Drupal\tripal_chado\TripalImporter\ChadoImporterBase Class Reference

Inheritance diagram for Drupal\tripal_chado\TripalImporter\ChadoImporterBase:

Collaboration diagram for Drupal\tripal_chado\TripalImporter\ChadoImporterBase:

Public Member Functions
	__construct (array $configuration, $plugin_id, $plugin_definition, ChadoConnection $connection)
	getChadoConnection ()
	form ($form, &$form_state)
	addAnalysis ($form, &$form_state)
Public Member Functions inherited from Drupal\tripal\TripalImporter\TripalImporterBase
	__construct (array $configuration, $plugin_id, $plugin_definition)
	describeUploadFileFormat ()
	setJob ($job)
	createImportJob ($run_args, $file_details=[])
	load ($import_id)
	submitJob ()
	prepareFiles ()
	cleanFile ()
	getArguments ()
Public Member Functions inherited from Drupal\tripal\TripalImporter\Interfaces\TripalImporterInterface
	formSubmit ($form, &$form_state)
	formValidate ($form, &$form_state)
	run ()
	postRun ()

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

Protected Attributes
	$chado_schema_main
	$messenger = NULL
	$connection
Protected Attributes inherited from Drupal\tripal\TripalImporter\TripalImporterBase
	$job
	$logger
	$arguments
	$import_id
	$is_prepared
	$messenger = NULL
	$reported
	$plugin_id
	$plugin_definition

Additional Inherited Members
Protected Member Functions inherited from Drupal\tripal\TripalImporter\TripalImporterBase
	setTotalItems ($total_items)
	addItemsHandled ($num_handled)
	setItemsHandled ($total_handled)
	setInterval ($interval)

Detailed Description

Defines an interface for tripal importer plugins.

Constructor & Destructor Documentation

__construct()

Drupal\tripal_chado\TripalImporter\ChadoImporterBase::__construct	(	array	$configuration,
			$plugin_id,
			$plugin_definition,
		ChadoConnection	$connection
	)

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_chado\Database\ChadoConnection	$connection

Member Function Documentation

addAnalysis()

Drupal\tripal_chado\TripalImporter\ChadoImporterBase::addAnalysis	(		$form,
		&	$form_state
	)

{Adds the form elements necessary for selecting an analaysis to the form.While every Importer must implement this function, Ideally it should be implomented by a child abstract Base class for each data store (e.g. Chado) and each importer should extend the new Base class to inherit the function. This will allow for consistency in the way the analysi form element is presented for all Importers working on the same data store.

Parameters

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

Returns

array An arrya definition containing the form elements for selecting an analysis.

}

Implements Drupal\tripal\TripalImporter\Interfaces\TripalImporterInterface.

create()

static Drupal\tripal_chado\TripalImporter\ChadoImporterBase::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

form()

Drupal\tripal_chado\TripalImporter\ChadoImporterBase::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.

}

Implements Drupal\tripal\TripalImporter\Interfaces\TripalImporterInterface.

Reimplemented in Drupal\tripal_chado\Plugin\TripalImporter\TaxonomyImporter, Drupal\tripal_chado\Plugin\TripalImporter\OBOImporter, Drupal\tripal_chado\Plugin\TripalImporter\NewickImporter, Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer, and Drupal\tripal_chado\Plugin\TripalImporter\FASTAImporter.

getChadoConnection()

Drupal\tripal_chado\TripalImporter\ChadoImporterBase::getChadoConnection

(

)

Gets a chado database connection set to the correct schema.

Requires you to call the parent::form in your form.

---

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

• tripal_chado/src/TripalImporter/ChadoImporterBase.php