Chado Schema

  1. 2.x tripal_core/api/tripal_core.chado_schema.api.inc tripal_chado_schema_api
  2. 3.x tripal_chado/api/tripal_chado.schema.api.inc tripal_chado_schema_api

Provides an application programming interface (API) for describing Chado tables. This API consists of a set of functions, one for each table in Chado. Each function simply returns a Drupal style array that defines the table.

Because Drupal 6 does not handle foreign key (FK) relationships, however FK relationships are needed to for Tripal Views. Therefore, FK relationships have been added to the schema defintitions below.

The functions provided in this documentation should not be called as is, but if you need the Drupal-style array definition for any table, use the following function call:

$table_desc = chado_get_schema($table)

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

Parent topics

Chado API
The Tripal Chado (tripal_chado) module provides an application programming interface (API) to support customizations and creation of new extensions using the Chado database schem as a data store.

File

tripal_chado/api/tripal_chado.schema.api.inc, line 10
Provides an application programming interface (API) for describing Chado tables.

Functions

Namesort descending Location Description
chado_column_exists tripal_chado/api/tripal_chado.schema.api.inc Check that any given column in a Chado table exists.
chado_dbschema_exists tripal_chado/api/tripal_chado.schema.api.inc Check that any given schema exists.
chado_get_base_tables tripal_chado/api/tripal_chado.schema.api.inc Returns all chado base tables.
chado_get_custom_table_schema tripal_chado/api/tripal_chado.schema.api.inc Retrieves the schema in an array for the specified custom table.
chado_get_schema tripal_chado/api/tripal_chado.schema.api.inc Retrieves the chado tables Schema API array.
chado_get_table_names tripal_chado/api/tripal_chado.schema.api.inc 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
chado_get_version tripal_chado/api/tripal_chado.schema.api.inc Returns the version number of the currently installed Chado instance. It can return the real or effective version. Note, this function is executed in the hook_init() of the tripal_chado module which then sets the…
chado_is_installed tripal_chado/api/tripal_chado.schema.api.inc Check whether chado is installed (either in the same or a different database)
chado_is_local tripal_chado/api/tripal_chado.schema.api.inc Check that the Chado schema exists within the local database
chado_sequence_exists tripal_chado/api/tripal_chado.schema.api.inc Check that any given column in a Chado table exists.
chado_table_exists tripal_chado/api/tripal_chado.schema.api.inc Check that any given Chado table exists.

Sub-Topics

Namesort descending Location Description
Chado v1.11 Schema tripal_chado/api/tripal_chado.schema_v1.11.api.inc Provides an application programming interface (API) for describing Chado tables. This API consists of a set of functions, one for each table in Chado. Each function simply returns a Drupal style array that defines the table.
Chado v1.2 Schema tripal_chado/api/tripal_chado.schema_v1.2.api.inc Provides an application programming interface (API) for describing Chado tables. This API consists of a set of functions, one for each table in Chado. Each function simply returns a Drupal style array that defines the table.
Chado v1.3 Schema tripal_chado/api/tripal_chado.schema_v1.3.api.inc Provides an application programming interface (API) for describing Chado tables. This API consists of a set of functions, one for each table in Chado. Each function simply returns a Drupal style array that defines the table.