tripal/tripal_entities/includes/tripal_entities.chado_entity.inc

<?php

/**
 *
 * Implements hook_entity_load().
 */
function tripal_entities_entity_presave($entity, $type) {

}
/**
 *
 * @param $entity
 * @param $type
 */
function tripal_entities_entity_postsave($entity, $type) {
  // Set the title for this entity using the chado data.
  $title = chado_get_entity_title($entity);
  $ec = new TripalEntityController($entity->type);
  $ec->setTitle($entity, $title);
}
/**
 *
 * Implements hook_entity_load().
 */
function tripal_entities_entity_load($entities, $type) {
  foreach ($entities as $entity) {

    // For Tripal created entities add in the chado_entity details.
    $dbs = tripal_entities_get_db_names_for_published_vocabularies();
    if (in_array($entity->type, $dbs)) {
      $details = db_select('chado_entity', 'ce')
        ->fields('ce')
        ->condition('entity_id', $entity->id)
        ->execute()
        ->fetchObject();

      // Add teh chado entity details to the entity in case it's needed
      // downstream (e.g. in field widget construction).
      $entity->chado_entity = $details;
    }
  }
}

/**
 *
 * Implements hook_entity_insert().
 */
function tripal_entities_entity_insert($entity, $type) {

}

/**
 *
 * Implements hook_entity_update().
 */
function tripal_entities_entity_update($entity, $type) {

}

/**
 *
 * Implements hook_entity_delete().
 */
function tripal_entities_entity_delete($entity, $type) {
  $record = db_select('chado_entity', 'ce')
   ->fields('ce', array('chado_entity_id', 'data_table', 'record_id'))
   ->condition('entity_id', $entity->id)
   ->execute()
   ->fetchObject();

  if ($record && property_exists($record, 'chado_entity_id')) {
    // Delete the corresponding record in Chado
    $table = $record->data_table;
    $record_id = $record->record_id;
    chado_delete_record($table, array($table . '_id' => $record_id));

    //Delete the record in the public.chado_entity table
    $sql = "DELETE FROM {chado_entity} WHERE chado_entity_id = :id";
    db_query($sql, array(':id' => $record->chado_entity_id));
  }
}

/**
 *
 * @param unknown $display
 * @param unknown $context
 */
function tripal_entities_field_widget_form_alter(&$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_entities_date_combo');
      }
    }
  }
}

/**
 * This theme function is meant to override the data_combo theme.
 *
 * @param $variables
 */
function theme_tripal_entities_date_combo($variables) {
  $element = $variables['element'];
  $field = field_info_field($element['#field_name']);
  $instance = field_info_instance($element['#entity_type'], $element['#field_name'], $element['#bundle']);

  // Group start/end items together in fieldset.
  $fieldset = array(
    '#title' => t($element['#title']) . ' ' . ($element['#delta'] > 0 ? intval($element['#delta'] + 1) : ''),
    '#value' => '',
    '#description' => !empty($element['#fieldset_description']) ? $element['#fieldset_description'] : '',
    '#attributes' => array(),
    '#children' => $element['#children'],
    '#attributes' => array('class' => array('collapsible', 'collapsed')),
  );
  return theme('fieldset', array('element' => $fieldset));
}
/**
 * Implements hook_chado_field_alter().
 *
 */
function tripal_entities_chado_field_alter(&$field) {
  // If the field doesn't list the Chado table or column then just return.
  if (!array_key_exists('chado_table', $field) or !array_key_exists('chado_column', $field)) {
    return;
  }
  // Here we provide new field types and widgets for FK fields
  // and fields that need special attention.
  if ($field['chado_column'] =='organism_id') {
    $field['field_type'] = 'organism_id';
    $field['widget_type'] = 'tripal_fields_organism_select_widget';
    $field['label'] = 'Organism';
    $field['description'] = 'Select an organism.';
  }
  else if ($field['chado_column'] =='dbxref_id') {
    $field['field_type'] = 'dbxref_id';
    $field['widget_type'] = 'tripal_fields_primary_dbxref_widget';
    $field['label'] = 'Primary Cross Reference';;
    $field['description'] = 'This record can be cross-referenced with a
        record in another online database. The primary reference is for the
        most prominent reference.  At a minimum, the database and accession
        must be provided.  To remove a set reference, change the database
        field to "Select a Database".';
  }
  else if ($field['chado_table'] == 'feature' and
    $field['chado_column'] == 'md5checksum') {
    $field['field_type'] = 'md5checksum';
    $field['widget_type'] = 'tripal_fields_md5checksum_checkbox_widget';
    $field['label'] = 'MD5 Checksum';
    $field['description'] = 'Generating MD5 checksum for the sequence.';
  }
  else if ($field['chado_table'] == 'feature' and $field['chado_column'] == 'seqlen') {
    $field['field_type'] = 'seqlen';
    $field['widget_type'] = 'tripal_fields_seqlen_hidden_widget';
    $field['label'] = 'Seqlen';
    $field['description'] = 'The length of the residues.';

  }
  else if ($field['chado_table'] == 'feature' and $field['chado_column'] == 'residues') {
    $field['field_type'] = 'residues';
    $field['widget_type'] = 'tripal_fields_residues_textarea_widget';
    $field['label'] = 'Residues';
    $field['description'] = 'Please provide an IUPAC compatible residues for this feature. Spaces and new lines are allowed.';
  }
  else if ($field['label'] == 'Timeaccessioned') {
    $field['label'] = 'Time Accessioned';
    $field['description'] = 'Please enter the time that this record was first added to the database.';
  }
  else if ($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.';
  }
}

/**
 * Determines whether the given user has access to a tripal data entity.
 *
 * @param $op
 *   The operation being performed. One of 'view', 'update', 'create', 'delete'
 *   or just 'edit' (being the same as 'create' or 'update').
 * @param $entity
 *   Optionally a tripal data entity or a tripal data type to check access for.
 *   If nothing is given, access for all types is determined.
 * @param $account
 *   The user to check for. Leave it to NULL to check for the global user.
 * @return boolean
 *   Whether access is allowed or not.
 */
function tripal_entities_entity_access($op, $entity = NULL, $account = NULL) {
  if (user_access('administer tripal data', $account)) {
    return TRUE;
  }
  if (isset($entity) && $type_name = $entity->type) {
    $op = ($op == 'view') ? 'view' : 'edit';
    if (user_access("$op any $type_name data", $account)) {
      return TRUE;
    }
  }
  return FALSE;
}

/**
 * Menu callback to display an entity.
 *
 * As we load the entity for display, we're responsible for invoking a number
 * of hooks in their proper order.
 *
 * @see hook_entity_prepare_view()
 * @see hook_entity_view()
 * @see hook_entity_view_alter()
 */
function tripal_entities_view_entity($entity, $view_mode = 'full') {
  $content = '';
  $controller = entity_get_controller($entity->type);
  $content = $controller->view(array($entity->id => $entity));
  drupal_set_title($entity->title);
  return $content;
}

/**
 * Menu title callback for showing individual entities
 */
function tripal_entities_entity_title($entity){
  if ($entity) {
    return $entity->title;
  }
}