tripal_chado.pub.api.inc File Reference

Functions
	chado_get_publication ($identifiers, $options=[])
	chado_publication_exists ($pub_details)
	chado_autocomplete_pub ($string='')
	chado_import_pub_by_dbxref ($pub_dbxref, $do_contact=FALSE, $publish=TRUE, $do_update=TRUE)
	chado_execute_active_pub_importers ($report_email=FALSE, $publish=TRUE, $do_update=FALSE)
	chado_execute_pub_importer ($import_id, $publish=TRUE, $do_update=FALSE, $job=NULL)
	_chado_execute_pub_importer_publish ($publish, $job, $message_type, $message_opts)
	chado_reimport_publications ($do_contact=FALSE, $dbxref=NULL, $db=NULL, $publish=TRUE)
	chado_pub_create_citations ($options)
	chado_pub_create_citation ($pub)
	chado_get_pub_dbxrefs ($pub_id)
	chado_get_minimal_pub_info ($pub)

Detailed Description

Provides API functions specifically for managing publication records in Chado.

Function Documentation

_chado_execute_pub_importer_publish()

_chado_execute_pub_importer_publish	(		$publish,
			$job,
			$message_type,
			$message_opts
	)

A helper function to dermine if imported publications should be published.

It supports backwards compatibility with Tripal v2 legacy mode.

Parameters

$publish

Set to TRUE if publications should be published after import. For Tripal v3 this value can be set to the string 'sync' or 'both' in the event that the site is in "legacy" mode. Setting this value to 'sync' will create nodes, setting to 'both' will create nodes and entities. If set to TRUE only entities are created.

chado_execute_pub_importer()

chado_execute_pub_importer	(		$import_id,
			$publish = TRUE,
			$do_update = FALSE,
			$job = NULL
	)

Imports all publications for a given publication import setup.

Parameters

$import_id	The ID of the import setup to use
$publish	Set to TRUE if publications should be published after import. For Tripal v3 this value can be set to the string 'sync' or 'both' in the event that the site is in "legacy" mode. Setting this value to 'sync' will create nodes, setting to 'both' will create nodes and entities. If set to TRUE only entities are created.
$do_update	If set to TRUE then publications that already exist in the Chado database will be updated, whereas if FALSE only new publications will be added.
$job	The jobs management object for the job if this function is run as a job. This argument is added by Tripal during a job run and is not needed if this function is run directly.

Returns

Returns an array containing the number of publications that were inserted, updated, skipped and which had an error during import.