'local', // The name of the term. 'term_name' => 'contact', // The unique ID (i.e. accession) of the term. 'term_accession' => 'contact', // Set to TRUE if the site admin is allowed to change the term // type. This will create form elements when editing the field instance // to allow the site admin to change the term settings above. 'term_fixed' => FALSE, ]; // The default widget for this field. public static $default_widget = 'chado_linker__contact_widget'; // The default formatter for this field. public static $default_formatter = 'chado_linker__contact_formatter'; // -------------------------------------------------------------------------- // PROTECTED CLASS MEMBERS -- DO NOT OVERRIDE // -------------------------------------------------------------------------- // An array containing details about the field. The format of this array // is the same as that returned by field_info_fields() protected $field; // An array containing details about an instance of the field. A field does // not have to have an instance. But if dealing with an instance (such as // when using the widgetForm, formatterSettingsForm, etc.) it should be set. protected $instance; /** * @see TripalField::elements() */ public function elementInfo() { $field_term = $this->getFieldTermID(); $type_term = chado_get_semweb_term('contact', 'type_id'); $name_term = chado_get_semweb_term('contact', 'name'); $description_term = chado_get_semweb_term('contact', 'description'); return [ $field_term => [ 'operations' => ['eq', 'contains', 'starts'], 'sortable' => TRUE, 'searchable' => TRUE, 'type' => 'xs:complexType', 'readonly' => FALSE, 'elements' => [ $type_term => [ 'searchable' => TRUE, 'label' => 'Contact Type', 'help' => 'The type of contact', 'operations' => ['eq', 'ne', 'contains', 'starts'], 'sortable' => TRUE, 'type' => 'xs:string', 'readonly' => FALSE, 'required' => TRUE, ], $name_term => [ 'searchable' => TRUE, 'label' => 'Contact Name', 'help' => 'The name of the contact.', 'operations' => ['eq', 'ne', 'contains', 'starts'], 'sortable' => TRUE, 'type' => 'xs:string', 'readonly' => FALSE, 'required' => TRUE, ], $description_term => [ 'searchable' => TRUE, 'label' => 'Contact Description', 'help' => 'A descriptoin of the contact.', 'operations' => ['contains'], 'sortable' => TRUE, 'type' => 'xs:string', 'readonly' => TRUE, 'required' => FALSE, ], 'entity' => [ 'searchable' => FALSE, ], ], ], ]; } /** * * @see TripalField::load() */ public function load($entity) { $record = $entity->chado_record; $field_name = $this->field['field_name']; $field_type = $this->field['type']; $field_table = $this->instance['settings']['chado_table']; $field_column = $this->instance['settings']['chado_column']; $base_table = $this->instance['settings']['base_table']; $type_term = chado_get_semweb_term('contact', 'type_id'); $name_term = chado_get_semweb_term('contact', 'name'); $description_term = chado_get_semweb_term('contact', 'description'); // Get the FK that links to the base record. $schema = chado_get_schema($field_table); $pkey = $schema['primary key'][0]; if (!isset($schema['foreign keys'][$base_table]['columns'])) { return; } $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']); $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn]; // If we don't have a chado record return before creating a stub for this field! if (!$record) { return; } // Set some defaults for the empty record. $entity->{$field_name}['und'][0] = [ 'value' => [], 'chado-' . $field_table . '__' . $pkey => '', 'chado-' . $field_table . '__' . $fkey_lcolumn => $record->$fkey_lcolumn, 'chado-' . $field_table . '__' . 'contact_id' => '', // Ignore the synonym_sgml column for now. ]; $linker_table = $base_table . '_contact'; $options = [ 'return_array' => 1, 'include_fk' => [ 'contact_id' => [ 'type_id' => [ 'dbxref_id' => [ 'db_id' => TRUE, ], ], ], $fkey_lcolumn => TRUE, ], ]; $record = chado_expand_var($record, 'table', $linker_table, $options); $contact_linkers = $record->$linker_table; if ($contact_linkers) { foreach ($contact_linkers as $i => $contact_linker) { $contact = $contact_linker->contact_id; $entity->{$field_name}['und'][$i] = [ 'value' => [ $type_term => $contact->type_id ? $contact->type_id->name : '', $name_term => $contact->name, $description_term => $contact->description, ], // Add elements that are not part of the values but used by // the chado storage back-end for saving values. 'chado-' . $field_table . '__' . $pkey => $contact_linker->$pkey, 'chado-' . $field_table . '__' . $fkey_lcolumn => $record->$fkey_lcolumn, 'chado-' . $field_table . '__' . 'contact_id' => $contact->contact_id, ]; if (property_exists($contact, 'entity_id')) { $entity->{$field_name}['und'][$i]['value']['entity'] = 'TripalEntity:' . $contact->entity_id; } } } } /** * @see ChadoField::query() */ public function query($query, $condition) { $alias = $this->field['field_name']; $operator = $condition['operator']; $field_term_id = $this->getFieldTermID(); $type_term = chado_get_semweb_term('contact', 'type_id'); $name_term = chado_get_semweb_term('contact', 'name'); $description_term = chado_get_semweb_term('contact', 'description'); $contact_linker = $this->instance['settings']['chado_table']; $base_table = $this->instance['settings']['base_table']; // Get the FK that links to the base record. $schema = chado_get_schema($contact_linker); $pkey = $schema['primary key'][0]; $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']); $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn]; // Join the contact linker table and then join the contact table. $calias = $contact_linker . '_contact'; $this->queryJoinOnce($query, $contact_linker, $alias, "base.$fkey_rcolumn = $alias.$fkey_lcolumn"); $this->queryJoinOnce($query, 'contact', $calias, "$calias.contact_id = $alias.contact_id"); // Search by the contact name if ($condition['column'] == $field_term_id or $condition['column'] == $field_term_id . ',' . $name_term) { $query->condition("$calias.name", $condition['value'], $operator); } // Search on the contact description. if ($condition['column'] == $field_term_id . ',' . $description_term) { $query->condition("$calias.description", $condition['value'], $operator); } // Search on the contact type. if ($condition['column'] == $field_term_id . ',' . $type_term) { $talias = $contact_linker . '_contact_type'; $this->queryJoinOnce($query, 'cvterm', $talias, "$calias.type_id = $talias.cvterm_id"); $query->condition("$talias.name", $condition['value'], $operator); } } /** * @see ChadoField::queryOrder() */ public function queryOrder($query, $order) { $alias = $this->field['field_name']; $field_term_id = $this->getFieldTermID(); $type_term = chado_get_semweb_term('contact', 'type_id'); $name_term = chado_get_semweb_term('contact', 'name'); $description_term = chado_get_semweb_term('contact', 'description'); $contact_linker = $this->instance['settings']['chado_table']; $base_table = $this->instance['settings']['base_table']; // Get the FK that links to the base record. $schema = chado_get_schema($contact_linker); $pkey = $schema['primary key'][0]; $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']); $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn]; // Join the contact linker table and then join the contact table. $calias = $contact_linker . '_contact'; $this->queryJoinOnce($query, $contact_linker, $alias, "base.$fkey_rcolumn = $alias.$fkey_lcolumn", "LEFT OUTER"); $this->queryJoinOnce($query, 'contact', $calias, "$calias.contact_id = $alias.contact_id", "LEFT OUTER"); // Search by the contact name if ($order['column'] == $field_term_id or $order['column'] == $field_term_id . ',' . $name_term) { $query->orderBy("$calias.name", $order['direction']); } // Search on the contact description. if ($order['column'] == $field_term_id . ',' . $description_term) { $query->orderBy("$calias.description", $order['direction']); } // Search on the contact type. if ($order['column'] == $field_term_id . ',' . $type_term) { $talias = $contact_linker . '_contact_type'; $this->queryJoinOnce($query, 'cvterm', $talias, "$calias.type_id = $talias.cvterm_id", "LEFT OUTER"); $query->orderBy("$talias.name", $order['direction']); } } } /** * An Ajax callback for the pub widget. */ function chado_linker__contact_widget_form_ajax_callback($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 $variables */ function theme_chado_linker__contact_widget($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']; $layout = "
" . drupal_render($element['name']) . "
"; return $layout; }