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

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

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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 ()

	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)

static	tripal_taxon_importer_set_ncbi_api_key ($form, &$form_state)

Protected Member Functions
	updateExisting ($root_taxon=NULL)

	findOrganism ($taxid, $sci_name)

	addOrganism ($sci_name, $rank)

	importRecord ($taxid, $root_taxon=NULL, $organism=NULL)

	addProperty ($organism_id, $term_name, $value, $rank=0)

	addDbxref ($organism_id, $taxId)

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)

Protected Attributes
	$all_orgs = []

	$ncbitaxon_db_id = NULL

object	$buddy_manager

object	$dbxref_buddy

object	$property_buddy

array	$retrieval_options

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

Constructor & Destructor Documentation

◆ __construct()

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

{}

Member Function Documentation

◆ addDbxref()

Drupal\tripal_chado\Plugin\TripalImporter\TaxonomyImporter::addDbxref	(	$organism_id,
		$taxId
	)

protected

Parameters

unknown	$organism_id
unknown	$taxId

◆ addOrganism()

Drupal\tripal_chado\Plugin\TripalImporter\TaxonomyImporter::addOrganism	(	$sci_name,
		$rank
	)

protected

Adds a new organism record to Chado.

Parameters

sci_name	The scientific name as provied by NCBI Taxonomy.
$rank	The rank of the organism as provied by NCBI Taxonomy.

◆ addProperty()

Drupal\tripal_chado\Plugin\TripalImporter\TaxonomyImporter::addProperty	(	$organism_id,
		$term_name,
		$value,
		$rank = `0`
	)

protected

Adds a property to an organism node.

Parameters

$organism_id	The organism ID to which the property is added.
$term_name	The name of the organism property term. This term must be present in the 'local' cv.
$value	The value of the property.
$rank	The order for this property. The first instance of this term for this organism should be zero. Defaults to zero.

◆ create()

static Drupal\tripal_chado\Plugin\TripalImporter\TaxonomyImporter::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.

◆ findOrganism()

Drupal\tripal_chado\Plugin\TripalImporter\TaxonomyImporter::findOrganism	(	$taxid,
		$sci_name
	)

protected

Checks the Chado database to see if the organism already exists.

Parameters

$taxid	The taxonomic ID for the organism.
$sci_name	The scientific name for the organism as returned by NCBI

◆ form()

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

See also: TripalImporter::form()

Reimplemented from Drupal\tripal_chado\TripalImporter\ChadoImporterBase.

◆ formSubmit()

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

See also: TripalImporter::formValidate()

Implements Drupal\tripal\TripalImporter\Interfaces\TripalImporterInterface.

◆ importRecord()

Drupal\tripal_chado\Plugin\TripalImporter\TaxonomyImporter::importRecord	(	$taxid,
		$root_taxon = `NULL`,
		$organism = `NULL`
	)

protected

Imports an organism from the NCBI taxonomy DB by its taxonomy ID

Parameters

$taxid	The NCBI Taxonomy ID.
$root_taxon	An optional taxon name for the root node if generating a sub-tree.
$organism	The organism object to which this taxonomy belongs. If the organism is NULL then it will be created.

◆ run()

Drupal\tripal_chado\Plugin\TripalImporter\TaxonomyImporter::run ( )

Performs the import.

Implements Drupal\tripal\TripalImporter\Interfaces\TripalImporterInterface.

◆ tripal_taxon_importer_set_ncbi_api_key()

static Drupal\tripal_chado\Plugin\TripalImporter\TaxonomyImporter::tripal_taxon_importer_set_ncbi_api_key	(		$form,
		&	$form_state
	)

static

Ajax callback for the TaxonomyImporter::form() function.

It is called when the user makes a change to the NCBI API key field and then moves their cursor out of the field.

Parameters

array	$form	The new form element.
\Drupal\Core\Form\FormStateInterface	$form_state	The state of the new form element.

Returns: array The new api key field.

◆ updateExisting()

Drupal\tripal_chado\Plugin\TripalImporter\TaxonomyImporter::updateExisting ( $root_taxon = NULL )

protected

Imports details from NCBI Taxonomy for organisms that already exist.

Member Data Documentation

◆ $all_orgs

Drupal\tripal_chado\Plugin\TripalImporter\TaxonomyImporter::$all_orgs = []

protected

Holds the list of all organisms currently in Chado. This list is needed when checking to see if an organism has already been loaded.

◆ $buddy_manager

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

protected

Used to store the manager so we can create various buddies

◆ $dbxref_buddy

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

protected

Provide the dbxref buddy instance

◆ $ncbitaxon_db_id

Drupal\tripal_chado\Plugin\TripalImporter\TaxonomyImporter::$ncbitaxon_db_id = NULL

protected

ID of the NCBITaxon database in Chado

◆ $property_buddy

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

protected

Provide the property buddy instance

◆ $retrieval_options

array Drupal\tripal_chado\Plugin\TripalImporter\TaxonomyImporter::$retrieval_options

protected

Initial value:

= [
    'rate_limit' => 0.334,
    'retry_delay' => 1.0,
  ]

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

tripal_chado/src/Plugin/TripalImporter/TaxonomyImporter.php

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

◆ __construct()

Member Function Documentation

◆ addDbxref()

◆ addOrganism()

◆ addProperty()

◆ create()

◆ findOrganism()

◆ form()

◆ formSubmit()

◆ formValidate()

◆ importRecord()

◆ run()

◆ tripal_taxon_importer_set_ncbi_api_key()

◆ updateExisting()

Member Data Documentation

◆ $all_orgs

◆ $buddy_manager

◆ $dbxref_buddy

◆ $ncbitaxon_db_id

◆ $property_buddy

◆ $retrieval_options