Inheritance diagram for Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase:

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Collaboration diagram for Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase:

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Public Member Functions
	__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)

Public Attributes
ChadoConnection	$connection

Protected Member Functions
	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)

Detailed Description

Base class for chado_buddy plugins.

Constructor & Destructor Documentation

◆ __construct()

Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase::__construct	(	array	$configuration,
			$plugin_id,
			$plugin_definition,
		ChadoConnection	$connection
	)

{}

Member Function Documentation

◆ addConditions()

Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase::addConditions	(	object &	$query,
		array	$conditions,
		array	$options
	)

protected

Adds the conditions to the database query. Implements case insensitive queries if requested.

Parameters

object	$query	Associative array where keys are table name+dot+table column.
array	$conditions	Associative array of conditions to add to the query.
object	$options	Associative array of options as passed to the calling buddy function. The option 'case_insensitive' can contain a single key string, or an array of multiple keys for which a case insensitive query is desired.

◆ addTableToCache()

Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase::addTableToCache	(	string	$chado_table,
		array &	$cached_tables
	)

protected

Add a chado table to the cache, used only by getTableColumns()

Parameters

string $chado_table Name of the table to add

array

$cached_tables

Schema information will be inserted in this array for the table indicated above. The array follows this format:

- 'all':
  - <field name>: TRUE
- 'required':
  - <field name>: TRUE|FALSE depending on if this field is not null and doesn't have a default.
- 'unique':
  - <field name>: TRUE|FALSE depending on if this field is in a unique constraint.

Returns: void

◆ create()

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

static

Implements ContainerFactoryPluginInterface->create().

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 in Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoCvtermBuddy, and Drupal\tripal_chado\Plugin\ChadoBuddy\ChadoPropertyBuddy.

◆ dereferenceBuddyRecord()

Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase::dereferenceBuddyRecord ( array $values )

protected

Used to dereference a ChadoBuddyRecord in the $values array into its component values.

Parameters

array $values An associative array to be validated. Keys are table+dot+column name, values are the database table values. The special case value of 'buddy_record' => ChadoBuddyRecord will have its component values appended to the values. In the case of a duplicated key, if the value in the ChadoBuddyRecord is different from the one in the array, then an exception is thrown.

Returns: array Merged associative array of values

Exceptions

Drupal

tripal_chado\ChadoBuddy\Exceptions\ChadoBuddyException If the key 'buddy_record' does not have a ChadoBuddyRecord as its value. If a value inside the ChadoBuddyRecord is different than one in the $values array.

◆ description()

Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase::description ( )

{}

◆ getTableCache()

Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase::getTableCache ( )

protected

Retrieves the chado table definition cache used by getTableColumns().

Returns

array An array describing the fields of any cached tables. The array follows this format:

- 'all':
  - <field name>: TRUE
- 'required':
  - <field name>: TRUE|FALSE depending on if this field is not null and doesn't have a default.
- 'unique':
  - <field name>: TRUE|FALSE depending on if this field is in a unique constraint.

◆ getTableColumns()

Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase::getTableColumns	(	array	$chado_tables,
		string	$filter = `'all'`
	)

protected

Retrieve a list of table columns for one or more chado tables. Schema information is cached for better performance.

Parameters

array	$chado_tables	One or more chado table names.
string	$filter	'required' = return columns that [1]: have a NOT NULL constraint, and [2]: do not have a default value and are not serial, such as a primary key. In other words, a column with a NOT NULL constraint but with some form of a default value is considered to be not required. 'unique' = return only columns that are part of any unique constraint. 'all' (default) or anything else = return all columns.

Returns: array An array of table+dot+column name, e.g. for 'db' table: ['db.db_id', 'db.name', 'db.description', 'db.urlprefix', 'db.url']

Exceptions

Drupal

tripal_chado\ChadoBuddy\Exceptions\ChadoBuddyException For invalid table name.

◆ label()

Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase::label ( )

{Returns the translated plugin label.}

Implements Drupal\tripal_chado\ChadoBuddy\Interfaces\ChadoBuddyInterface.

◆ makeAlias()

Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase::makeAlias ( string $name )

protected

Replace the first period with a double underscore This makes the string valid as a table column alias.

Parameters

string $name table name+dot+table column

Returns: string The first period is replaced with double underscore.

◆ makeUpsertConditions()

Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase::makeUpsertConditions	(	array	$values,
		array	$key_columns
	)

protected

Used by upsert functions to generate a subset of values using only key columns, e.g. 'name' for cv table. The key columns are those which are present in any of the unique constraints that the table may have.

Parameters

array	$values	An associative array where the key is the table.column_name.
array	$key_columns	Only column keys in this list should be returned.

Returns: array The subset of the passed $values array.

◆ removeTablePrefix()

Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase::removeTablePrefix ( array $values )

protected

Removes the table prefix from $values keys so that they can be used directly in an INSERT. The prefix is anything up to and including the first period.

Parameters

array $values Associative array where keys are table name+dot+table column.

Returns: array The keys have had the table name prefix removed, values are unchanged.

◆ subsetInput()

Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase::subsetInput	(	array	$user_values,
		array	$valid_tables
	)

protected

Used to return a subset of values applicable to a single chado table, e.g. remove db table columns when inserting a new dbxref.

Parameters

array	$user_values	An associative array to be filtered. Keys are table+dot+column name, values are for that table+column.
array	$valid_tables	An array listing which tables should have keys returned.

Returns: array The subset of passed $user_values with table prefixes present in the $valid_tables array.

Exceptions

Drupal

tripal_chado\ChadoBuddy\Exceptions\ChadoBuddyException If after subsetting there is nothing left.

◆ unmakeAlias()

Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase::unmakeAlias ( string $name )

protected

Replace the first double underscore with a period. This reverts the change made by the makeAlias() function.

Parameters

string $name table name+__+table column

Returns: string The first __ is replaced with a period.

◆ validateInput()

Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase::validateInput	(	array	$user_values,
		array	$valid_values
	)

protected

Used to validate input arrays to various buddy functions.

Parameters

array	$user_values	An associative array to be validated. Keys are table+dot+column name, values are the database table values.
array	$valid_values	An array listing all valid keys for $user_values.

Exceptions

Drupal

tripal_chado\ChadoBuddy\Exceptions\ChadoBuddyException If $user_values array is empty. If a key in $user_values is not in $valid_values.

◆ validateOutput()

Drupal\tripal_chado\ChadoBuddy\ChadoBuddyPluginBase::validateOutput	(		$output_records,
		array	$values
	)

protected

Used to validate results from a buddy function, to ensure there is exactly one record present.

Parameters

mixed	$output_records	An array of zero or more ChadoBuddyRecords. To be valid, it must contain exactly one ChadoBuddyRecord.
array	$values	Pass query values to print if an exception is thrown.

Exceptions

Drupal

tripal_chado\ChadoBuddy\Exceptions\ChadoBuddyException If not exactly one record is present.

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

tripal_chado/src/ChadoBuddy/ChadoBuddyPluginBase.php

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ __construct()

Member Function Documentation

◆ addConditions()

◆ addTableToCache()

◆ create()

◆ dereferenceBuddyRecord()

◆ description()

◆ getTableCache()

◆ getTableColumns()

◆ label()

◆ makeAlias()

◆ makeUpsertConditions()

◆ removeTablePrefix()

◆ subsetInput()

◆ unmakeAlias()

◆ validateInput()

◆ validateOutput()