Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoPropertyBuddy Class Reference

Inheritance diagram for Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoPropertyBuddy:

Collaboration diagram for Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoPropertyBuddy:

Public Member Functions
	__construct (array $configuration, $plugin_id, $plugin_definition, ChadoConnection $connection, ChadoBuddyPluginManager $buddy_manager)
	getProperty (string $base_table, int $record_id, array $conditions, array $options=[])
	insertProperty (string $base_table, int $record_id, array $values, array $options=[])
	updateProperty (string $base_table, int $record_id, array $values, array $conditions, array $options=[])
	upsertProperty (string $base_table, int $record_id, array $values, array $options=[])
	deleteProperty (string $base_table, int $record_id, array $conditions, array $options=[])
Public Member Functions inherited from Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase
	__construct (array $configuration, $plugin_id, $plugin_definition, ChadoConnection $connection)
	label ()
	description ()

Static Public Member Functions
static	create (ContainerInterface $container, array $configuration, $plugin_id, $plugin_definition)

Protected Attributes
object	$buddy_manager
object	$cvterm_instance

Additional Inherited Members
Public Attributes inherited from Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase
ChadoConnection	$connection
Protected Member Functions inherited from Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase
	getTableColumns (array $chado_tables, string $filter='all')
	getTableCache ()
	addTableToCache (string $chado_table, array &$cached_tables)
	makeUpsertConditions (array $values, array $key_columns)
	makeAlias (string $name)
	unmakeAlias (string $name)
	removeTablePrefix (array $values)
	addConditions (object &$query, array $conditions, array $options)
	validateInput (array $user_values, array $valid_values)
	dereferenceBuddyRecord (array $values)
	subsetInput (array $user_values, array $valid_tables)
	validateOutput ($output_records, array $values)

Constructor & Destructor Documentation

__construct()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoPropertyBuddy::__construct	(	array	$configuration,
			$plugin_id,
			$plugin_definition,
		ChadoConnection	$connection,
		ChadoBuddyPluginManager	$buddy_manager
	)

{}

Member Function Documentation

create()

static Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoPropertyBuddy::create ( ContainerInterface  $container, array  $configuration,   $plugin_id,   $plugin_definition  )

static

Implements ContainerFactoryPluginInterface->create().

We are injecting an additional dependency here, the ChadoBuddyPluginManager, so that this buddy can have access to the Dbxref buddy.

Since we have implemented the ContainerFactoryPluginInterface this static function will be called behind the scenes when a Plugin Manager uses createInstance(). Specifically this method is used to determine the parameters to pass to the constructor.

Parameters

\Symfony\Component\DependencyInjection\ContainerInterface	$container
array	$configuration
string	$plugin_id
mixed	$plugin_definition

Returns

static

Exceptions

Drupal

tripal_chado\ChadoBuddy\Exceptions\ChadoBuddyException If an error is encountered.

Reimplemented from Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase.

deleteProperty()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoPropertyBuddy::deleteProperty	(	string	$base_table,
		int	$record_id,
		array	$conditions,
		array	$options = []
	)

Deletes a chado property or multiple properties.

Parameters

string	$base_table	The base table for which the property should be associated. Thus to associate a property with a feature, the basetable=feature and a record is added to the featureprop table.
int	$record_id	The primary key of the basetable to that the property is associated with.
array	$conditions	An array where the key is a table+dot+column to describe the name of the property table and the column desired. Examples here are for the project table: projectprop.projectprop_id - (optional) property table primary key value projectprop.project_id - (optional) base table primary key value projectprop.type_id - a foreign key to cvterm_id projectprop.value - the value of the property projectprop.rank - optional rank of the property and possibly other columns for some property tables cv.cv_id cv.name cv.definition cvterm.cvterm_id cvterm.cv_id cvterm.name cvterm.definition cvterm.is_obsolete cvterm.is_relationshiptype dbxref.dbxref_id dbxref.db_id dbxref.description dbxref.accession dbxref.version db.db_id db.name db.description db.urlprefix db.url buddy_record = a ChadoBuddyRecord can be used in place of or in addition to other keys
array	$options	(Optional) property_table - if the default of $base_table . 'prop' needs to be changed fkey - if the default of $base_table . '_id' needs to be changed pkey - if the default of $property_table . '_id' needs to be changed max_delete - specifies the maximum number of properties that can be deleted. Default is 1. Set to -1 for unlimited. If the limit is exceeded, a ChadoBuddyException is thrown.

Returns

int Returns a count of the number of records that were deleted.

Exceptions

Drupal

tripal_chado\ChadoBuddy\Exceptions\ChadoBuddyException If an error is encountered.

getProperty()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoPropertyBuddy::getProperty	(	string	$base_table,
		int	$record_id,
		array	$conditions,
		array	$options = []
	)

Retrieves a chado property.

Parameters

string	$base_table	The base table for which the property should be associated. Thus to associate a property with a feature, the basetable=feature and a record is added to the featureprop table.
int	$record_id	The primary key of the basetable to that the property is associated with.
array	$conditions	An array where the key is a table+dot+column to describe the name of the property table and the column desired. Examples here are for the project table: projectprop.projectprop_id - (optional) property table primary key value projectprop.project_id - (optional) base table primary key value projectprop.type_id - a foreign key to cvterm_id projectprop.value - the value of the property projectprop.rank - optional rank of the property and possibly other columns for some property tables cv.cv_id cv.name cv.definition cvterm.cvterm_id cvterm.cv_id cvterm.name cvterm.definition cvterm.is_obsolete cvterm.is_relationshiptype dbxref.dbxref_id dbxref.db_id dbxref.description dbxref.accession dbxref.version db.db_id db.name db.description db.urlprefix db.url buddy_record = a ChadoBuddyRecord can be used in place of or in addition to other keys
array	$options	(Optional) property_table - if the default of $base_table . 'prop' needs to be changed fkey - if the default of $base_table . '_id' needs to be changed pkey - if the default of $property_table . '_id' needs to be changed

Returns

bool|array|ChadoBuddyRecord An array of ChadoBuddyRecord objects. More specifically, (1) if the select values return a single record then we return an array containing a single ChadoBuddyRecord describing the record. (2) if the select values return multiple records, then we return an array of ChadoBuddyRecords describing the results. (3) if there are no results then we return an empty array.

Exceptions

Drupal

tripal_chado\ChadoBuddy\Exceptions\ChadoBuddyException If an error is encountered.

insertProperty()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoPropertyBuddy::insertProperty	(	string	$base_table,
		int	$record_id,
		array	$values,
		array	$options = []
	)

Adds a new property linked to the specified base table and record

Parameters

string	$base_table	The base table for which the property should be associated. Thus to associate a property with a feature, the basetable=feature and a record is added to the featureprop table.
int	$record_id	The primary key of the basetable to that the property is associated with.
	$values	An array where the key is a table+dot+column to describe the name of the property table and the column desired. Examples here are for the project table: projectprop.projectprop_id - (optional) property table primary key value projectprop.project_id - (optional) base table primary key value projectprop.type_id - a foreign key to cvterm_id projectprop.value - the value of the property projectprop.rank - optional rank of the property and possibly other columns for some property tables cv.cv_id cv.name cv.definition cvterm.cvterm_id cvterm.cv_id cvterm.name cvterm.definition cvterm.is_obsolete cvterm.is_relationshiptype dbxref.dbxref_id dbxref.db_id dbxref.description dbxref.accession dbxref.version db.db_id db.name db.description db.urlprefix db.url buddy_record = a ChadoBuddyRecord can be used in place of or in addition to other keys
array	$options	(Optional) property_table - if the default of $base_table . 'prop' needs to be changed fkey - if the default of $base_table . '_id' needs to be changed pkey - if the default of $property_table . '_id' needs to be changed create_cvterm - set to TRUE (default FALSE) if you specified the necessary fields and want to create the dbxref and cvterm when creating this property, if they do not already exist.

Returns

ChadoBuddyRecord The inserted ChadoBuddyRecord will be returned on success and an exception will be thrown if an error is encountered. If the record already exists then an error will be thrown. If this is not the desired behaviour then use the upsert version of this method.

Exceptions

Drupal

tripal_chado\ChadoBuddy\Exceptions\ChadoBuddyException If an error is encountered.

updateProperty()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoPropertyBuddy::updateProperty	(	string	$base_table,
		int	$record_id,
		array	$values,
		array	$conditions,
		array	$options = []
	)

Updates an existing property.

Parameters

string	$base_table	The base table for which the property should be associated. Thus to associate a property with a feature, the basetable=feature and a record is added to the featureprop table.
int	$record_id	The primary key of the basetable to that the property is associated with.
array	$values	Values for what you want the updated propert to contaion. An array where the key is a table+dot+column to describe the name of the property table and the column desired. Examples here are for the project table: projectprop.projectprop_id - (optional) property table primary key value projectprop.project_id - (optional) base table primary key value projectprop.type_id - a foreign key to cvterm_id projectprop.value - the value of the property projectprop.rank - optional rank of the property and possibly other columns for some property tables cv.cv_id cv.name cv.definition cvterm.cvterm_id cvterm.cv_id cvterm.name cvterm.definition cvterm.is_obsolete cvterm.is_relationshiptype dbxref.dbxref_id dbxref.db_id dbxref.description dbxref.accession dbxref.version db.db_id db.name db.description db.urlprefix db.url buddy_record = a ChadoBuddyRecord can be used in place of or in addition to other keys
array	$conditions	An associative array of the conditions to find the record to update. Although the same keys are supported as those indicated for the $values, only columns that are part of a unique constraint will be used for the database query. e.g. you can't query on the property value.
array	$options	(Optional) property_table - if the default of $base_table . 'prop' needs to be changed fkey - if the default of $base_table . '_id' needs to be changed pkey - if the default of $property_table . '_id' needs to be changed

Returns

bool|ChadoBuddyRecord The updated ChadoBuddyRecord will be returned on success, FALSE will be returned if no record was found to update.

Exceptions

Drupal

tripal_chado\ChadoBuddy\Exceptions\ChadoBuddyException If an error is encountered.

upsertProperty()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoPropertyBuddy::upsertProperty	(	string	$base_table,
		int	$record_id,
		array	$values,
		array	$options = []
	)

Insert a property if it doesn't yet exist OR update it if does.

Parameters

string	$base_table	The base table for which the property should be associated. Thus to associate a property with a feature, the basetable=feature and a record is added to the featureprop table.
int	$record_id	The primary key of the basetable to that the property is associated with.
array	$values	An array where the key is a table+dot+column to describe the name of the property table and the column desired. Examples here are for the project table: projectprop.projectprop_id - (optional) property table primary key value projectprop.project_id - (optional) base table primary key value projectprop.type_id - a foreign key to cvterm_id projectprop.value - the value of the property projectprop.rank - optional rank of the property and possibly other columns for some property tables cv.cv_id cv.name cv.definition cvterm.cvterm_id cvterm.cv_id cvterm.name cvterm.definition cvterm.is_obsolete cvterm.is_relationshiptype dbxref.dbxref_id dbxref.db_id dbxref.description dbxref.accession dbxref.version db.db_id db.name db.description db.urlprefix db.url buddy_record = a ChadoBuddyRecord can be used in place of or in addition to other keys
array	$options	(Optional) property_table - if the default of $base_table . 'prop' needs to be changed fkey - if the default of $base_table . '_id' needs to be changed pkey - if the default of $property_table . '_id' needs to be changed create_cvterm - set to TRUE (default FALSE) if you have the necessary fields and want to create the dbxref and cvterm when creating this property, if they do not already exist.

Returns

ChadoBuddyRecord The inserted/updated ChadoBuddyRecord will be returned on success.

Exceptions

Drupal

tripal_chado\ChadoBuddy\Exceptions\ChadoBuddyException If an error is encountered.

Member Data Documentation

$buddy_manager

object Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoPropertyBuddy::$buddy_manager

protected

Used to store the manager so we can access the Cvterm buddy

$cvterm_instance

object Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoPropertyBuddy::$cvterm_instance

protected

Cache the cvterm instance here

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

• tripal_chado/src/Plugin/ChadoBuddy/ChadoPropertyBuddy.php