Drupal\tripal_chado\TripalField\ChadoFieldItemBase Class Reference

Inheritance diagram for Drupal\tripal_chado\TripalField\ChadoFieldItemBase:

Collaboration diagram for Drupal\tripal_chado\TripalField\ChadoFieldItemBase:

Public Member Functions
	storageSettingsFormBaseTableAjaxCallback ($form, &$form_state)
	storageSettingsFormLinkingMethodAjaxCallback ($form, &$form_state)
	isCompatible (TripalEntityType $entity_type)
Public Member Functions inherited from Drupal\tripal\TripalField\TripalFieldItemBase
	fieldSettingsForm (array $form, FormStateInterface $form_state)
	storageSettingsForm (array &$form, FormStateInterface $form_state, $has_data)
	tripalStorageId ()
	tripalSave ($field_item, $field_name, $prop_types, $prop_values, $entity)
	tripalLoad ($field_item, $field_name, $prop_types, $prop_values, $entity)
	tripalClear ($field_item, $field_name, $prop_types, $prop_values, $entity)
	sanitizeKey ($key)
	tripalValuesTemplate ($field_definition, $default_value=NULL)
	getFieldMaxDelta ()

Static Public Member Functions
static	defaultStorageSettings ()
static	storageSettingsFormValidateBaseTable (array $form, FormStateInterface $form_state)
static	storageSettingsFormValidateLinkingMethod (array $form, FormStateInterface $form_state)
static	get_linker_table_and_column ($storage_settings, $default_table, $default_column)
static	discoverPostprocess (array $field_list)
static	getChadoTableDefs (array $table_names, ?ChadoSchema $schema=NULL)
static	getChadoTableDef (string $table_name, ?ChadoSchema $schema=NULL)
static	getChadoForeignKeyDef (string $left_table, ?string $right_table=NULL, ?ChadoSchema $schema=NULL)
Static Public Member Functions inherited from Drupal\tripal\TripalField\TripalFieldItemBase
static	defaultFieldSettings ()
static	buildVocabularyTermTable (array &$elements, TripalTerm $term, TripalIdSpaceBase $idSpace, TripalVocabularyBase $vocabulary,)
static	buildFieldTermForm ($field, $form, FormStateInterface $form_state)
static	fieldSettingsFormValidate (array $form, FormStateInterface $form_state)
static	propertyDefinitions (FieldStorageDefinitionInterface $field_definition)
static	schema (FieldStorageDefinitionInterface $field_definition)
static	getFormStateSettings (FormStateInterface $form_state)
static	discover (TripalEntityType $bundle, string $field_id, array $field_types, array $field_instances)
static	generateFieldName (TripalEntityType $bundle, string $extra, int $cvterm_id=0)
Static Public Member Functions inherited from Drupal\tripal\TripalField\Interfaces\TripalFieldItemInterface
static	tripalTypes ($field_definition)

Protected Member Functions
	getBaseTables ($linked_table, $has_linker_table=FALSE)
	getTableColumnSelectOptions ($table_name='', $column_types=[])
	getTableColumns ($table_name, $column_types=[])
	getLinkerTableSelectOptions ($object_table, $base_table, $delimiter=" \u{2192} ")
	getLinkerTables ($object_table, $base_table)
	removeIncompatibleField (string $bundle, string $machine_name)

Static Protected Member Functions
static	parse_combined_table_and_column ($table_and_column)
static	createFieldEntry (TripalEntityType $bundle, array $options)
static	discoverBase (TripalEntityType $bundle, string $field_id, array $field_types, array $field_instances, array $options)
static	discoverDirect (TripalEntityType $bundle, string $field_id, array $field_types, array $field_instances, array $options)
static	discoverLinked (TripalEntityType $bundle, string $field_id, array $field_types, array $field_instances, array $options)
static	getPossibleLinkingTables (array $options)
static	getPrimaryKeys (array $table_names, ?ChadoSchema $schema=NULL)
static	getPrimaryKey (string $table_name, ?ChadoSchema $schema=NULL)

Static Protected Attributes
static	$record_id_term = 'SIO:000729'
static	$select_base_column = FALSE
static	$valid_base_column_types = []
static	$object_table = NULL
static	$table_column_delimiter = " \u{2192} "
static	$drupal_entity_term = 'schema:ItemPage'
static	$chadostorage_namespace = 'Drupal\tripal_chado\Plugin\TripalStorage\ChadoStorage'
static	$drupal_entity_callback = 'drupalEntityIdLookupCallback'
static	$mapping = NULL

Detailed Description

Defines the Tripal field item base class.

Member Function Documentation

createFieldEntry()

static Drupal\tripal_chado\TripalField\ChadoFieldItemBase::createFieldEntry ( TripalEntityType  $bundle, array  $options  )

staticprotected

Creates an array defining a single discovered field.

Parameters

TripalEntityType	$bundle	The bundle that the field will be added to
array	$options	All of the specific values for this field

defaultStorageSettings()

static Drupal\tripal_chado\TripalField\ChadoFieldItemBase::defaultStorageSettings ( )

static

{{}}

Reimplemented from Drupal\tripal\TripalField\TripalFieldItemBase.

Reimplemented in Drupal\tripal_chado\Plugin\Field\FieldType\ChadoAdditionalTypeTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoAnalysisTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoArrayDesignTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoAssayTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoBiomaterialTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoBooleanTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoContactByRoleTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoContactTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoDbxrefTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoFeatureMapTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoFeatureTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoIntegerTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoOrganismTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoProjectTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoPropertyTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoProtocolTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoRelationshipTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoSequenceChecksumTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoSequenceCoordinatesDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoSequenceLengthTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoSequenceTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoSourceDataTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoStockTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoStringTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoStudyTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoSynonymTypeDefault, and Drupal\tripal_chado\Plugin\Field\FieldType\ChadoTextTypeDefault.

discoverBase()

static Drupal\tripal_chado\TripalField\ChadoFieldItemBase::discoverBase ( TripalEntityType  $bundle, string  $field_id, array  $field_types, array  $field_instances, array  $options  )

staticprotected

Discover fields that use a column in the base table.

This is used by ChadoFieldItemBase::discover().

Parameters

\Drupal\tripal\Entity\TripalEntityType	$bundle	The entity type object for which new field instances should be found.
string	$field_id	The id of the field.
array	$field_types	An array where each item defines a field type that is attached to this bundle. Each item is itself an array of the annotation defined at the top of that particular field type class.
array	$field_instances	An array of FieldConfig objects where each object defines a field attached to this content type.
array	$options	Specific options from the field's discover() function. Required keys: id: the field id, e.g. 'chado_organism_type_default' name: the unique name for a specific field instance. The default is generated using generateFieldName(). base_table: the base table of the entity base_column: the column containing the field's value label: the field's label, e.g. 'Sequence' termIdSpace: The field term's DB termAccession: The field term's accession description: A text description for the discovered field

Returns

array An associative array of fields to suggest that follows the same structure as expected by tripal.tripalfield_collection.* configuration.

discoverDirect()

static Drupal\tripal_chado\TripalField\ChadoFieldItemBase::discoverDirect ( TripalEntityType  $bundle, string  $field_id, array  $field_types, array  $field_instances, array  $options  )

staticprotected

Discover fields that use a foreign key in the specified base table.

This is used by ChadoFieldItemBase::discover().

Parameters

\Drupal\tripal\Entity\TripalEntityType	$bundle	The entity type object for which new field instances should be found.
string	$field_id	The id of the field.
array	$field_types	An array where each item defines a field type that is attached to this bundle. Each item is itself an array of the annotation defined at the top of that particular field type class.
array	$field_instances	An array of FieldConfig objects where each object defines a field attached to this content type.
array	$options	Specific options from the field's discover() function. Required keys: id: the field id, e.g. 'chado_organism_type_default' name: the unique name for a specific field instance. The default is generated using generateFieldName(). base_table: the base table of the entity table: the field's table, e.g. 'organism' label: the field's label, e.g. 'Organism' termIdSpace: The field term's DB termAccession: The field term's accession description: A text description for the discovered field

Returns

array An associative array of fields to suggest that follows the same structure as expected by tripal.tripalfield_collection.* configuration.

discoverLinked()

static Drupal\tripal_chado\TripalField\ChadoFieldItemBase::discoverLinked ( TripalEntityType  $bundle, string  $field_id, array  $field_types, array  $field_instances, array  $options  )

staticprotected

Discover fields that link to the base table through a linking table.

This is used by ChadoFieldItemBase::discover().

Parameters

\Drupal\tripal\Entity\TripalEntityType	$bundle	The entity type object for which new field instances should be found.
string	$field_id	The id of the field.
array	$field_types	An array where each item defines a field type that is attached to this bundle. Each item is itself an array of the annotation defined at the top of that particular field type class.
array	$field_instances	An array of FieldConfig objects where each object defines a field attached to this content type.
array	$options	Specific options from the field's discover() function. Required keys: id: the field id, e.g. 'chado_organism_type_default' name: the unique name for a specific field instance. The default is generated using generateFieldName(). base_table: the base table of the entity table: the field's table, e.g. 'organism' label: the field's label, e.g. 'Organism' termIdSpace: The field term's DB termAccession: The field term's accession description: A text description for the discovered field custom_linker: either a string or an array of additional potential linker tables

Returns

array An associative array of fields to suggest that follows the same structure as expected by tripal.tripalfield_collection.* configuration.

discoverPostprocess()

static Drupal\tripal_chado\TripalField\ChadoFieldItemBase::discoverPostprocess ( array  $field_list )

static

Adds tripal term plugin IDs for the field's term.

Used for the field discovery process if a DB or CV is not a tripal collection yet.

Parameters

array

$field_list

Discoverd field definitions.

Returns

array The same array with plugin IDs added.

get_linker_table_and_column()

static Drupal\tripal_chado\TripalField\ChadoFieldItemBase::get_linker_table_and_column (   $storage_settings,   $default_table,   $default_column  )

static

Retrieve linker table and column from storage settings, used in a field's tripalTypes() function.

Parameters

array	$storage_settings	Storage settings for a field
string	$default_table	This will be the base table for the field
string	$default_column	This will be the object pkey column for the field

Returns

array Returns linker_table and linker_fkey_column

getBaseTables()

Drupal\tripal_chado\TripalField\ChadoFieldItemBase::getBaseTables (   $linked_table,   $has_linker_table = FALSE  )

protected

Return a list of candidate base tables. We only want to present valid tables to the user, which are those with an appropriate foreign key.

Parameters

string	$linked_table	The Chado table being linked to via a foreign key.
bool	$has_linker_table	When set to false (default), base tables are only those tables with a foreign key to $linked_table. When set to true, also include tables based on two foreign keys in linker tables, one to the specified $linked_table, and a second to a different table.

Returns

array The list of tables is returned in an alphabetized list ready to use in a form select.

getChadoForeignKeyDef()

static Drupal\tripal_chado\TripalField\ChadoFieldItemBase::getChadoForeignKeyDef ( string  $left_table, ?string  $right_table = NULL, ?ChadoSchema  $schema = NULL  )

static

Get a foreign key definition for a chado table.

Parameters

string	$left_table	The name of the table the foreign key resides in. E.g. 'feature' for the feature.type_id => cvterm.cvterm_id foreign key.
string | null	$right_table	The name of the table the foreign key refers to. For the example above it would be cvterm. If NULL, then all foreign keys are returned.
\tripal_chado\Database\ChadoSchema	?Drupal,$schema	The chado schema definition.

Returns

array The the foreign key definition, or an empty array if none exists.

getChadoTableDef()

static Drupal\tripal_chado\TripalField\ChadoFieldItemBase::getChadoTableDef ( string  $table_name, ?ChadoSchema  $schema = NULL  )

static

Get a single table definitions from the chado schema.

Parameters

string	$table_name	The table name to query.
Drupal\tripal_chado\Database\ChadoSchema | null	$schema	The chado schema definition.

Returns

array The table schema.

getChadoTableDefs()

static Drupal\tripal_chado\TripalField\ChadoFieldItemBase::getChadoTableDefs ( array  $table_names, ?ChadoSchema  $schema = NULL  )

static

Get multiple table definitions from the chado schema.

Parameters

array	$table_names	The table names to query.
Drupal\tripal_chado\Database\ChadoSchema | null	$schema	The chado schema definition.

Returns

array An associative array keyed by the table name, with value being the table schema.

getLinkerTables()

Drupal\tripal_chado\TripalField\ChadoFieldItemBase::getLinkerTables (   $object_table,   $base_table  )

protected

Return a list of candidate linking connections given a base table and a linked table. These can either be a column in the base table, or a connection through a linking table that connects the base table to the linked table.

Parameters

string	$base_table	The Chado table being used for the current entity (subject).
string	$object_table	The Chado table being linked to (object).

Returns

array The list of tables and columns.

getLinkerTableSelectOptions()

Drupal\tripal_chado\TripalField\ChadoFieldItemBase::getLinkerTableSelectOptions (   $object_table,   $base_table,   $delimiter = " \u{2192} "  )

protected

Return a list of candidate linking connections given a base table and a linked table. These can either be a column in the base table, or a connection through a linking table that connects the base table to the linked table. In some cases there may be more than one way to link the two tables, so the list generated here can be presented to the site administrator to select the desired linking method.

Parameters

string	$base_table	The Chado table being used for the current entity (subject).
string	$object_table	The Chado table being linked to (object).
string	$delimiter	The displayed delimiter between the table and column in the form select. This defaults to a right arrow.

Returns

array The list of tables is returned in an alphabetized list ready to use in a form select. The list elements will be in the format table.column

getPossibleLinkingTables()

static Drupal\tripal_chado\TripalField\ChadoFieldItemBase::getPossibleLinkingTables ( array  $options )

staticprotected

Constructs a list of possible linking tables

Parameters

array

$options

The options passed to discoverLinked(). Keys used here: base_table: the base table of the entity table: the field's table, e.g. 'organism' custom_linker: either a string or an array of additional potential linker tables

Returns

array The list of tables to check

getPrimaryKey()

static Drupal\tripal_chado\TripalField\ChadoFieldItemBase::getPrimaryKey ( string  $table_name, ?ChadoSchema  $schema = NULL  )

staticprotected

Retrieves the name of the primary key for a Chado table.

To also support custom chado tables, the definition is loaded from the database if necessary. Note that this may return a different definition array, specifically the value may be an array instead of a string.

Parameters

string	$table_name	The chado table to look up the primary key for.
Drupal\tripal_chado\Database\ChadoSchema | null	$schema	The chado schema definition.

Returns

string|null The primary key name, or NULL if the table does not have a primary key.

getPrimaryKeys()

static Drupal\tripal_chado\TripalField\ChadoFieldItemBase::getPrimaryKeys ( array  $table_names, ?ChadoSchema  $schema = NULL  )

staticprotected

Retrieves the name of the primary key for Chado tables.

To also support custom chado tables, the definition is loaded from the database if necessary. Note that this may return a different definition array, specifically the value may be an array instead of a string.

Parameters

string	$table_names	The chado tables to look up the primary key for.
Drupal\tripal_chado\Database\ChadoSchema | null	$schema	The chado schema definition.

Returns

array An associative array keyed by the table name, with the value being the table primary key name or NULL if the table does not have a primary key.

getTableColumns()

Drupal\tripal_chado\TripalField\ChadoFieldItemBase::getTableColumns (   $table_name,   $column_types = []  )

protected

Return a list of column names for the indicated table.

Parameters

string	$table_name	The Chado table of interest.
array	$column_types	If specified, limit to specified column types, e.g. "character varying", "text", "bigint", etc.

Returns

array The list of columns

getTableColumnSelectOptions()

Drupal\tripal_chado\TripalField\ChadoFieldItemBase::getTableColumnSelectOptions (   $table_name = '',   $column_types = []  )

protected

Return a list of column names for the indicated table.

Parameters

string	$table_name	The Chado table of interest.
array	$column_types	If specified, limit to specified column types, e.g. "character varying", "text", "bigint", etc.

Returns

array The list of columns is returned in an alphabetized list ready to use in a form select.

isCompatible()

Drupal\tripal_chado\TripalField\ChadoFieldItemBase::isCompatible

(

TripalEntityType

$entity_type

)

Indicates if the field is compatible with the content type.

This function should be implemented by all Chado-based fields and indicate if the field is compatible with the specified content type. By default, it returns TRUE.

Parameters

TripalEntityType

$entity_type

Returns

bool

Reimplemented in Drupal\tripal_chado\Plugin\Field\FieldType\ChadoAnalysisTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoArrayDesignTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoAssayTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoBiomaterialTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoBooleanTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoContactByRoleTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoContactTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoDbxrefTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoFeatureMapTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoFeatureTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoIntegerTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoOrganismTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoProjectTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoProtocolTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoRelationshipTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoSequenceChecksumTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoSequenceCoordinatesDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoSequenceLengthTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoSequenceTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoSourceDataTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoStockTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoStringTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoStudyTypeDefault, Drupal\tripal_chado\Plugin\Field\FieldType\ChadoSynonymTypeDefault, and Drupal\tripal_chado\Plugin\Field\FieldType\ChadoTextTypeDefault.

parse_combined_table_and_column()

static Drupal\tripal_chado\TripalField\ChadoFieldItemBase::parse_combined_table_and_column (   $table_and_column )

staticprotected

Parse a combined table + column string into its two parts

Parameters

string

$table_and_column

Table and column delimited by self::table_column_delimiter, a right arrow by default, e.g."project → contact"

Returns

array Will contain 2 elements if valid, empty array if not.

removeIncompatibleField()

Drupal\tripal_chado\TripalField\ChadoFieldItemBase::removeIncompatibleField ( string  $bundle, string  $machine_name  )

protected

Needed for Drupal ≤10.1 when an incompatible field was added to a content type, this will clean up the partially added field.

Parameters

string	$bundle	The bundle name.
string	$machine_name	The field identifier, including the 'field_' prefix.

storageSettingsFormBaseTableAjaxCallback()

Drupal\tripal_chado\TripalField\ChadoFieldItemBase::storageSettingsFormBaseTableAjaxCallback	(		$form,
		&	$form_state
	)

Ajax callback to update the base column select. The select can't be populated until we know the base table.

Parameters

array	$form	The form array.
\Drupal\Core\Form\FormStateInterface	$form_state	The form state object.

storageSettingsFormLinkingMethodAjaxCallback()

Drupal\tripal_chado\TripalField\ChadoFieldItemBase::storageSettingsFormLinkingMethodAjaxCallback	(		$form,
		&	$form_state
	)

Ajax callback to update the linking method select. The select can't be populated until we know the base table.

Parameters

array	$form	The form array.
\Drupal\Core\Form\FormStateInterface	$form_state	The form state object.

storageSettingsFormValidateBaseTable()

static Drupal\tripal_chado\TripalField\ChadoFieldItemBase::storageSettingsFormValidateBaseTable ( array  $form, FormStateInterface  $form_state  )

static

Form element validation handler for base table

Parameters

array	$form	The form where the settings form is being included in.
\Drupal\Core\Form\FormStateInterface	$form_state	The form state of the (entire) configuration form.

storageSettingsFormValidateLinkingMethod()

static Drupal\tripal_chado\TripalField\ChadoFieldItemBase::storageSettingsFormValidateLinkingMethod ( array  $form, FormStateInterface  $form_state  )

static

Form element validation handler for linking method (table + column)

Parameters

array	$form	The form where the settings form is being included in.
\Drupal\Core\Form\FormStateInterface	$form_state	The form state of the (entire) configuration form.

---

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

• tripal_chado/src/TripalField/ChadoFieldItemBase.php