'local', // The name of the term. 'term_name' => 'property', // The unique ID (i.e. accession) of the term. 'term_accession' => 'property', // 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 table in Chado that the instance maps to. 'chado_table' => '', // The primary key column of hte table in Dhado. 'chado_column' => '', // The base table. 'base_table' => '', // The number of default rows to show. The default is 1. 'rows' => 1, ]; // The default widget for this field. public static $default_widget = 'chado_linker__prop_widget'; // The default formatter for this field. public static $default_formatter = 'chado_linker__prop_formatter'; // A boolean specifying that users should not be allowed to create // fields and instances of this field type through the UI. Such // fields can only be created programmatically with field_create_field() // and field_create_instance(). public static $no_ui = FALSE; /** * * @see TripalField::load() */ public function load($entity) { $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']; $vocabulary = $this->instance['settings']['term_vocabulary']; $accession = $this->instance['settings']['term_accession']; $cvterm = chado_get_cvterm([ 'dbxref_id' => [ 'db_id' => [ 'name' => $vocabulary, ], 'accession' => $accession, ], ]); $cvterm_id = $cvterm->cvterm_id; // 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]; // Set some defaults for the empty record. $chado_record = $entity->chado_record; $entity->{$field_name}['und'][0] = [ 'value' => '', 'chado-' . $field_table . '__' . $pkey => '', 'chado-' . $field_table . '__' . $fkey_lcolumn => $chado_record->$fkey_lcolumn, 'chado-' . $field_table . '__value' => '', 'chado-' . $field_table . '__type_id' => $cvterm_id, 'chado-' . $field_table . '__rank' => '', ]; // Get the properties associated with this record for the given type. $columns = ['*']; $match = [ $fkey_lcolumn => $chado_record->{$fkey_lcolumn}, 'type_id' => $cvterm_id, ]; $options = [ 'return_array' => TRUE, 'order_by' => ['rank' => 'ASC'], ]; $properties = chado_select_record($field_table, $columns, $match, $options); for ($i = 0; $i < count($properties); $i++) { $property = $properties[$i]; foreach ($schema['fields'] as $fname => $details) { $entity->{$field_name}['und'][$i] = [ 'value' => $property->value, 'chado-' . $field_table . '__' . $pkey => $property->$pkey, 'chado-' . $field_table . '__' . $fkey_lcolumn => $property->$fkey_lcolumn, 'chado-' . $field_table . '__value' => $property->value, 'chado-' . $field_table . '__type_id' => $property->type_id, 'chado-' . $field_table . '__rank' => $property->rank, ]; } } // Ensure there are no values if there are no properties. // This is necessary to make sure the field is not rendered when there are no properies. // @todo: We should revisit this in the future as none of the other fields do this. // It was added here to make it easier to detect when the field was empty // but in hindsight, we would just check $entity->{$field_name}['und'][$i]['value'] // in the formatter. if (empty($properties)) { unset($entity->{$field_name}); } } /** * @see ChadoField::query() */ public function query($query, $condition) { $prop_linker = $this->instance['settings']['chado_table']; $base_table = $this->instance['settings']['base_table']; $bschema = chado_get_schema($base_table); $bpkey = $bschema['primary key'][0]; $alias = $this->field['field_name']; $operator = $condition['operator']; $vocab = $this->instance['settings']['term_vocabulary']; $accession = $this->instance['settings']['term_accession']; $cvterm = chado_get_cvterm(['id' => $vocab . ':' . $accession]); $this->queryJoinOnce($query, $prop_linker, $alias, "base.$bpkey = $alias.$bpkey"); $query->condition("$alias.type_id", $cvterm->cvterm_id); $query->condition("$alias.value", $condition['value'], $operator); } /** * @see ChadoField::query() */ public function queryOrder($query, $order) { $prop_linker = $this->instance['settings']['chado_table']; $base_table = $this->instance['settings']['base_table']; $bschema = chado_get_schema($base_table); $bpkey = $bschema['primary key'][0]; $alias = $this->field['field_name']; $vocab = $this->instance['settings']['term_vocabulary']; $accession = $this->instance['settings']['term_accession']; $cvterm = chado_get_cvterm(['id' => $vocab . ':' . $accession]); $this->queryJoinOnce($query, $prop_linker, $alias, "base.$bpkey = $alias.$bpkey AND $alias.type_id = $cvterm->cvterm_id", "LEFT OUTER"); $query->orderBy("$alias.value", $order['direction']); } }