Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy Class Reference

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

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

Public Member Functions
	__construct (array $configuration, $plugin_id, $plugin_definition, ChadoConnection $connection, ChadoBuddyPluginManager $buddy_manager)
	getCv (array $conditions, array $options=[])
	getCvterm (array $conditions, array $options=[])
	getCvtermSynonym (array $conditions, array $options=[])
	insertCv (array $values, array $options=[])
	insertCvterm (array $values, array $options=[])
	insertCvtermSynonym (array $values, array $options=[])
	updateCv (array $values, array $conditions, array $options=[])
	updateCvterm (array $values, array $conditions, array $options=[])
	updateCvtermSynonym (array $values, array $conditions, array $options=[])
	upsertCv (array $values, array $options=[])
	upsertCvterm (array $values, array $options=[])
	upsertCvtermSynonym (array $values, array $options=[])
	associateCvterm (string $base_table, int $record_id, ChadoBuddyRecord $cvterm, 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 Member Functions
	upsertDbxref (array $values, array $conditions, array $options=[])
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)

Protected Attributes
object	$buddy_manager
object	$dbxref_instance

Additional Inherited Members
Public Attributes inherited from Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase
ChadoConnection	$connection

Constructor & Destructor Documentation

__construct()

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

{}

Member Function Documentation

associateCvterm()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy::associateCvterm	(	string	$base_table,
		int	$record_id,
		ChadoBuddyRecord	$cvterm,
		array	$options = []
	)

Add a record to a controlled vocabulary term linking table (e.g. feature_cvterm).

Parameters

string	$base_table	The base table for which the cvterm should be associated. Thus to associate a cvterm with a feature the base_table=feature and cvterm_id is added to the feature_cvterm table.
int	$record_id	The primary key of the base_table to associate the cvterm with.
ChadoBuddyRecord	$cvterm	A cvterm object returned by any of the *Cvterm() in this service.
	$options	'pkey': Looking up the primary key for the base table is costly. If it is known, then pass it in as this option for better performance.

Also pass in any other columns used in the linking table, some of which may have a NOT NULL constraint. See the table below for a list of which of the following may be required: 'pub_id', 'is_not', 'rank', 'cvterm_type_id'. If not specified, then they will be looked up automatically, but this will be a slight performance hit. Disable this by specifying at least one additional column, or by setting the option 'lookup_columns' to FALSE.

Chado 1.3 defines these columns in the various linking tables: | table | pub_id | is_not | rank | cvterm_type_id | +--------------------------—+-------—+----------—+----------—+-------------—+ | analysis_cvterm | -absent | has default | has default | -absent | | cell_line_cvterm | not null | -absent | has default | -absent | | environment_cvterm | -absent | -absent | -absent | -absent | | expression_cvterm | -absent | -absent | has default | not null | | feature_cvterm | not null | has default | has default | -absent | | library_cvterm | not null | -absent | -absent | -absent | | organism_cvterm | not null | -absent | has default | -absent | | phenotype_comparison_cvterm | not null | -absent | has default | -absent | | phenotype_cvterm | -absent | -absent | has default | -absent | | stock_cvterm | not null | has default | has default | -absent | | stock_relationship_cvterm | yes null | -absent | -absent | -absent |

Returns

bool Returns TRUE if successful. Both the cvterm and the chado record indicated by $record_id MUST ALREADY EXIST.

Exceptions

Drupal

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

create()

static Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy::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

Reimplemented from Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase.

getCv()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy::getCv	(	array	$conditions,
		array	$options = []
	)

Retrieves a controlled vocabulary.

Parameters

array	$conditions	An array where the key is a column in chado and the value describes the cv you want to select. Valid keys include: cv.cv_id cv.name cv.definition buddy_record = a ChadoBuddyRecord can be used in place of or in addition to other keys
array	$options	(Optional) Associative array of options. 'case_insensitive' - a single key, or an array of keys to query case insensitively.

Returns

array 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.

getCvterm()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy::getCvterm	(	array	$conditions,
		array	$options = []
	)

Retrieves a controlled vocabulary term.

Parameters

array	$conditions	An array where the key is a column in chado and the value describes the cvterm you want to select. Valid keys include: 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) Associative array of options. 'case_insensitive' - a single key, or an array of keys to query case insensitively. 'synonyms' - set to true to enable synonym query, used internally be getCvtermSynonym()

Returns

array 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.

getCvtermSynonym()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy::getCvtermSynonym	(	array	$conditions,
		array	$options = []
	)

Retrieves a controlled vocabulary term.

Parameters

array	$conditions	An array where the key is a column in chado and the value describes the cvterm you want to select. Valid keys include: cv.cv_id cv.name cv.definition cvterm.cvterm_id cvterm.cv_id cvterm.name cvterm.definition cvterm.is_obsolete cvterm.is_relationshiptype cvtermsynonym.cvtermsynonym_id cvtermsynonym.cvterm_id cvtermsynonym.synonym cvtermsynonym.type_id 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) Associative array of options. 'case_insensitive' - a single key, or an array of keys to query case insensitively.

Returns

array 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.

insertCv()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy::insertCv	(	array	$values,
		array	$options = []
	)

Add a controlled vocabulary.

Parameters

$values	An associative array of the values to be inserted including: cv.cv_id cv.name cv.definition buddy_record = a ChadoBuddyRecord can be used in place of or in addition to other keys
$options	(Optional) None supported yet. Here for consistency.

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.

insertCvterm()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy::insertCvterm	(	array	$values,
		array	$options = []
	)

Add a controlled vocabulary term, including creating a dbxref entry if necessary.

Parameters

$values

An associative array of the values to be inserted including: cv.cv_id (either cv_id, cvterm.cv_id, or cv_name required) cv.name cv.definition cvterm.cvterm_id: Not valid for an insert. cvterm.cv_id cvterm.name: Required. cvterm.definition cvterm.is_obsolete cvterm.is_relationshiptype dbxref.dbxref_id dbxref.db_id: Required if generating a dbxref record. dbxref.description: Optional dbxref.accession: Required if generating a dbxref record. dbxref.version: Optional db.db_id: Can be used in place of dbxref.db_id db.name: valid, but has no effect for this function. db.description: valid, but has no effect for this function. db.urlprefix: valid, but has no effect for this function. db.url: valid, but has no effect for this function. buddy_record = a ChadoBuddyRecord can be used in place of or in addition to other keys

$options

(Optional) create_dbxref - set to FALSE (default TRUE) if you do not want to automatically create a dbxref if one does 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.

insertCvtermSynonym()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy::insertCvtermSynonym	(	array	$values,
		array	$options = []
	)

Add a controlled vocabulary term synonym. The existing Cvterm must already exist.

Parameters

$values

An associative array of the values to be inserted including: cv.cv_id (either cv_id, cvterm.cv_id, or cv_name required) cv.name cv.definition cvterm.cvterm_id: Not valid for an insert. cvterm.cv_id cvterm.name: Required. cvterm.definition cvterm.is_obsolete cvterm.is_relationshiptype cvtermsynonym.cvtermsynonym_id cvtermsynonym.cvterm_id cvtermsynonym.synonym cvtermsynonym.type_id dbxref.dbxref_id dbxref.db_id: Required if generating a dbxref record. dbxref.description: Optional dbxref.accession: Required if generating a dbxref record. dbxref.version: Optional db.db_id: Can be used in place of dbxref.db_id db.name: valid, but has no effect for this function. db.description: valid, but has no effect for this function. db.urlprefix: valid, but has no effect for this function. db.url: valid, but has no effect for this function. buddy_record = a ChadoBuddyRecord can be used in place of or in addition to other keys

$options

(Optional) None supported yet. Here for consistency.

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.

updateCv()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy::updateCv	(	array	$values,
		array	$conditions,
		array	$options = []
	)

Updates an existing controlled vocabulary.

Parameters

array	$values	An associative array of the values for the final record (i.e what you want to update the record to be) including: cv.cv_id (only used for $conditions) cv.name cv.definition 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. The same keys are supported as those indicated for the $values.
array	$options	(Optional) None supported yet. Here for consistency.

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.

updateCvterm()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy::updateCvterm	(	array	$values,
		array	$conditions,
		array	$options = []
	)

Updates an existing controlled vocabulary term.

Parameters

array	$values	An associative array of the values for the final record (i.e what you want to update the record to be) including: cv.cv_id (either cv_id, cvterm.cv_id, or cv_name required) cv.name cv.definition cvterm.cvterm_id: Not valid for an insert. cvterm.cv_id cvterm.name: Required. cvterm.definition cvterm.is_obsolete cvterm.is_relationshiptype dbxref.dbxref_id dbxref.db_id: Required if generating a dbxref record. dbxref.description: Optional dbxref.accession: Required if generating a dbxref record. dbxref.version: Optional db.db_id: Can be used in place of dbxref.db_id db.name: valid, but has no effect for this function. db.description: valid, but has no effect for this function. db.urlprefix: valid, but has no effect for this function. db.url: valid, but has no effect for this function. 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. The same keys are supported as those indicated for the $values.
array	$options	(Optional) None supported yet. Here for consistency.

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.

updateCvtermSynonym()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy::updateCvtermSynonym	(	array	$values,
		array	$conditions,
		array	$options = []
	)

Updates an existing controlled vocabulary term synonym.

Parameters

array	$values	An associative array of the values for the final record (i.e what you want to update the record to be) including: cv.cv_id (either cv_id, cvterm.cv_id, or cv_name required) cv.name cv.definition cvterm.cvterm_id: Not valid for an insert. cvterm.cv_id cvterm.name: Required. cvterm.definition cvterm.is_obsolete cvterm.is_relationshiptype cvtermsynonym.cvtermsynonym_id cvtermsynonym.cvterm_id cvtermsynonym.synonym cvtermsynonym.type_id dbxref.dbxref_id dbxref.db_id: Required if generating a dbxref record. dbxref.description: Optional dbxref.accession: Required if generating a dbxref record. dbxref.version: Optional db.db_id: Can be used in place of dbxref.db_id db.name: valid, but has no effect for this function. db.description: valid, but has no effect for this function. db.urlprefix: valid, but has no effect for this function. db.url: valid, but has no effect for this function. 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. The same keys are supported as those indicated for the $values.
array	$options	(Optional) None supported yet. Here for consistency.

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.

upsertCv()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy::upsertCv	(	array	$values,
		array	$options = []
	)

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

Parameters

array	$values	An associative array of the values for the final record including: cv.cv_id cv.name cv.definition buddy_record = a ChadoBuddyRecord can be used in place of or in addition to other keys
array	$options	(Optional) None supported yet. Here for consistency.

Returns

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

Exceptions

Drupal

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

upsertCvterm()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy::upsertCvterm	(	array	$values,
		array	$options = []
	)

Insert a controlled vocabulary term if it doesn't yet exist OR update it if it does.

Parameters

array	$values	An associative array of the values for the final record including: cv.cv_id (either cv_id, cvterm.cv_id, or cv_name required) cv.name cv.definition cvterm.cvterm_id: Not valid for an insert. cvterm.cv_id cvterm.name: Required. cvterm.definition cvterm.is_obsolete cvterm.is_relationshiptype dbxref.dbxref_id dbxref.db_id: Required if generating a dbxref record. dbxref.description: Optional dbxref.accession: Required if generating a dbxref record. dbxref.version: Optional db.db_id: Can be used in place of dbxref.db_id db.name: valid, but has no effect for this function. db.description: valid, but has no effect for this function. db.urlprefix: valid, but has no effect for this function. db.url: valid, but has no effect for this function. buddy_record = a ChadoBuddyRecord can be used in place of or in addition to other keys
array	$options	(Optional) None supported yet. Here for consistency.

Returns

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

Exceptions

Drupal

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

upsertCvtermSynonym()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy::upsertCvtermSynonym	(	array	$values,
		array	$options = []
	)

Insert a controlled vocabulary term synonym if it doesn't yet exist OR update it if it does.

Parameters

array	$values	An associative array of the values for the final record including: cv.cv_id (either cv_id, cvterm.cv_id, or cv_name required) cv.name cv.definition cvterm.cvterm_id: Not valid for an insert. cvterm.cv_id cvterm.name: Required. cvterm.definition cvterm.is_obsolete cvterm.is_relationshiptype cvtermsynonym.cvtermsynonym_id cvtermsynonym.cvterm_id cvtermsynonym.synonym cvtermsynonym.type_id dbxref.dbxref_id dbxref.db_id: Required if generating a dbxref record. dbxref.description: Optional dbxref.accession: Required if generating a dbxref record. dbxref.version: Optional db.db_id: Can be used in place of dbxref.db_id db.name: valid, but has no effect for this function. db.description: valid, but has no effect for this function. db.urlprefix: valid, but has no effect for this function. db.url: valid, but has no effect for this function. buddy_record = a ChadoBuddyRecord can be used in place of or in addition to other keys
array	$options	(Optional) None supported yet. Here for consistency.

Returns

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

Exceptions

Drupal

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

upsertDbxref()

Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy::upsertDbxref ( array  $values, array  $conditions, array  $options = []  )

protected

A helper function to add or update a dbxref for a cvterm, this will filter out extra non-applicable fields that the Cvterm function here may have.

Member Data Documentation

$buddy_manager

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

protected

Used to store the manager so we can create a buddy

$dbxref_instance

object Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy::$dbxref_instance

protected

Provide the dbxref instance

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

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