Drupal\tripal\Services\TripalEntityLookup Class Reference

Public Member Functions
	getRenderableItem ($displayed_string, $entity_id)
	getEntityId ($record_id, $termIdSpace, $termAccession, $base_table=NULL, $entity_type='tripal_entity')
	getBundleLabel (int $entity_id, string $entity_type='tripal_entity')
	getPublishedEntityIds ($bundle_id, $entity_type='tripal_entity')

Protected Member Functions
	getBundleFromCvTerm ($termIdSpace, $termAccession)
	getBundles (string $base_table)
	getEntityIdFromRecordId ($record_id, $bundle_id, $entity_type)
	getRequiredFields ($bundle_id, $entity_type)

Protected Attributes
array	$bundle_base_table_cache = []
array	$bundle_label_cache = []

Detailed Description

This class provides functions to assist with finding a Drupal entity that corresponds to a Chado record.

The two public functions defined here are: getEntityId() which looks up a Drupal entity id from a Chado record id getRenderableItem() is a helper function for field formatters, it will handle converting an entity_id into a render array element.

Member Function Documentation

getBundleFromCvTerm()

Drupal\tripal\Services\TripalEntityLookup::getBundleFromCvTerm (   $termIdSpace,   $termAccession  )

protected

Retrieve a Tripal bundle id based on its CV term.

Parameters

string	$termIdSpace	The bundle's CV Term namespace e.g. "NCIT"
string	$termAccession	The bundle's CV term accession e.g. "C47954"

Returns

string|null The bundle id, or null if no match found.

getBundleLabel()

Drupal\tripal\Services\TripalEntityLookup::getBundleLabel	(	int	$entity_id,
		string	$entity_type = 'tripal_entity'
	)

Retrieve the human-readable type (i.e. TripalEntityType label) for a given TripalEntity object.

Parameters

int	$entity_id	The TripalEntity ID value. This might be -1 for an unpublished entity.
string	$entity_type	The type of entity, only 'tripal_entity' is supported.

Returns

string The label, or an empty string if it could not be determined.

getBundles()

Drupal\tripal\Services\TripalEntityLookup::getBundles ( string  $base_table )

protected

Retrieve a list of Tripal bundles for a given base table.

Parameters

string

$base_table

The table name e.g. "contact"

Returns

array The bundle ids, or an empty array if no matches found.

getEntityId()

Drupal\tripal\Services\TripalEntityLookup::getEntityId	(		$record_id,
			$termIdSpace,
			$termAccession,
			$base_table = NULL,
			$entity_type = 'tripal_entity'
	)

Retrieve a Drupal entity ID for a record in a given bundle given the bundle's CV term.

Parameters

int	$record_id	The primary key value for the requested record
string	$termIdSpace	The bundle's CV Term namespace e.g. for gene "SO"
string	$termAccession	The bundle's CV term accession e.g. for gene "0000704" If IdSpace and Accession are NULL, then any bundle using the base table is checked.
string	$base_table	The Chado base table for the requested entity e.g. for gene "feature". Only needed if term does not map to a content type.
string	$entity_type	The type of entity, only 'tripal_entity' is supported.

Returns

int|null The Drupal entity ID, or null if no match found.

getEntityIdFromRecordId()

Drupal\tripal\Services\TripalEntityLookup::getEntityIdFromRecordId (   $record_id,   $bundle_id,   $entity_type  )

protected

Retrieve the pkey for an entity corresponding to a given record in a given table.

Parameters

int	$record_id	The primary key value for the requested record in its base table.
string	$bundle_id	The name of the drupal bundle, e.g. for base table 'arraydesign' it is 'array_design'
string	$entity_type	The type of entity, only 'tripal_entity' is supported.

Returns

array The id for the requested Drupal entity in the tripal_entity table. Will be an empty array if there was no corresponding entity. This can happen if the content is not published, or if this is not a content type. If a given record was published as more than one content type, the returned array may have more than one entity id. This would happen in Tripal 3, for example if an analysis is published as both "Analysis", and as "Genome Assembly".

getPublishedEntityIds()

Drupal\tripal\Services\TripalEntityLookup::getPublishedEntityIds	(		$bundle_id,
			$entity_type = 'tripal_entity'
	)

Find all published entities within a given bundle. Unfortunately the drupal entity API 'loadMultiple' function is too slow, taking a second or two per entity. We instead query the Drupal field tables directly, because we just want a simple list of two of the columns.

Parameters

string	$bundle_id	The name of the drupal bundle, e.g. for base table 'arraydesign' it is 'array_design'
string	$entity_type	The type of entity, only 'tripal_entity' is supported.

Returns

array A list of all published entities in the bundle. The key will be the chado table record ID, the values will be the entity IDs.

getRenderableItem()

Drupal\tripal\Services\TripalEntityLookup::getRenderableItem	(		$displayed_string,
			$entity_id
	)

This is used by field formatters to get a ready-to-use render array item to link to an entity.

Parameters

string	$displayed_string	The text that will be displayed as a url link.
int	$entity_id	The primary key value for the Drupal entity. We store -1 in the Drupal field tables to indicate when there is no Drupal entity because the TripalEntity class won't save a zero when drupal_store is TRUE.

Returns

array If a link is possible, then appropriate render array values to generate the link. If no link is possible, then appropriate render array values for simple markup.

getRequiredFields()

Drupal\tripal\Services\TripalEntityLookup::getRequiredFields (   $bundle_id,   $entity_type  )

protected

Retrieve a list of required fields in a given bundle

Parameters

string	$bundle_id	The name of the drupal bundle, e.g. 'analysis'
string	$entity_type	The type of entity, only 'tripal_entity' is supported.

Returns

array A list of required fields. Key is field name, value is base table.

Member Data Documentation

$bundle_base_table_cache

array Drupal\tripal\Services\TripalEntityLookup::$bundle_base_table_cache = []

protected

Caches bundle IDs used for a base table

$bundle_label_cache

array Drupal\tripal\Services\TripalEntityLookup::$bundle_label_cache = []

protected

Caches bundle information keyed by bundle machine ID

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

• tripal/src/Services/TripalEntityLookup.php