class taxrank__infraspecific_taxon
Hierarchy
- class \TripalField
- class \ChadoField
- class \taxrank__infraspecific_taxon
- class \ChadoField
Expanded class hierarchy of taxrank__infraspecific_taxon
4 string references to 'taxrank__infraspecific_taxon'
- taxrank__infraspecific_taxon_formatter.inc in tripal_chado/
includes/ TripalFields/ taxrank__infraspecific_taxon/ taxrank__infraspecific_taxon_formatter.inc - taxrank__infraspecific_taxon_widget.inc in tripal_chado/
includes/ TripalFields/ taxrank__infraspecific_taxon/ taxrank__infraspecific_taxon_widget.inc - tripal_chado_bundle_fields_info_custom in tripal_chado/
includes/ tripal_chado.fields.inc - tripal_chado_bundle_instances_info_custom in tripal_chado/
includes/ tripal_chado.fields.inc - Helper function for the hook_create_tripalfield_instance().
File
- tripal_chado/
includes/ TripalFields/ taxrank__infraspecific_taxon/ taxrank__infraspecific_taxon.inc, line 3
View source
class taxrank__infraspecific_taxon extends ChadoField {
// --------------------------------------------------------------------------
// EDITABLE STATIC CONSTANTS
//
// The following constants SHOULD be set for each descendent class. They are
// used by the static functions to provide information to Drupal about
// the field and it's default widget and formatter.
// --------------------------------------------------------------------------
// The default lable for this field.
public static $default_label = 'Infraspecific Taxon';
// The default description for this field.
public static $description = 'Specifies the infraspecific taxon of an organism.';
// Provide a list of instance specific settings. These can be access within
// the instanceSettingsForm. When the instanceSettingsForm is submitted
// then Drupal with automatically change these settings for the instnace.
// It is recommended to put settings at the instance level whenever possible.
// If you override this variable in a child class be sure to replicate the
// term_name, term_vocab, term_accession and term_fixed keys as these are
// required for all TripalFields.
public static $default_instance_settings = array(
// The short name for the vocabulary (e.g. shcema, SO, GO, PATO, etc.).
'term_vocabulary' => 'TAXRANK',
// The name of the term.
'term_name' => 'infraspecific_taxon',
// The unique ID (i.e. accession) of the term.
'term_accession' => '0000046',
// 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 = 'HERE_widget';
// The default formatter for this field.
public static $default_formatter = 'HERE_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::elementInfo()
*/
public function elementInfo() {
$field_term = $this->getFieldTermID();
$label_term = 'rdfs:label';
$infraspecific_name_term = chado_get_semweb_term('organism', 'infraspecific_name');
$infraspecific_type_term = chado_get_semweb_term('organism', 'type_id');
return array(
$field_term => array(
'sortable' => FALSE,
'searchable' => TRUE,
'readonly' => FALSE,
'type' => 'xs:complexType',
'elements' => array(
$label_term => array(
'name' => 'label',
'sortable' => FALSE,
'searchable' => TRUE,
'label' => 'Infraspecific Full Name',
'help' => 'The full infraspecific name including the rank and name.',
'type' => 'xsstring',
'readonly' => TRUE,
'required' => FALSE,
),
$infraspecific_name_term => array(
'name' => 'infraspecific_name',
'sortable' => TRUE,
'searchable' => TRUE,
'label' => 'Infraspecies Name',
'help' => 'The infraspecific name of the organism below the rank of species.',
'type' => 'xs:string',
'readonly' => FALSE,
'required' => TRUE,
),
$infraspecific_type_term => array(
'name' => 'infraspecific_rank',
'sortable' => TRUE,
'searchable' => TRUE,
'label' => 'Infraspecific Rank',
'help' => 'The infraspecific rank of the organism below the rank of species.',
'type' => 'xs:string',
'readonly' => FALSE,
'required' => TRUE,
),
),
),
);
}
/**
* @see ChadoField::query()
*/
public function query($query, $condition) {
$alias = $this->field['field_name'];
$operator = $condition['operator'];
$field_term_id = $this->getFieldTermID();
$label_term = $field_term_id . ',' . 'rdfs:label';
$infraspecific_name_term = $field_term_id . ',' . chado_get_semweb_term('organism', 'infraspecific_name');
$infraspecific_type_term = $field_term_id . ',' . chado_get_semweb_term('organism', 'type_id');
if ($condition['column'] == $label_term or $condition['column'] == $field_term_id) {
$this->queryJoinOnce($query, 'cvterm', $alias . '_cvterm', $alias . "_cvterm.cvterm_id = base.type_id");
$query->where("CONCAT(" . $alias . "_cvterm.name, ' ', base.infraspecific_name) $operator :full_name", array(':full_name' => $condition['value']));
}
if ($condition['column'] == $infraspecific_name_term) {
$query->condition('base.infraspecific_name', $condition['value'], $operator);
}
if ($condition['column'] == $infraspecific_type_term) {
$this->queryJoinOnce($query, 'cvterm', $alias . '_cvterm', $alias . "_cvterm.cvterm_id = base.type_id");
$query->condition($alias . '_cvterm.name', $condition['value'], $operator);
}
}
/**
* @see ChadoField::queryOrder()
*/
public function queryOrder($query, $order) {
$alias = $this->field['field_name'];
$field_term_id = $this->getFieldTermID();
$label_term = $field_term_id . ',' . 'rdfs:label';
$infraspecific_name_term = $field_term_id . ',' . chado_get_semweb_term('organism', 'infraspecific_name');
$infraspecific_type_term = $field_term_id . ',' . chado_get_semweb_term('organism', 'type_id');
if ($order['column'] == $infraspecific_name_term) {
$query->orderBy('base.infraspecific_name', $order['direction']);
}
if ($order['column'] == $infraspecific_type_term) {
$this->queryJoinOnce($query, 'cvterm', $alias . '_cvterm', $alias . "_cvterm.cvterm_id = base.type_id", "LEFT OUTER");
$query->orderBy($alias . '_cvterm.name', $order['direction']);
}
}
/**
*
* @see TripalField::load()
*/
public function load($entity) {
$record = $entity->chado_record;
$settings = $this->field['settings'];
$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'];
$entity->{$field_name}['und'][0]['value'] = '';
if (chado_get_version() < 1.3) {
return;
}
$label_term = 'rdfs:label';
$infraspecific_name_term = chado_get_semweb_term('organism', 'infraspecific_name');
$infraspecific_type_term = chado_get_semweb_term('organism', 'type_id');
// Set some defaults for the empty record.
$entity->{$field_name}['und'][0] = array(
'value' => array(),
'chado-organism__infraspecific_name' => '',
'chado-organism__type_id' => '',
);
if ($record->infraspecific_name) {
$label = $record->type_id->name . ' ' . $record->infraspecific_name;
$entity->{$field_name}['und'][0]['value'][$label_term] = $label;
$entity->{$field_name}['und'][0]['value'][$infraspecific_name_term] = $record->infraspecific_name;
$entity->{$field_name}['und'][0]['chado-organism__infraspecific_name'] = $record->infraspecific_name;
}
if ($record->type_id) {
$entity->{$field_name}['und'][0]['value'][$infraspecific_type_term] = $record->type_id->name;
$entity->{$field_name}['und'][0]['chado-organism__type_id'] = $record->type_id->cvterm_id;
}
}
}