Drupal\tripal_chado\api\ChadoSchema Class Reference

Public Member Functions
	__construct ($version=NULL, $schema_name=NULL)
	getVersion ()
	getSchemaName ()
	getTableNames ($include_custom=FALSE)
	getTableSchema ($table)
	getCustomTableSchema ($table)
	getBaseTables ()
	getSchemaDetails ()
	checkTableExists ($table)
	checkColumnExists ($table, $column)
	checkColumnType ($table, $column, $expected_type=NULL)
	checkSequenceExists ($table, $column, $sequence_name=NULL)
	checkPrimaryKey ($table, $column=NULL)
	checkConstraintExists ($table, $constraint_name, $type)
	checkFKConstraintExists ($base_table, $base_column)
	checkIndexExists ($table, $name, $no_suffix=FALSE)
	addIndex ($table, $name, $fields, $no_suffix=FALSE)
	createTableSql ($name, $table)
	createFieldSql ($name, $spec)
	processField ($field)
	ensureNotNullPrimaryKey (array $primary_key, array $fields)
	ensureIdentifiersLength ($table_identifier_part, $column_identifier_part, $tag, $separator='__')

Static Public Member Functions
static	schemaExists ($schema_name)

Protected Attributes
	$version = ''
	$schema_name = 'chado'
	$schema = []
	$logger = NULL
	$connection = NULL
	$default_db = NULL

Detailed Description

Provides an application programming interface (API) for describing Chado tables.

If you need the Drupal-style array definition for any table, use the following:

$chado_schema = new \ChadoSchema();
$table_schema = $chado_schema->getTableSchema($table_name);

where the variable $table contains the name of the table you want to retireve. The getTableSchema method determines the appropriate version of Chado and uses the Drupal hook infrastructure to call the appropriate hook function to retrieve the table schema.

Additionally, here are some other examples of how to use this class:

// Retrieve the schema array for the organism table in chado 1.2
$chado_schema = new \ChadoSchema('1.2');
$table_schema = $chado_schema->getTableSchema('organism');
 
// Retrieve all chado tables.
$chado_schema = new \ChadoSchema();
$tables = $chado_schema->getTableNames();
$base_tables = $chado_schema->getbaseTables();
 
// Check the feature.type_id foreign key constraint
$chado_schema = new \ChadoSchema();
$exists = $chado_schema ->checkFKConstraintExists('feature','type_id');
 
// Check Sequence exists
$chado_schema = new \ChadoSchema();
$exists = $chado_schema->checkSequenceExists('organism','organism_id');
// Or just check the primary key directly
$compliant = $chado_schema->checkPrimaryKey('organism');

Constructor & Destructor Documentation

__construct()

Drupal\tripal_chado\api\ChadoSchema::__construct	(		$version = NULL,
			$schema_name = NULL
	)

The ChadoSchema constructor.

Parameters

string

$version

The current version for this site. E.g. "1.3". If a version is not provided, the version of the current database will be looked up.

Member Function Documentation

addIndex()

Drupal\tripal_chado\api\ChadoSchema::addIndex	(		$table,
			$name,
			$fields,
			$no_suffix = FALSE
	)

A Chado-aware replacement for db_add_index().

Parameters

	$table	The table to be altered.
	$name	The name of the index.
string	$fields	An array of field names.

checkConstraintExists()

Drupal\tripal_chado\api\ChadoSchema::checkConstraintExists	(		$table,
			$constraint_name,
			$type
	)

Check that the constraint exists.

Parameters

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

Returns

TRUE if the constraint exists and false otherwise.

checkFKConstraintExists()

Drupal\tripal_chado\api\ChadoSchema::checkFKConstraintExists	(		$base_table,
			$base_column
	)

Check the foreign key constrain specified exists.

Parameters

$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.
$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.

checkIndexExists()

Drupal\tripal_chado\api\ChadoSchema::checkIndexExists	(		$table,
			$name,
			$no_suffix = FALSE
	)

A Chado-aware replacement for the db_index_exists() function.

Parameters

string	$table	The table to be altered.
string	$name	The name of the index.
bool	$no_suffix

checkPrimaryKey()

Drupal\tripal_chado\api\ChadoSchema::checkPrimaryKey	(		$table,
			$column = NULL
	)

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

Parameters

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

Returns

TRUE if the primary key meets all the requirements and false otherwise.

checkTableExists()

Drupal\tripal_chado\api\ChadoSchema::checkTableExists

(

$table

)

Get information about which Chado base table a cvterm is mapped to.

Vocabulary terms that represent content types in Tripal must be mapped to Chado tables. A cvterm can only be mapped to one base table in Chado. This function will return an object that contains the chado table and foreign key field to which the cvterm is mapped. The 'chado_table' property of the returned object contains the name of the table, and the 'chado_field' property contains the name of the foreign key field (e.g. type_id), and the 'cvterm' property contains a cvterm object.

@params An associative array that contains the following keys:

• cvterm_id: the cvterm ID value for the term.
• vocabulary: the short name for the vocabulary (e.g. SO, GO, PATO)
• accession: the accession for the term.
• bundle_id: the ID for the bundle to which a term is associated. The 'vocabulary' and 'accession' must be used together, the 'cvterm_id' can be used on it's own.

Returns

An object containing the chado_table and chado_field properties or NULL if if no mapping was found for the term.

public function getCvtermMapping($params) { return chado_get_cvterm_mapping($params); } Check that any given Chado table exists.

This function is necessary because Drupal's db_table_exists() function will not look in any other schema but the one where Drupal is installed

Parameters

$table

The name of the chado table whose existence should be checked.

Returns

TRUE if the table exists in the chado schema and FALSE if it does not.

getCustomTableSchema()

Drupal\tripal_chado\api\ChadoSchema::getCustomTableSchema

(

$table

)

Retrieves the schema array for the specified custom table.

Parameters

$table

The name of the table to create.

Returns

A Drupal-style Schema API array definition of the table. Returns FALSE on failure.

getSchemaDetails()

Drupal\tripal_chado\api\ChadoSchema::getSchemaDetails

(

)

Retrieve schema details from YAML file.

Returns

An array with details for the current schema version.

getSchemaName()

Drupal\tripal_chado\api\ChadoSchema::getSchemaName

(

)

Retrieve the name of the PostgreSQL schema housing Chado.

Returns

The name of the schema.

getTableNames()

Drupal\tripal_chado\api\ChadoSchema::getTableNames

(

$include_custom = FALSE

)

Retrieves the list of tables in the Chado schema. By default it only returns the default Chado tables, but can return custom tables added to the Chado schema if requested.

Parameters

$include_custom

Optional. Set as TRUE to include any custom tables created in the Chado schema. Custom tables are added to Chado using the tripal_chado_chado_create_table() function.

Returns

An associative array where the key and value pairs are the Chado table names.

getTableSchema()

Drupal\tripal_chado\api\ChadoSchema::getTableSchema

(

$table

)

Retrieves the chado tables Schema API array.

Parameters

$table

The name of the table to retrieve. The function will use the appopriate Tripal chado schema API hooks (e.g. v1.11 or v1.2).

Returns

A Drupal Schema API array defining the table.

getVersion()

Drupal\tripal_chado\api\ChadoSchema::getVersion

(

)

Returns the version number of the Chado this object references.

Returns

The version of Chado

schemaExists()

static Drupal\tripal_chado\api\ChadoSchema::schemaExists (   $schema_name )

static

Check that any given chado schema exists.

Parameters

string

$schema

The name of the schema to check the existence of

Returns

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

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

• tripal_chado/src/api/ChadoSchema.php