Inheritance diagram for Drupal\tripal_chado\TripalImporter\ChadoImporterBase:

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Collaboration diagram for Drupal\tripal_chado\TripalImporter\ChadoImporterBase:

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Public Member Functions
	__construct (array $configuration, $plugin_id, $plugin_definition, ChadoConnection $connection, ?Messenger $messenger=NULL, ?TripalLogger $logger=NULL, ?TripalFileRetriever $fileretriever=NULL, ?TripalBackendPublishManager $publish_manager=NULL,)

	getChadoConnection ()

	startTransactions ()

	form ($form, &$form_state)

	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 ()

Public Member Functions inherited from Drupal\tripal\TripalImporter\Interfaces\TripalImporterInterface
	formSubmit ($form, &$form_state)

	formValidate ($form, &$form_state)

	run ()

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

Protected Member Functions
	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)

Protected Attributes
	$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

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,
		?Messenger	$messenger = `NULL`,
		?TripalLogger	$logger = `NULL`,
		?TripalFileRetriever	$fileretriever = `NULL`,
		?TripalBackendPublishManager	$publish_manager = `NULL`
	)

Constructs a TripalImporterBase object.

Parameters

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.
Drupal\tripal_chado\Database\ChadoConnection	$connection	A connection to the Chado database.
Drupal\Core\Messenger\Messenger	$messenger	The Drupal messenger service.
Drupal\tripal\Services\TripalLogger	$logger	The Tripal logger service.
Drupal\tripal\Services\TripalFileRetriever	$fileretriever	The Tripal file retrieval service.
Drupal\tripal\TripalBackendPublish\PluginManager\TripalBackendPublishManager	$publish_manager	The Tripal publish manager service.

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.

◆ addBundleTypeProperty()

Drupal\tripal_chado\TripalImporter\ChadoImporterBase::addBundleTypeProperty	(	string	$pkey,
		int	$record_id,
		string	$property_table,
		string	$termIdSpace,
		string	$termAccession,
		string	$value = `''`,
		?int	$rank = `NULL`
	)

protected

Adds the bundle type property to a record

Parameters

string	$pkey	The primary key column name
int	$record_id	The pkey value for the record
string	$property_table	The name of the property table
string	$termIdSpace	The name in the chado.db table
string	$termAccession	The accession in the chado.dbxref table
string	$value	= '' Property value, can be empty string
	?int	$rank = NULL Optional rank

◆ create()

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

static

Implements ContainerFactoryPluginInterface->create().

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\TripalImporter\TripalImporterBase.

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

◆ 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\FASTAImporter, Drupal\tripal_chado\Plugin\TripalImporter\GFF3Importer, Drupal\tripal_chado\Plugin\TripalImporter\NewickImporter, Drupal\tripal_chado\Plugin\TripalImporter\OBOImporter, Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter, Drupal\tripal_chado\Plugin\TripalImporter\TaxonomyImporter, and Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator.

◆ 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.

◆ postRun()

Drupal\tripal_chado\TripalImporter\ChadoImporterBase::postRun ( )

Performs tasks after the importer has completed.

If the importer form specified one or more bundles to be published, these will be listed under the 'publish' key in the run arguments.

Returns: void No return value.

Reimplemented from Drupal\tripal\TripalImporter\TripalImporterBase.

Reimplemented in Drupal\tripal_chado\Plugin\TripalImporter\OBOImporter.

◆ startTransactions()

Drupal\tripal_chado\TripalImporter\ChadoImporterBase::startTransactions ( )

Creates a database transaction in the specific schema(s) this importer will be importing data into.

Returns: array An array of Drupal DatabaseTransaction objects. These are usually obtained by calling the startTransaction() method on the database connection object.

Reimplemented from Drupal\tripal\TripalImporter\TripalImporterBase.

Member Data Documentation

◆ $bundle_type_id

array Drupal\tripal_chado\TripalImporter\ChadoImporterBase::$bundle_type_id = []

protected

The type_id for the bundle(s)

Key is DB:accession, value is cvterm_id

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

tripal_chado/src/TripalImporter/ChadoImporterBase.php

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ __construct()

Member Function Documentation

◆ addAnalysis()

◆ addBundleTypeProperty()

◆ create()

◆ form()

◆ getChadoConnection()

◆ postRun()

◆ startTransactions()

Member Data Documentation

◆ $bundle_type_id