form
    'chado_node_properties_form_table' => array(
      'function' => 'theme_chado_add_node_form_properties',
      'render element' => 'element',
    ),
    // Additional Dbxrefs Nore Form
    'chado_node_additional_dbxrefs_form_table' => array(
      'function' => 'theme_chado_add_node_form_dbxrefs_table',
      'render element' => 'element',
    ),
    // Relationships Nore Form
    'chado_node_relationships_form_table' => array(
      'function' => 'theme_chado_add_node_form_relationships_table',
      'render element' => 'element',
    ),

    // Admin messages theme
    // --------------------------------
    'tripal_admin_message' => array(
      'function' => 'theme_tripal_admin_message',
      'variables' => array('message' => NULL),
    ),

    // Form and form element themes.
    // --------------------------------
    'tripal_node_toc_items_table' => array(
      'render element' => 'element',
    ),
    // Theme function for the extension admin page.
    'tripal_core_extensions_form_tables' => array(
      'render element' => 'element',
    )
  );
}


/**
 * Implements hook_job_describe_args().
 * Describes the arguements for the tripal_populate_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_populate_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,
  );
}

/**
 * Implements hook_node_view_alter()
 *
 * @param unknown $build
 */
function tripal_core_node_view_alter(&$build) {
  module_load_include('inc', 'tripal_core', 'includes/tripal_core.toc');
  tripal_core_node_view_build_toc($build);
}

/**
 * Implements hook_node_view()
 *
 * @ingroup tripal_core
 */
function tripal_core_node_view($node, $view_mode, $langcode) {

  // if this node type is a chado-based node (i.e. Tripal node)
  // the we want to add a table of contents to it's content list
  // this table of contents will be an empty
  if (preg_match('/^chado_/', $node->type)) {
    // Show feature browser and counts
    if ($view_mode == 'full') {
      if (!isset($node->content['#tripal_generic_node_template'])) {
        $node->content['#tripal_generic_node_template'] = TRUE;
      }
    }
  }
}

/**
 * Implements hook_exclude_type_by_default()
 *
 * This hooks allows fields of a specified type that match a specified criteria to be excluded by
 * default from any table when chado_generate_var() is called. Keep in mind that if
 * fields are excluded by default they can always be expanded at a later date using
 * chado_expand_var().
 *
 * Criteria are php strings that evaluate to either TRUE or FALSE. These strings are evaluated using
 * drupal_eval() which suppresses syntax errors and throws watchdog entries of type php. There are
 * also watchdog entries of type tripal_core stating the exact criteria evaluated. Criteria can
 * contain the following tokens:
 *   - <field_name>
 *       Replaced by the name of the field to be excluded
 *   - <field_value>
 *       Replaced by the value of the field in the current record
 * Also keep in mind that if your criteria doesn't contain the &gt;field_value&lt;  token then it will be
 * evaluated before the query is executed and if the field is excluded it won't be included in the
 * query.
 *
 * @return
 *   An array of type => criteria where the type is excluded if the criteria evaluates to TRUE
 *
 * @ingroup tripal_core
 */
function tripal_core_exclude_type_by_default() {
  return array('text' => 'strlen("<field_value> ") > 250');
}