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

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

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Public Member Functions
	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 ()

Protected Member Functions
	retrieveLineage ($root_taxon=NULL)

	initTree ($tree_name)

	removeTree ($tree_name)

	rebuildTree ($root_taxon=NULL)

	rebuildTreeOrganismLineage ($organism, $root_taxon, &$tree, &$lineage_good)

	queryPhylonode (int $phylotree_id, string $node_name, bool &$lineage_good, array &$lineage_nodes)

	getPhylonode (int $phylotree_id, int $organism_id)

	addOrganismNode ($organism, $root_taxon=NULL)

	addTaxonomyNode (&$tree, $node, $lineage_elements)

	trimLineage ($lineage, $root_taxon=NULL)

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 = []

	$phylotree = NULL

	$tree = NULL

	$rank_cvterm_id = NULL

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

Additional Inherited Members
Static Public Member Functions inherited from Drupal\tripal_chado\TripalImporter\ChadoImporterBase
static	create (ContainerInterface $container, array $configuration, $plugin_id, $plugin_definition,)

Member Function Documentation

◆ addOrganismNode()

Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator::addOrganismNode	(	$organism,
		$root_taxon = `NULL`
	)

protected

Adds an organism to the taxonomy tree using its lineage.

Parameters

$organism	An organism object.
$root_taxon	An optional taxon name for the root node if generating a sub-tree.

Returns: int Status. 1 = added 2 = not added, because not part of $root_taxon (if specified) 3 = no lineage available for this organism

◆ form()

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

See also: TripalImporter::form()

Reimplemented from Drupal\tripal_chado\TripalImporter\ChadoImporterBase.

◆ formSubmit()

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

See also: TripalImporter::formValidate()

Implements Drupal\tripal\TripalImporter\Interfaces\TripalImporterInterface.

◆ getPhylonode()

Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator::getPhylonode	(	int	$phylotree_id,
		int	$organism_id
	)

protected

Retrieves a phylonode in a phylotree for an organism

Parameters

int	$phylotree_id	The phylotree to query
int	$organism_id	The organism to query

Returns: object A phylonode object, or NULL if no match.

◆ initTree()

Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator::initTree ( $tree_name )

protected

Create the taxonomic tree in Chado.

If the tree already exists it will not be recreated.

Exceptions

Exception

Returns: Returns the phylotree object.

◆ queryPhylonode()

Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator::queryPhylonode	(	int	$phylotree_id,
		string	$node_name,
		bool &	$lineage_good,
		array &	$lineage_nodes
	)

protected

Called by rebuildTreeOrganismLineage(), selects a phylonode and its properties.

We need to find the node in the phylotree for this level of the lineage, but there are a lot of repeats and we don't want to keep doing the same queries over and over, so we store the nodes we've already seen in the $lineage_nodes array for fast lookup.

◆ rebuildTree()

Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator::rebuildTree ( $root_taxon = NULL )

protected

Iterates through all existing organisms and builds the taxonomy tree.

The phloytree API doesn't support adding nodes to existing trees, only importing whole trees. So, we must rebuild the tree using the current organisms.

Parameters

string $root_taxon If specified, this taxon is the root of the tree, and any organisms not part of this taxon are excluded from the tree.

◆ rebuildTreeOrganismLineage()

Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator::rebuildTreeOrganismLineage	(		$organism,
			$root_taxon,
		&	$tree,
		&	$lineage_good
	)

protected

Called by rebuildTree(), adds lineage nodes for one organism.

◆ removeTree()

Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator::removeTree ( $tree_name )

protected

Removes the chado.phylotree record. Used when tree generation is cancelled due to lack of any valid organisms.

◆ retrieveLineage()

Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator::retrieveLineage ( $root_taxon = NULL )

protected

Parses NCBI Taxonomy lineage details for organisms at this site. This is information previously generated in Chado by the taxonomy importer.

◆ run()

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

Performs the import.

Implements Drupal\tripal\TripalImporter\Interfaces\TripalImporterInterface.

◆ trimLineage()

Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator::trimLineage	(	$lineage,
		$root_taxon = `NULL`
	)

protected

Removes any part of a lineage above an optional root taxon, and returns the resulting lineage as an array.

Parameters

string	$lineage	The semicolon-delimited taxonomic lineage. If is lineageex it has colon-delimited parts.
string	$root_taxon	The root taxon, e.g. a family, or NULL.

Returns: array $lineage_elements Lineage string exploded into an array, starting at root taxon if specified.

Member Data Documentation

◆ $all_orgs

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

protected

Holds the list of all organisms currently in Chado.

◆ $phylotree

Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator::$phylotree = NULL

protected

The record from the Chado phylotree table that refers to this Taxonomic tree.

◆ $rank_cvterm_id

Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator::$rank_cvterm_id = NULL

protected

CV term id for local:rank

◆ $tree

Drupal\tripal_chado\Plugin\TripalImporter\TreeGenerator::$tree = NULL

protected

The temporary tree array used by the Tripal Phylotree API for importing a new tree.

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

tripal_chado/src/Plugin/TripalImporter/TreeGenerator.php

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Member Function Documentation

◆ addOrganismNode()

◆ form()

◆ formSubmit()

◆ formValidate()

◆ getPhylonode()

◆ initTree()

◆ queryPhylonode()

◆ rebuildTree()

◆ rebuildTreeOrganismLineage()

◆ removeTree()

◆ retrieveLineage()

◆ run()

◆ trimLineage()

Member Data Documentation

◆ $all_orgs

◆ $phylotree

◆ $rank_cvterm_id

◆ $tree