t('Synonyms'),
'description' => t('Adds an alternative name (synonym or alias) to this record.'),
'default_widget' => 'chado_linker__synonym_widget',
'default_formatter' => 'chado_linker__synonym_formatter',
'settings' => array(),
'storage' => array(
'type' => 'field_chado_storage',
'module' => 'tripal_chado',
'active' => TRUE
),
);
}
/**
* @see TripalField::attach_info()
*/
function attach_info($entity_type, $bundle, $target) {
$field_info = array();
$table_name = $target['data_table'];
$type_table = $target['type_table'];
$type_field = $target['field'];
$cv_id = $target['cv_id'];
$cvterm_id = $target['cvterm_id'];
// If the linker table does not exists then we don't want to add attach.
$syn_table = $table_name . '_synonym';
if (!chado_table_exists($syn_table)) {
return $field_info;
}
$schema = chado_get_schema($syn_table);
$pkey = $schema['primary key'][0];
// Initialize the field array.
$field_info = array(
'field_name' => $table_name . '__synonym',
'field_type' => 'chado_linker__synonym',
'widget_type' => 'chado_linker__synonym_widget',
'widget_settings' => array('display_label' => 1),
'description' => '',
'label' => 'Synonyms',
'is_required' => 0,
'cardinality' => FIELD_CARDINALITY_UNLIMITED,
'storage' => 'field_chado_storage',
'field_settings' => array(
'chado_table' => $syn_table,
'chado_column' => $pkey,
'base_table' => $table_name,
'semantic_web' => array(
'name' => 'alternateName',
'accession' => 'alternateName',
'ns' => 'schema',
'nsurl' => 'https://schema.org/',
),
),
);
return $field_info;
}
/**
* @see TripalField::widget_info()
*/
function widget_info() {
return array(
'label' => t('Synonyms'),
'field types' => array('chado_linker__synonym'),
);
}
/**
* @see TripalField::formatter_info()
*/
function formatter_info() {
return array(
'label' => t('Synonyms'),
'field types' => array('chado_linker__synonym'),
'settings' => array(
),
);
}
/**
* @see TripalField::formatter_view()
*/
function formatter_view(&$element, $entity_type, $entity, $field,
$instance, $langcode, $items, $display) {
$chado_table = $field['settings']['chado_table'];
foreach ($items as $delta => $item) {
if ($item[$chado_table . '__synonym_id']) {
$synonym = chado_generate_var('synonym', array('synonym_id' => $item[$chado_table . '__synonym_id']));
$name = $synonym->name;
if ($synonym->type_id->name != 'exact') {
$name .= ' (' . $synonym->type_id->name . ')';
}
$element[$delta] = array(
'#type' => 'markup',
'#markup' => $name,
);
}
}
}
/**
* @see TripalField::widget_form()
*/
function widget_form(&$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;
$synonym_id = '';
$pub_id = '';
$is_current = TRUE;
$is_internal = FALSE;
$syn_name = '';
$syn_type = '';
// 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]['value'];
$fkey_value = $items[$delta][$table_name . '__' . $fkey];
$synonym_id = $items[$delta][$table_name . '__synonym_id'];
$pub_id = $items[$delta][$table_name . '__pub_id'];
$is_current = $items[$delta][$table_name . '__is_current'];
$is_internal = $items[$delta][$table_name . '__is_internal'];
$syn_name = $items[$delta][$table_name . '--synonym__name'];
$syn_type = $items[$delta][$table_name . '--synonym__type_id'];
}
// 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);
$fkey_value = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__' . $fkey);
$synonym_id = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__synonym_id');
$pub_id = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__pub_id');
$is_current = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__is_current');
$is_internal = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__is_internal');
$syn_name = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '--synonym__name');
$syn_type = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '--synonym__type_id');
}
// Get the synonym type terms. There shouldn't be too many.
$cv = tripal_get_default_cv('synonym', 'type_id');
$options = tripal_get_cvterm_select_options($cv->cv_id);
// Get the schema for the synonym table so we can make sure we limit the
// size of the name field to the proper size.
$schema = chado_get_schema('synonym');
$widget['#table_name'] = $table_name;
$widget['#fkey_field'] = $fkey;
$widget['#element_validate'] = array('chado_linker__synonym_widget_validate');
$widget['#theme'] = 'chado_linker__synonym_widget';
$widget['#prefix'] = "";
$widget['#suffix'] = "";
$widget['value'] = array(
'#type' => 'value',
'#default_value' => $record_id,
);
$widget[$table_name . '__' . $fkey] = array(
'#type' => 'value',
'#default_value' => $fkey_value,
);
$widget[$table_name . '--synonym__type_id'] = array(
'#type' => 'select',
'#title' => t('Type'),
'#options' => $options,
'#default_value' => $syn_type,
);
$widget[$table_name . '--synonym__name'] = array(
'#type' => 'textfield',
'#title' => t('Synonym Name'),
'#default_value' => $syn_name,
'#size' => 25,
);
$widget[$table_name . '__is_current'] = array(
'#type' => 'checkbox',
'#title' => t('Is Current'),
'#default_value' => $is_current,
'#required' => $element['#required'],
);
$widget[$table_name . '__is_internal'] = array(
'#type' => 'checkbox',
'#title' => t('Is Internal'),
'#default_value' => $is_internal,
'#required' => $element['#required'],
);
}
/**
* @see TripalField::load()
*/
function load($field, $entity, $details) {
$record = $details['record'];
$base_table = $field['settings']['base_table'];
$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' => '',
$field_table . '__' . $fkey_lcolumn => '',
$field_table . '__' . 'synonym_id' => '',
$field_table . '__' . 'pub_id' => '',
$field_table . '__' . 'is_current' => TRUE,
$field_table . '__' . 'is_internal' => '',
$field_table . '--' . 'synonym__name' => '',
$field_table . '--' . 'synonym__type_id' => '',
// Ignore the synonym_sgml column for now.
);
$linker_table = $base_table . '_synonym';
$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) {
$synonym = $linker->synonym_id;
$entity->{$field_name}['und'][$i] = array(
'value' => $linker->$pkey,
$field_table . '__' . $fkey_lcolumn => $linker->$fkey_lcolumn->$fkey_lcolumn,
$field_table . '__' . 'synonym_id' => $synonym->synonym_id,
$field_table . '__' . 'pub_id' => $linker->pub_id->pub_id,
$field_table . '__' . 'is_current' => $linker->is_current,
$field_table . '__' . 'is_internal' => $linker->is_internal,
$field_table . '--' . 'synonym__name' => $synonym->name,
$field_table . '--' . 'synonym__type_id' => $synonym->type_id->cvterm_id,
);
$i++;
}
}
}
}
/**
* Theme function for the synonym widget.
*
* @param $variables
*/
function theme_chado_linker__synonym_widget($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 = "
";
return $layout;
}
/**
* Callback function for validating the chado_linker__synonym_widget.
*/
function chado_linker__synonym_widget_validate($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);
$synonym_id = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__synonym_id');
$pub_id = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__pub_id');
$is_current = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__is_current');
$is_internal = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__is_internal');
$syn_name = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '--synonym__name');
$syn_type = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '--synonym__type_id');
// Make sure that if a synonym is provided that a type is also
// provided.
if ($syn_name and !$syn_type) {
form_set_error(implode('][', $element ['#parents']) . '][' . $table_name . '--synonym__type_id', t("Please set a synonym type."));
}
if (!$syn_name and $syn_type) {
form_set_error(implode('][', $element ['#parents']) . '][' . $table_name . '--synonym__name', t("Please set a synonym name."));
}
// If the user provided a cv_id and a name then we want to set the
// foreign key value to be the chado_record_idd
if ($syn_name and $syn_type) {
// Get the synonym. If one with the same name and type is already present
// then use that. Otherwise, insert a new one.
if (!$synonym_id) {
$synonym = chado_generate_var('synonym', array('name' => $syn_name, 'type_id' => $syn_type));
if (!$synonym) {
$synonym = chado_insert_record('synonym', array(
'name' => $syn_name,
'type_id' => $syn_type,
'synonym_sgml' => '',
));
$synonym = (object) $synonym;
}
// Set the synonym_id and FK value
tripal_chado_set_field_form_values($field_name, $form_state, $synonym->synonym_id, $delta, $table_name . '__synonym_id');
$fkey_value = $element['#entity']->chado_record_id;
tripal_chado_set_field_form_values($field_name, $form_state, $fkey_value, $delta, $table_name . '__' . $fkey);
}
if (!$pub_id) {
$pub = chado_generate_var('pub', array('uniquename' => 'null'));
tripal_chado_set_field_form_values($field_name, $form_state, $pub->pub_id, $delta, $table_name . '__pub_id');
}
}
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, $table_name . '__synonym_id');
tripal_chado_set_field_form_values($field_name, $form_state, '', $delta, $table_name . '__is_internal');
tripal_chado_set_field_form_values($field_name, $form_state, '', $delta, $table_name . '__is_current');
}
}
/**
* An Ajax callback for the synonym widget.
*/
function chado_linker__synonym_widget_form_ajax_callback($form, $form_state) {
$field_name = $form_state['triggering_element']['#parents'][0];
$delta = $form_state['triggering_element']['#parents'][2];
return $form[$field_name]['und'][$delta];
}