Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer Class Reference

Inheritance diagram for Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer:

Collaboration diagram for Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer:

Public Member Functions
	__construct (array $configuration, $plugin_id, $plugin_definition, ChadoBuddyPluginManager $buddy_manager, ChadoConnection $connection, Messenger $messenger, TripalLogger $logger, TripalFileRetriever $fileretriever, TripalBackendPublishManager $publish_manager,)
	form ($form, &$form_state)
	formValidate ($form, &$form_state)
	run ()
	getLandmarkTypeID ($landmark_name)
	formSubmit ($form, &$form_state)
Public Member Functions inherited from Drupal\tripal_chado\TripalImporter\ChadoImporterBase
	__construct (array $configuration, $plugin_id, $plugin_definition, ChadoConnection $connection, ?Messenger $messenger=NULL, ?TripalLogger $logger=NULL, ?TripalFileRetriever $fileretriever=NULL, ?TripalBackendPublishManager $publish_manager=NULL,)
	getChadoConnection ()
	startTransactions ()
	addAnalysis ($form, &$form_state)
	postRun ()
Public Member Functions inherited from Drupal\tripal\TripalImporter\TripalImporterBase
	__construct (array $configuration, $plugin_id, $plugin_definition, ?Messenger $messenger=NULL, ?TripalLogger $logger=NULL, ?TripalFileRetriever $fileretriever=NULL, ?TripalBackendPublishManager $publish_manager=NULL,)
	describeUploadFileFormat ()
	setJob ($job)
	rollbackTransaction (string $stage)
	createImportJob ($run_args, $file_details=[])
	load ($import_id)
	submitJob ()
	prepareFiles ()
	cleanFile ()
	setArguments (array $arguments)
	getArguments ()

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

Protected Attributes
object	$buddy_manager
object	$dbxref_buddy
object	$cvterm_buddy
object	$property_buddy
Protected Attributes inherited from Drupal\tripal_chado\TripalImporter\ChadoImporterBase
	$chado_schema_main
	$messenger = NULL
	$connection
array	$bundle_type_id = []
Protected Attributes inherited from Drupal\tripal\TripalImporter\TripalImporterBase
	$messenger = NULL
	$logger = NULL
	$fileretriever = NULL
	$publish_manager = NULL
	$job
	$arguments
	$import_id
	$is_prepared
	$reported
	$plugin_id
	$plugin_definition

Additional Inherited Members
Protected Member Functions inherited from Drupal\tripal_chado\TripalImporter\ChadoImporterBase
	addBundleTypeProperty (string $pkey, int $record_id, string $property_table, string $termIdSpace, string $termAccession, string $value='', ?int $rank=NULL)
Protected Member Functions inherited from Drupal\tripal\TripalImporter\TripalImporterBase
	setTotalItems ($total_items)
	addItemsHandled ($num_handled)
	setItemsHandled ($total_handled)
	setInterval ($interval)
	xmlIsValid (string $xml)

Constructor & Destructor Documentation

__construct()

Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer::__construct	(	array	$configuration,
			$plugin_id,
			$plugin_definition,
		ChadoBuddyPluginManager	$buddy_manager,
		ChadoConnection	$connection,
		Messenger	$messenger,
		TripalLogger	$logger,
		TripalFileRetriever	$fileretriever,
		TripalBackendPublishManager	$publish_manager
	)

{}

Member Function Documentation

create()

static Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer::create ( ContainerInterface  $container, array  $configuration,   $plugin_id,   $plugin_definition  )

static

Implements ContainerFactoryPluginInterface->create().

We are injecting an additional dependency here, the ChadoBuddyPluginManager.

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	The container.
array	$configuration	A configuration array containing information about the plugin instance.
string	$plugin_id	The plugin ID for the plugin instance.
mixed	$plugin_definition	The plugin implementation definition.

Returns

static

Reimplemented from Drupal\tripal_chado\TripalImporter\ChadoImporterBase.

form()

Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer::form	(		$form,
		&	$form_state
	)

{Provides form elements to be added to the loader form.These form elements are added after the file uploader section that is automaticaly provided by the TripalImporter.

Parameters

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

Returns

array A new form array definition.

}

Reimplemented from Drupal\tripal_chado\TripalImporter\ChadoImporterBase.

formSubmit()

Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer::formSubmit	(		$form,
		&	$form_state
	)

{Handles submission of the form elements.The form elements provided in the implementation of the form() function can be used for special submit if needed.

Parameters

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

}

Implements Drupal\tripal\TripalImporter\Interfaces\TripalImporterInterface.

formValidate()

Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer::formValidate	(		$form,
		&	$form_state
	)

Handles validation of the form elements.The form elements provided in the implementation of the form() function should be validated using this function.

Parameters

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

Implements Drupal\tripal\TripalImporter\Interfaces\TripalImporterInterface.

getLandmarkTypeID()

Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer::getLandmarkTypeID

(

$landmark_name

)

This looks up the landmark type_id by utilizing the landmark_types associate array cached values and then checks the landmark_types_type_ids associate array cached values.

run()

Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer::run

(

)

Performs the import.

Implements Drupal\tripal\TripalImporter\Interfaces\TripalImporterInterface.

Member Data Documentation

$buddy_manager

object Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer::$buddy_manager

protected

Used to store the manager so we can create various buddies

$cvterm_buddy

object Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer::$cvterm_buddy

protected

Provide the cvterm buddy instance

$dbxref_buddy

object Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer::$dbxref_buddy

protected

Provide the dbxref buddy instance

$property_buddy

object Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer::$property_buddy

protected

Provide the property buddy instance

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

• tripal_chado/src/Plugin/TripalImporter/GFF3Importer.php