tripal/tripal_chado/tripal_chado.module

<?php

// APPLICATION PROGRAMMER INTERFACE -------------
// Chado API
require_once "api/tripal_chado.api.inc";
require_once 'api/tripal_chado.general.api.inc';
require_once 'api/tripal_chado.query.api.inc';
require_once 'api/tripal_chado.variables.api.inc';
require_once 'api/tripal_chado.schema.api.inc';
require_once 'api/tripal_chado.custom_tables.api.inc';
require_once 'api/tripal_chado.mviews.api.inc';
require_once 'api/tripal_chado.schema_v1.2.api.inc';
require_once 'api/tripal_chado.schema_v1.11.api.inc';

require_once 'api/modules/tripal_chado.analysis.api.inc';
require_once 'api/modules/tripal_chado.contact.api.inc';
require_once 'api/modules/tripal_chado.cv.api.inc';
require_once 'api/modules/tripal_chado.db.api.inc';
require_once 'api/modules/tripal_chado.feature.api.inc';
require_once 'api/modules/tripal_chado.organism.api.inc';
require_once 'api/modules/tripal_chado.pub.api.inc';
require_once 'api/modules/tripal_chado.stock.api.inc';

require_once "includes/tripal_chado.entity.inc";
require_once "includes/tripal_chado.schema.inc";
require_once "includes/tripal_chado.term_storage.inc";
require_once "includes/tripal_chado.field_storage.inc";

tripal_chado_set_globals();

/**
 * This function is used to set the global Chado variables
 *
 * @ingroup tripal_chado
*/
function tripal_chado_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_chado
 */
function tripal_chado_init() {

  // 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'");
    $cv = $results->fetchObject();
    if (!$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'");
    $db = $results->fetchObject();
    if (!$db) {
      $results = chado_query(
          "INSERT INTO {db} (name,description) " .
          "VALUES ('tripal', 'Used as a database placeholder for tripal defined objects such as tripal cvterms')"
      );
    }
  }
}

/**
 * Implements hook_menu().
 */
function tripal_chado_menu() {
  $items = array();

  $items['admin/tripal/loaders'] = array(
    'title' => 'Data Loaders',
    'description' => t('Tools facilitating data import.'),
    'access arguments' => array('administer tripal'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => 6
  );

  // 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_chado_load_form'),
    'access arguments' => array('install chado'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => -100
  );

  // 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_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_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_admin_custom_table', 'admin/tripal/storage/chado/custom_tables'),
    'access arguments' => array('administer tripal'),
    'type' => MENU_CALLBACK,
  );

  return $items;

}

/**
 * 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
 */
function tripal_chado_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.')
    ),
    'view chado_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_field_info().
 */
function tripal_chado_field_info() {
  $fields = array(
    'organism_id' => array(
      'label' => t('Organism'),
      'description' => t('A field for specifying an organism.'),
      'default_widget' => 'tripal_chado_organism_select_widget',
      'default_formatter' => 'tripal_chado_organism_formatter',
      'settings' => array(),
      'storage' => array(
        'type' => 'field_chado_storage',
        'module' => 'tripal_chado',
        'active' => TRUE
      ),
    ),
    'dbxref_id' => array(
      'label' => t('Cross-reference'),
      'description' => t('This record can be cross-referenced with a record in
          another online database. This field is intended for the most prominent
          reference.  At a minimum, the database and accession must be provided.'),
      'default_widget' => 'tripal_chado_dbxref_id_widget',
      'default_formatter' => 'tripal_chado_dbxref_id_formatter',
      'settings' => array(),
      'storage' => array(
        'type' => 'field_chado_storage',
        'module' => 'tripal_chado',
        'active' => TRUE
      ),
    ),
    'residues' => array(
      'label' => t('Residues'),
      'description' => t('A field for managing nucleotide and protein residues.'),
      'default_widget' => 'tripal_chado_residue_textarea_widget',
      'default_formatter' => 'tripal_chado_residues_formatter',
      'settings' => array(),
      'storage' => array(
        'type' => 'field_chado_storage',
        'module' => 'tripal_chado',
        'active' => TRUE
      ),
    ),
    'md5checksum' => array(
      'label' => t('MD5 checksum'),
      'description' => t('A field for generating MD5 checksum for a sequence.'),
      'default_widget' => 'tripal_chado_md5checksum_checkbox_widget',
      'default_formatter' => 'tripal_chado_md5checksum_formatter',
      'settings' => array(),
      'storage' => array(
        'type' => 'field_chado_storage',
        'module' => 'tripal_chado',
        'active' => TRUE
      ),
    ),
    'seqlen' => array(
      'label' => t('Sequence length'),
      'description' => t('A field for calculating the length of a sequence.'),
      'default_widget' => 'tripal_chado_seqlen_hidden_widget',
      'default_formatter' => 'tripal_chado_seqlen_formatter',
      'settings' => array(),
      'storage' => array(
        'type' => 'field_chado_storage',
        'module' => 'tripal_chado',
        'active' => TRUE
      ),
    ),
    // The field provides a widget for adding new properties
    // to an entity that is connected to a base table that has a prop table
    // in Chado.
    'kvproperty_adder' => array(
      'label' => t('Add a Property Type'),
      'description' => t('This record may have any number of properties. Use
          this field to first add the type.'),
      'default_widget' => 'tripal_chado_kvproperty_adder_widget',
      //'default_formatter' => 'tripal_chado_kvproperty_adder_formatter',
      'default_formatter' => 'hidden',
      'settings' => array(),
      'storage' => array(
        'type' => 'field_chado_storage',
        'module' => 'tripal_chado',
        'active' => TRUE
      ),
    ),
    // The field provides form elements for adding a property to an entity
    // that in turn gets stored in a prop table of Chado (e.g. featureprop,
    // stockprop, etc).
    'kvproperty' => array(
      'label' => t('Add a Property'),
      'description' => t('Add details about this property.'),
      'default_widget' => 'tripal_chado_kvproperty_widget',
      'default_formatter' => 'tripal_chado_kvproperty_formatter',
      'settings' => array(),
      'storage' => array(
        'type' => 'field_chado_storage',
        'module' => 'tripal_chado',
        'active' => TRUE
      ),
    ),
  );
  return $fields;
}

/**
 * Implements hook_field_widget_info().
 */
function tripal_chado_field_widget_info() {
  return array(
    'tripal_chado_organism_select_widget' => array(
      'label' => t('Organism Select'),
      'field types' => array('organism_id')
    ),
    'tripal_chado_dbxref_id_widget' => array(
      'label' => t('Cross-reference'),
      'field types' => array('dbxref_id'),
      'description' => t('This record can be cross-referenced with a record in another online database. This field is intended for the most prominent reference.  At a minimum, the database and accession must be provided.'),
    ),
    'tripal_chado_md5checksum_checkbox_widget' => array(
      'label' => t('MD5 Checksum Checkbox'),
      'field types' => array('md5checksum'),
    ),
    'tripal_chado_residues_textarea_widget' => array(
      'label' => t('Residues'),
      'field types' => array('residues'),
    ),
    'tripal_chado_seqlen_hidden_widget' => array(
      'label' => t('Sequence Length'),
      'field types' => array('seqlen'),
    ),
    'tripal_chado_kvproperty_adder_widget' => array(
      'label' => t('Add a Property'),
      'field types' => array('kvproperty_adder'),
    ),
    'tripal_chado_kvproperty_widget' => array(
      'label' => t('Property'),
      'field types' => array('kvproperty'),
    ),
  );
}
/**
 * Implements hook_field_formatter_info().
 */
function tripal_chado_field_formatter_info() {
  return array(
    'tripal_chado_organism_formatter' => array(
      'label' => t('Organism'),
      'field types' => array('organism_id')
    ),
    'tripal_chado_dbxref_id_formatter' => array(
      'label' => t('Cross-reference'),
      'field types' => array('dbxref_id')
    ),
    'tripal_chado_md5checksum_formatter' => array(
      'label' => t('MD5 checksum'),
      'field types' => array('md5checksum')
    ),
    'tripal_chado_residues_formatter' => array(
      'label' => t('Residues'),
      'field types' => array('residues')
    ),
    'tripal_chado_seqlen_formatter' => array(
      'label' => t('Sequence length'),
      'field types' => array('seqlen')
    ),
    'tripal_chado_kvproperty_adder_formatter' => array(
      'label' => t('Add a Property'),
      'field types' => array('kvproperty_adder')
    ),
    'tripal_chado_kvproperty_formatter' => array(
      'label' => t('Property'),
      'field types' => array('kvproperty')
    ),
  );
}

/**
 * Implements hook_chado_field_alter().
 *
 * This function is used to change the default field formatter and widget
 * that are assigned to fields of an Entity. This hook is only used for
 * those fields that correspond to a column in a Chado table.  An implementation
 * of this hook can be used to change the default formatters and widgets to
 * custom formatters and widgets that are created by the module creating
 * this hook.
 *
 * By default, Tripal will provide custom formatters and widgets for many
 * columns in Chado tables, therefore, this hook will most likely be of use
 * to extension modules that create custom table inside of Chado.
 *
 * @param $field
 */
function hook_chado_field_alter(&$field) {

  if (!array_key_exists('field_settings', $field)) {
    return;
  }
  // If the field doesn't list the Chado table or column then just return.
  if (!array_key_exists('chado_table', $field['field_settings']) or
      !array_key_exists('chado_column', $field['field_settings'])) {
    return;
  }
  // Here we provide new field types and widgets for FK fields
  // and fields that need special attention.
}

/**
 * Implements hook_field_widget_form_alter().
 */
function tripal_chado_field_widget_form_alter(&$element, &$form_state, $context) {

  if (array_key_exists('#field_name', $element)) {
    $field_name = $element['#field_name'];
    $matches = array();

    if (preg_match('/(.+?)__(.+?)$/', $field_name, $matches)) {
      $tablename = $matches[1];
      $colname = $matches[2];
      $schema = chado_get_schema($tablename);

      // The timelastmodified field exists in many Chado tables.  We want
      // the form element to update to the most recent time rather than the time
      // in the database.
      if ($colname == 'timelastmodified' and $schema['fields'][$colname]['type'] == 'datetime') {
        // We want the default value for the field to be the current time.
        $element['#default_value']['value'] = format_date(time(), 'custom', "Y-m-d H:i:s", 'UTC');
        $element['#date_items']['value'] = $element['#default_value']['value'];
      }
      // We want the date combo fieldset to be collaspible so we will
      // add our own theme_wrapper to replace the one added by the date
      // module.
      if (array_key_exists($colname, $schema['fields']) and $schema['fields'][$colname]['type'] == 'datetime') {
        $element['#theme_wrappers'] = array('tripal_chado_date_combo');
      }
    }
  }
}

/**
 * Implements hook_field_formatter_view().
 */
function tripal_chado_field_formatter_view($entity_type, $entity, $field,
    $instance, $langcode, $items, $display) {

      $element = array();
      switch ($display['type']) {
        case 'tripal_chado_organism_formatter':
          module_load_include('inc', 'tripal_chado', 'includes/fields/organism_id');
          tripal_chado_organism_select_formatter($element, $entity_type, $entity, $field,
              $instance, $langcode, $items, $display);
          break;
        case 'tripal_chado_dbxref_id_formatter':
          module_load_include('inc', 'tripal_chado', 'includes/fields/dbxref_id');
          tripal_chado_dbxref_id_formatter($element, $entity_type, $entity, $field,
              $instance, $langcode, $items, $display);
          break;
        case 'tripal_chado_md5checksum_formatter':
          module_load_include('inc', 'tripal_chado', 'includes/fields/md5checksum');
          tripal_chado_md5checksum_checkbox_formatter($element, $entity_type, $entity, $field,
              $instance, $langcode, $items, $display);
          break;
        case 'tripal_chado_residues_formatter':
          module_load_include('inc', 'tripal_chado', 'includes/fields/residues');
          tripal_chado_residues_textarea_formatter($element, $entity_type, $entity, $field,
              $instance, $langcode, $items, $display);
          break;
        case 'tripal_chado_seqlen_formatter':
          module_load_include('inc', 'tripal_chado', 'includes/fields/seqlen');
          tripal_chado_seqlen_hidden_formatter($element, $entity_type, $entity, $field,
              $instance, $langcode, $items, $display);
          break;
        case 'tripal_chado_kvproperty_adder_formatter':
          module_load_include('inc', 'tripal_chado', 'includes/fields/kvproperty_adder');
          tripal_chado_kvproperty_adder_formatter($element, $entity_type, $entity, $field,
              $instance, $langcode, $items, $display);
          break;
        case 'tripal_chado_kvproperty_formatter':
          module_load_include('inc', 'tripal_chado', 'includes/fields/kvproperty');
          tripal_chado_kvproperty_formatter($element, $entity_type, $entity, $field,
              $instance, $langcode, $items, $display);
          break;
      }
      return $element;
}

/**
 * Implements hook_field_widget_form().
 */
function tripal_chado_field_widget_form(&$form, &$form_state, $field,
    $instance, $langcode, $items, $delta, $element) {

  $widget = $element;
  switch ($instance['widget']['type']) {
    case 'tripal_chado_organism_select_widget':
      // Make sure the include files get parsed now and for the form submits.
      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/organism_id');
      module_load_include('inc', 'tripal_chado', 'includes/fields/organism_id');
      // Update the widget with the new field.
      tripal_chado_organism_select_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
      break;
    case 'tripal_chado_dbxref_id_widget':
      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/dbxref_id');
      module_load_include('inc', 'tripal_chado', 'includes/fields/dbxref_id');
      tripal_chado_dbxref_id_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
      break;
    case 'tripal_chado_md5checksum_checkbox_widget':
      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/md5checksum');
      module_load_include('inc', 'tripal_chado', 'includes/fields/md5checksum');
      tripal_chado_md5checksum_checkbox_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
      break;
    case 'tripal_chado_residues_textarea_widget':
      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/residues');
      module_load_include('inc', 'tripal_chado', 'includes/fields/residues');
      tripal_chado_residues_textarea_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
      break;
    case 'tripal_chado_seqlen_hidden_widget':
      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/seqlen');
      module_load_include('inc', 'tripal_chado', 'includes/fields/seqlen');
      tripal_chado_seqlen_hidden_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
      break;
    case 'tripal_chado_kvproperty_adder_widget':
      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/kvproperty_adder');
      module_load_include('inc', 'tripal_chado', 'includes/fields/kvproperty_adder');
      tripal_chado_kvproperty_adder_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
      break;
    case 'tripal_chado_kvproperty_widget':
      form_load_include($form_state, 'inc', 'tripal_chado', 'includes/fields/kvproperty');
      module_load_include('inc', 'tripal_chado', 'includes/fields/kvproperty');
      tripal_chado_kvproperty_widget($widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
      break;
  }
  return $widget;
}

/**
 * Implements hook_form_FORM_ID_alter().
 *
 * The field_ui_display_overview_form is used for formatting the display
 * or layout of fields attached to an entity and shown on the entity view page.
 */
function tripal_chado_form_field_ui_display_overview_form_alter(&$form, &$form_state, $form_id) {
  // Remove the kvproperty_addr field as it isn't ever displayed. It's just used
  // on the add/edit form of an entity for adding new property fields.
  $fields_names = element_children($form['fields']);
  foreach ($fields_names as $field_name) {
    $field_info = field_info_field($field_name);
    if ($field_info['type'] == 'kvproperty_adder') {
      unset($form['fields'][$field_name]);
    }
  }
}
/**
 * Implements hook_form_FORM_ID_alter().
 *
 * The field_ui_field_overview_form is used for ordering and configuring the
 * fields attached to an entity.
 */
function tripal_chado_form_field_ui_field_overview_form_alter(&$form, &$form_state, $form_id) {
  // Remove the kvproperty_addr field as it isn't ever displayed. It's just used
  // on the add/edit form of an entity for adding new property fields.
  $fields_names = element_children($form['fields']);
  foreach ($fields_names as $field_name) {
    $field_info = field_info_field($field_name);
    if ($field_info['type'] == 'kvproperty_adder') {
      unset($form['fields'][$field_name]);
    }
  }
}
/**
 * Implements hook_field_is_empty().
 */
function tripal_chado_field_is_empty($item, $field) {

  // If there is no value field then the field is empty.
  if (!array_key_exists('value', $item)) {
    return TRUE;
  }

  // Iterate through all of the fields and if at least one has a value
  // the field is not empty.
  foreach ($item as $form_field_name => $value) {
    if (isset($value) and $value != NULL and $value != '') {
      return FALSE;
    }
  }

  // Otherwise, the field is empty.
  return TRUE;
}

/**
 * Returns the values of the field from the $form_state.
 */
function tripal_chado_get_field_form_values($field_name, $form_state, $delta = 0, $child = NULL) {
  $value = NULL;
  // The form_state must have the 'values' key. If not then just return.
  if (!array_key_exists('values', $form_state)) {
    return $value;
  }

  // If the field name is not in the form_state['values'] then return.
  if (!array_key_exists($field_name, $form_state['values'])) {
    return $value;
  }

  // Iterate through the values looking for the field_name provided.
  foreach ($form_state['values'][$field_name] as $langcode => $items) {
    $item = $items[$delta];
    if ($child){
      if(array_key_exists($child, $item) and $item[$child] != '') {
        $value = $item[$child];
      }
    }
    else {
      $value = $item['value'];
    }
  }
  return $value;
}

/**
 * Sets the values of the field from the $form_state.
 */
function tripal_chado_set_field_form_values($field_name, &$form_state, $newvalue, $delta = 0, $child = NULL) {
  // The form_state must have the 'values' key. If not then just return.
  if (!array_key_exists('values', $form_state)) {
    return FALSE;
  }

  // If the field name is not in the form_state['values'] then reutrn.
  if (!array_key_exists($field_name, $form_state['values'])) {
    return FALSE;
  }

  foreach ($form_state['values'][$field_name] as $langcode => $items) {
    if ($child) {
      $form_state['values'][$field_name][$langcode][$delta][$child] = $newvalue;
    }
    else {
      $form_state['values'][$field_name][$langcode][$delta]['value'] = $newvalue;
    }
  }
  return TRUE;
}


/**
 * Implements hook_theme().
 */
function tripal_chado_theme($existing, $type, $theme, $path) {
  return array(
    'tripal_chado_dbxref_id_widget' => array(
      'render element' => 'element',
      'file' => 'includes/fields/dbxref_id.inc',
    ),
    'tripal_chado_kvproperty_addr_widget' => array(
      'render element' => 'element',
      'file' => 'includes/fields/dbxref_id.inc',
    ),
    'tripal_chado_date_combo' => array(
      'render element' => 'element',
      'file' => 'theme/tripal_chado.theme.inc',
    ),
  );
}

/**
 * Implements hook_add_bundle_fields().
 */
function tripal_chado_add_bundle_fields($entity_type, $bundle, $term) {

  $bundle_name = $bundle->name;

  // This array will hold details that map the bundle to tables in Chado.
  $bundle_data = array();

  // Get the cvterm that corresponds to this TripalTerm object.
  $vocab = entity_load('TripalVocab', array($term->vocab_id));
  $vocab = reset($vocab);
  $match = array(
    'dbxref_id' => array(
      'db_id' => array(
        'name' => $vocab->namespace,
      ),
      'accession' => $term->accession
    ),
  );
  $cvterm = chado_generate_var('cvterm', $match);

  // The organism table does not have a type_id so we won't ever find
  // a record for it in the tripal_cv_defaults table.
  if ($cvterm->name == 'organism') {
    $bundle_data = array(
      'cv_id' => $cvterm->cv_id->cv_id,
      'cvterm_id' => $cvterm->cvterm_id,
      'data_table' => 'organism',
      'type_table' => 'organism',
      'field' =>  '',
    );
  }
  // The analysis table does not have a type_id so we won't ever find
  // a record for it in the tripalcv_defaults table.
  else if ($cvterm->name == 'analysis') {
    $bundle_data = array(
      'cv_id' => $cvterm->cv_id->cv_id,
      'cvterm_id' => $cvterm->cvterm_id,
      'data_table' => 'analysis',
      'type_table' => 'analysis',
      'field' =>  '',
    );
  }
  else if ($cvterm->name == 'project') {
    $bundle_data = array(
      'cv_id' => $cvterm->cv_id->cv_id,
      'cvterm_id' => $cvterm->cvterm_id,
      'data_table' => 'project',
      'type_table' => 'project',
      'field' =>  '',
    );
  }
  else {
    // TODO: WHAT TO DO IF A VOCABULARY IS USED AS A DEFAULT FOR MULTIPLE
    // TABLES.
    // Look to see if this vocabulary is used as a default for any table.
    $default = db_select('tripal_cv_defaults', 't')
      ->fields('t')
      ->condition('cv_id', $cvterm->cv_id->cv_id)
      ->execute()
      ->fetchObject();
    if ($default) {
      $bundle_data = array(
        'cv_id' => $cvterm->cv_id->cv_id,
        'cvterm_id' => $cvterm->cvterm_id,
        'data_table' => $default->table_name,
        'type_table' => $default->table_name,
        'field' =>  $default->field_name,
      );
    }
  }

  // Adds the fields for the base table to the entity.
  tripal_chado_add_bundle_base_fields($entity_type, $bundle_name, $bundle_data);

  // Save the mapping information so that we can reuse it when we need to
  // look things up for later for an entity
  tripal_set_bundle_variable('chado_cvterm_id', $bundle->id, $bundle_data['cvterm_id']);
  tripal_set_bundle_variable('chado_table', $bundle->id, $bundle_data['data_table']);
  tripal_set_bundle_variable('chado_column', $bundle->id, $bundle_data['field']);

  // Check to see if there are any kv-property tables associated to this
  // base table. If so, add the fields for that type of table.
  // TODO: the 'featurprop' table should not be hardcoded.
  tripal_chado_add_bundle_kvproperty_adder_field($entity_type, $bundle_name, 'featureprop');
}

/**
 * Adds the fields for a kv-property table fields
 *
 * @param $entity_type_name
 * @param $bundle_name
 * @param $kv_table
 */
function tripal_chado_add_bundle_kvproperty_adder_field($entity_type_name, $bundle_name, $kv_table) {
  // First add a generic property field so that users can add new proeprty types.
  $field_name = $kv_table;

  // Initialize the field array.
  $field_info = array(
    'field_type' => 'kvproperty_adder',
    'widget_type' => 'tripal_fields_kvproperty_adder_widget',
    'field_settings' => array(),
    'widget_settings' => array('display_label' => 1),
    'description' => '',
    'label' => 'Additional Properties',
    'is_required' => 0,
  );
  tripal_add_bundle_field($field_name, $field_info, $entity_type_name, $bundle_name);
}

/**
 * Adds the fields for the base table to the entity.
 */
function tripal_chado_add_bundle_base_fields($entity_type_name, $bundle_name, $bundle_data) {

  $table_name = $bundle_data['data_table'];
  $type_table = $bundle_data['type_table'];
  $type_field = $bundle_data['field'];

  // Iterate through the columns of the table and see if fields have been
  // created for each one. If not, then create them.
  $schema = chado_get_schema($table_name);
  $columns = $schema['fields'];
  foreach ($columns as $column_name => $details) {
    $field_name = $table_name . '__' . $column_name;

    // Skip the primary key field.
    if ($column_name == $schema['primary key'][0]) {
      continue;
    }

    // Skip the type field.
    if ($table_name == $type_table and $column_name == $type_field) {
      continue;
    }

    // Get the field defaults for this column.
    $field_info = tripal_chado_get_table_column_field_default($table_name, $schema, $column_name);


    // Determine if the field is required.
    if (array_key_exists('not null', $details) and $details['not null'] === TRUE) {
      $field_info['is_required'] = array_key_exists('default', $details) ? 0 : 1;
    }

    // If we don't have a field type then we don't need to create a field.
    if (!$field_info['field_type']) {
      // If we don't have a field type but it is required and doesn't have
      // a default value then we are in trouble.
      if ($field_info['is_required'] and !array_key_exists('default', $details)) {
        throw new Exception(t('The %table.%field type, %type, is not yet supported for Entity fields, but it is required,',
            array('%table' => $table_name, '%field' => $column_name, '%type' => $details['type'])));
      }
      continue;
    }

    // If this field is a foreign key field then we will have a special custom
    // field provided by Tripal.
    $is_fk = FALSE;
    if (array_key_exists('foreign keys', $schema)) {
      foreach ($schema['foreign keys'] as $remote_table => $fk_details) {
        if (array_key_exists($column_name, $fk_details['columns'])) {
          $is_fk = TRUE;
        }
      }
    }

    // Add the field to the bundle.
    tripal_add_bundle_field($field_name, $field_info, $entity_type_name, $bundle_name);
  }
}

/**
 * Returns a $field_info array for a field based on a database column.
 *
 */
function tripal_chado_get_table_column_field_default($table_name, $schema, $column_name) {
  $details = $schema['fields'][$column_name];

  // Create an array with information about this field.
  $field = array(
    'field_type' => '',
    'widget_type' => '',
    'field_settings' => array(
      'chado_table' => $table_name,
      'chado_column' => $column_name,
      'semantic_web' => array(
        // The type is the term from a vocabulary that desribes this field..
        'type' => '',
        // The namepsace for the vocabulary (e.g. 'foaf').
        'ns' => '',
        // The URL for the namespace.  It must be that the type can be
        // appended to the URL.
        'nsurl' => '',
      ),
    ),
    'widget_settings' => array(
      'display_label' => 1
    ),
    'description' => '',
    'label' => ucwords(preg_replace('/_/', ' ', $column_name)),
    'is_required' => 0,
  );

  // Alter the field info array depending on the column details.
  switch($details['type']) {
    case 'char':
      $field['field_type'] = 'text';
      $field['widget_type'] = 'text_textfield';
      $field['field_settings']['max_length'] = $details['length'];
      break;
    case 'varchar':
      $field['field_type'] = 'text';
      $field['widget_type'] = 'text_textfield';
      $field['field_settings']['max_length'] = $details['length'];
      break;
    case 'text':
      $field['field_type'] = 'text';
      $field['widget_type'] = 'text_textarea';
      $field['field_settings']['max_length'] = 17179869184;
      $field['field_settings']['text_processing'] = 1;
      break;
    case 'blob':
      // not sure how to support a blob field.
      continue;
      break;
    case 'int':
      $field['field_type'] = 'number_integer';
      $field['widget_type'] = 'number';
      break;
    case 'float':
      $field['field_type'] = 'number_float';
      $field['widget_type'] = 'number';
      $field['field_settings']['precision'] = 10;
      $field['field_settings']['scale'] = 2;
      $field['field_settings']['decimal_separator'] = '.';
      break;
    case 'numeric':
      $field['field_type'] = 'number_decimal';
      $field['widget_type'] = 'number';
      break;
    case 'serial':
      // Serial fields are most likely not needed as a field.
      break;
    case 'boolean':
      $field['field_type'] = 'list_boolean';
      $field['widget_type'] = 'options_onoff';
      $field['field_settings']['allowed_values'] = array(0 => "No", 1 => "Yes");
      break;
    case 'datetime':
      // Use the Drupal Date and Date API to create the field/widget
      $field['field_type'] = 'datetime';
      $field['widget_type'] = 'date_select';
      $field['widget_settings']['increment'] = 1;
      $field['widget_settings']['tz_handling'] = 'none';
      $field['widget_settings']['collapsible'] = TRUE;

      // TODO: Add settings so that the minutes increment by 1.
      // And turn off the timezone, as the Chado field doesn't support it.
      break;
  }

  // Set some default semantic web information
  if ($column_name == 'name') {
    $field['field_settings']['semantic_web']['type'] = 'name';
    $field['field_settings']['semantic_web']['ns'] = 'foaf';
    $field['field_settings']['semantic_web']['nsurl'] = 'http://xmlns.com/foaf/0.1/';
  }
  if ($column_name == 'description' or $column_name == 'definition' or
      $column_name == 'comment') {
    $field['field_settings']['semantic_web']['type'] = 'description';
    $field['field_settings']['semantic_web']['ns'] = 'hydra';
    $field['field_settings']['semantic_web']['nsurl'] = 'http://www.w3.org/ns/hydra/core#';
  }

  //
  // GENERIC COLUMNS
  //
  if ($field['field_settings']['chado_column'] =='organism_id') {
    $field['field_type'] = 'organism_id';
    $field['widget_type'] = 'tripal_chado_organism_select_widget';
    $field['label'] = 'Organism';
    $field['description'] = 'Select an organism.';
  }
  elseif ($field['field_settings']['chado_column'] =='dbxref_id') {
    $field['field_type'] = 'dbxref_id';
    $field['widget_type'] = 'tripal_chado_primary_dbxref_widget';
    $field['label'] = 'Primary Cross Reference';;
    $field['description'] = 'This record can be cross-referenced with a ' .
      'record in another online database. The primary reference is for the ' .
      'most prominent reference.  At a minimum, the database and accession ' .
      'must be provided.  To remove a set reference, change the database ' .
      'field to "Select a Database".';
  }
  elseif ($field['label'] == 'Timeaccessioned') {
    $field['label'] = 'Time Accessioned';
    $field['description'] = 'Please enter the time that this record was first added to the database.';
  }
  elseif ($field['label'] == 'Timelastmodified') {
    $field['label'] = 'Time Last Modified';
    $field['description'] = 'Please enter the time that this record was last modified. The default is the current time.';
  }
  //
  // ORGANISM TABLE
  //
  elseif ($field['field_settings']['chado_table'] == 'organism' and $field['field_settings']['chado_column'] == 'comment') {
    $field['label'] = 'Description';
  }
  //
  // FEATURE TABLE
  //
  elseif ($field['field_settings']['chado_table'] == 'feature' and $field['field_settings']['chado_column'] == 'uniquename') {
    $field['field_type'] = 'text';
    $field['widget_type'] = 'text_textfield';
    $field['field_settings']['text_processing'] = 0;
    $field['field_settings']['semantic_web']['type'] = 'name';
    $field['field_settings']['semantic_web']['ns'] = 'foaf';
    $field['field_settings']['semantic_web']['nsurl'] = 'http://xmlns.com/foaf/0.1/';
  }
  elseif ($field['field_settings']['chado_table'] == 'feature' and $field['field_settings']['chado_column'] == 'md5checksum') {
    $field['field_type'] = 'md5checksum';
    $field['widget_type'] = 'tripal_chado_md5checksum_checkbox_widget';
    $field['label'] = 'MD5 Checksum';
    $field['description'] = 'Generating MD5 checksum for the sequence.';
  }
  elseif ($field['field_settings']['chado_table'] == 'feature' and $field['field_settings']['chado_column'] == 'seqlen') {
    $field['field_type'] = 'seqlen';
    $field['widget_type'] = 'tripal_chado_seqlen_hidden_widget';
    $field['label'] = 'Seqlen';
    $field['description'] = 'The length of the residues.';
  }
  elseif ($field['field_settings']['chado_table'] == 'feature' and $field['field_settings']['chado_column'] == 'residues') {
    $field['field_type'] = 'residues';
    $field['widget_type'] = 'tripal_chado_residues_textarea_widget';
    $field['label'] = 'Residues';
    $field['description'] = 'Please provide an IUPAC compatible residues for this feature. Spaces and new lines are allowed.';
  }

  return $field;
}

/**
 * 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 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
 */
function tripal_chado_exclude_type_by_default() {
  return array('text' => 'strlen("<field_value> ") > 250');
}

/**
 * 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 $args array
 *
 * @ingroup tripal
 */
function tripal_chado_describe_args($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_install_chado') {
    $new_args['Action'] = $args[0];
  }
  return $new_args;
}