class sep__protocol
@class Purpose: Provide a field for Protocol (typically the protocol_id column of a Chado table).
Data: Assumptions:
Hierarchy
- class \TripalField
- class \ChadoField
- class \sep__protocol
- class \ChadoField
Expanded class hierarchy of sep__protocol
4 string references to 'sep__protocol'
- sep__protocol_formatter.inc in tripal_chado/
includes/ TripalFields/ sep__protocol/ sep__protocol_formatter.inc - sep__protocol_widget.inc in tripal_chado/
includes/ TripalFields/ sep__protocol/ sep__protocol_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/ sep__protocol/ sep__protocol.inc, line 11
View source
class sep__protocol extends ChadoField {
// The default label for this field.
public static $default_label = 'Protocol';
// The default description for this field.
public static $default_description = 'The protocol followed to generate this resource.';
// The default widget for this field.
public static $default_widget = 'sep__protocol_widget';
// The default formatter for this field.
public static $default_formatter = 'sep__protocol_formatter';
// The module that manages this field.
public static $module = 'tripal_chado';
// A list of global settings. These can be accessed within the
// globalSettingsForm. When the globalSettingsForm is submitted then
// Drupal will automatically change these settings for all fields.
// Once instances exist for a field type then these settings cannot be
// changed.
public static $default_settings =[
'storage' 'field_chado_storage'
// It is expected that all fields set a 'value' in the load() function.
// In many cases, the value may be an associative array of key/value pairs.
// In order for Tripal to provide context for all data, the keys should
// be a controlled vocabulary term (e.g. rdfs:type). Keys in the load()
// function that are supported by the query() function should be
// listed here.
'searchable_keys'[]
];
// 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 instance.
// 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 =[
// The DATABASE name, as it appears in chado.db. This also builds the link-out url. In most cases this will simply be the CV name. In some cases (EDAM) this will be the SUBONTOLOGY.
'term_vocabulary' 'sep'
// The name of the term.
'term_name' 'protocol'
// The unique ID (i.e. accession) of the term.
'term_accession' '00101'
// Set to TRUE if the site admin is not allowed to change the term
// type, otherwise the admin can change the term mapped to a field.
'term_fixed' FALSE
// Indicates if this field should be automatically attached to display
// or web services or if this field should be loaded separately. This
// is convenient for speed. Fields that are slow should for loading
// should have auto_attach set to FALSE so tha their values can be
// attached asynchronously.
'auto_attach' FALSE
];
// 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;
// A boolean specifying that the field will not contain any data. This
// should exclude the field from web services or downloads. An example
// could be a quick search field that appears on the page that redirects
// the user but otherwise provides no data.
public static $no_data = FALSE;
/**
* Loads the field values from the underlying data store.
*
* @param $entity
*
* @return
* An array of the following format:
* $entity->{$field_name}['und'][0]['value'] = $value;
* where:
* - $entity is the entity object to which this field is attached.
* - $field_name is the name of this field
* - 'und' is the language code (in this case 'und' == undefined)
* - 0 is the cardinality. Increment by 1 when more than one item is
* available.
* - 'value' is the key indicating the value of this field. It should
* always be set. The value of the 'value' key will be the contents
* used for web services and for downloadable content. The value
* should be of the follow format types: 1) A single value (text,
* numeric, etc.) 2) An array of key value pair. 3) If multiple entries
* then cardinality should incremented and format types 1 and 2 should
* be used for each item.
* The array may contain as many other keys at the same level as 'value'
* but those keys are for internal field use and are not considered the
* value of the field.
*
*
*/
public function load($entity) {
parent::load($entity);
$record = $entity->chado_record;
$settings = $this->instance['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'];
$linker_field = 'chado-' . $field_table . '__protocol_id';
// Set some defaults for the empty record.
$entity->{$field_name}['und'][0] =[
'value'[]
];
if (!$record->protocol_id->protocol_id) {
return;
}
$protocol_id = $record->protocol_id->protocol_id;
$protocol_name = $record->protocol_id->name;
$entity_id = $record->entity_id;
$entity->{$field_name}['und'][0]['value'] =[
"protocol_id" $protocol_id
"protocol_name" $protocol_name
"entity_id" $entity_id
];
// Is there a published entity for this protocol?
if (property_exists($record->{$field_column}, 'entity_id')) {
$entity->{$field_name}['und'][0]['value']['entity_id'] = 'TripalEntity:' . $record->{$field_column}->entity_id;
}
}
}
Members
Name | Modifiers | Type | Description |
---|---|---|---|
ChadoField:: |
public static | property |
Overrides TripalField:: |
ChadoField:: |
public | function |
Overrides TripalField:: |
ChadoField:: |
public | function |
In addition to the rules to follow for the TripalField::query function
these should also be followed for the ChadoField::query implementation. Overrides TripalField:: |
ChadoField:: |
protected | function | A convient way to join a table to a query without duplicates. |
ChadoField:: |
public | function |
Overrides TripalField:: |
sep__protocol:: |
public static | property |
Overrides ChadoField:: |
sep__protocol:: |
public static | property |
Overrides TripalField:: |
sep__protocol:: |
public static | property |
Overrides ChadoField:: |
sep__protocol:: |
public static | property |
Overrides ChadoField:: |
sep__protocol:: |
public static | property |
Overrides ChadoField:: |
sep__protocol:: |
public static | property |
Overrides TripalField:: |
sep__protocol:: |
public static | property |
Overrides ChadoField:: |
sep__protocol:: |
public static | property |
Overrides TripalField:: |
sep__protocol:: |
public static | property |
Overrides TripalField:: |
sep__protocol:: |
public | function |
Loads the field values from the underlying data store. Overrides TripalField:: |
TripalField:: |
protected | property | |
TripalField:: |
protected | property | |
TripalField:: |
protected | property | |
TripalField:: |
public | function | After a field instance is created the following function is run. |
TripalField:: |
public | function | Provides the list of elements returned by the 'value' of the field. |
TripalField:: |
public | function | |
TripalField:: |
public | function | Retrives the name of this field. |
TripalField:: |
public | function | |
TripalField:: |
public | function | |
TripalField:: |
public | function | |
TripalField:: |
protected | function | When constructing a pager for use by a field, all pagers must have a unique ID |
TripalField:: |
public static | function | Provides default information about this field type |
TripalField:: |
public | function | Provides validation of the instance settings form. |
TripalField:: |
public | function | Provides a form for the 'Field Settings' of the field management page. |
TripalField:: |
public | function | _state |
TripalField:: |
public | function | Perform validation of the field regardless how it is updated. |
TripalField:: |
public | function | Describes this field to Views. |
TripalField:: |
public | function | Describes this field to Tripal web services. |
TripalField:: |
protected | function | |
TripalField:: |
protected | function | |
TripalField:: |
public | function | Instantiates a new TripalField object. |