Drupal\tripal_chado\Task\ChadoPreparer Class Reference

Inheritance diagram for Drupal\tripal_chado\Task\ChadoPreparer:

Collaboration diagram for Drupal\tripal_chado\Task\ChadoPreparer:

Public Member Functions
	validateParameters ()
	performTask ()
	createCustomTable_tripal_gffcds_temp ()
	createCustomTable_tripal_gffprotein_temp ()
	createCustomTable_tripal_obo_temp ()
	getProgress ()
	getStatus ()
Public Member Functions inherited from Drupal\tripal_chado\Task\ChadoTaskBase
	getTripalDbxClass ($class)
Public Member Functions inherited from Drupal\tripal_biodb\Task\BioTaskBase
	__construct (?\Drupal\Core\Database\Connection $database=NULL, ?\Psr\Log\LoggerInterface $logger=NULL, ?\Drupal\tripal_biodb\Lock\SharedLockBackendInterface $locker=NULL, ?\Drupal\Core\State\StateInterface $state=NULL)
	setParameters (array $parameters=[])
	getId ()
	getLogger ()

Public Attributes
const	TASK_NAME = 'preparer'
Public Attributes inherited from Drupal\tripal_chado\Task\ChadoTaskBase
const	TASK_NAME = 'chado'
Public Attributes inherited from Drupal\tripal_biodb\Task\BioTaskBase
const	TASK_NAME = 'task'
const	STATE_KEY_DATA_PREFIX = 'tripal_biodb_'

Protected Member Functions
	createCustomTables ()
	createCustomTable_tripal_gff_temp ()
	createMviews ()
	setProgress (float $value)
	importOntologies ()
Protected Member Functions inherited from Drupal\tripal_biodb\Task\BioTaskBase
	prepareSchemas (array $schema_list)
	getSchemaLockName (\Drupal\tripal\TripalDBX\TripalDbxConnection $db)
	initId ()
	acquireTaskLocks ()
	releaseTaskLocks ()

Protected Attributes
	$chado_schema_main
Protected Attributes inherited from Drupal\tripal_biodb\Task\BioTaskBase
	$id
	$connection
	$logger
	$locker
	$state
	$parameters = ['input_schemas' => [], 'output_schemas' => [], ]
	$inputSchemas = []
	$outputSchemas = []

Detailed Description

Chado preparer.

Usage:

// Where 'chado' is the name of the Chado schema to prepare.
$preparer = \Drupal::service('tripal_chado.preparer');
$preparer->setParameters([
  'output_schemas' => ['chado'],
]);
if (!$preparer->performTask()) {
  // Display a message telling the user the task failed and details are in
  // the site logs.
}

Member Function Documentation

createCustomTable_tripal_gff_temp()

Drupal\tripal_chado\Task\ChadoPreparer::createCustomTable_tripal_gff_temp ( )

protected

Creates the tripal_gff_temp table.

This table is used by the GFF Importer.

createCustomTable_tripal_gffcds_temp()

Drupal\tripal_chado\Task\ChadoPreparer::createCustomTable_tripal_gffcds_temp

(

)

Creates the tripal_gffcds_temp table.

This table is used by the GFF Importer.

createCustomTable_tripal_gffprotein_temp()

Drupal\tripal_chado\Task\ChadoPreparer::createCustomTable_tripal_gffprotein_temp

(

)

Create the tripal_gffproptein_temp table.

This table is used by the GFF Importer.

createCustomTable_tripal_obo_temp()

Drupal\tripal_chado\Task\ChadoPreparer::createCustomTable_tripal_obo_temp

(

)

Create the tripal_obo_temp table.

This table is used by the OBO Importer.

createCustomTables()

Drupal\tripal_chado\Task\ChadoPreparer::createCustomTables ( )

protected

Create the custom tables this module needs.

These are tables that Chado uses to manage the site (i.e. temporary loading tables) and not for primary data storage.

createMviews()

Drupal\tripal_chado\Task\ChadoPreparer::createMviews ( )

protected

Creates the materialized views used by this module.

getProgress()

Drupal\tripal_chado\Task\ChadoPreparer::getProgress

(

)

{Returns the percent of progress of current task.This method can also be used to check if a task is currently running if it has a > 0 value. A negative value means an error occured while running.

Returns

float A value between -1 and 1, 0 meaning the task has not been started yet, 1 meaning the task is completed with success and a negative value meaning that the task failed. The negative value may be used as a code to identify the error.

}

Implements Drupal\tripal_biodb\Task\BioTaskInterface.

getStatus()

Drupal\tripal_chado\Task\ChadoPreparer::getStatus

(

)

{{Returns a string describing current status of the performed task.This function returns the last known status, even if the task ended. In case of failure, this function may return the reason of the failure.

Returns

string A localized description.

}}

Reimplemented from Drupal\tripal_biodb\Task\BioTaskBase.

importOntologies()

Drupal\tripal_chado\Task\ChadoPreparer::importOntologies ( )

protected

Imports ontologies into Chado.

performTask()

Drupal\tripal_chado\Task\ChadoPreparer::performTask

(

)

Prepare a given chado schema by inserting minimal data.

Task parameter array provided to the class constructor includes:

• 'input_schemas' array: no input schema
• 'output_schemas' array: one output Chado schema that must exist (required)

Example:

['output_schemas' => ['chado_schema'], ]

Returns

bool TRUE if the task was performed with success and FALSE if the task was completed but without the expected success.

Exceptions

Drupal

Reimplemented from Drupal\tripal_biodb\Task\BioTaskBase.

setProgress()

Drupal\tripal_chado\Task\ChadoPreparer::setProgress ( float  $value )

protected

Set progress value.

Parameters

float

$value

New progress value.

validateParameters()

Drupal\tripal_chado\Task\ChadoPreparer::validateParameters

(

)

Validate task parameters.

Parameter array provided to the class constructor must include one output schema and no input schema as shown:

['output_schemas' => ['schema_name'], ]

Exceptions

Implements Drupal\tripal_biodb\Task\BioTaskInterface.

Member Data Documentation

TASK_NAME

const Drupal\tripal_chado\Task\ChadoPreparer::TASK_NAME = 'preparer'

Name of the task.

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

• tripal_chado/src/Task/ChadoPreparer.php