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

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

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Public Member Functions
	__construct (array $configuration, $plugin_id, $plugin_definition, TripalPubLibraryManager $pub_library_manager, Connection $public, ChadoConnection $connection, Messenger $messenger, TripalLogger $logger, TripalFileRetriever $fileretriever, TripalBackendPublishManager $publish_manager,)

	form ($form, &$form_state)

	formValidate ($form, &$form_state)

	formSubmit ($form, &$form_state)

	findExistingPublications (array $publications)

	run ()

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	test_click_on_change (array &$form, $form_state)

static	database_on_change (array &$form, $form_state)

Protected Member Functions
	formQueryIdNotSet (&$form, $form_state)

	getRemoteDbId (string $db_name)

	cachePublicationCvterms ()

	insertMissingPublicationsDbxref (array $publications)

	getNewPublicationAccessions (array $publications)

	insertPublications (array &$publications)

	getPublicationTypeId (array &$publications, int $index)

	insertPubDbxrefs ()

	insertPubProps (array $publications)

	specialCaseProps (&$publications)

	checkIfSupportedProperty (string $key, string\|array $value, array &$missing_cvterms)

	insertContacts (array $publications, bool $do_contact)

	addAuthors (string $accession, array $publication, bool $do_contact=FALSE)

	getContact (string $contact_name, string $type)

	getContactType (string $type_name)

	run_init ()

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
	$public = NULL

	$pub_library_manager = NULL

	$db_id = NULL

	$cvterm_lookups = NULL

	$contact_lookups = []

array	$pub_index = []

array	$new_accessions = []

int	$batch_size = 100

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\PubSearchQueryImporter::__construct	(	array	$configuration,
			$plugin_id,
			$plugin_definition,
		TripalPubLibraryManager	$pub_library_manager,
		Connection	$public,
		ChadoConnection	$connection,
		Messenger	$messenger,
		TripalLogger	$logger,
		TripalFileRetriever	$fileretriever,
		TripalBackendPublishManager	$publish_manager
	)

{}

Member Function Documentation

◆ addAuthors()

Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::addAuthors	(	string	$accession,
		array	$publication,
		bool	$do_contact = `FALSE`
	)

protected

Add one or more authors to a publication through the pubauthor table, and optionally the pubauthor_contact and contact tables

Parameters

string	$accession	The external database accession for this publication
array	$publication	A single publication query result.
bool	$do_contact	If TRUE, then create and link an entry in the chado.contact table

Returns: int A count of the number of records added Example PMID with a suffix: 38266644 Example PMID that is a collective: 12773082

◆ cachePublicationCvterms()

Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::cachePublicationCvterms ( )

protected

Caches cvterm_id values for all cvterms in the "tripal_pub" vocabulary, saving them in the class variable $this->cvterm_lookups

◆ checkIfSupportedProperty()

Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::checkIfSupportedProperty	(	string	$key,
		string\|array	$value,
		array &	$missing_cvterms
	)

protected

Helper function for insertPubProps to determine if the property CV term is supported.

Parameters

string	$key	The property key, which is a CV term.
string \| array	$value	The property value or values.
array	&$missing_cvterms	Array keys define a list of non-supported CV terms.

Returns: array An array of values to be saved, or NULL if the $key is not supported.

◆ create()

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

static

Implements ContainerFactoryPluginInterface->create().

We are injecting an additional dependency here, the TripalPubLibraryManager.

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.

◆ findExistingPublications()

Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::findExistingPublications ( array $publications )

Finds publication accessions that already are stored in Chado.

Results are stored in $this->pub_index

Parameters

array $publications Publications loaded from the external database

Returns: int The number of publications not currently stored in Chado

◆ form()

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

See also: TripalImporter::form()

Reimplemented from Drupal\tripal_chado\TripalImporter\ChadoImporterBase.

◆ formQueryIdNotSet()

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

protected

Helper function for form(), code to handle the case where the query ID is not yet set.

Parameters

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

◆ formSubmit()

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

See also: TripalImporter::formValidate()

Implements Drupal\tripal\TripalImporter\Interfaces\TripalImporterInterface.

◆ getContact()

Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::getContact	(	string	$contact_name,
		string	$type
	)

protected

Gets the contact_id of a person, will create the contact if it does not already exist

Parameters

string	$contact_name	The name of a contact
string	$type	The type of contact in the tripal_contact ontology, most commonly 'Person'

Returns: int The contact_id value

◆ getContactType()

Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::getContactType ( string $type_name )

protected

Gets a cvterm_id from the tripal_contact ontology.

Parameters

string $type_name Corresponds to the 'name' column of the cvterm table

Returns: int Corresponds to the 'cvterm_id' column of the cvterm table.

◆ getNewPublicationAccessions()

Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::getNewPublicationAccessions ( array $publications )

protected

Extract a list of new publication accessions that need to be imported

Parameters

array $publications The publications returned from the external database

Returns: void The list is stored at $this->new_accessions

◆ getPublicationTypeId()

Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::getPublicationTypeId	(	array &	$publications,
		int	$index
	)

protected

Get the cvterm_id for the publication type

Parameters

array	&$publications	Array of publication records returned by the external database.
int	$index	Array key for the publication of interest.

Returns: int The corresponding cvterm_id value

Exceptions

Exception If type is not defined in the publication, or if the type is not available in the tripal_pub ontology

◆ getRemoteDbId()

Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::getRemoteDbId ( string $db_name )

protected

Retrieves the pkey value from the chado.db table of the specified databse

Parameters

string $db_name The name of the remote database

Returns: void Stores the returned value in $this->db_id

Exceptions

Exception Exception if the database name does not exist

◆ insertContacts()

Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::insertContacts	(	array	$publications,
		bool	$do_contact
	)

protected

Add authors to all specified publications

Parameters

array	$publications	Results from the publication external database query
bool	$do_contact	If TRUE, then create and link an entry in the chado.contact table

Returns: int Count of number of contacts added

◆ insertMissingPublicationsDbxref()

Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::insertMissingPublicationsDbxref ( array $publications )

protected

Inserts new publication accessions into the dbxref table.

Parameters

array $publications All publications returned by the external database

Returns: int A count of the number of records inserted Inserted dbxref_id pkey values are stored in $this->pub_index

◆ insertPubDbxrefs()

Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::insertPubDbxrefs ( )

protected

Link publications to the database accessions through pub_dbxref table

◆ insertPublications()

Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::insertPublications ( array & $publications )

protected

Inserts new publications into the pub table

Parameters

array &$publications All publications returned by the external database

Returns: int A count of the number of publications inserted

◆ insertPubProps()

Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::insertPubProps ( array $publications )

protected

Add publication properties to the chado.pubprop table

Parameters

array $publications All publications returned by the external database

Returns: int A count of the number of properties inserted

◆ run()

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

See also: TripalImporter::run()

n.b. the calling function will wrap this in a database transaction

Implements Drupal\tripal\TripalImporter\Interfaces\TripalImporterInterface.

◆ run_init()

Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::run_init ( )

protected

Handles initialization for the run() function

Returns: array|NULL The criteria array, or NULL if an error occurred

◆ specialCaseProps()

Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::specialCaseProps ( & $publications )

protected

Special case handling for specific properties

Parameters

array &$publications The array of publications being imported

Member Data Documentation

◆ $batch_size

int Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::$batch_size = 100

protected

Stores the maximum size of database query batches

◆ $contact_lookups

array Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::$contact_lookups = []

protected

Stores a few cached cvterm_id values for the tripal_contact ontology

Key is CV name, value is cvterm_id

◆ $cvterm_lookups

array Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::$cvterm_lookups = NULL

protected

Stores all of the cvterm_id values for the tripal_pub ontology

Key is CV name, value is cvterm_id

◆ $db_id

int Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::$db_id = NULL

protected

db_id value from the chado.db table for the external database

◆ $new_accessions

array Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::$new_accessions = []

protected

Stores accessions of new publications not already stored in chado

◆ $pub_index

array Drupal\tripal_chado\Plugin\TripalImporter\PubSearchQueryImporter::$pub_index = []

protected

Stores information for retrieved publications keyed by the accession

First key is accession, second level keys implemented are:

'index' - int, the $publications array index
'pub_id' - int, the pkey of the chado.pub table
'is_new' - boolean, if TRUE we need to insert this as a new publication
'dbxref_id' - int, the pkey of the chado.dbxref table

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

tripal_chado/src/Plugin/TripalImporter/PubSearchQueryImporter.php

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

◆ __construct()

Member Function Documentation

◆ addAuthors()

◆ cachePublicationCvterms()

◆ checkIfSupportedProperty()

◆ create()

◆ findExistingPublications()

◆ form()

◆ formQueryIdNotSet()

◆ formSubmit()

◆ formValidate()

◆ getContact()

◆ getContactType()

◆ getNewPublicationAccessions()

◆ getPublicationTypeId()

◆ getRemoteDbId()

◆ insertContacts()

◆ insertMissingPublicationsDbxref()

◆ insertPubDbxrefs()

◆ insertPublications()

◆ insertPubProps()

◆ run()

◆ run_init()

◆ specialCaseProps()

Member Data Documentation

◆ $batch_size

◆ $contact_lookups

◆ $cvterm_lookups

◆ $db_id

◆ $new_accessions

◆ $pub_index