tripal/tripal_chado/includes/fields/chado_linker__pub.inc

<?php

class chado_linker_pub extends TripalField {
  /**
   * @see TripalField::fieldInfo()
   */
  static function fieldInfo() {
    return array(
      'label' => t('Publications'),
      'description' => t('Associates a publication (e.g. journal article,
            conference proceedings, book chapter, etc.) with this record.'),
      'default_widget' => 'chado_linker__pub_widget',
      'default_formatter' => 'chado_linker__pub_formatter',
      'settings' => array(),
      'storage' => array(
        'type' => 'field_chado_storage',
        'module' => 'tripal_chado',
        'active' => TRUE
      ),
    );
  }
  /**
   * @see TripalField::can_attach()
   */
  protected function setCanAttach() {
    $table_name = $this->details['chado_table'];
    $type_table = $this->details['chado_type_table'];
    $type_field = $this->details['chado_type_column'];
    $cv_id      = $this->details['chado_cv_id'];
    $cvterm_id  = $this->details['chado_cvterm_id'];

    // If the linker table does not exists then we don't want to add attach.
    $pub_table = $table_name . '_pub';
    if (chado_table_exists($pub_table)) {
      $this->can_attach = TRUE;
      return;
    }
    $this->can_attach = FALSE;
  }
  /**
   * @see TripalField::create_info()
   */
  function createInfo() {
    if (!$this->can_attach) {
      return;
    }

    $table_name = $this->details['chado_table'];
    $type_table = $this->details['chado_type_table'];
    $type_field = $this->details['chado_type_column'];
    $cv_id      = $this->details['chado_cv_id'];
    $cvterm_id  = $this->details['chado_cvterm_id'];

    $pub_table = $table_name . '_pub';
    $schema = chado_get_schema($pub_table);
    $pkey = $schema['primary key'][0];
    return array(
      'field_name' => $table_name . '__pub',
      'type' => 'chado_linker__pub',
      'cardinality' => FIELD_CARDINALITY_UNLIMITED,
      'locked' => FALSE,
      'storage' => array(
        'type' => 'field_chado_storage',
      ),
      'settings' => array(
        'chado_table' => $pub_table,
        'chado_column' => $pkey,
        'base_table' => $table_name,
        'semantic_web' => 'schema:publication',
      ),
    );
  }
  /**
   * @see TripalField::createInstanceInfo()
   */
  function createInstanceInfo() {
    if (!$this->can_attach) {
      return;
    }

    $table_name = $this->details['chado_table'];
    $type_table = $this->details['chado_type_table'];
    $type_field = $this->details['chado_type_column'];
    $cv_id      = $this->details['chado_cv_id'];
    $cvterm_id  = $this->details['chado_cvterm_id'];

    return array(
      'field_name' => $table_name . '__pub',
      'entity_type' => $this->entity_type,
      'bundle' => $this->bundle->name,
      'label' => 'Publications',
      'description' => 'This record has been referenced or is sourced from
        these publications.',
      'required' => FALSE,
      'settings' => array(
        'auto_attach' => FALSE,
      ),
      'widget' => array(
        'type' => 'chado_linker__pub_widget',
        'settings' => array(
          'display_label' => 1,
        ),
      ),
      'display' => array(
        'deafult' => array(
          'label' => 'above',
          'type' => 'chado_linker__pub_formatter',
          'settings' => array(),
        ),
      ),
    );

  }
  /**
   * @see TripalField::widgetInfo()
   */
  public static function widgetInfo() {
    return array(
      'chado_linker__pub_widget' => array(
        'label' => t('Publications'),
        'field types' => array('chado_linker__pub'),
      ),
    );
  }
  /**
   * @see TripalField::formatterInfo()
   */
  static function formatterInfo() {
    return array(
      'chado_linker__pub_formatter' => array(
        'label' => t('Publications'),
        'field types' => array('chado_linker__pub'),
        'settings' => array(
        ),
      ),
    );
  }
  /**
   * @see TripalField::formatterView()
   */
  static function formatterView(&$element, $entity_type, $entity, $field,
      $instance, $langcode, $items, $display) {

    $list_items = array();
    $chado_table = $field['settings']['chado_table'];
    foreach ($items as $delta => $item) {
      if ($item[$chado_table . '__pub_id']) {
        $pub = chado_generate_var('pub', array('pub_id' => $item[$chado_table . '__pub_id']));
        $list_items[$pub->pyear] = $pub->uniquename;
      }
    }

    krsort($list_items, SORT_NUMERIC);

    $list = array(
      'title' => '',
      'items' => $list_items,
      'type' => 'ol',
      'attributes' => array(),
    );

    if (count($items) > 0) {
      $element[0] = array(
        '#type' => 'markup',
        '#markup' => theme_item_list($list),
      );
    }
  }
  /**
   * @see TripalField::widgetForm()
   */
  public static function widgetForm(&$widget, &$form, &$form_state, $field, $instance,
      $langcode, $items, $delta, $element) {

    $entity = $form['#entity'];
    $field_name = $field['field_name'];

    // Get the FK column that links to the base table.
    $table_name = $field['settings']['chado_table'];
    $base_table = $field['settings']['base_table'];
    $schema = chado_get_schema($table_name);
    $pkey = $schema['primary key'][0];
    $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
    $fkey = $fkeys[0];

    // Get the field defaults.
    $record_id = '';
    $fkey_value = $element['#entity']->chado_record_id;
    $pub_id = '';
    $title = '';

    // If the field already has a value then it will come through the $items
    // array.  This happens when editing an existing record.
    if (array_key_exists($delta, $items)) {
      $record_id = $items[$delta][$table_name . '__' . $pkey];
      $fkey_value = $items[$delta][$table_name . '__' . $fkey];
      $pub_id = $items[$delta][$table_name . '__pub_id'];
      $title = $items[$delta][$table_name . '--pub__uniquename'];
    }

    // Check $form_state['values'] to see if an AJAX call set the values.
    if (array_key_exists('values', $form_state) and array_key_exists($delta, $form_state['values'])) {
      $record_id = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__' . $pkey);
      $fkey_value = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__' . $fkey);
      $pub_id = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__pub_id');
      $title = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__title');
    }

    $schema = chado_get_schema('pub');

    $widget['#table_name'] = $table_name;
    $widget['#fkey_field'] = $fkey;
    $widget['#element_validate'] = array('chado_linker__pub_widget_validate');
    $widget['#theme'] = 'chado_linker__pub_widget';
    $widget['#prefix'] =  "<span id='$table_name-$delta'>";
    $widget['#suffix'] =  "</span>";

    $widget['value'] = array(
      '#type' => 'value',
      '#value' => $items[$delta]['value'],
    );

    $widget[$table_name . '__' . $pkey] = array(
      '#type' => 'value',
      '#default_value' => $record_id,
    );
    $widget[$table_name . '__' . $fkey] = array(
      '#type' => 'value',
      '#default_value' => $fkey_value,
    );
    $widget[$table_name . '__pub_id'] = array(
      '#type' => 'value',
      '#default_value' => $pub_id,
    );

    $widget[$table_name . '--pub__uniquename'] = array(
      '#type' => 'textfield',
      '#title' => t('Publication ID'),
      '#default_value' => $title,
      '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/pub',
      '#ajax' => array(
        'callback' => "chado_linker__pub_widget_form_ajax_callback",
        'wrapper' => "$table_name-$delta",
        'effect' => 'fade',
        'method' => 'replace'
      ),
      '#maxlength' => 100000,
    );
  }

  /**
   * @see TripalField::load()
   */
  function load($field, $entity, $details) {

    $record = $details['record'];

    $field_name = $field['field_name'];
    $field_type = $field['type'];
    $field_table = $field['settings']['chado_table'];
    $field_column = $field['settings']['chado_column'];

    // Get the FK that links to the base record.
    $schema = chado_get_schema($field_table);
    $pkey = $schema['primary key'][0];
    $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
    $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];

    // Set some defaults for the empty record.
    $entity->{$field_name}['und'][0] = array(
      'value' => array(),
      $field_table . '__' . $pkey => '',
      $field_table . '__' . $fkey_lcolumn => '',
      $field_table . '__' . 'pub_id' => '',
      $field_table . '--' . 'pub__uniquename' => '',
    );

    $linker_table = $base_table . '_pub';
    $options = array(
      'return_array' => 1,
    );
    $record = chado_expand_var($record, 'table', $linker_table, $options);

    if (count($record->$linker_table) > 0) {
      $i = 0;
      foreach ($record->$linker_table as $index => $linker) {
        $pub = $linker->pub_id;
        $pub_details = tripal_get_minimal_pub_info($pub);
        $pub_details['@type'] = $pub->type_id->dbxref_id->db_id->name . ':' . $pub->type_id->dbxref_id->accession;
        $pub_details['publication']['type'] = $pub->type_id->name;

        $entity->{$field_name}['und'][$i]['value'] = $pub_details;
        $entity->{$field_name}['und'][$i][$field_table . '__' . $pkey] = $linker->$pkey;
        $entity->{$field_name}['und'][$i][$field_table . '__' . $fkey_lcolumn] = $linker->$fkey_lcolumn->$fkey_lcolumn;
        $entity->{$field_name}['und'][$i][$field_table . '__' . 'pub_id'] = $pub->pub_id;
        $entity->{$field_name}['und'][$i][$field_table . '--' . 'pub__uniquename'] =  $pub->uniquename;

        if (property_exists($pub, 'entity_id')) {
          $entity->{$field_name}['und'][$i]['entity_id'] = $pub->entity_id;
          $entity->{$field_name}['und'][$i]['entity_type'] = 'TripalEntity';
        }
        $i++;
      }
    }
  }
}

/**
 * Callback function for validating the chado_linker__pub_widget.
 */
function chado_linker__pub_widget_validate($element, &$form_state) {

  $field_name = $element['#field_name'];
  $delta = $element['#delta'];
  $table_name = $element['#table_name'];
  $fkey = $element['#fkey_field'];

  // If the form ID is field_ui_field_edit_form, then the user is editing the
  // field's values in the manage fields form of Drupal.  We don't want
  // to validate it as if it were being used in a data entry form.
  if ($form_state['build_info']['form_id'] =='field_ui_field_edit_form') {
    return;
  }

  // Get the field values.
  $fkey_value = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__' . $fkey);
  $pub_id = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__pub_id');
  $uname = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '--pub__uniquename');

  // If the user provided a uniquename then we want to set the
  // foreign key value to be the chado_record_idd
  if ($uname) {

    // Get the pub. If one with the same name and type is already present
    // then use that. Otherwise, insert a new one.
    if (!$pub_id) {
      $pub = chado_generate_var('pub', array('uniquename' => $uname));
      // Set the pub_id and FK value
      tripal_chado_set_field_form_values($field_name, $form_state, $pub->pub_id, $delta, $table_name . '__pub_id');
      $fkey_value = $element['#entity']->chado_record_id;
      tripal_chado_set_field_form_values($field_name, $form_state, $fkey_value, $delta, $table_name . '__' . $fkey);
    }

  }
  else {
    // If the $syn_name is not set, then remove the linker FK value to the base table.
    tripal_chado_set_field_form_values($field_name, $form_state, '', $delta, $table_name . '__' . $fkey);
    tripal_chado_set_field_form_values($field_name, $form_state, '', $delta, $table_name . '__pub_id');
  }

}
/**
 * An Ajax callback for the pub widget.
 */
function chado_linker__pub_widget_form_ajax_callback($form, $form_state) {

  $field_name = $form_state['triggering_element']['#parents'][0];
  $delta = $form_state['triggering_element']['#parents'][2];

  return $form[$field_name]['und'][$delta];
}
/**
 * Theme function for the pub widget.
 *
 * @param $variables
 */
function theme_chado_linker__pub_widget($variables) {
  $element = $variables['element'];

  // These two fields were added to the widget to help identify the fields
  // for layout.
  $table_name = $element['#table_name'];
  $fkey = $element['#fkey_field'];

  $layout = "
      <div class=\"pub-widget\">
        <div class=\"pub-widget-item\">" .
        drupal_render($element[$table_name . '--pub__uniquename']) . "
        </div>
      </div>
    ";

  return $layout;
}