Inheritance diagram for Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage:

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Collaboration diagram for Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage:

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Public Member Functions
	__construct (array $configuration, $plugin_id, $plugin_definition, TripalLogger $logger, ChadoConnection $connection, ChadoFieldDebugger $field_debugger)

Public Member Functions inherited from Drupal\tripal\TripalStorage\TripalStorageBase
	__construct (array $configuration, $plugin_id, $plugin_definition, TripalLogger $logger)

	getFieldDefinition (string $field_name)

	addTypes (string $field_name, array $types)

	getTypes ()

	getPropertyType (string $field_name, string $key)

	removeTypes (string $field_name, array $types)

	publishFormValidate ($form, FormStateInterface &$form_state)

	publishFromSubmit ($form, FormStateInterface &$form_state)

Public Member Functions inherited from Drupal\tripal\TripalStorage\Interfaces\TripalStorageInterface
	getStoredValues ()

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

Protected Attributes
	$connection

	$field_debugger

	$records = NULL

Protected Attributes inherited from Drupal\tripal\TripalStorage\TripalStorageBase
	$logger

	$field_definitions = []

	$property_types = []

	addFieldDefinition (string $field_name, object $field_definition)

	getStoredTypes ()

	insertValues (&$values)

	updateValues (&$values)

	loadValues (&$values)

	deleteValues ($values)

	findValues ($values)

	validateValues ($values)

	publishForm ($form, FormStateInterface &$form_state)

	setPropValues (&$values, ChadoRecords $records)

	buildChadoRecords ($values, bool $is_find=FALSE)

	handleStoreID (array $context, StoragePropertyValue $prop_value)

	handleStorePkey (array $context, StoragePropertyValue $prop_value)

	handleStoreLink (array $context, StoragePropertyValue $prop_value)

	handleStore (array $context, StoragePropertyValue $prop_value)

	handleReadValue (array $context, StoragePropertyValue $prop_value)

	parsePath (string $field_name, string $base_table, mixed $path, array $aliases=[], string $as='', string $full_path='')

	getPathValueColumn (array $path)

	handleJoins (array $path_array, array $context)

Additional Inherited Members
Protected Member Functions inherited from Drupal\tripal\TripalStorage\TripalStorageBase
	cloneValues ($values)

	addEmptyValuesItem (&$values, $field_name)

Detailed Description

Chado implementation of the TripalStorageInterface.

@TripalStorage( id = "chado_storage", label = @Translation("Chado Storage"), description = @Translation("Interfaces with GMOD Chado for field values."), )

Constructor & Destructor Documentation

◆ __construct()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::__construct	(	array	$configuration,
			$plugin_id,
			$plugin_definition,
		TripalLogger	$logger,
		ChadoConnection	$connection,
		ChadoFieldDebugger	$field_debugger
	)

Implements __contruct().

Since we have implemented the ContainerFactoryPluginInterface, the constructor will be passed additional parameters added by the create() function. This allows our plugin to use dependency injection without our plugin manager service needing to worry about it.

Parameters

array	$configuration
string	$plugin_id
mixed	$plugin_definition
\Drupal\tripal\Services\TripalLogger	$logger
\Drupal\tripal_chado\Database\ChadoConnection	$connection

Member Function Documentation

◆ addFieldDefinition()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::addFieldDefinition	(	string	$field_name,
		object	$field_definition
	)

inheritdoc}

Implements Drupal\tripal\TripalStorage\Interfaces\TripalStorageInterface.

◆ buildChadoRecords()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::buildChadoRecords	(		$values,
		bool	$is_find = `FALSE`
	)

protected

Indexes a values array for easy lookup.

Parameters

array	$values	Associative array 5-levels deep. The 1st level is the field name (e.g. ncbitaxon__common_name). The 2nd level is the delta value (e.g. 0). The 3rd level is a field key name (i.e. record_id and value). The 4th level must contain the following three keys/value pairs "value": a \Drupal\tripal\TripalStorage\StoragePropertyValue object "type": a\Drupal\tripal\TripalStorage\StoragePropertyType object "definition": a \Drupal\Field\Entity\FieldConfig object When the function returns, any values retrieved from the data store will be set in the StoragePropertyValue object.
bool	$is_find	Set to TRUE if we are building the record array for finding records.

◆ create()

static Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::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 contructor.

Parameters

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

Returns: static

Reimplemented from Drupal\tripal\TripalStorage\TripalStorageBase.

◆ deleteValues()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::deleteValues ( $values )

inheritdoc}

Implements Drupal\tripal\TripalStorage\Interfaces\TripalStorageInterface.

◆ findValues()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::findValues ( $values )

inheritdoc}

Implements Drupal\tripal\TripalStorage\Interfaces\TripalStorageInterface.

◆ getPathValueColumn()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::getPathValueColumn ( array $path )

protected

A helper function to quickly get the value column information from a path.

Parameters

array $path The parsed path of the field property.

◆ getStoredTypes()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::getStoredTypes ( )

Returns a list of property types that should be stored.In order to link data in the storage backend, the storage system must link the record in someway with Drupal entities. This most likely happens in tables in the Drupal schema (usually the public schema). This function should return the list of properties that must be stored in order to uniquely identify an entity in the datastore.

Returns: @array Array of \Drupal\tripal\Base\StoragePropertyTypeBase objects.

See also: \Drupal\tripal\TripalStorage\Interfaces\TripalStorageInterface::getStoredTypes()

Implements Drupal\tripal\TripalStorage\Interfaces\TripalStorageInterface.

◆ handleJoins()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::handleJoins	(	array	$path_array,
		array	$context
	)

protected

A helper function for the buildChadoRecords() function.

Adds the joins to the ChadoRecord object.

Parameters

array	$path_array	The join path array
array	$context	The field/property context provided by the buildChadoRecords() function.

◆ handleReadValue()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::handleReadValue	(	array	$context,
		StoragePropertyValue	$prop_value
	)

protected

A helper function for the buildChadoRecords() function.

Add chado record information for a specific ChadoStorageProperty where the action is read_value.

READ_VALUE: selecting a single column. This cannot be used for inserting or updating values. Instead we use store actions for that. If reading a value from a non-base table, then the path should be provided.

Parameters

array	$context	The field/property context provided by the buildChadoRecords() function.
StoragePropertyValue	$prop_value	The value object for the property we are adding records for. Note: We will always have a StoragePropertyValue for a property even if the value is not set. This method is expected to check if the value is empty or not.

◆ handleStore()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::handleStore	(	array	$context,
		StoragePropertyValue	$prop_value
	)

protected

A helper function for the buildChadoRecords() function.

Add chado record information for a specific ChadoStorageProperty where the action is store.

STORE: indicates that the value of this property can be loaded and stored in the Chado table indicated by this property.

Parameters

array	$context	The field/property context provided by the buildChadoRecords() function.
StoragePropertyValue	$prop_value	The value object for the property we are adding records for. Note: We will always have a StoragePropertyValue for a property even if the value is not set. This method is expected to check if the value is empty or not.

◆ handleStoreID()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::handleStoreID	(	array	$context,
		StoragePropertyValue	$prop_value
	)

protected

A helper function for the buildChadoRecords() function.

Add chado record information for a specific ChadoStorageProperty where the action is store_id.

STORE ID: stores the primary key value for a core table in chado.

Note: There may be more core tables in properties for this field then just the base table. For example, a field involving a two-join linker table will include two core tables.

Parameters

array	$context	The field/property context provided by the buildChadoRecords() function.
StoragePropertyValue	$prop_value	The value object for the property we are adding records for. Note: We will always have a StoragePropertyValue for a property even if the value is not set. This method is expected to check if the value is empty or not.

◆ handleStoreLink()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::handleStoreLink	(	array	$context,
		StoragePropertyValue	$prop_value
	)

protected

A helper function for the buildChadoRecords() function.

Add chado record information for a specific ChadoStorageProperty where the action is store_link.

STORE LINK: performs a join between two tables, one of which is a core table and one of which is a linking table. The value which is saved in this property is the left_table_id indicated in other key/value pairs.

NOTE: A JOIN is not added to the query but rather this property stores the id that a join would normally look up. This is much more performant.

Parameters

array	$context	The field/property context provided by the buildChadoRecords() function.
StoragePropertyValue	$prop_value	The value object for the property we are adding records for. Note: We will always have a StoragePropertyValue for a property even if the value is not set. This method is expected to check if the value is empty or not.

◆ handleStorePkey()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::handleStorePkey	(	array	$context,
		StoragePropertyValue	$prop_value
	)

protected

A helper function for the buildChadoRecords() function.

Add chado record information for a specific ChadoStorageProperty where the action is store_pkey.

STORE PKEY: stores the primary key value of a linking table.

NOTE: A linking table is not a core table. This is important because during insert and update, the core tables are handled first and then linking tables are handled after.

Parameters

array	$context	The field/property context provided by the buildChadoRecords() function.
StoragePropertyValue	$prop_value	The value object for the property we are adding records for. Note: We will always have a StoragePropertyValue for a property even if the value is not set. This method is expected to check if the value is empty or not.

◆ insertValues()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::insertValues ( & $values )

inheritdoc}

Implements Drupal\tripal\TripalStorage\Interfaces\TripalStorageInterface.

◆ loadValues()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::loadValues ( & $values )

inheritdoc}

Implements Drupal\tripal\TripalStorage\Interfaces\TripalStorageInterface.

◆ parsePath()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::parsePath	(	string	$field_name,
		string	$base_table,
		mixed	$path,
		array	$aliases = `[]`,
		string	$as = `''`,
		string	$full_path = `''`
	)

protected

Takes a path string for a field property and converts it to an array structure.

Parameters

mixed	$path	A string continaining the path. Note: this is a recursive function and on recursive calls this variable will be n array. Hence, the type is "mixed".*
array	$aliases	Optional. The list of table aliases provdied by the `table_alias_mapping` argument of a field. If this variable is an empty array then the function will use the table name provided in the path.
string	$as	An alias to be used for the Chado table column that contains the value. This argument will rename the column.
string	$full_path	This argument is used by recursion to build the string path for each level. It should not be set by the callee.

Returns: array

◆ publishForm()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::publishForm	(		$form,
		FormStateInterface &	$form_state
	)

Provides form elements to be added to the Tripal entity publish form.

Parameters

array	$form	The form array definition.
\Drupal\Core\Form\FormStateInterface	$form_state	The form state object.

Returns: array A new form array definition containing the form elements to add to the publish form.

See also: \Drupal\tripal\TripalStorage\Interfaces\TripalStorageInterface::publishFrom()

Implements Drupal\tripal\TripalStorage\Interfaces\TripalStorageInterface.

◆ setPropValues()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::setPropValues	(	&	$values,
		ChadoRecords	$records
	)

protected

Sets the property values using the records returned from Chado.

Parameters

array	$values	Array of \Drupal\tripal\TripalStorage\StoragePropertyValue objects.
ChadoRecords	$records	An instance of a ChadoRecords object from which values will be pulled. We don't use the built in member variable and instead allow it to be passed in because the findValues() functino can generate copies of the $records array and use that to set multiple values.

◆ updateValues()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::updateValues ( & $values )

inheritdoc}

Implements Drupal\tripal\TripalStorage\Interfaces\TripalStorageInterface.

◆ validateValues()

Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage::validateValues ( $values )

Performs validation checks on values.

Parameters

array $values Array of \Drupal\tripal\TripalStorage\StoragePropertyValue objects.

Returns: array An array of \Symfony\Component\Validator\ConstraintViolation objects.

Implements Drupal\tripal\TripalStorage\Interfaces\TripalStorageInterface.

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

tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php

Public Member Functions

Static Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ __construct()

Member Function Documentation

◆ addFieldDefinition()

◆ buildChadoRecords()

◆ create()

◆ deleteValues()

◆ findValues()

◆ getPathValueColumn()

◆ getStoredTypes()

◆ handleJoins()

◆ handleReadValue()

◆ handleStore()

◆ handleStoreID()

◆ handleStoreLink()

◆ handleStorePkey()

◆ insertValues()

◆ loadValues()

◆ parsePath()

◆ publishForm()

◆ setPropValues()

◆ updateValues()

◆ validateValues()