Inheritance diagram for Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish:

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Collaboration diagram for Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish:

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Public Member Functions
	publish (array $options)

	unpublish (array $options)

Public Member Functions inherited from Drupal\tripal\TripalBackendPublish\TripalBackendPublishBase
	__construct (array $configuration, $plugin_id, $plugin_definition, \Drupal\Core\Database\Connection $connection, \Drupal\Core\Entity\EntityTypeManagerInterface $entity_type_manager, \Drupal\Core\Entity\EntityFieldManagerInterface $entity_field_manager, \Drupal\Core\Field\FieldTypePluginManager $field_type_manager, \Drupal\tripal\Services\TripalLogger $logger, \Drupal\tripal\TripalStorage\PluginManager\TripalStorageManager $storage_manager, \Drupal\tripal\Services\TripalEntityLookup $entity_lookup_manager, \Drupal\tripal\Services\TripalTokenParser $token_parser)

Protected Member Functions
	loadMigrationData (string $filename)

	set_tripal_entity_id_seq ()

	getObjectTable (string $field_name, array $storage_plugin_settings)

	addRequiredValues ()

	addNonRequiredValues ()

	checkFieldIsSupported (string $field_name)

	getChadoRecordID (array $match)

	getEntityTitles (array $matches, string $title_format)

	getEntityIds ()

	findOrphanedEntities (array $entity_ids)

	getBundleTokenValues (string $tokenized_string, ?int $entity_id)

	updateExistingTitles (array $titles, array $existing_titles)

	findEntities (array $record_ids)

	validateMigrationData (array &$matches, bool $lenient)

	insertEntities ($matches, $titles)

	deleteEntities (array $entity_ids)

	findFieldItems ($field_name, $record_ids)

	countFieldMatches (string $field_name, array $matches)

	insertFieldItems ($field_name, $matches, $existing, $titles)

	deleteFieldItems (string $field_name, array $entity_ids)

	excludeExisting ($matches)

	divideIntoBatches ($record_ids)

	getRecordIds ()

	publish_summarize (bool $success, array $stats)

	getFindValuesOptions ()

Protected Attributes
	$base_table = ''

	$field_info = []

	$main_property_names = []

	$entity_type = NULL

	$uid = NULL

	$storage = NULL

	$required_types = []

	$non_required_types = []

	$supported_actions = ['store_id', 'store', 'store_link', 'store_pkey', 'read_value', 'replace', 'function']

	$unsupported_fields = []

	$existing_published_entities = []

	$published_or_updated_entities = []

	$search_values = []

array	$migration_data = []

int	$max_migrated_entity_id = 0

bool	$lenient_migration = FALSE

array	$token_values = []

int	$count_blank_titles = 0

	$republish = TRUE

int	$publish_global_max_delta

bool	$publish_global_max_delta_inhibit

Protected Attributes inherited from Drupal\tripal\TripalBackendPublish\TripalBackendPublishBase
	$connection

	$entity_type_manager = NULL

	$entity_field_manager = NULL

	$field_type_manager = NULL

	$logger = NULL

	$storage_manager = NULL

	$entity_lookup_manager = NULL

	$token_parser = NULL

	$batch_size = 1000

	$job = NULL

	$bundle = ''

	$datastore = ''

	$schema_name = ''

	$republish = FALSE

array	$allowed_title_tags = []

Additional Inherited Members
Static Public Member Functions inherited from Drupal\tripal\TripalBackendPublish\TripalBackendPublishBase
static	create (ContainerInterface $container, array $configuration, $plugin_id, $plugin_definition)

Member Function Documentation

◆ addNonRequiredValues()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::addNonRequiredValues ( )

protected

Adds to the search values array any remaining property values.

◆ addRequiredValues()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::addRequiredValues ( )

protected

Adds to the search values array the required property values.

◆ checkFieldIsSupported()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::checkFieldIsSupported ( string $field_name )

protected

Determines whether a field is supported for publishing.

Parameters

string $field_name The name of the field to check.

Returns: bool TRUE if supported, FALSE if not.

◆ countFieldMatches()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::countFieldMatches	(	string	$field_name,
		array	$matches
	)

protected

Counts the total items to insert for a field.

The matches array returned by the TripalStorage is organized by entity but fields can have a cardinality > 1. This function counts the number of items for the given field.

Parameters

string	$field_name	The name of the field
array	$matches	The array of matches for each entity.

Returns: int The number of items for the field

◆ deleteEntities()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::deleteEntities ( array $entity_ids )

protected

Performs bulk deletion of existing entities from the tripal_entity table.

Parameters

array $entity_ids A list of entities to delete.

Returns: int The number of entities deleted.

◆ deleteFieldItems()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::deleteFieldItems	(	string	$field_name,
		array	$entity_ids
	)

protected

Deletes records from the field tables for entities.

Parameters

string	$field_name	The name of the field.
array	$entity_ids	One or more entities having the field removed.

Returns: int The number of items deleted for the field.

◆ divideIntoBatches()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::divideIntoBatches ( $record_ids )

protected

Divides up a long list of record IDs into smaller batches for publishing, to reduce memory requirements.

Parameters

array $record_ids A list of primary key values.

Returns: array Original array values divided into a 2-D array of several batches. First level array key is a delta value starting at zero.

◆ excludeExisting()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::excludeExisting ( $matches )

protected

Removes existing records from the set of matched records.

Parameters

array $matches The array of matches for each entity.

Returns: array The passed $matches with already published entities excluded.

◆ findEntities()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::findEntities ( array $record_ids )

protected

Retrieves a list of chado record IDs that have already been published.

Parameters

array $record_ids A list of chado record IDs to process.

Returns: array An associative array of published entities keyed by the chado record ID with a value of the existing entity title.

◆ findFieldItems()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::findFieldItems	(	$field_name,
		$record_ids
	)

protected

Finds existing fields so that we will not be adding any duplicate fields.

Parameters

string	$field_name	The name of the field
array	$record_ids	Chado record IDs to process

Returns: array An associative array of matched entities keyed first by the entity_id and then by the delta. Value is always TRUE.

◆ findOrphanedEntities()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::findOrphanedEntities ( array $entity_ids )

protected

Filter entities for only those that are orphaned.

Orphaned entities are those without an underlying chado record.

Returns: array A list of orphaned numeric entity IDs.

◆ getBundleTokenValues()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::getBundleTokenValues	(	string	$tokenized_string,
		?int	$entity_id
	)

protected

Implements bundle token lookup similar to that done in Drupal\tripal\Entity\getBundleEntityTokenValues getBundleEntityTokenValues()

Parameters

string	$tokenized_string	The title format template
int \| null	$entity_id	The drupal entity numeric ID. Not known for a newly published entity.

Returns: array Associative array of all tokens and their values, ready to use for token replacement.

◆ getChadoRecordID()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::getChadoRecordID ( array $match )

protected

Retrieve the chado record ID for a single match record.

Parameters

array $match

Returns: int The chado record ID

◆ getEntityIds()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::getEntityIds ( )

protected

Retrieves a list of numeric entity ID values for the current bundle.

Returns: array A list of numeric entity IDs.

◆ getEntityTitles()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::getEntityTitles	(	array	$matches,
		string	$title_format
	)

protected

Retrieves a list of titles for the entities that should be published.

Parameters

array	$matches	The array of matches for each entity.
string	$title_format	The format for titles for this bundle, contains one or more tokens.

Returns: array A list of titles in order of the entities provided by the $matches array.

◆ getFindValuesOptions()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::getFindValuesOptions ( )

protected

Generates the options array for chado storage findValues().

These options include appropriate max_delta specifications. The cardinality value, if a positive integer greater than 1, will override the global setting.

Returns: array The options to pass to findValues().

◆ getObjectTable()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::getObjectTable	(	string	$field_name,
		array	$storage_plugin_settings
	)

protected

Retrieves the object_table storage plugin setting value for linking fields.

Parameters

string	$field_name	The name of the field.
array	$storage_plugin_settings	Storage settings for a field.

Returns: string The name of the linked object table, or an empty string for non-linking fields.

◆ getRecordIds()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::getRecordIds ( )

protected

Retrieves an array of chado record pkeys eligible for publishing.

Returns: array An array of chado record IDs in no particular order

◆ insertEntities()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::insertEntities	(	$matches,
		$titles
	)

protected

Performs bulk insert of new entities into the tripal_entity table

Parameters

array	$matches	The array of new matches for each entity.
array	$titles	The array of entity titles keyed by the record ID.

◆ insertFieldItems()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::insertFieldItems	(	$field_name,
		$matches,
		$existing,
		$titles
	)

protected

Inserts records into the field tables for entities.

Parameters

string	$field_name	The name of the field
array	$matches	The array of matches for each entity.
array	$existing	An associative array of entities that already have an existing item for this field.
array	$titles	The array of entity titles keyed by the record ID.

Returns: int The number of items inserted for the field.

◆ loadMigrationData()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::loadMigrationData ( string $filename )

protected

Loads migration data for preserving Tripal 3 entity IDs.

Parameters

string $filename If not an empty string, load this data file. If an empty string, do nothing.

Returns: string Empty string if successful, including no file specified. Error message if something went wrong.

◆ publish()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::publish ( array $options )

Publishes Chado content to Tripal entities.

Parameters

array $options Associative array defining what and how to publish. Required keys are: 'bundle' - The id of the bundle or entity type 'datastore' - The id of the TripalStorage plugin Optional keys are: 'republish' - If true, then republish existing entitites. 'job' - A Tripal job object 'batch_size' - Maximum number of records to publish per batch, defaults to 1000 'migration_file' - During migration of a Tripal 3 site, we would like to preserve the numeric entity IDs. This option specifies the name of a file generated by the tripal_chado/migration/export_tripal3_entity_mapping.php utility that was run on the Tripal 3 site. 'lenient_migration' - Do not stop if there are missing records in the migration data, rather just skip over them. 'unpublish' - A true value to instead unpublish content. 'orphaned' - Used for unpublish to only unpublish orphaned content.

Returns: array An associative array of the first 100 entities that were published, keyed by their titles, and the value being the entity_id.

◆ publish_summarize()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::publish_summarize	(	bool	$success,
		array	$stats
	)

protected

Provides a final summary message for publish

Parameters

bool	$success	TRUE if no errors encountered
array	$stats	Various statistics to display

Returns: void

◆ set_tripal_entity_id_seq()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::set_tripal_entity_id_seq ( )

protected

When migrating Tripal 3 entity ID values, makes sure the sequence "tripal_entity_id_seq" next value is higher than the maximum from the migration data.

◆ unpublish()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::unpublish ( array $options )

Unpublishes Tripal entities.

Parameters

array $options Associative array defining what and how to unpublish. Required keys are: 'bundle' - The id of the bundle or entity type 'datastore' - The id of the TripalStorage plugin Optional keys are: 'job' - A Tripal job object 'batch_size' - Max number of records per batch, defaults to 1000. 'unpublish' - When true unpublish content (i.e. delete entities) instead of publishing it. Must be present for this function to be called. 'orphaned' - When unpublishing, only unpublish orphaned content which are entities missing their chado record, defaults to TRUE.

Returns: array For publish the returned array is a list of titles. Here it is just a list of the entity ID values unpublished. This return value is only used for automated tests.

◆ updateExistingTitles()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::updateExistingTitles	(	array	$titles,
		array	$existing_titles
	)

protected

Check if the new title does not match the existing published title, and if so, update it. This can happen if the title format has been changed. Array keys for both input arrays are the chado record ID, array values are the titles.

Parameters

array	$titles	A list of new titles to check, key is chado record ID.
array	$existing_titles	A list of already published titles, key is chado record ID.

Returns: int Number of titles that were updated.

◆ validateMigrationData()

Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::validateMigrationData	(	array &	$matches,
		bool	$lenient
	)

protected

When using Tripal 3 migration data, validate that all values are present and available.

Parameters

array	&$matches	The array of matches for each entity.
bool	$lenient	If TRUE, allow records to be missing from migration data. This can happen if you had unpublished records on your Tripal 3 site.

Returns: bool Returns TRUE if validation passes, FALSE if not.

Member Data Documentation

◆ $base_table

string Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::$base_table = ''

protected

The base table of the bundle

◆ $count_blank_titles

int Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::$count_blank_titles = 0

protected

Number of entities with blank titles.

◆ $entity_type

Drupal tripal Entity TripalEntityType Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::$entity_type = NULL

protected

Stores the bundle (entity type) object.

◆ $existing_published_entities

array Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::$existing_published_entities = []

protected

All published entities for the current bundle. The key will be the chado record ID, the values will be the entity IDs.

◆ $lenient_migration

bool Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::$lenient_migration = FALSE

protected

Flag to permit a more lenient Tripal 3 migration. If a record is missing in the migration data, then skip it.

◆ $main_property_names

array Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::$main_property_names = []

protected

A list of the main properties for each field. The key is the field name, and the value is the name of the main property.

◆ $max_migrated_entity_id

int Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::$max_migrated_entity_id = 0

protected

Stores the maximum entity ID value present in $this->migration_data

◆ $migration_data

array Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::$migration_data = []

protected

Information used to migrate Tripal 3 entity values when first publishing a migrated chado instance.

◆ $non_required_types

array Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::$non_required_types = []

protected

A list of property types that are not one of the required types.

◆ $published_or_updated_entities

array Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::$published_or_updated_entities = []

protected

The first 100 published entities, key is entity_id, value is title. These are only used for unit tests, so don't need to use memory to store them all.

◆ $required_types

array Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::$required_types = []

protected

A list of property types that are required to uniquely identify an entity.

◆ $search_values

array Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::$search_values = []

protected

Array of values to search in chado storage.

◆ $storage

Drupal tripal TripalStorage TripalStorageBase Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::$storage = NULL

protected

The TripalStorage object.

◆ $supported_actions

array Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::$supported_actions = ['store_id', 'store', 'store_link', 'store_pkey', 'read_value', 'replace', 'function']

protected

Supported actions during publishing. Any field containing properties that are not in this list, will not be published!

◆ $token_values

array Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::$token_values = []

protected

Entity and field values used for token replacement, keyed by record_id.

◆ $uid

int Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::$uid = NULL

protected

Stores the user that is publishing content.

◆ $unsupported_fields

array Drupal\tripal_chado\Plugin\TripalBackendPublish\ChadoPublish::$unsupported_fields = []

protected

Keep track of fields which are not supported in order to let the user know.

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

tripal_chado/src/Plugin/TripalBackendPublish/ChadoPublish.php

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Member Function Documentation

◆ addNonRequiredValues()

◆ addRequiredValues()

◆ checkFieldIsSupported()

◆ countFieldMatches()

◆ deleteEntities()

◆ deleteFieldItems()

◆ divideIntoBatches()

◆ excludeExisting()

◆ findEntities()

◆ findFieldItems()

◆ findOrphanedEntities()

◆ getBundleTokenValues()

◆ getChadoRecordID()

◆ getEntityIds()

◆ getEntityTitles()

◆ getFindValuesOptions()

◆ getObjectTable()

◆ getRecordIds()

◆ insertEntities()

◆ insertFieldItems()

◆ loadMigrationData()

◆ publish()

◆ publish_summarize()

◆ set_tripal_entity_id_seq()

◆ unpublish()

◆ updateExistingTitles()

◆ validateMigrationData()

Member Data Documentation

◆ $base_table

◆ $count_blank_titles

◆ $entity_type

◆ $existing_published_entities

◆ $lenient_migration

◆ $main_property_names

◆ $max_migrated_entity_id

◆ $migration_data

◆ $non_required_types

◆ $published_or_updated_entities

◆ $required_types

◆ $search_values

◆ $storage

◆ $supported_actions

◆ $token_values

◆ $uid

◆ $unsupported_fields