tripal_chado.cv.api.inc File Reference

Functions
	chado_get_cv ($identifiers, $options=[])
	chado_get_cv_select_options ()
	chado_get_cvterm ($identifiers, $options=[])
	chado_get_cvterm_select_options ($cv_id, $rel_type=FALSE)
	tripal_update_cvtermpath_old ($cv_id, $job_id=NULL)
	chado_clear_cvtermpath ($cv_id)
	chado_update_cvtermpath ($cv_id, $job=NULL)
	_chado_update_cvtermpath_root ($cv_id, $root_id, $root_name, &$cache, $job, &$num_handled, $root_depth=0)
	_chado_update_cvtermpath_process_children ($cv_id, $root_id, $cvterm_id, $path, &$cache, $depth=1)
	_chado_update_cvtermpath_add_relationship ($type_id, $cvterm_id, $root_id, $cv_id, $depth)
	chado_insert_cv ($name, $definition)
	chado_insert_cvterm ($term, $options=[])
	chado_submit_obo_job ($obo)
	chado_insert_obo ($name, $path)
	chado_get_obo ($values)
	chado_autocomplete_cv ($string='')
	chado_autocomplete_cvterm ($cv_id, $string='')
	chado_associate_cvterm ($basetable, $record_id, $cvterm, $options=[])

Detailed Description

Provides API functions specifically for managing controlled vocabulary records in Chado.

Function Documentation

_chado_update_cvtermpath_add_relationship()

_chado_update_cvtermpath_add_relationship	(		$type_id,
			$cvterm_id,
			$root_id,
			$cv_id,
			$depth
	)

Inserts values into the cvtermpath table.

After the entire tree below the current root term is traversed, this function is called and inserts all of the relationships that were found into the cvtermpath table.

Parameters

$visited	The array contaiing relationships for all visited nodes in the tree. These elements will become the entries in the cvtermpath table.
$job	The TripalJob instance.

_chado_update_cvtermpath_process_children()

_chado_update_cvtermpath_process_children	(		$cv_id,
			$root_id,
			$cvterm_id,
			$path,
		&	$cache,
			$depth = 1
	)

Handles a single node in the tree.

This is a recursive function which calls itself as the tree is descended. It performs a depth-first search of the tree.

Parameters

$cv_id	The vocaulary Id
$root_id	This root term's cvterm Id.
$cvterm_id	This term's cvterm Id.
$path	An array used for storing the current path down the tree. This is the sequence of nodes visited to this point down a single branch.
$cache	The cache used for lookups.
$depth	The current depth in the tree.

_chado_update_cvtermpath_root()

_chado_update_cvtermpath_root	(		$cv_id,
			$root_id,
			$root_name,
		&	$cache,
			$job,
		&	$num_handled,
			$root_depth = 0
	)

Treats a term within the ontology as a root.

In order to add all relationships between a term and it's descendents each term gets it's turn as a "root". The first time this function is called it should be called with the actual root's of the ontology. This function will then recursively treat each child term within the tree as a root in order to find all relationships.

Parameters

$cv_id	The vocaulary Id
$root_id	This root term's cvterm Id.
$root_name	The name of this root term.
$cache	The cache used for lookups.
$job	The TripalJob instance.
$num_handled	Used to keep track of the number of nodes that have been handled for progress reporting.
$root_depth	The current depth in the tree of this term.

chado_clear_cvtermpath()

chado_clear_cvtermpath

(

$cv_id

)

Parameters

unknown

$cv_id