Tripal
Functions
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
$publishSet 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_idThe ID of the import setup to use
$publishSet 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_updateIf set to TRUE then publications that already exist in the Chado database will be updated, whereas if FALSE only new publications will be added.
$jobThe 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.