$item) { $accession = ''; if ($item['value']) { $dbxref = chado_generate_var('dbxref', array('dbxref_id' => $item['value'])); $accession = $dbxref->db_id->name . ':' . $dbxref->accession; if ($dbxref->db_id->urlprefix) { $accession = l($accession, $dbxref->db_id->urlprefix . '/' . $dbxref->accession, array('attributes' => array('target' => '_blank'))); } } $element[$delta] = array( '#type' => 'markup', '#markup' => $accession, ); } } /** * * @param unknown $field_name * @param unknown $widget * @param unknown $form * @param unknown $form_state * @param unknown $field * @param unknown $instance * @param unknown $langcode * @param unknown $items * @param unknown $delta * @param unknown $element */ function tripal_chado_dbxref_id_widget(&$widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element) { $field_name = $field['field_name']; // Get the field defaults. $dbxref_id = ''; $db_id = ''; $accession = ''; $version = ''; $description = ''; // 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)) { $dbxref_id = $items[$delta]['value']; $db_id = $items[$delta]['dbxref__db_id']; $accession = $items[$delta]['dbxref__accession']; $version = $items[$delta]['dbxref__version']; $description = $items[$delta]['dbxref__description']; } // Check $form_state['values'] to see if an AJAX call set the values. if (array_key_exists('values', $form_state)) { $dbxref_id = tripal_chado_get_field_form_values($field_name, $form_state, 0, $field_name); $db_id = tripal_chado_get_field_form_values($field_name, $form_state, 0, "dbxref__db_id"); $accession = tripal_chado_get_field_form_values($field_name, $form_state, 0, "dbxref__accession"); $version = tripal_chado_get_field_form_values($field_name, $form_state, 0, "dbxref__version"); $description = tripal_chado_get_field_form_values($field_name, $form_state, 0, "dbxref__description"); } // If we are here because our parent was triggered in a form submit // then that means an ajax call was made and we don't want the fieldset to // be closed when it returns from the ajax call. $collapsed = TRUE; if (array_key_exists('triggering_element', $form_state) and $form_state['triggering_element']['#parents'][0] == $field_name) { $collapsed = FALSE; } if ($dbxref_id) { $collapsed = FALSE; } $schema = chado_get_schema('dbxref'); $options = tripal_get_db_select_options(); $widget['#element_validate'] = array('tripal_chado_dbxref_id_widget_validate'); $widget['#theme'] = 'tripal_chado_dbxref_id_widget'; $widget['#prefix'] = ""; $widget['#suffix'] = ""; // A temporary element used for theming the fieldset. $widget['#theme_settings'] = array( '#title' => $element['#title'], '#description' => $element['#description'], '#weight' => isset($element['#weight']) ? $element['#weight'] : 0, '#theme' => 'tripal_chado_dbxref_id_widget', '#collapsible' => TRUE, '#collapsed' => $collapsed, ); $widget['value'] = array( '#type' => 'hidden', '#default_value' => $dbxref_id, ); $widget['dbxref__db_id'] = array( '#type' => 'select', '#title' => t('Database'), '#options' => $options, '#required' => $element['#required'], '#default_value' => $db_id, '#ajax' => array( 'callback' => "tripal_chado_dbxref_id_widget_form_ajax_callback", 'wrapper' => "$field_name-dbxref--db-id", 'effect' => 'fade', 'method' => 'replace' ), ); $widget['dbxref__accession'] = array( '#type' => 'textfield', '#title' => t('Accession'), '#default_value' => $accession, '#required' => $element['#required'], '#maxlength' => array_key_exists('length', $schema['fields']['accession']) ? $schema['fields']['accession']['length'] : 255, '#size' => 15, '#autocomplete_path' => "admin/tripal/chado/tripal_db/dbxref/auto_name/$db_id", '#ajax' => array( 'callback' => "tripal_chado_dbxref_id_widget_form_ajax_callback", 'wrapper' => "$field_name-dbxref--db-id", 'effect' => 'fade', 'method' => 'replace' ) ); $widget['dbxref__version'] = array( '#type' => 'textfield', '#title' => t('Version'), '#default_value' => $version, '#maxlength' => array_key_exists('length', $schema['fields']['version']) ? $schema['fields']['version']['length'] : 255, '#size' => 5, ); $widget['dbxref__description'] = array( '#type' => 'textfield', '#title' => t('Description'), '#default_value' => $description, '#size' => 20, ); $widget['links'] = array( '#type' => 'item', '#markup' => l('Add a new database', 'admin/tripal/chado/tripal_db/add', array('attributes' => array('target' => '_blank'))) ); } /** * An Ajax callback for the tripal_chado_admin_publish_form.. */ function tripal_chado_dbxref_id_widget_form_ajax_callback($form, $form_state) { $field_name = $form_state['triggering_element']['#parents'][0]; $db_id = tripal_chado_get_field_form_values($field_name, $form_state, 0, 'dbxref__db_id'); $accession = tripal_chado_get_field_form_values($field_name, $form_state, 0, 'dbxref__accession'); if ($db_id and $accession) { $values = array( 'db_id' => $db_id, 'accession' => $accession, ); $options = array('is_duplicate' => TRUE); $has_duplicate = chado_select_record('dbxref', array('*'), $values, $options); if (!$has_duplicate) { drupal_set_message('The selected cross reference is new and will be added for future auto completions.'); } } return $form[$field_name]; } /** * Callback function for validating the tripal_chado_organism_select_widget. */ function tripal_chado_dbxref_id_widget_validate($element, &$form_state) { $field_name = $element['#parents'][0]; // If the form ID is field_ui_field_edit_form, then the user is editing the // field's values in the manage fields form of Drupal. We don't want // to validate it as if it were being used in a data entry form. if ($form_state['build_info']['form_id'] =='field_ui_field_edit_form') { return; } // Get the field values. $dbxref_id = tripal_chado_get_field_form_values($field_name, $form_state, 0, $field_name); $db_id = tripal_chado_get_field_form_values($field_name, $form_state, 0, "dbxref__db_id"); $accession = tripal_chado_get_field_form_values($field_name, $form_state, 0, "dbxref__accession"); $version = tripal_chado_get_field_form_values($field_name, $form_state, 0, "dbxref__version"); $description = tripal_chado_get_field_form_values($field_name, $form_state, 0, "dbxref__description"); // Make sure that if a database ID is provided that an accession is also // provided. Here we use the form_set_error function rather than the // form_error function because the form_error will add a red_highlight // around all of the fields in the fieldset which is confusing as it's not // clear to the user what field is required and which isn't. Therefore, // we borrow the code from the 'form_error' function and append the field // so that the proper field is highlighted on error. if (!$db_id and $accession) { form_set_error(implode('][', $element ['#parents']) . '][dbxref__db_id', t("A database and the accession must both be provided for the primary cross reference.")); } if ($db_id and !$accession) { form_set_error(implode('][', $element ['#parents']) . '][dbxref__accession', t("A database and the accession must both be provided for the primary cross reference.")); } if (!$db_id and !$accession and ($version or $description)) { form_set_error(implode('][', $element ['#parents']) . '][dbxref__db_id', t("A database and the accession must both be provided for the primary cross reference.")); } // If user did not select a database, we want to remove dbxref_id from the // field. if (!$db_id) { tripal_chado_set_field_form_values($field_name, $form_state, '__NULL__'); } // If the dbxref_id does not match the db_id + accession then the user // has selected a new dbxref record and we need to update the hidden // value accordingly. if ($db_id and $accession) { $dbxref = chado_generate_var('dbxref', array('db_id' => $db_id, 'accession' => $accession)); if ($dbxref and $dbxref->dbxref_id != $dbxref_id) { tripal_chado_set_field_form_values($field_name, $form_state, $dbxref->dbxref_id); } } } /** * Theme function for the dbxref_id_widget. * * @param $variables */ function theme_tripal_chado_dbxref_id_widget($variables) { $element = $variables['element']; $layout = "
"; $classes = array(); $classes[] = 'collapsible'; $theme_settings = $element['#theme_settings']; if ($theme_settings['#collapsed'] == TRUE) { $classes[] = 'collapsed'; } $fieldset = array( '#title' => $element['#title'], '#value' => '', '#description' => $element['#description'], '#children' => $layout, '#attributes' => array('class' => $classes), ); return theme('fieldset', array('element' => $fieldset)); } /** * Loads the field values with appropriate data. * * This function is called by the tripal_chado_field_storage_load() for * each property managed by the field_chado_storage storage type. This is * an optional hook function that is only needed if the field has * multiple form elements. * * @param $field * @param $entity * @param $base_table * @param $record */ function tripal_chado_dbxref_id_field_load($field, $entity, $base_table, $record) { $field_name = $field['field_name']; $field_type = $field['type']; $field_table = $field['settings']['chado_table']; $field_column = $field['settings']['chado_column']; // Set some defauls for the empty record $entity->{$field_name}['und'][0] = array( 'value' => '', 'dbxref__db_id' => '', 'dbxref__accession' => '', 'dbxref__version' => '', 'dbxref__description' => '', ); // Get the primary dbxref record. Because we have a dbxref_id passed in // by the base record, we will only have one record. $columns = array('*'); $match = array('dbxref_id' => $record->$field_column); $options = array('return_array' => TRUE); $records = chado_select_record('dbxref', $columns, $match, $options); if (count($records) > 0) { $dbxref = $records[0]; $entity->{$field_name}['und'][0] = array( 'value' => $dbxref->dbxref_id, 'dbxref__db_id' => $dbxref->db_id, 'dbxref__accession' => $dbxref->accession, 'dbxref__version' => $dbxref->version, 'dbxref__description' => $dbxref->description, ); } }