ChadoField Class Reference

Inheritance diagram for ChadoField:

Collaboration diagram for ChadoField:

Public Member Functions
	query ($query, $condition)
	queryOrder ($query, $order)
	getValueList ($options=[], $keyword=NULL)
	instanceSettingsForm ()
Public Member Functions inherited from TripalField
	__construct ($field, $instance)
	getFieldName ()
	getField ()
	getInstance ()
	getFieldTerm ()
	getFieldTermID ()
	webServicesData ()
	viewsData ($view_base_id)
	validate ($entity_type, $entity, $langcode, $items, &$errors)
	load ($entity)
	elementInfo ()
	settingsForm ($has_data)
	settingsFormValidate ($form, &$form_state)
	settingsTheme ($element)
	instanceSettingsFormValidate ($form, &$form_state)
	createInstance ()

Static Public Attributes
static	$default_label = 'Chado Field'
static	$default_description = 'The generic base class for all Chado fields. Replace this text as appropriate for the child implementation.'
static	$default_settings
static	$default_instance_settings
static	$download_formatters
static	$module = 'tripal_chado'
Static Public Attributes inherited from TripalField
static	$default_label = 'Tripal Field'
static	$default_description = 'The generic base class for all Tripal fields. Replace this text as appropriate for the child implementation.'
static	$default_settings
static	$default_instance_settings
static	$download_formatters
static	$default_widget = ''
static	$default_formatter = ''
static	$module = 'tripal'
static	$no_ui = TRUE
static	$no_data = FALSE

Protected Member Functions
	queryJoinOnce ($query, $table, $alias, $condition, $type='INNER')
Protected Member Functions inherited from TripalField
	_addWebServiceElement (&$searchable_keys, &$sortable_keys, $parent_term_name, $parent_term, $element_name, $element_details)
	_addViewsDataElement (&$data, $view_base_id, $parent, $element_name, $element_details)

Additional Inherited Members
Static Public Member Functions inherited from TripalField
static	info ()
Protected Attributes inherited from TripalField
	$field
	$instance
	$term

Member Function Documentation

getValueList()

ChadoField::getValueList	(		$options = [],
			$keyword = NULL
	)

Used to retrieve a distinct list of values already used for the current field instance.

Parameters

$keyword	A string option used to filter the distinct list. This is used when creating an autocomplete. For all distinct values, set this to NULL.
$options	An array where options for how to generate this list can be specified. Supported options include: limit: how many results to limit to (Default: 25) label_string: a string with tokens that should be used to generate the human-readable values in the returned list.

The following example shows you how to pull all the value list for a specific instance of a field.

// In this example we want the values for the obi__organism field
// attached to the Tripal Content Type with a machine name of bio_data_17:
$field_name = 'obi__organism';
$bundle_name = 'bio_data_17';
 
// The following two calls get information about the field we want the
  values for.
$field_info = field_info_field($field_name);
$instance_info = field_info_instance('TripalEntity', $field_name,
  $bundle_name);
// Construct the Field instance we want the values for.
$instance = new ChadoField($field_info, $instance_info);
 
// Retrieve the values.
// $values will be an array containing the distinct set of values for this
  field instance.
$values = $instance->getValueList();

Returns

An array of values.

Reimplemented from TripalField.

instanceSettingsForm()

ChadoField::instanceSettingsForm

(

)

See also

TripalField::instanceSettingsForm()

Reimplemented from TripalField.

Reimplemented in so__transcript, schema__additional_type, sbo__relationship, and obi__organism.

query()

ChadoField::query	(		$query,
			$condition
	)

See also

TripalField::query()

In addition to the rules to follow for the TripalField::query function these should also be followed for the ChadoField::query implementation.

• When giving alias to joined tables be sure to use aliases that are unique to avoid conflicts with other fields.
• When joining with the base table its alias is 'base'.
• You may join to materialized views if need be to help speed queries.

Reimplemented from TripalField.

Reimplemented in uo__unit, taxrank__infraspecific_taxon, sio__vocabulary, sio__annotation, sep__protocol, schema__alternate_name, schema__additional_type, sbo__relationship, sbo__database_cross_reference, operation__analysis, ogi__location_on_map, obi__organism, local__source_data, local__contact, efo__array_design, data__sequence_coordinates, data__accession, chado_linker__prop, and chado_linker__contact.

queryJoinOnce()

ChadoField::queryJoinOnce (   $query,   $table,   $alias,   $condition,   $type = 'INNER'  )

protected

A convient way to join a table to a query without duplicates.

Parameters

$query	The SelectQuery object.
$table	The table to join.
$alias	The table alias to use.
$condition	The join condition.
$type	The type of join: INNER, LEFT OUTER, or RIGHT OUTER.

queryOrder()

ChadoField::queryOrder	(		$query,
			$order
	)

See also

TripalField::queryOrder()

Reimplemented from TripalField.

Reimplemented in uo__unit, taxrank__infraspecific_taxon, sio__vocabulary, sio__annotation, sep__protocol, schema__alternate_name, schema__additional_type, sbo__relationship, sbo__database_cross_reference, operation__analysis, ogi__location_on_map, obi__organism, local__source_data, local__contact, efo__array_design, data__sequence_coordinates, data__accession, chado_linker__prop, and chado_linker__contact.

Member Data Documentation

$default_instance_settings

ChadoField::$default_instance_settings

static

Initial value:

= [
    
    'term_vocabulary' => 'schema',
    
    'term_name' => 'Thing',
    
    'term_accession' => 'Thing',
    
    
    
    'term_fixed' => FALSE,
    
    'chado_table' => '',
    
    'chado_column' => '',
    
    'base_table' => '',
  ]

$default_settings

ChadoField::$default_settings

static

Initial value:

= [
    'storage' => 'field_chado_storage',
  ]

$download_formatters

ChadoField::$download_formatters

static

Initial value:

= [
    'TripalTabDownloader',
    'TripalCSVDownloader',
  ]

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The documentation for this class was generated from the following file:

• tripal_chado/includes/TripalFields/ChadoField.inc