<?php
class chado_base__dbxref_id extends TripalField {
/**
* @see TripalField::field_info()
*/
function field_info() {
return 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' => 'chado_base__dbxref_id_widget',
'default_formatter' => 'chado_base__dbxref_id_formatter',
'settings' => array(),
'storage' => array(
'type' => 'field_chado_storage',
'module' => 'tripal_chado',
'active' => TRUE
),
);
}
/**
* @see TripalField::attach_info()
*/
function attach_info($entity_type, $bundle, $settings) {
$field_info = array();
$table_name = $settings['data_table'];
$type_table = $settings['type_table'];
$type_field = $settings['field'];
$cv_id = $settings['cv_id'];
$cvterm_id = $settings['cvterm_id'];
// Check the schema for the data table if it does not have
// a 'dbxref_id' column then we don't want to attach this field.
$schema = chado_get_schema($table_name);
if (!array_key_exists('dbxref_id', $schema['fields'])) {
return $field_info;
}
// There is an dbxref_id column so attach the field!
$field_info = array(
'field_name' => $table_name . '__dbxref_id',
'field_type' => 'chado_base__dbxref_id',
'widget_type' => 'chado_base__dbxref_id_widget',
'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".',
'label' => 'Cross Reference',
'is_required' => 0,
'storage' => 'field_chado_storage',
'widget_settings' => array(
'display_label' => 1
),
'field_settings' => array(
'chado_table' => $table_name,
'chado_column' => 'dbxref_id',
'semantic_web' => array(
'name' => '',
'accession' => '',
'ns' => '',
'nsurl' => '',
),
),
);
return $field_info;
}
/**
* @see TripalField::widget_info()
*/
function widget_info() {
return array(
'label' => t('Cross reference'),
'field types' => array('chado_base__dbxref_id'),
'description' => t('This record can be cross referenced with a record in
another online database. This field is intended for the most
prominent reference. At a minimum, the database and accession
must be provided.'),
);
}
/**
* @see TripalField::formatter_info()
*/
function formatter_info() {
return array(
'label' => t('Database Cross Reference'),
'field types' => array('chado_base__dbxref_id'),
'settings' => array(
),
);
}
/**
* @see TripalField::formatter_view()
*/
function formatter_view(&$element, $entity_type, $entity, $field,
$instance, $langcode, $items, $display) {
$record = $entity->chado_record;
foreach ($items as $delta => $item) {
$accession = '';
if ($item['value']) {
$dbxref = $record->dbxref_id;
$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' => $accession,
);
}
}
/**
* @see TripalField::widget_form()
*/
function widget_form(&$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('chado_base__dbxref_id_widget_validate');
$widget['#theme'] = 'chado_base__dbxref_id_widget';
$widget['#prefix'] = "<span id='$field_name-dbxref--db-id'>";
$widget['#suffix'] = "</span>";
// 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' => 'chado_base__dbxref_id_widget',
//'#collapsible' => TRUE,
//'#collapsed' => $collapsed,
);
$widget['value'] = array(
'#type' => 'value',
'#default_value' => $dbxref_id,
);
$widget['dbxref__db_id'] = array(
'#type' => 'select',
'#title' => t('Database'),
'#options' => $options,
'#required' => $element['#required'],
'#default_value' => $db_id,
'#ajax' => array(
'callback' => "chado_base__dbxref_id_widget_form_ajax_callback",
'wrapper' => "$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/storage/chado/auto_name/dbxref/' . $db_id,
'#ajax' => array(
'callback' => "tripal_chado_dbxref_widget_form_ajax_callback",
'wrapper' => "$field_name-dbxref--db-id",
'effect' => 'fade',
'method' => 'replace'
),
'#disabled' => $db_id ? FALSE : TRUE,
);
$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,
'#disabled' => $db_id ? FALSE : TRUE,
);
$widget['dbxref__description'] = array(
'#type' => 'textfield',
'#title' => t('Description'),
'#default_value' => $description,
'#size' => 20,
'#disabled' => $db_id ? FALSE : TRUE,
);
$widget['links'] = array(
'#type' => 'item',
'#markup' => l('Add a new database', 'admin/tripal/chado/tripal_db/add', array('attributes' => array('target' => '_blank')))
);
}
/**
* @see TripalField::load()
*/
function load($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'];
// 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 (if it's not NULL). Because we have a
// dbxref_id passed in by the base record, we will only have one record.
if ($record->$field_column) {
$columns = array('*');
$match = array('dbxref_id' => $record->$field_column->$field_column);
$options = array('return_array' => TRUE);
$dbxrefs = chado_select_record('dbxref', $columns, $match, $options);
if (count($dbxrefs) > 0) {
$dbxref = $dbxrefs[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' => $dbxref->description,
);
}
}
}
}
/**
* Callback function for validating the tripal_chado_dbxref_select_widget.
*/
function chado_base__dbxref_id_widget_validate($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, $dbxref->dbxref_id);
}
}
}
/**
* An Ajax callback for the tripal_chado_admin_publish_form..
*/
function chado_base__dbxref_id_widget_form_ajax_callback($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];
}
function theme_chado_base__dbxref_id_widget($variables) {
$element = $variables['element'];
$layout = "
<div class=\"primary-dbxref-widget\">
<div class=\"primary-dbxref-widget-item\">" .
drupal_render($element['dbxref__db_id']) . "
</div>
<div class=\"primary-dbxref-widget-item\">" .
drupal_render($element['dbxref__accession']) . "
</div>
<div class=\"primary-dbxref-widget-item\">" .
drupal_render($element['dbxref__version']) . "
</div>
<div class=\"primary-dbxref-widget-item\">" .
drupal_render($element['dbxref__description']) . "
</div>
<div class=\"primary-dbxref-widget-links\">" . drupal_render($element['links']) . "</div>
</div>
";
// $classes = array();
// $classes[] = 'collapsible';
// $theme_settings = $element['#theme_settings'];
// if ($theme_settings['#collapsed'] == FALSE) {
// $classes[] = 'collapsed';
// }
$fieldset = array(
'#title' => $element['#title'],
'#value' => '',
'#description' => $element['#description'],
'#children' => $layout,
// '#attributes' => array('class' => $classes),
);
return theme('fieldset', array('element' => $fieldset));
}