Inheritance diagram for Drupal\tripal\TripalDBX\TripalDbxSchema:

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Collaboration diagram for Drupal\tripal\TripalDBX\TripalDbxSchema:

Public Member Functions
	getSchemaDef (array $parameters)

	__construct (\Drupal\tripal\TripalDBX\TripalDbxConnection $connection)

	initialize ()

	getSchemaName ()

	findTables ($table_expression)

	queryTableInformation ($table)

	indexExists ($table, $index_name, bool $exact_name=FALSE)

	getSchemaSize ()

	schemaExists ()

	functionExists (string $function_name, array $function_parameters)

	sequenceExists (?string $table_name=NULL, ?string $column_name=NULL, ?string &$sequence_name=NULL)

	constraintExists ( $table, $constraint_name, ?string $type=NULL)

	primaryKeyExists (string $table, ?string $column=NULL)

	foreignKeyConstraintExists (string $base_table, string $base_column)

	getTables (array $include=[])

	getTableDef (string $table, array $parameters)

	getTableDdl (string $table_name, bool $clear_cache=FALSE)

	getReferencingTables (string $table_name, bool $clear_cache=FALSE)

	createSchema ()

	cloneSchema (string $source_schema)

	renameSchema (string $new_schema_name)

	dropSchema ()

	tableExists ($table)

Protected Attributes
	$defaultSchema = ''

	$quotedDefaultSchema = ''

	$initialized = FALSE

	$tripalDbxApi = NULL

Detailed Description

Tripal DBX API Schema class.

NOTE: This class should not be instantiated directly but rather it should be accessed through a TripalDbxConnection object using the schema() method.

This class provides a Tripal-specific implementation of the Drupal Schema abstract class. The Drupal PostgreSQL (and other database driver) implementations of the base Drupal Schema class follow the assumption that there is a single schema. As such the core Drupal implementations focus on managing tables within a single schema.

This implementation extends that table-management functionality to also include Schema-focused management including creation, cloning, renaming, dropping and definition export. Additionally, it removes the assumption of a single schema by allowing the default schema to be set based on a Tripal DBX connection.

Here are some useful functions to know that are inherited from Drupal Schema classes (core + PgSchema implementation):

addField(), addIndex(), addPrimaryKey(), addUniqueKey(),
createTable(), dropTable()
dropField(), dropIndex(), dropPrimaryKey(), dropUniqueKey(),
fieldExists(), findPrimaryKeyColumns(),
renameTable() and more from the documentation.

See also: https://api.drupal.org/api/drupal/core!lib!Drupal!Core!Database!Driver!pgsql!Schema.php/class/Schema/9.0.x; https://api.drupal.org/api/drupal/core%21lib%21Drupal%21Core%21Database%21Schema.php/class/Schema/9.0.x

Constructor & Destructor Documentation

◆ __construct()

Drupal\tripal\TripalDBX\TripalDbxSchema::__construct ( \Drupal\tripal\TripalDBX\TripalDbxConnection $connection )

Constructor.

OVERRIDES \Drupal\Core\Database\Schema:__construct().

Overrides default constructor to manage the Tripal DBX managed schema name.

The TripalDbxSchema object should be instantiated by the TripalDbxConnection::schema() method in order to avoid issues when the default Tripal DBX managed schema name is changed in the TripalDbxConnection object which could lead to issues.

If you choose to instantiate a TripalDbxSchema object yourself, you are responsible to not change the Tripal DBX managed schema name of the connection object used to instantiate this TripalDbxSchema.

Parameters

\Drupal\tripal\TripalDBX\TripalDbxConnection $connection A Tripal DBX connection object.

Exceptions

Member Function Documentation

◆ cloneSchema()

Drupal\tripal\TripalDBX\TripalDbxSchema::cloneSchema ( string $source_schema )

Clones a schema into new (unexisting) one.

The target schema must not exist. If $target_schema is omitted, current schema will be used. For instance, if you want to clone "chado" schema into a "chado_copy" schema, you would do something like this:

// We assume 'chado_copy' schema does not exist.
$new_schema = new ChadoConnection('chado_copy');
$new_schema->clone('chado');

Parameters

string	$source_schema	Source schema to clone.
	?string	$target_schema Destination schema that will be created and filled with a copy of $source_schema. If not set, current schema will be the target.

Returns: int The new schema size in bytes or 0 if the operation failed or the schema to clone was empty.

◆ constraintExists()

Drupal\tripal\TripalDBX\TripalDbxSchema::constraintExists	(		$table,
			$constraint_name,
		?string	$type = `NULL`
	)

Check that the constraint exists.

OVERRIDES \Drupal\Core\Database\Schema:constraintExists().

Our version of this method adds an optional parameter $type to support type-specific searching and exact name matches since many biological data-focused databases will not follow the Drupal naming patterns. For example, Chado does not follow these patterns.

Parameters

string	$table	The table the constraint applies to.
string	$constraint_name	The name of the constraint you want to check.
	?string	$type The type of constraint. Should be one of "PRIMARY KEY", "UNIQUE", or "FOREIGN KEY".

Returns: TRUE if the constraint exists and FALSE otherwise.

◆ createSchema()

Drupal\tripal\TripalDBX\TripalDbxSchema::createSchema ( )

Creates the given schema.

The schema to create must not exist. If an error occurs, an exception is thrown.

Exceptions

◆ dropSchema()

Drupal\tripal\TripalDBX\TripalDbxSchema::dropSchema ( )

Removes the given schema.

The schema to remove must exist. If an error occurs, an exception is thrown.

Exceptions

◆ findTables()

Drupal\tripal\TripalDBX\TripalDbxSchema::findTables ( $table_expression )

Finds all tables that are like the specified base table name.

OVERRIDES \Drupal\Core\Database\Schema:findTables().

NOTE: In Drupal 10 individually prefixed tables will no longer be supported. At this point we should re-evaluate if this override is still needed.

Overrides the PostgreSQL implementation for two reasons:

Switch back to the generic Drupal implementation to prepare for other database driver support in the future.
To override where tablePrefix() is called to include the optional parameter indicating to use the Tripal DBX API.

Parameters

string $table_expression An SQL expression, for example "cache_%" (without the quotes).

Returns: array Both the keys and the values are the matching tables.

◆ foreignKeyConstraintExists()

Drupal\tripal\TripalDBX\TripalDbxSchema::foreignKeyConstraintExists	(	string	$base_table,
		string	$base_column
	)

Check the foreign key constrain specified exists.

Parameters

string	$base_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	$base_column	The name of the column that is a foreign key in. E.g. 'type_id' for the feature.type_id => cvterm.cvterm_id foreign key.

Returns: TRUE if the constraint exists and FALSE otherwise.

◆ functionExists()

Drupal\tripal\TripalDBX\TripalDbxSchema::functionExists	(	string	$function_name,
		array	$function_parameters
	)

Check that the given function exists.

Example:

$exists = $tripaldbx_schema->functionExists('dummyfunc', ['bigint', 'varchar']);

Parameters

string	$function_name	The name of the function.
array	$func_parameters	An ordered array of input parameter types that are part of the function signature.

Returns: bool TRUE if the function exists in the schema and FALSE otherwise.

Exceptions

◆ getReferencingTables()

Drupal\tripal\TripalDBX\TripalDbxSchema::getReferencingTables	(	string	$table_name,
		bool	$clear_cache = `FALSE`
	)

Retrieves tables referencing a given one.

Parameters

string	$table	The name of the table used as foreign table by other tables.
bool	$clear_cache	If TRUE, cache is cleared.

Returns: array First level are referencing table names and values are local table column names => referencing table column name. If no referencing tables are found, returns an empty array.

◆ getSchemaDef()

Drupal\tripal\TripalDBX\TripalDbxSchema::getSchemaDef ( array $parameters )

abstract

Retrieve schema details from selected source in the requested format.

Parameters

array

$parameters

An array of key-value parameters:

'source': either 'database' to extract data from database or 'file' to get the data from a static YAML file. Default: 'file'.
'version': version of the Tripal DBX managed schema to fetch from a file. Ignored for 'database' source. Default: implementation specific.
'format': return format, either 'SQL' for an array of SQL string, 'Drupal' for Drupal schema API, 'none' to return nothing or anything else to provide a data structure as returned by TripalDbx::parseTableDdl. If the selected source is 'file', the format parameter will be ignored and 'Drupal' format will be used. Default: TripalDbx::parseTableDdl data structure structure.
'clear': if not empty, cache will be cleared.

Returns: An array with details for the current schema version as defined by $parameters values.

Exceptions

Reimplemented in Drupal\tripal_chado\Database\ChadoSchema, and Drupal\Tests\tripal\Kernel\TripalDBX\Subclass\TripalDbxSchemaFake.

◆ getSchemaName()

Drupal\tripal\TripalDBX\TripalDbxSchema::getSchemaName ( )

Returns current schema name.

Returns: string Current schema name.

◆ getSchemaSize()

Drupal\tripal\TripalDBX\TripalDbxSchema::getSchemaSize ( )

Returns the size in bytes of a PostgreSQL schema.

Returns: integer The size in bytes of the schema or 0 if the size is not available.

Exceptions

◆ getTableDdl()

Drupal\tripal\TripalDBX\TripalDbxSchema::getTableDdl	(	string	$table_name,
		bool	$clear_cache = `FALSE`
	)

Retrieves the table DDL (table data definition language).

Parameters

string	$table	The name of the table to retrieve.
bool	$clear_cache	If TRUE, cache is cleared.

Returns: string A set of SQL queries used to create the table including its constraints or an empty string if the table was not found.

◆ getTableDef()

Drupal\tripal\TripalDBX\TripalDbxSchema::getTableDef	(	string	$table,
		array	$parameters
	)

Returns the specified table structure details.

Parameters

string	$table	The name of the table.
array	$parameters	An array of key-value parameters: 'source': either 'database' to extract data from database or 'file' to get the data from a static YAML file or 'tripal' to get the data from Tripal records. Default: 'file'. 'version': version of the Tripal DBX managed schema to fetch from a file. Ignored fot 'database' source. Default: implementation specific. 'format': return format, either 'sql' for an array of SQL string, 'drupal' for Drupal schema API, 'none' to return nothing or anything else (like 'default') to provide a data structure as returned by TripalDbx::parseTableDdl plus a 'referenced_by' key containing all the referencing tables returned by ::getReferencingTables. If the selected source is 'file' or 'tripal', the format parameter will be ignored and 'Drupal' format will be used. Default: TripalDbx::parseTableDdl data structure structure. 'clear': if not empty, cache will be cleared.

Returns: An array with details from the specified source for the specified table using the specified format or an empty array if table not found.

◆ getTables()

Drupal\tripal\TripalDBX\TripalDbxSchema::getTables ( array $include = [] )

Retrieves the list of tables in the given schema.

Note: only peristant tables (ie. no unlogged or temporary tables) visible by current DB user are returned.

Parameters

array $include An associative array to select other element type to include. Supported keys are: 'table': include all tables; 'base': include only base tables (as defined in the original Tripal Dbx schema definition); 'custom': include only custom tables (not part of the original Tripal Dbx schema definition); 'view': include views; 'partition': include partitions; 'materialized view': include PostgreSQL materialized views (not to be confused with Tripal materialized views which currently are regular tables); If both 'base' and 'custom' are specified, all tables are returned. Default: tables only (empty array).

Returns: array An associative array where the keys are the table names and values are array of properties such as: -'name': table name -'type': one of 'table', 'view', 'partition' and 'materialized view' for PostgreSQL materialized views. -'status': either 'base' for a base table, or 'custom' for a custom table or a tripal materialized view, or 'other' for other elements.

◆ indexExists()

Drupal\tripal\TripalDBX\TripalDbxSchema::indexExists	(		$table,
			$index_name,
		bool	$exact_name = `FALSE`
	)

Checks if an index exists in the given table.

OVERRIDES \Drupal\Core\Database\Schema:indexExists().

Our version of this method adds an optional parameter $exact_name to support exact name matches since many biological data-focused databases will not follow the Drupal index naming pattern. For example, Chado does not follow this pattern.

Parameters

	$table	The name of the table in Tripal DBX managed schema.
	$name	The full name of the index (including the '_idx' part for instance).
bool	$exact_name	If FALSE, Drupal will append to the given name the '__idx' suffix (added when ::addIndex is used) and will adjust the name if needed (length). If TRUE, the function assumes the given index name is complete.

Returns: TRUE if the given index exists, otherwise FALSE.

◆ primaryKeyExists()

Drupal\tripal\TripalDBX\TripalDbxSchema::primaryKeyExists	(	string	$table,
		?string	$column = `NULL`
	)

Check that the primary key exists, has a sequence and a constraint.

Parameters

string	$table	The table you want to check the primary key for.
	?string	$column (optional) The name of the primary key column.

Returns: TRUE if the primary key meets all the requirements and FALSE otherwise.

◆ queryTableInformation()

Drupal\tripal\TripalDBX\TripalDbxSchema::queryTableInformation ( $table )

Fetch the list of blobs and sequences used on a table.

OVERRIDES \Drupal\Core\Database\Schema:queryTableInformation().

Override is required for proper table prefixing. While the exact mechanism isn't clear, if this function is removed then tests will fail due to incorrect table prefixing.

Parameters

string $table_name The non-prefixed name of the table.

Returns

object An object with two member variables:

'blob_fields' that lists all the blob fields in the table.
'sequences' that lists the sequences used in that table.

◆ renameSchema()

Drupal\tripal\TripalDBX\TripalDbxSchema::renameSchema ( string $new_schema_name )

Renames a schema.

The new schema name must not be used by an existing schema. If an error occurs, an exception is thrown.

Parameters

string $new_schema_name New name to use.

Exceptions

◆ schemaExists()

Drupal\tripal\TripalDBX\TripalDbxSchema::schemaExists ( )

Check that the given schema exists.

Returns: bool TRUE/FALSE depending upon whether or not the schema exists.

◆ sequenceExists()

Drupal\tripal\TripalDBX\TripalDbxSchema::sequenceExists	(	?string	$table_name = `NULL`,
		?string	$column_name = `NULL`,
		?string &	$sequence_name = `NULL`
	)

Check that any given sequence in a table exists.

When the sequence name is not known, a table name and a column name can be specified instead. Then, the sequence name will be guessed from those and returned into the given $sequence_name variable if provided. If both the sequence name and the table and column names are specified, only the sequence name will be taken into account.

This information can also be extracted from ::queryTableInformation()['sequences'].

Parameters

string	$table_name	The name of the table the sequence is used in.
string	$column_name	The name of the column the sequence is used to populate.
string	&$sequence_name	The name of the sequence is to check if known. Otherwise, the function will set it.

Returns: bool TRUE if the seqeuence exists and FALSE if it does not.

Exceptions

◆ tableExists()

Drupal\tripal\TripalDBX\TripalDbxSchema::tableExists ( $table )

Overrides Drupal\Core\Database\Schema->tableExists().

We needed to override it because core Drupal makes some assumptions when building the where condition that do not match our multi-schema setup.

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

tripal/src/TripalDBX/TripalDbxSchema.php

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ __construct()

Member Function Documentation

◆ cloneSchema()

◆ constraintExists()

◆ createSchema()

◆ dropSchema()

◆ findTables()

◆ foreignKeyConstraintExists()

◆ functionExists()

◆ getReferencingTables()

◆ getSchemaDef()

◆ getSchemaName()

◆ getSchemaSize()

◆ getTableDdl()

◆ getTableDef()

◆ getTables()

◆ indexExists()

◆ primaryKeyExists()

◆ queryTableInformation()

◆ renameSchema()

◆ schemaExists()

◆ sequenceExists()

◆ tableExists()